bluuebunny/crossref_metadata_2025_split huggingface dataset:
The PEPSI Exoplanet Transit Survey (PETS) – V. New Na d transmission spectra indicate a quieter atmosphere on HD 189733b
Authors: Keles E , Czesla S , Poppenhaeger K , Hauschildt P , Carroll T A , Ilyin I , Baratella M , Steffen M , Strassmeier K G , Bonomo A S , Gaudi B S , Henning T , Johnson M C , Molaverdikhani K , Nascimbeni V , Patience J , Reiners A , Scandariato G , Schlawin E , Shkolnik E , Sicilia D , Sozzetti A , Mallonn M , Veillet C , Wang J , Yan F 
Published: April 2024

ABSTRACT
Absorption lines from exoplanet atmospheres observed in transmission allow us to study atmospheric characteristics such as winds. We present a new high-resolution transit time-series of HD 189733b, acquired with the PEPSI instrument at the LBT and analyse the transmission spectrum around the Na d lines. We model the spectral signature of the RM-CLV-effect using synthetic PHOENIX spectra based on spherical LTE atmospheric models. We find an Na d absorption signature between the second and third contact but not during the ingress and egress phases, which casts doubt on the planetary origin of the signal. Presupposing a planetary origin of the signal, the results suggest a weak day-to-nightside streaming wind in the order of 0.7 km s−1 and a moderate super-rotational streaming wind in the order of 3–4 km s−1, challenging claims of prevailing strong winds on HD 189733b.
Cosmological constraints from density-split clustering in the BOSS CMASS galaxy sample
Authors: Paillas Enrique , Cuesta-Lazaro Carolina , Percival Will J , Nadathur Seshadri , Cai Yan-Chuan , Yuan Sihan , Beutler Florian , de Mattia Arnaud , Eisenstein Daniel J , Forero-Sanchez Daniel , Padilla Nelson , Pinon Mathilde , Ruhlmann-Kleider Vanina , Sánchez Ariel G , Valogiannis Georgios , Zarrouk Pauline 
Published: April 2024

ABSTRACT
We present a clustering analysis of the BOSS DR12 CMASS galaxy sample, combining measurements of the galaxy two-point correlation function and density-split clustering down to a scale of $1 \, h^{-1}\, \text{Mpc}$. Our theoretical framework is based on emulators trained on high-fidelity mock galaxy catalogues that forward model the cosmological dependence of the clustering statistics within an extended-ΛCDM framework, including redshift-space and Alcock–Paczynski distortions. Our base-ΛCDM analysis finds ωcdm = 0.1201 ± 0.0022, σ8 = 0.792 ± 0.034, and ns = 0.970 ± 0.018, corresponding to fσ8 = 0.462 ± 0.020 at z ≈ 0.525, which is in agreement with Planck 2018 predictions and various clustering studies in the literature. We test single-parameter extensions to base-ΛCDM, varying the running of the spectral index, the dark energy equation of state, and the density of mass-less relic neutrinos, finding no compelling evidence for deviations from the base model. We model the galaxy–halo connection using a halo occupation distribution framework, finding signatures of environment-based assembly bias in the data. We validate our pipeline against mock catalogues that match the clustering and selection properties of CMASS, showing that we can recover unbiased cosmological constraints even with a volume 84 times larger than the one used in this study.
RABBITS – II. The impact of AGN feedback on coalescing supermassive black holes in disc and elliptical galaxy mergers
Authors: Liao Shihong , Irodotou Dimitrios , Johansson Peter H , Naab Thorsten , Rizzuto Francesco Paolo , Hislop Jessica M , Wright Ruby J , Rawlings Alexander 
Published: April 2024

ABSTRACT
In this study of the ‘Resolving supermAssive Black hole Binaries In galacTic hydrodynamical Simulations’ (RABBITS) series, we investigate the orbital evolution of supermassive black holes (SMBHs) during galaxy mergers. We simulate both disc and elliptical galaxy mergers using the ketju code, which can simultaneously follow galaxy (hydro-)dynamics and small-scale SMBH dynamics with post-Newtonian corrections. With our SMBH binary subgrid model, we show how active galactic nuclei (AGNs) feedback affects galaxy properties and SMBH coalescence. We find that simulations without AGN feedback exhibit excessive star formation, resulting in merger remnants that deviate from observed properties. Kinetic AGN feedback proves more effective than thermal AGN feedback in expelling gas from the centre and quenching star formation. The different central galaxy properties, which are a result of distinct AGN feedback models, lead to varying rates of SMBH orbital decay. In the dynamical friction phase, galaxies with higher star formation and higher SMBH masses possess denser centres, become more resistant to tidal stripping, experience greater dynamical friction, and consequently form SMBH binaries earlier. As AGN feedback reduces gas densities in the centres, dynamical friction by stars dominates over gas. In the SMBH hardening phase, compared to elliptical mergers, disc mergers exhibit higher central densities of newly formed stars, resulting in accelerated SMBH hardening and shorter merger time-scales (i.e. $\lesssim 500$ Myr versus $\gtrsim 1$ Gyr). Our findings highlight the importance of AGN feedback and its numerical implementation in understanding the SMBH coalescing process, a key focus for low-frequency gravitational wave observatories.
Emergence of hot corona and truncated disc in simulations of accreting stellar mass black holes
Authors: Nemmen Rodrigo , Vemado Artur , Almeida Ivan , Garcia Javier , Motta Pedro N 
Published: April 2024

ABSTRACT
Stellar mass black holes in X-ray binaries (XRBs) are known to display different states characterized by different spectral and timing properties, understood in the framework of a hot corona coexisting with a thin accretion disc whose inner edge is truncated. There are several open questions related to the nature and properties of the corona, the thin disc, and dynamics behind the hard state. This motivated us to perform 2D hydrodynamical simulations of accretion flows onto a $10 \, \mathrm{M}_\odot$ black hole. We consider a two-temperature plasma, incorporate radiative cooling with bremmstrahlung, synchrotron, and Comptonization losses and approximate the Schwarzschild space–time via a pseudo-Newtonian potential. We varied the mass accretion rate in the range $0.02 \le \dot{M}/\dot{M}_{\rm Edd} \le 0.35$. Our simulations show the natural emergence of a colder truncated thin disc embedded in a hot corona, as required to explain the hard state of XRBs. We found that as $\dot{M}$ increases, the corona contracts and the inner edge of the thin disc gets closer to the event horizon. At a critical accretion rate $0.02 \le \dot{M}_{\text{crit }}/\dot{M}_{\rm Edd} \le 0.06$, the thin disc disappears entirely. We discuss how our simulations compare with XRB observations in the hard state.
Mercury and selenium distribution in human brain tissue using synchrotron micro-X-ray fluorescence
Authors: Webb Alexis N , Antipova Olga , Shughoury Serena , Farfel Jose M , Bennett David A , Du Yansheng , Zheng Wei , Nie Linda H 
Published: April 2024

Abstract
Mercury is a well-recognized environmental contaminant and neurotoxin, having been associated with a number of deleterious neurological conditions including neurodegenerative diseases, such as Alzheimer's disease. To investigate how mercury and other metals behave in the brain, we used synchrotron micro-X-ray fluorescence to map the distribution pattern and quantify concentrations of metals in human brain. Brain tissue was provided by the Rush Alzheimer's Disease Center and samples originated from individuals diagnosed with Alzheimer's disease and without cognitive impairment. Data were collected at the 2-ID-E beamline at the Advanced Photon Source at Argonne National Laboratory with an incident beam energy of 13 keV. Course scans were performed at low resolution to determine gross tissue features, after which smaller regions were selected to image at higher resolution. The findings revealed (1) the existence of mercury particles in the brain samples of two subjects; (2) co-localization and linear correlation of mercury and selenium in all particles; (3) co-localization of these particles with zinc structures; and (4) association with sulfur in some of these particles. These results suggest that selenium and sulfur may play protective roles against mercury in the brain, potentially binding with the metal to reduce the induced toxicity, although at different affinities. Our findings call for further studies to investigate the relationship between mercury, selenium, and sulfur, as well as the potential implications in Alzheimer's disease and related dementias.
Smoking and Idiopathic Pulmonary Fibrosis: A Meta-analysis
Authors: Fang Min , He Bixiu , Xiao Jian 
Published: April 2024

Abstract

Introduction
In this study, we aimed to systematically explore the relationship between smoking and idiopathic pulmonary fibrosis (IPF).

Aims and Methods
The PubMed, Web of Science, and Embase databases were searched to systematically identify eligible studies. The Newcastle‒Ottawa Quality Assessment Scale (NOS) was used to evaluate the quality of the selected studies. The pooled odds ratio (OR) and survival hazard ratio (HR) were calculated with a random effects model using Stata 16.0 software.

Results
Thirty studies were enrolled. All of the included studies were considered to have intermediate or high quality. Nine studies were suitable for meta-analysis of ORs, and 21 studies were suitable for meta-analysis of survival HR. The pooled analysis revealed a significant difference in the risk of IPF between the smoking group and the never-smoking group (OR 1.71, 95% CI: 1.27 to 2.30, p &lt; .001), indicating that smoking is a risk factor for IPF. When analyzing pooled survival HRs, never smoking was compared to former smoking or current smoking. Former smoking was shown to be a poor prognostic factor for IPF (HR 1.43, 95% CI: 1.18 to 1.74, p &lt; .001), but current smoking was not a significant factor.

Conclusions
Our results indicated that smoking is a risk factor for IPF patients.

Implications
In this study, we mainly concluded that smoking is a risk factor for IPF and that former smoking is a poor prognostic factor for IPF. To the best of our knowledge, this is the first meta-analysis report focusing on the association between smoking per se and IPF. Through our current study, we hope to further raise awareness of the relationship between smoking and IPF.
Mayer-Rokitansky-Kuster-Hauser syndrome complicated with giant mucinous cystadenoma and inguinal herniation: case report
Authors: Susilo Artha Falentin Putri , Suryawan Alfonsus Zeus , Tjandraprawira Kevin Dominique , Rachmawati Anita 
Published: April 2024

Abstract
Introduction: Coexistence of Mayer-Rokitansky-Kuster-Hauster syndrome (MRKH) with other conditions is rare, especially when MRKH was found in a young woman presenting with ovarian malignancy. This case report wishes to highlight MRKH complicated with giant mucinous cystadenoma and bilateral inguinal hernia. Case report: A 22-year-old nulligravid woman was admitted with primary amenorrhea and abdominal mass. Abdominal examination revealed a cystic mass 25 × 25 × 20 cm in size and a vagina 1 cm in length. Pelvic magnetic resonance imaging (MRI) showed a giant multiloculated left ovarian mass amidst the absence of uterus. During the surgery, the giant multiloculated cystic mass was identified as mucinous cystadenoma on frozen section. Bilateral medial inguinal hernia was also identified. Discussion: MRKH coexisting with other disease is rare but considering other structures arising from paramesonephric duct (PMD) may exist, allows the possibility of other structural anomalies. Conclusions: The present report illustrates a rare case of MRKH syndrome with giant ovarian cystadenoma and inguinal hernia.
Spider mite herbivory induces an ABA-driven stomatal defense
Authors: Rosa-Diaz Irene , Rowe James , Cayuela-Lopez Ana , Arbona Vicent , Díaz Isabel , Jones Alexander M 
Published: April 2024

Abstract
Arthropod herbivory poses a serious threat to crop yield, prompting plants to employ intricate defense mechanisms against pest feeding. The generalist pest 2-spotted spider mite (Tetranychus urticae) inflicts rapid damage and remains challenging due to its broad target range. In this study, we explored the Arabidopsis (Arabidopsis thaliana) response to T. urticae infestation, revealing the induction of abscisic acid (ABA), a hormone typically associated with abiotic stress adaptation, and stomatal closure during water stress. Leveraging a Forster resonance energy transfer (FRET)-based ABA biosensor (nlsABACUS2-400n), we observed elevated ABA levels in various leaf cell types postmite feeding. While ABA's role in pest resistance or susceptibility has been debated, an ABA-deficient mutant exhibited increased mite infestation alongside intact canonical biotic stress signaling, indicating an independent function of ABA in mite defense. We established that ABA-triggered stomatal closure effectively hinders mite feeding and minimizes leaf cell damage through genetic and pharmacological interventions targeting ABA levels, ABA signaling, stomatal aperture, and density. This study underscores the critical interplay between biotic and abiotic stresses in plants, highlighting how the vulnerability to mite infestation arising from open stomata, crucial for transpiration and photosynthesis, reinforces the intricate relationship between these stress types.
Histone H3K27 demethylase SlJMJ3 modulates fruit ripening in tomato
Authors: Li Zhiwei , Zeng Jing , Zhou Yijie , Ding Xiaochun , Jiang Guoxiang , Wu Keqiang , Jiang Yueming , Duan Xuewu 
Published: April 2024

Abstract
The histone lysine (K) demethylase 4 (KDM4/JHDM3) subfamily of jumonji domain–containing demethylases (JMJs) has been implicated in various aspects of plant development. However, their involvement in regulating the ripening of fleshy fruits remains unclear. In this study, we identified SlJMJ3, a member of the KDM4/JHDM3 family, as an H3K27me3 demethylase in tomato (Solanum lycopersicum) that plays an important role in fruit ripening regulation. Overexpression of SlJMJ3 leads to accelerated fruit ripening, whereas loss of function of SlJMJ3 delays this process. Furthermore, we determined that SlJMJ3 exerts its regulatory function by modulating the expression of multiple ripening-related genes involved in ethylene biosynthesis and response, carotenoid metabolism, cell wall modification, transcriptional control, and DNA methylation modification. SlJMJ3 binds directly to the promoters of ripening-related genes harboring the CTCTGYTY motif and activates their expression. Additionally, SlJMJ3 reduces the levels of H3K27me3 at its target genes, thereby upregulating their expression. In summary, our findings highlight the role of SlJMJ3 in the regulation of fruit ripening in tomato. By removing the methyl group from trimethylated histone H3 lysine 27 at ripening-related genes, SlJMJ3 acts as an epigenetic regulator that orchestrates the complex molecular processes underlying fruit ripening.
Transcription factors HB21/40/53 trigger inflorescence arrest through abscisic acid accumulation at the end of flowering
Authors: Sánchez-Gerschon Verónica , Martínez-Fernández Irene , González-Bermúdez María R , de la Hoz-Rodríguez Sergio , González Florenci V , Lozano-Juste Jorge , Ferrándiz Cristina , Balanzà Vicente 
Published: April 2024

Abstract
Flowers, and hence, fruits and seeds, are produced by the activity of the inflorescence meristem after the floral transition. In plants with indeterminate inflorescences, the final number of flowers produced by the inflorescence meristem is determined by the length of the flowering period, which ends with inflorescence arrest. Inflorescence arrest depends on many different factors, such as the presence of seeds, the influence of the environment, or endogenous factors such as phytohormone levels and age, which modulate inflorescence meristem activity. The FRUITFULL-APETALA2 (FUL-AP2) pathway plays a major role in regulating the end of flowering, likely integrating both endogenous cues and those related to seed formation. Among AP2 targets, HOMEOBOX PROTEIN21 (HB21) has been identified as a putative mediator of AP2 function in the control of inflorescence arrest. HB21 is a homeodomain leucine zipper transcription factor involved in establishing axillary bud dormancy. Here, we characterized the role of HB21 in the control of the inflorescence arrest at the end of flowering in Arabidopsis (Arabidopsis thaliana). HB21, together with HB40 and HB53, are upregulated in the inflorescence apex at the end of flowering, promoting floral bud arrest. We also show that abscisic acid (ABA) accumulation occurs in the inflorescence apex in an HB-dependent manner. Our work suggests a physiological role of ABA in floral bud arrest at the end of flowering, pointing to ABA as a regulator of inflorescence arrest downstream of the HB21/40/53 genes.
Transcription factor CmHSFA4–CmMYBS3 complex enhances salt tolerance in chrysanthemum by repressing CmMYB121 expression
Authors: Wang Xinhui , Wang Yue , Jiang Yuhan , Wang Han , Zhou Lijie , Li Fei , Wang Likai , Jiang Jiafu , Chen Fadi , Chen Sumei 
Published: April 2024

Abstract
Excessive soil salinity not only hampers plant growth and development but can also lead to plant death. Previously, we found that heat-shock factor A4 (CmHSFA4) enhances the tolerance of chrysanthemum (Chrysanthemum morifolium) to salt. However, the underlying molecular mechanism remains unclear. In this study, we identified a candidate MYB transcription factor, CmMYB121, which responded to salt stress. We observed that the CmMYB121 transcription is suppressed by CmHSFA4. Moreover, overexpression of CmMYB121 exacerbated chrysanthemum sensitivity to salt stress. CmHSFA4 directly bound to the promoter of CmMYB121 at the heat-shock element. Protein–protein interaction assays identified an interaction between CmHSFA4 and CmMYBS3, a transcriptional repressor, and recruited the corepressor TOPLESS (CmTPL) to inhibit CmMYB121 transcription by impairing the H3 and H4 histone acetylation levels of CmMYB121. Our study demonstrated that a CmHSFA4–CmMYBS3–CmTPL complex modulates CmMYB121 expression, consequently regulating the tolerance of chrysanthemum to salt. The findings shed light on the responses of plants to salt stress.
Reconstructing robust background integral field unit spectra using machine learning
Authors: Rhea Carter Lee , Hlavacek-Larrondo Julie , Giroux Justine , Thilloy Auriane , Choi Hyunseop , Rousseau-Nepton Laurie , Gendron-Marsolais Marie-Lou , Pasquato Mario , Prunet Simon 
Published: April 2024

ABSTRACT
In astronomy, spectroscopy consists of observing an astrophysical source and extracting its spectrum of electromagnetic radiation. Once extracted, a model is fit to the spectra to measure the observables, leading to an understanding of the underlying physics of the emission mechanism. One crucial, and often overlooked, aspect of this model is the background emission, which contains foreground and background astrophysical sources, intervening atmospheric emission, and artefacts related to the instrument such as noise. This paper proposes an algorithmic approach to constructing a background model for SITELLE observations using statistical tools and supervised machine learning algorithms. SITELLE is an imaging Fourier transform spectrometer located at the Canada-France-Hawaii Telescope, which produces a three-dimensional data cube containing the position of the emission (two dimensions) and the spectrum of the emission. SITELLE has a wide field of view (11 arcmin × 11 arcmin), which makes the background emission particularly challenging to model. We apply a segmentation algorithm implemented in photutils to divide the data cube into background and source spaxels. After applying a principal component analysis (PCA) on the background spaxels, we train an artificial neural network to interpolate from the background to the source spaxels in the PCA coefficient space, which allows us to generate a local background model over the entire data cube. We highlight the performance of this methodology by applying it to SITELLE observations obtained of a Star-formation, Ionized Gas and Nebular Abundances Legacy Survey galaxy, NGC 4449, and the Perseus galaxy cluster of galaxies, NGC 1275. We discuss the physical interpretation of the principal components and noise reduction in the resulting PCA-based reconstructions. Additionally, we compare the fit results using our new background modelling approach with standard methods used in the literature and find that our method better captures the emission from H ii regions in NGC 4449 and the faint emission regions in NGC 1275. These methods also demonstrate that the background does change as a function of the position of the data cube. While the approach is applied explicitly to SITELLE data in this study, we argue that it can be readily adapted to any integral field unit style data, enabling the user to obtain more robust measurements on the flux of the emission lines.
Topological Perturbations in the Functional Connectome Support the Deficit/Non-deficit Distinction in Antipsychotic Medication-Naïve First Episode Psychosis Patients
Authors: Teles Matheus , Maximo Jose Omar , Lahti Adrienne Carol , Kraguljac Nina Vanessa 
Published: April 2024

Abstract

Background
Heterogeneity in the etiology, pathophysiology, and clinical features of schizophrenia challenges clinicians and researchers. A helpful approach could be stratifying patients according to the presence or absence of clinical features of the deficit syndrome (DS). DS is characterized by enduring and primary negative symptoms, a clinically less heterogeneous subtype of the illness, and patients with features of DS are thought to present abnormal brain network characteristics, however, this idea has received limited attention. We investigated functional brain network topology in patients displaying deficit features and those who do not.

Design
We applied graph theory analytics to resting-state functional magnetic resonance imaging data of 61 antipsychotic medication-naïve first episode psychosis patients, 18 DS and 43 non-deficit schizophrenia (NDS), and 72 healthy controls (HC). We quantified small-worldness, global and nodal efficiency measures, shortest path length, nodal local efficiency, and synchronization and contrasted them among the 3 groups.

Results
DS presented decreased network integration and segregation compared to HC and NDS. DS showed lower global efficiency, longer global path lengths, and lower global local efficiency. Nodal efficiency was lower and the shortest path length was longer in DS in default mode, ventral attention, dorsal attention, frontoparietal, limbic, somatomotor, and visual networks compared to HC. Compared to NDS, DS showed lower efficiency and longer shortest path length in default mode, limbic, somatomotor, and visual networks.

Conclusions
Our data supports increasing evidence, based on topological perturbations of the functional connectome, that deficit syndrome may be a distinct form of the illness.