bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three-Dimensional Ultrastructural Analysis of the Head-Most Mitochondrial Roots of Mice Spermatozoa Using Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) Tomography
Authors: Uemura Kei-ichiro , Miyazono Yoshihiro , Hiroshige Tasuku , Ohta Keisuke , Ueda Kosuke , Nishihara Kiyoaki , Nakiri Makoto , Hirashima Shingo , Igawa Tsukasa , Nakamura Kei-ichiro 
Published: July 2023

Abstract
This study aimed to clarify the three-dimensional ultrastructure of head-side mice spermatozoa mitochondria. Six 13-week-old male C57BL/6 mice were deeply anesthetized, perfused with 2% paraformaldehyde, and placed in 2.5% glutaraldehyde in 0.1 M cacodylate buffer (pH 7.3) for electron microscopy. After perfusion, the vas deferens was removed, and the specimens were cut into small cubes and subjected to postfixation and en bloc staining. Three-dimensional ultrastructural analysis was performed on five mitochondria on the spermatozoa head using conventional transmission electron microscopy (TEM) and focused ion beam/scanning electron microscopy (FIB/SEM) tomography. Conventional TEM analysis showed that head-side mitochondria were not spiral in morphology but clearly horizontal to the sperm axis. However, this was difficult to evaluate further using conventional TEM. In the FIB/SEM analysis, the first and second head-most mitochondria were flat and straight, with no helix, and shaped as an attachment plug with two electrodes, and their tail side contacted the third mitochondrion. The third mitochondrion was shorter than the fourth and fifth and had a semicircular arching structure. The fourth and fifth mitochondria were spiral-shaped and intertwined. The redundant nuclear envelope encircled the head-most mitochondria. This ultrastructural analysis clarified that the head-most mitochondria have a unique morphology.
A Retrofittable Photoelectron Gun for Low-Voltage Imaging Applications in the Scanning Electron Microscope
Authors: Quigley Frances , Downing Clive , McGuinness Cormac , Jones Lewys 
Published: July 2023

Abstract
Low-voltage scanning electron microscopy is a powerful tool for examining surface features and imaging beam-sensitive materials. Improving resolution during low-voltage imaging is then an important area of development. Decreasing the effect of chromatic aberration is one solution to improving the resolution and can be achieved by reducing the energy spread of the electron source. Our approach involves retrofitting a light source onto a thermionic lanthanum hexaboride (LaB6) electron gun as a cost-effective low energy-spread photoelectron emitter. The energy spread of the emitter's photoelectrons is theorized to be between 0.11 and 0.38 eV, depending on the photon energy of the ultraviolet (UV) light source. Proof-of-principle images have been recorded using this retrofitted photoelectron gun, and an analysis of its performance is presented.
Axisymmetric oscillation modes of relativistic tori in the vicinity of a distorted, deformed compact object
Authors: Faraji S , Trova A 
Published: July 2023

ABSTRACT
This paper studies the oscillation properties of relativistic, non-self-gravitating tori in the background of a distorted, deformed compact object. This work concentrates on a static and axially symmetric metric containing two quadrupole parameters; relating to the central object and the external fields. This metric may associate the observable effects of these parameters as dynamical degrees of freedom. The astrophysical motivation for choosing such a field is the possibility of constituting a reasonable model for an actual scenario occurring in the vicinity of compact objects. Following our previous works, this paper aims to investigate the radial epicyclic frequency in a perfect fluid disc and not a test particle scenario via a local analysis. To achieve this goal, we employ the vertically integrated technique to be able to treat the equations analytically. The tori configuration is also modelled with Keplerian and non-Keplerian distributions of specific angular momentum. In this set-up, we also discuss the dependence of oscillation properties on the model’s variables related to angular momentum distribution and quadrupoles. In the present contribution, we further explore these properties with the possibility of relating oscillatory frequencies to some high-frequency quasi-periodic oscillations models and observed data in some microquasar and neutron star sources, and test the ability of this fluid approach to fit with observational data.
On the impact of the galaxy window function on cosmological parameter estimation
Authors: Karim Tanveer , Rezaie Mehdi , Singh Sukhdeep , Eisenstein Daniel 
Published: July 2023

ABSTRACT
One important source of systematics in galaxy redshift surveys comes from the estimation of the galaxy window function. Up until now, the impact of the uncertainty in estimating the galaxy window function on parameter inference has not been properly studied. In this paper, we show that the uncertainty and the bias in estimating the galaxy window function will be salient for ongoing and next-generation galaxy surveys using a simulation-based approach. With a specific case study of cross-correlating emission-line galaxies from the DESI Legacy Imaging Surveys and the Planck cosmic microwave background lensing map, we show that neural network-based regression approaches to modelling the window function are superior in comparison to linear regression-based models. We additionally show that the definition of the galaxy overdensity estimator can impact the overall signal-to-noise of observed power spectra. Finally, we show that the additive biases coming from the window functions can significantly bias the modes of the inferred parameters and also degrade their precision. Thus, a careful understanding of the window functions will be essential to conduct cosmological experiments.
X-ray metal line emission from the hot circumgalactic medium: probing the effects of supermassive black hole feedback
Authors: Truong Nhut , Pillepich Annalisa , Nelson Dylan , Bogdán Ákos , Schellenberger Gerrit , Chakraborty Priyanka , Forman William R , Kraft Ralph , Markevitch Maxim , Ogorzalek Anna , Oppenheimer Benjamin D , Sarkar Arnab , Veilleux Sylvain , Vogelsberger Mark , Wang Q Daniel , Werner Norbert , Zhuravleva Irina , Zuhone John 
Published: July 2023

ABSTRACT
We derive predictions from state-of-the-art cosmological galaxy simulations for the spatial distribution of the hot circumgalactic medium (CGM, [0.1–1]R200c) through its emission lines in the X-ray soft band ([0.3–1.3] keV). In particular, we compare IllustrisTNG, EAGLE, and SIMBA and focus on galaxies with stellar mass $10^{10-11.6}\, \rm {M}_{\odot }$ at z = 0. The three simulation models return significantly different surface brightness radial profiles of prominent emission lines from ionized metals such as O vii(f), O viii, and Fe xvii as a function of galaxy mass. Likewise, the three simulations predict varying azimuthal distributions of line emission with respect to the galactic stellar planes, with IllustrisTNG predicting the strongest angular modulation of CGM physical properties at radial range ${{\gtrsim}0.3{-}0.5\, R_{200c}}$. This anisotropic signal is more prominent for higher energy lines, where it can manifest as X-ray eROSITA-like bubbles. Despite different models of stellar and supermassive black hole (SMBH) feedback, the three simulations consistently predict a dichotomy between star-forming and quiescent galaxies at the Milky Way and Andromeda mass range, where the former are X-ray brighter than the latter. This is a signature of SMBH-driven outflows, which are responsible for quenching star formation. Finally, we explore the prospect of testing these predictions with a microcalorimeter-based X-ray mission concept with a large field of view. Such a mission would probe the extended hot CGM via soft X-ray line emission, determine the physical properties of the CGM, including temperature, from the measurement of line ratios, and provide critical constraints on the efficiency and impact of SMBH feedback on the CGM.
Orbital period changes for 14 novae and the critical failures of the predictions of standard theories, the Hibernation Model, and the Magnetic Braking Model
Authors: Schaefer Bradley E 
Published: July 2023

ABSTRACT
The evolution of novae and cataclysmic variables (CVs) is driven by changes in the binary orbital periods. In a direct and critical test for various evolution models and their physical mechanisms, I measure the sudden changes in the period (ΔP) across 14 nova eruptions, and I measure the steady period change during quiescence (Ṗ) for 20 inter-eruption intervals. The standard theory for ΔP is dominated by the mechanism of mass loss, and this fails completely for the five novae with negative values, and it fails to permit the ΔP for U Sco eruptions to change by one order of magnitude eruption to eruption. The Hibernation Model of evolution is refuted because all the ΔP measures are orders of magnitude too small to cause any significant drop in accretion luminosity, and indeed, near half of the nova have negative ΔP as the opposite of the required mechanism for any hibernation state. As for the Magnetic Braking Model, this fails by many orders of magnitude in its predictions of the required Ṗ for 9 out of 13 novae. The observed Ṗ values scatter, both positively and negatively, over a range of ±10−9, while the predicted values are from −10−13 to −10−11. This huge scatter is not possible with standard theory, and there must be some currently unknown mechanism to be added in, with this new mechanism 100–10 000× larger in effect than the current theory allows. In all, these failed predictions demonstrate that nova systems must have unknown physical mechanisms for both ΔP and Ṗ that dominate over all other effects.
General relativistic pulsations of ultra-massive ZZ Ceti stars
Authors: Córsico Alejandro H , Boston S Reece , Althaus Leandro G , Kilic Mukremin , Kepler S O , Camisassa María E , Torres Santiago 
Published: July 2023

ABSTRACT
Ultra-massive white dwarf stars are currently being discovered at a considerable rate, thanks to surveys such as the Gaia space mission. These dense and compact stellar remnants likely play a major role in Type Ia supernova explosions. It is possible to probe the interiors of ultra-massive white dwarfs through asteroseismology. In the case of the most massive white dwarfs, general relativity could affect their structure and pulsations substantially. In this work, we present results of relativistic pulsation calculations employing relativistic ultra-massive ONe-core white dwarf models with hydrogen-rich atmospheres and masses ranging from 1.29 to $1.369 \ \mathrm{M}_{\odot }$ with the aim of assessing the impact of general relativity on the adiabatic gravity (g)-mode period spectrum of very high mass ZZ Ceti stars. Employing the relativistic Cowling approximation for the pulsation analysis, we find that the critical buoyancy (Brunt–Väisälä) and acoustic (Lamb) frequencies are larger for the relativistic case, compared to the Newtonian case, due to the relativistic white dwarf models having smaller radii and higher gravities for a fixed stellar mass. In addition, the g-mode periods are shorter in the relativistic case than those in the Newtonian computations, with relative differences of up to ∼$50$ per cent for the highest mass models ($1.369 \ \mathrm{M}_{\odot }$) and for effective temperatures typical of the ZZ Ceti instability strip. Hence, the effects of general relativity on the structure, evolution, and pulsations of white dwarfs with masses larger than ∼$1.29 \ \mathrm{M}_{\odot }$ cannot be ignored in the asteroseismological analysis of ultra-massive ZZ Ceti stars.
Whole Genome Duplication and Gene Evolution in the Hyperdiverse Venomous Gastropods
Authors: Farhat Sarah , Modica Maria Vittoria , Puillandre Nicolas 
Published: July 2023

Abstract
The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied. Among the available gastropods genomes, only eight, with uneven quality assemblies, belong to neogastropods. Here, we generated chromosome-level assemblies of two species belonging to the Tonnoidea and Muricoidea superfamilies (Monoplex corrugatus and Stramonita haemastoma). The two obtained high-quality genomes had 3 and 2.2 Gb, respectively, and 92–89% of the total assembly conformed 35 pseudochromosomes in each species. Through the analysis of syntenic blocks, Hox gene cluster duplication, and synonymous substitutions distribution pattern, we inferred the occurrence of a whole genome duplication event in both genomes. As these species are known to release venom, toxins were annotated in both genomes, but few of them were found in homologous chromosomes. A comparison of the expression of ohnolog genes (using transcriptomes from osphradium and salivary glands in S. haemastoma), where both copies were differentially expressed, showed that most of them had similar expression profiles. The high quality of these genomes makes them valuable reference in their respective taxa, facilitating the identification of genome-level processes at the origin of their evolutionary success.
Survival of juvenile Florida Scrub-Jays is positively correlated with month and negatively correlated with male breeder death
Authors: Carter Geoffrey M , Stolen Eric D , Breininger David R , Legare Stephanie A , Hunt Danny K , Schumann Christopher D , Payne William V 
Published: July 2023

AbstractJuvenile survival in birds is difficult to estimate, but this vital rate can be an important consideration for management decisions. We estimated juvenile survival of cooperatively breeding Florida Scrub-Jays (Aphelocoma coerulescens) in a landscape degraded by fire suppression and fragmentation using data from marked (n = 325) and unmarked juveniles (n = 1,306) with an integrated hierarchical Bayesian model. To assess the combined analyses, we also analyzed these datasets separately, with a Cormack–Jolly–Seber model (marked) and young model (unmarked). Our data consisted of monthly censuses of territorial family groups from Florida Scrub-Jay populations in East Central Florida collected over a 22-year period. Juvenile survival was estimated from July when young Florida Scrub-Jays begin developing independence to March when they become first-year individuals and grouped according to the habitat quality class of their natal territory that were based on shrub height (with intermediate shrub heights being optimal and short and tall shrub heights being suboptimal) and the presence of sandy openings (the preferred open having many sandy openings; closed not having enough). Parameter estimates in the combined analysis were intermediate to the separate analyses. Notable differences among the separate analyses were that suboptimal habitat survival was lower in the unmarked analysis, the unmarked analysis showed a linear effect of time not seen in the marked analysis, and there was an effect of male breeder death in the marked but not unmarked analysis. The combined data analysis provided more inference than did either dataset analyzed separately including juveniles in optimal-closed territories unexpectedly had higher survival than those in optimal-open, survival increased through time, and male breeder death had a negative effect on survival. This study suggests that optimal-closed habitat may play an important role in juvenile Florida Scrub-Jay survival perhaps by providing better cover from predators and warrants further investigation for management implications.
Increasing perceived predation risk through playbacks reduces Red-winged Blackbird abundance in agriculture late in the breeding season
Authors: Enos Janice K , Smith Emma B , Ward Michael P , Swaddle John P , Hauber Mark E 
Published: July 2023

Abstract
Perceived predation and brood parasitism risks strongly influence nesting habitat selection in several bird species. Here, we report on a playback experiment evaluating whether perceived predation or brood parasitism risk can reduce Red-winged Blackbird (Agelaius phoeniceus) abundances in agricultural nesting habitat. We broadcast Cooper’s Hawk vocalizations (Accipiter cooperii, a predator of adult blackbirds and nests), Brown-headed Cowbird vocalizations (Molothrus ater, a brood parasite of many passerine species, including blackbirds), and the “Sonic Net” as treatments, the latter of which is broadcast of frequencies that overlap with blackbird vocalizations and prevent blackbirds from accessing intraspecific communication informing of predator and brood parasite risks. Neither the hawk, cowbird, nor Sonic Net treatments reduced blackbird abundances at sites early in the breeding season (April to May), when blackbirds were selecting nesting habitat. In contrast, late in the breeding season (July to August), hawk vocalizations and the Sonic Net reduced blackbird abundances at sites, but cowbird vocalizations did not. Our late-breeding season results suggest that blackbirds may flexibly change responses to perceived predation risk based on their stage of reproductive investment. Perceived predation risk could potentially be used to manage pest birds that nest in agricultural landscapes, at least for crops that are vulnerable to birds late in the breeding season.
Mice lacking intestinal Nr1i2 have normal intestinal homeostasis under steady‐state conditions and are not hypersensitive to inflammation under lipopolysaccharide treatment
Authors: Amini Salah Edden , Bresson Sophie Emilie , Ruzzin Jérôme 
Published: July 2023

AbstractNr1i2, a nuclear receptor known for its key function in xenobiotic detoxification, has emerged as a potential regulator of intestinal homeostasis and inflammation. However, the role of Nr1i2 in different intestinal segments remains poorly known. Moreover, in vivo investigations on intestinal Nr1i2 have essentially been performed in whole‐body Nr1i2 knockout (Nr1i2−/−) mice where the deletion of Nr1i2 in all tissues may affect the intestinal phenotype. To better understand the role of Nr1i2 in the intestine, we generated intestinal epithelial‐specific Nr1i2 knockout (iNr1i2−/−) mice and studied the duodenum, jejunum, ileum, and colon of these animals during steady‐state conditions and lipopolysaccharide (LPS)‐induced inflammation. As compared to control (iNr1i2+/+) mice, iNr1i2−/− mice showed normal intestinal permeability as assessed by in vivo FITC‐dextran test. The expression of genes involved in inflammation, tight‐ and adherens‐junction, proliferation, glucose, and lipid metabolism was comparable in the duodenum, jejunum, ileum, and colon of iNr1i2−/− and iNr1i2+/+ mice. In line with these findings, histological analyses of the jejunum revealed no difference between iNr1i2−/− and iNr1i2+/+ mice. When treated with LPS, the intestine of iNr1i2−/− mice had no increased inflammatory response as compared to iNr1i2+/+ mice. Moreover, the health monitoring of LPS‐treated iNr1i2−/− and iNr1i2+/+ mice was similar. Taken together, our results demonstrate that the specific deletion of Nr1i2 in the intestinal epithelium does not cause major intestinal damages in mice during both steady‐state and inflammatory conditions.
Isoliquiritigenin induces HMOX1 and GPX4-mediated ferroptosis in gallbladder cancer cells
Authors: Wang Zeyu , Li Weijian , Wang Xue , Zhu Qin , Liu Liguo , Qiu Shimei , Zou Lu , Liu Ke , Li Guoqiang , Miao Huijie , Yang Yang , Jiang Chengkai , Liu Yong , Shao Rong , Wang Xu'an , Liu Yingbin 
Published: July 2023

Abstract

Background:
Gallbladder cancer (GBC) is the most common malignant tumor of biliary tract. Isoliquiritigenin (ISL) is a natural compound with chalcone structure extracted from the roots of licorice and other plants. Relevant studies have shown that ISL has a strong anti-tumor ability in various types of tumors. However, the research of ISL against GBC has not been reported, which needs to be further investigated.

Methods:
The effects of ISL against GBC cells in vitro and in vivo were characterized by cytotoxicity test, RNA-sequencing, quantitative real-time polymerase chain reaction, reactive oxygen species (ROS) detection, lipid peroxidation detection, ferrous ion detection, glutathione disulphide/glutathione (GSSG/GSH) detection, lentivirus transfection, nude mice tumorigenesis experiment and immunohistochemistry.

Results:
ISL significantly inhibited the proliferation of GBC cells in vitro. The results of transcriptome sequencing and bioinformatics analysis showed that ferroptosis was the main pathway of ISL inhibiting the proliferation of GBC, and HMOX1 and GPX4 were the key molecules of ISL-induced ferroptosis. Knockdown of HMOX1 or overexpression of GPX4 can reduce the sensitivity of GBC cells to ISL-induced ferroptosis and significantly restore the viability of GBC cells. Moreover, ISL significantly reversed the iron content, ROS level, lipid peroxidation level and GSSG/GSH ratio of GBC cells. Finally, ISL significantly inhibited the growth of GBC in vivo and regulated the ferroptosis of GBC by mediating HMOX1 and GPX4.

Conclusion:
ISL induced ferroptosis in GBC mainly by activating p62-Keap1-Nrf2-HMOX1 signaling pathway and down-regulating GPX4 in vitro and in vivo. This evidence may provide a new direction for the treatment of GBC.
Prenatal exposure to perfluoroalkyl substances and inflammatory biomarker concentrations
Authors: Palaniyandi Jana , Bruin Jennifer E. , Kumarathasan Premkumari , MacPherson Susan , Borghese Michael M. , Ashley-Martin Jillian 
Published: July 2023

Background:
Per- and polyfluoroalkyl substances (PFAS) are persistent environmental contaminants that induce immunotoxicity in experimental studies; however, epidemiological evidence—particularly during pregnancy—is scarce. We quantified associations between first trimester plasma perfluorooctanoic acid (PFOA), perfluorooctane sulfonate (PFOS), and perfluorohexane sulfonate (PFHxS) concentrations and third trimester concentrations of inflammatory biomarkers and determined if these associations were modified by fetal sex.

Methods:
We analyzed data from 1411 participants, recruited between 2008 and 2011, in the Maternal-Infant Research on Environmental Chemicals study. Our primary outcome was a composite inflammatory index derived by summing the z-scores of eight proinflammatory biomarkers. Using multivariable linear regression models, we quantified associations between each PFAS and the inflammatory index and individual biomarkers. We quantified the effects of the PFAS mixture using weighted quantile sum regression, and evaluated effect modification using product terms and sex-stratified models.

Results:
Each doubling of PFOA and PFHxS was associated with a 0.38 (95% CI, 0.09, 0.67) and 0.21 (95% CI, 0.01, 0.41) SD increase in the proinflammatory index, respectively. A one-quartile increase in the PFAS mixture was associated with a 0.40 (95% CI, 0.09, 0.71) SD increase in the proinflammatory index. In individual models, we observed positive associations between PFAS and concentrations of monocyte chemoattractant protein-1, macrophage inflammatory protein-1β, and matrix metalloproteinases-9; however, the magnitude and precision varied according to the specific PFAS. Sex-specific findings were identified in few PFAS-biomarker associations.

Conclusions:
PFOA, PFOS, and PFHxS, individually and as a mixture, were positively associated with proinflammatory biomarkers during pregnancy.