bluuebunny/crossref_metadata_2025_split huggingface dataset:
LGS‐PPIS: A Local–Global Structural Information Aggregation Framework for Predicting Protein–Protein Interaction Sites
Authors: Zhai Zhengli , Xu Shiya , Ma Wenjian , Niu Niuwangjie , Qu Chunyu , Zong Chao 
Published: November 2024

ABSTRACTExploring protein–protein interaction sites (PPIS) is of significance to elucidating the intrinsic mechanisms of diverse biological processes. On this basis, recent studies have applied deep learning‐based technologies to overcome the high cost of wet experiments for PPIS determination. However, the existing methods still suffer from two limitations that remain to be solved. Firstly, the process of feature aggregation in most methods only took into account node features, but ignored the complex edge features of the target residue to its neighbor residues, resulting in insufficient local feature extraction. Secondly, such feature aggregation was limited to aggregating spatially adjacent residues, and could not capture the “remote” residues that played a critical role in determining PPIS, which can be summed up as the lack of global feature at the residue level. To break the above limitations, a local–global structural information aggregation framework, LGS‐PPIS, was proposed in this study, including two modules of edge‐aware graph convolutional network (EA‐GCN) and self‐attention integrated with initial residual and identity mapping (SA‐RIM), which achieved the aggregation of local and global information for PPIS prediction. Evaluation results of LGS‐PPIS showed that the proposed method outperformed state‐of‐the‐art deep learning methods on three widely used PPIS prediction benchmarks. Besides, the results of ablation experiments demonstrated that the local features from spatially adjacent residues and global features from “remote” residues separately captured by EA‐GCN and SA‐RIM could benefit the model performance. Among them, the former was shown to have a more significant role in the PPIS prediction.
Population pharmacokinetics and pharmacodynamics of edoxaban in pediatric patients
Authors: Zou Peng , Atluri Akhilesh , Chang Peter , Goedecke Michael , Leil Tarek A. 
Published: November 2024

AbstractEdoxaban is an orally active inhibitor of activated factor X (FXa). Population pharmacokinetic (PK) and pharmacodynamic (PD) analyses were performed to characterize the PK and PK–PD relationships of edoxaban in pediatric patients to identify the covariates that may contribute to inter‐subject variability in PK and PD of edoxaban in pediatric patients, and to compare the PK and PD data between pediatric and adult patients. The pediatric PK of edoxaban was best described by a two‐compartment model with transit compartments, first‐order oral absorption, and linear elimination. The estimated glomerular filtration rate (eGFR), body weight, and post‐menstrual age were the significant covariates explaining variability in edoxaban PK among pediatric patients. A function based on renal maturation was applied to edoxaban clearance. The clearance for a 70 kg patient with an eGFR of 110 mL/min/1.73 m2 was estimated to be 42.9 L/h (CV ~ 31.8%). PK simulation showed that exposures across five pediatric age groups were comparable to that in adult patients receiving 60 mg once daily dose. The PK–PD relationship for anti‐factor Xa was best fit with an Emax (8.65 IU/mL) model with an EC50 of 631 ng/mL. The PK–PD relationships for activated partial thromboplastin time and prothrombin time were best fit with linear models (slopes of 0.0467, and 0.0415 s mL/ng, respectively). In addition, due to the small number of efficacy and safety events, an exploratory analysis did not detect a correlation between efficacy events (recurrent venous thromboembolism) or safety events (clinically relevant bleeding) and edoxaban exposure.
Oxyberberine Inhibits Hepatic Gluconeogenesis via AMPK‐Mediated Suppression of FoxO1 and CRTC2 Signaling Axes
Authors: Wu Fan , Lu Fuer , Dong Hui , Hu Meilin , Xu Lijun , Wang Dingkun 
Published: November 2024

ABSTRACTOxyberberine (OBB), a natural metabolite of berberine, has been shown to exhibit inhibitory effects on gluconeogenesis in our previous work. This work was designed to investigate the potential effects and underlying mechanisms of OBB on hepatic gluconeogenesis. Our work found that OBB significantly inhibited the expressions of glucose 6‐phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PEPCK), and decreased the glucose production in palmitic acid‐induced HepG2 cells. Then, AMPK/Akt/FoxO1 and AMPK/CRTC2 signaling pathways were confirmed by transcriptomics and network pharmacology analyses. It was shown that AMPK activation may phosphorylate and promote nuclear exclusion of FoxO1 and CRTC2, two key regulators of hepatic gluconeogenesis transcriptional pathways, resulting in the inhibition of gluconeogenesis under OBB administration. Afterwards, AMPK/Akt/FoxO1, AMPK/CRTC2 signaling pathways were evidenced by western blot, immunoprecipitation and confocal immunofluorescence, and the targeted inhibitor (Compound C) and siRNA of AMPK were applied for further mechanism verification. Moreover, it was found that OBB treatment activated AMPK/Akt/FoxO1 and AMPK/CRTC2 signaling pathways to decrease hepatic gluconeogenesis in db/db mice. Similarly, the in vivo inhibitory effects of OBB on gluconeogenesis were also diminished by AMPK inhibition. Our work demonstrated that OBB can inhibit hepatic gluconeogenesis in vitro and in vivo, and its underlying mechanisms were associated with AMPK‐mediated suppression of FoxO1 and CRTC2 signaling axes.
Performance of Minnesota Functionals on Vibrational Frequency
Authors: Wang Jiaxu , Zhang Cheng , Li Yaqi , Zhou Yini , Shu Yuanyuan , Liang Songping , Zhang Gaihua , Liu Zhonghua , Wang Ying 
Published: November 2024

ABSTRACTMolecular geometry and harmonic frequency calculations are essential in thermochemical computations, with density functional theory (DFT) being widely employed for vibrational frequency predictions due to its efficiency and accuracy. In this study, we assessed the precision of 28 Minnesota based functionals with three different basis sets using the VIBFREQ1295 dataset. Scaling factors are necessary for predicting fundamental frequencies, global scaling factors were fitted by using F38/10 and VIBFREQ1295 datasets. The superior performing functionals were then fitted based on vibrational frequency ranges to obtain frequency‐range‐specific scaling factors. We observed consistent outlier across various model chemistries in vibrational frequency predictions, with alternative scaling factors showing minimal impact on reducing outlier occurrences. Besides, large basis sets are not indispensably required for fundamental frequency predictions. M06‐L, revM06‐L, SOGGA11‐X, PW6B95‐D3(BJ), CF22D, and M06‐2X consistently exhibit excellent performance across the three basis sets. When using frequency‐range‐specific scaling factors, the root mean squard errors (RMSEs) and median absolute errors (MedAEs) of almost all the selected functionals were reduced. PW6B95‐D3(BJ), CF22D, and MN12‐SX exhibited the lowest RMSEs. Comparisons were also done for different data classifications; the dataset was classified by the elements of the molecules, vibrational frequency intervals, and vibrational modes.
Association between anti‐Müllerian hormone levels and polycystic ovary syndrome in a general cohort of young women in Japan
Authors: Miyake Natsuki , Osuka Satoko , Ohsawa Isao , Tonoike Takashi , Uno Tomoko , Tsuzuki Kazuo , Bayasula  , Sonehara Reina , Muraoka Ayako , Nakamura Tomoko , Goto Maki , Iwase Akira , Kajiyama Hiroaki 
Published: November 2024

AbstractPurposePolycystic ovary syndrome (PCOS) significantly affects women. This study investigated the association between serum anti‐Müllerian hormone (AMH) levels and menstrual cycle disorders, and AMH for PCOS in a general cohort of young Japanese women.MethodsWe measured serum AMH levels in 528 healthy female students at two universities in Japan between 2014 and 2020. We investigated the association between serum AMH levels and hormone levels, menstrual cycle, and body mass index.ResultsThe mean (±standard deviation) AMH level was 4.78 ± 2.88 ng/mL. Correlations were observed between serum AMH and luteinizing hormone (LH) or LH/follicle‐stimulating hormone (FSH) levels in women with irregular menstruation (LH: r = 0.542, p < 0.001; LH/FSH: r = 0.584, p < 0.001). The optimal serum AMH cutoff value that predicted LH ≥7.1 IU/L and LH/FSH ≥1.21 (PCOS diagnostic criteria revised by Japan Society of Obstetrics and Gynecology) in women with menstrual irregularities was 5.30 ng/mL (area under the curve: 0.815, sensitivity: 84.2%, specificity: 70.3%).ConclusionsSerum AMH can be measured during annual health checkups and may be a useful biomarker for early and arcuate diagnosis and intervention in women with PCOS.
Reinforcing Photogenerated Carrier Extraction of Environment‐Friendly InP/ZnSeS Quantum Dots for High‐Performing Photoelectrochemical Photodetection and Solar Energy Conversion
Authors: Mi Guohua , Yao Yisen , Xia Li , Zhao Hongyang , Yang Qian , Wang Zhiming M. , Tong Xin 
Published: November 2024

AbstractColloidal InP/ZnSeS‐based quantum dots (QDs) are considered promising building blocks for light‐emitting devices due to their environmental friendliness, high quantum yield (QY), and narrow emission. However, the intrinsic type‐I band structure severely hinders potential photoelectrochemical (PEC) applications requiring efficient photoexcited carrier separation and transfer. In this study, the optoelectronic properties of InP/ZnSeS QDs are tailored by introducing Al dopants in the ZnSeS layer, which concurrently passivate the surface defects and act as shallow donor states for suppressed non‐radiative recombination and improved charge extraction efficiency. Consequently, as‐fabricated InP/ZnSeS:Al QDs‐based PEC‐type photodetector exhibited a high detectivity up to 1011 Jones and a remarkable responsivity of 0.66 A W−1 at 600 nm even under self‐powered condition (0V bias). In addition, as‐prepared InP/ZnSeS:Al QDs‐based photoanode can be alternatively used for PEC hydrogen generation, showing an H2 production rate of 73.7 µmol cm−2 h−1 under 1 sun illumination (AM 1.5G, 100 mW cm−2). The results offer a prospective strategy for optimizing eco‐friendly QDs for high‐performance multifunctional light detection/conversion devices.
Precise Methylation Detection of Tumor Suppressor Gene Promoters by Magnetic Enrichment and Nano Silver Adduct–Promoted Surface‐Enhanced Raman Scattering
Authors: Singh Shubham , Lin Yu‐Wei , Wang Wen‐Jyun , Chang Yu‐Cheng , Chien Yi‐Hsin , Li Wei‐Peng 
Published: November 2024

AbstractNoninvasive liquid biopsies can be used for early tumor diagnosis by identifying the methylation level of the tumor suppressor genes (TSGs)—a reliable index for cancer evaluation. However, identifying trace circulating genes from specimens remains challenging. This work introduces a novel method that combines magnetic isolation and surface‐enhanced Raman scattering (SERS) to concentrate and detect the methylated TSG promotors. A superparamagnetic iron oxide nanoparticle modified with streptavidin is prepared as a universal magnetic bead. Biotin‐terminated probe single‐strand DNA (ssDNA) is immobilized on the magnetic beads through biotin–streptavidin bioconjugation. Artificial target ssDNA fragments with various methylation levels are applied as a promoter gene model. Concentrated double‐strand DNA (dsDNA) is produced by a hybridizing probe and target ssDNA on magnetic nanobeads, as well as an additional magnetic isolation process. The well‐prepared DNA adduct, which consists of 3 nm cisplatin‐modified Ag nanoclusters, can specifically bind with guanine‐cytosine base pairs of dsDNA. Ag‐nanoparticle‐induced localized SERS amplified signals of 5‐methylcytosine (5‐mC) from the dsDNA in Raman spectra, enabling accurate methylation level measurement in mixtures of 0–1 µm methylated DNA, with a detection limit of 0.05 µm. This method shows promise for enabling the methylation level evaluation of various TSGs and promoters in early cancer liquid biopsies.
Peierls Distortion Induced Giant Linear Dichroism, Second‐Harmonic Generation, and In‐Plane Ferroelectricity in NbOBr2
Authors: Li Zhuolun , Wang Shaolong , Wang Chong , Zhang Xi , Yu Zhipeng , Du Shanzheng , Zeng Zhongming , Dai Yang , Zhang Yuchao , Liu Xiaochi , Sun Jian , Xue Jiawei , Wu Zheng , Fan Luyuan , Dai Junfeng , Zhai Kun , Nie Anmin , Liu Zhongyuan , Cheng Yingchun 
Published: November 2024

AbstractThe Peierls distortion plays an essential role in governing the in‐plane ferroelectricity and nonlinear optical characteristics of anisotropic niobium oxide dihalides, such as NbOCl2 and NbOI2. Despite its significance, experimental investigation into the structural, optical, and ferroelectric properties of NbOBr2 has been lacking. Here, the successful fabrication of centimeter‐sized, high‐quality NbOBr2 single crystals, enabling direct observation of Peierls distortion using aberration‐corrected scanning transmission electron microscopy, is reported. Notably, the magnitude of Peierls distortion in NbOBr2 falls between that observed in NbOCl2 and NbOI2. Furthermore, the existence of giant linear dichroism absorption and second‐harmonic generation (SHG) phenomena associated with Peierls distortion is confirmed. Exfoliated NbOBr2 flakes exhibit single‐domain ferroelectricity, with the polarization switchable by an electric field. Temperature‐dependent SHG measurements reveal a Curie temperature of ≈502 K for ferroelectric NbOBr2. This work demonstrates that NbOBr2 holds promise for polarized nonlinear optical devices, as well as for nonvolatile information processing and storage devices.
Bioorthogonal Janus microparticles for photothermal and chemo‐therapy
Authors: Zhang Qingfei , Kuang Gaizhen , Chen Kai , Zhao Miaoqing , Shang Luoran 
Published: November 2024

AbstractBioorthogonal chemistry, recognized as a highly efficient tool in chemical biology, has shown significant value in cancer treatment. The primary objective is to develop efficient delivery strategies to achieve enhanced bioorthogonal drug treatment for tumors. Here, Janus microparticles (JMs) loaded with cyclooctene‐modified doxorubicin prodrug (TCO‐DOX) and tetrazine‐modified indocyanine green (Tz‐ICG) triggers are reported. Besides activating TCO‐DOX, Tz‐ICG is also a photothermal agent used in photothermal therapy (PTT), enabling the simultaneous use of biorthogonal chemotherapy and PTT. Additionally, the DOX could be significantly reduced in systemic toxicity with the modification of cyclooctene. Thus, the developed drug‐carrying JMs system exhibits effective tumor cell killing in vitro and effectively inhibits tumor local progress and distant lung metastasis after postoperative treatment with good safety. These results demonstrate that the prepared JMs provide a paradigm for bioorthogonal prodrug activation and localized delivery, and hold great promise for cancer therapy as well as other related applications.
Student perspectives on learning transfer from online postgraduate sonography courses to traineeships: A pilot survey
Authors: Maranna Sandhya , Joksimovic Srecko , Willison John , MacDougall Margaret , Parange Nayana , Costabile Maurizio 
Published: November 2024

AbstractIntroductionThis survey aims to understand how postgraduate sonography students perceive to apply knowledge from online coursework to traineeships. It also explores the impact of students' age, gender, traineeship duration and geographic location on learning transfer. The ability to apply learnt knowledge is a key factor for student success in higher education and the workplace, yet it is an under‐researched topic.MethodThe Human Research Ethics Committee of an Australian university granted ethical approval. A pilot online survey was sent to 279 medical sonography students enrolled in an online postgraduate program. These students had an industry traineeship as a corequisite to online coursework. The survey was sent via email on Microsoft Forms from October to December 2023. Descriptive, Likert scale and free‐text data were analysed using Microsoft Excel, IBM SPSS Statistics (version 29) and Lumivero NVivo (version 14).ResultsThe response rate was 38% (n = 106). Most respondents agreed that they developed transfer skills from online courses. Practice questions, lectures and interactive sessions emerged as the key online learning activities that helped to facilitate knowledge transfer. With summative assessments, case studies enhanced knowledge transfer. No significant difference was seen in the transfer ability based on geographical location, age and gender.ConclusionIt is challenging for online educators to foster transfer skills to prepare safe, competent, job‐ready graduates. Our study has provided initial insights on enablers of online learning transfer to online educators on students' perspectives of how they see the relevance and how they apply knowledge from online courses to traineeships.
Advancements to the equivalent compression flange method
Authors: Jörg Fabian , Schaper Lukas , Kuhlmann Ulrike , Knobloch Markus 
Published: November 2024

AbstractThe simplified method of the equivalent compression flange represents an illustrative and easy‐to‐use engineering model for lateral torsional buckling. The basic concept of the verification procedure has existed since its introduction in the 1950s. It is still frequently used today for preliminary design and application cases where the solution of the ‘correct lateral torsional buckling problem’ is complex and time‐consuming. To adapt the method to the current state of the art, it was further developed in the framework of the Eurocode 3 evolution. This ‘new’ method is part of the second generation of Eurocode 3, Part 1‐1 and is valid for classes 1 to 3 cross sections in major axis bending. The method must be adapted for use in other contexts and for specific applications. Applying the equivalent compression flange verification method to the structural fire design of building structures must consider the temperature‐dependent material properties of steel and their impact on the stability behaviour. Moreover, typical applications for bridge structures, runway beams, and H‐piles in combined walls require additional consideration of class 4 cross sections and various combined loadings, e. g., N–M interaction behaviour. This article presents theoretical studies on extending the simplified method of the equivalent compression flange to meet these demands. Finally, the application of the verification method is demonstrated in working examples.
Nonlinear Dynamic Analysis Using the Force Analogy Method and the Ibarra–Medina–Krawinkler Model
Authors: Patlán Carlos M. , Hernández‐Barrios Hugo , Gomez Roberto 
Published: November 2024

ABSTRACTA methodology to integrate the Ibarra–Medina–Krawinkler (IMK) hysteretic model with the force analogy method (FAM) is proposed. FAM is a powerful tool for performing nonlinear structural analysis that reduces analysis time, addressing the main limitation of nonlinear analysis. One area of opportunity for FAM lies in its access to material nonlinearity models, which enable the reproduction of inelastic behavior in structures. The IMK model, utilized in nonlinear analysis for updating the stiffness matrix, incorporates various rules of material nonlinear behavior and considers cyclic deterioration of stiffness and strength. By combining the IMK model with FAM, the capability to model material nonlinear behavior in a computationally efficient manner is enhanced. The proposed methodology is validated through four numerical examples, demonstrating its effectiveness in replicating experimental behaviors and enhancing FAM capabilities in inelastic structural analysis.
Insights Into the Adsorption Behavior of Polyethylene Microplastics Towards Lead(II) Ions
Authors: Saravanakumar Krishnan , Sathyamoorthy Manickam , Prasad Donipathi Mogili Reddy , Prasad Balakrishna Sankari Naveen , Senthilkumar Ramalingham , Lakshmanarao Govindarajan 
Published: November 2024

ABSTRACTMicroplastics and metals represent widespread contaminants which can cause significant damage to aquatic ecosystems and organisms. However, the complex interactions between microplastics and various metals in water environments remains to be understood. This study aims to investigate the interaction dynamics between lead(II) ions and polyethylene in freshwater environments. Adsorption trials were conducted systematically by adjusting operational parameters such as initial Pb(II) concentration, equilibrium pH value, and residence times. An in‐depth characterization study using scanning electron microscopy (SEM), x‐ray diffraction and Fourier transform infrared (FTIR) analysis was conducted to explain the adsorption mechanism of polyethylene microplastics (PEM). The data indicated the porous surface of PEM, highlighting the presence of diverse functional groups. According to the Langmuir model, the PEM exhibited maximum Pb(II) uptake of 3.69 mg/g at pH 4.5. The pseudo‐first‐order model demonstrated superior fitting to Pb(II)‐PEM kinetics. Desorption trials were performed to assess the release of Pb(II) from Pb(II)‐bounded PEM using various chemical agents. It was observed that 0.01 M HNO₃ desorbed Pb(II) ions optimally, achieving a desorption efficiency exceeding 99.9%. Consequently, desorption trials provided evidence that Pb(II)‐bounded PEM may release Pb(II) ions in acidic environments, facilitating the transfer of Pb(II) to the digestive tracts of aquatic organisms.
Analysis of Heavy Metal Pollution in the Water of the Halda River: A Distinctive Breeding Habitat for Carp Fish in Bangladesh
Authors: Kamal Afsana , Kibria Md. Manzoorul , Hossain Shahadat , Mahmud Chowdhury Kaiser , Roy Rashmi , Resma Nighat Sultana 
Published: November 2024

ABSTRACTBackgroundThe present study aimed to assess the heavy metal concentrations in water from different sampling sites of the Halda River, the only natural breeding ground of Indian major carps.ObjectivesWe have analysed the contamination level and seasonal variations of heavy metals (viz. Fe, Cu, Zn, Cr, Cd and Pb). The favourability of the breeding environment was assessed by different contamination indices.MethodsSamples were collected from six sampling sites for four different seasons, and the metal concentrations were determined for water samples using Flame atomic absorption spectrophotometer.ResultsThe obtained order of mean concentrations of heavy metals for four seasons was winter > spring > monsoon > pre‐monsoon, and the assessed mean concentrations (mg/L) of heavy metals follow the trend: Fe (9.129) > Pb (0.033) > Zn (0.024) > Cr (0.017) > Cu (0.012) > Cd (0.002). The concentration of Fe was found above the permissible limit set by the World Health Organization (WHO) (Guidelines for Water Quality) and ECR (1997), and the concentrations for Pb were found above the USEPA (2006) limit in all four seasons. Contamination indices (heavy metal pollution Index [HPI] and metal index [MI]) indicate that during winter and monsoon, the river water metal condition is critical (HPI > 100) and the sites are moderately as well as slightly (1< MI <2) affected by the studied heavy metals. Contamination indices, such as contamination factors (Cf), degree of contamination (Cdeg) and the pollution load index (PLI), demonstrate the fact that Fe and Pb remarkably contaminated the studied sampling sites. The Pearson correlation matrix and the principal component analysis (PCA) revealed that the studied metals are connected by their sources, which can be geological or anthropogenic.ConclusionUrgent initiatives need to be taken, and effective strategies must be implemented to control the different sources responsible for the entry of heavy metals into the Halda River water.