Search results for: molecular differentiation

Authors: Wilmer Esteban Vallejo Narváez, Serguei Fomine

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The theoretical investigation of Si-doped graphene nanoflakes (NFs) was conducted to understand their catalytic impact on CO₂ reduction using molecular hydrogen at the Density Functional Theory (DFT) level. The introduction of silicon by substituting carbon induces defects in the NF structure, resulting in a polyradical ground state. This silicon defect significantly boosts reactivity towards substrates, making Si-doped graphene NFs more catalytically active in CO₂ reduction to formic acid compared to silicene. Notably, Si-doped graphene demonstrates a preference for formic acid over carbon monoxide, mirroring the behavior of silicene. Furthermore, investigations into formic acid-to-formaldehyde and formaldehyde-to-methanol conversions reveal instances where Si-doped graphene outperforms silicene in terms of efficacy. In the final reduction step, the methanol-to-methane reaction unfolds in four stages, with the rate-determining step involving hydrogen transfer from silicon to methyl. Notably, the activation energy for this step is lower in Si-doped graphene compared to silicene. Consequently, Si-doped graphene NFs emerge as superior catalysts with lower activation energies overall. Remarkably, throughout these catalytic processes, Si-doped graphene maintains environmental stability, further highlighting its enhanced catalytic activity without compromising graphene's inherent stability.

Keywords: silicon-doped graphene, CO₂ reduction, DFT, catalysis

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Authors: Aigul Manapova

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We consider an optimal control problem in the higher coefficient of nonlinear equations with a divergent elliptic operator and unbounded nonlinearity, and the Dirichlet boundary condition. The conditions imposed on the coefficients of the state equation are assumed to hold only in a small neighborhood of the exact solution to the original problem. This assumption suggests that the state equation involves nonlinearities of unlimited growth and considerably expands the class of admissible functions as solutions of the state equation. We obtain formulas for the first partial derivatives of the objective functional with respect to the control functions. To calculate the gradients the numerical solutions of the state and adjoint problems are used. We also prove that the gradient of the cost function is Lipchitz continuous.

Keywords: cost functional, differentiability, divergent elliptic operator, optimal control, unbounded nonlinearity

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Authors: Jennifer Cuellar, Angie L. Parada, Kevin N. S. Chacon, Sol M. Mejia

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The purification of bio-ethanol through distillation methods is an unresolved issue at the biofuel industry because of the ethanol-water azeotrope formation, which increases the steps of the purification process and subsequently increases the production costs. Therefore, understanding the mixture nature at the molecular level could provide new insights for improving the current methods and/or designing new and more efficient purification methods. For that reason, the present study focuses on the evaluation and analysis of (ethanol)₉-water heterodecamers, as the systems with the minimum molecular proportion that represents the azeotropic concentration (96 %m/m in ethanol). The computational modelling was carried out with B3LYP-D3/6-311++G(d,p) in Gaussian 09. Initial explorations of the potential energy surface were done through two methods: annealing simulated runs and molecular dynamics trajectories besides intuitive structures obtained from smaller (ethanol)n-water heteroclusters, n = 7, 8 and 9. The energetic order of the seven stable heterodecamers determines the most stable heterodecamer (Hdec-1) as a structure forming a bicyclic geometry with the O-H---O hydrogen bonds (HBs) where the water is a double proton donor molecule. Hdec-1 combines 1 water molecule and the same quantity of every ethanol conformer; this is, 3 trans, 3 gauche 1 and 3 gauche 2; its abundance is 89%, its decamerization energy is -80.4 kcal/mol, i.e. 13 kcal/mol most stable than the less stable heterodecamer. Besides, a way to understand why methanol does not form an azeotropic mixture with water, analogous systems ((ethanol)10, (methanol)10, and (methanol)9-water)) were optimized. Topologic analysis of the electron density reveals that Hec-1 forms 33 weak interactions in total: 11 O-H---O, 8 C-H---O, 2 C-H---C hydrogen bonds and 12 H---H interactions. The strength and abundance of the most unconventional interactions (H---H, C-H---O and C-H---O) seem to explain the preference of the ethanol for forming heteroclusters instead of clusters. Besides, O-H---O HBs present a significant covalent character according to topologic parameters as the Laplacian of electron density and the relationship between potential and kinetic energy densities evaluated at the bond critical points; obtaining negatives values and values between 1 and 2, for those two topological parameters, respectively.

Keywords: ADMP, DFT, ethanol-water azeotrope, Grimme dispersion correction, simulated annealing, weak interactions

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Authors: Khalid Alhudaib

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Potato is considered as one of the most important and potential vegetable crops in Saudi Arabia. Alfalfa mosaic virus (AMV), genus Alfamovirus, family Bromoviridae is among the broad spread of viruses in potato. During spring and fall growing seasons of potato in 2015 and 2016, several field visits were conducted in the four major growing areas of potato cultivation (Riyadh-Qaseem-Hail-Hard). The presence of AMV was detected in samples using ELISA, dot blot hybridization and/or RT-PCR. The highest occurrence of AMV was observed as 18.6% in Qaseem followed by Riyadh with 15.2% while; the lowest infection rates were recorded in Hard and Hail, 8.3 and 10.4%, respectively. The sequences of seven isolates of AMV obtained in this study were determined and the sequences were aligned with the other sequences available in the GenBank database. Analyses confirmed the low variability among AMV isolated in this study, which means that all AMV isolates may originate from the same source. Due to high incidence of AMV, other economic susceptible crops may become affected by high incidence of this virus in potato crops. This requires accurate examination of potato seed tubers to prevent the spread of the virus in Saudi Arabia. The obtained results indicated that the hybridization and ELISA are suitable techniques in the routine detection of AMV in a large number of samples while RT-PCR is more sensitive and essential for molecular characterization of AMV.

Keywords: Alfamovirus, AMV, Alfalfa mosaic virus, PCR, potato

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Authors: Acheampong Addo, Emmanuel Odartei Armah, Seth Koranteng Agyakwah, Ruby Asmah, Emmanuel Tetteh-Doku Mensah, Rhoda Lims Diyie, Sena Amewu, Catherine Ragasa, Edward Kofi Abban, Mike Yaw Osei-Atweneboana

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The study investigated genetic variation and relationships among populations of Nile tilapia cultured in small-scale fish farms in selected regions of Ghana. A total of 700 samples were collected. All samples were screened with five microsatellite markers and results were analyzed using (Genetic Analysis in Excel), (Molecular and Evolutionary Genetic Analysis software, and Genpop on the web for Heterozygosity and Shannon diversity, (Analysis of Molecular Variance), and (Principal Coordinate Analysis). Fish from the 16 populations (made up of 14 farms and 2 selectively bred populations) clustered into three groups: 7 populations clustered with the GIFT-derived strain, 4 populations clustered with the Akosombo strain, and three populations were in a separate cluster. The clustering pattern indicated groups of different strains of Nile tilapia cultured. Mantel correlation test also showed low genetic variations among the 16 populations hence the need to boost seed quality in order to accelerate aquaculture production in Ghana.

Keywords: microsatellites, small- scale, Nile tilapia, akosombo strain, GIFT strain

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Authors: Giovanni Meloni

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Recent results are presented from experiments carried out at the Advanced Light Source (ALS) at the Chemical Dynamics Beamline of Lawrence Berkeley National Laboratory using multiplexed synchrotron photoionization mass spectrometry. The reaction mixture and a buffer gas (He) are introduced through individually calibrated mass flow controllers into a quartz slow flow reactor held at constant pressure and temperature. The gaseous mixture effuses through a 650 μm pinhole into a 1.5 mm skimmer, forming a molecular beam that enters a differentially pumped ionizing chamber. The molecular beam is orthogonally intersected by a tunable synchrotron radiation produced by the ALS in the 8-11 eV energy range. Resultant ions are accelerated, collimated, and focused into an orthogonal time-of-flight mass spectrometer. Reaction species are identified by their mass-to-charge ratios and photoionization (PI) spectra. Comparison of experimental PI spectra with literature and/or simulated curves is routinely done to assure the identity of a given species. With the aid of electronic structure calculations, potential energy surface scans are performed, and Franck-Condon spectral simulations are obtained. Examples of these experiments are discussed, ranging from new intermediates characterization to reaction mechanisms elucidation and biofuels oxidation pathways identification.

Keywords: mass spectrometry, reaction intermediates, synchrotron photoionization, oxidation reactions

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Authors: Bright Chukwunwike Uzuegbunam, Wojciech Paslawski, Hans Agren, Christer Halldin, Wolfgang Weber, Markus Luster, Thomas Arzberger, Behrooz Hooshyar Yousefi

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There is a need to develop a PET tracer that will enable to diagnosis and track the progression of Alpha-synucleinopathies (Parkinson’s disease [PD], dementia with Lewy bodies [DLB], multiple system atrophy [MSA]) in living subjects over time. Alpha-synuclein aggregates (a-syn), which are present in all the stages of disease progression, for instance, in PD, are a suitable target for in vivo PET imaging. For this reason, we have developed some promising a-syn tracers based on a disarylbisthiazole (DABTA) scaffold. The precursors are synthesized via a modified Hantzsch thiazole synthesis. The precursors were then radiolabeled via one- or two-step radiofluorination methods. The ligands were initially screened using a combination of molecular dynamics and quantum/molecular mechanics approaches in order to calculate the binding affinity to a-syn (in silico binding experiments). Experimental in vitro binding assays were also performed. The ligands were further screened in other experiments such as log D, in vitro plasma protein binding & plasma stability, biodistribution & brain metabolite analyses in healthy mice. Radiochemical yields were up to 30% - 72% in some cases. Molecular docking revealed possible binding sites in a-syn and also the free energy of binding to those sites (-28.9 - -66.9 kcal/mol), which correlated to the high binding affinity of the DABTAs to a-syn (Ki as low as 0.5 nM) and selectivity (> 100-fold) over Aβ and tau, which usually co-exist with a-synin some pathologies. The log D values range from 2.88 - 2.34, which correlated with free-protein fraction of 0.28% - 0.5%. Biodistribution experiments revealed that the tracers are taken up (5.6 %ID/g - 7.3 %ID/g) in the brain at 5 min (post-injection) p.i., and cleared out (values as low as 0.39 %ID/g were obtained at 120 min p.i. Analyses of the mice brain 20 min p.i. Revealed almost no radiometabolites in the brain in most cases. It can be concluded that in silico study presents a new venue for the rational development of radioligands with suitable features. The results obtained so far are promising and encourage us to further validate the DABTAs in autoradiography, immunohistochemistry, and in vivo imaging in non-human primates and humans.

Keywords: alpha-synuclein aggregates, alpha-synucleinopathies, PET imaging, tracer development

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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In last decade, metal-organic complexes have captured intensive attention because of their wide range of biological activities such as antibacterial, antifungal, anticancerous, antimicrobial and antiHIV. Therefore, it is of great importance for the development of coordination chemistry to explore the assembly of functional organic ligands with metal ion and to investigate the relationship between the structure and property. In view of our studies, we reasoned that benzimidazoles complexed to metal ions could act as a potent antibacterial agents. Thus, we have bioassayed the inhibitory potency of benzimidazoles and their metal salts (Co or Ni) against Gram negative bacteria Escherichia coli. In order to validate our in vitro study, we performed in silico studies using molecular docking software’s. The investigated compounds and their metal complexes (Co, Ni) showed good antibacterial activity against Escherichia coli. In silico docking studies of the synthesized compounds suggested that complexed benzimidazoles have a greater binding affinity and enhanced antibacterial activity in comparison with noncomplexed ligands. In view of their enhanced inhibitory properties we propose that the studied complexes can be used as potential pharmaceuticals. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, complexes, antibacterial, Escherichia coli, metal

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Authors: Nishaben Dholakiya, Anirban Roy, Ranjan Dey

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The unprecedented rise in global temperatures has triggered complex changes in marine ecosystems, necessitating a deeper understanding of seawater's thermophysical properties by experimentally measuring ultrasonic velocity and density at varying temperatures and salinity. This study investigates the critical relationship between temperature variations and molecular-level interactions in Arabian Sea surface waters, specifically focusing on internal pressure (π) and cohesion energy density (CED) as key indicators of ecosystem disruption. Our experimental findings reveal that elevated temperatures significantly reduce internal pressure, weakening the intermolecular forces that maintain seawater's structural integrity. This reduction in π correlates directly with decreased habitat stability for marine organisms, particularly affecting pressure-sensitive species and their physiological processes. Similarly, the observed decline in cohesion energy density at higher temperatures indicates a fundamental shift in water molecule organization, impacting the dissolution and distribution of vital nutrients and gases. These molecular-level changes cascade through the ecosystem, affecting everything from planktonic organisms to complex food webs. By employing advanced machine learning techniques, including Stacked Ensemble Machine Learning (SEML) and AdaBoost (AB), we developed highly accurate predictive models (>99% accuracy) for these thermophysical parameters. The results provide crucial insights into the mechanistic relationship between climate warming and marine ecosystem degradation, offering valuable data for environmental policymaking and conservation strategies. The novelty of this research serves as no such thermodynamic investigation has been conducted before in literature, whereas this research establishes a quantitative framework for understanding how molecular-level changes in seawater properties directly influence marine ecosystem stability, emphasizing the urgent need for climate change mitigation efforts.

Keywords: thermophysical properties, Arabian Sea, internal pressure, cohesion energy density, machine learning

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Authors: Chang-Hui Shen, Paulina Konarzewska

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Cell homeostasis is regulated by vacuolar activity and it has been shown that lipid composition of the vacuole plays an important role in vacuolar function. The major phosphoinositide species present in the vacuolar membrane include phosphatidylinositol 3,5-biphosphate (PI(3,5)P₂) which is generated from PI(3)P controlled by Fab1p. Deletion of FAB1 gene reduce the synthesis of PI(3,5)P₂ and thus result in enlarged or fragmented vacuoles, with neutral vacuolar pH due to reduced vacuolar H⁺-ATPase activity. These mutants also exhibited poor growth at high extracellular pH and in the presence of CaCl₂. Conversely, VPS34 regulates the synthesis of PI(3)P from phosphatidylinositol (PI), and the lack of Vps34p results in the reduction of vacuolar activity. Although the cellular observations are clear, it is still unknown about the molecular mechanism between the phospholipid biosynthesis pathway and vacuolar activity. Since both VPS34 and FAB1 are important in vacuolar activity, we hypothesize that the molecular mechanism of vacuolar function might be regulated by the transcriptional regulators of phospholipid biosynthesis. In this study, we study the role of the major phospholipid biosynthesis transcription factor, INO2, in the regulation of vacuolar activity. We first performed qRT-PCR to examine the effect of Ino2p on the expression of VPS34 and FAB1. Our results showed that VPS34 was upregulated in the presence of inositol for both WT and ino2Δ cells. However, FAB1 was only upregulated significantly in ino2Δ cells. This indicated that Ino2p might be the negative regulator for FAB1 expression. Next, growth sensitivity experiment showed that WT, vma3Δ, and ino2Δ grew well in growth medium buffered to pH 5.5 containing 10 mM CaCl₂. As cells were switched to growth medium buffered to pH 7 containing CaCl₂ WT, ino2Δ and opi1Δ showed growth reduction, whereas vma3Δ was completely nonviable. As the concentration of CaCl₂ was increased to 60 mM, ino2Δ cells showed moderate growth reduction compared to WT. This result suggests that ino2Δ cells have better vacuolar activity. Microscopic analysis and vacuolar acidification were employed to further elucidate the importance of INO2 in vacuolar homeostasis. Analysis of vacuolar morphology indicated that WT and vma3Δ cells displayed vacuoles that occupied a small area of the cell when grown in media buffered to pH 5.5. Whereas, ino2Δ displayed fragmented vacuoles. On the other hand, all strains grown in media buffered to pH 7, exhibited enlarged vacuoles that occupied most of the cell’s surface. This indicated that the presence of INO2 may play negative effect in vacuolar morphology when cells are grown in media buffered to pH 5.5. Furthermore, vacuolar acidification assay showed that only vma3Δ cells displayed notably less acidic vacuoles as cells were grown in media buffered to pH 5.5 and pH 7. Whereas, ino2Δ cells displayed more acidic pH compared to WT at pH7. Taken together, our results demonstrated the molecular mechanism of the vacuolar activity regulated by the phospholipid biosynthesis transcription factors Ino2p. Ino2p negatively regulates vacuolar activity through the expression of FAB1.

Keywords: vacuole, phospholipid, homeostasis, Ino2p, FAB1

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Authors: Masoud Sheidaei, Mohammad-Reza Kordasti, Fahimeh Koohdar

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Calotropis procera (Aiton) W.T.Aiton, (Apocynaceae), is an economically and medicinally important plant species which is an evergreen, perennial shrub growing in arid and semi-arid climates, and can tolerate very low annual rainfall (150 mm) and a dry season. The plant can also tolerate temperature ran off 20 to30°C and is not frost tolerant. This plant species prefers free-draining sandy soils but can grow also in alkaline and saline soils.It is found at a range of altitudes from exposed coastal sites to medium elevations up to 1300 m. Due to morpho-physiological adaptations of C. procera and its ability to tolerate various abiotic stresses. This taxa can compete with desirable pasture species and forms dense thickets that interfere with stock management, particularly mustering activities. Caloteropis procera grows only in southern part of Iran where in comprises a limited number of geographical populations. We used different population genetics and r landscape analysis to produce data on geographical populations of C. procera based on molecular genetic study using SCoT molecular markers. First, we used spatial principal components (sPCA), as it can analyze data in a reduced space and can be used for co-dominant markers as well as presence / absence data as is the case in SCoT molecular markers. This method also carries out Moran I and Mantel tests to reveal spatial autocorrelation and test for the occurrence of Isolation by distance (IBD). We also performed Random Forest analysis to identify the importance of spatial and geographical variables on genetic diversity. Moreover, we used both RDA (Redundency analysis), and LFMM (Latent factor mixed model), to identify the genetic loci significantly associated with geographical variables. A niche modellng analysis was carried our to predict present potential area for distribution of these plants and also the area present by the year 2050. The results obtained will be discussed in this paper.

Keywords: population genetics, landscape genetic, Calotreropis procera, niche modeling, SCoT markers

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Authors: C. Maphosa, Ndileleni Mudzielwana, Lufuno Phillip Netshifhefhe

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In line with established mission and vision, a university articulates its focus and purpose of existence. The conduct of business in a university should be for the furtherance of the mission and vision. Teaching and learning should play a pivotal role in driving the purpose of a university. In this paper, the researchers examine how service learning could be significant in driving the purpose of a rural-based university whose focus is to promote rural development. The importance of institutions’ vision and mission statement is explored and the vision and mission of the said university examined closely. The concept rural development and the contribution of a university in its promotion is discussed. Service learning as a teaching and learning approach is examined and its significance in driving the purpose of a rural-based university explained.

Keywords: relevance, differentiation, purpose, teaching, learning

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Authors: Sarthak S. Salunke

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Development, as a notion, is seen in perspective of western philosophical conceptions, and the western developed nations have become a yardstick for setting up development goals for developing and underdeveloped nations around the world. This blanket term of development becomes superficial and materialistic in context of the vast geopolitical, territorial, cultural and behavioral diversities existing in countries of the Africa and the Asia, and tends to undermine the atomistic aspect of development. Indian political theories, which are often seen as religious philosophies, have inherent structure of development of human being as an individual and as a part of the society, and, in result, development of the State. These theories, primarily individualistic in nature, have a combination of altruism and rationalism which guides human beings towards constructing a collectively developed and morally sustainable society. This research focuses on the application of this Indian thought in combination of classical liberal thought to tackle the issues of development in diverse societies. The proposed restructured model of development is based on molecular individualism, instead of atomic individual approach of liberalists, which lets development modelers to target meaningful clusters for designating goals for development based on the particular needs based on geopolitical, cultural and ethical requirements, and making it meaningful in conjunction with global development to establish a harmony between western and eastern worlds.

Keywords: Indian political thought, development, liberalism, molecular individualism

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Authors: Harish Rajak, Preeti Patel

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HDAC inhibitors can reactivate gene expression and inhibit the growth and survival of cancer cells. The 3D-QSAR and Pharmacophore modeling studies were performed to identify important pharmacophoric features and correlate 3D-chemical structure with biological activity. The pharmacophore hypotheses were developed using e-pharmacophore script and phase module. Pharmacophore hypothesis represents the 3D arrangement of molecular features necessary for activity. A series of 55 compounds with well-assigned HDAC inhibitory activity was used for 3D-QSAR model development. Best 3D-QSAR model, which is a five PLS factor model with good statistics and predictive ability, acquired Q2 (0.7293), R2 (0.9811) and standard deviation (0.0952). Molecular docking were performed using Histone Deacetylase protein (PDB ID: 1t69) and prepared series of hydroxamic acid based HDAC inhibitors. Docking study of compound 43 show significant binding interactions Ser 276 and oxygen atom of dioxine cap region, Gly 151 and amino group and Asp 267 with carboxyl group of CONHOH, which are essential for anticancer activity. On docking, most of the compounds exhibited better glide score values between -8 to -10.5. We have established structure activity correlation using docking, energetic based pharmacophore modelling, pharmacophore and atom based 3D QSAR model. The results of these studies were further used for the design and testing of new HDAC analogs.

Keywords: Docking, e-pharmacophore, HDACIs, QSAR, Suberoylanilidehydroxamic acid.

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Authors: A. K. Faizah, G. Vadamalai, S. K. Balasundram, W. L. Lim

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Pineapple (Ananas comosus) is a common crop in tropical and subtropical areas of the world. Malaysia once ranked as one of the top 3 pineapple producers in the world in the 60's and early 70's, after Hawaii and Brazil. Moreover, government’s recognition of the pineapple crop as one of priority commodities to be developed for the domestics and international markets in the National Agriculture Policy. However, pineapple industry in Malaysia still faces numerous challenges, one of which is the management of disease and pest. Red tip disease on pineapple was first recognized about 20 years ago in a commercial pineapple stand located in Simpang Renggam, Johor, Peninsular Malaysia. Since its discovery, there has been no confirmation on its causal agent of this disease. The epidemiology of red tip disease is still not fully understood. Nevertheless, the disease symptoms and the spread within the field seem to point toward viral infection. Bioassay test on nucleic acid extracted from the red tip-affected pineapple was done on Nicotiana tabacum cv. Coker by rubbing the extracted sap. Localised lesions were observed 3 weeks after inoculation. Negative staining of the fresh inoculated Nicotiana tabacum cv. Coker showed the presence of membrane-bound spherical particles with an average diameter of 94.25nm under transmission electron microscope. The shape and size of the particles were similar to tospovirus. SDS-PAGE analysis of partial purified virions from inoculated N. tabacum produced a strong and a faint protein bands with molecular mass of approximately 29 kDa and 55 kDa. Partial purified virions of symptomatic pineapple leaves from field showed bands with molecular mass of approximately 29 kDa, 39 kDa and 55kDa. These bands may indicate the nucleocapsid protein identity of tospovirus. Furthermore, a handheld sensor, Greenseeker, was used to detect red tip symptoms on pineapple non-destructively based on spectral reflectance, measured as Normalized Difference Vegetation Index (NDVI). Red tip severity was estimated and correlated with NDVI. Linear regression models were calibrated and tested developed in order to estimate red tip disease severity based on NDVI. Results showed a strong positive relationship between red tip disease severity and NDVI (r= 0.84).

Keywords: pineapple, diagnosis, virus, NDVI

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Authors: P. Sindhumole, K. Soumya, R. Renjimol

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Rice (Oryza sativa L.) is the major staple food crop over the world. It is prone to a number of biotic and abiotic stresses, out of which Bacterial Leaf Blight (BLB), caused by Xanthomonas oryzae pv. oryzae, is the most rampant. Management of this disease through chemicals or any other means is very difficult. The best way to control BLB is by the development of Host Plant Resistance. BLB resistance is not an activity of a single gene but it involves a cluster of more than thirty genes reported. Among these, Xa5 and Xa13 genes are two important ones, which can be diagnosed through marker assisted selection using closely linked molecular markers. During 2014, the first phase of field screening using forty traditional rice genotypes was carried out and twenty resistant symptomless genotypes were identified. Molecular characterisation of these genotypes using RM 122 SSR marker revealed the presence of Xa5 gene in thirteen genotypes. Forty-two traditional rice genotypes were used for the second phase of field screening for BLB resistance. Among these, sixteen resistant genotypes were identified. These genotypes, along with two susceptible check genotypes, were subjected to marker assisted selection for Xa13 gene, using the linked STS marker RG-136. During this process, presence of Xa13 gene could be detected in ten resistant genotypes. In future, these selected genotypes can be directly utilised as donors in Marker assisted breeding programmes for BLB resistance in rice.

Keywords: oryza sativa, SSR, STS, marker, disease, breeding

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Authors: Md. Shoffikul Islam, Hongqing Hu

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Immobilizing trace elements by reducing their mobility and bioavailability through amendment application, especially biochar (BC), is a cost-effective and efficient method to address their toxicity in the soil environment. However, the low molecular weight organic acids (LMWOAs) in the rhizosphere could affect BC's efficiency to immobilize trace metals as the LMWOAs could either mobilize or fix metals in the soils. Therefore, understanding the BC's and LMWOAs' interaction mechanisms on metals stabilization in the rhizosphere is crucial. The present study examined the impact of BC derived from rice husk, tartaric acid (TA), and oxalic acid (OA), and the combination of BC and TA/OA on the changes of cadmium (Cd), lead (Pb), and zinc (Zn) among their geochemical forms through incubation experiment. The changes of zeta potential and X-ray diffraction (XRD) pattern of BC and BC-amended soils to investigate the probable mechanisms of trace elements' immobilization by BC under the attacks of TA and OA were also examined. The rice husk BC at 5% (w/w) was mixed with the air-dry soil (an Anthrosols) contaminated with Cd, Pb, and Zn in the plastic pot. The TA and OA each at 2, 5, 10, and 20 mM kg-1 (w/v) were added separately into the pot. All the ingredients were mixed thoroughly with the soil. A control (CK) treatment was also prepared without BC, TA, and OA addition. After 7, 15, and 60 days of incubation with 60% (w/v) moisture level at 25 °C, the incubated soils were determined for pH and EC and were sequentially extracted to assess the metals' transformation in soil. The electronegative charges and XRD peaks of BC and BC-amended soils were also measured. The BC, low level of TA (2 mM kg-1 soil), and BC plus the low concentration of TA (BC-TA2) addition considerably declined the acid-soluble Cd, Pb, and Zn in which BC-TA2 was found to be the most effective treatment. The trends were reversed concerning the high levels of TA (>5-20 mM kg-1 soil), all levels of OA (2-20 mM kg-1 soil), and the BC plus high levels of TA/OA treatments. BC-TA2 changed the highest amounts of acid-soluble and reducible metals to the oxidizable and residual fractions with time. The most increased electronegative charges of BC-TA2 indicate its (BC-TA2) highest metals' immobilizing efficiency, probably through metals adsorption and fixation with the negative charge sites. The XRD study revealed the presence of P, O, CO32-, and Cl1- in BC, which might be responsible for the precipitation of CdCO3, pyromorphite, and hopeite concerning Cd, Pb, and Zn immobilization, respectively. The findings demonstrated that the low level of TA increased metals immobilization, while the high levels of TA and all levels of OA enhanced their mobilization. The BC-TA2 was the best treatment in stabilizing metals in soil.

Keywords: biochar, immobilization, low molecular weight organic acids, trace elements contaminated soil

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Authors: Guanlin Wu, Jiajia Yao, Fang Liu, Junshuai Xue, Jincheng Zhang, Yue Hao

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Owing to the excellent thermal conductivity and ultra-wide bandgap, Aluminum nitride (AlN)/Gallium nitride (GaN) is a highly promising material to achieve high breakdown voltage and output power devices among III-nitrides. In this study, we explore the growth and characterization of polarization-induced AlN/GaN heterostructures using plasma-assisted molecular beam epitaxy (PA-MBE) on AlN-on-sapphire templates. To improve the crystal quality and demonstrate the effectiveness of the PA-MBE approach, a thick AlN buffer of 180 nm was first grown on the AlN-on sapphire template. This buffer acts as a back-barrier to enhance the breakdown characteristic and isolate leakage paths that exist in the interface between the AlN epilayer and the AlN template. A root-mean-square roughness of 0.2 nm over a scanned area of 2×2 µm2 was measured by atomic force microscopy (AFM), and the full-width at half-maximum of (002) and (102) planes on the X-ray rocking curve was 101 and 206 arcsec, respectively, using by high-resolution X-ray diffraction (HR-XRD). The electron mobility of 443 cm2/Vs with a carrier concentration of 2.50×1013 cm-2 at room temperature was achieved in the AlN/GaN heterostructures by using a polarization-induced GaN channel. The low depletion capacitance of 15 pF is resolved by the capacitance-voltage. These results indicate that the polarization-induced AlN/GaN heterostructures have great potential for next-generation high-temperature, high-frequency, and high-power electronics.

Keywords: AlN, GaN, MBE, heterostructures

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Authors: L. Heidari, M. Jalili Ghazizade

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In recent years, different petrochemical complexes have been established to produce aromatic compounds. Among them, Nouri Petrochemical Complex (NPC) is the largest producer of aromatic raw materials in the world, and is located in south of Iran. Environmental concerns have been raised in this region due to generation of different types of solid waste generated in the process of aromatics production, and subsequently, industrial waste characterization has been thoroughly considered. The aim of this study is qualitative and quantitative characterization of industrial waste generated in the aromatics production process and determination of the best method for industrial waste management. For this purpose, all generated industrial waste during the production process was determined using a checklist. Four main industrial wastes were identified as follows: spent industrial soil, spent catalyst, spent molecular sieves and spent N-formyl morpholine (NFM) solvent. The amount of heavy metals and organic compounds in these wastes were further measured in order to identify the nature and toxicity of such a dangerous compound. Then industrial wastes were classified based on lab analysis results as well as using different international lists of hazardous waste identification such as EPA, UNEP and Basel Convention. Finally, the best method of waste disposal is selected based on environmental, economic and technical aspects. 

Keywords: aromatic compounds, industrial soil, molecular sieve, normal formyl morpholine solvent

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Authors: Sinethemba Yakobi, Lindiwe Zuma, Ofentse Pooe

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Gonococcal infections present a notable public health issue, and the major approach for treatment involves using β-lactam antibiotics that specifically target penicillin-binding protein 2 (PBP2) in Neisseria gonorrhoeae. This study examines the influence of flavonoids, namely rutin, on the structural changes of PBP2 in both penicillin-resistant (FA6140) and penicillin-susceptible (FA19) strains. The research clarifies the structural effects of particular mutations, such as inserting an aspartate residue at position 345 (Asp-345a) in the PBP2 protein. The strain FA6140, which is resistant to penicillin, shows specific changes that lead to a decrease in penicillin binding. These mutations, namely P551S and F504L, significantly impact the pace at which acylation occurs and the stability of the strain under high temperatures. Molecular docking analyses investigate the antibacterial activities of rutin and other phytocompounds, emphasizing its exceptional binding affinity and potential as an inhibitor of PBP2. Quercetin and protocatechuic acid have encouraging antibacterial effectiveness, with quercetin displaying characteristics similar to those of drugs. Molecular dynamics simulations offer a detailed comprehension of the interactions between flavonoids and PBP2, highlighting rutin's exceptional antioxidant effects and strong affinity for the substrate binding site. The study's wider ramifications pertain to the pressing requirement for antiviral treatments in the context of the ongoing COVID-19 epidemic. Flavonoids have a strong affinity for binding to PBP2, indicating their potential as inhibitors to impair cell wall formation in N. gonorrhoeae. Ultimately, this study provides extensive knowledge on the interactions between proteins and ligands, the dynamics of the structure, and the ability of flavonoids to combat penicillin-resistant N. gonorrhoeae bacteria. The verified simulation outcomes establish a basis for creating potent inhibitors and medicinal therapies to combat infectious illnesses.

Keywords: phytochemicals, penicillin-binding protein 2, gonococcal infection, ligand-protein interaction, binding energy, neisseria gonorrhoeae FA19, neisseria gonorrhoeae FA6140, flavonoids

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Authors: Avigail Moor

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Rape by an acquaintance is a prevalent type of sexual assault that is often misperceived and downplayed. To date, there has been no empirical investigation of the prevailing social attitudes towards this type of rape as compared to stranger rape. The present study seeks to address this issue by evaluating widely held attitudes towards these different types of rape. The mediating role of gender and rape myths acceptance is assessed as well. Three hundred and twenty participants, equally divided by gender, completed self-report questionnaires. The results indicate that sexual coercion by strangers is perceived as rape to a significantly greater degree than forced sex by an acquaintance, which in turn is believed to be more harmful than coercion within a steady relationship, particularly by men who view rape in accordance with prevailing rape-supportive attitudes. The same pattern of differentiation emerged in the participants' attitudes toward the psychological harm expected following each, as well as the advisability of reporting the incidents to the police. Implications for preventive efforts are discussed.

Keywords: rape supportive attitudes, acquaintance rape, sexual assault, gender differences

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Authors: Takahiro Ishizaki, Shutaro Hisada, Oi Lun Li

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Control of surface wettability is very important in various industrial fields. Thus, contact angle hysteresis which is defined as the difference between advancing and receding water contact angles has been paid attention because the surface having low contact angle hysteresis can control wetting behavior of water droplet. Self-assembled monolayer (SAM) formed using organic silane molecules has been used to control surface wettability, in particular, static contact angles, however, the effect of alkyl-chain length in organic silane molecules on the contact angle hysteresis has not yet clarified. In this study, we aimed to investigate the effect of alkyl-chain length (C1-C18) in organic silane molecules on the contact angle hysteresis. SAMs were formed on Si wafer by thermal CVD method using silane coupling agents having different alkyl-chain length. The static water contact angles increased with an increase in the alkyl-chain length. On the other hand, although the water contact angle hysteresis tended to decrease with an increase in the alkyl-chain length, in case of the alkyl-chain length of more than C16 the contact angle hysteresis increased. This could be due to the decrease in the molecular mobility because of the increase in the molecular packing density in chemisorbed silane molecules.

Keywords: alkyl-chain length, self-assembled monolayer, silane coupling agent, surface wettability

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Authors: Amanda C. Evans

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Enabling technologies such as continuous processing (CP) approaches can provide the tools needed to control and manipulate reactivities and transform chemical reactions into micro-controlled in-flow processes. Traditional synthetic approaches can be radically transformed by the application of CP, facilitating the pairing of chemical methodologies with technologies from other disciplines. CP supports sustainable processes that controllably generate reaction specificity utilizing supramolecular interactions. Continuous photochemical processing is an emerging field of investigation. The use of light to drive chemical reactivity is not novel, but the controlled use of specific and tunable wavelengths of light to selectively generate molecular structure under continuous processing conditions is an innovative approach towards chemical synthesis. This investigation focuses on the use of circularly polarized (cp) light as a sustainable catalyst for the CP generation of asymmetric molecules. Chiral photolysis has already been achieved under batch, solid-phase conditions: using synchrotron-sourced cp light, asymmetric photolytic selectivities of up to 4.2% enantiomeric excess (e.e.) have been reported. In order to determine the optimal wavelengths to use for irradiation with cp light for any given molecular building block, CD and anisotropy spectra for each building block of interest have been generated in two different solvents (water, hexafluoroisopropanol) across a range of wavelengths (130-400 nm). These spectra are being used to support a series of CP experiments using cp light to generate enantioselectivity.

Keywords: anisotropy, asymmetry, flow chemistry, active pharmaceutical ingredients

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Authors: Phatthanan Chaiyabut

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This research paper investigates whether the development of environmentally friendly practices by luxury hotel resorts can be used as a strategy for gaining competitive advantage through differentiation, and suggests ways to do it. The focus is on luxury hotel resorts in Samut Songkram Province, Thailand. A questionnaire was utilized as a tool to collect data. Statistics utilized in this research included frequency, percentage, mean, standard deviation, and multiple regression analysis. Findings indicate that environmentally friendly development of hotel resorts in Samut Songkram Province has a very limited use as a corporate strategy. Only two luxury hotel resorts had it incorporated in their strategy, it is not much used in marketing indicating environmental issues are not seen as important. This was confirmed through the interviews with the managers that it is not seen as important issue to promote.

Keywords: competitive advantage, competitive strategy, Samut Songkram Province, hotel and resort

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Authors: Thian Khoon Tan, Poi Sim Khiew, Wee Siong Chiu, Chin Hua Chia

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This study investigates the efficacy of magnetically enhanced zinc oxide (MZnO) nanoparticles as a photocatalyst in the photodegradation of synthetic dyes, especially azo dyes. This magnetised zinc oxide has been simply fabricated by mechanical mixing through low-temperature calcination. This MZnO has been analysed through several analytical measurements, including FESEM, XRD, BET, EDX, and TEM, as well as VSM analysis which reflects successful fabrication. A high volume of azo dyes was found in industries effluent wastewater. They contribute to serious environmental stability and are very harmful to human health due to their high stability and carcinogenic properties. Therefore, five azo dyes, Reactive Red 120 (RR120), Disperse Blue 15 (DB15), Acid Brown 14 (AB14), Orange G (OG), and Acid Orange 7 (AO7), have been randomly selected to study their photodegradation property with reference to few characteristics, such as number of azo functional groups, benzene groups, molecular mass, and absorbance. The photocatalytic degradation efficiency was analysed by using a UV-vis spectrophotometer, where the reaction rate constant was obtained. It was found that azo dyes were significantly degraded through the first-order rate constant, which shows a higher kinetic constant as the number of azo functional groups and benzene group increases. However, the kinetic constant is inversely proportional to the molecular weight of these azo dyes.

Keywords: nanoparticles, photocatalyst, magnetically enhanced, wastewater, synthetic dyes, azo dyes

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Authors: Nigatu Tadesse, Ying Liu, Juan Li, Hong Ming Liu

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Gastric carcinogenesis is a lengthy process of histopathological transition from normal to atrophic gastritis (AG) to intestinal metaplasia (GIM), dysplasia toward gastric cancer (GC). The stage of GIM identified as precancerous lesions with resistance to H-pylori eradication and recurrence after endoscopic surgical resection therapies. GIM divided in to two morphologically distinct phenotypes such as complete GIM bearing intestinal type morphology whereas the incomplete type has colonic type morphology. The incomplete type GIM considered to be the greatest risk factor for the development of GC. Studies indicated the expression of the caudal type homeobox 2 (CDX2) gene is responsible for the development of complete GIM but its progressive downregulation from incomplete metaplasia toward advanced GC identified as the risk for IM progression and neoplastic transformation. The downregulation of CDX2 gene have promoted cell growth and proliferation in gastric and colon cancers and ascribed in chemo-treatment inefficacies. CDX2 downregulated through promoter region hypermethylation in which the methylation frequency positively correlated with the dietary history of the patients, suggesting the role of diet as methyl carbon donor sources such as methionine. However, the metabolism of exogenous methionine is yet unclear. Targeting exogenous methionine metabolism has become a promising approach to limits tumor cell growth, proliferation and progression and increase treatment outcome. This review article discusses molecular alterations that could shed light on the potential of exogenous methionine metabolisms, such as gut microbiota alteration as sources of methionine to host cells, metabolic pathway signaling via PI3K/AKt/mTORC1-c-MYC to rewire exogenous methionine and signature of increased gene methylation index, cell growth and proliferation in GIM, with insights to new treatment avenue via targeting methionine metabolism, and the need for future integrated studies on molecular alterations and metabolomics to uncover altered methionine metabolism and characterization of CDX2 methylation in gastric intestinal metaplasia for potential therapeutic exploitation.

Keywords: altered methionine metabolism, Intestinal metaplesia, CDX2 gene, gastric cancer

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Authors: Geetakshi Arora, Danish Malhotra

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Diabetic wounds are serious health issues and often fail to heal, leading to limb amputation that makes the life of the patient miserable. Delayed wound healing has been characterized by an increase in matrix metalloproteinase-9 (MMP-9). Thus research throughout the world has been going on to develop selective MMP-9 inhibitors for aiding diabetic wound healing. Bioactive constituents from natural sources always served as potential leads in drug development with high rates of success. Considering the need for novel selective MMP-9 inhibitors and the importance of natural bioactive compounds in drug development, we have screened a library of bioactive constituents from plant sources that were effective in diabetic wound healing on human MMP-9 (hMMP-9) using molecular docking studies. Screened constituents are ranked according to their dock score, ∆G value (binding affinity), and Ligand efficiency evaluated from FleXX docking and Hyde scoring modules available with drug designing platform LeadIT. Rhamnocitrin showed the highest correlation between dock score, ∆G value (binding affinity), and Ligand efficiency was further explored for binding interactions with hMMP-9. The overall study suggest that Rhamnocitrin is sufficiently decorated with both hydrophilic and hydrophobic substitutions that perfectly block hMMP-9 and act as a potential lead in the design and development of selective hMMP-9 inhibitors.

Keywords: MMP-9, diabetic wound, molecular docking, phytoconstituents

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Authors: Mohammad Moezzibadi, Isabelle Charpentier, Adrien Wanko, Robert Mosé

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The calibration of hydrodynamic parameters for subsurface constructed wetlands (CWs) is a sensitive process since highly non-linear equations are involved in unsaturated flow modeling. CW systems are engineered systems designed to favour natural treatment processes involving wetland vegetation, soil, and their microbial flora. Their significant efficiency at reducing the ecological impact of urban runoff has been recently proved in the field. Numerical flow modeling in a vertical variably saturated CW is here carried out by implementing the Richards model by means of a mixed hybrid finite element method (MHFEM), particularly well adapted to the simulation of heterogeneous media, and the van Genuchten-Mualem parametrization. For validation purposes, MHFEM results were compared to those of HYDRUS (a software based on a finite element discretization). As van Genuchten-Mualem soil hydrodynamic parameters depend on water content, their estimation is subject to considerable experimental and numerical studies. In particular, the sensitivity analysis performed with respect to the van Genuchten-Mualem parameters reveals a predominant influence of the shape parameters α, n and the saturated conductivity of the filter on the piezometric heads, during saturation and desaturation. Modeling issues arise when the soil reaches oven-dry conditions. A particular attention should also be brought to boundary condition modeling (surface ponding or evaporation) to be able to tackle different sequences of rainfall-runoff events. For proper parameter identification, large field datasets would be needed. As these are usually not available, notably due to the randomness of the storm events, we thus propose a simple, robust and low-cost numerical method for the inverse modeling of the soil hydrodynamic properties. Among the methods, the variational data assimilation technique introduced by Le Dimet and Talagrand is applied. To that end, a variational data assimilation technique is implemented by applying automatic differentiation (AD) to augment computer codes with derivative computations. Note that very little effort is needed to obtain the differentiated code using the on-line Tapenade AD engine. Field data are collected for a three-layered CW located in Strasbourg (Alsace, France) at the water edge of the urban water stream Ostwaldergraben, during several months. Identification experiments are conducted by comparing measured and computed piezometric head by means of the least square objective function. The temporal variability of hydrodynamic parameter is then assessed and analyzed.

Keywords: automatic differentiation, constructed wetland, inverse method, mixed hybrid FEM, sensitivity analysis

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Authors: Jiajia Yao, Guanlin Wu, Fang Liu, Junshuai Xue, Yue Hao

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This study reports on the epitaxial growth of a GaN-based resonant tunneling diode (RTD) structure with stable and repeatable double negative differential resistance (NDR) characteristics at room temperature on a c-plane GaN-on-sapphire template using plasma-assisted molecular beam epitaxy (PA-MBE) technology. In this structure, two independent AlN/GaN RTDs are epitaxially connected in series in the vertical growth direction through a silicon-doped GaN layer. As the collector electrode bias voltage increases, the two RTDs respectively align the ground state energy level in the quantum well with the 2DEG energy level in the emitter accumulation well to achieve quantum resonant tunneling and then reach the negative differential resistance (NDR) region. The two NDR regions exhibit similar peak current densities and peak-to-valley current ratios, which are 230 kA/cm² and 249 kA/cm², 1.33 and 1.38, respectively, for a device with a collector electrode mesa diameter of 1 µm. The consistency of the NDR is much higher than the results of on-chip discrete RTD device interconnection, resulting from the smaller chip area, fewer interconnect parasitic parameters, and less process complexity. The methods and results presented in this paper show the brilliant prospects of GaN RTDs in the development of multi-value logic digital circuits.

Keywords: MBE, AlN/GaN, RTDs, double NDR

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Authors: Mohammad Anvari, Helen S. Joyner (Melito)

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Camelina sativa (L.) Crantz is an oilseed crop currently used for the production of biofuels. However, the low price of diesel and gasoline has made camelina an unprofitable crop for farmers, leading to declining camelina production in the US. Hence, the ability to utilize camelina byproduct (defatted meal) after oil extraction would be a pivotal factor for promoting the economic value of the plant. Camelina defatted meal is rich in proteins and polysaccharides. The great diversity in the polysaccharide structural features provides a unique opportunity for use in food formulations as thickeners, gelling agents, emulsifiers, and stabilizers. There is currently a great degree of interest in the study of novel plant polysaccharides, as they can be derived from readily accessible sources and have potential application in a wide range of food formulations. However, there are no published studies on the polysaccharide extracted from camelina meal, and its potential industrial applications remain largely underexploited. Rheological properties are a key functional feature of polysaccharides and are highly dependent on the material composition and molecular structure. Therefore, the objective of this study was to evaluate the rheological properties of the polysaccharide extracted from camelina meal at different conditions to obtain insight on the molecular characteristics of the polysaccharide. Flow and dynamic mechanical behaviors were determined under different temperatures (5-50°C) and concentrations (1-6% w/v). Additionally, the zeta potential of the polysaccharide dispersion was measured at different pHs (2-11) and a biopolymer concentration of 0.05% (w/v). Shear rate sweep data revealed that the camelina polysaccharide displayed shear thinning (pseudoplastic) behavior, which is typical of polymer systems. The polysaccharide dispersion (1% w/v) showed no significant changes in viscosity with temperature, which makes it a promising ingredient in products requiring texture stability over a range of temperatures. However, the viscosity increased significantly with increased concentration, indicating that camelina polysaccharide can be used in food products at different concentrations to produce a range of textures. Dynamic mechanical spectra showed similar trends. The temperature had little effect on viscoelastic moduli. However, moduli were strongly affected by concentration: samples exhibited concentrated solution behavior at low concentrations (1-2% w/v) and weak gel behavior at higher concentrations (4-6% w/v). These rheological properties can be used for designing and modeling of liquid and semisolid products. Zeta potential affects the intensity of molecular interactions and molecular conformation and can alter solubility, stability, and eventually, the functionality of the materials as their environment changes. In this study, the zeta potential value significantly decreased from 0.0 to -62.5 as pH increased from 2 to 11, indicating that pH may affect the functional properties of the polysaccharide. The results obtained in the current study showed that camelina polysaccharide has significant potential for application in various food systems and can be introduced as a novel anionic thickening agent with unique properties.

Keywords: Camelina meal, polysaccharide, rheology, zeta potential

Procedia PDF Downloads 245