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Keywords = site-selectivity excitation

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21 pages, 12507 KiB  
Article
Soil Amplification and Code Compliance: A Case Study of the 2023 Kahramanmaraş Earthquakes in Hayrullah Neighborhood
by Eyübhan Avcı, Kamil Bekir Afacan, Emre Deveci, Melih Uysal, Suna Altundaş and Mehmet Can Balcı
Buildings 2025, 15(15), 2746; https://doi.org/10.3390/buildings15152746 - 4 Aug 2025
Abstract
In the earthquakes that occurred in the Pazarcık (Mw = 7.7) and Elbistan (Mw = 7.6) districts of Kahramanmaraş Province on 6 February 2023, many buildings collapsed in the Hayrullah neighborhood of the Onikişubat district. In this study, we investigated whether there was [...] Read more.
In the earthquakes that occurred in the Pazarcık (Mw = 7.7) and Elbistan (Mw = 7.6) districts of Kahramanmaraş Province on 6 February 2023, many buildings collapsed in the Hayrullah neighborhood of the Onikişubat district. In this study, we investigated whether there was a soil amplification effect on the damage occurring in the Hayrullah neighborhood of the Onikişubat district of Kahramanmaraş Province. Firstly, borehole, SPT, MASW (multi-channel surface wave analysis), microtremor, electrical resistivity tomography (ERT), and vertical electrical sounding (VES) tests were carried out in the field to determine the engineering properties and behavior of soil. Laboratory tests were also conducted using samples obtained from bore holes and field tests. Then, an idealized soil profile was created using the laboratory and field test results, and site dynamic soil behavior analyses were performed on the extracted profile. According to The Turkish Building Code (TBC 2018), the earthquake level DD-2 design spectra of the project site were determined and the average design spectrum was created. Considering the seismicity of the project site and TBC (2018) criteria (according to site-specific faulting, distance, and average shear wave velocity), 11 earthquake ground motion sets were selected and harmonized with DD-2 spectra in short, medium, and long periods. Using scaled motions, the soil profile was excited with 22 different earthquake scenarios and the results were obtained for the equivalent and non-linear models. The analysis showed that the soft soil conditions in the area amplified ground shaking by up to 2.8 times, especially for longer periods (1.0–2.5 s). This level of amplification was consistent with the damage observed in mid- to high-rise buildings, highlighting the important role of local site effects in the structural losses seen during the Kahramanmaraş earthquakes. Full article
(This article belongs to the Section Building Structures)
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29 pages, 5719 KiB  
Article
Cross-Floor Vibration Wave Propagation in High-Rise Industrial Buildings Under TMD Control
by Ruoyang Zhou and Xiaoxiong Zha
Infrastructures 2025, 10(7), 169; https://doi.org/10.3390/infrastructures10070169 - 3 Jul 2025
Viewed by 275
Abstract
High-rise industrial buildings are particularly susceptible to vibration-induced comfort issues, which can negatively impact both the health and productivity of workers and office staff. Unlike most existing studies that focus on local structural components, this study proposes and validates a wave propagation analysis [...] Read more.
High-rise industrial buildings are particularly susceptible to vibration-induced comfort issues, which can negatively impact both the health and productivity of workers and office staff. Unlike most existing studies that focus on local structural components, this study proposes and validates a wave propagation analysis (WPA) method to predict peak accelerations of the floor caused by excitations located on different floors. The method is validated through on-site vibration tests conducted on a high-rise industrial building with shared factory and office space. A simplified regression-based propagation equation is further developed to facilitate practical design applications. The regression parameters are fitted using theoretical calculation results, enabling rapid prediction of peak acceleration responses on the same or different floors. To enhance vibration control, tuned mass dampers (TMDs) are installed on selected floors, and additional tests are conducted with the TMDs activated. An insertion loss-based correction is introduced into the WPA framework to account for the TMD’s frequency-dependent attenuation effects. The extended method supports both accurate prediction of vibration reduction and optimisation of TMD placement across multiple floors in high-rise industrial buildings. Full article
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17 pages, 2746 KiB  
Article
Semi-Supervised Class-Incremental Sucker-Rod Pumping Well Operating Condition Recognition Based on Multi-Source Data Distillation
by Weiwei Zhao, Bin Zhou, Yanjiang Wang and Weifeng Liu
Sensors 2025, 25(8), 2372; https://doi.org/10.3390/s25082372 - 9 Apr 2025
Cited by 1 | Viewed by 555
Abstract
The complex and variable operating conditions of sucker-rod pumping wells pose a significant challenge for the timely and accurate identification of oil well operating conditions. Effective deep learning based on measured multi-source data obtained from the sucker-rod pumping well production site offers a [...] Read more.
The complex and variable operating conditions of sucker-rod pumping wells pose a significant challenge for the timely and accurate identification of oil well operating conditions. Effective deep learning based on measured multi-source data obtained from the sucker-rod pumping well production site offers a promising solution to the challenge. However, existing deep learning-based operating condition recognition methods are constrained by several factors: the limitations of traditional operating condition recognition methods based on single-source and multi-source data, the need for large amounts of labeled data for training, and the high robustness requirement for recognizing complex and variable data. Therefore, we propose a semi-supervised class-incremental sucker-rod pumping well operating condition recognition method based on measured multi-source data distillation. Firstly, we select measured ground dynamometer cards and measured electrical power cards as information sources, and construct the graph neural network teacher models for data sources, and dynamically fuse the prediction probability of each teacher model through the Squeeze-and-Excitation attention mechanism. Then, we introduce a multi-source data distillation loss. It uses Kullback-Leibler (KL) divergence to measure the difference between the output logic of the teacher and student models. This helps reduce the forgetting of old operating condition category knowledge during class-incremental learning. Finally, we employ a multi-source semi-supervised graph classification method based on enhanced label propagation, which improves the label propagation method through a logistic regression classifier. This method can deeply explore the potential relationship between labeled and unlabeled samples, so as to further enhance the classification performance. Extensive experimental results show that the proposed method achieves superior recognition performance and enhanced engineering practicality in real-world class-incremental oil extraction production scenarios with complex and variable operating conditions. Full article
(This article belongs to the Section Internet of Things)
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41 pages, 10214 KiB  
Review
A Review of Parameters and Methods for Seismic Site Response
by A. S. M. Fahad Hossain, Ali Saeidi, Mohammad Salsabili, Miroslav Nastev, Juliana Ruiz Suescun and Zeinab Bayati
Geosciences 2025, 15(4), 128; https://doi.org/10.3390/geosciences15040128 - 1 Apr 2025
Cited by 1 | Viewed by 2946
Abstract
Prediction of the intensity of earthquake-induced motions at the ground surface attracts extensive attention from the geoscience community due to the significant threat it poses to humans and the built environment. Several factors are involved, including earthquake magnitude, epicentral distance, and local soil [...] Read more.
Prediction of the intensity of earthquake-induced motions at the ground surface attracts extensive attention from the geoscience community due to the significant threat it poses to humans and the built environment. Several factors are involved, including earthquake magnitude, epicentral distance, and local soil conditions. The local site effects, such as resonance amplification, topographic focusing, and basin-edge interactions, can significantly influence the amplitude–frequency content and duration of the incoming seismic waves. They are commonly predicted using site effect proxies or applying more sophisticated analytical and numerical models with advanced constitutive stress–strain relationships. The seismic excitation in numerical simulations consists of a set of input ground motions compatible with the seismo-tectonic settings at the studied location and the probability of exceedance of a specific level of ground shaking over a given period. These motions are applied at the base of the considered soil profiles, and their vertical propagation is simulated using linear and nonlinear approaches in time or frequency domains. This paper provides a comprehensive literature review of the major input parameters for site response analyses, evaluates the efficiency of site response proxies, and discusses the significance of accurate modeling approaches for predicting bedrock motion amplification. The important dynamic soil parameters include shear-wave velocity, shear modulus reduction, and damping ratio curves, along with the selection and scaling of earthquake ground motions, the evaluation of site effects through site response proxies, and experimental and numerical analysis, all of which are described in this article. Full article
(This article belongs to the Special Issue Geotechnical Earthquake Engineering and Geohazard Prevention)
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14 pages, 6876 KiB  
Article
Near-Edge X-Ray Absorption Fine-Structure Spectra and Specific Dissociation of Phe-Gly and Gly-Phe
by Tse-Fu Shen, Yu-Ju Chiang, Yi-Shiue Lin, Chen-Lin Liu, Yu-Chiao Wang, Kuan-Yi Chou, Cheng-Cheng Tsai and Wei-Ping Hu
Int. J. Mol. Sci. 2025, 26(6), 2515; https://doi.org/10.3390/ijms26062515 - 11 Mar 2025
Viewed by 819
Abstract
The total-ion-yield (TIY) near-edge X-ray absorption fine-structure (NEXAFS) spectra of two dipeptides were measured and analyzed to identify the excitation sites of core electrons and the corresponding destination molecular orbitals. Peptide molecules were transferred to the gaseous phase using traditional heating and MALDI [...] Read more.
The total-ion-yield (TIY) near-edge X-ray absorption fine-structure (NEXAFS) spectra of two dipeptides were measured and analyzed to identify the excitation sites of core electrons and the corresponding destination molecular orbitals. Peptide molecules were transferred to the gaseous phase using traditional heating and MALDI methods, ensuring that the resulting NEXAFS spectra and fragmentation products were consistent across both approaches. Mass spectra obtained at various excitation energies revealed the branching ratios of products at each energy level, offering insights into specific dissociation phenomena. Notably, variations in excitation energy demonstrated a selective dissociation process, with certain products forming more efficiently. This specificity appears closely linked to dissociations near the peptide bond, where the nodal planes of destination molecular orbitals are located. These findings were validated using both small peptide models and peptoid molecules, highlighting consistent patterns in the dissociation behavior. Full article
(This article belongs to the Section Molecular Informatics)
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24 pages, 5937 KiB  
Article
Nonstationary Stochastic Responses of Transmission Tower-Line System with Viscoelastic Material Dampers Under Seismic Excitations
by Mingjing Chang, Bo Chen, Xiang Xiao and Yanzhou Chen
Materials 2025, 18(5), 1138; https://doi.org/10.3390/ma18051138 - 3 Mar 2025
Cited by 1 | Viewed by 756
Abstract
The excessive vibration or collapse of a transmission tower-line (TTL) system under seismic excitation can result in significant losses. Viscoelastic material dampers (VMDs) have been recognized as an effective method for structural vibration mitigation. Most existing studies have focused solely on the dynamic [...] Read more.
The excessive vibration or collapse of a transmission tower-line (TTL) system under seismic excitation can result in significant losses. Viscoelastic material dampers (VMDs) have been recognized as an effective method for structural vibration mitigation. Most existing studies have focused solely on the dynamic analysis of TTL systems with control devices under deterministic seismic excitations. Studies focusing on the nonstationary stochastic control of TTL systems with VMDs have not been reported. To this end, this study proposes a comprehensive analytical framework for the nonstationary stochastic responses of TTL systems with VMDs under stochastic seismic excitations. The analytical model of the TTL system is formulated using the Lagrange equation. The six-parameter model of VMDs and the vibration control method are established. Following this, the pseudo-excitation method (PEM) is applied to compute the stochastic response of the controlled TTL system under nonstationary seismic excitations, and a probabilistic framework for analyzing extreme value responses is developed. A real TTL system in China is selected to verify the validity of the proposed method. The accuracy of the proposed framework is validated based on the Monte Carlo method (MCM). A detailed parametric investigation is conducted to determine the optimal damper installation scheme and examine the effects of the service temperature and site type on stochastic seismic responses. VMDs can effectively suppress the structural dynamic responses, with particularly stable control over displacement. The temperature and site type have a notable influence on the stochastic seismic responses of the TTL system. The research findings provide important references for improving the seismic performance of VMDs in TTL systems. Full article
(This article belongs to the Special Issue From Materials to Applications: High-Performance Steel Structures)
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81 pages, 50947 KiB  
Review
Towards Completion of the “Periodic Table” of Di-2-Pyridyl Ketoxime
by Christina Stamou, Christina D. Polyzou, Zoi G. Lada, Konstantis F. Konidaris and Spyros P. Perlepes
Molecules 2025, 30(4), 791; https://doi.org/10.3390/molecules30040791 - 8 Feb 2025
Viewed by 1046
Abstract
The oxime group is important in organic and inorganic chemistry. In most cases, this group is part of an organic molecule possessing one or more donor sites capable of forming bonds to metal ions. One family of such compounds is the group of [...] Read more.
The oxime group is important in organic and inorganic chemistry. In most cases, this group is part of an organic molecule possessing one or more donor sites capable of forming bonds to metal ions. One family of such compounds is the group of 2-pyridyl (aldo)ketoximes. Metal complexes of 2-pyridyl oximes continue to attract the intense interest of many inorganic chemistry groups around the world for a variety of reasons, including their interesting structures, physical and biological properties, and applications. A unique member of 2-pyridyl ketoximes is di-2-pyridyl ketoxime (dpkoxH), which contains two 2-pyridyl groups and an oxime functionality that can be easily deprotonated giving the deprotonated ligand (dpkox). The extra 2-pyridyl site confers a remarkable flexibility resulting in metal complexes with exciting structural and reactivity features. Our and other research groups have prepared and characterized many metal complexes of dpkoxH and dpkox over the past 30 years or so. This work is an attempt to build a “periodic table” of dpkoxH, which is near completion. The filled spaces of this “periodic table” contain metal ions whose dpkoxH/dpkox complexes have been structurally characterized. This work reviews comprehensively the to-date published coordination chemistry of dpkoxH with emphasis on the syntheses, reactivity, relationship to metallacrown chemistry, structures, and properties of the metal complexes; selected unpublished results from our group are also reported. The sixteen coordination modes adopted by dpkoxH and dpkox have provided access to monomeric and dimeric complexes, trinuclear, tetranuclear, pentanuclear, hexanuclear, heptanuclear, enneanuclear, and decanuclear clusters, as well as to a small number of 1D coordination polymers. With few exceptions ({MIILnIII2} and {NiII2MnIII2}; M = Ni, Cu, Pd, and Ln = lanthanoid), most complexes are homometallic. The metals whose ions have yielded complexes with dpkoxH and dpkox are Cr, Mn, Fe, Co, Ni, Cu, Zn, Ru, Rh, Pd, Ag, Cd, Re, Os, Ir, Au, Hg, lanthanoids (mainly Pr and Nd), and U. Most metal complexes are homovalent, but some mixed-valence Mn, Fe, and Co compounds have been studied. Metal ion-assisted/promoted transformations of dpkoxH, i.e., reactivity patterns of the coordinated ligand, are also critically discussed. Some perspectives concerning the coordination chemistry of dpkoxH and research work for the future are outlined. Full article
(This article belongs to the Section Inorganic Chemistry)
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12 pages, 2936 KiB  
Article
First-Principles Understanding of Mono- and Dual-Emissions in AZnOS:Bi3+ (A = Ba, Ca) Phosphors
by Quanzhi Kougong, Bibo Lou and Mikhail G. Brik
Materials 2025, 18(3), 657; https://doi.org/10.3390/ma18030657 - 2 Feb 2025
Viewed by 898
Abstract
The AZnOS:Bi3+ (A = Ba, Ca) phosphors exhibit mono- and dual-emission phenomena based on the different choices of cation, making them an ideal prototype for dual-emission mechanism studies of Bi3+ ions. Here, first-principles calculations were performed to investigate the site occupancy, [...] Read more.
The AZnOS:Bi3+ (A = Ba, Ca) phosphors exhibit mono- and dual-emission phenomena based on the different choices of cation, making them an ideal prototype for dual-emission mechanism studies of Bi3+ ions. Here, first-principles calculations were performed to investigate the site occupancy, defect levels, and luminescence properties of the AZnOS:Bi3+ systems. The formation energy calculations show that the bismuth dopants are mainly in the trivalent charge state, with the Bi3+ ions preferring the Ca sites in CaZnOS but the Zn sites in BaZnOS. Such cation-selective occupancy mainly results in the difference between the mono- and dual-emission phenomena in the two hosts. The excitation and emission energies predicted by calculations are in good agreement with the measurements. Our calculations show that the lowest excited state 3P0,1 provides the dominant emission in both CaZnOS:Bi3+ and BaZnOS:Bi3+ phosphors. In light of the experimental and theoretical results, the metastable excited state of Bi2+ + hVBM (hole at the valence band maximum) is the origin of the additional emission bands in BaZnOS:Bi3+. These results provide the basis of emission band tuning and novel material design for Bi3+-doped phosphors. Full article
(This article belongs to the Section Materials Simulation and Design)
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15 pages, 2199 KiB  
Article
Human Serum Albumin and Human Serum Albumin Nanoparticles as Carriers of 10-(2′-Pyrimidyl)-3,6-diazaphenothiazine: In Vitro Spectroscopic Studies
by Aleksandra Owczarzy, Karolina Kulig, Beata Morak-Młodawska, Małgorzata Jeleń, Tammam Muhammetoglu, Wojciech Rogóż and Małgorzata Maciążek-Jurczyk
Molecules 2025, 30(2), 315; https://doi.org/10.3390/molecules30020315 - 15 Jan 2025
Viewed by 1260
Abstract
Human serum albumin (HSA) plays a fundamental role in the human body, including the transport of exogenous and endogenous substances. HSA is also a biopolymer with a great medical and pharmaceutical potential. Due to nontoxicity and biocompatibility, this protein can be used as [...] Read more.
Human serum albumin (HSA) plays a fundamental role in the human body, including the transport of exogenous and endogenous substances. HSA is also a biopolymer with a great medical and pharmaceutical potential. Due to nontoxicity and biocompatibility, this protein can be used as a nanocarrier. 10-(2′-Pyrimidyl)-3,6-diazaphenothiazine (10-Pyr-3,6-DAPT) is a phenothiazine showing high anticancer potential in vitro against glioma, melanoma and breast cancer cells. Additionally, this compound is characterized by selectivity of action towards MCF-7 breast cancer and has low cytotoxicity towards normal cells. Considering the promising pharmacological potential of this compound and using spectroscopic techniques, HSA and human serum albumin nanoparticles (HSA-NP) were tested as carriers of this molecule. Based on the obtained data and the appropriate mathematical models (Stern-Volmer and Klotz models), it can be concluded that 10-Pyr-3,6-DAPT probably forms a weak (Ka = (5.24 ± 0.57) × 104 and Ka = (4.67 ± 0.59) × 104) for excitation wavelengths λex 275 nm and λex 295 nm, respectively) static complex (kq > 1010) with HSA (at Sudlow site II (subdomain IIIA), and the phenomenon of it having both strong therapeutic and toxic effects is possible. High encapsulation efficiency of 10-Pyr-3,6-DAPT into the HSA-NPs was obtained, and the changes in albumin secondary structure due to the presence of 10-Pyr-3,6-DAPT were registered. Based on the data presented, it can be concluded that due to the high toxic effects of 10-Pyr-3,6-DAPT, a better carrier may be HSA-NPs. Full article
(This article belongs to the Special Issue Protein-Ligand Interactions)
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19 pages, 8204 KiB  
Article
Rapid Detection of Aluminium and Iron Impurities in Lithium Carbonate Using Water-Soluble Fluorescent Probes
by Hong-Mei Wu, Huai-Gang Cheng, Zi-Wen Zhu and Li Cui
Molecules 2025, 30(1), 135; https://doi.org/10.3390/molecules30010135 - 31 Dec 2024
Cited by 2 | Viewed by 874
Abstract
The real-time measurement of the content of impurities such as iron and aluminium ions is one of the keys to quality evaluation in the production process of high-purity lithium carbonate; however, impurity detection has been a time-consuming process for many years, which limits [...] Read more.
The real-time measurement of the content of impurities such as iron and aluminium ions is one of the keys to quality evaluation in the production process of high-purity lithium carbonate; however, impurity detection has been a time-consuming process for many years, which limits the optimisation of the production of high-purity lithium carbonate. In this context, this work explores the possibility of using water-soluble fluorescent probes for the rapid detection of impurity ions. Salicylaldehyde was modified with the hydrophilic group dl-alanine to synthesise a water-soluble Al3+ fluorescent probe (Probe A). Moreover, a water-soluble Fe3+ fluorescent probe (Probe B) was synthesised from coumarin-3-carboxylic acid and 3-hydroxyaminomethane. Probe A and Probe B exhibited good stability in the pH range of 4–9 in aqueous solutions, high sensitivity, as well as high selectivity for Al3+ and Fe3+; the detection limits for Al3+ and Fe3+ were 1.180 and 1.683 μmol/L, whereas the response times for Al3+ and Fe3+ were as low as 10 and 30 s, respectively. Electrostatic potential (ESP) analysis and density functional theory calculations identified the binding sites and fluorescence recognition mechanism; theoretical calculations showed that the enhanced fluorescence emission of Probe A when detecting Al3+ was due to the excited intramolecular proton transfer (ESIPT) effect, whereas the fluorescence quenching of Probe B when detecting Fe3+ was due to the electrons turning off fluorescence when binding through the photoelectron transfer (PET) mechanism. Full article
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19 pages, 15502 KiB  
Article
Train-Induced Vibration and Structure-Borne Noise Measurement and Prediction of Low-Rise Building
by Jialiang Chen, Sen Hou, Bokai Zheng, Xuming Li, Fangling Peng, Yingying Wang and Junjie Chen
Buildings 2024, 14(9), 2883; https://doi.org/10.3390/buildings14092883 - 12 Sep 2024
Cited by 3 | Viewed by 1811
Abstract
The advancement of urban rail transit is increasingly confronted with environmental challenges related to vibration and noise. To investigate the critical issues surrounding vibration propagation and the generation of structure-borne noise, a two-story frame building was selected for on-site measurements of both vibration [...] Read more.
The advancement of urban rail transit is increasingly confronted with environmental challenges related to vibration and noise. To investigate the critical issues surrounding vibration propagation and the generation of structure-borne noise, a two-story frame building was selected for on-site measurements of both vibration and its induced structure-borne noise. The collected data were analyzed in both the time and frequency domains to explore the correlation between these phenomena, leading to the proposal of a hybrid prediction method for structural noise that was subsequently compared with measured results. The findings indicate that the excitation of structure-borne noise produces significant waveforms within sound signals. The characteristic frequency of the structure-borne noise is 25–80 Hz, as well as that of the train-induced vibration. Furthermore, there exists a positive correlation between structural vibration and structure-borne noise, whereby increased levels of vibration correspond to more pronounced structure-borne noise; additionally, indoor distribution patterns of structure-borne noise are non-uniform, with corner wall areas exhibiting greater intensity than central room locations. Finally, a hybrid prediction methodology that is both semi-analytical and semi-empirical is introduced. The approach derives dynamic response predictions of the structure through analytical solutions, subsequently estimating the secondary noise within the building’s interior using a newly formulated empirical equation to facilitate rapid predictions regarding indoor building vibrations and structure-borne noises induced by subway train operations. Full article
(This article belongs to the Special Issue Vibration Prediction and Noise Assessment of Building Structures)
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18 pages, 3031 KiB  
Article
In Silico Analysis: Molecular Characterization and Evolutionary Study of CLCN Gene Family in Buffalo
by Yiheng Fu, Muhammad Farhan Khan, Yingqi Wang, Shakeela Parveen, Mehwish Sultana, Qingyou Liu and Laiba Shafique
Genes 2024, 15(9), 1163; https://doi.org/10.3390/genes15091163 - 3 Sep 2024
Cited by 3 | Viewed by 1563
Abstract
Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating [...] Read more.
Chloride channels (ClCs) have received global interest due to their significant role in the regulation of ion homeostasis, fluid transport, and electrical excitability of tissues and organs in different mammals and contributing to various functions, such as neuronal signaling, muscle contraction, and regulating the electrolytes’ balance in kidneys and other organs. In order to define the chloride voltage-gated channel (CLCN) gene family in buffalo, this study used in silico analyses to examine physicochemical properties, evolutionary patterns, and genome-wide identification. We identified eight CLCN genes in buffalo. The ProtParam tool analysis identified a number of important physicochemical properties of these proteins, including hydrophilicity, thermostability, in vitro instability, and basic nature. Based on their evolutionary relationships, a phylogenetic analysis divided the eight discovered genes into three subfamilies. Furthermore, a gene structure analysis, motif patterns, and conserved domains using TBtool demonstrated the significant conservation of this gene family among selected species over the course of evolution. A comparative amino acid analysis using ClustalW revealed similarities and differences between buffalo and cattle CLCN proteins. Three duplicated gene pairs were identified, all of which were segmental duplications except for CLCN4-CLCN5, which was a tandem duplication in buffalo. For each gene pair, the Ka/Ks test ratio findings showed that none of the ratios was more than one, indicating that these proteins were likely subject to positive selection. A synteny analysis confirmed a conserved pattern of genomic blocks between buffalo and cattle. Transcriptional control in cells relies on the binding of transcription factors to specific sites in the genome. The number of transcription factor binding sites (TFBSs) was higher in cattle compared to buffalo. Five main recombination breakpoints were identified at various places in the recombination analysis. The outcomes of our study provide new knowledge about the CLCN gene family in buffalo and open the door for further research on candidate genes in vertebrates through genome-wide studies. Full article
(This article belongs to the Special Issue Buffalo Genetics and Genomics)
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18 pages, 3436 KiB  
Article
Polycations as Aptamer-Binding Modulators for Sensitive Fluorescence Anisotropy Assay of Aflatoxin B1
by Alexey V. Samokhvalov, Alena A. Mironova, Sergei A. Eremin, Anatoly V. Zherdev and Boris B. Dzantiev
Sensors 2024, 24(10), 3230; https://doi.org/10.3390/s24103230 - 19 May 2024
Cited by 3 | Viewed by 1879
Abstract
Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte [...] Read more.
Fluorescence induced by the excitation of a fluorophore with plane-polarized light has a different polarization depending on the size of the fluorophore-containing reagent and the rate of its rotation. Based on this effect, many analytical systems have been implemented in which an analyte contained in a sample and labeled with a fluorophore (usually fluorescein) competes to bind to antibodies. Replacing antibodies in such assays with aptamers, low-cost and stable oligonucleotide receptors, is complicated because binding a fluorophore to them causes a less significant change in the polarization of emissions. This work proposes and characterizes the compounds of the reaction medium that improve analyte binding and reduce the mobility of the aptamer–fluorophore complex, providing a higher analytical signal and a lower detection limit. This study was conducted on aflatoxin B1 (AFB1), a ubiquitous toxicant contaminating foods of plant origins. Eight aptamers specific to AFB1 with the same binding site and different regions stabilizing their structures were compared for affinity, based on which the aptamer with 38 nucleotides in length was selected. The polymers that interact reversibly with oligonucleotides, such as poly-L-lysine and polyethylene glycol, were tested. It was found that they provide the desired reduction in the depolarization of emitted light as well as high concentrations of magnesium cations. In the selected optimal medium, AFB1 detection reached a limit of 1 ng/mL, which was 12 times lower than in the tris buffer commonly used for anti-AFB1 aptamers. The assay time was 30 min. This method is suitable for controlling almond samples according to the maximum permissible levels of their contamination by AFB1. The proposed approach could be applied to improve other aptamer-based analytical systems. Full article
(This article belongs to the Special Issue Fluorescence Sensors for Biological and Medical Applications)
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17 pages, 10304 KiB  
Article
Fluorinated TiO2 Hollow Spheres for Detecting Formaldehyde under UV Irradiation
by Jianwei Zhang, Baoyu Huang, Xinlei Li, Chao Yang, Wenzhuo Zhao, Xiuhua Xie, Nan Wang and Xiaogan Li
Materials 2024, 17(4), 904; https://doi.org/10.3390/ma17040904 - 15 Feb 2024
Cited by 2 | Viewed by 1621
Abstract
The fluorinated titanium dioxide (F-TiO2) hollow spheres with varying F to Ti molar ratios were prepared by a simple one-step hydrothermal method followed by thermal processing. The diameter of the F-TiO2-0.3 hollow spheres with a nominal ratio of F:Ti [...] Read more.
The fluorinated titanium dioxide (F-TiO2) hollow spheres with varying F to Ti molar ratios were prepared by a simple one-step hydrothermal method followed by thermal processing. The diameter of the F-TiO2-0.3 hollow spheres with a nominal ratio of F:Ti = 0.3:1 was about 200–400 nm. Compared with the sensor based on pristine TiO2 sensing materials, the F-TiO2-0.3 sensor displayed an enhanced sensing performance toward gaseous formaldehyde (HCHO) vapor at room temperature under ultraviolet (UV) light irradiation. The F-TiO2-0.3 sensor demonstrated an approximately 18-fold enhanced response (1.56) compared to the pristine TiO2 sensor (0.085). The response and recovery times of the F-TiO2-0.3 sensor to 10 ppm HCHO were about 56 s and 64 s, respectively, and a limit-of-detection value of 0.5 ppm HCHO was estimated. The F-TiO2-0.3 sensor also demonstrated good repeatability and selectivity to HCHO gas under UV light irradiation. The outstanding HCHO gas-sensing properties of the F-TiO2-0.3 sensor were related to the following factors: the excitation effect caused by the UV light facilitated surface chemical reactions with analyte gas species; the hollow sphere structure provided sufficient active sites; and the surface fluoride (≡Ti−F) created additional chemisorption sites on the surface of the TiO2 material. Full article
(This article belongs to the Section Advanced Nanomaterials and Nanotechnology)
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13 pages, 1875 KiB  
Article
Water Splitting Reaction Mechanism on Transition Metal (Fe-Cu) Sulphide and Selenide Clusters—А DFT Study
by Ellie Uzunova, Ivelina Georgieva and Tsvetan Zahariev
Materials 2024, 17(1), 56; https://doi.org/10.3390/ma17010056 - 22 Dec 2023
Viewed by 1630
Abstract
The tetracarbonyl complexes of transition metal chalcogenides M2X2(CO)4, where M = Fe, Co, Ni, Cu and X = S, Se, are examined by density functional theory (DFT). The M2X2 core is cyclic with either [...] Read more.
The tetracarbonyl complexes of transition metal chalcogenides M2X2(CO)4, where M = Fe, Co, Ni, Cu and X = S, Se, are examined by density functional theory (DFT). The M2X2 core is cyclic with either planar or non-planar geometry. As a sulfide, it is present in natural enzymes and has a selective redox capacity. The reduced forms of the selenide and sulfide complexes are relevant to the hydrogen evolution reaction (HER) and they provide different positions of hydride ligand binding: (i) at a chalcogenide site, (ii) at a particular cation site and (iii) in a midway position forming equal bonds to both cation sites. The full pathway of water decomposition to molecular hydrogen and oxygen is traced by transition state theory. The iron and cobalt complexes, cobalt selenide, in particular, provide lower energy barriers in HER as compared to the nickel and copper complexes. In the oxygen evolution reaction (OER), cobalt and iron selenide tetracarbonyls provide a low energy barrier via OOH* intermediate. All of the intermediate species possess favorable excitation transitions in the visible light spectrum, as evidenced by TD-DFT calculations and they allow photoactivation. In conclusion, cobalt and iron selenide tetracarbonyl complexes emerge as promising photocatalysts in water splitting. Full article
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