bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of obesity on the CCR6-CCL20 axis in epidermal γδ T cells and IL-17A production in murine wound healing and psoriasis
Authors: Lawler William , Castellanos Tanya , Engel Emma , Alvizo Cristian R , Kasler Antolette , Bshara-Corson Savannah , Jameson Julie M 
Published: January 2025

Abstract
Obesity is associated with comorbidities including type 2 diabetes, chronic nonhealing wounds, and psoriasis. Normally, skin homeostasis and repair is regulated through the production of cytokines and growth factors derived from skin-resident cells including epidermal γδ T cells. However, epidermal γδ T cells exhibit reduced proliferation and defective growth factor and cytokine production during obesity and type 2 diabetes. One of the genes modulated in epidermal γδ T cells during obesity and type 2 diabetes is CCR6, which is the receptor for CCL20. CCL20 is elevated in the skin during obesity and type 2 diabetes. Here, we identify a subset of murine epidermal γδ T cells that express CCR6 upon activation, both in vitro and in vivo. We show that CCL20 stimulates epidermal γδ T cells to produce interleukin (IL)-17, indicating that CCR6 regulates the IL-17 axis in epidermal γδ T cells. In murine models of wound repair and psoriasis, these epidermal γδ T cells upregulate CCR6 and produce IL-17, with obesity amplifying this response during wound repair but having less effect during psoriasis. These findings have novel implications for the regulation of a specific population of IL-17–producing epidermal γδ T cells during skin damage and inflammation.
Genetic evidence for the suppressive role of zebrafish vhl targeting mavs in antiviral innate immunity during RNA virus infection
Authors: Sun Xueyi , Liu Wen , Zhu Chunchun , Wang Zixuan , Deng Hongyan , Liao Qian , Xiao Wuhan , Liu Xing 
Published: January 2025

Abstract
The von Hippel-Lindau (VHL) tumor suppressor gene VHL is a classic tumor suppressor that has been identified in family members with clear cell renal cell carcinomas, central nervous system and retinal hemangioblastomas, phaeochromocytomas, and pancreatic neuroendocrine tumors. The well-defined function of VHL is to mediate proteasomal degradation of hydroxylated hypoxia-inducible factor α proteins, resulting in the downregulation of hypoxia-responsive gene expression. Previously, we reported that VHL inhibits antiviral signaling by targeting mitochondrial antiviral signaling protein (MAVS) for proteasomal degradation. However, due to the lack of a viable animal model, the physiological role and underlying mechanism of VHL in antiviral immunity remains to be elucidated. In this study, we found that heterozygous vhl-deficient zebrafish have normal neutrophils and no gross phenotypic alterations. However, upon spring viremia of carp virus or grass carp reovirus infection, antiviral gene expression is induced in vhl+/− zebrafish compared with wild-type zebrafish. In addition, spring viremia of carp virus replication is suppressed in vhl+/− zebrafish, owing to the enhancement of antiviral ability. Furthermore, by crossing with mavs−/− zebrafish line, we observed that disruption of mavs in vhl+/− zebrafish abrogates the viral resistance exhibited in vhl+/− zebrafish. Thus, we reveal that heterozygous vhl deficiency enhances the antiviral ability of zebrafish against RNA virus infection, and we provide genetic evidence to support that zebrafish mavs serves as a mediator for the suppressive role of vhl in antiviral innate immunity.
Self-absorption effect in soft X-ray emission spectra utilized for bandgap evaluation of semiconductors
Authors: Terauchi Masami , Sato Yohei K 
Published: January 2025

Abstract
The self-absorption effects observed in the background intensity just above the Si L-emission spectra of Si and β-Si3N4, and the C K-emission spectra of diamond and graphite were examined. Based on comparisons with reported results, the energy positions of absorption edges – representing the bottom of conduction bands (CBs) – were assigned. The self-absorption profiles in the background intensities were consistent with previously reported data. The simultaneous observation of valence band and CB edges allowed the determination of a bandgap energy of 1.1 eV for Si, which agrees with the indirect bandgap energy of Si. For β-Si3N4, the bandgap energy was evaluated as 5.1 eV. For diamond, the edge positions were matched with reported values, and the bandgap energy was calculated to be 5.0 eV, slightly smaller than the optical gap of 5.5 eV. These observations suggest that both edges can be expected for semiconductors in principle. On the other hand, C K-emission spectrum of graphite, a semimetal also showed an edge structure, which was assigned to the self-absorption edge due to the transitions from 1s to σ* antibonding state of sp2 bonding.
Calothrixin B by docking JAK2 is a potential therapeutic inhibitor for pancreatic ductal adenocarcinoma
Authors: Wang Yang , Esa Sayed S , Yu Rongji , Ibrahim Sherif Abdelaziz , Li Yixin , Sheng Zhi , Wu Jinzheng , Jiang Hao , Di Xiaotang , Wen Doudou , Liu Sheng , Zhang Shubing 
Published: January 2025

Abstract

Objectives
Pancreatic cancer, a highly invasive and prognostically unfavorable malignant tumor, consistently exhibits resistance to conventional chemotherapy, leading to substantial side effects and diminished patient quality of life. This highlights the critical need for the discovery of novel, effective, and safe chemotherapy drugs. This study aimed to explore bioactive compounds, particularly natural products, as an alternative for JAK2 protein inhibitor in cancer treatment.

Methods
Molecular docking, molecular dynamics, and Western blot experiments were conducted to verify the binding of Calothrixin B to JAK2 and its inhibitory effect on the JAK2-STAT3 signaling axis.

Key findings
Recognizing the significant impact of JAK-STAT3 signaling pathway in pancreatic cancer, we screened the Zinc database to discover potential JAK2 inhibitors, and identified the small molecule Calothrixin B as a promising drug. Molecular simulations revealed stable interactions and the formation of hydrogen bonds between Calothrixin B and specific amino acids (Asp 994, Leu 855, and Arg 980) after a 100 ns simulation. Furthermore, we show that Calothrixin B inhibited the activity of the JAK2-STAT3 signaling pathway, arrested pancreatic cancer cells in the G1 phase, induced apoptosis, and significantly inhibited cell migration. Moreover, in vivo on a subcutaneous tumor model in nude mice confirmed that Calothrixin B effectively inhibited tumor growth in nude mice. In addition, the combination of Carlothrixin B and gemcitabine had a better inhibitory effect on pancreatic cancer cells.

Conclusion
These findings introduce new avenues for Calothrixin B as promising therapy for pancreatic cancer.
Reductions in mesophyll conductance under drought stress are influenced by increases in cell wall chelator-soluble pectin content and denser microfibril alignment in cotton
Authors: Sun Dongsheng , Lei Zhangying , Carriquí Marc , Zhang Yujie , Liu Tianyang , Wang Shengnan , Song Kunhao , Zhu Lan , Zhang Wangfeng , Zhang Yali 
Published: January 2025

Abstract
Plants commonly undergo leaf morphoanatomy and composition modifications to cope with drought stress, and these tend to reduce mesophyll conductance to CO2 diffusion (gm), a key limitation to photosynthesis. The cell wall appears to play a crucial role in this reduction, yet the specific effect of cell wall component on gm and the underlying regulatory mechanisms of cell wall thickness (Tcw) variation are not well understood. In this study, we subjected cotton plants to varying levels of water deficit to investigate the impact of leaf cell wall component and the arrangement patterns of microfibrils within cell walls on Tcw and leaf gas exchange. Drought stress resulted in a significant thickening of cell walls and a decrease in gm. Concurrently, drought stress increased the content of chelator-soluble pectin and cellulose while reducing hemicellulose content. The alignment of cellulose microfibrils became more parallel and their diameter increased under drought conditions, suggesting a decrease in cell wall effective porosity which coincides with the observed reduction in gm. This research demonstrates that reduced gm typically observed under drought stress is related not only to thickened cell walls, but also to ultra-anatomical and compositional variations. Specifically, increases in cellulose content, diameter, and a highly aligned arrangement of cellulose microfibrils collectively contributed to an increase in Tcw, which, together with increases in chelator-soluble pectin content, resulted in an increased cell wall resistance to CO2 diffusion.
The luminous, slow-rising orphan afterglow AT2019pim as a candidate moderately relativistic outflow
Authors: Perley Daniel A , Ho Anna Y Q , Fausnaugh Michael , Lamb Gavin P , Kasliwal Mansi M , Ahumada Tomas , Anand Shreya , Andreoni Igor , Bellm Eric , Bhalerao Varun , Bolin Bryce , Brink Thomas G , Burns Eric , Cenko S Bradley , Corsi Alessandra , Filippenko Alexei V , Frederiks Dmitry , Goldstein Adam , Hamburg Rachel , Jayaraman Rahul , Jonker Peter G , Kool Erik C , Kulkarni Shrinivas R , Kumar Harsh , Laher Russ , Levan Andrew , Lysenko Alexandra , Perley Richard A , Ricker George R , Riddle Reed , Ridnaia Anna , Rusholme Ben , Smith Roger , Svinkin Dmitry , Ulanov Mikhail , Vanderspek Roland , Waratkar Gaurav , Yao Yuhan 
Published: January 2025

ABSTRACT
Classical gamma-ray bursts (GRBs) have two distinct emission episodes: prompt emission from ultrarelativistic ejecta and afterglow from shocked circumstellar material. While both components are extremely luminous in known GRBs, a variety of scenarios predict the existence of luminous afterglow emission with little or no associated high-energy prompt emission. We present AT 2019pim, the first spectroscopically confirmed afterglow with no observed high-energy emission to be identified. Serendipitously discovered during follow-up observations of a gravitational-wave trigger and located in a contemporaneous TESS sector, it is hallmarked by a fast-rising ($t \approx 2$ h), luminous ($M_{\rm UV,peak} \approx -24.4$ mag) optical transient with accompanying luminous X-ray and radio emission. No gamma-ray emission consistent with the time and location of the transient was detected by Fermi-GBM or by Konus, placing constraining limits on an accompanying GRB. We investigate several independent observational aspects of the afterglow in the context of constraints on relativistic motion and find all of them are consistent with an initial Lorentz factor of $\Gamma _0 \approx$ 10–30 for the on-axis material, significantly lower than in any well-observed GRB and consistent with the theoretically predicted ‘dirty fireball’ scenario in which the high-energy prompt emission is stifled by pair production. However, we cannot rule out a structured jet model in which only the line-of-sight material was ejected at low-$\Gamma$, off-axis from a classical high-$\Gamma$ jet core, and an on-axis GRB with below-average gamma-ray efficiency also remains a possibility. This event represents a milestone in orphan afterglow searches, demonstrating that luminous optical afterglows lacking detected GRB counterparts can be identified and spectroscopically confirmed in real time.
Inferring the ionizing photon contributions of high-redshift galaxies to reionization with JWST NIRCam photometry
Authors: Choustikov Nicholas , Stiskalek Richard , Saxena Aayush , Katz Harley , Devriendt Julien , Slyz Adrianne 
Published: January 2025

ABSTRACT
JWST observations are providing unprecedented constraints on the history of reionization owing to the ability to detect faint galaxies at $z\gg 6$. Modelling this history requires understanding both the ionizing photon production rate ($\xi _{\rm ion}$) and the fraction of those photons that escape into the intergalactic medium ($f_{\rm esc}$). Observational estimates of these quantities generally rely on spectroscopy for which large samples with well-defined selection functions remain limited. To overcome this challenge, we present and release a novel implicit likelihood inference pipeline, PHOTONIOn, trained on mock photometry to predict the escaped ionizing luminosity of individual galaxies ($\dot{N}_{\rm ion}$) based on photometric magnitudes and redshifts. We show that PHOTONIOn is able to reliably infer $\dot{N}_{\rm ion}$ from photometry. This is in contrast to traditional spectral energy distribution-fitting approaches which rely on $f_{\rm esc}$ prescriptions that often overpredict $\dot{N}_{\rm ion}$ for Lyman Continuum (LyC)-dim galaxies, even when given access to spectroscopic data. We have deployed PHOTONIOn on a sample of 4559 high-redshift galaxies from the JWST Advanced Deep Extragalactic Survey (JADES), finding gentle redshift evolutions of $\log _{10}(\dot{N}_{\rm ion}) = (0.08\pm 0.01)z + (51.60\pm 0.06)$ and $\log _{10}(f_{\rm esc}\xi _{\rm ion}) = (0.07\pm 0.01)z + (24.12\pm 0.07)$. Late-time values for the ionizing photon production rate density are consistent with both theoretical models and observations. Finally, we measure the evolution of the intergalactic medium ionized fraction to find that observed populations of star-forming galaxies are capable of driving reionization in this field to completion by $z\sim 5.3$ without the need for active galactic nucleus or other exotic sources, consistent with other studies of the same field. The 20 per cent of UV-brightest galaxies ($M_{\rm UV}\lt -18.5$) reionize roughly 35 per cent of the survey volume, demonstrating that UV faint LyC emitters are crucial for reionization.
Age-dating early quiescent galaxies: high star formation efficiency, but consistent with direct, higher-redshift observations
Authors: Turner Crispin , Tacchella Sandro , D’Eugenio Francesco , Carniani Stefano , Curti Mirko , Glazebrook Karl , Johnson Benjamin D , Lim Seunghwan , Looser Tobias , Maiolino Roberto , Nanayakkara Themiya , Wan Jenny 
Published: January 2025

ABSTRACT
We present a detailed analysis of JWST/NIRSpec and NIRCam observations of ZF-UDS-7329, a massive, quiescent galaxy at redshift $z=3.2$, which has been put forward to challenge cosmology and galaxy formation physics. We study on the impact of different star formation history (SFH) priors, stellar libraries, metallicity, and initial mass function assumptions. Our results show that ZF-UDS-7329, with a formed stellar mass of $M_{\star } \approx 10^{11.4}~{\rm M}_\odot $ (surviving mass $M_{\star \mathrm{,surv}} \approx 10^{11.2}~{\rm M}_\odot $) and a specific star formation rate of $\mathrm{sSFR} \approx 0.03~{\rm Gyr} ^{-1}$, formed efficiently in the first billion years of the Universe. In agreement with previous work, we find that the spectrum is consistent with mass-weighted stellar ages of $1.3{\!-\!}1.8$ Gyr, depending on the SFH prior used. A physically motivated rising SFH prior makes the formation history of ZF-UDS-7329 compatible with stellar mass and star formation rate estimates of $z\gt 6$ galaxies. Using NIRCam imaging, we identify a colour gradient indicative of an old, quiescent bulge and a younger disc component, as expected from a complex formation history. The inferred SFH is consistent a high stellar fraction of $f_{\star }=M_{\star }/(f_b \cdot M_{\rm h}) \approx 100{{\ \rm per\ cent}}$ at $z=7{\!-\!}12$, implying an extremely high integrated star formation efficiency. However, when considering cosmic variance and possible mergers as expected in overdense environments – as traced by ZF-UDS-7329 – the stellar fractions could be reduced to $f_{\star } \approx 50{{\ \rm per\ cent}}$, which is more consistent with galaxy formation models and the stellar-to-halo mass relation at lower redshifts. We conclude that ZF-UDS-7329 forms extremely efficient in the early universe, but does not necessitate unseen galaxies at higher redshifts since the inferred SFR of ancestors are consistent with those seen in $z\gt 6$ galaxies.
Stellar population and metal production in AGN discs
Authors: Fryer Chris L , Huang Jiamu , Ali-Dib Mohamad , Andrews Amaya , Xu Zhenghao , Lin Douglas N C 
Published: January 2025

ABSTRACT
As gravitational wave detections increase the number of observed compact binaries (consisting of neutron stars or blacks), we begin to probe the different conditions producing these binaries. Most studies of compact remnant formation focus either on stellar collapse from the evolution of field binary stars in gas-free environments or on the formation of stars in clusters where dynamical interactions capture the compact objects, forming binaries. But a third scenario exists. In this paper, we study the fate of massive stars formed, accrete gas, and evolve in the dense discs surrounding supermassive black holes. We calculate the explosions produced and compact objects formed by the collapse of these massive stars. Nucleosynthetic yields may provide an ideal, directly observable, diagnostic of the formation and fate of these stars in active galactic nuclei. We present a first study of the explosive yields from these stars, comparing these yields with the observed nucleosynthetic signatures in the discs around supermassive stars with quasars. We show that, even though these stars tend to form black holes, their rapid rotation leads to discs that can eject a considerable amount of iron during the collapse of the star. The nucleosynthetic yields from these stars can produce constraints on the number of systems formed in this manner, but further work is needed to exploit variations from the initial models presented in this paper.
Orbital stability of hierarchical three- and four-body systems with inclination: results for Kepler-1625, 1708, and HD 23079
Authors: Patel Shaan D , Quarles Billy , Cuntz Manfred 
Published: January 2025

ABSTRACT
As the number of potential exomoon candidates grows, there is a heightened motivation of pursing orbital stability analyses. In this work, we provide an in-depth investigation into four-body systems, consisting of a star, planet, moon, and submoon by using the N-body simulator rebound.. Particularly, we focus on the system of Kepler-1625, where evidence of a possible exomoon has been obtained. We investigate the three-body star–planet–moon system for the proposed exomoon parameters allowing us to identify stable regions associated with most of the space parameters. Thereafter, we consider a four-body system including a potential submoon. We find that there are both stable and unstable regions, as expected, as well as resonance patterns that are further explored using numerical and analytical methods including secular perturbation theory. We are able to identify these resonances as secular in nature. In addition, we investigate three-body versions of two other systems, Kepler-1708 and HD 23079, while also studying a four-body version of HD 23079. Our work may serve as a generalized framework for exploring other planet–moon cases in the future while noting that the current four-body study may be an incentive for studying further exomoon and submoon systems.
Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences
Authors: Fonseca Emanuel M , Tran Linh N , Mendoza Hannah , Gutenkunst Ryan N 
Published: January 2025

Abstract
Low-pass genome sequencing is cost-effective and enables analysis of large cohorts. However, it introduces biases by reducing heterozygous genotypes and low-frequency alleles, impacting subsequent analyses such as model-based demographic history inference. Several approaches exist for inferring an unbiased allele frequency spectrum (AFS) from low-pass data, but they can introduce spurious noise into the AFS. Rather than correcting the AFS, here, we developed an approach that incorporates low-pass biases into the demographic modeling and directly analyzes the AFS from low-pass data. Our probabilistic model captures biases from the Genome Analysis Toolkit multisample calling pipeline, and we implemented it in the population genomic inference software dadi. We evaluated the model using simulated low-pass datasets and found that it alleviated low-pass biases in inferred demographic parameters. We further validated the model by downsampling 1000 Genomes Project data, demonstrating its effectiveness on real data. Our model is widely applicable and substantially improves model-based inferences from low-pass population genomic data.
CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR
Authors: Harris David T , Jan Calvin H 
Published: January 2025

Abstract
Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.
Periodic instability and restoration of cratonic lithosphere
Authors: Liu Lijun , Chen Ling , Cao Zebin , Yang Xiaotao , Goddard Andrea Stevens , Zhu Rixiang 
Published: January 2025

Abstract
The longevity of cratons implies that the entire cratonic lithosphere remained unchanged over billions of years, attributed to their intrinsically buoyant and strong lithospheric roots. By reviewing relevant studies and recent observational constraints, we show that the present cratonic roots are notably denser than the ambient mantle, with the compositional buoyancy offsetting only 1/5 of the negative thermal buoyancy. In addition, the presence of a weak mid-lithospheric discontinuity could decouple the upper and lower lithosphere upon perturbation, allowing delamination of the lower portion, while the delaminated lithosphere would eventually relaminate to the base of the lithosphere after sufficient warming inside the convective mantle. This process generates enduring (&gt;100 Myr) and prominent (&gt;1 km) surface uplifts within continents, a mechanism more compatible with data, especially those reflecting lithospheric deformation and delamination, than the model of all continents climbing up a steady region of dynamic uplift. Subsequent lithospheric cooling gradually draws the surface down to even below sea level, where the lithospheric mantle density reaches a maximum upon formation of the next supercontinent. We argue that such cratonic deformation happened repeatedly over supercontinent cycles since the Neoproterozoic and largely shaped the properties of the cratonic lithosphere. A few new research directions are also suggested.