Search results for: molecular dynamics

Authors: Alaa M. M. Badr Eldin, Marwa I. Ezzat, Mohammed S. Sedeek, Manal S. Afifi, Omar M. Sabry

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Cytotoxic activity of the total methanol extract against breast cancer cell line MCF-7 was amazing IC50 at 54 ug/ml. 130 polyphenolic compounds were tentatively identified in pomegranate peel (Punica granatum L.) methanol extract using HPLC-MS/MS technique. The antiestrogenic activity of the polyphenolic constituents found in pomegranate extract was confirmed experimentally in-vitro and by the in-silico molecular docking using gallagic acid, ellagic acid, and Punicalagin as these are considered model compounds confirmed in pomegranate peel extract. The methanolic extract was found to suppress ER, TGF-β, and NF-kB in-vitro gene expression strongly, and that was verified by qPCR and Western Blot gel electrophoresis techniques.

Keywords: HPLC-MS/MS, pomegranate, breast cancer, ovarian cancer, ER, TGF-β, NF-kB

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Authors: Zdzislaw Kaminski, Zbigniew Czyz, Krzysztof Skiba

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This paper discusses the CFD simulation of a flow around a rotor of a Vertical Axis Wind Turbine. Numerical simulation, unlike experiments, enables us to validate project assumptions when it is designed and avoid a costly preparation of a model or a prototype for a bench test. CFD simulation enables us to compare characteristics of aerodynamic forces acting on rotor working surfaces and define operational parameters like torque or power generated by a turbine assembly. This research focused on the rotor with the blades capable of modifying their working surfaces, i.e. absorbing wind kinetic energy. The operation of this rotor is based on adjusting angular aperture α of the top and bottom parts of the blades mounted on an axis. If this angular aperture α increases, the working surface which absorbs wind kinetic energy also increases. The operation of turbines is characterized by parameters like the angular aperture of blades, power, torque, speed for a given wind speed. These parameters have an impact on the efficiency of assemblies. The distribution of forces acting on the working surfaces in our turbine changes according to the angular velocity of the rotor. Moreover, the resultant force from the force acting on an advancing blade and retreating blade should be as high as possible. This paper is part of the research to improve an efficiency of a rotor assembly. Therefore, using simulation, the courses of the above parameters were studied in three full rotations individually for each of the blades for three angular apertures of blade working surfaces, i.e. 30 °, 60 °, 90 °, at three wind speeds, i.e. 4 m / s, 6 m / s, 8 m / s and rotor speeds ranging from 100 to 500 rpm. Finally, there were created the characteristics of torque coefficients and power as a function of time for each blade separately and for the entire rotor. Accordingly, the correlation between the turbine rotor power as a function of wind speed for varied values of rotor rotational speed. By processing this data, the correlation between the power of the turbine rotor and its rotational speed for each of the angular aperture of the working surfaces was specified. Finally, the optimal values, i.e. of the highest output power for given wind speeds were read. The research results in receiving the basic characteristics of turbine rotor power as a function of wind speed for the three angular apertures of the blades. Given the nature of rotor operation, the growth in the output turbine can be estimated if angular aperture of the blades increases. The controlled adjustment of angle α enables a smooth adjustment of power generated by a turbine rotor. If wind speed is significant, this type of adjustment enables this output power to remain at the same level (by reducing angle α) with no risk of damaging a construction. This work has been financed by the Polish Ministry of Science and Higher Education.

Keywords: computational fluid dynamics, numerical analysis, renewable energy, wind turbine

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Authors: H. Nacef, L. Larous

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Salin soils occupy about 7% of land area; they are characterized by unsuitable physical conditions for the growth of living organisms. However, researches showed that some microorganisms especially fungi are able to grow and adapt to such extreme conditions; it is due to their ability to develop different physiological mechanisms in their adaptation. The aim of this study is to identify qualitatively the osmolytes that the biotechnological important fungus A. oryzae accumulated and/or produced in its adaptation, which they were detected by Thin-layer chromatography technique (TLC) using several systems, from different media (Wheat brane, MNM medium and MM medium). The results showed that The moderately halotolerant fungus A. oryzae, accumulates mixture of molecules, containing polyols and sugars , some amino acids in addition to some molecules which were not defined. Wheat bran was the best medium for the extraction of these molecules, where the proportion was 85.71%, followed by MNM medium 64.28%, then the minimum medium MM 14.28%. Properties of osmolytes are becoming increasingly useful in molecular biology, agriculture pharmaceutical, medicinal, and biotechnological interests.

Keywords: salinity, aspergillus oryzae, halo tolerance, osmolytes, compatible solutes

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Authors: Rim Ben Kalifa, Sabra Habli, Nejla Mahjoub Saïd, Hervé Bournot, Georges Le Palec

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The present study treats different phenomena taking place in a configuration of air jet impinging on a flat surface in a coflow stream. A Computational Fluid Dynamics study is performed using the Reynolds-averaged Navier–Stokes equations by means of the Reynolds Stress Model (RSM) second order turbulent closure model. The results include mean and turbulent velocities and quantify the large effects of the coflow stream on an impinging air jet. The study of the jet in a no-directed coflow stream shows the presence of a phenomenon of recirculation near the flat plate. The influence of the coflow velocity ratio on the behavior of an impinging plane jet was also numerically investigated. The coflow stream imposed noticeable restrictions on the spreading of the impinging jet. The results show that the coflow stream decreases considerably the entrainment of air jet.

Keywords: turbulent jet, turbulence models, coflow stream, velocity ratio

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Authors: Xiaolin Tang, Wei Yang, Xiaoan Chen

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The research described in this paper was aimed at exploring the torsional vibration characteristics of a power-split hybrid powertrain equipped with a dual mass flywheel. The dynamic equations of governing torsional vibration for this hybrid driveline are presented, and the multi-body dynamic model for the powertrain is established with the software of ADAMS. Accordingly, different parameters of dual mass flywheel are investigated by forced vibration to reduce the torsional vibration of hybrid drive train. The analysis shows that the implementation of a dual mass flywheel is an effective way to decrease the torsional vibration of the hybrid powertrain. At last, the optimal combination of parameters yielding the lowest vibration is provided.

Keywords: dual mass flywheel, hybrid electric vehicle, torsional vibration, powertrain, dynamics

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Authors: Pakize Ozlem Kurt Polat

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GMO (genetically modified organism) is the result of a laboratory process where genes from the DNA of one species are extracted and artificially forced into the genes of an unrelated plant or animal. This technology includes; nucleic acid hybridization, recombinant DNA, RNA, PCR, cell culture and gene cloning techniques. The studies are divided into three groups of properties transferred to the transgenic plant. Up to 59% herbicide resistance characteristic of the transfer, 28% resistance to insects and the virus seems to be related to quality characteristics of 13%. Transgenic crops are not included in the commercial production of each product; mostly commercial plant is soybean, maize, canola, and cotton. Day by day increasing GMO interest can be listed as follows; Use in the health area (Organ transplantation, gene therapy, vaccines and drug), Use in the industrial area (vitamins, monoclonal antibodies, vaccines, anti-cancer compounds, anti -oxidants, plastics, fibers, polyethers, human blood proteins, and are used to produce carotenoids, emulsifiers, sweeteners, enzymes , food preservatives structure is used as a flavor enhancer or color changer),Use in agriculture (Herbicide resistance, Resistance to insects, Viruses, bacteria, fungi resistance to disease, Extend shelf life, Improving quality, Drought , salinity, resistance to extreme conditions such as frost, Improve the nutritional value and quality), we explain all this methods step by step in this research. GMO has advantages and disadvantages, which we explain all of them clearly in full text, because of this topic, worldwide researchers have divided into two. Some researchers thought that the GMO has lots of disadvantages and not to be in use, some of the researchers has opposite thought. If we look the countries law about GMO, we should know Biosafety law for each country and union. For this Biosecurity reasons, the problems caused by the transgenic plants, including Turkey, to minimize 130 countries on 24 May 2000, ‘the United Nations Biosafety Protocol’ signed nudes. This protocol has been prepared in addition to Cartagena Biosafety Protocol entered into force on September 11, 2003. This protocol GMOs in general use by addressing the risks to human health, biodiversity and sustainable transboundary movement of all GMOs that may affect the prevention, transit covers were dealt and used. Under this protocol we have to know the, ‘US Regulations GMO’, ‘European Union Regulations GMO’, ‘Turkey Regulations GMO’. These three different protocols have different applications and rules. World population increasing day by day and agricultural fields getting smaller for this reason feeding human and animal we should improve agricultural product yield and quality. Scientists trying to solve this problem and one solution way is molecular biotechnology which is including the methods of GMO too. Before decide to support or against the GMO, should know the GMO protocols and it effects.

Keywords: biotechnology, GMO (genetically modified organism), molecular marker

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Authors: Arpit Patil, Atharav Bhagwat, Rajas Bhope, Pramod Bide

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This research integrates IoT and ML to predict heart failure risks, utilizing the Framingham dataset. IoT devices gather real-time physiological data, focusing on heart rate dynamics, while ML, specifically Random Forest, predicts heart failure. Rigorous feature selection enhances accuracy, achieving over 90% prediction rate. This amalgamation marks a transformative step in proactive healthcare, highlighting early detection's critical role in cardiovascular risk mitigation. Challenges persist, necessitating continual refinement for improved predictive capabilities.

Keywords: cardiovascular diseases, internet of things, machine learning, cardiac risk assessment, heart failure prediction, early detection, cardio data analysis

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Authors: Aran Abd Al Rahman

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Joubert syndrome regards as a congenital cerebellar ataxia caused by autosomal recessive carried on X chromosome. The disease diagnosed by brain imaging—the so-called molar tooth sign. Neurological signs were present from the neonatal period and include hypotonia progressing to ataxia, global developmental delay, ocular motor apraxia, and breathing dysregulation. These signs are variably associated with multiorgan involvement, mainly of the retina, kidneys, skeleton, and liver. 30 causative genes have been identified so far, all of which encode for proteins of the primary cilium or its apparatus, The purpose of our project was to detect the mutant gene (INPP5E gene) which cause Joubert syndrome. There were many methods used for diagnosis such as MRI and CT- scan and molecular diagnosis by doing ARMS PCR for detection of mutant gene that we were used in this research project. In this research for individual family which reported, the two children with parents, the two children were affected and were carrier.

Keywords: Joubert syndrome, genetic disease, Kurdistan region, Sulaimani

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Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: Vinay Kumar Vanjakula, Frank Adam

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The generation of electricity through wind power is one of the leading renewable energy generation methods. Due to abundant higher wind speeds far away from shore, the construction of offshore wind turbines began in the last decades. However, the installation of offshore foundation-based (monopiles) wind turbines in deep waters are often associated with technical and financial challenges. To overcome such challenges, the concept of floating wind turbines is expanded as the basis of the oil and gas industry. For such a floating system, stabilization in harsh conditions is a challenging task. For that, a robust heavy-weight gravity anchor is needed. Transportation of such anchor requires a heavy vessel that increases the cost. To lower the cost, the gravity anchor is designed with ballast chambers that allow the anchor to float while towing and filled with water when lowering to the planned seabed location. The presence of such a large structure may influence the flow field around it. The changes in the flow field include, formation of vortices, turbulence generation, waves or currents flow breaking and pressure differentials around the seabed sediment. These changes influence the installation process. Also, after installation and under operating conditions, the flow around the anchor may allow the local seabed sediment to be carried off and results in Scour (erosion). These are a threat to the structure's stability. In recent decades, rapid developments of research work and the knowledge of scouring on fixed structures (bridges and monopiles) in rivers and oceans have been carried out, and very limited research work on scouring around a bluff-shaped gravity anchor. The objective of this study involves the application of different numerical models to simulate the anchor towing under waves and calm water conditions. Anchor lowering involves the investigation of anchor movements at certain water depths under wave/current. The motions of anchor drift, heave, and pitch is of special focus. The further study involves anchor scour, where the anchor is installed in the seabed; the flow of underwater current around the anchor induces vortices mainly at the front and corners that develop soil erosion. The study of scouring on a submerged gravity anchor is an interesting research question since the flow not only passes around the anchor but also over the structure that forms different flow vortices. The achieved results and the numerical model will be a basis for the development of other designs and concepts for marine structures. The Computational Fluid Dynamics (CFD) numerical model will build in OpenFOAM and other similar software.

Keywords: anchor lowering, anchor towing, gravity anchor, computational fluid dynamics, scour

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Authors: J. Fernandez, N. Aguilar, R. Fernandez de Canete, J. C. Ramos-Diaz

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In this paper, a simulation model of the glucose-insulin system for a patient undergoing diabetes Type 1 is developed by using a causal modeling approach under system dynamics. The OpenModelica simulation environment has been employed to build the so called causal model, while the glucose-insulin model parameters were adjusted to fit recorded mean data of a diabetic patient database. Model results under different conditions of a three-meal glucose and exogenous insulin ingestion patterns have been obtained. This simulation model can be useful to evaluate glucose-insulin performance in several circumstances, including insulin infusion algorithms in open-loop and decision support systems in closed-loop.

Keywords: causal modeling, diabetes, glucose-insulin system, diabetes, causal modeling, OpenModelica software

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Authors: Nusrat Masood, Vijaya Dubey, Suaib Luqman

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Caspase 3, a member of cysteine-aspartic acid protease family, is an imperative indicator for cell death particularly when substantiating apoptosis. Thus, caspase 3 is an interesting target for the discovery and development of anticancer agent. We adopted a four level assessment of both terpenoids and flavonoids and thus experimentally performed the enzymatic assay in cell free system as well as in cancer cell line which was validated through real time expression and molecular interaction studies. A significant difference was observed with both the class of natural products indicating terpenoids as better activators of caspase 3 compared to flavonoids both in the cell free system as well as in cell lines. The expression analysis, activation constant and binding energy also correlate well with the enzyme activity. Overall, terpenoids had an unswerving effect on caspase 3 in all the tested system while flavonoids indirectly affect enzyme activity.

Keywords: Caspase 3, terpenoids, flavonoids, activation constant, binding energy

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Authors: Nourhan Hussein Fanaki, Hoda Mohamed Gamal El-Din Omar, Nihal Kadry Moussa, Eva Adel Edward Farid

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The resistance of staphylococci to various antibiotics has become a major concern for health care professionals. The efficacy of the combinations of selected glycopeptides (vancomycin and teicoplanin) with gentamicin or rifampicin, as well as that of gentamicin/rifampicin combination, was studied against selected pathogenic staphylococcus isolated from Egypt. The molecular distribution of genes conferring resistance to these four antibiotics was detected among tested clinical isolates. Antibiotic combinations were studied using the checkerboard technique and the time-kill assay (in both the stationary and log phases). Induction of resistance to glycopeptides in staphylococci was tried in the absence and presence of diclofenac sodium as inducer. Transmission electron microscopy was used to study the effect of glycopeptides on the ultrastructure of the cell wall of staphylococci. Attempts were made to cure gentamicin resistance plasmids and to study the transfer of these plasmids by conjugation. Trials for the transformation of the successfully isolated gentamicin resistance plasmid to competent cells were carried out. The detection of genes conferring resistance to the tested antibiotics was performed using the polymerase chain reaction. The studied antibiotic combinations proved their efficacy, especially when tested during the log phase. Induction of resistance to glycopeptides in staphylococci was more promising in presence of diclofenac sodium, compared to its absence. Transmission electron microscopy revealed the thickening of bacterial cell wall in staphylococcus clinical isolates due to the presence of tested glycopeptides. Curing of gentamicin resistance plasmids was only successful in 2 out of 9 tested isolates, with a curing rate of 1 percent for each. Both isolates, when used as donors in conjugation experiments, yielded promising conjugation frequencies ranging between 5.4 X 10-2 and 7.48 X 10-2 colony forming unit/donor cells. Plasmid isolation was only successful in one out of the two tested isolates. However, low transformation efficiency (59.7 transformants/microgram plasmid DNA) of such plasmids was obtained. Negative regulators of autolysis, such as arlR, lytR and lrgB, as well as cell-wall associated genes, such as pbp4 and/or pbp2, were detected in staphylococcus isolates with reduced susceptibility to the tested glycopeptides. Concerning rifampicin resistance genes, rpoBstaph was detected in 75 percent of the tested staphylococcus isolates. It could be concluded that in vitro studies emphasized the usefulness of the combination of vancomycin or teicoplanin with gentamicin or rifampicin, as well as that of gentamicin with rifampicin, against staphylococci showing varying resistance patterns. However, further in vivo studies are required to ensure the safety and efficacy of such combinations. Diclofenac sodium can act as an inducer of resistance to glycopeptides in staphylococci. Cell-wall thickness is a major contributor to such resistance among them. Gentamicin resistance in these strains could be chromosomally or plasmid mediated. Multiple mutations in the rpoB gene could mediate staphylococcus resistance to rifampicin.

Keywords: glycopeptides, combinations, induction, diclofenac, transmission electron microscopy, polymerase chain reaction

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Authors: Shiuh-Jer Huang, Shin-Ham Lee, Sheam-Chyun Lin

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A two wheel inverted pendulum (TWIP) vehicle is built with two hub DC motors for motion control evaluation. Arduino Nano micro-processor is chosen as the control kernel for this electric test plant. Accelerometer and gyroscope sensors are built in to measure the tilt angle and angular velocity of the inverted pendulum vehicle. Since the TWIP has significantly hub motor dead zone and nonlinear system dynamics characteristics, the vehicle system is difficult to control by traditional model based controller. The intelligent model-free fuzzy sliding mode controller (FSMC) was employed as the main control algorithm. Then, intelligent controllers are designed for TWIP balance control, and two wheels synchronization control purposes.

Keywords: balance control, synchronization control, two-wheel inverted pendulum, TWIP

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Authors: Hasan Jumaah Mrayeh, Fue-Sang Lien

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ANSYS Fluent will be used to simulate Computational Fluid Dynamics (CFD) for an efficient lens and nozzle design which will be explained in this paper. We have designed and characterized an aerodynamic lens and a divergent nozzle for focusing flow that transmits sub 25 nm particles through the aerodynamic lens. The design of the lens and nozzle has been improved using CFD for particle trajectories. We obtained a case for calculating nanoparticles (25 nm) flowing through the aerodynamic lens and divergent nozzle. Nanoparticles are transported by air, which is pumped into the aerodynamic lens through the nozzle at 1 atmospheric pressure. We have also developed a computational methodology that can determine the exact focus characteristics of aerodynamic lens systems. Particle trajectories were traced using the Lagrange approach. The simulation shows the ability of the aerodynamic lens to focus on 25 nm particles after using a divergent nozzle.

Keywords: aerodynamic lens, divergent nozzle, ANSYS Fluent, Lagrange approach

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Authors: Ujjwall Sai Sunder Uppuluri

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Group theory is a powerful tool that researchers can use to provide a structural foundation for their Agent Based Models. These Agent Based models are argued by this paper to be the future of the Social Science Disciplines. More specifically, researchers can use them to apply evolutionary theory to the study of complex social systems. This paper illustrates one such example of how theoretically an Agent Based Model can be formulated from the application of Group Theory, Systems Dynamics, and Evolutionary Biology to analyze the strategies pursued by states to mitigate risk and maximize usage of resources to achieve the objective of economic growth. This example can be applied to other social phenomena and this makes group theory so useful to the analysis of complex systems, because the theory provides the mathematical formulaic proof for validating the complex system models that researchers build and this will be discussed by the paper. The aim of this research, is to also provide researchers with a framework that can be used to model political entities such as states on a 3-dimensional plane. The x-axis representing resources (tangible and intangible) available to them, y the risks, and z the objective. There also exist other states with different constraints pursuing different strategies to climb the mountain. This mountain’s environment is made up of risks the state faces and resource endowments. This mountain is also layered in the sense that it has multiple peaks that must be overcome to reach the tallest peak. A state that sticks to a single strategy or pursues a strategy that is not conducive to the climbing of that specific peak it has reached is not able to continue advancement. To overcome the obstacle in the state’s path, it must innovate. Based on the definition of a group, we can categorize each state as being its own group. Each state is a closed system, one which is made up of micro level agents who have their own vectors and pursue strategies (actions) to achieve some sub objectives. The state also has an identity, the inverse being anarchy and/or inaction. Finally, the agents making up a state interact with each other through competition and collaboration to mitigate risks and achieve sub objectives that fall within the primary objective. Thus, researchers can categorize the state as an organism that reflects the sum of the output of the interactions pursued by agents at the micro level. When states compete, they employ a strategy and that state which has the better strategy (reflected by the strategies pursued by her parts) is able to out-compete her counterpart to acquire some resource, mitigate some risk or fulfil some objective. This paper will attempt to illustrate how group theory combined with evolutionary theory and systems dynamics can allow researchers to model the long run development, evolution, and growth of political entities through the use of a bottom up approach.

Keywords: complex systems, evolutionary theory, group theory, international political economy

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Authors: Omar S. Sharaf

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The mitochondrial 12s rRNA (mt-12s rDNA) gene for pig-specific was developed to detect material from pork species in different products collected from Jordanian market. The amplification PCR products of 359 bp and 531 bp were successfully amplified from the cyt b gene of pig the amplification product using mt-12S rDNA gene were successfully produced a single band with a molecular size of 456 bp. In the present work, the PCR amplification of mtDNA of cytochrome b has been shown as a suitable tool for rapid detection of pig DNA. 100 samples from different dairy, gelatin and chocolate based products and 50 samples from baby food formula were collected and tested to a presence of any pig derivatives. It was found that 10% of chocolate based products, 12% of gelatin and 56% from dairy products and 5.2% from baby food formula showed single band from mt-12S rDNA gene.

Keywords: halal food, baby infant formula, chocolate based products, PCR, Jordan

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Authors: Jie Lin, Yiwen Pan, Li Zhang, Zhangyong Xia

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Atherosclerosis is a chronic inflammatory disease characterized by the accumulation of lipids, immune cells, and extracellular matrix in the arterial walls. This pathological process can lead to the formation of plaques that can obstruct blood flow and trigger various cardiovascular diseases such as heart attack and stroke. The underlying molecular mechanisms still remain unclear, although many studies revealed the dysfunction of endothelial cells, recruitment and activation of monocytes and macrophages, and the production of pro-inflammatory cytokines and chemokines in atherosclerosis. This study aimed to identify hub genes involved in the progression of atherosclerosis and to analyze their biological function in silico, thereby enhancing our understanding of the disease’s molecular mechanisms. Through the analysis of microarray data, we examined the gene expression in media and neo-intima from plaques, as well as distant macroscopically intact tissue, across a cohort of 32 hypertensive patients. Initially, 112 differentially expressed genes (DEGs) were identified. Subsequent immune infiltration analysis indicated a predominant presence of 27 immune cell types in the atherosclerosis group, particularly noting an increase in monocytes and macrophages. In the Weighted gene co-expression network analysis (WGCNA), 10 modules with a minimum of 30 genes were defined as key modules, with blue, dark, Oliver green and sky-blue modules being the most significant. These modules corresponded respectively to monocyte, activated B cell, and activated CD4 T cell gene patterns, revealing a strong morphological-genetic correlation. From these three gene patterns (modules morphology), a total of 2509 key genes (Gene Significance >0.2, module membership>0.8) were extracted. Six hub genes (CD36, DPP4, HMOX1, PLA2G7, PLN2, and ACADL) were then identified by intersecting 2509 key genes, 102 DEGs with lipid-related genes from the Genecard database. The bio-functional analysis of six hub genes was estimated by a robust classifier with an area under the curve (AUC) of 0.873 in the ROC plot, indicating excellent efficacy in differentiating between the disease and control group. Moreover, PCA visualization demonstrated clear separation between the groups based on these six hub genes, suggesting their potential utility as classification features in predictive models. Protein-protein interaction (PPI) analysis highlighted DPP4 as the most interconnected gene. Within the constructed key gene-drug network, 462 drugs were predicted, with ursodeoxycholic acid (UDCA) being identified as a potential therapeutic agent for modulating DPP4 expression. In summary, our study identified critical hub genes implicated in the progression of atherosclerosis through comprehensive bioinformatic analyses. These findings not only advance our understanding of the disease but also pave the way for applying similar analytical frameworks and predictive models to other diseases, thereby broadening the potential for clinical applications and therapeutic discoveries.

Keywords: atherosclerosis, hub genes, drug prediction, bioinformatics

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Authors: Ahmed Bensreti, Mohamed Gouarsha

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This paper presents a review of the pressure surge simulations carried out for Phase III of the Man Made River project in Libya with particular emphasis on the transient generated by simultaneous pump trips at Al Gardabiya Pump Station. The omission of the surge vessel check valve and bypass system on the grounds of cost, ease of design, and construction will result in, as expected, increased surge fluctuations as the damping effect in the form was removed. From the hydraulic and control requirements, it is recommended for Al Gardabiya Pump station that the check valve and check valve bypass be included in the final surge vessel design.

Keywords: computational fluid dynamics, surge vessel design, transient surge analysis, water pipe hydraulics

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Authors: Julianne Mullen-Williams

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This paper will provide an overview of a three year mixed methods research project that explores if methods from the supervision of dramatherapy can augment the occupational psychology of newly qualified secondary school teachers. It will consider how creativity and the use of metaphor, as applied in the supervision of dramatherapists, can be translated to an educational context in order to explore the explicit / implicit dynamics between the teacher trainee/ newly qualified teacher and the organisation in order to support the super objective in training for teaching; how to ‘be a teacher.’ There is growing evidence that attrition rates among teachers are rising after only five years of service owing to too many national initiatives, an unmanageable curriculum and deteriorating student discipline. The fieldwork conducted entailed facilitating a reflective space for Newly Qualified Teachers from all subject areas, using methods from the supervision of dramatherapy, to explore the social and emotional aspects of teaching and learning with the ultimate aim of improving the occupational psychology of teachers. Clinical supervision is a formal process of professional support and learning which permits individual practitioners in frontline service jobs; counsellors, psychologists, dramatherapists, social workers and nurses to expand their knowledge and proficiency, take responsibility for their own practice, and improve client protection and safety of care in complex clinical situations. It is deemed integral to continued professional practice to safeguard vulnerable people and to reduce practitioner burnout. Dramatherapy supervision incorporates all of the above but utilises creative methods as a tool to gain insight and a deeper understanding of the situation. Creativity and the use of metaphor enable the supervisee to gain an aerial view of the situation they are exploring. The word metaphor in Greek means to ‘carry across’ indicating a transfer of meaning form one frame of reference to another. The supervision support was incorporated into each group’s induction training programme. The first year group attended fortnightly one hour sessions, the second group received two one hour sessions every term. The existing literature on the supervision and mentoring of secondary school teacher trainees calls for changes in pre-service teacher education and in the induction period. There is a particular emphasis on the need to include reflective and experiential learning, within training programmes and within the induction period, in order to help teachers manage the interpersonal dynamics and emotional impact within a high pressurised environment

Keywords: dramatherapy supervision, newly qualified secondary school teachers, professional development, teacher education

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Authors: Yankun Yang, Xinggang Yan, Konstantinos Sirlantzis, Gareth Howells

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This paper presents a static output feedback sliding mode control method to regulate a two-wheeled inverted pendulum system with considerations of matched and unmatched uncertainties. A sliding surface is designed and the associated sliding motion stability is analysed based on the reduced-order dynamics. A static output sliding mode control law is synthesised to drive the system to the sliding surface and maintain a sliding motion afterwards. The nonlinear bounds on the uncertainties are employed in the stability analysis and control design to improve the robustness. The simulation results demonstrate the effectiveness of the proposed control.

Keywords: two-wheeled inverted pendulum, output feedback sliding mode control, nonlinear systems, robotics

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Authors: Ayse Ozturk

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The study extends the prior research on modeling competencies by positioning students’ cognitive and language resources as the fundamentals for pursuing their own inquiry and expression lines through mathematical modeling. This strategy aims to answer the question that guides this study, “How do students’ group approaches to modeling tasks affect their modeling competencies over a unit of instruction?” Six bilingual tenth-grade students worked on open-ended modeling problems along with the content focused on quantities over six weeks. Each group was found to have a unique cognitive approach for solving these problems. Three different problem-solving strategies affected how the groups’ modeling competencies changed. The results provide evidence that the discussion around groups’ solutions, coupled with their reflections, advances group interpreting and validating competencies in the mathematical modeling process

Keywords: cognition, collective learning, mathematical modeling competencies, problem-solving

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Authors: Biao Sun, Tejas Bhatelia, Vishnu Pareek, Ranjeet Utikar, Moses Tadé

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Additive manufacturing (AM), commonly known as 3D printing, with the continuing advances in parallel processing and computational modeling, has created a paradigm shift (with significant radical thinking) in the design and operation of chemical processing plants, especially LNG plants. With the rising energy demands, environmental pressures, and economic challenges, there is a continuing industrial need for disruptive technologies such as AM, which possess capabilities that can drastically reduce the cost of manufacturing and operations of chemical processing plants in the future. However, the continuing challenge for 3D printing is its lack of adaptability in re-designing the process plant equipment coupled with the non-existent theory or models that could assist in selecting the optimal candidates out of the countless potential fabrications that are possible using AM. One of the most common packings used in the LNG process is structured packing in the packed column (which is a unit operation) in the process. In this work, we present an example of an optimum strategy for the application of AM to this important unit operation. Packed columns use a packing material through which the gas phase passes and comes into contact with the liquid phase flowing over the packing, typically performing the necessary mass transfer to enrich the products, etc. Structured packing consists of stacks of corrugated sheets, typically inclined between 40-70° from the plane. Computational Fluid Dynamics (CFD) was used to test and model various geometries to study the governing hydrodynamic characteristics. The results demonstrate that the costly iterative experimental process can be minimized. Furthermore, they also improve the understanding of the fundamental physics of the system at the multiscale level. SpiroPak, patented by Curtin University, represents an innovative structured packing solution currently at a technology readiness level (TRL) of 5~6. This packing exhibits remarkable characteristics, offering a substantial increase in surface area while significantly enhancing hydrodynamic and mass transfer performance. Recent studies have revealed that SpiroPak can reduce pressure drop by 50~70% compared to commonly used commercial packings, and it can achieve 20~50% greater mass transfer efficiency (particularly in CO2 absorption applications). The implementation of SpiroPak has the potential to reduce the overall size of columns and decrease power consumption, resulting in cost savings for both capital expenditure (CAPEX) and operational expenditure (OPEX) when applied to retrofitting existing systems or incorporated into new processes. Furthermore, pilot to large-scale tests is currently underway to further advance and refine this technology.

Keywords: Additive Manufacturing (AM), 3D printing, Computational Fluid Dynamics (CFD, structured packing (SpiroPak)

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Authors: Homin Kim, Hyungjo Byun, Jinyoung Do, Yongil Lee, Hyunho Shin, Seungbae Lee

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Engine room of mobile hydraulic vehicle is densely packed with an engine and many hydraulic components mostly generating heat and sound. Though hydraulic oil cooler, ATF cooler, and axle oil cooler etc. are added to vehicle cooling system of mobile vehicle, the overheating may cause downgraded performance and frequent failures. In order to improve thermal and acoustic environment of engine room, the computational approaches by Computational Fluid Dynamics (CFD) and Boundary Element Method (BEM) are used together with necessary modal analysis of belt-driven system. The engine room design layout and process, which satisfies the design objectives of sound power level and temperature levels of radiator water, charged air cooler, transmission and hydraulic oil coolers, is discussed.

Keywords: acoustics, CFD, engine room design, mobile hydraulics

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Authors: Endrik Mifta Shaiful, Firman Riyudha

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Acquired Immunodeficiency Syndrome (AIDS) is one of the world's deadliest diseases caused by the Human Immunodeficiency Virus (HIV) that infects white blood cells and cause a decline in the immune system. AIDS quickly became a world epidemic disease that affects almost all countries. Therefore, mathematical modeling approach to the spread of HIV and AIDS is needed to anticipate the spread of HIV and AIDS which are widespread. The purpose of this study is to determine the parameter estimation on mathematical models of HIV transmission and AIDS using cumulative data of people with HIV and AIDS each year in Indonesia. In this model, there are parameters of r ∈ [0,1) which is the effectiveness of the treatment in patients with HIV. If the value of r is close to 1, the number of people with HIV and AIDS will decline toward zero. The estimation results indicate when the value of r is close to unity, there will be a significant decline in HIV patients, whereas in AIDS patients constantly decreases towards zero.

Keywords: HIV, AIDS, parameter estimation, mathematical models

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Authors: Katherine Dropiewski, Michael Yakimov, Vadim Tokranov, Allan Minns, Pavel Murat, Serge Oktyabrsky

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InAs Quantum Dots (QDs) in a GaAs matrix is a well-documented luminescent material with high light yield, as well as thermal and ionizing radiation tolerance due to quantum confinement. These benefits can be leveraged for high-efficiency, room temperature scintillation detectors. The proposed scintillator is composed of InAs QDs acting as luminescence centers in a GaAs stopping medium, which also acts as a waveguide. This system has appealing potential properties, including high light yield (~240,000 photons/MeV) and fast capture of photoelectrons (2-5ps), orders of magnitude better than currently used inorganic scintillators, such as LYSO or BaF2. The high refractive index of the GaAs matrix (n=3.4) ensures light emitted by the QDs is waveguided, which can be collected by an integrated photodiode (PD). Scintillation structures were grown using Molecular Beam Epitaxy (MBE) and consist of thick GaAs waveguiding layers with embedded sheets of modulation p-type doped InAs QDs. An AlAs sacrificial layer is grown between the waveguide and the GaAs substrate for epitaxial lift-off to separate the scintillator film and transfer it to a low-index substrate for waveguiding measurements. One consideration when using a low-density material like GaAs (~5.32 g/cm³) as a stopping medium is the matrix thickness in the dimension of radiation collection. Therefore, luminescence properties of very thick (4-20 microns) waveguides with up to 100 QD layers were studied. The optimization of the medium included QD shape, density, doping, and AlGaAs barriers at the waveguide surfaces to prevent non-radiative recombination. To characterize the efficiency of QD luminescence, low temperature photoluminescence (PL) (77-450 K) was measured and fitted using a kinetic model. The PL intensity degrades by only 40% at RT, with an activation energy for electron escape from QDs to the barrier of ~60 meV. Attenuation within the waveguide (WG) is a limiting factor for the lateral size of a scintillation detector, so PL spectroscopy in the waveguiding configuration was studied. Spectra were measured while the laser (630 nm) excitation point was scanned away from the collecting fiber coupled to the edge of the WG. The QD ground state PL peak at 1.04 eV (1190 nm) was inhomogeneously broadened with FWHM of 28 meV (33 nm) and showed a distinct red-shift due to self-absorption in the QDs. Attenuation stabilized after traveling over 1 mm through the WG, at about 3 cm⁻¹. Finally, a scintillator sample was used to test detection and evaluate timing characteristics using 5.5 MeV alpha particles. With a 2D waveguide and a small area of integrated PD, the collected charge averaged 8.4 x10⁴ electrons, corresponding to a collection efficiency of about 7%. The scintillation response had 80 ps noise-limited time resolution and a QD decay time of 0.6 ns. The data confirms unique properties of this scintillation detector which can be potentially much faster than any currently used inorganic scintillator.

Keywords: GaAs, InAs, molecular beam epitaxy, quantum dots, III-V semiconductor

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Authors: Ritika Chaturvedi

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Introduction: Sexual objectification, characterized by the reduction of an individual to a mere object of sexual desire, remains a pervasive societal issue with profound repercussions on individual well-being. Such experiences, often rooted in systemic and cultural norms, have long-lasting implications for mental and emotional health. This study aims to explore the intricate relationship between experiences of sexual objectification and insidious trauma, further investigating the potential moderating effects of overexcitability as proposed by Dabrowski's theory of positive disintegration. Methodology: The research involved a comprehensive cohort of 204 women, spanning ages from 18 to 65 years. Participants were tasked with completing self-administered questionnaires designed to capture their experiences with sexual objectification. Additionally, the questionnaire assessed symptoms indicative of insidious trauma and explored overexcitability across five distinct domains: emotional, intellectual, psychomotor, sensory, and imaginational. Employing advanced statistical techniques, including multiple regression and moderation analysis, the study sought to decipher the intricate interplay among these variables. Findings: The study's results revealed a compelling positive correlation between experiences of sexual objectification and the onset of symptoms indicative of insidious trauma. This correlation underscores the profound and detrimental effects of sexual objectification on an individual's psychological well-being. Interestingly, the moderation analyses introduced a nuanced understanding, highlighting the differential roles of various overexcitability. Specifically, emotional, intellectual, and sensual overexcitability were found to exacerbate trauma symptomatology. In contrast, psychomotor overexcitability emerged as a protective factor, demonstrating a mitigating influence on the relationship between sexual objectification and trauma. Implications: The study's findings hold significant implications for a diverse array of stakeholders, encompassing mental health practitioners, educators, policymakers, and advocacy groups. The identified moderating effects of overexcitability emphasize the need for tailored interventions that consider individual differences in coping and resilience mechanisms. By recognizing the pivotal role of overexcitability in modulating the traumatic consequences of sexual objectification, this research advocates for the development of more nuanced and targeted support frameworks. Moreover, the study underscores the importance of continued research endeavors to unravel the intricate mechanisms and dynamics underpinning these relationships. Such endeavors are crucial for fostering the evolution of informed, evidence-based interventions and strategies aimed at mitigating the adverse effects of sexual objectification and promoting holistic well-being.

Keywords: sexual objectification, insidious trauma, emotional overexcitability, intellectual overexcitability, sensual overexcitability, psychomotor overexcitability, imaginational overexcitability

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Authors: N. Manjunatha, K. T. Rangswamy, N. Nagaraju, H. A. Prameela, P. Rudraswamy, M. Krishnareddy

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The identification of virus in cowpea especially potyviruses is confusing. Even though there are several studies on viruses causing diseases in cowpea, difficult to distinguish based on symptoms and serological detection. The differentiation of potyviruses considering as a constraint, the present study is initiated for molecular characterization, host plant resistance and epidemiology of the BCMV infecting cowpea. The etiological agent causing cowpea mosaic was identified as Bean Common Mosaic Virus (BCMV) on the basis of RT-PCR and electron microscopy. An approximately 750bp PCR product corresponding to coat protein (CP) region of the virus and the presence of long flexuous filamentous particles measuring about 952 nm in size typical to genus potyvirus were observed under electron microscope. The characterized virus isolate genome had 10054 nucleotides, excluding the 3’ terminal poly (A) tail. Comparison of polyprotein of the virus with other potyviruses showed similar genome organization with 9 cleavage sites resulted in 10 functional proteins. The pairwise sequence comparison of individual genes, P1 showed most divergent, but CP gene was less divergent at nucleotide and amino acid level. A phylogenetic tree constructed based on multiple sequence alignments of the polyprotein nucleotide and amino acid sequences of cowpea BCMV and potyviruses showed virus is closely related to BCMV-HB. Whereas, Soybean variant of china (KJ807806) and NL1 isolate (AY112735) showed 93.8 % (5’UTR) and 94.9 % (3’UTR) homology respectively with other BCMV isolates. This virus transmitted to different leguminous plant species and produced systemic symptoms under greenhouse conditions. Out of 100 cowpea genotypes screened, three genotypes viz., IC 8966, V 5 and IC 202806 showed immune reaction in both field and greenhouse conditions. Single marker analysis (SMA) was revealed out of 4 SSR markers linked to BCMV resistance, M135 marker explains 28.2 % of phenotypic variation (R2) and Polymorphic information content (PIC) value of these markers was ranged from 0.23 to 0.37. The correlation and regression analysis showed rainfall, and minimum temperature had significant negative impact and strong relationship with aphid population, whereas weak correlation was observed with disease incidence. Path coefficient analysis revealed most of the weather parameters exerted their indirect contributions to the aphid population and disease incidence except minimum temperature. This study helps to identify specific gaps in knowledge for researchers who may wish to further analyse the science behind complex interactions between vector-virus and host in relation to the environment. The resistant genotypes identified are could be effectively used in resistance breeding programme.

Keywords: cowpea, epidemiology, genotypes, virus

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Authors: Ibrahim M. Elmojtaba, Rayan M. Altayeb

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Visceral leishmaniasis (VL) is a vector-borne disease caused by the protozoa parasite of the genus leishmania. The transmission of the parasite to humans and animals occurs via the bite of adult female sandflies previously infected by biting and sucking blood of an infectious humans or animals. In this paper we use a previously proposed model, and then applied two optimal controls, namely treatment and vaccination to that model to investigate optimal strategies for controlling the spread of the disease using treatment and vaccination as the system control variables. The possible impact of using combinations of the two controls, either one at a time or two at a time on the spread of the disease is also examined. Our results provide a framework for vaccination and treatment strategies to reduce susceptible and infection individuals of VL in five years.

Keywords: visceral leishmaniasis, treatment, vaccination, optimal control, numerical simulation

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Authors: Jong H. Kim, Kathleen L. Chan, Luisa W. Cheng

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Control of fungal pathogens, such as foodborne mycotoxin producers, is problematic as effective antimycotic agents are often very limited. Mycotoxin contamination significantly interferes with the safe production of foods or crops worldwide. Moreover, expansion of fungal resistance to commercial drugs or fungicides is a global human health concern. Therefore, there is a persistent need to enhance the efficacy of commercial antimycotic agents or to develop new intervention strategies. Disruption of the cellular antioxidant system should be an effective method for pathogen control. Such disruption can be achieved with safe, redox-active compounds. Natural phenolic derivatives are potent redox cyclers that inhibit fungal growth through destabilization of the cellular antioxidant system. The goal of this study is to identify novel, redox-active compounds that disrupt the fungal antioxidant system. The identified compounds could also function as sensitizing agents to conventional antimycotics (i.e., chemosensitization) to improve antifungal efficacy. Various benzo derivatives were tested against fungal pathogens. Gene deletion mutants of the yeast Saccharomyces cerevisiae were used as model systems for identifying molecular targets of benzo analogs. The efficacy of identified compounds as potent antifungal agents or as chemosensitizing agents to commercial drugs or fungicides was examined with methods outlined by the Clinical Laboratory Standards Institute or the European Committee on Antimicrobial Susceptibility Testing. Selected benzo derivatives possessed potent antifungal or antimycotoxigenic activity. Molecular analyses by using S. cerevisiae mutants indicated antifungal activity of benzo derivatives was through disruption of cellular antioxidant or cell wall integrity system. Certain benzo analogs screened overcame tolerance of Aspergillus signaling mutants, namely mitogen-activated protein kinase mutants, to fludioxonil fungicide. Synergistic antifungal chemosensitization greatly lowered minimum inhibitory or fungicidal concentrations of test compounds, including inhibitors of mitochondrial respiration. Of note, salicylaldehyde is a potent antimycotic volatile that has some practical application as a fumigant. Altogether, benzo derivatives targeting cellular antioxidant system of fungi (along with cell wall integrity system) effectively suppress fungal growth. Candidate compounds possess the antifungal, antimycotoxigenic or chemosensitizing capacity to augment the efficacy of commercial antifungals. Therefore, chemogenetic approaches can lead to the development of novel antifungal intervention strategies, which enhance the efficacy of established microbe intervention practices and overcome drug/fungicide resistance. Chemosensitization further reduces costs and alleviates negative side effects associated with current antifungal treatments.

Keywords: antifungals, antioxidant system, benzo derivatives, chemosensitization

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