bluuebunny/crossref_metadata_2025_split huggingface dataset:
The diplomatic authority of William Davison
Authors: Cousins Rosalyn 
Published: July 2024

Abstract
Secretary William Davison (d. 1608) is best known for his involvement in the execution of Mary, queen of Scots, in 1587. This article explores Davison’s earlier diplomatic career, specifically his mission to the Low Countries in autumn 1585. It argues, first, that Davison was an influential political actor prior to his elevation to the privy council, as he fulfilled significant diplomatic responsibilities and was highly regarded by his conciliar patrons; and second, that study of Davison’s diplomatic career casts new light on familiar debates over mid-Elizabethan diplomacy, men of business and patron-client relationships.
Genomic data provides insights into the evolutionary history and adaptive differentiation of two tetraploid strawberries
Authors: Lin Hanyang , Chen Luxi , Cai Chaonan , Ma Junxia , Li Junmin , Ashman Tia-Lynn , Liston Aaron , Dong Ming 
Published: July 2024

Abstract
Over the decades, evolutionists and ecologists have shown intense interest in the role of polyploidization in plant evolution. Without clear knowledge of the diploid ancestor(s) of polyploids, we would not be able to answer fundamental ecological questions such as the evolution of niche differences between them or its underlying genetic basis. Here, we explored the evolutionary history of two Fragaria tetraploids, Fragaria corymbosa and Fragaria moupinensis. We de novo assembled five genomes including these two tetraploids and three diploid relatives. Based on multiple lines of evidence, we found no evidence of subgenomes in either of the two tetraploids, suggesting autopolyploid origins. We determined that Fragaria chinensis was the diploid ancestor of F. corymbosa while either an extinct species affinitive to F. chinensis or an unsampled population of F. chinensis could be the progenitor of F. moupinensis. Meanwhile, we found introgression signals between F. chinensis and Fragaria pentaphylla, leading to the genomic similarity between these two diploids. Compared to F. chinensis, gene families related to high ultraviolet (UV)-B and DNA repair were expanded, while those that responded towards abiotic and biotic stresses (such as salt stress, wounding, and various pathogens) were contracted in both tetraploids. Furthermore, the two tetraploids tended to down-regulate defense response genes but up-regulate UV-B response, DNA repairing, and cell division gene expression compared to F. chinensis. These findings may reflect adaptions toward high-altitude habitats. In summary, our work provides insights into the genome evolution of wild Fragaria tetraploids and opens up an avenue for future works to answer deeper evolutionary and ecological questions regarding the strawberry genus.
SlDELLA interacts with SlPIF4 to regulate arbuscular mycorrhizal symbiosis and phosphate uptake in tomato
Authors: Li Lan , Ge Shibei , He Liqun , Liu Ruicheng , Mei Yuhong , Xia Xiaojian , Yu Jingquan , Zhou Yanhong 
Published: July 2024

Abstract
Arbuscular mycorrhizal symbiosis (AMS), a complex and delicate process, is precisely regulated by a multitude of transcription factors. PHYTOCHROME-INTERACTING FACTORS (PIFs) are critical in plant growth and stress responses. However, the involvement of PIFs in AMS and the molecular mechanisms underlying their regulator functions have not been well elucidated. Here, we show that SlPIF4 negatively regulates the arbuscular mycorrhizal fungi (AMF) colonization and AMS-induced phosphate uptake in tomato. Protein–protein interaction studies suggest that SlDELLA interacts with SlPIF4, reducing its protein stability and inhibiting its transcriptional activity towards downstream target genes. This interaction promotes the accumulation of strigolactones (SLs), facilitating AMS development and phosphate uptake. As a transcription factor, SlPIF4 directly transcriptionally regulates genes involved in SLs biosynthesis, including SlCCD7, SlCDD8, and SlMAX1, as well as the AMS-specific phosphate transporter genes PT4 and PT5. Collectively, our findings uncover a molecular mechanism by which the SlDELLA-SlPIF4 module regulates AMS and phosphate uptake in tomato. We clarify a molecular basis for how SlPIF4 interacts with SLs to regulate the AMS and propose a potential strategy to improve phosphate utilization efficiency by targeting the AMS-specific phosphate transporter genes PTs.
Agricultural intensification reduces selection of putative plant growth-promoting rhizobacteria in wheat
Authors: Reid Tessa E , Kavamura Vanessa N , Torres-Ballesteros Adriana , Smith Monique E , Abadie Maïder , Pawlett Mark , Clark Ian M , Harris Jim A , Mauchline Tim H 
Published: July 2024

Abstract
The complex evolutionary history of wheat has shaped its associated root microbial community. However, consideration of impacts from agricultural intensification has been limited. This study investigated how endogenous (genome polyploidization) and exogenous (introduction of chemical fertilizers) factors have shaped beneficial rhizobacterial selection. We combined culture-independent and -dependent methods to analyze rhizobacterial community composition and its associated functions at the root–soil interface from a range of ancestral and modern wheat genotypes, grown with and without the addition of chemical fertilizer. In controlled pot experiments, fertilization and soil compartment (rhizosphere, rhizoplane) were the dominant factors shaping rhizobacterial community composition, whereas the expansion of the wheat genome from diploid to allopolyploid caused the next greatest variation. Rhizoplane-derived culturable bacterial collections tested for plant growth-promoting (PGP) traits revealed that fertilization reduced the abundance of putative plant growth-promoting rhizobacteria in allopolyploid wheats but not in wild wheat progenitors. Taxonomic classification of these isolates showed that these differences were largely driven by reduced selection of beneficial root bacteria representative of the Bacteroidota phylum in allopolyploid wheats. Furthermore, the complexity of supported beneficial bacterial populations in hexaploid wheats was greatly reduced in comparison to diploid wild wheats. We therefore propose that the selection of root-associated bacterial genera with PGP functions may be impaired by crop domestication in a fertilizer-dependent manner, a potentially crucial finding to direct future plant breeding programs to improve crop production systems in a changing environment.
Clinical Characteristics and Treatment of Marjolin’s Ulcer at a Major Burn Center in Northwest China: A Retrospective Review of 126 Cases
Authors: Luo Yuming , Liu Mengdong , Zhang Siyu , Yang Qiying , Gao Xiaowen , Han Juntao , Zhu Liang , Li Jun 
Published: July 2024

Abstract
Marjolin’s ulcer (MU) is a rare, aggressive skin tumor. There are numerous case reports but large long-term studies are lacking, necessitating further exploration of its treatment. This study aimed to summarize and analyze the characteristics, treatment methods, and prognosis of MU. We retrospectively analyzed the clinical data of 126 patients with MU, treated between January 2013 and January 2023 at the burn center. Demographic data, clinical characteristics, treatment, and prognosis were statistically analyzed. Of the 126 included patients, 104 were followed up for 0.1–10.2 years. The most common cause of the primary injury was flame burn (50.8%). Lesions were commonly observed on the lower limbs (47.6%). The predominant histopathological type was squamous cell carcinoma (92.8%). Among the 126 patients, 35 (27.8%) presented with bone invasion, 37 (29.4%) presented with enlarged lymph nodes, and 9 (7.1%) had lymph node metastasis. Extensive local excision (83.3%) was the most common surgical procedure; the defect was repaired using skin grafting (41.9%), free flaps (37.1%), and local flaps (21.0%). Multivariate analysis revealed that bone invasion and lymph node involvement were risk factors for postoperative recurrence. Survival analysis showed that age, latency period, pathological type, and recurrence were significant risk factors for survival. Extensive local resection is necessary to eradicate tumors, and patient follow-up should be more frequent within 1 year postoperatively. As MU is preventable, it is essential to reach a quick diagnosis and avoid delayed management before the occurrence of deadly metastases.
A molecular approach to unravel trophic interactions between parasitoids and hyperparasitoids associated with pecan aphids
Authors: Slusher Eddie K , Cottrell Ted , Gariepy Tara , Acebes-Doria Angelita , Querejeta Coma Marina , Toledo Pedro F S , Schmidt Jason M 
Published: July 2024

Abstract
Advances in molecular ecology can overcome many challenges in understanding host–parasitoid interactions. Genetic characterization of the key-players in systems helps to confirm species and identify trophic linkages essential for ecological service delivery by biological control agents; however, relatively few agroecosystems have been explored using this approach. Pecan production consists of a large tree perennial system containing an assortment of seasonal pests and natural enemies. As a first step to characterizing host–parasitoid associations in pecan food webs, we focus on aphid species and their parasitoids. Based on DNA barcoding of field-collected and reared specimens, we confirmed the presence of 3 species of aphid, one family of primary parasitoids, and 5 species of hyperparasitoids. By applying metabarcoding to field-collected aphid mummies, we were able to identify multiple species within each aphid mummy to unravel a complex food web of 3 aphids, 2 primary parasitoids, and upward of 8 hyperparasitoid species. The results of this study demonstrate that multiple hyperparasitoid species attack a single primary parasitoid of pecan aphids, which may have negative consequences for successful aphid biological control. Although further research is needed on a broader spatial scale, our results suggest multiple species exist in this system and may suggest a complex set of interactions between parasitoids, hyperparasitoids, and the 3 aphid species. This was the first time that many of these species have been characterized and demonstrates the application of novel approaches to analyze the aphid-parasitoid food webs in pecans and other tree crop systems.
A censored quantile transformation model for Alzheimer’s Disease data with multiple functional covariates
Authors: Ma Shaopei , Tang Man-lai , Yu Keming , Härdle Wolfgang Karl , Wang Zhihao , Xiong Wei , Zhang Xueliang , Wang Kai , Zhang Liping , Tian Maozai 
Published: July 2024

Abstract
Alzheimer’s disease (AD) is a progressive disease that starts from mild cognitive impairment and may eventually lead to irreversible memory loss. It is imperative to explore the risk factors associated with the conversion time to AD that is usually right-censored. Classical statistical models like mean regression and Cox models fail to quantify the impact of risk factors across different quantiles of a response distribution, and previous research has primarily focused on modelling a single functional covariate, possibly overlooking the interdependence among multiple functional covariates and other crucial features of the distribution. To address these issues, this paper proposes a multivariate functional censored quantile regression model based on dynamic power transformations, which relaxes the global linear assumption and provides more robustness and flexibility. Uniform consistency and weak convergence of the quantile process are established. Simulation studies suggest that the proposed method outperforms the existing approaches. Real data analysis shows the importance of both left and right hippocampal radial distance curves for predicting the conversion time to AD at different quantile levels.
Variable importance based interaction modelling with an application on initial spread of COVID-19 in China
Authors: Zhang Jianqiang , Chen Ze , Yang Yuhong , Xu Wangli 
Published: July 2024

Abstract
Interaction selection for linear regression is useful in many fields of modern science, yet very challenging. Existing methods focus on finding one optimal model but they may perform poorly in terms of stability for high-dimensional data, and they do not typically deal with categorical predictors. In this paper, we introduce a variable importance based interaction modelling (VIBIM) procedure for learning interactions in a linear regression model with both continuous and categorical predictors. We apply the VIBIM procedure to a COVID-19 data and show that the VIBIM approach leads to better models in terms of interpretability, stability, reliability, and prediction.
Encephalocele as a complication post-craniosynostosis surgery
Authors: Talahma Imad , Abuzneid Yousef S , Ismail Ameer , Alqam Lina , Mufreh Amaal , Shama'a Bara Abu 
Published: July 2024

Abstract
Duraplasty is one of the most common neurosurgical procedures which complications include iatrogenic pseudomeningocele, which is common, but ossification of pseudomeningocele following cranial surgery is a rare event. We present a case of a 2-year-old male patient who came to our hospital with a huge bulge in his head and weakness in the right arm and leg. He had a history of sagittal craniosynostosis with a postoperative cranioplasty complication of left parital pseudomeningocele. He underwent a duraplasty, but the bulge recurred with failed cerebrospinal fluid aspiration and external ventricular drain, changing in size periodically. Computed tomography showed that the bulge was a median and left paramedian parital encephalocele, so encephalocele with ossification was diagnosed and a cranioplasty was done. This case highlights that iatrogenic encephaloceles with ossification can develop after duraplasty repair in the parital region. Also, if a postoperative pseudomeningocele changes in size or consistency, clinicians should look for ossification.
A rare case of leiomyosarcoma with a pleomorphic component of the sigmoid colon
Authors: Omameuda Takahiko , Koizumi Masaru , Miyahara Yuzo , Kitabayashi Hiroyuki , Shiozawa Mikio , Kondo Satoru , Kawai Shigeo , Kodama Masaaki 
Published: July 2024

Abstract
A 66-year-old man presented to our institution with a positive fecal occult blood test and lower abdominal pain. Although a tumor was found in the sigmoid colon, biopsy and imaging studies failed to enable the diagnosis of the cancer, and the patient underwent surgery for treatment and diagnosis. The tumor had two distinct areas with differing features shown both histopathologically and on imaging; it was thus diagnosed as a leiomyosarcoma of the sigmoid colon with a pleomorphic component. Here, we describe a rare case of leiomyosarcoma of the sigmoid colon with a pleomorphic component. There are no reports of leiomyosarcoma with pleomorphic components arising in the colon in the literature; thus, the recurrence and metastatic characteristics are unknown. Therefore, accumulating cases in the literature may provide valuable insights into diagnosing and treating these rare tumors.
The fusicoccin story revisited
Authors: de Boer Albertus H 
Published: July 2024

Abstract
Fusicoccin (FC) is one of the most studied fungal metabolites to date. The finding that the plasma membrane H+-ATPase in combination with 14-3-3 proteins acts as a high-affinity receptor for FC was a breakthrough in the field. Ever since, the binding of FC to the ATPase–14-3-3 receptor complex has taken center stage in explaining all FC-induced physiological effects. However, a more critical review shows that this is not evident for a number of FC-induced effects. This review challenges the notion that all FC-affected processes start with the binding to and activation of the plasma membrane ATPase, and raises the question of whether other proteins with a key role in the respective processes are directly targeted by FC. A second unresolved question is whether FC may be another example of a fungal molecule turning out to be a ‘copy’ of an as yet unknown plant molecule. In view of the evidence, albeit not conclusive, that plants indeed produce ‘FC-like ligands’, it is worthwhile making a renewed attempt with modern improved technology to answer this question; the answer might upgrade FC or its structural analogue(s) to the classification of plant hormone.
CyCoNP lncRNA establishes cis and trans RNA–RNA interactions to supervise neuron physiology
Authors: Desideri Fabio , Grazzi Alessandro , Lisi Michela , Setti Adriano , Santini Tiziana , Colantoni Alessio , Proietti Gabriele , Carvelli Andrea , Tartaglia Gian Gaetano , Ballarino Monica , Bozzoni Irene 
Published: July 2024

Abstract
The combination of morphogenetic and transcription factors together with the synergic aid of noncoding RNAs and their cognate RNA binding proteins contribute to shape motor neurons (MN) identity. Here, we extend the noncoding perspective of human MN, by detailing the molecular and biological activity of CyCoNP (as Cytoplasmic Coordinator of Neural Progenitors) a highly expressed and MN-enriched human lncRNA. Through in silico prediction, in vivo RNA purification and loss of function experiments followed by RNA-sequencing, we found that CyCoNP sustains a specific neuron differentiation program, required for the physiology of both neuroblastoma cells and hiPSC-derived MN, which mainly involves miR-4492 and NCAM1 mRNA. We propose a novel lncRNA-mediated ‘dual mode’ of action, in which CyCoNP acts in trans as a classical RNA sponge by sequestering miR-4492 from its pro-neuronal targets, including NCAM1 mRNA, and at the same time it plays an additional role in cis by interacting with NCAM1 mRNA and regulating the availability and localization of the miR-4492 in its proximity. These data highlight novel insights into the noncoding RNA-mediated control of human neuron physiology and point out the importance of lncRNA-mediated interactions for the spatial distribution of regulatory molecules.
BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A
Authors: Hoshii Takayuki , Kikuchi Sota , Kujirai Tomoya , Masuda Takeshi , Ito Tomoko , Yasuda Satoshi , Matsumoto Makoto , Rahmutulla Bahityar , Fukuyo Masaki , Murata Takeshi , Kurumizaka Hitoshi , Kaneda Atsushi 
Published: July 2024

Abstract
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism
Authors: Li Shen , Xu Tianhao , Meng Xinru , Yan Yujuan , Zhou Ying , Duan Lei , Tang Yulong , Zhu Li , Sun Litao 
Published: July 2024

Abstract
The burgeoning crisis of antibiotic resistance has directed attention to bacteriophages as natural antibacterial agents capable of circumventing bacterial defenses. Central to this are the bacterial defense mechanisms, such as the BREX system, which utilizes the methyltransferase BrxX to protect against phage infection. This study presents the first in vitro characterization of BrxX from Escherichia coli, revealing its substrate-specific recognition and catalytic activity. We demonstrate that BrxX exhibits nonspecific DNA binding but selectively methylates adenine within specific motifs. Kinetic analysis indicates a potential regulation of BrxX by the concentration of its co-substrate, S-adenosylmethionine, and suggests a role for other BREX components in modulating BrxX activity. Furthermore, we elucidate the molecular mechanism by which the T7 phage protein Ocr (Overcoming classical restriction) inhibits BrxX. Despite low sequence homology between BrxX from different bacterial species, Ocr effectively suppresses BrxX’s enzymatic activity through high-affinity binding. Cryo-electron microscopy and biophysical analyses reveal that Ocr, a DNA mimic, forms a stable complex with BrxX, highlighting a conserved interaction interface across diverse BrxX variants. Our findings provide insights into the strategic counteraction by phages against bacterial defense systems and offer a foundational understanding of the complex interplay between phages and their bacterial hosts, with implications for the development of phage therapy to combat antibiotic resistance.
Veteran's Health Administration HIV Care Continuum: 2019 vs 2022
Authors: Maier Marissa , Beste Lauren A , Lowy Elliott , Hauser Ronald G , Van Epps Puja , Yakovchenko Vera , Rogal Shari , Chartier Maggie , Ross David 
Published: July 2024

Abstract

Background
The diagnosis-based Human Immunodeficiency Virus (HIV) Care Continuum offers a well-established framework for measuring HIV care quality. It is used by the government agencies, community organizations, and health care institutions to “guide the nation's response to HIV” and assesses HIV care from the time of HIV diagnosis through viral suppression. Our objective is to present the Veteran Health Administration's (VHA) HIV Care Continuum, assess postpandemic versus prepandemic performance, and compare VHA performance to Centers for Disease Control and Prevention–published data.

Methods
We conducted a nationwide retrospective cohort analysis examining the care continuum for people with HIV (PWH) in VHA care in 2019 versus 2022. Measurements included linkage to care, receipt of care, retention in care, and viral suppression. We used multivariable logistic regression of virological suppression to identify factors associated with viral suppression.

Results
In VHA in 2019, 83% of individuals newly diagnosed with HIV were linked to care, 84% of PWH received care, 76% were retained in care, and viral suppression was 76% among those with HIV and 93% of those with viral load (VL) results. In 2022, 74% were linked to care, 79% received care, 67% were retained in care, and viral suppression was 70% among those with HIV and 94% of those with a VL result.

Conclusions
VHA has achieved &gt;90% viral suppression among those with a VL result. Among all PWH, viral suppression decreased an absolute 5.2% between 2019 and 2022. VHA's performance on the HIV Care Continuum exceeds the national HIV Care Continuum reported by the Centers for Disease Control and Prevention.