Search results for: molecular modelling

Authors: Sfiso Radebe

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The design models dealing with flawless composite structures are in abundance, where the mechanical properties of composite structures are assumed to be known a priori. However, if the worst case scenario is assumed, where material defects combined with processing anomalies in composite structures are expected, a different solution is attained. Furthermore, if the system being designed combines in series hybrid elements, individually affected by material constant variations, it implies that a different approach needs to be taken. In the body of literature, there is a compendium of research that investigates different modes of failure affecting hybrid metal-composite structures. It covers areas pertaining to the failure of the hybrid joints, structural deformation, transverse displacement, the suppression of vibration and noise. In the present study a system employing a combination of two or more hybrid power transmitting elements will be explored for the least favourable dynamic loads as well as weight minimization, subject to uncertain material properties. Elastic constants are assumed to be uncertain-but-bounded quantities varying slightly around their nominal values where the solution is determined using convex models of uncertainty. Convex analysis of the problem leads to the computation of the least favourable solution and ultimately to a robust design. This approach contrasts with a deterministic analysis where the average values of elastic constants are employed in the calculations, neglecting the variations in the material properties.

Keywords: convex modelling, hybrid, metal-composite, robust design

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Authors: Yegnanew A. Shiferaw

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Background: commodity price volatility originating from excessive commodity price fluctuation has been a global problem especially after the recent financial crises. Volatility is a measure of risk or uncertainty in financial analysis. It plays a vital role in risk management, portfolio management, and pricing equity. Objectives: the core objective of this paper is to examine the relationship between the prices of agricultural commodities with oil price, gas price, coal price and exchange rate (USD/Rand). In addition, the paper tries to fit an appropriate model that best describes the log return price volatility and estimate Value-at-Risk and expected shortfall. Data and methods: the data used in this study are the daily returns of agricultural commodity prices from 02 January 2007 to 31st October 2016. The data sets consists of the daily returns of agricultural commodity prices namely: white maize, yellow maize, wheat, sunflower, soya, corn, and sorghum. The paper applies the three-state Markov-switching (MS) regression, the standard single-regime GARCH and the two regime Markov-switching GARCH (MS-GARCH) models. Results: to choose the best fit model, the log-likelihood function, Akaike information criterion (AIC), Bayesian information criterion (BIC) and deviance information criterion (DIC) are employed under three distributions for innovations. The results indicate that: (i) the price of agricultural commodities was found to be significantly associated with the price of coal, price of natural gas, price of oil and exchange rate, (ii) for all agricultural commodities except sunflower, k=3 had higher log-likelihood values and lower AIC and BIC values. Thus, the three-state MS regression model outperformed the two-state MS regression model (iii) MS-GARCH(1,1) with generalized error distribution (ged) innovation performs best for white maize and yellow maize; MS-GARCH(1,1) with student-t distribution (std) innovation performs better for sorghum; MS-gjrGARCH(1,1) with ged innovation performs better for wheat, sunflower and soya and MS-GARCH(1,1) with std innovation performs better for corn. In conclusion, this paper provided a practical guide for modelling agricultural commodity prices by MS regression and MS-GARCH processes. This paper can be good as a reference when facing modelling agricultural commodity price problems.

Keywords: commodity prices, MS-GARCH model, MS regression model, South Africa, volatility

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Authors: Lise Retat, Maria Carmen Huerta, Laura Webber, Franco Sassi

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Background: Intra-generational social mobility (ISM) can be defined as the extent to which individuals change their socio-economic position over a period of time or during their entire life course. The relationship between poor health and ISM is established. Therefore, quantifying the impact that potential health policies have on ISM now and into the future would provide evidence for how social inequality could be reduced. This paper takes the condition of overweight and obesity as an example and estimates the mean earning change per individual if the UK were to introduce policies to effectively reduce overweight and obesity. Methods: The HealthLumen individual-based model was used to estimate the impact of obesity on social mobility measures, such as earnings, occupation, and wealth. The HL tool models each individual's probability of experiencing downward ISM as a result of their overweight and obesity status. For example, one outcome of interest was the cumulative mean earning per person of implementing a policy which would reduce adult overweight and obesity by 1% each year between 2020 and 2030 in the UK. Results: Preliminary analysis showed that by reducing adult overweight and obesity by 1% each year between 2020 and 2030, the cumulative additional mean earnings would be ~1,000 Euro per adult by 2030. Additional analysis will include other social mobility indicators. Conclusions: These projections are important for illustrating the role of health in social mobility and for providing evidence for how health policy can make a difference to social mobility outcomes and, in turn, help to reduce inequality.

Keywords: modelling, social mobility, obesity, health

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Authors: A. A. Dare, E. U. Iniegbedion

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Industrial furnaces generally involve enclosures of fire typically initiated by the combustion of gases. The fire leads to temperature distribution inside the enclosure. A proper understanding of the temperature and velocity distribution within the enclosure is often required for optimal design and use of the furnace. This study was therefore directed at numerical modeling of temperature distribution inside an enclosure as typical in a furnace. A mathematical model was developed from the conservation of mass, momentum and energy. The stream function-vorticity formulation of the governing equations was solved by an alternating direction implicit (ADI) finite difference technique. The finite difference formulation obtained were then developed into a computer code. This was used to determine the temperature, velocities, stream function and vorticity. The effect of the wall heat conduction was also considered, by assuming a one-dimensional heat flow through the wall. The computer code (MATLAB program) developed was used for the determination of the aforementioned variables. The results obtained showed that the transient temperature distribution assumed a uniform profile which becomes more chaotic with increasing time. The vertical velocity showed increasing turbulent behavior with time, while the horizontal velocity assumed decreasing laminar behavior with time. All of these behaviours were equally reported in the literature. The developed model has provided understanding of heat transfer process in an industrial furnace.

Keywords: heat source, modelling, enclosure, furnace

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Authors: Matthew B. Davis, Amit Kumar

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With potentially dangerous impacts of climate change on the horizon, Canada has an opportunity to take a lead role on the international stage to demonstrate how energy use intensity and greenhouse gas emission intensity may be effectively reduced. Through bottom-up modelling of Canada’s energy sector using Long-range Energy Alternative Planning (LEAP) software, it can be determined where efforts should to be concentrated to produce the most positive energy management results. By analyzing a provincially integrated Canada, one can develop strategies to minimize the country’s economic downfall while transitioning to lower-emission energy technologies. Canada’s electricity sector plays an important role in accommodating these transitionary technologies as fossil-fuel based power production is prevalent in many parts of the country and is responsible for a large portion (17%) of Canada’s greenhouse gas emissions. Current findings incorporate an in-depth model of Canada’s current energy supply and demand sectors, as well as a business-as-usual scenario up to the year 2035. This allows for in-depth analysis of energy flow from resource potential, to extraction, to fuel and electricity production, to energy end use and emissions in Canada’s residential, transportation, commercial, institutional, industrial, and agricultural sectors. Bottom-up modelling techniques such as these are useful to critically analyze and compare the various possible scenarios of implementing sustainable energy measures. This work can aid government in creating effective energy and environmental policies, as well as guide industry to what technology or process changes would be most worthwhile to pursue.

Keywords: energy management, LEAP, energy end-use, GHG emissions

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Authors: Hyeon Su Kim, Sungjin Park, Hae Ryung Chang, Hae Rim Jung, Young Zoo Ahn, Yon Hui Kim, Seungyoon Nam

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Ependymoma, one of the most common parenchymal spinal cord tumor, represents 3-6% of all CNS tumor. Especially intracranial ependymomas, which are more frequent in childhood, have a more poor prognosis and more malignant than spinal ependymomas. Although there are growing needs to understand pathogenesis, detailed molecular understanding of pathogenesis remains to be explored. A cancer cell is composed of complex signaling pathway networks, and identifying interaction between genes and/or proteins are crucial for understanding these pathways. Therefore, we explored each ependymoma in terms of differential expressed genes and signaling networks. We used Microsoft Excel™ to manipulate microarray data gathered from NCBI’s GEO Database. To analyze and visualize signaling network, we used web-based PATHOME algorithm and Cytoscape. We show HOX family and NEFL are down-regulated but SCL family is up-regulated in cerebrum and posterior fossa cancers over a spinal cancer, and JAK/STAT signaling pathway and Chemokine signaling pathway are significantly different in the both intracranial ependymoma comparing to spinal ependymoma. We are considering there may be an age-dependent mechanism under different histological pathogenesis. We annotated mutation data of each gene subsequently in order to find potential target genes.

Keywords: systems biology, ependymoma, deg, network analysis

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Authors: Margaret Schmuhl, Michelle Cubellis

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Violence against women (VAW) is a widespread social problem affecting nearly two million women in the United States each year. Recently, feminist criminologists have sought to examine patriarchy as a guiding framework for understanding violence against women. Literature on VAW often examines measures of structural gender equality, often overlooking ideological patriarchy which is necessary for structural inequality to remain unchallenged. Additionally, empirical literature generally focuses on extreme forms of VAW, rape, and femicide, often neglecting more common types of violence. This literature, under the theoretical guidance of the Liberal, Radical, and Marxist feminist traditions, finds mixed support for the relationship of patriarchy and VAW. Explanations for these inconsistencies may include data availability, and the use of different operationalizations of structural patriarchy. Research is needed to examine fuller operationalizations of patriarchy in social institutions and to extend this theoretical framework to the criminal justice response to VAW (i.e., clearance rates). This study examines sexual violence clearance rates under the theoretical guidance of these feminist traditions using incident- and county-level data from National Incident Based Reporting System and other sources in multilevel modelling. The findings suggest mixed support for the feminist hypotheses and that patriarchy and gender equality differentially affect arrest clearance rates and clearance through exceptional means for sexual violence.

Keywords: clearance rates, gender equality, multilevel modelling, patriarchy, sexual victimization, violence against women

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Authors: Pedro A. S. Bergamo, Emilia S. Streng, Jan Rosenkranz, Yousef Ghorbani

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Within the often-hazardous mineral industry, simulation training has speedily gained appreciation as an important method of increasing site safety and productivity through enhanced operator skill and knowledge. Performance calculations related to froth flotation, one of the most important concentration methods, is probably the hardest topic taught during the training of plant operators. Currently, most training teach those skills by traditional methods like slide presentations and hand-written exercises with a heavy focus on memorization. To optimize certain aspects of these pieces of training, we developed “MinFloat”, which teaches the operation formulas of the froth flotation process with the help of gamification. The simulation core based on a first-principles flotation model was implemented in Unity3D and an instructor tutoring system was developed, which presents didactic content and reviews the selected answers. The game was tested by 25 professionals with extensive experience in the mining industry based on a questionnaire formulated for training evaluations. According to their feedback, the game scored well in terms of quality, didactic efficacy and inspiring character. The feedback of the testers on the main target audience and the outlook of the mentioned solution is presented. This paper aims to provide technical background on the construction of educational games for the mining industry besides showing how feedback from experts can more efficiently be gathered thanks to new technologies such as online forms.

Keywords: training evaluation, simulation based training, modelling, and simulation, froth flotation

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Authors: Laura Pytel, Georg Baumann, Gregor Gstrein, Corina Klug

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Premium cars often coat the instrument panels with a bilaminate consisting of a soft foam and a plastic skin. The coating is torn open during the passenger airbag deployment under high strain rates. Characterizing and simulating the top coat layer is crucial for predicting the attenuation that delays the airbag deployment, effecting the design of the restrain system and to reduce the demand of simulation adjustments through expensive physical component testing.Up to now, bilaminates used within cars either have been modelled by using a two-dimensional shell formulation for the whole coating system as one which misses out the interaction of the two layers or by combining a three-dimensional formulation foam layer with a two-dimensional skin layer but omitting the foam in the significant parts like the expected tear line area and the hinge where high compression is expected. In both cases, the properties of the coating causing the attenuation are not considered. Further, at present, the availability of material information, as there are failure dependencies of the two layers, as well as the strain rate of up to 200 1/s, are insufficient. The velocity of the passenger airbag flap during an airbag shot has been measured with about 11.5 m/s during first ripping; the digital image correlation evaluation showed resulting strain rates of above 1500 1/s. This paper provides a high strain rate material characterization of a bilaminate consisting of a thin polypropylene foam and a thermoplasctic olefins (TPO) skin and the creation of validated material models. With the help of a Split Hopkinson tension bar, strain rates of 1500 1/s were within reach. The experimental data was used to calibrate and validate a more physical modelling approach of the forced ripping of the bilaminate. In the presented model, the three-dimensional foam layer is continuously tied to the two-dimensional skin layer, allowing failure in both layers at any possible position. The simulation results show a higher agreement in terms of the trajectory of the flaps and its velocity during ripping. The resulting attenuation of the airbag deployment measured by the contact force between airbag and flaps increases and serves usable data for dimensioning modules of an airbag system.

Keywords: bilaminate ripping behavior, High strain rate material characterization and modelling, induced material failure, TPO and foam

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Authors: Md. Alauddin, Md. Ruhul Amin, Md. Omar Faruque, Muhammad Ali Siddiquee, Zakir Hossain Howlader, Mohammad Asaduzzaman

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Diabetes and hypertension are the major lifestyle related diseases. The α-amylase and angiotensin converting enzymes (ACE) are the key enzymes that regulate diabetes and hypertension. The aim was to develop a drug for the treatment of diabetes and hypertension. The Rice Bran (RB) sample (Oryza sativa; BRRI-Dhan-84) was collected from the Bangladesh Rice Research Institute (BRRI), and rice bran proteins were isolated and hydrolyzed by hydrolyzing enzyme alcalase and trypsin. In vivo experiment suggested that rice bran bioactives has an effect on regulating the expression of several key gluconeogenesis and lipogenesis-regulating genes, such as glucose-6-phosphatase, phosphoenolpyruvate carboxykinase, and fatty acid synthase. The above genes have a connection of regulating the glucose level, lipids profile as well as act as an anti-inflammatory agent. A molecular docking, bioinformatics and in vitro experiments were performed. We found rice bran protein hydrolysates significantly (<0.05) influence the peptide concentration in the case of trypsin, alcalase, and (trypsin + alcalase) digestion. The in vitro analysis found that protein hydrolysate significantly (<0.05) reduced diabetic and hypertension as well as oxidative stress. A molecular docking study showed that the YY and IP peptide have a significantly strong binding affinity to the active site of the ACE enzyme and α-amylase with -7.8Kcal/mol and -6.2Kcal/mol, respectively. The Molecular dynamics (MD) simulation and Swiss ADME data analysis showed that less toxicity risk, good physicochemical properties, pharmacokinetics, and drug-likeness with drug scores 0.45 and 0.55 of YY and IP peptides, respectively. Thus, rice bran bioactive could be a good candidate for the treatment of diabetes and hypertension.

Keywords: anti-hypertensive and anti-hyperglycemic, anti-oxidative, bioinformatics, in vitro study, rice bran proteins and peptides

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Authors: Zhong-Dan Tu, Wang-Xi Fan, Yi-Chen Huang, Jen-Taut Yeh

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Novel ultrahigh molecular weight polyethylene (UHMWPE)/cellulose nanofiber (CNF) (F100CNFy) and UHMWPE/modified cellulose nanofiber (MCNF) (F100MCNFxy) as-prepared nanocomposite fibers were prepared by spinning F100CNFy and F100MCNFxy gel solutions, respectively. Cellulose nanofibers were successfully prepared by proper acid treatment of cotton fibers using sulfuric acid solutions. The best prepared CNF is with specific surface areas around 120 m2/g and a nanofiber diameter of 20 nm. Modified cellulose nanofiber was prepared by grafting maleic anhydride grafted polyethylene (PE-g-MAH) onto cellulose nanofibers. The achievable draw ratio (Dra) values of each F100MCNFxy as-prepared fiber series specimens approached a maximal value as their MCNF contents reached the optimal value at 0.05 phr. In which, the maximum Dra value obtained for F100MCNFx0.05 as-prepared fiber specimen prepared at the optimal MCNF content reached another maximum value as the weight ratio of PE-g-MAH to CNF approach an optimal value at 6. Similar to those found for the achievable drawing properties of the as-prepared fibers, the orientation factor, tensile strength (σ f) and initial modulus (E) values of drawn F100MCNF6y fiber series specimens with a fixed draw ratio reach a maximal value as their MCNF contents approach the optimal value, wherein the σ f and E values of the drawn F100MCNFxy fiber specimens are significantly higher than those of the drawn F100 fiber specimens and corresponding drawn F100CNFy fiber specimens prepared at the same draw ratios and CNF contents but without modification. To understand the interesting ultradrawing, thermal, orientation and tensile properties of F100CNFy and F100MCNFxy fiber specimens, Fourier transform infra-red, specific surface areas, and transmission electron microcopic analyses of the original and modified CNF nanofillers were performed in this study.

Keywords: ultradrawing, cellulose nanofibers, ultrahigh molecular weight polyethylene, nanocomposite fibers

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Authors: Nicolaas Unland, John Webb

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The acidification and mobilisation of metals during the oxidation of acid sulfate soils exposed during lake bed drying is an increasingly common phenomenon under climate scenarios with reduced rainfall. In order to assess the risk of generating high concentrations of acidity and dissolved metals, chromium suite analysis are fundamental, but sometimes limited in characterising the potential risks they pose. This study combines such fundamental test work, along with incubation tests and 1D modelling to investigate the risks associated with the drying of Third Reedy Lake in South East Australia. Core samples were collected from a variable depth of 0.5 m below the lake bed, at 19 locations across the lake’s footprint, using a boat platform. Samples were subjected to a chromium suite of analysis, including titratable actual acidity, chromium reducible sulfur and acid neutralising capacity. Concentrations of reduced sulfur up to 0.08 %S and net acidities up to 0.15 %S indicate that acid sulfate soils have formed on the lake bed during permanent inundation over the last century. A further sub-set of samples were prepared in 7 columns and subject to accelerated heating, drying and wetting over a period of 64 days in laboratory. Results from the incubation trial indicate that while pyrite oxidation proceeded, minimal change to soil pH or the acidity of leachate occurred, suggesting that the internal buffering capacity of lake bed sediments was sufficient to neutralise a large proportion of the acidity produced. A 1D mass balance model was developed to assess potential changes in lake water quality during drying based on the results of chromium suite and incubation tests. Results from the above test work and modelling suggest that acid sulfate soils pose a moderate to low risk to the Third Reedy Lake system. Further, the risks can be effectively managed during the initial stages of lake drying via flushing with available mildly alkaline water. The study finds that while test work such as chromium suite analysis are fundamental in characterizing acid sulfate soil environments, they can the overestimate risks associated with the soils. Subsequent incubation test work may more accurately characterise such soils and lead to better-informed management strategies.

Keywords: acid sulfate soil, incubation, management, model, risk

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Authors: Fatimah A. Alhomaid

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The present study was planned to investigate the role of molecular changes and immunohistochemical in early detection of liver cancer in Saudi patients. our results were carried out on 54 patients liver cancer. We obtained our data from laboratory in King Khalid University Hospital. The specimens were taken (54) patients with liver cancer 34 male and 14 female and 2 control. The average age of varied from 37-85 years. The tumor was diagnosed as grade I in tow patients (male and female) and grade 2 in 45 patients (28 male and 17 female) while the grade 3 in 4 patients (all males). The specimens were processed for haematoxylin and eosin staining, immunohistochemical technique and flow cytometry analysis. Our study noted that most patients had adenocarcinoma which characterized by presence of signet-ring cells were very clear in advanced patients with adenocarcinoma. Our sections in adenocarcinoma in grade 2 and stage 3 had an increase in signet ring cells,an increase in the acini of glands and an increase in number of lymphocytes which spread to the muscular layer. With advancing the disease, there were haemorrhage in blood and increase in lymphocytes and increase in the number of nuclei in the tubular glands. Our study was carried on 48 patients, immunohistochemical diagnosis (CK20, PCNA, P53) and the analysis of DNA content by flow cytometry technique. Our study indicated that the presence of correlation between the immunohistochemical analysis for P53 and the grades. The reaction of P53 appeared as strong in nucleus in grades &stage 3 and appeared in other sections as dark brown pigment. Our study indicated that the absence of correlation between the immunohistochemical analysis for PCAN and the grades. In our sections there were strong reaction in the more 80% of nuclei in grade 1& stage 2. Our study indicated that the presence of correlation between the immunohistochemical analysis for CK20 and the grades. Our results indicated the presence of positive reaction in cytoplasm varied from weak to moderate in grade 3 & stage 4. Concerning the Flow cytometry technique our results indicated that the presence of correlation between the DNA and different stages of liver cancer.

Keywords: cancer, CK20, DNA, cytometry analysis, liver, immunohistochemical, molecular changes, PCNA, p53

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Authors: Arpita Roy, Navneeta Bharadvaja

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Cancer is an uncontrolled growth of abnormal cells in the body. It is one of the most serious diseases on which extensive research work has been going on all over the world. Structure-based drug designing is a computational approach which helps in the identification of potential leads that can be used for the development of a drug. Plumbagin is a naphthoquinone derivative from Plumbago zeylanica roots and belongs to one of the largest and diverse groups of plant metabolites. Anticancer and antiproliferative activities of plumbagin have been observed in animal models as well as in cell cultures. Plumbagin shows inhibitory effects on multiple cancer-signaling proteins; however, the binding mode and the molecular interactions have not yet been elucidated for most of these protein targets. In this investigation, an attempt to provide structural insights into the binding mode of plumbagin against four cancer receptors using molecular docking was performed. Plumbagin showed minimal energy against targeted cancer receptors, therefore suggested its stability and potential towards different cancers. The least binding energies of plumbagin with COX-2, TACE, and CDK6 are -5.39, -4.93, -and 4.81 kcal/mol, respectively. Comparison studies of plumbagin with different receptors showed that it is a promising compound for cancer treatment. It was also found that plumbagin obeys the Lipinski’s Rule of 5 and computed ADMET properties which showed drug likeliness and improved bioavailability. Since plumbagin is from a natural source, it has reduced side effects, and these results would be useful for cancer treatment.

Keywords: cancer, receptor, plumbagin, docking

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Authors: Rodrigo Pacheco-Ruiz, Jonathan Adams, Felix Pedrotti

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This paper introduces the applicability of underwater photogrammetric survey within challenging conditions as the main tool to enhance and enrich the process of documenting archaeological excavation through the creation of 4D models. Photogrammetry was being attempted on underwater archaeological sites at least as early as the 1970s’ and today the production of traditional 3D models is becoming a common practice within the discipline. Photogrammetry underwater is more often implemented to record exposed underwater archaeological remains and less so as a dynamic interpretative tool.  Therefore, it tends to be applied in bright environments and when underwater visibility is > 1m, reducing its implementation on most submerged archaeological sites in more turbid conditions. Recent years have seen significant development of better digital photographic sensors and the improvement of optical technology, ideal for darker environments. Such developments, in tandem with powerful processing computing systems, have allowed underwater photogrammetry to be used by this research as a standard recording and interpretative tool. Using multi-source photogrammetry (5, GoPro5 Hero Black cameras) this paper presents the accumulation of daily (4D) underwater surveys carried out in the Early Bronze Age (3,300 BC) to Late Ottoman (17th Century AD) archaeological site of Ropotamo in the Bulgarian Black Sea under challenging conditions (< 0.5m visibility). It proves that underwater photogrammetry can and should be used as one of the main recording methods even in low light and poor underwater conditions as a way to better understand the complexity of the underwater archaeological record.

Keywords: 4D modelling, Black Sea Maritime Archaeology Project, multi-source photogrammetry, low visibility underwater survey

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Authors: Md. Baki Billah, Suraiya Parveen, Shuvra Kanti Dey

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Bangladesh is earning a lot of foreign currency by exporting shrimp, but this industry is facing a tremendous problem due to the infection of white spot syndrome virus (WSSV). This study was undermined to develop rapid detection method of WSSV. A total of shrimp samples 240 collected from the 12 shrimp farms of different coastal regions (Satkhira, Khulna, and Bagerhat) were analyzed by conventional PCR using VP28 and VP664 gene-specific primers. In satkhira, Bagerhat and Khulna 39, 41 and 29 samples were found WSSV positive respectively. Real-time PCR using 71-bp amplicon for VP664 gene correlated well with conventional PCR data. The prevalence rates of WSSV among the collected 240 samples were Satkhira 38%, Khulna 47% and Bagerhat 50%. Molecular analysis of the VP28 gene sequences of WSSV revealed that Bangladeshi strains phylogenetically affiliated to the strains belong to India. This work concluded that WSSV infections are widely distributed in the coastal regions cultured shrimp in Bangladesh. Physico-chemical parameters were within the range of fish culture.

Keywords: coastal regions of Bangladesh, PCR, shrimp, white spot syndrome virus

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Authors: Eleni Stefanidou, Nikolaos Katsenios, Ioanna Karamichali, Aspasia Efthimiadou, Panagiotis Madesis

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The excessive use of pesticides and fertilizers has significant environmental and human health-related negative effects. In the frame of the development of sustainable agriculture practices, especially in the context of extreme environmental changes (climate change), it is important to develop alternative practices to increase productivity and biotic and abiotic stress tolerance. Beneficial bacteria, such as symbiotic bacteria in legumes (rhizobia) and symbiotic or free-living Plant Growth Promoting Rhizobacteria (PGPR), which could act as "plant probiotics", can promote plant growth and significantly increase the resistance of crops under adverse environmental conditions. In this study, we explored the symbiotic relationships between Faba bean (Vicia faba L.) cultivars with different PGPR bacteria, aiming to identify the possible influence on yield and biotic-abiotic phytoprotection benefits. Transcriptomic analysis of root and whole plant samples was executed for two Vicia faba L. cultivars (Polikarpi and Solon) treated with selected PGPR bacteria (6 treatments: B. subtilis + Rhizobium-mixture, A. chroococcum + Rhizobium-mixture, B. subtilis, A. chroococcum and Rhizobium-mixture). Preliminary results indicate a significant yield (Seed weight and Total number of pods) increase in both varieties, ranging around 25%, in comparison to the control, especially for the Solon cultivar. The increase was observed for all treatments, with the B. subtilis + Rhizobium-mixture treatment being the highest performing. The correlation of the physiological and morphological data with the transcriptome analysis revealed molecular mechanisms and molecular targets underlying the observed yield increase, opening perspectives for the use of nitrogen-fixing bacteria as a natural, more ecological enhancer of legume crop productivity.

Keywords: plant probiotics, PGPR, legumes, sustainable agriculture

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Authors: Maria Amodeo, Pasquale Arpaia, Marco Buzio, Vincenzo Di Capua, Francesco Donnarumma

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Different deep neural network architectures have been compared and tested to predict magnetic hysteresis in the context of pulsed electromagnets for experimental physics applications. Modelling quasi-static or dynamic major and especially minor hysteresis loops is one of the most challenging topics for computational magnetism. Recent attempts at mathematical prediction in this context using Preisach models could not attain better than percent-level accuracy. Hence, this work explores neural network approaches and shows that the architecture that best fits the measured magnetic field behaviour, including the effects of hysteresis and eddy currents, is the nonlinear autoregressive exogenous neural network (NARX) model. This architecture aims to achieve a relative RMSE of the order of a few 100 ppm for complex magnetic field cycling, including arbitrary sequences of pseudo-random high field and low field cycles. The NARX-based architecture is compared with the state-of-the-art, showing better performance than the classical operator-based and differential models, and is tested on a reference quadrupole magnetic lens used for CERN particle beams, chosen as a case study. The training and test datasets are a representative example of real-world magnet operation; this makes the good result obtained very promising for future applications in this context.

Keywords: deep neural network, magnetic modelling, measurement and empirical software engineering, NARX

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Authors: Ramin Mehdiabadi, Neda Menbari, Mohammad Nazir Menbari

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As a pressing public health concern, breast cancer stands as the predominant oncological diagnosis and principal cause of cancer-related mortality among women globally, accounting for 11.7% of new cancer incidences and 6.9% of cancer-related deaths. The annual figures indicate that approximately 230,480 women are diagnosed with breast cancer in the United States alone, with 39,520 succumbing to the disease. While developed economies have reported a deceleration in both incidence and mortality rates across various forms of cancer, including breast cancer, emerging and low-income economies manifest a contrary escalation, largely attributable to lifestyle-mediated risk factors such as tobacco usage, physical inactivity, and high caloric intake. Breast cancer is distinctly characterized by molecular heterogeneity, manifesting in specific subtypes delineated by biomarkers—Estrogen Receptors (ER), Progesterone Receptors (PR), and Human Epidermal Growth Factor Receptor 2 (HER2). These subtypes, comprising Luminal A, Luminal B, HER2-enriched, triple-negative/basal-like, and normal-like, necessitate nuanced, subtype-specific therapeutic regimens, thereby challenging the applicability of generalized treatment protocols. Within this molecular complexity, the transcription factor Forkhead Box M1 (FoxM1) has garnered attention as a significant driver of cellular proliferation, tumorigenesis, metastatic progression, and treatment resistance in a spectrum of human malignancies, including breast cancer. Concurrently, microRNAs (miRs), specifically miR-216b-5p, have been identified as post-transcriptional gene expression regulators and potential tumor suppressors. The overarching objective of this academic investigation is to explicate the multifaceted interrelationship between FoxM1 and miR-216b-5p across the disparate molecular subtypes of breast cancer. Employing a methodologically rigorous, interdisciplinary research design that incorporates cutting-edge molecular biology techniques, sophisticated bioinformatics analytics, and exhaustive meta-analyses of extant clinical data, this scholarly endeavor aims to unveil novel biomarker-specific therapeutic pathways. By doing so, this research is positioned to make a seminal contribution to the advancement of personalized, efficacious, and minimally toxic treatment paradigms, thus profoundly impacting the global efforts to ameliorate the burden of breast cancer.

Keywords: breast cancer, fox m1, microRNAs, mir-216b-5p, gene expression

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Authors: A. Ascenso, C. Silveira, B. Augusto, S. Rafael, S. Coelho, J. Ferreira, A. Monteiro, P. Roebeling, A. I. Miranda

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Innovative nature-based solutions (NBSs) can provide answers to the challenges that urban areas are currently facing due to urban densification and extreme weather conditions. The effects of NBSs are recognized and include improved quality of life, mental and physical health and improvement of air quality, among others. Part of the work developed in the scope of the UNaLab project, which aims to guide cities in developing and implementing their own co-creative NBSs, intends to assess the impacts of NBSs on air quality, using Eindhoven city as a case study. The state-of-the-art online air quality modelling system WRF-CHEM was applied to simulate meteorological and concentration fields over the study area with a spatial resolution of 1 km2 for the year 2015. The baseline simulation (without NBSs) was validated by comparing the model results with monitored data retrieved from the Eindhoven air quality database, showing an adequate model performance. In addition, land use changes were applied in a set of simulations to assess the effects of different types of NBSs. Finally, these simulations were compared with the baseline scenario and the impacts of the NBSs were assessed. Reductions on pollutant concentrations, namely for NOx and PM, were found after the application of the NBSs in the Eindhoven study area. The present work is particularly important to support public planners and decision makers in understanding the effects of their actions and planning more sustainable cities for the future.

Keywords: air quality, modelling approach, nature based solutions, urban area

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Authors: Masoud Sheidai, Fahimeh Koohdar, Hashem Sharifi

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Juglans regia (L.) commonly known as Persian walnut of the genus Juglans L. (Juglandaceae) is one of the most important cultivated plant species due to its high-quality wood and edible nuts. The genetic diversity analysis is essential for conservation and management of tree species. Persian walnut is native from South-Eastern Europe to North-Western China through Tibet, Nepal, Northern India, Pakistan, and Iran. The species like Persian walnut, which has a wide range of geographical distribution, should harbor extensive genetic variability to adapt to environmental fluctuations they face. We aimed to study the population genetic structure of seven Persian walnut populations including three wild and four cultivated populations by using ISSR (Inter simple sequence repeats) and SRAP (Sequence related amplified polymorphism) molecular markers. We also aimed to compare the genetic variability revealed by ISSR neutral multilocus marker and rDNA ITS sequences. The studied populations differed in morphological features as the samples in each population were clustered together and were separate from the other populations. Three wild populations studied were placed close to each other. The mantel test after 5000 times permutation performed between geographical distance and morphological distance in Persian walnut populations produced significant correlation (r = 0.48, P = 0.002). Therefore, as the populations become farther apart, they become more divergent in morphological features. ISSR analysis produced 47 bands/ loci, while we obtained 15 SRAP bands. Gst and other differentiation statistics determined for these loci revealed that most of the ISSR and SRAP loci have very good discrimination power and can differentiate the studied populations. AMOVA performed for these loci produced a significant difference (< 0.05) supporting the above-said result. AMOVA produced significant genetic difference based on ISSR data among the studied populations (PhiPT = 0.52, P = 0.001). AMOVA revealed that 53% of the total variability is due to among population genetic difference, while 47% is due to within population genetic variability. The results showed that both multilocus molecular markers and ITS sequences can differentiate Persian walnut populations. The studied populations differed genetically and showed isolation by distance (IBD). ITS sequence based MP and Bayesian phylogenetic trees revealed that Iranian walnut cultivars form a distinct clade separated from the cultivars studied from elsewhere. Almost all clades obtained have high bootstrap value. The results indicated that a combination of multilpcus and sequencing molecular markers can be used in genetic differentiation of Persian walnut.

Keywords: genetic diversity, population, molecular markers, genetic difference

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Authors: Vineeth Siripuram, Abhineet Nigam

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A bioreactor is an engineered system that supports a biologically active environment. Along the years, the advancements in bioreactors have been widely accepted all over the world for varied applications ranging from sewage treatment to tissue cloning. Driven by tissue and organ shortage, tissue engineering has emerged as an alternative to transplantation for the reconstruction of lost or damaged organs. In this study, Computational fluid dynamics (CFD) has been used to model porous medium flow in scaffolds (taken from the literature) with different flow patterns. A detailed analysis of different scaffold geometries and their influence on cell deposition in the perfusion system is been carried out using Computational fluid dynamics (CFD). Considering the fact that, the scaffold should mimic the organs or tissues structures in a three-dimensional manner, certain assumptions were made accordingly. The research on scaffolds has been extensively carried out in different bioreactors. However, there has been less focus on the morphology of the scaffolds and the flow patterns in which the perfusion system is laid upon. The objective of this paper is to employ a computational approach using CFD simulation to determine the optimal morphology and the anisotropic measurements of the various samples of scaffolds. Using predictive computational modelling approach, variables which exert dominant effects on the cell deposition within the scaffold were prioritised and corresponding changes in morphology of scaffold and flow patterns in the perfusion systems are made. A Eulerian approach was carried on in multiple CFD simulations, and it is observed that the morphological and topological changes in the scaffold perfusion system are of great importance in the commercial applications of scaffolds.

Keywords: cell seeding, CFD, flow patterns, modelling, perfusion systems, scaffold

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Authors: Bharti Saini, Sukanta K. Dash

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In this work polymeric Nanofiltration (NF) membranes of polysulfone (PSF) (average molecular weight of 22400 Da) were prepared using polyethylene glycol (PEG) (average molecular weight of 200 Da) as an organic additive and ZnCl2 as an inorganic additive. Dimethyl acetamide (DMAc) was used as the solvent, and Deionised water as nonsolvent. The membranes were prepared by phase inversion (immersion precipitation) method. PEG 200 and ZnCl2 in varying concentration are directly added into the casting solution of PSF and DMAc. PEG 200 was used in concentration varying from 0 to 10 % (w/w) in the solution of PSF and DMAc, while ZnCl2 is varied from 0 to 2% (w/w). Membranes were characterized for surface morphology, water uptake, porosity and contact angle, with respect to concentration of PEG and ZnCl2. It was observed that with the increase in additive PEG 200, the porosity and hence, hydrophilicity increase. As a result, the number of pores increases as justified by the SEM analysis as well. The study revealed that the synergistic effect of PEG with ZnCl2 is more effective, and the best results were produced by the solution containing 2% PEG 200 and 1% ZnCl2. It was inferred that with the increase in concentration of additives, the pore size goes on decreasing. The membranes obtained gradually move from microfiltration range to nanofiltration range, and this change is primarily brought about by the addition of ZnCl2.

Keywords: membrane, phase inversion method, polysulfone, porous structure

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Authors: E. Esra Kasapbaşı, Büşra Yıldırım

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Weak oxidizing radicals, such as alkyl peroxyl derivatives, react with carotenoids through hydrogen atom transfer to form neutral carotenoid radicals. Using the DFT method, it has been observed that s-cis-β-carotene is more stable than all-transforms. In the context of this study, an attempt is made to explain the reaction mechanism of the isomers of β-carotene, which exhibits antioxidant properties, with n-pentyl peroxide, one of the alkyl peroxyl molecules, using the Density Functional Theory (DFT) method. The cis and transforms of β-carotene are used in the study to determine which form is more reactive. For this purpose, Natural Bond Orbital (NBO) charges of all optimized structures are calculated, and electron transfer is determined by examining electron transitions between Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). Additionally, the radical character and reaction mechanism of β-carotene in a radical environment are attempted to be explained based on the calculations. The theoretical inclination of whether β-carotene in cis or transforms is more active in reaction is also discussed. All these calculations are performed in the gas phase using the Integral Equation Formalism Polarizable Continuum Model IEFPCM method with dichloromethane as the solvent.

Keywords: β-carotene, n-pentyl peroxyl radical, DFT, TD-DFT

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Authors: Mohamed Al-Hazmi, Abdullah Al-Arfaj, Moussa Ihab

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Raw, unpasteurized milk can carry dangerous bacteria such as Salmonella, E. coli, and Listeria, which are responsible for causing numerous foodborne illnesses. The objective of this study was molecular characterization of shiga toxogenic E. coli in raw milk collected from different Egyptian governorates by multiplex PCR. During the period of 25th May to 25th October 2012, a total of 320 bulk-tank milk samples were collected from 10 cow farms located in different Egyptian governorates. Bacteriological examination of milk samples revealed the presence of E. coli organisms in 65 samples (20.3%), serotyping of the E. coli isolates revealed, 35 strains (10.94%) O111, 15 strains (4.69%) O157: H7, 10 strains (3.13%) O128 and 5 strains (1.56%) O119. Multiplex PCR for detection of shiga toxin type 2 and intimin genes revealed positive amplification of 255 bp fragment of shiga toxin type 2 gene and 384 bp fragment of intimin gene from all E. coli serovar O157: H7, while from serovar O111 were 25 (71.43%), 20 (57.14%) and from serovar O128 were 6 (60%), 8 (80%), respectively. The results of multiplex PCR assay are useful for identification of STEC possessing the eaeA and stx2 genes.

Keywords: raw milk, E. coli, multiplex PCR, Shiga toxin type 2, intimin gene

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Authors: Amr A. El Hanafy, Yasser M. Saad, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group).

Keywords: milk yield, beta-casein precursor (CSN2), Saudi camel, molecular markers

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Authors: Yiannis Vacanas, Kyriacos Themistocleous, Athos Agapiou, Diofantos Hadjimitsis

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Building Information Modelling (BIM) technology is considered by construction professionals as a very valuable process in modern design, procurement and project management. Construction professionals of all disciplines can use a single 3D model which BIM technology provides, to design a project accurately and furthermore monitor the progress of construction works effectively and efficiently. Unmanned Aerial Vehicles (UAVs), a technology initially developed for military applications, is now without any difficulty accessible and has already been used by commercial industries, including the construction industry. UAV technology has mainly been used for collection of images that allow visual monitoring of building and civil engineering projects conditions in various circumstances. UAVs, nevertheless, have undergone significant advances in equipment capabilities and now have the capacity to acquire high-resolution imagery from many angles in a cost effective manner, and by using photogrammetry methods, someone can determine characteristics such as distances, angles, areas, volumes and elevations of an area within overlapping images. In order to examine the potential of using a combination of BIM and UAV technologies in construction project management, this paper presents the results of a case study of a typical road construction project where the combined use of the two technologies was used in order to achieve efficient and accurate as-built data collection of the works progress, with outcomes such as volumes, and production of sections and 3D models, information necessary in project progress monitoring and efficient project management.

Keywords: BIM, project management, project monitoring, UAV

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Authors: Hiroyuki Aoki

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The physical properties of polymer materials are dependent on the conformation and molecular motion of a polymer chain. Therefore, the structure and dynamic behavior of the single polymer chain have been the most important concerns in the field of polymer physics. However, it has been impossible to directly observe the conformation of the single polymer chain in a bulk medium. In the current work, the novel techniques to study the conformation and dynamics of a single polymer chain are proposed. Since a fluorescence method is extremely sensitive, the fluorescence microscopy enables the direct detection of a single molecule. However, the structure of the polymer chain as large as 100 nm cannot be resolved by conventional fluorescence methods because of the diffraction limit of light. In order to observe the single chains, we developed the labeling method of polymer materials with a photo-switchable dye and the super-resolution microscopy. The real-space conformational analysis of single polymer chains with the spatial resolution of 15-20 nm was achieved. The super-resolution microscopy enables us to obtain the three-dimensional coordinates; therefore, we succeeded the conformational analysis in three dimensions. The direct observation by the nanometric optical microscopy would reveal the detailed information on the molecular processes in the various polymer systems.

Keywords: polymer materials, single molecule, super-resolution techniques, conformation

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Authors: Kiran Fatima, Kashif Ali

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Staphylococcus aureus is an opportunistic human as well as animal pathogen that causes a variety of diseases. A total of 70 staphylococci isolates were obtained from soil, water, yogurt, and clinical samples. The likely staphylococci clinical isolates were identified phenotypically by different biochemical tests. Molecular identification was done by PCR using species-specific 16S rRNA primer pairs, and finally, 50 isolates were found to be positive as Staphylococcus aureus, sciuri, xylous and cohnii. Screened isolates were further analyzed by several microbiological diagnostics tests, including gram staining, coagulase, capsule, hemolysis, fermentation of glucose, lactose, maltose, and sucrose tests enzymatic reactions. It was found that 78%, 81%, and 51% of isolates were positive for gelatin hydrolysis, protease, and lipase activities, respectively. Antibiogram analysis of isolated Staphylococcus aureus strains with respect to different antimicrobial agents revealed resistance patterns ranging from 57 to 96%. Our study also shows 70% of strains to be MRSA, 54.3% as VRSA, and 54.3% as both MRSA and VRSA. All the identified isolates were subjected to detection of mecA, nuc, and hlb genes, and 70%, 84%, and 40% were found to harbour mecA, nuc, and hlb genes, respectively. The current investigation is highly important and informative for the high-level multidrug-resistant Staphylococcus aureus infections inclusive also of methicillin and vancomycin.

Keywords: MRSA, VRSA, mecA, MSSA

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Authors: Apisaraporn Baicharoen, Prapasiri Pongprayoon

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Betaine aldehyde dehydrogenase 2 (BADH2) is an enzyme that inhibits the accumulation of 2-acetyl-1-pyrroline (2AP), a potent flavor compound in rice fragrance. BADH2 contains three domains (NAD-binding, substrate-binding, and oligomerization domains). It catalyzes the oxidation of amino aldehydes. The lack of BADH2 results in the formation of 2AP and consequently an increase in rice fragrance. To date, inadequate data on BADH2 structure and function are available. An insight into the nature of BADH2 can serve as one of key starting points for the production of high quality fragrant rice. In this study, we therefore constructed the homology model of BADH2 and employed 500-ns Molecular Dynamics simulations (MD) to primarily understand the structural and dynamic properties of BADH2. Initially, Ramachandran plot confirms the good quality of modeled protein structure. Principle Component Analysis (PCA) was also calculated to capture the protein dynamics. Among 3 domains, the results show that NAD binding site is found to be more flexible. Moreover, interactions from key amino acids (N162, E260, C294, and Y419) that are crucial for function are investigated.

Keywords: betaine aldehyde dehydrogenase 2, fragrant rice, homology modeling, molecular dynamics simulations

Procedia PDF Downloads 194