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Authors = Asad Riaz

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27 pages, 3031 KiB  
Review
Plant Secondary Metabolites—Central Regulators Against Abiotic and Biotic Stresses
by Ameer Khan, Farah Kanwal, Sana Ullah, Muhammad Fahad, Leeza Tariq, Muhammad Tanveer Altaf, Asad Riaz and Guoping Zhang
Metabolites 2025, 15(4), 276; https://doi.org/10.3390/metabo15040276 - 16 Apr 2025
Cited by 5 | Viewed by 2323
Abstract
As global climates shift, plants are increasingly exposed to biotic and abiotic stresses that adversely affect their growth and development, ultimately reducing agricultural productivity. To counter these stresses, plants produce secondary metabolites (SMs), which are critical biochemical and essential compounds that serve as [...] Read more.
As global climates shift, plants are increasingly exposed to biotic and abiotic stresses that adversely affect their growth and development, ultimately reducing agricultural productivity. To counter these stresses, plants produce secondary metabolites (SMs), which are critical biochemical and essential compounds that serve as primary defense mechanisms. These diverse compounds, such as alkaloids, flavonoids, phenolic compounds, and nitrogen/sulfur-containing compounds, act as natural protectants against herbivores, pathogens, and oxidative stress. Despite the well-documented protective roles of SMs, the precise mechanisms by which environmental factors modulate their accumulation under different stress conditions are not fully understood. This review provides comprehensive insights into the recent advances in understanding the functions of SMs in plant defense against abiotic and biotic stresses, emphasizing their regulatory networks and biosynthetic pathways. Furthermore, we explored the unique contributions of individual SM classes to stress responses while integrating the findings across the entire spectrum of SM diversity, providing a comprehensive understanding of their roles in plant resilience under multiple stress conditions. Finally, we highlight the emerging strategies for harnessing SMs to improve crop resilience through genetic engineering and present novel solutions to enhance agricultural sustainability in a changing climate. Full article
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17 pages, 14240 KiB  
Article
Dual-Planar Monopole Antenna-Based Remote Sensing System for Microwave Medical Applications
by Minghui Zhao, Asad Riaz, Imran M. Saied, Zain Shami and Tughrul Arslan
Sensors 2024, 24(2), 328; https://doi.org/10.3390/s24020328 - 5 Jan 2024
Cited by 4 | Viewed by 1942
Abstract
Neurodegenerative diseases (NDs) can be life threatening and have chronic impacts on patients and society. Timely diagnosis and treatment are imperative to prevent deterioration. Conventional imaging modalities, such as Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and Positron Emission Tomography (PET), are expensive [...] Read more.
Neurodegenerative diseases (NDs) can be life threatening and have chronic impacts on patients and society. Timely diagnosis and treatment are imperative to prevent deterioration. Conventional imaging modalities, such as Computed Tomography (CT), Magnetic Resonance Imaging (MRI), and Positron Emission Tomography (PET), are expensive and not readily accessible to patients. Microwave sensing and imaging (MSI) systems are promising tools for monitoring pathological changes, namely the lateral ventricle enlargement associated with ND, in a non-invasive and convenient way. This paper presents a dual-planar monopole antenna-based remote sensing system for ND monitoring. First, planar monopole antennas were designed using the simulation software CST Studio Suite. The antenna analysis was carried out regarding the reflection coefficient, gain, radiation pattern, time domain characterization, E-field distribution, and Specific Absorption Rate (SAR). The designed antennas were then integrated with a controlling circuit as a remote sensing system. The system was experimentally validated on brain phantoms using a vector network analyzer and a laptop. The collected reflection coefficient data were processed using a radar-based imaging algorithm to reconstruct images indicating brain abnormality in ND. The results suggest that the system could serve as a low-cost and efficient tool for long-term monitoring of ND, particularly in clinics and care home scenarios. Full article
(This article belongs to the Section Biomedical Sensors)
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17 pages, 5141 KiB  
Article
A Blockchain-Based Framework to Make the Rice Crop Supply Chain Transparent and Reliable in Agriculture
by Muhammad Shoaib Farooq, Shamyla Riaz, Ibtesam Ur Rehman, Muhammad Asad Khan and Bilal Hassan
Systems 2023, 11(9), 476; https://doi.org/10.3390/systems11090476 - 17 Sep 2023
Cited by 12 | Viewed by 6634
Abstract
Rice is one of the major food crops across the globe, and its quality and safety highly influence human health. It is the basis of many different products, including rice flour, rice bread, noodles, rice vinegar, and others. Therefore, the rice supply chain [...] Read more.
Rice is one of the major food crops across the globe, and its quality and safety highly influence human health. It is the basis of many different products, including rice flour, rice bread, noodles, rice vinegar, and others. Therefore, the rice supply chain has garnered increasing attention due to the high demand for food safety. Furthermore, malpractices in the rice supply chain can impact farmers by generating low revenues despite their great efforts in rice cultivation. In addition, they would cause governments to suffer significant economic losses due to the high cost of importing rice crops from other countries during the off-season. These issues derive from the lack of reliability, trust, transparency, traceability, and security in the rice supply chain. In this research, we propose a secure, trusted, reliable, and transparent framework based on a Blockchain for rice crop supply chain’s traceability from farm to fork. A new crypto token, the Rice Coin (RC), is introduced to keep a record of all transactions between the stakeholders of the rice supply chain. Moreover, the proposed framework includes an economic model and a crypto wallet and introduces an Initial Coin Offering (ICO) for the RC. Based on smart contracts, a transaction processing system was developed for the transparency and traceability of rice crops, including the conversion of the RC to fiat currency. Furthermore, the InterPlanetary File System (IPFS) is proposed in this research to store encrypted data of companies, retailers, and farmers, so to increase data security, transparency, and availability. In the end, the experimental results showed a better performance of the proposed framework compared to already available supply chain solutions in terms of transaction verification time, transaction average gas cost, and new block latency. Full article
(This article belongs to the Special Issue Blockchain Technology for Future Supply Chain Management)
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19 pages, 882 KiB  
Article
Pesticides, Heavy Metals and Plasticizers: Contamination and Risk Assessment of Drinking-Water Quality
by Noman Adil, Kamran Ashraf, Masooma Munir, Muhammad Mohiuddin, Asim Abbasi, Umair Riaz, Asad Aslam, Samy A. Marey, Ashraf Atef Hatamleh and Qamar uz Zaman
Sustainability 2023, 15(17), 13263; https://doi.org/10.3390/su151713263 - 4 Sep 2023
Cited by 13 | Viewed by 6689
Abstract
This study highlights the impact of formal agricultural practices and their adverse effect on the deterioration of underground water quality, with special emphasis on toxic elements, including pesticides, herbicides, fungicides, plasticizer accumulation and heavy-metal contamination. A comprehensive study was conducted at various recently [...] Read more.
This study highlights the impact of formal agricultural practices and their adverse effect on the deterioration of underground water quality, with special emphasis on toxic elements, including pesticides, herbicides, fungicides, plasticizer accumulation and heavy-metal contamination. A comprehensive study was conducted at various recently developed societies of Sadiqabad that were formerly used for agricultural purposes. Ten various societies were selected, and three samples from each society were collected from different regions of these areas. Data regarding the physicochemical properties, metal contamination and accumulation of pesticide residues were determined using standard protocols. The results revealed that almost all the physicochemical properties of water samples selected from these sites were close to the WHO’s recommended limits. The range for physicochemical properties was pH (6.4–7.7), electrical conductivity (168–766 µ S cm−1), turbidity (6–17 NTU), total hardness (218–1030 mg L−1), chloride contents (130–870 mg L−1) and phosphate contents (2.55–5.11 mg L−1). Among heavy metals, lead and arsenic concentrations in all sampling sites were found to be above the recommended limits. The decreasing pattern in terms of water-quality deterioration with respect to physicochemical properties was FFT > USM > CRH > UCS > CHS > MAH > FFC > CGA > GIH > AGS. Overall, 95 different kinds of toxic elements, including pesticides, herbicides, plasticizer, etc., were detected in the groundwater samples. The toxic compounds in the groundwater were categorized into pesticides, herbicides, plasticizer, plant growth regulators, fungicides, acaricides and insecticides. Most of these parameters showed peak values at the Fatima Fertilizer Company area and Chief Residencia Housing Society. Pesticide contamination showed that water-filtration plants have a big positive impact on the drinking quality of water. Proper monitoring of the pesticides must be performed, as the majority of the pesticides showed low priority. The monitoring method of the pesticides needs to be updated so that the occurrence of recently authorized pesticides is demonstrated. Full article
(This article belongs to the Special Issue Urban Environment and Human Health)
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18 pages, 5486 KiB  
Article
Bioremediation of Azo Dye Brown 703 by Pseudomonas aeruginosa: An Effective Treatment Technique for Dye-Polluted Wastewater
by Asad Ullah Khan, Muhammad Zahoor, Mujaddad Ur Rehman, Muhammad Ikram, Daochen Zhu, Muhammad Naveed Umar, Riaz Ullah and Essam A. Ali
Microbiol. Res. 2023, 14(3), 1049-1066; https://doi.org/10.3390/microbiolres14030070 - 2 Aug 2023
Cited by 25 | Viewed by 4263
Abstract
Dye-polluted wastewater poses a serious threat to humans’, animals’ and plants’ health, and to avoid these health risks in the future, the treatment of wastewater containing dyes is necessary before its release to environment. Herein, a biological approach is used; the textile azo [...] Read more.
Dye-polluted wastewater poses a serious threat to humans’, animals’ and plants’ health, and to avoid these health risks in the future, the treatment of wastewater containing dyes is necessary before its release to environment. Herein, a biological approach is used; the textile azo dye brown 703 is degraded utilizing Pseudomonas aeruginosa. The bacterial strain was isolated from textile wastewater dumping sites in Mingora, Swat. The optimization for bacterial degradation was carried out on the nutrient broth medium, which was then subjected to a variety of environmental physicochemical conditions and nutritional source supplementation before being tested. Under micro-aerophilic circumstances, the maximum decolorization and degradation of dye occurred at a 20 ppm dye concentration within 3 days of incubation at a neutral pH and 38 °C. The decrease in the intensity of the absorbance peak in the UV–Vis spectrum was used to measure the extent of decolorization. Initially, 15 bacterial strains were isolated from the textile effluent. Out of these strains, Pseudomonas aeruginosa was found to be the most potent degrading bacteria, with a degradation extent of around 71.36% at optimum conditions. The appearance and disappearance of some new peaks in the FT-IR analysis after the degradation of brown 703 showed that the dye was degraded by Pseudomonas aeruginosa. The GC–MS analysis performed helped in identifying the degraded compounds of azo dye that were utilized in illustrating the under-study process of brown 703 degradation. The biodegradation brought about by Pseudomonas aeruginosa can be employed successfully in the future as an eco-friendly approach with far reaching results. Full article
(This article belongs to the Special Issue Microorganisms as a Tool for Restoring the Environment)
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32 pages, 8286 KiB  
Article
Machine Learning-Based Predictive Model for Tensile and Flexural Strength of 3D-Printed Concrete
by Ammar Ali, Raja Dilawar Riaz, Umair Jalil Malik, Syed Baqar Abbas, Muhammad Usman, Mati Ullah Shah, In-Ho Kim, Asad Hanif and Muhammad Faizan
Materials 2023, 16(11), 4149; https://doi.org/10.3390/ma16114149 - 2 Jun 2023
Cited by 41 | Viewed by 5990
Abstract
The additive manufacturing of concrete, also known as 3D-printed concrete, is produced layer by layer using a 3D printer. The three-dimensional printing of concrete offers several benefits compared to conventional concrete construction, such as reduced labor costs and wastage of materials. It can [...] Read more.
The additive manufacturing of concrete, also known as 3D-printed concrete, is produced layer by layer using a 3D printer. The three-dimensional printing of concrete offers several benefits compared to conventional concrete construction, such as reduced labor costs and wastage of materials. It can also be used to build complex structures with high precision and accuracy. However, optimizing the mix design of 3D-printed concrete is challenging, involving numerous factors and extensive hit-and-trail experimentation. This study addresses this issue by developing predictive models, such as the Gaussian Process Regression model, Decision Tree Regression model, Support Vector Machine model, and XGBoost Regression models. The input parameters were water (Kg/m3), cement (Kg/m3), silica fume (Kg/m3), fly ash (Kg/m3), coarse aggregate (Kg/m3 & mm for diameter), fine aggregate (Kg/m3 & mm for diameter), viscosity modifying agent (Kg/m3), fibers (Kg/m3), fiber properties (mm for diameter and MPa for strength), print speed (mm/sec), and nozzle area (mm2), while target properties were the flexural and tensile strength of concrete (MPa data from 25 literature studies were collected. The water/binder ratio used in the dataset ranged from 0.27 to 0.67. Different types of sands and fibers have been used, with fibers having a maximum length of 23 mm. Based upon the Coefficient of Determination (R2), Root Mean Square Error (RMSE), Mean Square Error (MSE), and Mean Absolute Error (MAE) for casted and printed concrete, the SVM model performed better than other models. All models’ cast and printed flexural strength values were also correlated. The model’s performance has also been checked on six different mix proportions from the dataset to show its accuracy. It is worth noting that the lack of ML-based predictive models for the flexural and tensile properties of 3D-printed concrete in the literature makes this study a novel innovation in the field. This model could reduce the computational and experimental effort required to formulate the mixed design of printed concrete. Full article
(This article belongs to the Special Issue Design and Properties of 3D Printing Concrete)
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16 pages, 5466 KiB  
Article
Co-Doped CeO2/Activated C Nanocomposite Functionalized with Ionic Liquid for Colorimetric Biosensing of H2O2 via Peroxidase Mimicking
by Abdul Khaliq, Ruqia Nazir, Muslim Khan, Abdur Rahim, Muhammad Asad, Mohibullah Shah, Mansoor Khan, Riaz Ullah, Essam A. Ali, Ajmir Khan and Umar Nishan
Molecules 2023, 28(8), 3325; https://doi.org/10.3390/molecules28083325 - 9 Apr 2023
Cited by 18 | Viewed by 2953
Abstract
Hydrogen peroxide acts as a byproduct of oxidative metabolism, and oxidative stress caused by its excess amount, causes different types of cancer. Thus, fast and cost-friendly analytical methods need to be developed for H2O2. Ionic liquid (IL)-coated cobalt (Co)-doped [...] Read more.
Hydrogen peroxide acts as a byproduct of oxidative metabolism, and oxidative stress caused by its excess amount, causes different types of cancer. Thus, fast and cost-friendly analytical methods need to be developed for H2O2. Ionic liquid (IL)-coated cobalt (Co)-doped cerium oxide (CeO2)/activated carbon (C) nanocomposite has been used to assess the peroxidase-like activity for the colorimetric detection of H2O2. Both activated C and IL have a synergistic effect on the electrical conductivity of the nanocomposites to catalyze the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB). The Co-doped CeO2/activated C nanocomposite has been synthesized by the co-precipitation method and characterized by UV–Vis spectrophotometry, FTIR, SEM, EDX, Raman spectroscopy, and XRD. The prepared nanocomposite was functionalized with IL to avoid agglomeration. H2O2 concentration, incubation time, pH, TMB concentration, and quantity of the capped nanocomposite were tuned. The proposed sensing probe gave a limit of detection of 1.3 × 10−8 M, a limit of quantification of 1.4 × 10−8 M, and an R2 of 0.999. The sensor gave a colorimetric response within 2 min at pH 6 at room temperature. The co-existing species did not show any interference during the sensing probe. The proposed sensor showed high sensitivity and selectivity and was used to detect H2O2 in cancer patients’ urine samples. Full article
(This article belongs to the Section Materials Chemistry)
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17 pages, 3416 KiB  
Article
Design and Modelling of Graphene-Based Flexible 5G Antenna for Next-Generation Wearable Head Imaging Systems
by Asad Riaz, Sagheer Khan and Tughrul Arslan
Micromachines 2023, 14(3), 610; https://doi.org/10.3390/mi14030610 - 6 Mar 2023
Cited by 15 | Viewed by 3901
Abstract
Arguably, 5G and next-generation technology with its key features (specifically, supporting high data rates and high mobility platforms) make it valuable for coping with the emerging needs of medical healthcare. A 5G-enabled portable device receives the sensitive detection signals from the head imaging [...] Read more.
Arguably, 5G and next-generation technology with its key features (specifically, supporting high data rates and high mobility platforms) make it valuable for coping with the emerging needs of medical healthcare. A 5G-enabled portable device receives the sensitive detection signals from the head imaging system and transmits them over the 5G network for real-time monitoring, analysis, and storage purposes. In terms of material, graphene-based flexible electronics have become very popular for wearable and healthcare devices due to their exceptional mechanical strength, thermal stability, high electrical conductivity, and biocompatibility. A graphene-based flexible antenna for data communication from wearable head imaging devices over a 5G network was designed and modelled. The antenna operated at the 34.5 GHz range and was designed using an 18 µm thin graphene film for the conductive radiative patch and ground with electric conductivity of 3.5 × 105 S/m. The radiative patch was designed in a fractal fashion to provide sufficient antenna flexibility for wearable uses. The patch was designed over a 1.5 mm thick flexible polyamide substrate that made the design suitable for wearable applications. This paper presented the 3D modelling and analysis of the 5G flexible antenna for communication in a digital care-home model. The analyses were carried out based on the antenna’s reflection coefficient, gain, radiation pattern, and power balance. The time-domain signal analysis was carried out between the two antennas to mimic real-time communication in wearable devices. Full article
(This article belongs to the Special Issue Recent Advances in Flexible Sensors)
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14 pages, 2975 KiB  
Article
Fabrication and Characterization of Dextranase Nano-Entrapped Enzymes in Polymeric Particles Using a Novel Ultrasonication–Microwave Approach
by Mohanad Bashari, Hani Ahmed, Ayman Balla Mustafa, Asad Riaz, Jinpeng Wang, Salina Yahya Saddick, Abdulkader Shaikh Omar, Mohamed Afifi, Ammar Al-Farga, Lulwah Zeyad AlJumaiah, Mohammed A. S. Abourehab, Amany Belal and Mohamed Y. Zaky
Catalysts 2023, 13(1), 125; https://doi.org/10.3390/catal13010125 - 5 Jan 2023
Cited by 1 | Viewed by 2408
Abstract
In the current study, a novel method to improve the nano-entrapment of enzymes into Ca-alginate gel was investigated to determine the synergistic effects of ultrasound combined with microwave shock (UMS). The effects of UMS treatment on dextranase enzymes’ loading effectiveness (LE) and immobilization [...] Read more.
In the current study, a novel method to improve the nano-entrapment of enzymes into Ca-alginate gel was investigated to determine the synergistic effects of ultrasound combined with microwave shock (UMS). The effects of UMS treatment on dextranase enzymes’ loading effectiveness (LE) and immobilization yield (IY) were investigated. By using FT-IR spectra and SEM, the microstructure of the immobilized enzyme (IE) was characterized. Additionally, the free enzyme was used as a control to compare the reusability and enzyme-kinetics characteristics of IEs produced with and without UMS treatments. The results demonstrated that the highest LE and IY were obtained when the IE was produced with a US of 40 W at 25 kHz for 15 min combined with an MS of 60 W at a shock rate of 20 s/min for 20 min, increasing the LE and the IY by 97.32 and 78.25%, respectively, when compared with an immobilized enzyme prepared without UMS treatment. In comparison with the control, UMS treatment dramatically raised the Vmax, KM, catalytic, and specificity constant values for the IE. The outcomes suggested that a microwave shock and ultrasound combination would be an efficient way to improve the immobilization of enzymes in biopolymer gel. Full article
(This article belongs to the Section Biocatalysis)
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31 pages, 2299 KiB  
Article
Sensitive Demonstration of the Twin-Core Couplers including Kerr Law Non-Linearity via Beta Derivative Evolution
by Adeel Asad, Muhammad Bilal Riaz and Yanfeng Geng
Fractal Fract. 2022, 6(12), 697; https://doi.org/10.3390/fractalfract6120697 - 24 Nov 2022
Cited by 5 | Viewed by 1742
Abstract
To obtain new solitary wave solutions for non-linear directional couplers using optical meta-materials, a new extended direct algebraic technique (EDAT) is used. This model investigates solitary wave propagation inside a fiber. As a result, twin couplers are the subject of this study. Kerr [...] Read more.
To obtain new solitary wave solutions for non-linear directional couplers using optical meta-materials, a new extended direct algebraic technique (EDAT) is used. This model investigates solitary wave propagation inside a fiber. As a result, twin couplers are the subject of this study. Kerr law is the sort of non-linearity addressed there. Because it offers solutions to problems with large tails or infinite fluctuations, the resulting solution set is more generalized than the current solution because it is turned into a fractional-order derivative. Furthermore, the found solutions are fractional solitons with spatial–temporal fractional beta derivative evolution. In intensity-dependent switches, these nonlinear directional couplers also serve as limiters. Non-linearity alters the transmission constants of a system’s modes. The significance of the beta derivative parameter and mathematical approach is demonstrated graphically, with a few of the extracted solutions. A parametric analysis revealed that the fractional beta derivative parameter has a significant impact on the soliton amplitudes. With the aid of the advanced software tools for numerical computations, the categories of semi-dark solitons, singular dark-pitch solitons, single solitons of Type-1 along with 2, intermingled hyperbolically, trigonometric, and rational solitons were established and evaluated. We also discussed sensitivity analysis, which is an inquiry that determines how sensitive our system is. A comparative investigation via different fractional derivatives was also studied in this paper so that one can easily understand the correlation with other fractional derivatives. The findings demonstrate that the approach is simple and efficient and that it yields generalized analytical results. The findings will be extremely beneficial in examining and comprehending physical issues in nonlinear optics, specifically in twin-core couplers with optical metamaterials. Full article
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20 pages, 4054 KiB  
Article
Advanced Modulation Scheme of a Dual-Active-Bridge Series Resonant Converter (DABSRC) for Enhanced Performance
by Asad Hameed, Ali Nauman, Munleef Quadir, Irfan Latif Khan, Adeel Iqbal, Riaz Hussain and Tahir Khurshaid
Mathematics 2022, 10(23), 4402; https://doi.org/10.3390/math10234402 - 22 Nov 2022
Cited by 1 | Viewed by 2649
Abstract
This paper proposes a two-degree-of-freedom (2-DoF) modulation technique for the efficient optimization of an open-loop three-phase dual-active-bridge series resonant converter (3P-DABSRC). The efficiency and performance of an conventional dual-active-bridge (DAB) converter decrease when it is operated over a wide range of voltage gain. [...] Read more.
This paper proposes a two-degree-of-freedom (2-DoF) modulation technique for the efficient optimization of an open-loop three-phase dual-active-bridge series resonant converter (3P-DABSRC). The efficiency and performance of an conventional dual-active-bridge (DAB) converter decrease when it is operated over a wide range of voltage gain. The efficiency and performance of a DAB converter depend upon the switching and conduction losses. Circulating current is the main cause of conduction loss, and hard switching of active switches adds a switching loss. To increase the performance of DAB converters, the first objective is to minimize the conduction loss, and the second objective is to reduce the switching loss. Still, unfortunately, it is not easy to achieve these two objectives simultaneously. Circulating current helps us to reduce the switching loss, but the unbridled amount of circulating current will increase the root-mean-square inductor tank current, and as a result, the conduction loss will be increased. This paper presents an advanced modulation scheme for a 3P-DABSRC that can be used not only in low-power applications, but also in high-power applications. The DABSRC consists of a series LC resonant tank, isolated high-frequency transformer, and dual active bridge connected with the primary and secondary sides of the transformer. The proposed 2-DoF modulation technique not only minimizes the circulating current, but also eliminates the switching loss. Keeping the minimum phase shift between the primary and secondary bridges reduces the circulating current, and thus, all switches can be operated with zero-voltage switching (ZVS) for the entire power range. The power is controlled by changing the switching frequency from 45 to 63 kHz. To confirm the proposed topology and modulation scheme, a 1500 W DABSRC, which interfaces a 300 V DC bus with a 75 V DC bus, is simulated. A loss model of the proposed topology is also made to verify the results. The simulation results are used to confirm the proper operation of the 3P-DABSRC. Full article
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24 pages, 3867 KiB  
Article
Genome-Based Multi-Antigenic Epitopes Vaccine Construct Designing against Staphylococcus hominis Using Reverse Vaccinology and Biophysical Approaches
by Mahreen Nawaz, Asad Ullah, Alhanouf I. Al-Harbi, Mahboob Ul Haq, Alaa R. Hameed, Sajjad Ahmad, Aamir Aziz, Khadija Raziq, Saifullah Khan, Muhammad Irfan and Riaz Muhammad
Vaccines 2022, 10(10), 1729; https://doi.org/10.3390/vaccines10101729 - 16 Oct 2022
Cited by 10 | Viewed by 3886
Abstract
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for [...] Read more.
Staphylococcus hominis is a Gram-positive bacterium from the staphylococcus genus; it is also a member of coagulase-negative staphylococci because of its opportunistic nature and ability to cause life-threatening bloodstream infections in immunocompromised patients. Gram-positive and opportunistic bacteria have become a major concern for the medical community. It has also drawn the attention of scientists due to the evaluation of immune evasion tactics and the development of multidrug-resistant strains. This prompted the need to explore novel therapeutic approaches as an alternative to antibiotics. The current study aimed to develop a broad-spectrum, multi-epitope vaccine to control bacterial infections and reduce the burden on healthcare systems. A computational framework was designed to filter the immunogenic potent vaccine candidate. This framework consists of pan-genomics, subtractive proteomics, and immunoinformatics approaches to prioritize vaccine candidates. A total of 12,285 core proteins were obtained using a pan-genome analysis of all strains. The screening of the core proteins resulted in the selection of only two proteins for the next epitope prediction phase. Eleven B-cell derived T-cell epitopes were selected that met the criteria of different immunoinformatics approaches such as allergenicity, antigenicity, immunogenicity, and toxicity. A vaccine construct was formulated using EAAAK and GPGPG linkers and a cholera toxin B subunit. This formulated vaccine construct was further used for downward analysis. The vaccine was loop refined and improved for structure stability through disulfide engineering. For an efficient expression, the codons were optimized as per the usage pattern of the E coli (K12) expression system. The top three refined docked complexes of the vaccine that docked with the MHC-I, MHC-II, and TLR-4 receptors were selected, which proved the best binding potential of the vaccine with immune receptors; this was followed by molecular dynamic simulations. The results indicate the best intermolecular bonding between immune receptors and vaccine epitopes and that they are exposed to the host’s immune system. Finally, the binding energies were calculated to confirm the binding stability of the docked complexes. This work aimed to provide a manageable list of immunogenic and antigenic epitopes that could be used as potent vaccine candidates for experimental in vivo and in vitro studies. Full article
(This article belongs to the Special Issue Advances in Epitope-Based Vaccine Design)
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19 pages, 4823 KiB  
Article
Phytohormones and Transcriptome Analyses Revealed the Dynamics Involved in Spikelet Abortion and Inflorescence Development in Rice
by Asif Ali, Tingkai Wu, Zhengjun Xu, Asad Riaz, Ahmad M. Alqudah, Muhammad Zafar Iqbal, Hongyu Zhang, Yongxiang Liao, Xiaoqiong Chen, Yutong Liu, Tahir Mujtaba, Hao Zhou, Wenming Wang, Peizhou Xu and Xianjun Wu
Int. J. Mol. Sci. 2022, 23(14), 7887; https://doi.org/10.3390/ijms23147887 - 17 Jul 2022
Cited by 7 | Viewed by 3671
Abstract
Panicle degeneration, sometimes known as abortion, causes heavy losses in grain yield. However, the mechanism of naturally occurring panicle abortion is still elusive. In a previous study, we characterized a mutant, apical panicle abortion1331 (apa1331), exhibiting abortion in apical spikelets starting from the [...] Read more.
Panicle degeneration, sometimes known as abortion, causes heavy losses in grain yield. However, the mechanism of naturally occurring panicle abortion is still elusive. In a previous study, we characterized a mutant, apical panicle abortion1331 (apa1331), exhibiting abortion in apical spikelets starting from the 6 cm stage of panicle development. In this study, we have quantified the five phytohormones, gibberellins (GA), auxins (IAA), abscisic acid (ABA), cytokinins (CTK), and brassinosteroids (BR), in the lower, middle, and upper parts of apa1331 and compared these with those exhibited in its wild type (WT). In apa331, the lower and middle parts of the panicle showed contrasting concentrations of all studied phytohormones, but highly significant changes in IAA and ABA, compared to the upper part of the panicle. A comparative transcriptome of apa1331 and WT apical spikelets was performed to explore genes causing the physiological basis of spikelet abortion. The differential expression analysis revealed a significant downregulation and upregulation of 1587 and 978 genes, respectively. Hierarchical clustering of differentially expressed genes (DEGs) revealed the correlation of gene ontology (GO) terms associated with antioxidant activity, peroxidase activity, and oxidoreductase activity. KEGG pathway analysis using parametric gene set enrichment analysis (PGSEA) revealed the downregulation of the biological processes, including cell wall polysaccharides and fatty acids derivatives, in apa1331 compared to its WT. Based on fold change (FC) value and high variation in expression during late inflorescence, early inflorescence, and antherdevelopment, we predicted a list of novel genes, which presumably can be the potential targets of inflorescence development. Our study not only provides novel insights into the role of the physiological dynamics involved in panicle abortion, but also highlights the potential targets involved in reproductive development. Full article
(This article belongs to the Section Molecular Plant Sciences)
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22 pages, 6424 KiB  
Article
Mechanical Performance of Amorphous Metallic Fiber-Reinforced and Rubberized Thin Bonded Cement-Based Overlays
by Ayesha Javed, Syed Asad Ali Gillani, Wasim Abbass, Muhammad Rizwan Riaz, Rashid Hameed, Safeer Abbas, Abdelatif Salmi and Ahmed Farouk Deifalla
Sustainability 2022, 14(13), 8226; https://doi.org/10.3390/su14138226 - 5 Jul 2022
Cited by 5 | Viewed by 2791
Abstract
To improve the flexural behavior of thin bonded cement-based overlays, this study was carried out on the use of repair material incorporating amorphous metallic fibers (AMFs) in combination with the rubber aggregates obtained from grinding of worn-out tires. For this study, sixteen mortar [...] Read more.
To improve the flexural behavior of thin bonded cement-based overlays, this study was carried out on the use of repair material incorporating amorphous metallic fibers (AMFs) in combination with the rubber aggregates obtained from grinding of worn-out tires. For this study, sixteen mortar mix compositions were prepared to contain AMFs and/or rubber aggregates to be used as overlay material while the substrate used was plain cement mortar. Rubber aggregates were incorporated at three different replacement ratios (i.e., 10%, 20% and 30%) by an equivalent volume of sand, and AMFs were added in three different dosages (i.e., 10 kg/m3, 20 kg/m3 and 30 kg/m3). In this study, composite beams (500 × 100 × 140 mm) comprising substrate (500 × 100 × 100 mm) and repair layer (500 × 100 × 40 mm) were prepared and investigated under flexural loading. Experimental results showed that the increase in rubber content resulted in a decrease compressive strength, flexural strength and modulus of elasticity. Rubberized fiber-reinforced cementitious composites (30R30F) exhibited higher flexural toughness and the flexural toughness improved up to 400%. Toughness and maximum deflection of composite beams enhanced significantly due to synergetic effect of AMF and rubber aggregates. It was observed that before peak load, rubber plays its role by delaying the micro-crack propagation. Results also revealed that the steel fibers reinforcement plays an important role in restraining the crack openings under flexure loading. In the post-peak region, steel fibers control the cracks from propagating further by bridging action and provide higher post-peak residual strength. Full article
(This article belongs to the Special Issue Concrete with Recycled and Sustainable Materials)
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16 pages, 5030 KiB  
Article
Biological Mineralization of Methyl Orange by Pseudomonas aeruginosa
by Asad Ullah Khan, Muhammad Zahoor, Mujaddad Ur Rehman, Abdul Bari Shah, Ivar Zekker, Farhat Ali Khan, Riaz Ullah, Ghadeer M. Albadrani, Roula Bayram and Hanan R. H. Mohamed
Water 2022, 14(10), 1551; https://doi.org/10.3390/w14101551 - 12 May 2022
Cited by 58 | Viewed by 6300
Abstract
Due to its recalcitrant and carcinogenic nature, the presence of methyl orange (MO) in the environment is a serious threat to human and animal life and is also toxic to plants. MO being recalcitrant cannot be effectively reclaimed from industrial effluents through physical [...] Read more.
Due to its recalcitrant and carcinogenic nature, the presence of methyl orange (MO) in the environment is a serious threat to human and animal life and is also toxic to plants. MO being recalcitrant cannot be effectively reclaimed from industrial effluents through physical and chemical approaches. Biological methods on the other hand have the potential to degrade such dyes because of their compatibility with nature and low chances of adverse effects on the environment. Bacteria, due to their fast growth rate and capability of surviving in extreme environments can effectively be used for this purpose. In the current research study, Pseudomonas aeruginosa was isolated and characterized using 16rRNA from textile wastewater. In the preliminary tests it was found that Pseudomonas aeruginosa has the ability to degrade and mineralize methyl orange effectively. The physicochemical conditions were then optimized, in order to get maximum degradation of MO which was achieved at 37 °C, a pH of 7, a low salt concentration of 0.1 g/15 mL, a high carbon source of 0.6 g/15 mL, and 72 h experimental time. In a single set of experiments where all these optimum conditions were combined, 88.23% decolorization of the selected dye was achieved. At the end of the experimental cycle, the aliquots were homogenized and filtered. The filtrates were subjected to FTIR and GC-MS analysis where azo linkage breaking was confirmed from the FTIR spectra. The filtrates were then extracted with ethyl acetate and then passed through a silica gel column. On the basis of Rf value (TLC plates used) similar fraction were combined which were then subjected to NMR analysis. The compounds detected through GC-MS, peaks were not observed in proton and C-13 NMR. Instead, solvent and some impurity peaks were present, showing that complete mineralization of the dye had occurred due to the action of different bacterial enzymes such as azoreductase, peroxidases, and classes on MO. The prosed mechanism of complete mineralization is based on spectral data that needs to be verified by trapping the individual step products through the use of appropriate inhibitors of individual enzymes. Full article
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