bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of cyclophosphamide on the morphological and histological changes in polyglycolic acid spacers
Authors: Tsuzuki Yusuke , Kamei Michi , Iwata Hiromitsu , Takeda Risa , Kimura Hiroaki , Aiba Hisaki , Murase Takayuki , Tsuchiya Takahiro , Sasaki Ryohei , Hiwatashi Akio 
Published: September 2024

Abstract
In radiotherapy for pediatric abdominal tumors, determining the effect of concurrent chemotherapy on polyglycolic acid (PGA) spacers is crucial; yet this effect has not been validated. Therefore, we aimed to evaluate the impact of cyclophosphamide (CPA) chemotherapy on the PGA spacer using a rat model. Twenty-four rats were implanted with the spacer, and morphological changes in the spacer were assessed on CT for both the CPA-dosed group (40 mg/kg) and the control group. The size and volume of the spacer were quantified using CT, while the degree of adhesion and microscopic examination of the tissue were determined using pathology specimens. Morphologically, the size of the spacer decreased over time in both the CPA-dosed and control groups, with no significant differences observed between groups. No significant differences in adhesion were observed between the two groups. Macrophages were observed around the PGA fibers, suggesting their involvement in the degradation of the PGA spacer. These results suggest that CPA does not cause significant clinically problematic degradation or adverse tissue reactions to the PGA spacer. This study reinforced the benefits of PGA spacers; however, future research focusing on in vivo longitudinal monitoring of individual rats, as well as on humans, is required.
Mixtures of Dirichlet processes for joint spatial modelling of transcranial magnetic stimulation mapping data
Authors: Egbon Osafu Augustine , Heumann Christian , Nascimento Diego Carvalho , Louzada Francisco 
Published: September 2024

Abstract
A patient’s responses to Transcranial Magnetic Stimulation (TMS) pulses on the motor cortex have a complex spatial pattern, making it challenging to understand the response patterns across multiple patients. We developed a mixture of Dirichlet process models to distinguish between patient-specific and shared spatial patterns across multiple patients to provide insight into consistent response patterns essential for developing personalized treatment procedures. The Metropolis–Hastings within Gibbs sampler of the Markov Chain Monte Carlo algorithm was developed for estimation. The model was used to analyse the TMS data of 3 healthy subjects. The study revealed that the primary motor cortex of the hand consistently emerges as a promising region for eliciting optimal responses. This area serves as a key target for brain mapping using TMS to identify cortical hotspots. However, the excitability patterns in this region can vary significantly among patients.
Nucleotides and nucleotide derivatives as signal molecules in plants
Authors: Witte Claus-Peter , Herde Marco 
Published: September 2024

Abstract
In reaction to a stimulus, signaling molecules are made, generate a response, and are then degraded. Nucleotides are classically associated with central metabolism and nucleic acid biosynthesis, but there are a number of nucleotides and nucleotide derivatives in plants to which this simple definition of a signaling molecule applies in whole or at least in part. These include cytokinins and chloroplast guanosine tetraposphate (ppGpp), as well as extracellular canonical nucleotides such as extracellular ATP (eATP) and NAD+ (eNAD+). In addition, there is a whole series of compounds derived from NAD+ such as ADP ribose (ADPR), and ATP–ADPR dinucleotides and their hydrolysis products (e.g. pRib-AMP) together with different variants of cyclic ADPR (cADPR, 2´-cADPR, 3´-cADPR), and also cyclic nucleotides such as 3´,5´-cAMP and 2´,3´-cyclic nucleoside monophosphates. Interestingly, some of these compounds have recently been shown to play a central role in pathogen defense. In this review, we highlight these exciting new developments. We also review nucleotide derivatives that are considered as candidates for signaling molecules, for example purine deoxynucleosides, and discuss more controversial cases.
Temporal trends in asteroid behaviour: a machine learning and N-body integration approach
Authors: Bora Chetan Abhijnanam , Kushvah Badam Singh , Mouli Gunda Chandra , Yousuf Saleem 
Published: September 2024

ABSTRACT
Asteroids pose significant threats to Earth, necessitating early detection for potential deflection. Leveraging machine learning (ML), we classify asteroids into near-Earth Asteroids (particularly Atens, Amors, Apollos, and Apoheles) and non-near-Earth asteroids, further categorizing them based on hazard potential. Training the seven models on a comprehensive data set of 4687 asteroids, we achieve high accuracy in prediction. The predictive capability of these models is critical for informed decision-making in planetary defense strategies. We apply different regularization techniques to prevent overfitting and validate the models using a large unseen data set. A rigorous long-term N-body integration spanning 1 Myr is executed utilizing the Mercury N-body integrator to illuminate the evolution of asteroid properties over extended temporal scales. Following this integration process, the best-performing ML model is employed to classify asteroids based on their orbital characteristics and hazardous status respectively. Our findings highlight the effectiveness of ML in asteroid classification and prediction, paving the way for large-scale applications. By dividing a 1 Myr integration into intervals, we uncover temporal trends in asteroid behaviour, revealing insights into hazard evolution and ejection patterns. Notably, initially, hazardous asteroids tend to transition to non-hazardous states over time, elucidating key dynamics in planetary defense. We illustrate these findings through plotted graphs, providing valuable insights into asteroid dynamics. These insights are instrumental in advancing our understanding of long-term asteroid behaviour, with significant implications for future research and planetary protection efforts.
Photospheric signatures of CME onset
Authors: Aslam O P M , MacTaggart D , Williams T , Fletcher L , Romano P 
Published: September 2024

ABSTRACT
Coronal mass ejections (CMEs) are solar eruptions that involve large-scale changes to the magnetic topology of an active region. There exists a range of models for CME onset which are based on twisted or sheared magnetic field above a polarity inversion line (PIL). We present observational evidence that topological changes at PILs, in the photosphere, form a key part of CME onset, as implied by many models. In particular, we study the onset of 30 CMEs and investigate topological changes in the photosphere by calculating the magnetic winding flux, using the artop code. By matching the times and locations of winding signatures with CME observations produced by the almanac code, we confirm that these signatures are indeed associated with CMEs. Therefore, as well as presenting evidence that changes in magnetic topology at the photosphere are a common signature of CME onset, our approach also allows for the finding of the source location of a CME within an active region.
Trinucleotide cap analogs with triphosphate chain modifications: synthesis, properties, and evaluation as mRNA capping reagents
Authors: Warminski Marcin , Depaix Anais , Ziemkiewicz Kamil , Spiewla Tomasz , Zuberek Joanna , Drazkowska Karolina , Kedzierska Hanna , Popielec Agnieszka , Baranowski Marek R , Sklucka Marta , Bednarczyk Marcelina , Smietanski Miroslaw , Wolosewicz Karol , Majewski Bartosz , Serwa Remigiusz A , Nowis Dominika , Golab Jakub , Kowalska Joanna , Jemielity Jacek 
Published: September 2024

Abstract
The recent COVID-19 pandemics have demonstrated the great therapeutic potential of in vitro transcribed (IVT) mRNAs, but improvements in their biochemical properties, such as cellular stability, reactogenicity and translational activity, are critical for further practical applications in gene replacement therapy and anticancer immunotherapy. One of the strategies to overcome these limitations is the chemical modification of a unique mRNA 5′-end structure, the 5′-cap, which is responsible for regulating translation at multiple levels. This could be achieved by priming the in vitro transcription reaction with synthetic cap analogs. In this study, we combined a highly efficient trinucleotide IVT capping technology with several modifications of the 5′ cap triphosphate bridge to synthesize a series of 16 new cap analogs. We also combined these modifications with epigenetic marks (2′-O-methylation and m6Am) characteristic of mRNA 5′-ends in higher eukaryotes, which was not possible with dinucleotide caps. All analogs were compared for their effect on the interactions with eIF4E protein, IVT priming, susceptibility to decapping, and mRNA translation efficiency in model cell lines. The most promising α-phosphorothiolate modification was also evaluated in an in vivo mouse model. Unexpected differences between some of the analogs were analyzed using a protein cell extract pull-down assay.
Mary McCarthy
Authors: Wilson Niehaus Sophia 
Published: September 2024

Mary McCarthy (b. 1912–d. 1989) was an American essayist, novelist, critic, and public intellectual known for her biting satire and incisive criticism. From the 1930s to 1980s, her book reviews and other essays appeared in periodicals such as Partisan Review, Harper’s, The New Yorker and The New York Review of Books. The Group, McCarthy’s 1963 novel about the lives of eight Vassar College graduates, was considered scandalous for its satirical and frank depiction of sex, contraception, and the private lives of women; it is now regarded as a classic of postwar fiction. Born in Seattle to an Irish-Catholic father and half-Jewish, half-Protestant mother, Mary McCarthy was the oldest of four children. She was six years old when her parents died in 1918 during the flu epidemic. In Memories of a Catholic Girlhood (1957), she recalls the shock of becoming an orphan followed by years of abuse at the hands of sadistic guardians and her loss of religious faith at age twelve. McCarthy attended Vassar and graduated in 1933. Soon she married an aspiring playwright (whom she would divorce three years later) and grew close to a circle of leftist intellectuals that included Dwight Macdonald, William Phillips, Philip Rahv, and Nicola Chiaromonte. She married the critic Edmund Wilson in 1938; the same year, the couple had one son, Reuel. In the midst of their tumultuous marriage, McCarthy––with Wilson’s encouragement––published her first work of fiction, The Company She Keeps (1942). One of the collection’s stories, “The Man in the Brooks Brothers Shirt,” was considered daring for its description of the heroine’s casual sexual encounter with a married Midwestern businessman in a Pullman car. In the 1940s and 1950s, McCarthy’s record, at once finely observed and satirically recreated, of political, social, and indeed conjugal life in America, gained recognition in works such as The Oasis (1949), The Groves of Academe (1952), and A Charmed Life (1955). By the time of the publication of The Group in 1963, McCarthy had left New York to live in Paris, France and Castine, Maine. She contributed regularly to the New York Review of Books, including reports on the Vietnam War and Watergate hearings. She also published two more novels, Birds of America (1971) and Cannibals and Missionaries (1979). In a much discussed cause célèbre, McCarthy accused Lillian Hellman of being a “dishonest writer” on a live recording of the Dick Cavett Show in 1980; Hellman sued for libel but died before the case could go to trial.
Aquaporin CmPIP2;3 links H2O2 signal and antioxidation to modulate trehalose-induced cold tolerance in melon seedlings
Authors: Han Yuqing , Luo Fei , Liang Adan , Xu Dongdong , Zhang Hongyi , Liu Tao , Qi Hongyan 
Published: September 2024

Abstract
Cold stress severely restricts the growth and development of cold-sensitive crops. Trehalose (Tre), known as the “sugar of life”, plays key roles in regulating plant cold tolerance by triggering antioxidation. However, the relevant regulatory mechanism remains unclear. Here, we confirmed that Tre triggers apoplastic hydrogen peroxide (H2O2) production and thus plays key roles in improving the cold tolerance of melon (Cucumis melo var. makuwa Makino) seedlings. Moreover, Tre treatment can promote the transport of apoplastic H2O2 to the cytoplasm. This physiological process may depend on aquaporins. Further studies showed that a Tre-responsive plasma membrane intrinsic protein 2;3 (CmPIP2;3) had strong H2O2 transport function and that silencing CmPIP2;3 significantly weakened apoplastic H2O2 transport and reduced the cold tolerance of melon seedlings. Yeast library and protein–DNA interaction technology were then used to screen 2 Tre-responsive transcription factors, abscisic acid–responsive element (ABRE)–binding factor 2 (CmABF2) and ABRE-binding factor 3 (CmABF3), which can bind to the ABRE motif of the CmPIP2;3 promoter and activate its expression. Silencing of CmABF2 and CmABF3 further dramatically increased the ratio of apoplastic H2O2/cytoplasm H2O2 and reduced the cold tolerance of melon seedlings. This study uncovered that Tre treatment induces CmABF2/3 to positively regulate CmPIP2;3 expression. CmPIP2;3 subsequently enhances the cold tolerance of melon seedlings by promoting the transport of apoplastic H2O2 into the cytoplasm for conducting redox signals and stimulating downstream antioxidation.
A hierarchical ubiquitination-mediated regulatory module controls bamboo lignin biosynthesis
Authors: Yang Kebin , Li Ziyang , Zhu Chenglei , Liu Yan , Li Hui , Di Xiaolin , Song Xinzhang , Ren Haiqing , Gao Zhimin 
Published: September 2024

Abstract
The lignocellulosic feedstock of woody bamboo shows promising potential as an alternative to conventional wood, attributed to its excellent properties. The content and distribution of lignin serve as the foundation of these properties. While the regulation of lignin biosynthesis in bamboo has been extensively studied at the transcriptional level, its posttranslational control has remained poorly understood. This study provides a ubiquitinome dataset for moso bamboo (Phyllostachys edulis), identifying 13,015 ubiquitinated sites in 4,849 unique proteins. We further identified Kelch repeat F-box protein 9 (PeKFB9) that plays a negative role in lignin biosynthesis. Heterologous expression of PeKFB9 resulted in reduced accumulation of lignin and decreased phenylalanine ammonia lyase (PAL) activities. Both in vitro and in vivo assays identified interaction between PeKFB9 and PePAL10. Further examination revealed that SCFPeKFB9 mediated the ubiquitination and degradation of PePAL10 via the 26S proteasome pathway. Moreover, PebZIP28667 could bind to the PePAL10 promoter to significantly inhibit its transcription, and ubiquitination of PebZIP28667 weakened this inhibition. Collectively, our findings reveal a PeKFB9-PePAL10/PebZIP28667-PePAL10 module that acts as a negative regulator of lignin biosynthesis. This study advances our understanding of posttranslational regulation in plant lignification, which will facilitate the improvement of the properties of bamboo wood and the breeding of varieties.
The lysogenic filamentous Pseudomonas bacteriophage phage Pf slows mucociliary transport
Authors: Burgener Elizabeth B , Cai Pamela C , Kratochvil Michael J , Rojas-Hernandez Laura S , Joo Nam Soo , Gupta Aditi , Secor Patrick R , Heilshorn Sarah C , Spakowitz Andrew J , Wine Jeffrey J , Bollyky Paul L , Milla Carlos E 
Published: September 2024

Abstract
Pseudomonas aeruginosa is a major pulmonary pathogen causing chronic pulmonary infections in people with cystic fibrosis (CF). The P. aeruginosa filamentous and lysogenic bacteriophage, Pf phage, is abundant in the airways of many people with CF and has been associated with poor outcomes in a cross-sectional cohort study. Previous studies have identified roles for Pf phage in biofilm formation, specifically forming higher-order birefringent, liquid crystals when in contact with other biopolymers in biofilms. Liquid crystalline biofilms are more adherent and viscous than those without liquid crystals. A key feature of biofilms is to enhance bacterial adherence and resist physical clearance. The effect of Pf phage on mucociliary transport is unknown. We found that primary CF and non-CF nasal epithelial cells cultured at air–liquid interface treated with Pf phage exhibit liquid crystalline structures in the overlying mucus. On these cell cultures, Pf phage entangles cilia but does not affect ciliary beat frequency. In both these in vitro cell cultures and in an ex vivo porcine trachea model, introduction of Pf phage decreases mucociliary transport velocity. Pf phage also blocks the rescue of mucociliary transport by CF transmembrane conductance regulator modulators in CF cultures. Thus, Pf phage may contribute to the pathogenesis of P. aeruginosa-associated CF lung disease via induction of liquid crystalline characteristics to airway secretions, leading to impaired mucociliary transport. Targeting Pf phage may be useful in treatment CF as well as other settings of chronic P. aeruginosa infections.
Association of gut commensal translocation with autoantibody production in systemic lupus erythematosus
Authors: Katsushima Masao , Nakayama Yoichi , Yoshida Tsuneyasu , Nishida Yuri , Shirakashi Mirei , Nakashima Ran , Yoshifuji Hajime , Ito Shinji , Satoh Junko , Yamamoto Masaki , Watanabe Ryu , Emori Takashi , Kamiya Tomonori , Nitahara Yuko , Nakagama Yu , Ohtani Naoko , Kido Yasutoshi , Morinobu Akio , Hashimoto Motomu 
Published: September 2024

Abstract

Objective
Bacterial translocation across the gut barrier has been implicated in the pathogenesis of SLE, though the underlying mechanisms remain unclear. This study aimed to investigate the role of translocated bacteria in the context of molecular mimicry by utilizing lupus model mice and blood samples from untreated SLE patients.

Methods
Bacterial translocation was evaluated using nonselective cultured mesenteric lymph nodes (MLNs) from B6SKG mice, a lupus model characterized by impaired TCR signalling and gut dysbiosis. The relationships of detected pathobionts with autoantibody production were examined using in vivo experiments, ELISA, immunoblotting and epitope mapping.

Results
Culture-based bacterial profiling in MLNs demonstrated that Lactobacillus murinus was enriched in B6SKG mice with elevated anti-dsDNA IgG levels. Subcutaneous injection of heat-killed L. murinus induced anti-dsDNA IgG production without altering T- or B-cell subset composition. Immunoblotting and mass spectrometry analysis identified a peptide ATP-binding cassette (ABC) transporter as a molecular mimicry antigen, with its cross-reactivity in lupus mice confirmed by serological assays and in vivo immunization. The L. murinus ABC transporter exhibited surface epitopes that were cross-reactive with sera from lupus mice and patients. The ABC transporter from R. gnavus, known for its pathogenic role in lupus patients, had a similar epitope sequence to that of the L. murinus ABC transporter and reacted with lupus sera.

Conclusion
ABC transporters from gut bacteria can serve as cross-reactive antigens that may promote anti-dsDNA antibody production in genetically susceptible mice. These findings underscore the role of commensal-derived molecular mimicry and bacterial translocation in lupus pathogenesis.
The Limits of the Metapopulation: Lineage Fragmentation in a Widespread Terrestrial Salamander (Plethodon cinereus)
Authors: Waldron Brian P , Watts Emily F , Morgan Donald J , Hantak Maggie M , Lemmon Alan R , Lemmon Emily C Moriarty , Kuchta Shawn R 
Published: September 2024

Abstract
In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here, we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least 6 divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in Bayesian Phylogenetics and Phylogeography supported 5 lineages of P. cinereus, genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence.
Elevated concentrations of amyloid‐β oligomers and their proapoptotic effects on age‐related cataract
Authors: Lin Peimin , Xu Jie , Yang Fan , Li Dan , Zhang Rong , Jiang Yongxiang , Zheng Tianyu 
Published: September 2024

AbstractRecently, amyloid‐β oligomers (AβOs) have been studied as the primary pathogenic substances in Alzheimer's disease (AD). Our previous study revealed that the Aβ expression level is closely related to ARC progression. Here, we demonstrated that the accumulation of AβOs in the lens epithelium of age‐related cataract (ARC) patients increased during ARC progression and that this alteration was consistent with the changes in mitochondrial function, oxidative stress, and cellular apoptosis. In vitro, human lens epithelial cells (HLECs) treated with AβOs exhibited Ca2+ dyshomeostasis, impaired mitochondrial function, elevated oxidative stress levels, and increased apoptosis. Moreover, the proapoptotic effect of AβOs was alleviated after the uptake of mitochondrial Ca2+ was inhibited. These results establish that AβOs may promote HLEC apoptosis by inducing mitochondrial Ca2+ overload, thus preliminarily revealing the possible association between the accumulation of AβOs and other pathological processes in ARC.