bluuebunny/crossref_metadata_2025_split huggingface dataset:
LIPID RICH 1 Modulates Allocation of Carbon between Starch and Triacylglycerol in Arabidopsis Leaves
Authors: Yamaguchi Mebae , Shigenobu Shuji , Yamaguchi Katsushi , Higashi Yasuhiro , Okazaki Yozo , Saito Kazuki , Mishiro-Sato Emi , Kano Keiko , Sugiyama Ryosuke , Yamazaki Mami , Sugano Shigeo S , Fukuyoshi Shuichi , Ueda Haruko , Hara-Nishimura Ikuko , Shimada Takashi L 
Published: February 2025

Abstract
Plants accumulate starch and triacylglycerols (TAGs) as carbon sources. Leaves primarily store starch in chloroplasts, with some TAGs stored in lipid droplets, but how carbon resource allocation is regulated in leaves during cellular metabolism is largely unknown. Using a forward genetics approach, we isolated an Arabidopsis thaliana mutant with more lipid droplets in its leaves than the wild type, named lipid rich 1 (liri1). The overaccumulation of lipid droplets was caused by the loss of function in the causal gene, encoding an uncharacterized protein. TAG levels were five-fold higher and starch levels two-fold lower in the leaves of liri1 than the wild type. LIRI1 localized to the chloroplasts, and the contents of chloroplast membrane lipids were 20% higher in liri1 leaves than in wild-type leaves. Co-immunoprecipitation assays revealed that LIRI1 interacts with acetyl-coenzyme A carboxylase carboxyltransferase alpha subunit (an enzyme for fatty acid biosynthesis) and starch synthase 4 (an enzyme for starch biosynthesis). In isotope tracer experiments using [1-13C]-sodium acetate, more 13C was incorporated into TAGs in liri1 leaves than in wild-type leaves. Moreover, liri1 plants showed growth defects and irregular chloroplasts. These results suggest that LIRI1 affects the carbon trade-off to inhibit lipid production in leaves.
The characterization of Herbaspirillum huttiense isolated from a uremic patient: virulence and antimicrobial efficacy in the Galleria mellonella model
Authors: Liu Yuchun , Zhu Rui , Liu Dongmei , Hu Yue , Xia Qing , Liu Xinwei , Wang Chunxia , Li Yongwei 
Published: February 2025

Abstract
Herbaspirillum species are typically isolated from plants and are known for their role in crop nitrogen fixation. Recently, they have been found to colonize humans and cause infections. This study aimed to identify and characterize two Herbaspirillum huttiense strains (CLJ01 and CLJ02) isolated from the blood of a uremic patient, with a focus on evaluating their pathogenicity and antibiotic efficacy. The strains were identified using the VITEK2 system, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry , and 16S rRNA gene sequencing, confirming their identity as H. huttiense. High-throughput sequencing further revealed the presence of the resistance gene arnA, which confers resistance to polymyxin. For the first time, the pathogenicity of H. huttiense was assessed using a Galleria mellonella infection model. The results demonstrated a concentration-dependent virulence, with CLJ01 exhibiting slightly higher pathogenicity. Additionally, meropenem showed significant antimicrobial efficacy in the G. mellonella infection model, particularly under conditions of high bacterial load, indicating strong therapeutic potential. In conclusion, this study provides experimental evidence supporting the correct diagnosis and treatment of H. huttiense infections. Furthermore, the findings underscore the importance of accurately identifying rare pathogens in clinical settings for effective treatment.
Development of cyclopeptide inhibitors specifically disrupting FXR-coactivator interaction in the intestine as a novel therapeutic strategy for MASH
Authors: Li Yazhou , Jiao Tingying , Cheng Xi , Liu Lu , Zhang Mengjiao , Li Jian , Wang Jue , Hu Shulei , Li Cuina , Yu Tao , Liu Yameng , Li Yangtai , Zhang Yu , Sun Chuying , Sun Jina , Wang Jiang , Xie Cen , Liu Hong 
Published: February 2025

Abstract
Intestinal farnesoid X receptor (FXR) antagonists have been proven to be efficacious in ameliorating metabolic diseases, particularly for the treatment of metabolic dysfunction-associated steatohepatitis (MASH). All the reported FXR antagonists target to the ligand-binding pocket (LBP) of the receptor, whereas antagonist acting on the non-LBP site of nuclear receptor (NR) is conceived as a promising strategy to discover novel FXR antagonist. Here, we have postulated the hypothesis of antagonizing FXR by disrupting the interaction between FXR and coactivators, and have successfully developed a series of macrocyclic peptides as FXR antagonists based on this premise. The cyclopeptide DC646 not only exhibits potent inhibitory activity of FXR, but also demonstrates a high degree of selectivity towards other NRs. Moreover, cyclopeptide DC646 has high potential therapeutic benefit for the treatment of MASH in an intestinal FXR-dependent manner, along with a commendable safety profile. Mechanistically, distinct from other known FXR antagonists, cyclopeptide DC646 specifically binds to the coactivator binding site of FXR, which can block the coactivator recruitment, reducing the circulation of intestine-derived ceramides to the liver, and promoting the release of glucagon-like peptide-1 (GLP-1). Overall, we identify a novel cyclopeptide that targets FXR-coactivator interaction, paving the way for a new approach to treating MASH with FXR antagonists.
Modelling a transiting circumbinary disc in the HD98800 system
Authors: Faruqi Amena , Kennedy Grant , Nealon Rebecca , Rowther Sahl 
Published: February 2025

ABSTRACT
We present synthetic optical light curves of the hierarchical HD 98800 quadruple system over a decade-long period when the circumbinary disc encircling the system’s B binary is expected to eclipse the light from the A binary. We produce and compare light curves of this transit event using hydrodynamical models with different values of the disc’s gas mass, dust mass, and $\alpha$-viscosity to determine the observable effect of each parameter. These comparisons provide insight that could aid in the analysis of observational data from the system when the real transit occurs and provide recommendations for how such observations should be made. We find that a higher dust mass or higher value of $\alpha$ correspond to a longer transit, with the gas mass having a more minor effect on the overall shape and duration of the transit. A higher $\alpha$ has an observable effect on the viscous spreading at the outer edge of the disc, though is countered through truncation by the outer binary. It is also shown that long-term interactions between the outer binary and disc can excite spiral arms in the disc, which introduce observable asymmetries to the light curve. Our models suggest that the transit should have begun at the time of writing, but no dimming has yet been observed. It is likely that the disc has a smaller radial extent than our models, due to a lower viscosity than can be simulated with Smoothed Particle Hydrodynamics. The transit is expected to last 8–11 yr, ending in late 2034 at the latest.
Optical evolution of AT 2024wpp: the high-velocity outflows in Cow-like transients are consistent with high spherical symmetry
Authors: Pursiainen M , Killestein T L , Kuncarayakti H , Charalampopoulos P , Warwick B , Lyman J , Kotak R , Leloudas G , Coppejans D , Kravtsov T , Maeda K , Nagao T , Taguchi K , Ackley K , Dhillon V S , Galloway D K , Kumar A , O’Neill D , Ramsay G , Steeghs D 
Published: February 2025

ABSTRACT
We present the analysis of optical/near-infrared (NIR) data and host galaxy properties of a bright, extremely rapidly evolving transient, AT 2024wpp, which resembles the enigmatic AT 2018cow. AT 2024wpp rose to a peak brightness of $c=-21.9$ mag in 4.3 d and remained above the half-maximum brightness for only 6.7 d. The blackbody fits to the photometry show that the event remained persistently hot ($T\gtrsim 20\, 000$ K) with a rapidly receding photosphere ($v\sim 11\, 500$ km s$^{-1}$), similarly to AT 2018cow albeit with a several times larger photosphere. $JH$ photometry reveals an NIR excess over the thermal emission at $\sim +20$ d, indicating a presence of an additional component. The spectra are consistent with blackbody emission throughout our spectral sequence ending at $+21.9$ d, showing a tentative, very broad emission feature at $\sim 5500$ Å – implying that the optical photosphere is likely within a near-relativistic outflow. Furthermore, reports of strong X-ray and radio emission cement the nature of AT 2024wpp as a likely Cow-like transient. AT 2024wpp is the second event of the class with optical polarimetry. Our $BVRI$ observations obtained from $+6.1$ to $+14.4$ d show a low polarization of $P\lesssim 0.5$ per cent across all bands, similar to AT 2018cow that was consistent with $P\sim 0$ per cent during the same outflow-driven phase. In the absence of evidence for a preferential viewing angle, it is unlikely that both events would have shown low polarization in the case that their photospheres were aspherical. As such, we conclude that the near-relativistic outflows launched in these events are likely highly spherical, but polarimetric observations of further events are crucial to constrain their ejecta geometry and stratification in detail.
The quenching of star formation in dwarf galaxies: new perspectives from deep-wide surveys
Authors: Kaviraj S , Lazar I , Watkins A E , Laigle C , Martin G , Jackson R A 
Published: February 2025

Abstract
Dwarf galaxies dominate the galaxy number density, making them critical to our understanding of galaxy evolution. However, typical dwarfs are too faint to be visible outside the very local Universe in past surveys like the SDSS, which offer large footprints but are shallow. Dwarfs in such surveys have relatively high star formation rates, which boost their luminosity, making them detectable in shallow surveys, but also biased and potentially unrepresentative of dwarfs as a whole. Here, we use deep data to perform an unbiased statistical study of ∼7,000 nearby (z &lt; 0.25) dwarfs (108 M⊙ &lt; M⋆ &lt; 109.5 M⊙) in the COSMOS field which, at these redshifts, is a relatively low-density field. At z ∼ 0.05, ∼40 per cent of dwarfs in low-density environments are red/quenched, falling to ∼30 per cent by z ∼ 0.25. Red dwarfs reside closer to nodes, filaments and massive galaxies. Proximity to a massive galaxy appears to be more important in determining whether a dwarf is red, rather than simply its distance from nodes and filaments or the mean density of its local environment. Interestingly, around half of the red dwarfs reside outside the virial radii of massive galaxies and around a third of those also inhabit regions in the lower 50 per cent in density percentile (i.e. regions of very low ambient density). Around half of the red dwarf population is, therefore, quenched by mechanisms unrelated to environment, which are likely to be internal processes such as stellar and AGN feedback.
Structural decomposition of merger-free galaxies hosting luminous AGNs
Authors: Fahey Matthew J , Garland Izzy L , Simmons Brooke D , Keel William C , Shanahan Jesse , Coil Alison , Glikman Eilat , Lintott Chris J , Masters Karen L , Moran Ed , Smethurst Rebecca J , Géron Tobias , Thorne Matthew R 
Published: February 2025

ABSTRACT
Active galactic nucleus (AGN) growth in disc-dominated, merger-free galaxies is poorly understood, largely due to the difficulty in disentangling the AGN emission from that of the host galaxy. By carefully separating this emission, we examine the differences between AGNs in galaxies hosting a (possibly) merger-grown, classical bulge, and AGNs in secularly grown, truly bulgeless disc galaxies. We use galfit to obtain robust, accurate morphologies of 100 disc-dominated galaxies imaged with the Hubble Space Telescope. Adopting an inclusive definition of classical bulges, we detect a classical bulge component in $53.3 \pm 0.5$ per cent of the galaxies. These bulges were not visible in Sloan Digital Sky Survey photometry, however these galaxies are still unambiguously disc-dominated, with an average bulge-to-total luminosity ratio of $0.1 \pm 0.1$. We find some correlation between bulge mass and black hole mass for disc-dominated galaxies, though this correlation is significantly weaker in comparison to the relation for bulge-dominated or elliptical galaxies. Furthermore, a significant fraction ($\gtrsim 90$ per cent) of our black holes are overly massive when compared to b the relationship for elliptical galaxies. We find a weak correlation between total stellar mass and black hole mass for the disc-dominated galaxies, hinting that the stochasticity of black hole–galaxy co-evolution may be higher in disc-dominated than bulge-dominated systems.
Two-temperature treatments in magnetically arrested disk GRMHD simulations more accurately predict light curves of Sagittarius A*
Authors: Salas L D S , Liska M T P , Markoff S B , Chatterjee K , Musoke G , Porth O , Ripperda B , Yoon D , Mulaudzi W 
Published: February 2025

Abstract
The Event Horizon Telescope Collaboration (EHTC) observed the Galactic centre source Sagittarius A* (Sgr A*) and used emission models primarily based on single ion temperature (1T) general relativistic magnetohydrodynamic (GRMHD) simulations. This predicted emission is strongly dependent on a modelled prescription of the ion-to-electron temperature ratio. The most promising models are magnetically arrested disk (MAD) states. However, nearly all MAD models exhibit larger temporal fluctuations in radiative 230 GHz emission compared to observations. This limitation possibly stems from the fact that the actual temperature ratio depends on microphysical dissipation, radiative processes and other effects not captured in ideal fluid simulations. Therefore, we investigate the effects of two-temperature (2T) thermodynamics in MAD GRMHD simulations of Sgr A*, where the temperatures of both species are evolved. We find that the 230 GHz synchrotron flux variability more closely matches historical observations when we include the 2T treatment compared to 1T simulations. For the low accretion rates of Sgr A*, a common assumption is to neglect radiative cooling. However, we find that the radiative cooling of electrons—via synchrotron, inverse Compton, and bremsstrahlung processes—reduces the electron temperature in the inner disk, where the EHT observes, by about 10 %, which, in turn, decreases both the (sub)millimetre synchrotron flux and its temporal fluctuations compared to uncooled simulations.
The protective effect of low-dose nicotine on ischemia stroke by maintaining the integrity of the blood-brain barrier
Authors: Pang Qianqian , Yan Xinyang , Chen Zheng , Yun Liang , Qian Jiang , Dong Zeyi , Wang Miao , Deng Wei , Fu Yao , Hai Tao , Chen Zhichao , Rong Xianfang 
Published: February 2025

Abstract

Introduction
Increasing evidence has shown that low-dose nicotine could have preventive and therapeutic effects on ischemic stroke (IS). Nevertheless, direct evidence is still missing, especially key molecules and signal pathways.

Methods
Mice were randomly assigned to one of three groups: the sham group, the control group, and the nicotine-treated group. In the control group, mice were subjected to middle cerebral artery occlusion/reperfusion (MCAO/R). In the nicotine-treated group, mice were exposed to 12 μg/ml nicotine in their drinking water for 1 month prior to undergoing surgery. For in vitro blood-brain barrier (BBB) model, hCMEC/D3 monolayers were prepared on Transwells and pre-treated with nicotine for 48 hours and then subjected to oxygen-glucose deprivation/reoxygenation (OGD/R). Moreover, RNA-seq was adopted to explore the potential targets and signaling pathways regarding the protective role of nicotine.

Results
MCAO/R resulted in significantly compromised BBB integrity and serious brain damage. Notably, pretreatment of mice with 12μg/ml nicotine for one month significantly reduced IS-induced BBB damage and its associated brain injury. In addition, the permeability of hCMEC/D3 monolayer endothelial cells was significantly reduced under OGD/R conditions, which could be ameliorated by nicotine pretreatment. The RNA-seq results showed that TGF-β and Wnt signaling pathways were associated with pathways associated with DEGs between OGD/R and OGD/R plus nicotine treatment. Finally, the activation of Wnt/β-catenin pathways could be antagonized by the α7 nicotine acetylcholine receptor (α7 nAChR) inhibitor α-BTX.

Conclusions
These results demonstrate that nicotine treatment could alleviates the IS-compromised integrity of BBB by regulating the Wnt signal pathway through α7 nAChR.

Implications
The study demonstrates that nicotine at low concentrations exerts neuro-protective effects by supporting the integrity of BBB and subsequent endothelial viability after ischemic stroke. This finding suggests that targeting the BBB, especially endothelial cells, with nicotine treatment is a promising therapeutic strategy for brain injury after ischemic stroke.
Evaluation of phenotypic and behavioral toxicity of micro- and nano-plastic polystyrene particles in larval zebrafish (Danio rerio)
Authors: Levesque Bailey , Hrapovic Sabahudin , Berrué Fabrice , Vogt Anja , Ellis Lee D , Hermabessiere Ludovic 
Published: February 2025

Abstract
Plastic particles have been found in all environments and it is necessary to understand the risks these particles pose in, and to, the environment. The objectives of this work were to understand the toxic effects of varying size and concentration of polystyrene (PS) micro- and nano-plastics in zebrafish embryos and their fate within the larvae. In this work, larval zebrafish (Danio rerio) were exposed to six sizes (0.05, 0.25, 0.53, 2.1, 6.02, and 10.2 µm diameter) and concentrations (0.0005 to 0.2 µg/µL) of PS micro/nanoplastics particles. The zebrafish embryo toxicity (ZET) and the general and behavioral toxicity (GBT) assays were used to determine particle toxicity in embryos. Behavioral analysis was performed and micro/nanoplastics uptake and organ distribution were assessed. Phenotypic and behavioral toxicity was observed in all exposures with the exception of 0.25 µm particle-exposed larvae. Significant phenotypic toxicity was seen at the highest tested exposure concentration, with some sizes showing potential recovery as time increased in the assay. Behavioral analysis demonstrated a decrease in baseline activity across all micro- and nano-plastic sizes. Significant increases in light–dark responses were recorded in ZET assays of smaller-sized particles and no significant effects were observed at larger sizes. Significant decreases in this response were reported in the GBT assays of all tested sizes with the exception of the 0.05-µm particles. These assays demonstrate the general, developmental, and neurotoxicity of micro/nanoplastics to a model organism, which can be used to infer individual and population-level effects of exposure.
Machine learning-based unsupervised phenotypic clustering analysis of patients with IgA nephropathy: Distinct therapeutic responses of different groups
Authors: Wang Yiqin , Wen Qiong , Lian Xingji , Liu Lingling , Zhou Qian , Zhang Yunfang , Chen Chao , Wu Gengmao , Wang Cheng , Liu Qinghua , Chen Wei 
Published: February 2025

Abstract

Background:
Immunoglobulin A nephropathy (IgAN) has a heterogeneous clinical presentation. Comparison of different IgAN subgroups may facilitate the application of more targeted therapies. This study was aimed to distinct disease phenotypes in IgAN and to develop prognostic models for renal composite outcomes.

Methods:
Clinical and pathological data were from 2000 patients with biopsy-proven primary IgAN from four centers, including the First Affiliated Hospital of Sun Yat-sen University (SYSU), the Fifth Affiliated Hospital of Sun Yat-sen University, the Huadu District People’s Hospital of Guangzhou, and Jieyang Affiliated Hospital of SYSU in China between January 2009 and December 2018 (training cohort: 1203 patients, validation cohort: 797 patients). Components from principal components analysis (PCA) were used to fit a k-means clustering algorithm and identify distinct subgroups. A subgroup-based prediction model was developed to assess prognosis and therapeutic efficacy in each subgroup.

Results:
The PCA-k-means clustering algorithm identified four subgroups. Subgroup 1 had significantly better long-term renal survival upon administration of a renin-angiotensin system blocker (adjusted hazard ratio [aHR]: 0.16, 95% confidence interval [CI]: 0.10–0.27, P <0.001). Subgroup 2 had a significant improvement from corticosteroid therapy (aHR: 0.19, 95% CI: 0.06–0.61, P = 0.005). Subgroups 3 and 4 had milder pathological changes and relatively stable kidney function for several years. Subgroup 3 (predominantly males) had a high incidence of metabolic risk factors, necessitating more intensive monitoring; subgroup 4 (predominantly females) had a high incidence of recurrent macroscopic hematuria. These patterns were similar in the validation cohort. A subgroup-based prognosis prediction model demonstrated an area under the curve of 0.856 in the validation dataset.

Conclusion:
The unsupervised clustering method provided reliable classification of IgAN patients into different subgroups according to clinical features, prognoses, and treatment responsiveness. Our subgroup-based prediction model has significant clinical utility for the assessment of risk and treatment in patients with IgAN.
Transcription factor ATF3 aggravates kidney fibrosis by maintaining the state of histone H3 lysine 27 acetylation
Authors: Yang Lina , Chen Yilong , Guo Fan , Wang Bo , Ying Zhiye , Kuang Yalan , Zeng Xiaoxi , Ma Liang , Yu Haopeng , Fu Ping 
Published: February 2025

Abstract

Background:
Chronic kidney disease (CKD) is a global health issue, with renal fibrosis being a common pathway in CKD development. Histone modification plays crucial roles in transcriptional regulation, but their pathological functions and mechanisms in CKD are not well understood.

Methods:
We utilized chromatin immunoprecipitation with next-generation DNA sequencing (ChIP-seq) and RNA-seq to evaluate the states and functions of H3 lysine 27 acetylation (H3K27ac) and H3 lysine 4 trimethylation (H3K4me3) in kidney of CKD mice. We identified epigenetic factors regulating H3K27ac through motif analysis. Expression of activating transcription factor 3 (ATF3) in CKD mouse models and patients’ kidneys was validated via immunofluorescence staining or Western blot. We further generated the Atf3 deficient (Atf3
-/-) mice to explore its effect in kidney function and fibrosis. ChIP-seq of H3K27ac from Atf3
-/- CKD mice was employed to validate ATF3’s regulatory effects. We explored how ATF3 maintains the state of H3K27ac by integrating the data sources from multiple databases.

Results:
The states of H3K27ac and H3K4me3 were changed during CKD, and positively correlated with differential gene expression. ATF3 was highly expressed in kidney of both patients and mice with CKD, and co-localized with H3K27ac in genome, epigenetically regulating H3K27ac state. Atf3 deficient in CKD mice significantly ameliorated kidney dysfunction and fibrotic phenotype, and reduced H3K27ac levels at the ATF3 binding sites. Mechanically, ATF3 may recruit the histone acetyltransferases (HATs) network to maintain the H3K27ac state during CKD.

Conclusion:
ATF3 promotes kidney injury and fibrosis in CKD by maintaining the state of H3k27ac via recruiting HATs network.