bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal inhomogeneous pattern of a predator-prey model with delay and chemotaxis
Authors: Chen Mengxin 
Published: July 2023

Abstract
In this paper, we investigate the spatiotemporal inhomogeneous pattern phenomenon of a predatorprey model with chemotaxis and time delay. The precise intervals of the Turing instability are yielded so that we can obtain sufficient conditions to ensure the existence of the Turing instability by adjusting the ranges of the control parameters of time delay and chemotaxis. Also, we perform the occurrence conditions of the Turing-Hopf bifurcation by employing the time delay control parameter and chemotaxis sensitivity coefficient as the bifurcation parameter. Theoretically, there are no Hopf bifurcation, Turing instability, and Turing-Hopf bifurcation as the chemotaxis effect and time delay are absent. Of course, complicated spatiotemporal inhomogeneous patterns are displayed with the help of numerical experiments. Particularly, we find that both the time delay control parameter and chemotaxis sensitivity coefficient can affect the formation of the spatiotemporal inhomogeneous patterns. Certainly, our method could be applied in other reaction-diffusion models with the chemotaxis and full/non-full time delay in reaction kinetics terms.
The combination of nanotechnology and potassium: Applications in agriculture
Authors: Wang Qibin , Shan Chen , Zhang Peng , Zhao Weichen , Zhu Guikai , Sun Yi , Wang Quanlong , Jiang Yaqi , Shakoor Noman , Rui Yukui 
Published: July 2023

Abstract
Potassium fertilizer is essential to ensure crop production and thus global food supply and safe fertilizer. Potassium resources are mainly located in the Northern Hemisphere, and as a result, there is currently a scarcity of cheap potash and severe soil deficiencies in some areas of the Southern Hemisphere. There is a shift from mined salts to locally available potassium resources. such as silicates containing K, may be an option to improve this situation. The goal of increasing crop productivity and improving quality dictates an increase in potassium availability or a efficient use of potassium. The development of plants that use potassium more efficiently may be a valuable goal for geneticists. Nanomaterials are increasingly used in people's working life as a new type of material, and this technology is gradually being applied in agriculture with a view to increase crop yields and reduce environmental pollution. This paper reviews the applications of common potassium-containing materials and the effects and mechanisms of nano-fertilizers on plants, and also gives an outlook on the future applications of nano-potassium fertilizers in agriculture, and also hopes that it can provide a reference for more researchers working in this field.
A green vehicle routing problem with picking up and delivery based on an improved firefly algorithm
Authors: Zhou Qian , Wu Zhibin 
Published: July 2023

Abstract
Transportation which plays an essential role in distribution impacts climate change and global warming. So, one of the critical problems in distribution is the green vehicle routing problem. This paper investigates a green vehicle routing problem with picking up and delivery and soft time windows for a single depot. The problem is developed as a single-objective mixed integer nonlinear programming model. The model aims to minimize fuel costs based on vehicle load and penalty costs for violating time windows while satisfying customer pickup and delivery demands simultaneously. This paper proposes an improved firefly algorithm based on chaotic initialization and differential evolution to solve the model. Results show that the proposed model minimizes carbon emissions while maximizing customer satisfaction. Compared with a traditional heuristic algorithm, the improved firefly algorithm has higher solved precision.
Belowground biomass changed the regulatory factors of soil N2O fluxes under N and water additions in a temperate steppe of Inner Mongolia
Authors: Dong Qi , Liu Yinghui , He Pei , Du Wei 
Published: July 2023

Abstract
Purpose：
Simulations of N deposition and precipitation via N and water addition experiments are important for studying how soil nitrous oxide (N2O) fluxes in temperate steppes will respond to future global climate change.
Methods：
In June 2017, we conducted an N and water application experiment on a temperate steppe in Inner Mongolia, Northeast China, to investigate the impacts of N and water additions upon N2O fluxes and how the soil physicochemical properties, vegetation, and microbes regulate this process regulate this process. In this study, we collected samples and measured the variations in soil N2O fluxes and physicochemical and biological properties under N, and water additions in July and August of 2019 and 2020.
Results：
The results indicated that N addition significantly decreased soil pH, increased the NH4 + -N and DON contents, decreased the MBC content, and promoted PER activity, while water addition significantly increased soil pH, SWC, and the root-shoot ratio. Soil N2O fluxes were significantly increased by a factor of 2.2 under the 2020 N treatment alone. A structural equation model (SEM) showed that the soil N2O fluxes in response to N and water additions were mainly driven by DON in 2019, and pH was the key factor that affected the N2O fluxes in 2020.
Conclusions：
Our findings suggested that the leading factors differed between the two years due to the differences in BGB caused by different distribution of precipitation during the growing season.
Exploring the Biosynthetic Gene Clusters in Brevibacterium: A Comparative Genomic Analysis of Diversity and Distribution
Authors: Cumsille Andrés , Serna-Cardona Néstor , González Valentina , Claverías Fernanda , Undabarrena Agustina , Molina Vania , Salvà-Serra Francisco , Moore Edward R. B. , Cámara Beatriz 
Published: July 2023

Abstract
Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. The genome of Brevibacterium sp. H-BE7 was sequenced and a phenazine-like biosynthetic gene clusters (BGCs) is not present within the genome. To study the biosynthetic potential of strain H-BE7 and Brevibacterium genus, the genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs and could be related to the production of 1-methoxyphenazine in HBE-7’s crude extract. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.
Biomechanical effects of cranial closing wedge osteotomy on joint stability in normal canine stifles: An ex vivo study
Authors: Shimada Masakazu , Huang Chenxu , Yamakawa Satoshi , Fujie Hiromichi , Murakami Sawako , Kanno Nobuo , Hara Yasushi 
Published: July 2023

Abstract
Cranial closing wedge osteotomy (CCWO) is a functional stabilization technique for cranial cruciate ligament (CrCL) ruptures. This biomechanical study aimed to evaluate the influence of CCWO on the stability of the stifle joint. Eighteen Beagle stifle joints were divided into two groups, Control and CCWO. The stifle joints were then analyzed using a six-degree-of-freedom robotic joint biomechanical testing system. The joints were subjected to 30 N in the craniocaudal (CrCd) drawer and proximal compression tests and 1 Nm in the internal-external (IE) rotation test. Each test was performed with an extension position, 135 degrees, and 120 degrees of joint angle. The stifle joints were tested while the CrCLs were intact, then transected. In the drawer test, the CCWO procedure, CrCL transection, and stifle joint flexion increased CrCd displacement. The CCWO procedure and CrCL transection showed an interaction effect. In the compression test, the CCWO procedure decreased, and CrCL transection and stifle joint flexion increased displacement. In the IE rotation test, CCWO, CrCL transection, and stifle joint flexion increased the range of motion. Therefore, CCWO was expected to provide stability against compressive force, but it does not contribute to stabilities in the drawer and rotational tests. Particularly in the CCWO-treated stifle joint, instability during the drawer test worsened with CrCL transection. In other words, performing the CCWO procedure when CrCL function is present is desirable for the stabilization of the stifle joint.
Patient-derived tumoroids of advanced high-grade neuroendocrine neoplasms mimic patient chemotherapy responses and guide the design of personalized combination therapies
Authors: Perren Aurel , April-Monn Simon , Detjen Katharina , Kirchner Philippe , Bräutigam Konstantin , Trippel Mafalda , Grob Tobias , Statzer Cyril , Maire Renaud , Kollàr Attila , Couchane Aziz , Kunze Catarina , Horst David , Sadowski Martin , Schrader Jörg , Marinoni Ilaria , Wiedenmann Bertram 
Published: July 2023

Abstract
There are no therapeutic predictive biomarkers or representative preclinical models for high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN), a highly aggressive, fatal, and heterogeneous epithelial malignancy. We established patient-derived (PD) tumoroids from biobanked tissue samples of advanced high-grade GEP-NEN patients and applied this model for targeted rapid ex vivo pharmacotyping, next-generation sequencing, and perturbational profiling. We used tissue-matched PD tumoroids to profile individual patients, compared ex vivo drug response to patients’ clinical response to chemotherapy, and investigated treatment-induced adaptive stress responses.
PD tumoroids recapitulated biological key features of high-grade GEP-NEN and mimicked clinical response to cisplatin and temozolomide ex vivo. When we investigated treatment-induced adaptive stress responses in PD tumoroids in silico, we discovered and functionally validated Lysine demethylase 5A and interferon-beta, which act synergistically in combination with cisplatin. Since ex vivo drug response in PD tumoroids matched clinical patient responses to standard-of-care chemotherapeutics for GEP-NEN, our rapid and functional precision oncology approach could expand personalized therapeutic options for patients with advanced high-grade GEP-NEN.
Metabuli: sensitive and specific metagenomic classification via joint analysis of amino-acid and DNA
Authors: Steinegger Martin , KIM JAEBEOM 
Published: July 2023

Abstract

Current metagenomic classifiers analyze either DNA or amino-acid (AA) sequences. DNA-based methods have better specificity in distinguishing well-studied clades, but they have limited sensitivity in detecting under-studied clades. AA-based methods suffer the opposite problem. To tackle this trade-off, we developed Metabuli for a joint analysis of DNA and AA using a novel k-mer, metamer. In benchmarks, Metabuli was simultaneously as specific as DNA-based methods and as sensitive as AA-based methods. In the CAMI2 plant-associated dataset, Metabuli covers 99% and 98% of classifications of state-of-the-art DNA-based and AA-based classifiers, respectively. Metabuli is available as free and open-source software for Linux and macOS at metabuli.steineggerlab.com.
Development of new systems based on hydrotalcites for stabilization and deacidification of paper information carriers
Authors: Guzikiewiczová Eva , Malečková Soňa , Jurišová Jana , Králik Milan , Vizárová Katarína 
Published: July 2023

Abstract
Stabilization and deacidification of paper information carriers is still a highly discussed topic. It is very important to continue in searching for new, more effective, and affordable methods of paper stabilization because none of the currently known processes is ideal. This study focuses on the effectiveness of a new substance in stabilizing paper information carriers - hydrotalcite, applied to the paper in a partially polar environment. The effect of modification on the stabilization of paper during accelerated aging was investigated by measuring chemical (surface pH, rate of glycosidic bond cleavage), mechanical (coefficient of the relative increase of the lifetime for folding endurance), optical (colorimetry - CIE L*a*b*), and spectral (FTIR) properties. Three types of hydrotalcites differing in composition, particle size, and preparation conditions, were tested and compared. After the modification, all the properties of acidic test papers improved. The most promising type of hydrotalcite was prepared under nucleation action of citric acid. The atomic ratio of Mg2+ to Al3+ of this hydrotalcite was equal to 5. Modification by this hydrotalcite led to an increase in surface pH by 1.3 to 2.7 units.
Chemical exchange rate study by NMR CPMG method
Authors: Mohorič Aleš , Stepišnik Janez 
Published: July 2023

Abstract
Detailed analysis of NMR CPMG method is presented that enables direct sampling of the spectrum of the chemical exchange rate. The experiment on sucrose solution
gives the spectrum that cannot be described single parameter of chemical exchange rate and indicates a much more complicated dynamics of molecular conformations in these processes. The result confirms that the method can provide insight into the details of the dynamics of molecular conformations, which are not limited to a single one, but can include chemical exchanges with multiple molecules.
Synergy-based functional electrical stimulation and robotic-assisted for retraining reach-to-grasp in stroke: a study protocol for randomised controlled trial
Authors: Zhou Huan-xia , Hu Jun , Yun Rui-sheng , Zhao Zhong-zhi , Lai Ming-hui , Sun Li-hui-zi , Luo Kai-liang 
Published: July 2023

Abstract
Background Customized multi-muscle Functional Electrical Stimulation (FES) based on muscle synergy of the healthy adults, may provide opportunity for improve the upper limb motor function of the stroke survivors. Additionally, synergy-based FES combined with Robotic-assisted Therapy (RAT) can be a novel and more effective therapy for improving upper limb function of the stroke survivors from the perspective of synergistic enhancement. However, few studies examined the effectiveness of combined synergy-based FES and RAT for stroke upper limb function improvement, especially for the motor control evaluated by the Reach-To-Grasp (RTG) behavior.
Methods This study will be an assessor-blind randomized controlled trial involving 12-week intervention and 6-month follow-up. The stratified randomization will be used to randomly assign the 120 stroke patients into FES + conventional rehabilitation programs (CRP) group, RAT + CRP group and FES-RAT + CRP group equally. Intervention will be 3 sessions a week, with a total of 36 sessions. The primary outcome measurements will include Fugl-Meyer Assessment and Biomechanical Assessment of RTG behavior. The secondary outcome measurements will include Quality of life and Brain Neuroplasticity assessment by MRI. There are five time points for the evaluation, including baseline, 6 weeks and 12 weeks from the start of treatment, and 3 months, 6 months following the end of treatment. Two-way of variance with repeated measures will be applied to examine the main effects of the group, the time factor and group-time interaction effects.
Discussion The results of the study protocol will provide evidence with high quality for integrated synergy-based FES and RAT, and synergy-based FES alone, and guide significance for design more effective treatment methods in stroke rehabilitation.
Trial registration number ChiCTR2300071588.
Causal effects between inflammatory bowel disease and oral diseases based on Oral-GUT Axis: a Mendelian randomization study
Authors: Xu Yaxin , Luo Jingsong , Gao Yanan , Tao Yanmin , Xu Jun , Yao Ting , Chen Yamei 
Published: July 2023

Abstract
Objective
Several previous studies have suggested oral diseases was correlated to Inflammatory bowel disease (IBD), Crohn's disease (CD) and ulcerative colitis (UC), but the causality and direction of action remained largely unclear. Therefore, this study will through a bidirectional two-sample Mendelian randomization (MR) based on the oral-gut axis to explore evidence for oral diseases with IBD and its two main subtypes.
Methods
We sourced summary statistics from the GWAS database on four oral diseases with each of the three IBD databases for exposure-outcome by bidirectional MR. The MR analyses were performed using IVW as the main effect estimate measure and a series of sensitivity analyses and potential heterogeneity tests were applied to make the results more reliable. And then, we chose either a random-effects model or a fixed-effects model for the meta-analysis based on the presence or absence of heterogeneity thereby.
Results
From oral diseases to IBD, we found a significant effect of genetically predict lichen planus on IBD [OR: 1.069; 95%CI: 1.043–1.097; P < 0.01], CD [OR: 1.090; 95%CI: 1.056–1.125; P < 0.01] and UC [OR: 1.075; 95%CI: 1.040–1.111; P < 0.01]. From IBD to oral diseases, we found a positive effect of whole IBD on periodontal disease [OR: 1.051; 95%CI: 1.020–1.083; P < 0.01], lichen planus [OR: 1.166; 95%CI: 1.011–1.344; P = 0.04] and oral ulcer [OR: 1.003; 95%CI: 1.001–1.004; P < 0.01]. In subtype analysis, we found a suggestive association between UC and periodontal disease [OR: 1.043; 95%CI: 1.009–1.077; P = 0.01], as well as a significant effect of CD on lichen planus [OR: 1.088; 95%CI: 1.038–1.141; P < 0.01].
Conclusion
Our study provides modest evidence for a causal effect between oral diseases and IBD, which can help guide clinical treatment and decision-making for the oral health of patients with IBD, and also somewhat supports the clinical need to predict the extent of IBD disease activity in patients with oral problems.
Diagnosis of inter-turn short-circuit faults and power supply faults of a PMSM controlled by input-output linearization without speed sensor
Authors: MAANANI Yacine , BENAKCHA Abdelhamid , MAANANI Aimen Acil 
Published: July 2023

Abstract
It is generally known that the most common causes of faults in permanent magnets synchronous motors (PMSM) are short circuits between turns and supply problems with unbalanced voltages. Early fault detection prevents some eventual damage to the PMSM and lowers repair costs. This article discusses the detection of supply faults and short circuit faults between turns for the control of synchronous motors with permanent magnets via input-output linearization without a speed sensor in order to accomplish this goal. The Extended Kalman Filter (EKF) will estimate this. The Fast Fourier Transform (FFT) for the steady state, and the Discrete Wavelet Transform (DWT) and the associated energy for the non-stationary state of the electrical variables under study will both be used in the defect detection procedure. To differentiate between turn to turn short-circuits and unbalanced power supply faults, the stator resistance will also be estimated using the extended Kalman filter (EKF). Simulated fault detection and sensorless control algorithms are demonstrated for effectiveness in the MATLAB/Simulink system softaware.
SELEX based aptamers with diagnostic and entry inhibitor therapeutic potential for SARS-CoV-2
Authors: Halder Sayanti , Thakur Abhishek , Keshry Supriya Suman , Acevedo Orlando , Swain Rajeeb K. , Mondal Arindam , Chattopadhyay Soma , Jayaprakash Venkatesan , Dev Abhimanyu , Jana Pradip , Karothia Divyanshi , Jana Indrani Das 
Published: July 2023

Abstract
Frequent mutation and variable immunological protection against vaccination is a common feature for COVID-19 pandemic. Early detection and confinement remain key to controlling further spread of infection. In response, we have developed an aptamer-based system that possesses both diagnostic and therapeutic potential towards the virus. A random aptamer library (~ 1017 molecules) was screened using systematic evolution of ligands by exponential enrichment (SELEX) and aptamer R was identified as a potent binder for the SARS-CoV-2 spike receptor binding domain (RBD) using in vitro binding assay. Using a pseudotyped viral entry assay we have shown that aptamer R specifically inhibited the entry of a SARS-CoV-2 pseudotyped virus in HEK293T-ACE2 cells but did not inhibit the entry of a Vesicular Stomatitis Virus (VSV) glycoprotein (G) pseudotyped virus, hence establishing its specificity towards SARS-CoV-2 spike protein. The antiviral potential of aptamers R and J (same central sequence as R but lacking flanked primer regions) was tested and showed 95.4% and 82.5% inhibition, respectively, against the SARS-CoV-2 virus. Finally, intermolecular interactions between the aptamers and the RBD domain were analyzed using in silico docking and molecular dynamics simulations that provided additional insight into the binding and inhibitory action of aptamers R and J.