bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparing Neural Style Transfer and Gradient-Based Algorithms in Brushstroke Rendering Tasks
Authors: Karimov Artur , Kopets Ekaterina , Shpilevaya Tatiana , Katser Evgenii , Leonov Sergey , Butusov Denis
Published: May 2023

Non-photorealistic rendering (NPR) with explicit brushstroke representation is essential for both high-grade imitating of artistic paintings and generating commands for artistically skilled robots. Some algorithms for this purpose have been recently developed based on simple heuristics, e.g., using an image gradient for driving brushstroke orientation. The notable drawback of such algorithms is the impossibility of automatic learning to reproduce an individual artist’s style. In contrast, popular neural style transfer (NST) algorithms are aimed at this goal by their design. The question arises: how good is the performance of neural style transfer methods in comparison with the heuristic approaches? To answer this question, we develop a novel method for experimentally quantifying brushstroke rendering algorithms. This method is based on correlation analysis applied to histograms of six brushstroke parameters: length, orientation, straightness, number of neighboring brushstrokes (NBS-NB), number of brushstrokes with similar orientations in the neighborhood (NBS-SO), and orientation standard deviation in the neighborhood (OSD-NB). This method numerically captures similarities and differences in the distributions of brushstroke parameters and allows comparison of two NPR algorithms. We perform an investigation of the brushstrokes generated by the heuristic algorithm and the NST algorithm. The results imply that while the neural style transfer and the heuristic algorithms give rather different parameter histograms, their capabilities of mimicking individual artistic manner are limited comparably. A direct comparison of NBS-NB histograms of brushstrokes generated by these algorithms and of brushstrokes extracted from a real painting confirms this finding.
Interpreting Deep Graph Convolutional Networks with Spectrum Perspective
Authors: Zhang Sisi , Li Fan , Zhang Tiancheng , Yu Ge
Published: May 2023

Graph convolutional network (GCN) architecture is the basis of many neural networks and has been widely used in processing graph-structured data. When dealing with large and sparse data, deeper GCN models are often required. However, the models suffer from performance degradation as the number of layers increases. The mainstream attribution of the current research is over-smoothing, and there are also gradient vanishing, training difficulties, etc., so a consensus cannot be reached. In this paper, we theoretically analyze the degradation problem by adopting spectral graph theory to globally consider the propagation and transformation components of the GCN architecture, and conclude that the over-smoothing problem caused by the propagation matrices is not the key factor for performance degradation. Afterwards, in addition to using conventional experimental methods, we proposed an experimental analysis strategy under the guidance of random matrix theory to analyze the singular value distribution of the model weight matrix. We concluded that the key factor leading to the degradation of model performance is the transformation component. In the context of a lack of consensus on the problem of model performance degradation, the paper proposes a systematic analysis strategy, as well as theoretical and empirical evidence.
Grey-Wolf-Optimization-Algorithm-Based Tuned P-PI Cascade Controller for Dual-Ball-Screw Feed Drive Systems
Authors: Liu Qi , Lu Hong , Yonezawa Heisei , Yonezawa Ansei , Kajiwara Itsuro , Wang Ben
Published: May 2023

Dual-ball-screw feed drive systems (DBSFDSs) are designed for most high-end manufacturing equipment. However, the mismatch between the dynamic characteristic parameters (e.g., stiffness and inertia) and the P-PI cascade control method reduces the accuracy of the DBSFDSs owing to the structural characteristic changes in the motion. Moreover, the parameters of the P-PI cascade controller of the DBSFDSs are always the same even though the two axes have different dynamic characteristics, and it is difficult to tune two-axis parameters simultaneously. A new application of the combination of the grey wolf optimization (GWO) algorithm and the P-PI cascade controller is presented to solve these problems and enhance the motion performance of DBSFDSs. The novelty is that the flexible coupling model and dynamic stiffness obtained from the motor current can better represent the two-axis coupling dynamic characteristics, and the GWO algorithm is used to adjust the P-PI controller parameters to address variations in the positions of the moving parts and reflect characteristic differences between the two axes. Comparison of simulation and experimental results validated the superiority of the proposed controller over existing ones in practical applications, showing a decrease in the tracking error of the tool center and non-synchronization error of over 34% and 39%, respectively.
Fractional-Order Variational Image Fusion and Denoising Based on Data-Driven Tight Frame
Authors: Zhao Ru , Liu Jingjing
Published: May 2023

Multi-modal image fusion can provide more image information, which improves the image quality for subsequent image processing tasks. Because the images acquired using photon counting devices always suffer from Poisson noise, this paper proposes a new three-step method based on the fractional-order variational method and data-driven tight frame to solve the problem of multi-modal image fusion for images corrupted by Poisson noise. Thus, this article obtains fused high-quality images while removing Poisson noise. The proposed image fusion model can be solved by the split Bregman algorithm which has significant stability and fast convergence. The numerical results on various modal images show the excellent performance of the proposed three-step method in terms of numerical evaluation metrics and visual quality. Extensive experiments demonstrate that our method outperforms state-of-the-art methods on image fusion with Poisson noise.
Wake Control of Flow Past Twin Cylinders via Small Cylinders
Authors: Yang Jinghua , Peng Bo , Zhao Ying , Zhang Hongfu
Published: May 2023

The drag and lift force of a twin-cylinder structure are often greater than those of a single cylinder, causing serious structural safety problems. However, there are few studies on the passive control of twin cylinders. The study aimed to investigate the performance of passive drag reduction measures using small cylinders on twin cylinders at a Reynolds number of 100. The effects of small cylinder height (HD/D = 0~1.0, D is the side length of the twin cylinder) and cross-sectional shape on fluid force and flow structures were studied by direct numerical simulations. The control mechanism was analyzed using high-order dynamic mode decomposition (HODMD). The results showed that significant drag reduction occurred in the co-shedding state, particularly when the gap length of the twin cylinders L/D = 6.0. The small control cylinders with HD = 0.6, by contrast, showed the best performance in reducing the mean drag and fluctuating lift of the twin cylinders. It reduced the mean drag of the upstream cylinder (UC) by 2.58% and the downstream cylinder (DC) by more than 62.97%. The fluctuating lift coefficient for UC (DC) was also decreased by more than 70.41% (59.74%). The flow structures showed that when the flow hit UC under the action of small control cylinders, a virtual missile-like aerodynamic shape was formed at the leading edge of UC. In this way, the gap vortex consisted of two asymmetric steady vortices and the vortex length significantly increased. This was also confirmed by HODMD. The coherence modes in the gap were suppressed and thus the interaction between gap flow and wake flow was mitigated, which resulted in the fluid force reduction.
A Study on the Choice of Online Marketplace Co-Opetition Strategy Considering the Promotional Behavior of a Store on an E-Commerce Platform
Authors: Wang Tao
Published: May 2023

The huge traffic of e-commerce platforms provides a wide market for stores, but the fierce competition among stores for onsite traffic increases the cost of onsite promotion for stores, and it also reduces the effectiveness of promotion. Therefore, more and more stores on e-commerce platforms are using content platforms for offsite promotion. In the face of stores’ onsite and offsite promotion behaviors, the choice of competition and cooperation strategies among participants in the promotion process is the key to solving the problem of increasing traffic. Accordingly, this paper constructs an onsite and offsite promotion decision model consisting of an e-commerce platform, a store on the e-commerce platform, and a content platform, and it compares the results based on the decentralized decision situation, centralized decision situation, and promotion investment sharing situation. In addition, some results are presented in more detail in the form of numerical analysis. The results show that the promotion investment sharing does not change the level of onsite promotion investment, but the centralized decision makes the onsite promotion investment decrease; promotion investment sharing and centralized decision scenarios increase the promotion investment of the e-commerce platform and the content platform. When the sum of the parts of promotion investments shared by the store and the content platform for the e-commerce platform is relatively small, each participant will be willing to participate in the promotion investment sharing agreement. We believe that this study will provide important implications for the resolution of stores’ traffic dilemmas on e-commerce platforms.
A Family of Multi-Step Subgradient Minimization Methods
Authors: Tovbis Elena , Krutikov Vladimir , Stanimirović Predrag , Meshechkin Vladimir , Popov Aleksey , Kazakovtsev Lev
Published: May 2023

For solving non-smooth multidimensional optimization problems, we present a family of relaxation subgradient methods (RSMs) with a built-in algorithm for finding the descent direction that forms an acute angle with all subgradients in the neighborhood of the current minimum. Minimizing the function along the opposite direction (with a minus sign) enables the algorithm to go beyond the neighborhood of the current minimum. The family of algorithms for finding the descent direction is based on solving systems of inequalities. The finite convergence of the algorithms on separable bounded sets is proved. Algorithms for solving systems of inequalities are used to organize the RSM family. On quadratic functions, the methods of the RSM family are equivalent to the conjugate gradient method (CGM). The methods are intended for solving high-dimensional problems and are studied theoretically and numerically. Examples of solving convex and non-convex smooth and non-smooth problems of large dimensions are given.
A Methodology for the Analysis of Collaboration Networks with Higher-Order Interactions
Authors: Aguirre-Guerrero Daniela , Bernal-Jaquez Roberto
Published: May 2023

Scientific research often involves collaboration among researchers, and coauthorship networks are a common means of exploring these collaborations. However, traditional coauthorship networks represent coauthorship relations using simple links, i.e., pairwise interactions, which fail to capture the strength of scientific collaborations in either small or large groups. In this study, we propose a novel methodology to address this issue, which involves using a multilayer network model that captures the strength of coauthorship relations and employs a convergence index to identify the collaboration order in which these properties converge. We apply this methodology to investigate the collaborative behavior of researchers in the context of the three main public universities in Mexico over the last decade, using Scopus data as the primary source of information. Our study reveals that community structure emerges in low-order collaborations, and higher-order collaborations lead to increased clustering and centrality measures. Our methodology provides a comprehensive and insightful way of analyzing scientific collaborations and sheds light on the dynamics of scientific collaboration, providing a valuable tool for future studies. Our proposed model and convergence index can be applied to other scientific domains to better capture the strength of collaborations among researchers.
Computing Nash Equilibria for Multiplayer Symmetric Games Based on Tensor Form
Authors: Liu Qilong , Liao Qingshui
Published: May 2023

In an m-person symmetric game, all players are identical and indistinguishable. In this paper, we find that the payoff tensor of the player k in an m-person symmetric game is k-mode symmetric, and the payoff tensors of two different individuals are the transpose of each other. Furthermore, we reformulate the m-person symmetric game as a tensor complementary problem and demonstrate that locating a symmetric Nash equilibrium is equivalent to finding a solution to the resulting tensor complementary problem. Finally, we use the hyperplane projection algorithm to solve the resulting tensor complementary problem, and we present some numerical results to find the symmetric Nash equilibrium.
Hierarchical Control Strategy with Battery Dynamic Consideration for a Dual Fuel Cell/Battery Tramway
Authors: Do Tri-Cuong , Trinh Hoai-An , Ahn Kyoung-Kwan
Published: May 2023

This paper proposes a hierarchical energy control strategy for a hybrid dual fuel cell/battery tramway, combining online and offline optimization methods while considering the battery’s dynamic behavior. In the upper layer, an online band-pass filter-based extremum-seeking control (BFESC) is employed to estimate the reference power between the dual fuel cell system and battery. In addition, the battery’s dynamic behavior is considered a penalty function of the BFESC to maintain its parameters within the desired boundaries. In the middle layer, the power requirement for each fuel cell system is calculated by using an offline method called the map search method. Finally, the fuel cell and battery provide the required power to the DC bus through DC/DC converters, which are controlled by PID controllers in the lower layer. To verify the effectiveness of the proposed control strategy, a simulation model is built in Matlab/Simulink. The results demonstrate that the dual fuel cell/battery system under the control of the proposed energy management strategy (EMS) can operate efficiently while improving the battery’s durability. The efficiency of the fuel cell system when using the proposed EMS was lower than 4% compared with the non-constraint EMS. However, the capacity loss of the battery could improve up to 25.9% in high-current and high-SOC cases.
Neural Network Trajectory Tracking Control on Electromagnetic Suspension Systems
Authors: Beltran-Carbajal Francisco , Yañez-Badillo Hugo , Tapia-Olvera Ruben , Rosas-Caro Julio C. , Sotelo Carlos , Sotelo David
Published: May 2023

A new adaptive-like neural control strategy for motion reference trajectory tracking for a nonlinear electromagnetic suspension dynamic system is introduced. Artificial neural networks, differential flatness and sliding modes are strategically integrated in the presented adaptive neural network control design approach. The robustness and efficiency of the magnetic suspension control system on desired smooth position reference profile tracking can be improved in this fashion. A single levitation control parameter is tuned on-line from a neural adaptive perspective by using information of the reference trajectory tracking error signal only. The sliding mode discontinuous control action is approximated by a neural network-based adaptive continuous control function. Control design is firstly developed from theoretical modelling of the nonlinear physical system. Next, dependency on theoretical modelling of the nonlinear dynamic system is substantially reduced by integrating B-spline neural networks and sliding modes in the electromagnetic levitation control technique. On-line accurate estimation of uncertainty, unmeasured external disturbances and uncertain nonlinearities are conveniently evaded. The effective performance of the robust trajectory tracking levitation control approach is depicted for multiple simulation operating scenarios. The capability of active disturbance suppression is furthermore evidenced. The presented B-spline neural network trajectory tracking control design approach based on sliding modes and differential flatness can be extended to other controllable complex uncertain nonlinear dynamic systems where internal and external disturbances represent a relevant issue. Computer simulations and analytical results demonstrate the effective performance of the new adaptive neural control method.
A Hybrid Algorithm Based on Social Engineering and Artificial Neural Network for Fault Warning Detection in Hydraulic Turbines
Authors: Tan Yun , Zhan Changshu , Pi Youchun , Zhang Chunhui , Song Jinghui , Chen Yan , Golmohammadi Amir-Mohammad
Published: May 2023

Hydraulic turbines constitute an essential component within the hydroelectric power generation industry, contributing to renewable energy production with minimal environmental pollution. Maintaining stable turbine operation presents a considerable challenge, which necessitates effective fault diagnosis and warning systems. Timely and efficient fault w arnings are particularly vital, as they enable personnel to address emerging issues promptly. Although backpropagation (BP) networks are frequently employed in fault warning systems, they exhibit several limitations, such as susceptibility to local optima. To mitigate this issue, this paper introduces an improved social engineering optimizer (ISEO) method aimed at optimizing BP networks for developing a hydraulic turbine warning system. Experimental results reveal that the ISEO-BP-based approach offers a highly effective fault warning system, as evidenced by superior performance metrics when compared to alternative methods.
Evaluation of the Appropriate LigaSure™ Device to Transect the Appendix—A Comparison between 5 mm and 10 mm Laparoscopic Devices in an Ex Vivo Trial
Authors: Turial Salmai , Schwind Martin , Nyiredi Alexandra
Published: May 2023

Background and Objectives: A topic of greatinterest in the surgical field comprises cost and time reduction operative techniques with high efficiency rates. Thus, the aim of this paper is to evaluate whether a transection of the appendix using only a laparoscopic LigaSure™ device is feasible and, if so, which size of the laparoscopic device is optimal. Materials and Methods: Appendectomy specimens were sealed and cut using LigaSureTM V (5 mm) and LigaSure AtlasTM (10 mm) devices ex vivo. Analysis criteria included handling, resistance to bursting pressure of the appendicular stump (adequacy), eligibility, durability and airtightness. Results: Twenty sealed areas were measured. While the 5 mm instrument was not able to transect the appendix in one attempt in any of the cases, the 10 mm device could be applied successfully without any handling difficulties. The adequacy of the sealed area was rated as complete and dry in all 10 cases using the 10 mm device and as oozing in 8 of the cases using the 5 mm device. There was no leakage in terms of air and liquid tightness using the 10 mm device, in contrast to six sealed segments with air and liquid leakage when using the 5 mm device. The resistance to bursting pressure was on average 285 mmHg and 60.5 mmHg with the 10 mm and 5 mm devices, respectively. The durability and eligibility of the 10 mm device were rated as very sufficient in 9 of 10 cases (1 perforation) in contrast to the 5 mm device, where the sealing in 9 of 10 cases was not sufficient (9 perforations). Conclusions: Using the 10 mm laparoscopic LigaSure™ device for the transection of the appendix seems to be feasible, safe and resistant to 300 mmHg bursting pressure. The 5 mm LigaSure™ instrument is inadequate to seal the appendix in humans.
Clinical Symptoms Influencing Parkinson’s Patients’ Quality of Life in Latvia: A Single-Center Cohort Study
Authors: Minibajeva Olga , Zeltiņa Estere , Karelis Guntis , Kurjāne Nataļja , Ķēniņa Viktorija
Published: May 2023

Background and Objectives: Parkinson’s disease (PD) is a chronic, progressive illness with a profound impact on health-related quality of life, and it is crucial to know what factors influence the quality of life throughout the course of the disease. This study aimed to evaluate PD patients’ motor and non-motor symptoms to compare symptom severity between PD clinical phenotypes and to assess the impact of disease symptoms on quality of life in a cohort of Latvian patients. Materials and Methods: We evaluated 43 patients with Parkinson’s disease. Fourteen patients had tremor dominant (TD) PD, twenty-five patients had postural instability/gait difficulty (PIGD), and four patients had a mixed phenotype. Results: The patients’ mean age was 65.21 years, and the disease’s mean duration was 7 years. The most common non-motor symptoms were fatigue (95.3%), sleep disturbance (83.7%), daytime sleepiness (83.7%), and pain and other sensations (81.4%). PIGD patients had a higher prevalence of depressed mood, daytime sleepiness, constipation, lightheadedness on standing, cognitive impairment, and severe gastrointestinal and urinary disturbances (as assessed using the SCOPA-AUT domains) compared with TD patients. A high prevalence of fatigue was assessed in both disease subtypes. Health-related quality of life significantly statistically correlated with MDS-UPDRS parts III and IV (r = 0.704), the Hoehn and Yahr scale (r = 0.723), as well as the SCOPA-AUT scale’s gastrointestinal (r = 0.639), cardiovascular (r = 0.586), thermoregulatory (r = 0.566) and pupillomotor domains (r = 0.597). Conclusions: The severity of motor symptoms, as well as non-motor symptoms, such as fatigue, apathy, sleep problems and daytime sleepiness, pain, and disturbances in gastrointestinal and cardiovascular function, negatively affect PD patients’ health-related quality of life. Thermoregulatory and pupillomotor symptoms also significantly affect PD patients’ well-being.
Odontogenic Sinusitis with Oroantral Communication and Fistula Management: Role of Regenerative Surgery
Authors: Sabatino Lorenzo , Lopez Michele Antonio , Di Giovanni Simone , Pierri Michelangelo , Iafrati Francesco , De Benedetto Luigi , Moffa Antonio , Casale Manuele
Published: May 2023

Objective: The aim of this study is to show our experience with the correct management of patients suffering from odontogenic sinusitis with oroantral communication and fistula. Methods: According to the inclusion criteria, 41 patients were enrolled in this retrospective study with a diagnosis of odontogenic sinusitis with oroantral communication and fistula; 1 patient with pre-implantological complication, 14 with implantological complications, and 26 with classical complications. Results: Two patients were treated with a fractioned combined approach, 13 patients were treated with an oral approach only, and 26 patients were treated with a combination. There was a complete resolution of the symptoms and closure of the fistula in all the patients enrolled. Conclusions: In our study, in all 41 patients, there was a surgical success. The best option is to use a multidisciplinary approach for patients suffering from odontogenic sinusitis.
Evaluation of Efficiently Removing Secondary Effluent Organic Matters (EfOM) by Al-Based Coagulant for Wastewater Recycling: A Case Study with an Industrial-Scale Food-Processing Wastewater Treatment Plant
Authors: Cheng Yu , Cheng Qiangqiang , Zhao Chengjin , Ren Xianghao , Wang Yu , Kou Yingying , Chon Kangmin , Ko Myung-Han , Hwang Moon-Hyun
Published: May 2023

The reuse of wastewater has been identified as an important initiative for the sustainable development of the environment; thus, the removal of secondary effluent organic matter (EfOM) to ensure the safety of reused wastewater is the key step and a subject of extensive research. In this study, Al2(SO4)3 and anionic polyacrylamide were selected as coagulant and flocculant, respectively, for the treatment of secondary effluent from a food-processing industry wastewater treatment plant to meet the standard regulatory specifications for water reuse. In this process, the removal efficiencies of chemical oxygen demand (COD), components with UV254, and specific ultraviolet absorbance (SUVA) were 44.61%, 25.13%, and 9.13%, respectively, with an associated reduction in chroma and turbidity. The fluorescence intensities (Fmax) of two humic-like components were reduced during coagulation, and microbial humic-like components of EfOM had a better removal efficiency because of a higher Log Km value of 4.12. Fourier transform infrared spectroscopy showed that Al2(SO4)3 could remove the protein fraction of the soluble microbial products (SMP) of EfOM by forming a loose SMP protein complex with enhanced hydrophobicity. Furthermore, flocculation reduced the aromaticity of secondary effluent. The cost of the proposed secondary effluent treatment was 0.034 CNY t−1 %COD−1. These results demonstrate that the process is efficient and economically viable for EfOM removal to realize food-processing wastewater reuse.
Microstructure, Mechanical and Wear Properties of W-Si-C Composites Consolidated by Spark Plasma Sintering
Authors: Wang Chuanbin , Cheng Yongxin , Hu Sumeng , Kang Kejia , Han Yuzhe , Zhang Xudan , Wei Ronghan , Luo Guoqiang
Published: May 2023

W-Si-C composites with high relative densities and good mechanical and wear properties were successfully prepared by spark plasma sintering. The influence of SiC content on the relative density, microstructure, mechanical properties and wear characteristics was investigated. The results indicated that the reaction between SiC and W at their interface produced W2C and W5Si3. SiC also reacted with oxygen impurities at the W grain boundary to form SiO2. The purification of the grain boundaries of W was carried out by SiO2 synthesis. Reactive sintering reduces the free energy of the system and facilitates the densification process of W-Si-C composites. This results in a significant increase in the relative density of W-Si-C composites, which reaches a maximum of 98.12%, higher than the 94.32% of pure tungsten. The hardness significantly increases from 4.33 GPa to 8.40 GPa when the SiC content is 2 wt% compared to pure tungsten due to the generation of the hard ceramic phase and the increase in relative density. The wear resistance of the W-Si-C composites was significantly improved with little SiC addition. The wear rate significantly decreased from 313.27 × 10−3 mm3/N·m of pure tungsten to 5.71 × 10−3 mm3/N·m of W-0.5 wt% SiC. SEM analyses revealed that the dominant wear mechanism of pure tungsten was attributed to fatigue wear, while that of W-Si-C composites was due to abrasive wear.
Editorial for the Special Issue on Broadband Terahertz Devices and Communication Technologies
Authors: Zhang Lu , Pang Xiaodan , Pitchappa Prakash
Published: May 2023

The remarkable explosion of wireless devices and bandwidth-consuming Internet applications have boosted the demand for wireless communications with ultra-high data rate [...]
In Silico and In Vitro Investigation of the Distribution and Expression of Key Genes in the Fucose Operon of Escherichia coli
Authors: Saif Nehal A. , Hashem Yomna A. , Amin Heba M. , Aziz Ramy K.
Published: May 2023

Many gut bacteria degrade polysaccharides, providing nutritional advantages to their hosts. Fucose, a mucin degradation product, was suggested as a communication molecule between the resident microbiota and external pathogens. However, the precise role and variants of the fucose utilization pathway remain to be elucidated. Here, we computationally and experimentally investigated the fucose utilization operon of E. coli. While the operon is conserved among E. coli genomes, a variant pathway, in which an ABC transporter system replaces the fucose permease gene (fucP), was computationally identified in 50 out of 1058 genomes. Comparative genomics and subsystems analysis results were confirmed by polymerase chain reaction-based screening of 40 human E. coli isolates, which indicated the conservation of fucP in 92.5% of the isolates (vs. 7.5% of its suggested alternative, yjfF). The in silico predictions were confirmed by in vitro experiments comparing the growth of E. coli strains K12, BL21, and isogenic fucose-utilization K12 mutants. Additionally, fucP and fucI transcripts were quantified in E. coli K12 and BL21, after in silico analysis of their expression in 483 public transcriptomes. In conclusion, E. coli utilizes fucose by two pathway variants, with measurable transcriptional differences. Future studies will explore this variation’s impact on signaling and virulence.
Comparative Analysis Using Raman Spectroscopy of the Cellular Constituents of Lacticaseibacillus paracasei Zhang in a Normal and Viable but Nonculturable State
Authors: Bao Qiuhua , Bo Xiaoyu , Chen Lu , Ren Yan , Wang Huiying , Kwok Lai-Yu , Liu Wenjun
Published: May 2023

This study aimed to investigate the molecular composition of a viable but nonculturable (VBNC) state of a probiotic strain, Lacticaseibacillus paracasei Zhang (L. paracasei Zhang), using single-cell Raman spectroscopy (SCRS). Fluorescent microcopy with live/dead cell staining (propidium iodide and SYTO 9), plate counting, and scanning electron microscopy were used in combination to observe bacteria in an induced VBNC state. We induced the VBNC state by incubating the cells in de Man, Rogosa, and Sharpe broth (MRS) at 4 °C. Cells were sampled for subsequent analyses before VBNC induction, during it, and up to 220 days afterwards. We found that, after cold incubation for 220 days, the viable plate count was zero, but active cells could still be observed (as green fluorescent cells) under a fluorescence microscope, indicating that Lacticaseibacillus paracasei Zhang entered the VBNC state under these conditions. Scanning electron microscopy revealed the altered ultra-morphology of the VBNC cells, characterized by a shortened cell length and a wrinkled cell surface. Principal component analysis of the Raman spectra profiles revealed obvious differences in the intracellular biochemical constituents between normal and VBNC cells. Comparative analysis of the Raman spectra identified 12 main differential peaks between normal and VBNC cells, corresponding to carbohydrates, lipids, nucleic acids, and proteins. Our results suggested that there were obvious cellular structural intracellular macromolecular differences between normal and VBNC cells. During the induction of the VBNC state, the relative contents of carbohydrates (such as fructose), saturated fatty acids (such as palmitic acid), nucleic acid constituents, and some amino acids changed obviously, which could constitute a bacterial adaptive mechanism against adverse environmental conditions. Our study provides a theoretical basis for revealing the formation mechanism of a VBNC state in lactic acid bacteria.
Insights from the Endophytic Fungi in Amphisphaeria (Sordariomycetes): A. orixae sp. nov. from Orixa japonica and Its Secondary Metabolites
Authors: Wang Xiaojie , Wanasinghe Dhanushka N. , Zhang Jingyi , Ma Jian , Zhou Peifeng , Zhang Lijuan , Lu Yongzhong , Zhang Zhen
Published: May 2023

Endophytic fungi are a remarkably diverse group of microorganisms that have imperceptible associations with their hosts for at least a part of their life cycle. The enormous biological diversity and the capability of producing bioactive secondary metabolites such as alkaloids, terpenoids, and polyketides have attracted the attention of different scientific communities, resulting in numerous investigations on these fungal endophytes. During our surveys of plant-root-based fungi in the mountain areas of Qingzhen, Guizhou Province, several isolates of endophytic fungi were identified. In this study, a novel endophytic fungus was discovered in the roots of a medicinal plant (Orixa japonica) in Southern China and introduced as a new species (Amphisphaeria orixae) based on morphological evidence and molecular phylogenetic analysis (combined ITS and LSU sequence data). To the best of our knowledge, A. orixae is the first reported endophyte as well as the first hyphomycetous asexual morph in Amphisphaeria. A new isocoumarin, (R)-4,6,8-trihydroxy-5-methylisochroman-1-one (1), and 12 known compounds (2–13) were isolated from the rice fermentation products of this fungus. Using 1D- and 2D-NMR, mass spectrometry, and ECD studies, their structures were identified. The antitumor activity of these compounds was tested. Unfortunately, none of the compounds tested showed significant antitumor activity.
Systemic Inflammatory Molecules Are Associated with Advanced Fibrosis in Patients from Brazil Infected with Hepatitis Delta Virus Genotype 3 (HDV-3)
Authors: Souza Campos Mauricio , Villalobos-Salcedo Juan Miguel , Vieira Dallacqua Deusilene Souza , Lopes Borges Andrade Caio , Meyer Nascimento Roberto José , Menezes Freire Songeli , Paraná Raymundo , Schinoni Maria Isabel
Published: May 2023

Background and Aims: Hepatitis Delta virus (HDV) genotype 3 is responsible for outbreaks of fulminant hepatitis in Northeastern South America. This study investigates if systemic inflammatory molecules are differentially expressed in patients with advanced fibrosis chronically infected with Hepatitis Delta virusgenotype 3(HDV-3). Methods: Sixty-one patients from the north of Brazil coinfected with hepatitis B virus (HBV)/HDV-3 were analyzed. HDV quantification and genotyping were performed by semi-nested real-time polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP) methodologies. Ninety-two systemic inflammatory molecules (SIMs) were measured by Proximity Extension Assay (PEA) technology. The Shapiro–Wilk, Student’s t-test, Mann–Whitney tests, and logistic regression analysis were used when appropriate. Results: The median age was 41 years, and all patients were HBeAg negative. Advanced fibrosis or cirrhosis was diagnosed by histological staging in 17 patients, while 44 presented with minimal or no fibrosis. Advanced necroinflammatory activity correlated positively with serum levels of aspartate aminotransferase (AST) and alanine aminotransferase (ALT). Established non-invasive fibrosis scores (APRI, FIB-4, and AST/ALT ratio) revealed low sensitivities and positive predictive values (PPVs) with an AUROC maximum of 0.586. Among the 92 SIMs analyzed, MCP.4, CCL19, EN.RAGE, SCF, and IL18 showed a positive correlation with fibrosis stage. A combined score including CCL19 and MCP.4 revealed a sensitivity of 81% and an odds ratio of 2.202 for advanced fibrosis. Conclusions: Standard non-invasive fibrosis scores showed poor performance in HDV-3 infection. We here suggest that the determination of CCL19 and MCP.4 may be used to identify patients with advanced fibrosis. Moreover, this study gives novel insights into the immunopathogenesis of HDV-3 infection.
Quorum Sensing in Halorubrum saccharovorum Facilitates Cross-Domain Signaling between Archaea and Bacteria
Authors: Thompson Thomas P. , Busetti Alessandro , Gilmore Brendan F.
Published: May 2023

Quorum Sensing (QS) is a well-studied intercellular communication mechanism in bacteria, regulating collective behaviors such as biofilm formation, virulence, and antibiotic resistance. However, cell–cell signaling in haloarchaea remains largely unexplored. The coexistence of bacteria and archaea in various environments, coupled with the known cell–cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms and the presence of cell–cell signaling mechanisms in both prokaryotic and eukaryotic microorganisms, suggests a possibility for haloarchaea to possess analogous cell–cell signaling or QS systems. Recently, N-acylhomoserine lactone (AHL)-like compounds were identified in haloarchaea; yet, their precise role—for example, persister cell formation—remains ambiguous. This study investigated the capacity of crude supernatant extract from the haloarchaeon Halorubrum saccharovorum CSM52 to stimulate bacterial AHL-dependent QS phenotypes using bioreporter strains. Our findings reveal that these crude extracts induced several AHL-dependent bioreporters and modulated pyocyanin and pyoverdine production in Pseudomonas aeruginosa. Importantly, our study suggests cross-domain communication between archaea and bacterial pathogens, providing evidence for archaea potentially influencing bacterial virulence. Using Thin Layer Chromatography overlay assays, lactonolysis, and colorimetric quantification, the bioactive compound was inferred to be a chemically modified AHL-like compound or a diketopiperazine-like molecule, potentially involved in biofilm formation in H. saccharovorum CSM52. This study offers new insights into putative QS mechanisms in haloarchaea and their potential role in interspecies communication and coordination, thereby enriching our understanding of microbial interactions in diverse environments.
Selecting Nanobodies Specific for the Epidermal Growth Factor from a Synthetic Nanobody Library
Authors: Serrano-Rivero Yunier , Salazar-Uribe Julieta , Rubio-Carrasquilla Marcela , Camacho-Casanova Frank , Sánchez-Ramos Oliberto , González-Pose Alaín , Moreno Ernesto
Published: May 2023

The epidermal growth factor (EGF) is one of the most critical ligands of the EGF receptor (EGFR), a well-known oncogene frequently overexpressed in cancerous cells and an important therapeutic target in cancer. The EGF is the target of a therapeutic vaccine aimed at inducing an anti-EGF antibody response to sequester this molecule from serum. However, strikingly, very few investigations have focused on EGF immunotargeting. Since the use of nanobodies (Nbs) for EGF neutralization may be an effective therapeutic strategy in several types of cancer, in this study, we decided to generate anti-EGF Nbs from a recently constructed, phage-displaying synthetic nanobody library. To our knowledge, this is the first attempt to obtain anti-EGF Nbs from a synthetic library. By applying a selection strategy that uses four different sequential elution steps along with three rounds of selection, we obtained four different EGF-specific Nb clones, and also tested their binding capabilities as recombinant proteins. The obtained results are very encouraging and demonstrate the feasibility of selecting nanobodies against small antigens, such as the EGF, from synthetic libraries.
Machine Learning Generation of Dynamic Protein Conformational Ensembles
Authors: Zheng Li-E , Barethiya Shrishti , Nordquist Erik , Chen Jianhan
Published: May 2023

Machine learning has achieved remarkable success across a broad range of scientific and engineering disciplines, particularly its use for predicting native protein structures from sequence information alone. However, biomolecules are inherently dynamic, and there is a pressing need for accurate predictions of dynamic structural ensembles across multiple functional levels. These problems range from the relatively well-defined task of predicting conformational dynamics around the native state of a protein, which traditional molecular dynamics (MD) simulations are particularly adept at handling, to generating large-scale conformational transitions connecting distinct functional states of structured proteins or numerous marginally stable states within the dynamic ensembles of intrinsically disordered proteins. Machine learning has been increasingly applied to learn low-dimensional representations of protein conformational spaces, which can then be used to drive additional MD sampling or directly generate novel conformations. These methods promise to greatly reduce the computational cost of generating dynamic protein ensembles, compared to traditional MD simulations. In this review, we examine recent progress in machine learning approaches towards generative modeling of dynamic protein ensembles and emphasize the crucial importance of integrating advances in machine learning, structural data, and physical principles to achieve these ambitious goals.
Synthesis and Application of a New Polymer with Imprinted Ions for the Preconcentration of Uranium in Natural Water Samples and Determination by Digital Imaging
Authors: Felix Caio S. A. , Chagas Adriano V. B. , de Jesus Rafael F. , Barbosa Willams T. , Barbosa Josiane D. V. , Ferreira Sergio L. C. , Cerdà Víctor
Published: May 2023

This work proposes the synthesis of a new polymer with imprinted ions (IIP) for the pre-concentration of uranium in natural waters using digital imaging as a detection technique. The polymer was synthesized using 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol (Br-PADAP) for complex formation, ethylene glycol dimethacrylate (EGDMA) as a crosslinking reagent, methacrylic acid (AMA) as functional monomer, and 2,2′-azobisisobutyronitrile as a radical initiator. The IIP was characterized by Fourier transform infrared spectroscopy and scanning electron microscopy (FTIR). Uranium determination was performed using digital imaging (ID), and some experimental conditions (sample pH, eluent concentration, and sampling flow rate) were optimized using a two-level full factorial design and Doelhert response surface methodology. Thus, using the optimized conditions, the system allowed the determination of uranium with detection and quantification limits of 2.55 and 8.51 µg L−1, respectively, and a pre-concentration factor of 8.2. All parameters were determined using a 25 mL sample volume. The precision expressed as relative deviation (RSD%) was 3.5% for a solution with a concentration of 50 µg L−1. Given this, the proposed method was used for the determination of uranium in four samples of natural waters collected in the city of Caetité, Bahia, Brazil. The concentrations obtained ranged from 35 to 75.4 μg L−1. The accuracy was evaluated by the addition/recovery test, and the values found ranged between 91 and 109%.
Photocatalysis in Water-Soluble Supramolecular Metal Organic Complex
Authors: Hong Dongfeng , Shi Linlin , Liu Xianghui , Ya Huiyuan , Han Xin
Published: May 2023

As an emerging subset of organic complexes, metal complexes have garnered considerable attention owing to their outstanding structures, properties, and applications. In this content, metal-organic cages (MOCs) with defined shapes and sizes provide internal spaces to isolate water for guest molecules, which can be selectively captured, isolated, and released to achieve control over chemical reactions. Complex supramolecules are constructed by simulating the self-assembly behavior of the molecules or structures in nature. For this purpose, massive amounts of cavity-containing supramolecules, such as metal-organic cages (MOCs), have been extensively explored for a large variety of reactions with a high degree of reactivity and selectivity. Because sunlight and water are necessary for the process of photosynthesis, water-soluble metal-organic cages (WSMOCs) are ideal platforms for photo-responsive stimulation and photo-mediated transformation by simulating photosynthesis due to their defined sizes, shapes, and high modularization of metal centers and ligands. Therefore, the design and synthesis of WSMOCs with uncommon geometries embedded with functional building units is of immense importance for artificial photo-responsive stimulation and photo-mediated transformation. In this review, we introduce the general synthetic strategies of WSMOCs and their applications in this sparking field.
Liposome Formulations for the Strategic Delivery of PARP1 Inhibitors: Development and Optimization
Authors: Conceição Carlota J. F. , Moe Elin , Ribeiro Paulo A. , Raposo Maria
Published: May 2023

The development of a lipid nano-delivery system was attempted for three specific poly (ADP-ribose) polymerase 1 (PARP1) inhibitors: Veliparib, Rucaparib, and Niraparib. Simple lipid and dual lipid formulations with 1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1′-glycerol) sodium salt (DPPG) and 1,2-dipalmitoyl-sn-glycero-3-phosphocoline (DPPC) were developed and tested following the thin-film method. DPPG-encapsulating inhibitors presented the best fit in terms of encapsulation efficiency (>40%, translates into concentrations as high as 100 µM), zeta potential values (below −30 mV), and population distribution (single population profile). The particle size of the main population of interest was ~130 nm in diameter. Kinetic release studies showed that DPPG-encapsulating PARP1 inhibitors present slower drug release rates than liposome control samples, and complex drug release mechanisms were identified. DPPG + Veliparib/Niraparib presented a combination of diffusion-controlled and non-Fickian diffusion, while anomalous and super case II transport was verified for DPPG + Rucaparib. Spectroscopic analysis revealed that PARP1 inhibitors interact with the DPPG lipid membrane, promoting membrane water displacement from hydration centers. A preferential membrane interaction with lipid carbonyl groups was observed through hydrogen bonding, where the inhibitors’ protonated amine groups may be the major players in the PARP1 inhibitor encapsulation mode.
3D Hierarchically Structured Tin Oxide and Iron Oxide-Embedded Carbon Nanofiber with Outermost Polypyrrole Layer for High-Performance Asymmetric Supercapacitor
Authors: Yoon Chang-Min , Jekal Suk , Kim Dong-Hyun , Noh Jungchul , Kim Jiwon , Kim Ha-Yeong , Kim Chan-Gyo , Chu Yeon-Ryong , Oh Won-Chun
Published: May 2023

Herein, unique three-dimensional (3D) hierarchically structured carbon nanofiber (CNF)/metal oxide/conducting polymer composite materials were successfully synthesized by combinations of various experimental methods. Firstly, base CNFs were synthesized by carbonization of electrospun PAN/PVP fibers to attain electric double-layer capacitor (EDLC) characteristics. To further enhance the capacitance, tin oxide (SnO2) and iron oxide (Fe2O3) were coated onto the CNFs via facile hydrothermal treatment. Finally, polypyrrole (PPy) was introduced as the outermost layer by a dispersion polymerization method under static condition to obtain 3D-structured CNF/SnO2/PPy and CNF/Fe2O3/PPy materials. With each synthesis step, the morphology and dimension of materials were transformed, which also added the benign characteristic for supercapacitor application. For the practical application, as-synthesized CNF/SnO2/PPy and CNF/Fe2O3/PPy were applied as active materials for supercapacitor electrodes, and superb specific capacitances of 508.1 and 426.8 F g−1 (at 1 A g−1) were obtained (three-electrode system). Furthermore, an asymmetric supercapacitor (ASC) device was assembled using CNF/SnO2/PPy as the positive electrode and CNF/Fe2O3/PPy as the negative electrode. The resulting CNF/SnO2/PPy//CNF/Fe2O3/PPy device exhibited excellent specific capacitance of 101.2 F g−1 (at 1 A g−1). Notably, the ASC device displayed a long-term cyclability (at 2000 cycles) with a retention rate of 81.1%, compared to a CNF/SnO2//CNF/Fe2O3 device of 70.3% without an outermost PPy layer. By introducing the outermost PPy layer, metal oxide detachment from CNFs were prevented to facilitate long-term cyclability of electrodes. Accordingly, this study provides an effective method for manufacturing a high-performance and stable supercapacitor by utilizing unique 3D hierarchical materials, comprised of CNF, metal oxide, and conducting polymer.