bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and mechanistic insights into Quinolone Synthase to address its functional promiscuity
Authors: Vijayanathan Mallika , Vadakkepat Abhinav Koyamangalath , Mahendran Kozhinjampara R. , Sharaf Abdoallah , Frandsen Kristian E. H. , Bandyopadhyay Debashree , Pillai M. Radhakrishna , Soniya Eppurath Vasudevan 
Published: May 2024

AbstractQuinolone synthase from Aegle marmelos (AmQNS) is a type III polyketide synthase that yields therapeutically effective quinolone and acridone compounds. Addressing the structural and molecular underpinnings of AmQNS and its substrate interaction in terms of its high selectivity and specificity can aid in the development of numerous novel compounds. This paper presents a high-resolution AmQNS crystal structure and explains its mechanistic role in synthetic selectivity. Additionally, we provide a model framework to comprehend structural constraints on ketide insertion and postulate that AmQNS’s steric and electrostatic selectivity plays a role in its ability to bind to various core substrates, resulting in its synthetic diversity. AmQNS prefers quinolone synthesis and can accommodate large substrates because of its wide active site entrance. However, our research suggests that acridone is exclusively synthesized in the presence of high malonyl-CoA concentrations. Potential implications of functionally relevant residue mutations were also investigated, which will assist in harnessing the benefits of mutations for targeted polyketide production. The pharmaceutical industry stands to gain from these findings as they expand the pool of potential drug candidates, and these methodologies can also be applied to additional promising enzymes.
EP4-induced mitochondrial localization and cell migration mediated by CALML6 in human oral squamous cell carcinoma
Authors: Ishikawa Soichiro , Umemura Masanari , Nakakaji Rina , Nagasako Akane , Nagao Kagemichi , Mizuno Yuto , Sugiura Kei , Kioi Mitomu , Mitsudo Kenji , Ishikawa Yoshihiro 
Published: May 2024

AbstractLymph node metastasis, primarily caused by the migration of oral squamous cell carcinoma (OSCC) cells, stands as a crucial prognostic marker. We have previously demonstrated that EP4, a subtype of the prostaglandin E2 (PGE2) receptor, orchestrates OSCC cell migration via Ca2+ signaling. The exact mechanisms by which EP4 influences cell migration through Ca2+ signaling, however, is unclear. Our study aims to clarify how EP4 controls OSCC cell migration through this pathway. We find that activating EP4 with an agonist (ONO-AE1-473) increased intracellular Ca2+ levels and the migration of human oral cancer cells (HSC-3), but not human gingival fibroblasts (HGnF). Further RNA sequencing linked EP4 to calmodulin-like protein 6 (CALML6), whose role remains undefined in OSCC. Through protein-protein interaction network analysis, a strong connection is identified between CALML6 and calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), with EP4 activation also boosting mitochondrial function. Overexpressing EP4 in HSC-3 cells increases experimental lung metastasis in mice, whereas inhibiting CaMKK2 with STO-609 markedly lowers these metastases. This positions CaMKK2 as a potential new target for treating OSCC metastasis. Our findings highlight CALML6 as a pivotal regulator in EP4-driven mitochondrial respiration, affecting cell migration and metastasis via the CaMKK2 pathway.
ALKBH5-mediated m6A modification of circFOXP1 promotes gastric cancer progression by regulating SOX4 expression and sponging miR-338-3p
Authors: Wang Shouhua , Zhu Xiang , Hao Yuan , Su Ting ting , Shi Weibin 
Published: May 2024

AbstractCircular RNAs (circRNAs) have recently been suggested as potential functional modulators of cellular physiology processes in gastric cancer (GC). In this study, we demonstrated that circFOXP1 was more highly expressed in GC tissues. High circFOXP1 expression was positively associated with tumor size, lymph node metastasis, TNM stage, and poor prognosis in patients with GC. Cox multivariate analysis revealed that higher circFOXP1 expression was an independent risk factor for disease-free survival (DFS) and overall survival (OS) in GC patients. Functional studies showed that increased circFOXP1 expression promoted cell proliferation, cell invasion, and cell cycle progression in GC in vitro. In vivo, the knockdown of circFOXP1 inhibited tumor growth. Mechanistically, we observed ALKBH5-mediated m6A modification of circFOXP1 and circFOXP1 promoted GC progression by regulating SOX4 expression and sponging miR-338-3p in GC cells. Thus, our findings highlight that circFOXP1 could serve as a novel diagnostic and prognostic biomarker and potential therapeutic target for GC.
Data-driven insights can transform women’s reproductive health
Authors: Oskotsky Tomiko T. , Yin Ophelia , Khan Umair , Arnaout Leen , Sirota Marina 
Published: May 2024

AbstractThis perspective explores the transformative potential of data-driven insights to understand and address women’s reproductive health conditions. Historically, clinical studies often excluded women, hindering comprehensive research into conditions such as adverse pregnancy outcomes and endometriosis. Recent advances in technology (e.g., next-generation sequencing techniques, electronic medical records (EMRs), computational power) provide unprecedented opportunities for research in women’s reproductive health. Studies of molecular data, including large-scale meta-analyses, provide valuable insights into conditions like preterm birth and preeclampsia. Moreover, EMRs and other clinical data sources enable researchers to study populations of individuals, uncovering trends and associations in women’s reproductive health conditions. Despite these advancements, challenges such as data completeness, accuracy, and representation persist. We emphasize the importance of holistic approaches, greater inclusion, and refining and expanding on how we leverage data and computational integrative approaches for discoveries so that we can benefit not only women’s reproductive health but overall human health.
The kinase ZYG-1 phosphorylates the cartwheel protein SAS-5 to drive centriole assembly in C. elegans
Authors: Sankaralingam Prabhu , Wang Shaohe , Liu Yan , Oegema Karen F , O’Connell Kevin F 
Published: May 2024

AbstractCentrioles organize centrosomes, the cell’s primary microtubule-organizing centers (MTOCs). Centrioles double in number each cell cycle, and mis-regulation of this process is linked to diseases such as cancer and microcephaly. In C. elegans, centriole assembly is controlled by the Plk4 related-kinase ZYG-1, which recruits the SAS-5–SAS-6 complex. While the kinase activity of ZYG-1 is required for centriole assembly, how it functions has not been established. Here we report that ZYG-1 physically interacts with and phosphorylates SAS-5 on 17 conserved serine and threonine residues in vitro. Mutational scanning reveals that serine 10 and serines 331/338/340 are indispensable for proper centriole assembly. Embryos expressing SAS-5S10A exhibit centriole assembly failure, while those expressing SAS-5S331/338/340A possess extra centrioles. We show that in the absence of serine 10 phosphorylation, the SAS-5–SAS-6 complex is recruited to centrioles, but is not stably incorporated, possibly due to a failure to coordinately recruit the microtubule-binding protein SAS-4. Our work defines the critical role of phosphorylation during centriole assembly and reveals that ZYG-1 might play a role in preventing the formation of excess centrioles.
Diet-driven differential response of Akkermansia muciniphila modulates pathogen susceptibility
Authors: Wolter Mathis , Grant Erica T , Boudaud Marie , Pudlo Nicholas A , Pereira Gabriel V , Eaton Kathryn A , Martens Eric C , Desai Mahesh S 
Published: May 2024

AbstractThe erosion of the colonic mucus layer by a dietary fiber-deprived gut microbiota results in heightened susceptibility to an attaching and effacing pathogen, Citrobacter rodentium. Nevertheless, the questions of whether and how specific mucolytic bacteria aid in the increased pathogen susceptibility remain unexplored. Here, we leverage a functionally characterized, 14-member synthetic human microbiota in gnotobiotic mice to deduce which bacteria and functions are responsible for the pathogen susceptibility. Using strain dropouts of mucolytic bacteria from the community, we show that Akkermansia muciniphila renders the host more vulnerable to the mucosal pathogen during fiber deprivation. However, the presence of A. muciniphila reduces pathogen load on a fiber-sufficient diet, highlighting the context-dependent beneficial effects of this mucin specialist. The enhanced pathogen susceptibility is not owing to altered host immune or pathogen responses, but is driven by a combination of increased mucus penetrability and altered activities of A. muciniphila and other community members. Our study provides novel insights into the mechanisms of how discrete functional responses of the same mucolytic bacterium either resist or enhance enteric pathogen susceptibility.
Characterisation of the morphology of surface-assembled Au nanoclusters on amorphous carbon
Authors: Dearg Malcolm , Lethbridge Sean , McCormack James , Palmer Richard E. , Slater Thomas J. A. 
Published: May 2024

Au nanoparticles over 100 atoms in size formed via surface-growth of sputtered atoms on amorphous carbon are approximately spherical in morphology. The distribution of particle structural isomers was found to match those formed via gas-condensation.
Multi‐objective interval type‐2 fuzzy linear programming problem with vagueness in coefficient
Authors: Sargolzaei Shokouh , Mishmast Nehi Hassan 
Published: May 2024

AbstractOne of the most widely used fuzzy linear programming models is the multi‐objective interval type‐2 fuzzy linear programming (IT2FLP) model, which is of particular importance due to the simultaneous integration of multiple criteria and objectives in a single problem, the fuzzy nature of this type of problems, and thus, its closer similarity to real‐world problems. So far, many studies have been done for the IT2FLP problem with uncertainties of the vagueness type. However, not enough studies have been done regarding the multi‐objective interval type‐2 fuzzy linear programming (MOIT2FLP) problem with uncertainties of the vagueness type. As an innovation, this study investigates the MOIT2FLP problem with vagueness‐type uncertainties, which are represented by membership functions (MFs) in the problem. Depending on the localisation of vagueness in the problem, that is, vagueness in the objective function vector, vagueness in the technological coefficients, vagueness in the resources vector, and any possible combination of them, various problems may arise. Furthermore, to solve problems with MOIT2FLP, first, using the weighted sum method as an efficient and effective method, each of the MOIT2FLP problems is converted into a single‐objective problem. In this research, these types of problems are introduced, their MFs are stated, and different solution methods are suggested. For each of the proposed methods, the authors have provided an example and presented the results in the corresponding tables.
CLaSP: Cross‐view 6‐DoF localisation assisted by synthetic panorama
Authors: Zhu Juelin , Yan Shen , Cheng Xiaoya , Wu Rouwan , Liu Yuxiang , Zhang Maojun 
Published: May 2024

AbstractDespite the impressive progress in visual localisation, 6‐DoF cross‐view localisation is still a challenging task in the computer vision community due to the huge appearance changes. To address this issue, the authors propose the CLaSP, a coarse‐to‐fine framework, which leverages a synthetic panorama to facilitate cross‐view 6‐DoF localisation in a large‐scale scene. The authors first leverage a segmentation map to correct the prior pose, followed by a synthetic panorama on the ground to enable coarse pose estimation combined with a template matching method. The authors finally formulate the refine localisation process as feature matching and pose refinement to obtain the final result. The authors evaluate the performance of the CLaSP and several state‐of‐the‐art baselines on the Airloc dataset, which demonstrates the effectiveness of our proposed framework.
Traditional vs. modified Ringer lactate-based del Nido cardioplegia impacts on clinical outcomes in patients undergoing coronary artery bypass grafting: Results from a prospective, randomized, blinded trial
Authors: Kachoueian Naser , Janghorban Salimeh , Gorjipour Farhad , Torkashvand Majid , Mahjoob Mohammad Parsa , Aslani Hossein , Mehrabanian Mohamadjavad , Gorjipour Fazel 
Published: May 2024

Introduction: Myocardial protection with cardioplegia is a crucial approach to mitigate myocardial damage during coronary bypass grafting surgery (CABG) with cardiopulmonary bypass (CPB). The major component of the del Nido cardioplegia solution, Plasma-Lyte A, is difficult to obtain in Iran due to high cost. The objective of the current study was to study if the lactated Ringer’s solution as the base for del Nido solution (LR DN) usage is a viable option as a substitute for Plasma-Lyte A in adult patients presenting for CABG surgery. Study design and methods: The present prospective, randomized, blinded study was performed on 18–75-year-old patients ejection fraction (EF) > 35% undergoing CABG with CPB. Patients were randomly allocated to LR DN (modified del Nido cardioplegia) and PL DN (standard del Nido cardioplegia solution) groups. Serum level of cardiac troponin I (cTnI), the type and dosage of inotrope agents, EF, rate of arrhythmia after clamp removal and lactate level were measured and compared between patients of LR DN and PL DN groups. Results: 109 patients were recruited. There were no statistically significant differences between groups for cardiopulmonary bypass times, cardiac enzymes, transfusion requirements, and arterial blood gases. There was no mortality for study patients. Postoperative serum levels of cTnI among patients in the LR DN group was significantly higher than patients of the PL DN group after ICU admission and 24 h post-ICU. Also, more patients needed epinephrine administration in the operating room in the LR DN group (29.8% vs. 11.5%; p: 0.019 vs. PL DN group). Conclusion: We concluded that the standard del Nido cardioplegia solution offers better myocardial protection compared with Ringer’s lactate-based del Nido cardioplegia in adult patients undergoing CABG with CPB. We recommend using standard del Nido cardioplegia with a PL base for patients presenting for CABG surgery.
The Influence of Streptococcus mutans Biofilm Formation in a Polymicrobial Environment (Streptococcus gordonii & Porphyromonas gingivalis)
Authors: Kriswandini Indah Listiana , Sidarningsih Sidarningsih , Hermanto Adelheid Chrissanda , Tyas Pinta Rahayuning , Aljunaid Mohammed Ahmed 
Published: May 2024

Abstract
Objectives Biofilms play a vital role in the occurrence or worsening of an infectious disease. Streptococcus mutans is a bacterium with the ability to form biofilms that plays a key role in the development of infectious diseases such as dental caries. The formation of biofilms in S. mutans is mediated by quorum sensing. Inhibiting quorum sensing can be considered as one of the approaches to prevent caries. This study aims to investigate the ability of Streptococcus gordonii and Porphyromonas gingivalis bacteria to inhibit the formation of S. mutans biofilm.
Materials and Methods This research was conducted to analyze bacterial biofilm formation and metabolism. The bacteria used are S. mutans (serotype C), S. gordonii (ATCC 5165), and P. gingivalis (ATCC 33277). Biofilm formation was analyzed using the crystal violet assay. Bacterial metabolism was analyzed using the methylthiazol tetrazolium (MTT) assay.
Results The results of the crystal violet assay indicate a decrease in biofilm formation in S. mutans when in the presence of S. gordonii and S. mutans in the presence of P. gingivalis. The results of the MTT assay show no significant change in the bacterial metabolism of S. mutans in the presence of S. gordonii and S. mutans in the presence of P. gingivalis. However, S. mutans with the presence of S. gordonii and P. gingivalis show an increase in biofilm formation and bacterial metabolism.
Conclusion S. gordonii and P. gingivalis are each capable of inhibiting the formation of S. mutans biofilm in a polymicrobial environment.
The Effect of Different Chemical Surface Treatments on the Bond Strength of Resin-Matrix Ceramic Repaired with Resin Composite
Authors: Prabriputaloong Satit , Krajangta Nantawan , Klaisiri Awiruth 
Published: May 2024

Abstract
Objective This study investigates the effect of different chemical surface treatment protocols with different functional monomers of universal adhesives on the shear bond strength between resin-matrix ceramic and resin composite.
Materials and Methods Eighty resin-matrix ceramics (Shofu block HC) were built and designed into eight groups of ten specimens and surface treated with HC primer (HC) and/or three universal adhesives (single bond universal [SBU], Scotchbond universal plus [SBP], and Tetric N-bond universal [TNU]) assigning follows; group 1, nonsurface treated; group 2, HC; group 3, SBU; group 4, HC + SBU; group 5, SBP; group 6, HC + SBP; group 7, TNU; group 8, HC + TNU. A template was put on the specimen center, and then pushed packable resin composite. Mechanical testing machinery was used to examine the samples' shear bond strength (SBS) values. To examine failure patterns, the debonded specimen surfaces were examined by a stereomicroscope.
Statistical Analysis The one-way analysis of variance method was used to evaluate the data, and the Tukey's test was used to determine the significant level (p < 0.05).
Results The highest SBS was obtained in group 6 (39.25 ± 1.65 MPa). Group 1 (4.15 ± 0.54 MPa) had the lowest SBS. Group 6 exhibited the highest percentage of cohesive failure patterns (70%). High SBS values were frequently correlated with the surface treatment groups and the cohesive failure patterns.
Conclusion The application of HC primer prior to the universal adhesive is an alternative protocol for enhancing the repair bond strength between resin-matrix ceramic and resin composite interfaces. Moreover, the application of HC primer prior to the SBP is the best strategy for resin-matrix ceramic and resin composite repairs.
On-chip quasi-light storage for long optical delays using Brillouin scattering
Authors: Merklein Moritz , Goulden Lachlan , Kiewiet Max , Liu Yang , Lai Choon Kong , Choi Duk-Yong , Madden Stephen J. , Poulton Christopher G. , Eggleton Benjamin J. 
Published: May 2024

Efficient and extended light storage mechanisms are pivotal in photonics, particularly in optical communications, microwave photonics, and quantum networks, as they offer a direct route to circumvent electrical conversion losses and surmount bandwidth constraints. Stimulated Brillouin Scattering (SBS) is an established method to store optical information by transferring it to the acoustic domain, but current on-chip SBS efforts have limited bandwidth or storage time due to the phonon lifetime of several nanoseconds. An alternate approach known as quasi-light storage (QLS), which involves the creation of delayed replicas of optical data pulses via SBS in conjunction with a frequency comb, has been proposed to lift the storage time constraint; however, its realization has been confined to lengthy optical fibers, constraining integration with on-chip optical elements and form factors. Here, we present an experimental demonstration of QLS on a photonic chip leveraging the large SBS gain of chalcogenide glass, achieving delays of up to 500 ns for 1 ns long signal pulses, surpassing typical Brillouin storage processes' acoustic lifetime by more than an order of magnitude and waveguide transit time by two orders of magnitude. We experimentally and numerically investigate the dynamics of on-chip QLS and reveal that the interplay between the acoustic wave that stores the optical signal and subsequent optical pump pulses leads to a reshaping of the acoustic field. Our demonstrations illustrate the potential for achieving ultra-long storage times of individual pulses by several hundred pulse widths, marking a significant stride toward advancing the field of all-optical storage and delay mechanisms.
Investigation of melt flow index and tensile properties of dual metal reinforced polymer composites for 3D printing using machine learning approach: Biomedical and engineering applications
Authors: Manola Mukesh Singh , Singh Balwant , Singla Manoj Kumar , Chohan Jasgurpreet Singh , Kumar Raman , Bisht Yashwant Singh , Kumar Raman , Alkahtani Meshel Q. , Islam Saiful , Ammarullah Muhammad Imam 
Published: May 2024

This study investigates the enhancement of mechanical properties of metal/polymer composites produced through fused deposition modeling and the prediction of the ultimate tensile strength (UTS) by machine learning using a Classification and Regression Tree (CART). The composites, comprising 80% acrylonitrile butadiene styrene matrix and 10% each of aluminum (Al) and copper (Cu) fillers, were subjected to a comprehensive exploration of printing parameters, including printing temperature, infill pattern, and infill density using the Taguchi method. The CART unveiled a hierarchical tree structure with four terminal nodes, each representing distinct subgroups of materials characterized by similar UTS properties. The predictors’ importance was assessed, highlighting their role in determining material strength. The model exhibited a high predictive power with an R-squared value of 0.9154 on the training data and 0.8922 on the test data, demonstrating its efficacy in capturing variability. The optimal combination of parameters for maximizing UTS was a zigzag infill pattern, a printing temperature of 245 °C, and an infill density of 10%, which is associated with the highest UTS of 680 N. The model’s reliability was confirmed through a paired t-test and test and confidence interval for two variances, revealing no significant difference between the observed and predicted UTS values. This research contributes to advancing additive manufacturing processes by leveraging CART analysis to optimize printing parameters and predict material strength. The identified optimal conditions and subgroup characteristics pave the way for developing robust and predictable metal/polymer composites, offering valuable insights for material design in the era of advanced manufacturing technologies.