bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of prenatal alcohol consumption on maternal anemia among pregnant women in Gondar town, Northwest Ethiopia: a retrospective cohort study
Authors: Addila Alemu Earsido , Azale Telake , Yitayal Mezgebu
Published: February 2025

Background

Alcohol consumption during pregnancy can lead to multiple health, social and behavioral problems for both the mother and the offspring. Anemia is one of the major public health concerns and causes of morbidity and mortality among pregnant women with poor maternal and fetal outcomes in developing countries. This study aimed to identify the link between prenatal alcohol consumption and anemia among pregnant women in Gondar town, Northwest Ethiopia.

Methods

A facility-based retrospective cohort study was conducted among 1669 pregnant women who were booked in for antenatal care in Gondar town. We used a two-stage random sampling technique to recruit and include study participants in the cohort. Data were collected using an interviewer-administered questionnaire. Multivariable analysis was performed to examine the association between reported prenatal alcohol exposure (non-hazardous and hazardous) and anemia in pregnancy using log-binomial regression modeling. The burden of anemia in pregnancy was reported using the adjusted risk ratio (ARR) and population-attributable risk.

Results

The prevalence of anemia during pregnancy was 14.86% (95% CI 13.23 to 16.65%). Hazardous alcohol consumption during pregnancy was significantly associated with anemia in pregnancy (ARR=2.24; 95% CI 1.60, 3.15). The adjusted population-attributable risk of anemia in pregnancy related to hazardous alcohol consumption during pregnancy was 7.68%.

Conclusions

This study revealed that anemia during pregnancy continues to be a public health concern. Regardless of timing, there is a clear association between prenatal alcohol consumption and anemia during pregnancy that suggests a need for targeted prenatal alcohol use screening, and ongoing intervention for alcoholic pregnant women.
Distinct phytoplankton size classes respond differently to biotic and abiotic factors
Authors: Eyring Stefanie , Merz Ewa , Reyes Marta , Ntetsika Pinelopi , Dennis Stuart R , Isles Peter D F , Kyathanahally Sreenath , Baity-Jesi Marco , To Sze-Wing , Merico Agostino , Pomati Francesco
Published: February 2025

The interplay between abiotic (resource supply, temperature) and biotic (grazing) factors determines growth and loss processes in phytoplankton through resource competition and trophic interactions, which are mediated by morphological traits like size. Here, we study the relative importance of grazers, water physics, and chemistry on the daily net accumulation rates (ARs) of individual phytoplankton from natural communities, grouped into six size classes from circa 10 to 500 μm. Using a Random Forest modelling approach and 4 years of daily data from a lake, we find that water temperature is generally a pivotal control of all phytoplankton ARs. At the same time, nutrients and light are important for the smallest and the largest classes. Mesozooplankton abundance is a key predictor of the AR for small phytoplankton, with microzooplankton being important for the middle-size range. In our data, large and small phytoplankton have different (seasonal) blooming patterns: small forms are favoured by low temperature and grazing, and high phosphorus levels. Larger forms show positive ARs at high temperatures and low phosphorus (being relatively insensitive to zooplankton grazing). These results help us understand the opportunities and limitations of using size to explain and model phytoplankton responses to biotic and abiotic environmental change.
Effect of Luteolin on cadmium-inhibited bone growth via suppressing osteoclastogenesis in laying chickens
Authors: Tong Xishuai , Fu Xiaohui , Gong Anqing , Yu Gengsheng , Chen Naineng , Chen Bing , Gu Jianhong , Liu Zongping
Published: February 2025

Luteolin (Lut) is a flavonoid derived from several plant sources. Cadmium (Cd) is a widespread environmental contaminant and potential toxin with detrimental effects on animal health. However, the effect of Lut on Cd-induced inhibition of bone growth in laying chickens remains unclear. This study investigates the effects of Lut on Cd-induced inhibition of bone growth in the femur and tibia of laying chickens. A total of sixty 1-day-old green-eggshell yellow feather laying chickens were randomly assigned to four groups after a 5-day of acclimation period: basal diet (Con), cadmium chloride (CdCl2, Cd), Lut, and Lut + Cd. Bone microstructure, serum biomarkers of bone remodeling, the levels of Cd, calcium (Ca), phosphorus (P), and trace metal elements were assessed using the micro-computed tomography (Micro-CT), enzyme-linked immunosorbent assay (ELISA), and microwave digestion, respectively. Bone remodeling biomarkers, late endosomal/lysosomal adaptor and MAPK and mTOR activator 1 (LAMTOR1), as well as the phosphorylation of AMP-activated protein kinase α (AMPKα) and protein kinase B (Akt), were quantified using the qRT-PCR and western blot. The results indicated that Lut effectively mitigated Cd-induced bone mass loss compared to the Cd group, resulting in increased bone volume (BV), bone surface/bone volume (BS/BV), connectivity density (Conn.Dn), and the length and weight of the femur and tibia in laying chickens. Mechanistically, compared to Cd group, Lut restored the ratio of osteoprotegerin (OPG)/receptor activator of NF-κB ligand (RANKL) in serum and bone tissue, enhanced the expression of bone morphogenetic protein-2 (BMP-2), runt-related transcription factor 2 (Runx2), osteocalcin (OCN), and Osterix (OSX), while reducing the levels of Ca, Cd, and alkaline phosphatase (ALP) activity, as well as the expression of osteopontin (OPN), c-Fos, osteoclast stimulatory-transmembrane protein (OC-STAMP), tartrate-resistant acid phosphatase (TRAP), cathepsin K (CTSK), matrix metalloprotein-9 (MMP-9), LAMTOR1, and the phosphorylation of AMPKα and Akt. Therefore, Lut alleviates Cd-induced damage to the femur and tibia of chickens by promoting osteogenesis and inhibiting osteoclastogenesis, positioning Lut as a potential therapeutic plant extract for enhancing bone growth in laying chickens.
Acute enhanced liquid aspirin administration improves performance and intestinal function in nursery pigs
Authors: Pearce Sarah C , Kerr Brian J
Published: February 2025

Aspirin (acetylsalicylic acid) is a nonsteroidal anti-inflammatory drug which has been a widely used analgesic for pain relief as well as an anti-inflammatory medication. However, it also causes negative effects to the gastrointestinal (GI) tract including GI bleeding, peptic ulcers, and can also impact the small intestine. Enhanced liquid aspirin (ELA) contains a combination of a salicylate compound, glycerin, triacetate, and saccharin which is more stable than aspirin alone and may reduce negative effects on the GI tract, while still exerting positive effects on inflammatory processes. The objective of this pilot study was to evaluate oral ELA on healthy weaning pigs. 8 pigs per treatment were gavaged daily for 5 d with either saline controls (CON) or 2 mg/kg body weight ELA. After the 5-d dosing period, pigs were weighed and then euthanized for intestinal sample collection. ELA-administered pigs gained significantly more body weight relative to initial body weights compared to CON pigs (8% vs. 13.7%; P<0.05). Additionally, there was tendency for an increase of 24% in villus height in ELA pigs compared to CON (P = 0.06) and significant increases in relative protein expression of Claudins (CLDN) 3 and 7 (P<0.05). Finally, several genes were altered in ELA-fed pigs compared to CON including stem cell markers and immune markers. All in all, this data showed that ELA was well tolerated in a pig model, showed a preliminary improvement in body weight, and had no observable negative impacts.
Sketch-based Modeling with Perception-aware Extraction and Intention-aware Snapping of Contours
Authors: Jin Yinghan , Huang Hao , Li Jituo , Guo Liuqia , Zheng Yifan , Zhang Dongliang
Published: February 2025

Using 2D sketches as input is an intuitive way to create 3D models. However, accurately sketching freeform strokes by hand from a reference drawing can be time-consuming and repetitive. This paper addresses this issue by proposing an efficient sketch modeling method based on structural part extracting and intention-aware snapping of an input drawing. Based on drawing contours, perceptually completed parts are decomposed after completing occlusions, then the boundaries of parts are used as construction curves to inflate 3D shapes. Moreover, user-drawn strokes can be seamlessly snapped onto drawing contours while preserving the user’s intention, allowing users to create shapes with different semantics. This approach enables users to easily obtain desired and accurate construction curves without the need for careful contour alignment. To achieve irregular shape design, 3D shapes can be further deformed by a contour deformation method from different viewpoints. We evaluate the method on several drawings and demonstrate our method effectively facilitates the creation of desired 3D models from a guide drawing.
Comprehensive seismic physical modeling study for carbonate reservoirs in Tarim area
Authors: Wei Li , Ju Linbo , Wei Jianxin , Ding Pinbo , Di Bangrang
Published: February 2025

Carbonate reservoirs in the Tarim area are characterized by diverse types, complex geological structures, and overlapping layers. As a result, capturing the seismic response characteristics in local areas is challenging, hindering defined analysis, model construction, and reservoir prediction owing to multiple influencing factors. Seismic forward physics is effective in characterizing specific wave fields. Seismic physical modeling technology allows for the modeling and analysis of the seismic response characteristics in carbonate reservoirs. In response to the challenges in the Tarim area, we designed a multi-type of comprehensive physical model that included dolomite/limestone of various strata from the Yijianfang Formation to the Cambrian and six types of reservoirs. The model formation, diverse reservoirs, and their distribution patterns were designed in the laboratory according to field seismic data. We analyzed and developed 11 suitable materials for modeling and their combinations based on the physical measurement results of rock cores. The ‘embedding method’ and ‘overlapping pouring’ improved the model development and construction. 3D seismic acquisition was conducted, and high-quality seismic data were obtained from building a model aligning with the field observation system. By analyzing the 3D post-stack profile, the response characteristics of various strata were relatively recognizable, and the response characteristics of reservoirs were more evident. We can use the high-quality, reliable 3D model seismic data and physical model to compare and analyze the seismic response characteristics of multiple carbonate reservoir types. This method greatly enhances the performance of seismic physical modeling of complex carbonate reservoirs, facilitating its application for evaluating diverse lithofacies and reservoirs commonly found in carbonate formations.
Robust reconstruction of non-uniformly sampled 3D seismic data with outliers
Authors: Dong Lieqian , Zhang Mugang , Xu Yingjie , Wang Changhui , Yu Siwei , Zhang Yingming
Published: February 2025

Compressive sensing (CS) acquisition utilizes non-uniform sampling along spatial directions, allowing for the reconstruction of seismic data without satisfying the requirements of Nyquist sampling theory. However, the reconstruction of CS data may fail in case of measurement outliers. Moreover, realistic environmental conditions often alter the sampling geometry, resulting in both missing samples and non-uniform samples relative to the designed grid. To reconstruct non-uniformly sampled data with outlier noise, we propose a reconstruction model that incorporates an interpolation operator and a robust measurement term within the data misfit. The robust measurement term utilizes the Huber norm to align the reconstructed data and sampled data with outliers, thereby enhancing robustness to realistic noise. The interpolation operator maps data from a uniform grid to a non-uniform grid using a barycentric Lagrangian interpolator. We apply the robust projection onto convex sets (RPOCS) algorithm to solve this optimization problem. Numerical tests demonstrate the effectiveness of the proposed approach. Superior reconstruction results are achieved compared to methods that do not incorporate robust measurements or consider true coordinates.
Pseudoalteromonas agarivorans-derived novel ulvan lyase of polysaccharide lyase family 40: Potential application of ulvan and partially hydrolyzed products in cosmetic industry
Authors: Gajanayaka Navindu Dinara , Jo Eunyoung , Bandara Minthari Sakethanika , Marasinghe Svini Dileepa , Hettiarachchi Sachithra Amarin , Wijewickrama Sithumini , Park Gun-Hoo , Oh Chulhong , Lee Youngdeuk
Published: February 2025

Ulvan is a complex sulfated polysaccharide in the cell walls of green algae with extensive applications in food, pharmaceutical, and agricultural industries, prompting extensive studies on ulvan, its oligosaccharides, monosaccharides, and cost-effective depolymerization methods. Our primary objectives were to investigate novel ulvan-utilizing marine bacteria, perform recombinant engineering of genes responsible for ulvan depolymerization, and determine their potential industrial applications. Samples were collected from Jeju Island, which is a South Korean region with significant excessive green algal growth, especially that of Ulva species. The marine bacterium Pseudoalteromonas agarivorans efficiently uses ulvan as its primary carbon source, indicating its potential for ulvan degradation. Through whole-genome sequencing the paul40 gene, which is a polysaccharide lyase family 40 (PL40) member, was identified and subsequently engineered into the pET-16b vector for expression as a His-tagged 95 kDa fusion protein. The ulvan depolymerization process was evaluated and confirmed using various analytical techniques including dinitrosalicylic acid assay, thin-layer chromatography, and gel permeation chromatography. Optimal enzyme activity occurred at 35°C, pH 8.0 in phosphate buffer, and 2.5 mM of NaCl. Furthermore, enzyme characterization and specific activity measurements were performed. This study is the first to report hyaluronidase and elastase inhibition by ulvan and its derivatives along with the characterization of an ulvan lyase enzyme from the PL40 family.

One-Sentence Summary

This study reports the identification and recombinant expression of a novel ulvan-degrading enzyme from Pseudoalteromonas agarivorans, demonstrating its potential for cosmetic industrial applications by revealing ulvan’s and partially hydrolyzed ulvan’s hyaluronidase and elastase inhibition properties.
The use of large language models to enhance cancer clinical trial educational materials
Authors: Gao Mingye , Varshney Aman , Chen Shan , Goddla Vikram , Gallifant Jack , Doyle Patrick , Novack Claire , Dillon-Martin Maeve , Perkins Teresia , Correia Xinrong , Duhaime Erik , Isenstein Howard , Sharon Elad , Lehmann Lisa Soleymani , Kozono David , Anthony Brian , Dligach Dmitriy , Bitterman Danielle S
Published: February 2025

Background

Adequate patient awareness and understanding of cancer clinical trials is essential for trial recruitment, informed decision-making, and protocol adherence. While Large Language Models (LLMs) have shown promise for patient education, their role in enhancing patient awareness of clinical trials remains unexplored. This study explored the performance and risks of LLMs in generating trial-specific educational content for potential participants.

Methods

GPT4 was prompted to generate short clinical trial summaries and multiple-choice question-answer pairs from informed consent forms (ICFs) from ClinicalTrials.gov. Zero-shot learning was used for summaries, using a direct summarization, sequential extraction, and summarization approach. One-shot learning was used for question-answer pairs development. We evaluated performance through patient surveys of summary effectiveness and crowdsourced annotation of question-answer pair accuracy, using held-out cancer trial ICFs not used in prompt development.

Results

For summaries, both prompting approaches achieved comparable results for readability and core content. Patients found summaries to be understandable, and to improve clinical trial comprehension and interest in learning more about trials. The generated multiple-choice questions achieved high accuracy and agreement with crowdsourced annotators. For both summaries and multiple-choice questions, GPT4 was most likely to include inaccurate information when prompted to provide information that was not adequately described in the ICFs.

Conclusions

LLMs such as GPT4 show promise in generating patient-friendly educational content for clinical trials with minimal trial-specific engineering. The findings serve as a proof-of-concept for the role of LLMs in improving patient education and engagement in clinical trials, as well as the need for ongoing human oversight.
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

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

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

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

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

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

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 < 0.25) dwarfs (108 M⊙ < M⋆ < 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

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

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

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

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.
First Report of Pseudopithomyces chartarum associated with a leaf spot of corn in the United States
Authors: Jimenez Madrid Alejandra Maria , Sanders III Hunt , Munoz Gabriel , Beasley Edward , Kemerait Robert C.
Published: February 2025

In October 2023, during scouting operations, two symptomatic corn plants (cv. Dekalb 68-95) with large circular, light brown/tan lesions with concentric rings covering the stalks and leaves were observed on a commercial field in Grady County, Georgia (USA). Foliar lesions resembled Hyalothyridium leaf spot of maize, a prevalent disease in Latin America countries, but that has not been observed in the United States. The identification of the causal agent was confirmed by morphological and molecular features of the isolated fungus. Sequencing of isolates using nuclear ribosomal DNA markers showed 100% similarity to Pseudopithomyces chartarum (Berk. & M.A. Curtis). To our knowledge, this is the first report of P. chartarum on corn in the USA. The origin and potential environmental conditions that trigger the development of the disease in these plants are currently unknown, so further research and monitoring is needed to better understand this observation.
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

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

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.
Safety of LEEP in Treating CIN 2–3 During Pregnancy
Authors: Siegler Yoav , Bornstein Jacob , Lavie Ofer , Vaknin Zvi , Kugelman Nir ,   Israeli Society of Colposcopy and Cervical Pathology, Siegler Efraim
Published: February 2025

Cervical intraepithelial neoplasia (CIN) 2–3, a premalignant lesion usually treated by Loop Electrosurgical Excision Procedure (LEEP) in nonpregnant women, is addressed differently in pregnant women.

Data from 2006 to 2023 on 178 pregnant women with CIN 2–3 were provided by the Israeli Society of Colposcopy. Sixty-seven underwent LEEP within 15 weeks of gestation with only minor complications. Of the 57 continuing pregnancies, 53 (93%) delivered at term, 2 (3.5%) at 34–37 weeks, and 2 (3.5%) experienced missed abortions. One hundred eleven women were followed through pregnancy without LEEP. Of that group, 5 women were lost to follow-up. From 173 women on whom we have follow-up data, 9 (5.2%) were finally diagnosed with cervical cancer, 132 women (76.3%) remained CIN 2–3, and 32 women (18.5%) were CIN 1 or normal.

Loop Electrosurgical Excision Procedure (LEEP) performed within the first 15 weeks of pregnancy in 67 women was safe. In 5.2% of pregnant women with CIN 2–3, the final diagnosis was invasive cancer.
HIT-EC: Trustworthy prediction of enzyme commission numbers using a hierarchical interpretable transformer
Authors: Dumontet Louis , Han So-Ra , Oh Tae-Jin , Kang Mingon
Published: February 2025

Accurate and trustworthy prediction of Enzyme Commission (EC) numbers is critical for understanding enzyme functions and their roles in biological processes. Despite the success of recently proposed deep learning-based models, there remain limitations, such as low performance in underrepresented EC numbers, lack of learning strategy with incomplete annotations, and limited interpretability. To address these challenges, we propose a novel hierarchical interpretable transformer model, HIT-EC, for trustworthy EC number prediction. HIT-EC employs a four-level transformer architecture that aligns with the hierarchical structure of EC numbers, and leverages both local and global dependencies within protein sequences for this multi-label classification task. We also propose a novel learning strategy to handle incomplete EC numbers. HIT-EC, as an evidential deep learning model, produces trustworthy predictions by providing domain-specific evidence through a biologically meaningful interpretation scheme. The predictive performance of HIT-EC was assessed by multiple experiments: a cross-validation with a large dataset, a validation with external data, and a species-based performance evaluation. HIT-EC showed statistically significant improvement in predictive performance when compared to the current state-of-the-art benchmark models. HIT-EC’s robust interpretability was further validated by identifying well-known conserved motifs and functional regions in the CYP106A2 enzyme family. HIT-EC would be a robust, interpretable, and reliable solution for EC number prediction, with significant implications for enzymology, drug discovery, and metabolic engineering. The open-source code is publicly available at:https://github.com/datax-lab/HIT-EC.
Spatiotemporal analysis of pericyte-induced dynamics in nascent angiogenic morphogenesis and heterogeneity using a microvessel-on-a-chip platform
Authors: Zeng Hedele , Sano Takanori , Kawabe Jun-ichi , Matsunaga Yukiko T.
Published: February 2025

The recent emergence of in vitro microvessel models has boosted research on angiogenesis and vascularization in tissue engineering, due to their superior control over in controlling culture conditions and enabling real-time observation compared to in vivo models. However, conventional two-dimensional (2D) observation and analysis fail to capture the heterogeneity of three-dimensional (3D) morphological dynamics. To overcome this issue, here, a novel morphological registration method for spatiotemporal quantification of angiogenic deformation dynamics by combining confocal microscopy of an engineered microvessel with computer vision techniques is proposed. Using a coculture system of a microvessel and pericytes, the spatiotemporal measurements reveals: (i) distinct deformation patterns and growth/regression zonation on the parent vessel and angiogenic sprouts; (ii) spatiotemporal changes in pericyte localization and coverage; and (iii) the enhancing effect of pericyte-microvessel contact on local Notch signaling activation, the distribution of matrix metalloproteinase-1 (MMP-1), the heterogeneity of angiogenic dynamics, and morphological maturation. This pilot system offers a characterization of the comprehensive effects of cocultured cells during angiogenesis and enables the interactive fusion of multimodal data in future studies on vascular morphogenesis.
Integrated detection and quantification of aberrant transcripts with novel splicing events
Authors: Agrawal Ira , Lim Yong Shan , Sanford Emma May , Yun Wan , Ling Shuo-Chien , Tucker-Kellogg Greg
Published: February 2025

Splicing misregulation, such as the inclusion of previously unknown cryptic exons, is implicated in numerous diseases. Recent methods have increased accurate and efficient detection of such splicing alterations occurring in disease phenotypes. However, the quantification and differential analyses of non-canonical splicing alterations remains focused at a splice event level, thus preventing a complete view of the effects on the downstream transcriptomic landscape. Here, we present a novel and integrated pipeline, SpliCeAT, that (1) detects and quantifies differential non-canonical splicing events from short-read bulk RNA-seq data, (2) augments the canonical transcriptome with novel transcripts containing these non-canonical splicing events, and (3) performs transcript-level differential analysis to identify and quantify aberrant cryptic exon-containing transcripts based on this augmented transcriptome. Using TDP-43, an ALS/FTD-associated RNA-binding protein as an example, we identified and catalogued aberrant splicing events in embryonic mouse brains. The accuracy of our integrated pipeline was further confirmed and validated with long-read isoform sequencing. Furthermore, by comparing neuronal TDP-43 knockouts in mice with a publicly available human dataset with TDP-43 pathology, we identified and validated 4 common genes, namely, Kalrn/KALRN, Poldip3/POLDIP3, Rnf144a/RNF144A, and Unc13a/UNC13A, with cryptic exons. In summary, our integrated pipeline, novel splice events are identified, incorporated and quantified at the transcript level, thereby enabling more complete transcriptome profiling of well-annotated genomes in in the case of pathological splicing misregulation