bluuebunny/crossref_metadata_2025_split huggingface dataset:
Weak allelopathic effects of bracken fern (Pteridium esculentum subsp. arachnoideum) on early life stages of native tree species in a Neotropical montane forest
Authors: Maidana-Tuco Yamil , Pacheco Luis F. , Hensen Isabell , Gallegos Silvia C. 
Published: December 2024

Abstract

The allelopathic effect of Pteridium ferns (hereafter bracken) is considered an important factor hindering forest recovery. We examined the effects of bracken allelopathy on seed germination, seedling emergence, survival, and relative growth rate (RGR) of two native tree species, Morella pubescens and Vismia plicatifolia, in a tropical montane forest. Two potential allelopathic sources, fronds and litter, were considered, along with site age (using soils from young and old bracken-dominated sites, burned <5 and >10 years ago, respectively). In a greenhouse experiment, resembling bracken conditions of shade, we conducted a fully crossed block experiment with four treatments: Control, soil + activated carbon (AC, to adsorb allelopathic compounds), soil + bracken (Bracken), and soil + activated carbon + bracken (Bracken + AC), using soils from old and young sites. In a laboratory experiment, four aqueous extracts of rhizomes, litter, and fronds (from old and young sites) were used to water seeds at low and high concentrations and to compare their effects with the control treatment (water). Results showed low allelopathic effects on seedling emergence in soils from young sites for both species, with activated carbon mitigating these effects. Soils from young sites positively influenced the RGR of M. pubescens seedlings, contrasting with soils from old sites. Aqueous extracts from bracken fronds exhibited a 20% reduction on seedling survival of V. plicatifolia, while other extracts had no significant impact on germination or seedling survival. We discuss the implications of these mild allelopathic effects on the impediment to forest succession in tropical bracken-dominated areas.
Transcription factor FOXD1 and miRNA-204-5p play a major role in B4GALNT2 downregulation in colon cancer
Authors: Duca Martina , Malagolini Nadia , Pucci Michela , Cogez Virginie , Harduin-Lepers Anne , Dall’Olio Fabio 
Published: December 2024

Abstract

The β1,4-N-acetylgalactosaminyltransferase 2 (B4GALNT2) which synthesizes the histo-blood group antigen Sda is highly expressed by normal colon, but it is dramatically down-regulated in colorectal cancer (CRC). High B4GALNT2 expression in CRC tissues is a marker of longer survival. The molecular bases of B4GALNT2 inhibition in CRC are largely obscure. A key role may be played by transcription factors and miRNA. Through an in silico analysis of The Cancer Genome Atlas (TCGA) and of the Cancer Cell Line Encyclopedia (CCLE), we identified the transcription factors FOXD1, FOXF2 and PGR as well as mir-204-5p as potential inhibitory agents. Their transient transfection in the cell line GP2d, whose B4GALNT2 is closer to that of a normal mucosa, confirmed their inhibitory activity with a crucial role for FOXD1. The latter inhibited B4GALNT2 also in the middle B4GALNT2 expresser cell line Caco2. Deletion experiments of the putative FOXD1 binding sites in the ~ 2800 bp sequence upstream of the B4GALNT2 transcriptional start site cloned in frame with the luciferase reporter gene, confirmed the regulatory role of FOXD1. Finally, FOXD1 knock down in the non-B4GALNT2 expresser cell line SW948 stimulated B4GALNT2. Thus, FOXD1 and miR-204-5p emerged as crucial new player of B4GALNT2 down-regulation in CRC.
Effect of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) on the immune system maternal-fetal interface during palatal development
Authors: Yongkai Wang , Shuhui Zhang , li ma 
Published: December 2024

Abstract

The maternal immune system during pregnancy is crucial for generating a balance between maternal immunity and the fetus. Our understanding of the potential impact of teratogens on the maternal-fetal interface (MFI) immune system and if such influences could precipitate the development of cleft palate (CP) remains limited. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a widely prevalent environmental pollutant, was used as a teratogen to induce a CP animal model. Fifteen C57BL/6J mice were selected and randomly assigned to three groups: a control group, TCDD group, and TCDD plus Freund's complete adjuvant (FCA) group. Peripheral blood, placentas, and palatal tissues were collected for H&E, flow cytometry, and ELISA.In the TCDD group, the placental diameter, the number of placental labyrinth vessels, and the area of sponge layer cells were all significantly reduced. At embryonic day (E) 17.0, there was a significant decrease in T-helper 1 (Th1) and Th2 cells in the peripheral blood of pregnant mice. Additionally, the levels of Interferon-γ(IFN-γ) and Interleukin-4(IL-4), particularly IL-4, were significantly decreased. However, after treatment with FCA, the distance between the palatal shelves was reduced, and the placental weight, the number of labyrinth vessels and the area of the cavernous cells in the placenta also increased. The number of Th1 and Th2 cells significantly increased, returning to the levels observed in the control group, with a more pronounced increase in the number of Th2 cells.TCDD may induce CP by disrupting the homeostasis of the MFI. The precise mechanisms by which TCDD impact immune system at the MFI require further investigation.
Mitochondrial metabolism and epigenetic crosstalk drive the SASP
Authors: Passos Joao , Martini Helene , Birch Jodie , Marques Francisco , Victorelli Stella , Lagnado Anthony , Pirius Nicholas , Franco Ana , Lee Gung , Han Yeaeun , Rowsey Jennifer , Gaspar-Maia Alexandre , Havas Aaron , Murad Rabi , Lei Xue , Porritt Rebecca , Maddocks Oliver , Jurk Diana , Khosla Sundeep , Adams Peter 
Published: December 2024

Abstract

Senescent cells drive tissue dysfunction through the senescence-associated secretory phenotype (SASP). We uncovered a central role for mitochondria in the epigenetic regulation of the SASP, where mitochondrial-derived metabolites, specifically citrate and acetyl-CoA, fuel histone acetylation at SASP gene loci, promoting their expression. We identified the mitochondrial citrate carrier (SLC25A1) and ATP-citrate lyase (ACLY) as critical for this process. Inhibiting these pathways selectively suppresses SASP without affecting cell cycle arrest, highlighting their potential as therapeutic targets for age-related inflammation. Notably, SLC25A1 inhibition reduces systemic inflammation and extends healthspan in aged mice, establishing mitochondrial metabolism as pivotal to the epigenetic control of aging.
The role of a novel marine protein LeAlkB in BMSCs osteogenic differentiation with mechanical stress
Authors: Zhao Qihang , Ren Zhiheng , Hu Zhengxuan , Chen Zhenggang , Zhao Xiaomeng , Yang Fang , Yuan Rongtao , Guo Qingyuan 
Published: December 2024

Abstract

LeAlkB is a marine protein derived from the Lysobacter enzymogenes. It has a dependence on Fe2+and α- Ketoglutaric acid. The ALKBH family of methylases, which are functionally conserved for ketoglutarate, have a similar structure. FTO（Fat Mass and Obesity-associated Protein） in the ALKBH family is a key promoter of osteogenic differentiation under mechanical stress and has an upregulation effect on inducing osteogenic differentiation phenotype markers. Research has found that ALKBH5 also has osteogenic ability, and the application of marine drugs in bone disease and bone regeneration research is gradually increasing. The structure similarly to the ALKBH family enables LeAlkB to have the same osteogenic differentiation ability. To explore the potential application of the novel marine protein LeAlkB in bone reconstruction, this study investigated the bone regeneration characteristics induced by LeAlkB. It has been demonstrated that mechanical stress encourages bone marrow mesenchymal stem cells (BMSCs) to differentiate into osteogenic tissue. This study discovered that BMSCs' expression of osteogenic differentiation markers in LeAlkB dramatically increased under mechanical stress settings. Furthermore, LeAlkB significantly raises the expression of FTO. This suggests that BMSCs' osteogenic differentiation can be stimulated by the marine protein LeAlkB. LeAlkB is a marine new protein that exhibits much greater osteogenic ability and minimal cytotoxicity when compared to FTO and ALKBH5. This suggests that LeAlkB has better therapeutic potential. LeAlkB is therefore anticipated to be used in the clinical treatment of orthodontics in the future. Our study's conclusions, however, offer fresh concepts for the potential uses of marine naturally occurring bioactive compounds in the future.
Multiples Elimination to enhance Seismic Imaging for Safe Wind Farm Establishment: A case study from Baltic Sea
Authors: Roshdy Eslam , Mabrouk Walid , Metwally Ahmed 
Published: December 2024

Abstract

The primary objective of this paper is to eliminate the effect of multiples on seismic data using different multiple attenuation techniques, ultimately enhancing seismic imaging for the establishment of wind farms in the study area. Seismic reflection data processing is a highly effective method for detecting potential hazards such as mines and shallow gas bubbles, making it crucial for environmental hazard assessments. In this study, multiple elimination methods were combined to attenuate different types of multiples in 2D raw shallow marine seismic data from the Baltic Sea region. The demultiple workflow combined several robust techniques: Surface-Related Multiple Elimination (SRME), Tau-P deconvolution, high-resolution (HR) radon demultiple, and Common Depth Point (CDP) stacking. SRME was used to remove surface-related multiples by subtracting predicted multiple models from the seismic data, followed by Tau-P deconvolution to attenuate short-period multiples. HR radon demultiple was then employed to attenuate any remaining multiples, which could not be eliminated by previous methods, and finally, CDP stacking of normal moveout-corrected data was applied to improve the alignment of primary reflections and eliminate non-aligned multiples. The improvement in data quality was not solely due to the individual demultiple techniques but from their integration. Each method addresses specific types of multiples and noise, and the combined workflow ensures the optimal suppression of unwanted energy without losing important seismic signal. The final stacked seismic section showed significant improvement in image clarity, confirming the absence of predicted mines or shallow gas bubbles beneath the surface. Based on these findings, the study concludes that the area is suitable for wind farm construction.
Co-design of a Mobile Stroke Unit pathway highlights uncertainties and trade-offs for viable system-wide implementation in the English and Welsh NHS
Authors: Moseley Lisa , McMeekin Peter , Allen Michael , Ford Gary A , James Martin , Laws Anna , McCarthy Stephen , McClelland Graham , Park Laura J , Pearn Kerry , Phillips Daniel , Price Christopher , Shaw Lisa , White Phil , Wilson David , Scott Jason 
Published: December 2024

Abstract

Background: Mobile stroke units (MSUs) are specialist ambulances equipped with scanning and point of care testing that can identify patients eligible for intravenous thrombolysis – medication to dissolve a clot used in ischaemic strokes – and provide this on location. While benefits of MSUs have been demonstrated, this has been highly context dependent. Routine use of MSUs across the English and Welsh National Health Service (NHS) has not yet been considered, with only one MSU currently deployed as part of a research project, and as such no pathway for their operation exists. This study aimed to co-design a viable pathway for MSUs within the NHS context.
Methods: The study used interdisciplinary co-design alongside Nominal Group Technique (NGT) to generate consensus. Participants were recruited using a combination of purposive, opportunistic and snowball sampling. Data collection took place in online workshops, across three rounds, with supplemental interviews conducted where required. Data were analysed as an ongoing process, with participants checking interpretations after each round, and then further analysed deductively to identify key uncertainties following all the rounds. The consensus threshold for the NGT was set a priori at ≥80%.
Results: The study resulted in a developed MSU pathway that reached consensus for being viable within the NHS, with consideration for current systems and pressures. In developing the pathway key uncertainties were identified such as where to base the MSU. We also identified where participants had to make trade-offs in the co-designed pathway, such as staffing considerations. Together, the identified uncertainties and trade-offs represent challenges to MSU implementation and are presented alongside the process to reach the finalised pathway. Future developments which may have implications for the implementation of MSUs were also explored.
Conclusions: The co-designed MSU pathway provides a foundation for MSU implementation in the English and Welsh NHS and can be subjected to local and regional modifications required for implementation. However, optimal implementation is likely hindered by several uncertainties and trade-offs that represent challenges to implementation of MSUs at scale, though future developments in acute stroke care may help to mitigate these challenges.
A retrospective cohort study of 203 patients with Takayasu’s arteritis: Experience from a Brazilian tertiary center
Authors: De Araujo Pedro Cargnelutti , Donato Arthur Ney Alves , Franco Andre Silva , Echauri Carlos Insfrán , Shinjo Samuel Katsuyuki 
Published: December 2024

Abstract

Background. Takayasu arteritis (TAK) is a rare form of systemic vasculitis that primarily affects the aorta and its major branches. Despite several epidemiological studies on TAK, only a few descriptive studies have been conducted in our country, which motivated us to conduct this study.
Methods. This single-center retrospective cohort study included Brazilian TAK patients who underwent follow-up at a tertiary outpatient clinic between January 2000 and June 2024. Patient data were extracted from the electronic medical records via standardized and parameterized information.
Results. A total of 203 patients with TAK were included with a predominance of Caucasians (83.7%) and females (79.8%). The median age at disease diagnosis was 28.0 (interquartile range: 20.0-38.0) years, and the median follow-up period was 122.0 (49.0-177.0) months. During the initial or follow-up period, 65.0% of patients used glucocorticoids and 80.0% used immunosuppressive/immunobiological drugs. The three most common Hata classifications were V (46.8%), IV (23.2%), and I (22.7%). There was a high burden of cardiovascular risk factors, including hypertension (72.9%), dyslipidemia (59.1%), and renovascular hypertension (22.7%). When patients were analyzed by age quartile, elderly patients were predominantly without glucocorticoids and immunosuppressants and maintained sustained disease control.
Conclusions. This is the largest cohort study to include Brazilian patients with TAK. Even with higher cardiovascular risk factors than in other series, we observed lower rates of ischemic or cardiovascular events. Moreover, the frequency of disease activity and current treatment was restricted to the patients’ ages.
Spatial and temporal pattern of phytoplankton community assembly processes in the largest tributary of the Yangtze River, China
Authors: Wang Jie , Sun Fuhong , Guo Yiding , Zhao Qianyu , Huang Nannan , Wang Ziteng , Wu Fengchang 
Published: December 2024

Abstract

Background
Elucidating phytoplankton community assembly processes is crucial for understanding the mechanisms of river bloom formation. The blooms in the Hanjiang River, the largest tributary of the Yangtze River, have garnered significant attention. However, research on the phytoplankton community assembly processes and their driving mechanisms in this river remains limited.
Results
Based on a comprehensive survey of phytoplankton communities in the Hanjiang River during both dry and wet seasons in 2023, this study employed statistical methodologies, including similarity and correlation analyses, to investigate these assembly processes. Furthermore, it quantified the relative contributions of stochastic and deterministic processes. The results indicated significant heterogeneity in the distribution and composition of phytoplankton communities. Phytoplankton community dissimilarity increased significantly with geographical distance. VPA results showed that spatial variables had a stronger effect on phytoplankton communities than environmental factors. Fitting results from the neutral community and null models revealed that stochastic processes played a more significant role in phytoplankton community construction in the Hanjiang River than deterministic processes, with undominated stochastic processes being predominant during both the dry (82%) and wet (64%) seasons. The roles of diatoms and cyanobacteria in community construction were systematically analyzed based on the dominant species in the Hanjiang River blooms. Compared to other phytoplankton species (such as diatoms), cyanobacteria were more influenced by deterministic factors, suggesting a risk of cyanobacteria blooms in the middle and lower reaches of the Hanjiang River during the wet season.
Conclusions
This study elucidated the phytoplankton community assembly processes and their influencing factors in the Hanjiang River, playing an important role in revealing bloom outbreak mechanisms and providing insights for future studies on the assembly processes of phytoplankton and other aquatic organisms.
Intermediates of Forming Transition Metal Dichalcogenides Heterostructures Revealed by Machine Learning Simulations
Authors: Gao Junfeng , Zhao Luneng , Liu Hongsheng , Chang Yuan , Shi Xiaoran , Zhao Jijun , Ding Feng 
Published: December 2024

Abstract

The primary restrictions on 2D transition metal dichalcogenide (TMD) van der Waals heterostructures (vdWHs) are size limitation and alloying. Recently, a two-step vapor deposition method was reported to grow wafer-scale TMD vdWHs with little contamination [Nature 621, 499 (2023)]. In this study, we developed a machine learning potential (MLP) which can accurately simulate the growth processes of bilayer MoS2/WS2 vdWHs under various conditions. Importantly, a SMMS (where M is Mo or W) structure is revealed as a highly stable intermediate easily introduces metal atom exchange and alloying. Eliminating the alloying contamination in TMD vdWHs is avoiding SMMS structure by preventing the landing of bare metal atoms. However, SMMS is revealed as an ideal electrode for MoS2 FETs with low Schottky barrier.
Integrating Quantum Mechanics into Protein-Ligand Docking: Toward Higher Accuracy and Reliability
Authors: Fusti-Molnar Laszlo 
Published: December 2024

Abstract

I introduce two new methods, QFVina and QFVinardo, for protein-ligand docking that leverage precomputed high-quality conformational libraries with QM-optimized geometries and ab initio DFT-D4-based conformational rankings and strain energies. These methods provide greater accuracy in docking-based virtual screening by addressing the inaccuracies in intramolecular relative energies of conformations, a critical component often misrepresented in flexible ligand docking calculations. I demonstrate that numerous force field-based methods widely used today exhibit substantial errors in conformational relative energies, and that it is unrealistic to expect better accuracy from the faster scoring functions typically employed in docking. Consistent with these findings, I show that traditional flexible ligand docking often produces geometries with significant strain energies and large deviations, with magnitudes comparable to the protein-ligand binding energies themselves and much larger than the differences we aim to estimate in docking hitlists. By using physically realistic ligand conformations with accurate strain energies in the scoring function, QFVina and QFVinardo produce markedly different docking results, even with the same docking parameters and scoring functions for protein-ligand interaction energies. I analyzed these differences in docking hitlists and selected protein-ligand interactions using three protein targets from COVID-19 research.
Glioblastoma chemoattract migratory interneuron precursors modified to deliver therapeutic proteins
Authors: De Raedt Thomas , Brosius Stephanie , Manley William , Harvey Kyra , Galanaugh Jamie , Rohacek Deborah , Anderson Stewart 
Published: December 2024

Abstract

Glioblastoma has a poor prognosis with limited therapeutic options, in part due to the presence of the blood brain barrier, which often prevents the delivery of therapeutic agents, and the immune suppressive tumor environment (TME), which is a challenge for T-cell based immunotherapies. We developed a cellular delivery vector where implanted modified post-mitotic Migratory Inhibitory Interneuron Precursors (MIPs) are chemoattracted to high-grade glioma (HGG), independent of expressed antigens and unhindered by the TME, to deliver therapeutic proteins of choice.
Fatty Acid Synthase-Derived Lipid Stores Support Breast Cancer Metastasis
Authors: Andolino Chaylen , Cotul Eylem Kulkoyluoglu , Xianyu Zilin , Li Yun , Bhat Divya , Ayers Mitchell , Buhman Kimberly K. , Hursting Stephen D. , Wendt Michael K. , Teegarden Dorothy 
Published: December 2024

Abstract

Lipid accumulation is associated with breast cancer metastasis. However, the mechanisms underlying how breast cancer cells increase lipid stores and their functional role in disease progression remain incompletely understood. Herein we quantified changes in lipid metabolism and characterized cytoplasmic lipid droplets in metastatic versus non-metastatic breast cancer cells. 14C-labeled palmitate was used to determine differences in fatty acid (FA) uptake and oxidation. Despite similar levels of palmitate uptake, metastatic cells increase lipid accumulation and oxidation of endogenous FAs compared to non-metastatic cells. Isotope tracing also demonstrated that metastatic cells support increased de novo lipogenesis by converting higher levels of glutamine and glucose into the FA precursor, citrate. Consistent with this, metastatic cells displayed increased levels of fatty acid synthase (FASN) and de novo lipogenesis. Genetic depletion or pharmacologic inhibition of FASN reduced cell migration, survival in anoikis assays, and in vivo metastasis. Finally, global proteomic analysis indicated that proteins involved in proteasome function, mitotic cell cycle, and intracellular protein transport were reduced following FASN inhibition of metastatic cells. Overall, these studies demonstrate that breast cancer metastases accumulate FAs by increasing de novo lipogenesis, storing TAG as cytoplasmic lipid droplets, and catabolizing these stores to drive several FAO-dependent steps in metastasis.