Search results for: molecular modelling

Authors: Habib Alehossein, M. S. K. Fernando

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Soil density depends on the volume of the voids and the proportion of the water and air in the voids. However, there is a limit to the contraction of the voids at any given compaction energy, whereby additional water is used to reduce the void volume further by lubricating the particles' frictional contacts. Hence, at an optimum moisture content and specific compaction energy, the density of unsaturated soil can be maximized where the void volume is minimum. However, when considering a full compaction curve and permutations and variations of all these components (soil, air, water, and energy), laboratory soil compaction tests can become expensive, time-consuming, and exhausting. Therefore, analytical methods constructed on a few test data can be developed and used to reduce such unnecessary efforts significantly. Concentrating on the compaction testing results, this study discusses the analytical modelling method developed for some fine-grained and coarse-grained soils of Queensland. Soil properties and characteristics, such as full functional compaction curves under various compaction energy conditions, were studied and developed for a few soil types. Using MATLAB, several generic analytical codes were created for this study, covering all possible compaction parameters and results as they occur in a soil mechanics lab. These MATLAB codes produce a family of curves to determine the relationships between the density, moisture content, void ratio, saturation, and compaction energy.

Keywords: analytical, MATLAB, modelling, compaction curve, void ratio, saturation, moisture content

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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

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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: Nicola G. G. Cecca

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In Italian IPSSEOAs, high schools that give a vocational education to students that will work in the field of Enogastronomy and Hotel Management, the course of Food Science allows the students to start and see food as a mixture of substances that they will transform during their profession. These substances are characterized not only by a chemical composition but also by a molecular structure that makes them nutritionally active. But the increasing number of new products proposed by Food Industry, the modern techniques of production and transformation, the innovative preparations required by customers have made many information reported in the most wide spread Food Science textbooks not up-to-date or too poor for the people who will work in catering sector. Often Authors offer information aged to Bohr’s Atomic Model and to the ‘Octet Rule’ proposed by G.N. Lewis to describe the Chemical Bond, without giving any reference to new as Orbital Atomic Model and Molecular Orbital Theory that, in the meantime, start to be old themselves. Furthermore, this antiquated information precludes an easy understanding of a wide range of properties of nutritive substances and many reactions in which the food constituents are involved. In this paper, our attention is pointed out to use GEOMAG™ to represent the dynamics with which the chemical bond is formed during the synthesis of the molecules. GEOMAG™ is a toy, produced by the Swiss Company Geomagword S.A., pointed to stimulate in children, aged between 6-10 years, their fantasy and their handling ability and constituted by metallic spheres and metallic magnetic bars coated by coloured plastic materials. The simulation carried out with GEOMAG™ is based on the similitude existing between the Coulomb’s force and the magnetic attraction’s force and in particular between the formulae with which they are calculated. The electrostatic force (F in Newton) that allows the formation of the chemical bond can be calculated by mean Fc = kc q1 q2/d2 where: q1 e q2 are the charge of particles [in Coulomb], d is the distance between the particles [in meters] and kc is the Coulomb’s constant. It is surprising to observe that the attraction’s force (Fm) acting between the magnetic extremities of GEOMAG™ used to simulate the chemical bond can be calculated in the same way by using the formula Fm = km m1 m2/d2 where: m1 e m2 represent the strength of the poles [A•m], d is the distance between the particles [m], km = μ/4π in which μ is the magnetic permeability of medium [N•A-2]. The magnetic attraction can be tested by students by trying to keep the magnetic elements of GEOMAG™ separate by hands or trying to measure by mean an appropriate dynamometric system. Furthermore, by using a dynamometric system to measure the magnetic attraction between the GEOMAG™ elements is possible draw a graphic F=f(d) to verify that the curve obtained during the simulation is very similar to that one hypnotized, around the 1920’s by Linus Pauling to describe the formation of H2+ in according with Molecular Orbital Theory.

Keywords: chemical bond, molecular orbital theory, magnetic attraction force, GEOMAG™

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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: Rumana Keyani, Haleema Sadia, Asia Nosheen, Rabia Naz, Humaira Yasmin, Sidra Zahoor

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Tomato is a significant crop of the world and is one of the staple foods of Pakistan. A vast number of plant pathogens from simple viruses to complex parasites cause diseases in tomatoes but fungal infection in our country is quite high. Sometimes the symptoms are too harsh destroying the crop altogether. Countries like our own with continuously increasing massive population and limited resources cannot afford such an economic loss. There is an array of morphological, genetic, biochemical and molecular processes involved in plant resistance mechanisms to biotic stress. The study of different metabolic pathways like Jasmonic acid (JA) pathways and most importantly signaling molecules like ROS/RNS and their redoxin enzymes i.e. TRX and NRX is crucial to disease management, contributing to healthy plant growth. So, improving tolerance in crop plants against biotic stresses is a dire need of our country and world as whole. In the current study, fungal pathogenic strains Alternaria solani and Rhizoctonia solani were used to inoculate tomatoes to check the defense responses of tomato plant against these pathogens at molecular as well as phenotypic level with jasmonic acid and spermidine pretreatment. All the growth parameters (root and shoot length, dry and weight root, shoot weight measured 7 days post-inoculation, exhibited that infection drastically declined the growth of the plant whereas jasmonic acid and spermidine assisted the plants to cope up with the infection. Thus, JA and Spermidine treatments maintained comparatively better growth factors. Antioxidant assays and expression analysis through real time quantitative PCR following time course experiment at 24, 48 and 72 hours intervals also exhibited that activation of JA defense genes and a polyamine Spermidine helps in mediating tomato responses against fungal infection when used alone but the two treatments combined mask the effect of each other.

Keywords: fungal infection, jasmonic acid defence, tomato, spermidine

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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: Mohammad Nazri Abdul Bahari, Nurshafika Mohd Sakeh, Siti Nor Akmar Abdullah

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Basal stem rot (BSR) is the most devastating disease in oil palm. Among the oil palm pathogenic fungi, the most prevalent and virulent species associated with BSR is Ganoderma boninense. Early detection of G. boninense attack in oil palm wherein physical symptoms has not yet appeared can offer opportunities to prevent the spread of the necrotrophic fungus. However, poor understanding of molecular defense responses and roles of antifungal metabolites in oil palm against G. boninense has complicated the resolving measures. Hence, characterization of defense-related molecular responses and production of antifungal compounds during early interaction with G. boninense is of utmost important. Four month-old oil palm (Elaeis guineensis) seedlings were artificially infected with G. boninense-inoculated rubber wood block via sitting technique. RNA of samples were extracted from roots and leaves tissues at 0, 3, 7 and 11 days post inoculation (d.p.i) followed with sequencing using RNA-Seq method. Differentially-expressed genes (DEGs) of oil palm-G. boninense interaction were identified, while changes in metabolite profile will be scrutinized related to the DEGs. The RNA-Seq data generated a total of 113,829,376 and 313,293,229 paired-end clean reads from untreated (0 d.p.i) and treated (3, 7, 11 d.p.i) samples respectively, each with two biological replicates. The paired-end reads were mapped to Elaeis guineensis reference genome to screen out non-oil palm genes and subsequently generated 74,794 coding sequences. DEG analysis of phytohormone biosynthetic genes in oil palm roots revealed that at p-value ≤ 0.01, ethylene and jasmonic acid may act in antagonistic manner with salicylic acid to coordinate defense response at early interaction with G. boninense. Findings on metabolite profiling of G. boninense-infected oil palm roots and leaves are hoped to explain the defense-related compounds elicited by Elaeis guineensis in response to G. boninense colonization. The study aims to shed light on molecular defense response of oil palm at early interaction with G. boninense and promote prevention measures against Ganoderma infection.

Keywords: Ganoderma boninense, metabolites, phytohormones, RNA-Seq

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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: Elmira Ghanbari, Jan Van Esch, Stephen J. Picken, Sahil Aggarwal

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Organogels are formed by the assembly of low molecular weight gelators (LMWG) into fibrous structures. The assembly of these molecules into crystalline fibrous structures occurs as a result of reversible interactions such as π-stacking, hydrogen-bonding, and van der Waals interactions. Bisamide organogelators with two amide groups have been used as one of LMWGs which show efficient assembly behavior via hydrogen bonding for network formation, the formation of a crystalline network for solvent entrapment. In this study, different bisamide gelators with different lengths of alkyl chains have been added to the bisamide parent gels. The effect of the addition of bisamide additives on the gelation of bisamide gels is described. Investigation of the thermal properties of the gels by differential scanning calorimetry and dropping ball techniques indicated that the bisamide gels can be formed by the addition of a high concentration of the second bisamide components. The microstructure of the gels with different gelator components has been visualized with scanning electron microscopy (SEM) which has shown systematic woven, platelet-like, and a combination of those morphologies for different gels. Examining the addition of a range of bisamide additives with different structural characteristics than the parent bisamide gels has confirmed the effect of the molecular structure on the morphology of the bisamide gels and their final properties.

Keywords: bisamide organogelator additives, gel morphology, gel properties, self-assembly

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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: Abdulwahab Kammon, Tan Sheau Wei, Abdul Rahman Omar, Abdunaser Dayhum, Ibrahim Eldghayes, Monier Sharif

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Infectious bronchitis virus (IBV) is a very dynamic and evolving virus which causing major economic losses to the global poultry industry. Recently, the Libyan poultry industry faced severe outbreak of respiratory distress associated with high mortality and dramatic drop in egg production. Tracheal and cloacal swabs were analyzed for several poultry viruses. IBV was detected using SYBR Green I real-time PCR detection based on the nucleocapsid (N) gene. Sequence analysis of the partial N gene indicated high similarity (~ 94%) to IBV strain 3382/06 that was isolated from Taiwan. Even though the IBV strain 3382/06 is more similar to that of the Mass type H120, the isolate has been implicated associated with intertypic recombinant of 3 putative parental IBV strains namely H120, Taiwan strain 1171/92 and China strain CK/CH/LDL/97I. Complete sequencing and antigenicity studies of the Libya IBV strains are currently underway to determine the evolution of the virus and its importance in vaccine induced immunity. In this paper, we documented for the first time the presence of possibly variant IBV strain from Libya which required a dramatic change in the vaccination program.

Keywords: Libya, infectious bronchitis, molecular characterization, viruses, vaccine

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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: Hamza Javar Magnier, Leslie V. Woodcock

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It has been reported that at temperatures above the critical there is no “continuity of liquid and gas”, as originally hypothesized by van der Waals. Rather, both gas and liquid phases, with characteristic properties as such, extend to supercritical temperatures. Each phase is bounded by the locus of a percolation transition, i.e. a higher-order thermodynamic phase change associated with percolation of gas clusters in a large void, or liquid interstitial vacancies in a large cluster. Between these two-phase bounds, it is reported there exists a mesophase that resembles an otherwise homogeneous dispersion of gas micro-bubbles in liquid (foam) and a dispersion of liquid micro-droplets in gas (mist). Such a colloidal-like state of a pure one-component fluid represents a hitherto unchartered equilibrium state of matter besides pure solid, liquid or gas. Here we provide compelling evidence, from molecular dynamics (MD) simulations, for the existence of this supercritical mesophase and its colloidal nature. We report preliminary results of computer simulations for a model fluid using a simplistic representation of atoms or molecules, i.e. a hard-core repulsion with an attraction so short that the atoms are referred to as “adhesive spheres”. Molecular clusters, and hence percolation transitions, are unambiguously defined. Graphics of color-coded clusters show colloidal characteristics of the supercritical mesophase.

Keywords: critical phenomena, mesophase, supercritical, square-well, critical parameters

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Authors: B. Gonzalez-Yebra, H. Barajas, P. Palomares, M. Hernandez, O. Torres, M. Ayala, A. L. González, G. Vazquez-Ortiz, M. L. Guzman

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Leukemia arises by molecular alterations of the normal hematopoietic stem cell (HSC) transforming it into a leukemic stem cell (LSC) with high cell proliferation, self-renewal, and cell differentiation. Chronic myeloid leukemia (CML) originates from an LSC-leading to elevated proliferation of myeloid cells and acute lymphoblastic leukemia (ALL) originates from an LSC development leading to elevated proliferation of lymphoid cells. In both cases, LSC can be identified by multicolor flow cytometry using several antibodies. However, to date, LSC levels in peripheral blood (PB) are not established well enough in ALL and CML patients. On the other hand, the detection of the minimal residue disease (MRD) in leukemia is mainly based on the identification of the mRNA bcr-abl gene in CML patients and some other genes in ALL patients. There is no a properly biomarker to detect MDR in both types of leukemia. The objective of this study was to determine mRNA bcr-abl and the percentage of LSC in peripheral blood of patients with CML and ALL and identify a possible association between the amount of LSC in PB and clinical data. We included in this study 19 patients with Leukemia. A PB sample was collected per patient and leukocytes were obtained by Ficoll gradient. The immunophenotype for LSC CD34+ was done by flow cytometry analysis with CD33, CD2, CD14, CD16, CD64, HLA-DR, CD13, CD15, CD19, CD10, CD20, CD34, CD38, CD71, CD90, CD117, CD123 monoclonal antibodies. In addition, to identify the presence of the mRNA bcr-abl by RT-PCR, the RNA was isolated using TRIZOL reagent. Molecular (presence of mRNA bcr-abl and LSC CD34+) and clinical results were analyzed with descriptive statistics and a multiple regression analysis was performed to determine statistically significant association. In total, 19 patients (8 patients with ALL and 11 patients with CML) were analyzed, 9 patients with de novo leukemia (ALL = 6 and CML = 3) and 10 under treatment (ALL = 5 and CML = 5). The overall frequency of mRNA bcr-abl was 31% (6/19), and it was negative in ALL patients and positive in 80% in CML patients. On the other hand, LSC was determined in 16/19 leukemia patients (%LSC= 0.02-17.3). The Novo patients had higher percentage of LSC (0.26 to 17.3%) than patients under treatment (0 to 5.93%). The amount of LSC was significantly associated with the amount of LSC were: absence of treatment, the absence of splenomegaly, and a lower number of leukocytes, negative association for the clinical variables age, sex, blasts, and mRNA bcr-abl. In conclusion, patients with de novo leukemia had a higher percentage of circulating LSC than patients under treatment, and it was associated with clinical parameters as lack of treatment, absence of splenomegaly and a lower number of leukocytes. The mRNA bcr-abl detection was only possible in the series of patients with CML, and molecular detection of LSC could be identified in the peripheral blood of all leukemia patients, we believe the identification of circulating LSC may be used as biomarker for the detection of the MRD in leukemia patients.

Keywords: stem cells, leukemia, biomarkers, flow cytometry

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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: 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: Seyed Hassan Moosa-kazemi, Jalal Mohammadi Soleimani, Hassan Vatandoost, Mohammad Hassan Shirazi, Sara Hajikhani, Roonak Bakhtiari, Morteza Akbari, Siamak Hydarzadeh

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Malaria is an infectious disease and considered most important health problems in the southeast of Iran. Iran is elimination malaria phase and new tool need to vector control. Paraterasgenesis is a new way to cut of life cycle of the malaria parasite. In this study, the microflora of the surface and gut of various stages of Anopheles fluviatilis James as one of the important malaria vector was studied using biochemical and molecular techniques during 2013-2014. Twelve bacteria species were found including; Providencia rettgeri, Morganella morganii, Enterobacter aerogenes, Pseudomonas oryzihabitans, Citrobacter braakii، Citrobacter freundii، Aeromonas hydrophila، Klebsiella oxytoca, Citrobacter koseri, Serratia fonticola، Enterobacter sakazakii and Yersinia pseudotuberculosis. The species of Alcaligenes faecalis, Providencia vermicola and Enterobacter hormaechei were identified in various stages of the vector and confirmed by biochemical and molecular techniques. We found Providencia rettgeri proper candidate for paratransgenesis.

Keywords: Anopheles fluviatilis, bacteria, malaria, Paraterasgenesis, Southern Iran

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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: Thangaraj Arasakumar, Athar Ata, Palathurai Subramaniam Mohan

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A series of novel 4-quinolone-3-carboxylic acid grafted spiropyrrolidines as new type of antibacterial agents were synthesized via multicomponent 1,3-dipolar cycloaddition reaction of an azomethine ylides with a newly prepared (E)-4-oxo-6-(3-phenyl-acryloyl)-1,4-dihydro-quinoline-3-carboxylic acids in high regioselectivity with good yields. The structure of cycloadduct characterized by FT IR, mass, 1H, 13C, 2D NMR techniques and elemental analysis. Structure and spectrometry of compound 8a has been investigated theoretically by using HF and DFT approach at B3LYP, M05-2x/6-31G* levels of theories. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. A good agreement is found between the measured and calculated values. The DFT studies support the molecular mechanism of this cycloaddition reaction and determine the molecular electrostatic potential and thermodynamic properties. Furthermore, the antibacterial activities of synthesized compounds were evaluated against Gram-positive bacteria (Staphylococcus aureus, Bacillus subtilis) and Gram-negative bacteria strains (Escherichia coli, Klebsiella pneumoniae). Among 21 compounds screened, 8f and 8p were found to be more active against tested bacteria.

Keywords: antibacterial activity, azomethine ylide, DFT calculation, spirooxindole

Procedia PDF Downloads 215

Authors: S. Taghavi Kalajahi, A. Koerdt, T. Lund Skovhus

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Cathodic protection (CP) is an electrochemical method to control and manage corrosion in different industries and environments. CP which is widely used, especially in buried and sub-merged environments, which both environments are susceptible to microbiologically influenced corrosion (MIC). Most of the standards recommend performing CP using -800 mV, however, if MIC threats are high or sulfate reducing bacteria (SRB) is present, the recommendation is to use more negative potentials for adequate protection of the metal. Due to the lack of knowledge and research on the effectiveness of CP on MIC, to the author’s best knowledge, there is no information about what MIC threat is and how much more negative potentials should be used enabling adequate protection and not overprotection (due to hydrogen embrittlement risk). Recently, the development and cheaper price of molecular microbial methods (MMMs) open the door for more effective investigations on the corrosion in the presence of microorganisms, along with other electrochemical methods and surface analysis. In this work, using MMMs, the gene expression of SRB biofilm under different potentials of CP will be investigated. The specific genes, such as pH buffering, metal oxidizing, etc., will be compared at different potentials, enabling to determine the precise potential that protect the metal effectively from SRB. This work is the initial step to be able to standardize the recommended potential under MIC condition, resulting better protection for the infrastructures.

Keywords: cathodic protection, microbiologically influenced corrosion, molecular microbial methods, sulfate reducing bacteria

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Authors: El-Sohaimy Sobhy A., Androsova Natalia, Toshev Abuvali Djabarovec

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The conditions of the isolation of proteins from the hemp seeds were optimized in the current work. Moreover, the physicochemical and functional properties of hemp protein isolate were evaluated for its potential application in food manufacturing. The elastin protein is the most predominant protein in the protein profile with a molecular weight of 58.1 KDa, besides albumin, with a molecular weight of 31.5 KDa. The FTIR spectrum detected the absorption peaks of the amide I in 1750 and 1600 cm⁻¹, which pointed to C=O stretching while N-H was stretching at 1650-1580 cm⁻¹. The peak at 3250 was related to N-H stretching of primary aliphatic amine (3400-3300 cm⁻¹), and the N-H stretching for secondary (II) amine appeared at 3350-3310 cm⁻¹. Hemp protein isolate (HPI) was showed high content of arginine (15.52 g/100 g), phenylalanine+tyrosine (9.63 g/100 g), methionine + cysteine (5.49 g/100 g), leucine + isoleucine (5.21 g/100 g) and valine (4.53 g/100 g). It contains a moderate level of threonine (3.29 g/100 g) and lysine (2.50 g/100 g), with the limiting amino acid being a tryptophan (0.22 g/100 g HPI). HPI showed high water-holding capacity (4.5 ± 2.95 ml/g protein) and oil holding capacity (2.33 ± 1.88 ml/g) values. The foaming capacity of HPI was increased with increasing the pH values to reach the maximum value at pH 11 (67.23±3.20 %). The highest emulsion ability index of HPI was noted at pH 9 (91.3±2.57 m2/g) with low stability (19.15±2.03).

Keywords: Cannabis sativa ssp., protein isolate, isolation conditions, amino acid composition, chemical properties, functional properties

Procedia PDF Downloads 180

Authors: Beata Lachtara, Renata Szewczyk, Katarzyna Bielinska, Kinga Wieczorek, Jacek Osek

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Listeria monocytogenes is an important human and animal pathogen that causes foodborne outbreaks. The bacteria may be present in different types of food: cheese, raw vegetables, sliced meat products and vacuum-packed sausages, poultry, meat, fish. The most common method, which has been used for the investigation of genetic diversity of L. monocytogenes, is PFGE. This technique is reliable and reproducible and established as gold standard for typing of L. monocytogenes. The aim of the study was characterization by molecular serotyping and PFGE analysis of L. monocytogenes strains isolated from fresh fish and fish products in Poland. A total of 301 samples, including fresh fish (n = 129) and fish products (n = 172) were, collected between January 2014 and March 2016. The bacteria were detected using the ISO 11290-1 standard method. Molecular serotyping was performed with PCR. The isolates were tested with the PFGE method according to the protocol developed by the European Union Reference Laboratory for L. monocytogenes with some modifications. Based on the PFGE profiles, two dendrograms were generated for strains digested separately with two restriction enzymes: AscI and ApaI. Analysis of the fingerprint profiles was performed using Bionumerics software version 6.6 (Applied Maths, Belgium). The 95% of similarity was applied to differentiate the PFGE pulsotypes. The study revealed that 57 of 301 (18.9%) samples were positive for L. monocytogenes. The bacteria were identified in 29 (50.9%) ready-to-eat fish products and in 28 (49.1%) fresh fish. It was found that 40 (70.2%) strains were of serotype 1/2a, 14 (24.6%) 1/2b, two (4.3%) 4b and one (1.8%) 1/2c. Serotypes 1/2a, 1/2b, and 4b were presented with the same frequency in both categories of food, whereas serotype 1/2c was detected only in fresh fish. The PFGE analysis with AscI demonstrated 43 different pulsotypes; among them 33 (76.7%) were represented by only one strain. The remaining 10 profiles contained more than one isolate. Among them 8 pulsotypes comprised of two L. monocytogenes isolates, one profile of three isolates and one restriction type of 5 strains. In case of ApaI typing, the PFGE analysis showed 27 different pulsotypes including 17 (63.0%) types represented by only one strain. Ten (37.0%) clusters contained more than one strain among which four profiles covered two strains; three had three isolates, one with five strains, one with eight strains and one with ten isolates. It was observed that the isolates assigned to the same PFGE type were usually of the same serotype (1/2a or 1/2b). The majority of the clusters had strains of both sources (fresh fish and fish products) isolated at different time. Most of the strains grouped in one cluster of the AscI restriction was assigned to the same groups in ApaI investigation. In conclusion, PFGE used in the study showed a high genetic diversity among L. monocytogenes. The strains were grouped into varied clonal clusters, which may suggest different sources of contamination. The results demonstrated that 1/2a serotype was the most common among isolates from fresh fish and fish products in Poland.

Keywords: Listeria monocytogenes, molecular characteristic, PFGE, serotyping

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

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The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene

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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: Purva Mishra, Rajesh Potlia, Kuljeet Singh Sandhu

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The role of glycyl residues in the protein structure has lingered within the research community for the last several decades. Glycyl residue is the only amino acid that is achiral due to the lack of a side chain and can, therefore, exhibit Ramachandran conformations that are disallowed for L-amino acids. The structural and functional significance of glycyl residues with L-disallowed conformation, however, remains obscure. Through statistical analysis of various datasets, we found that the glycyls with L-disallowed conformations are over-represented at disease-associated sites and tend to be evolutionarily conserved. The mutations of L-disallowed glycyls tend to destabilize the native conformation, reduce protein solubility, and promote inter-molecular aggregations. We uncovered a structural motif referred to as “β-crescent” formed around the L-disallowed glycyl, which prevents β-sheet aggregation by disrupting the alternating pattern of β-pleats. The L-disallowed conformation of glycyls also holds predictive power to infer the pathogenic missense variants. Altogether, our observations highlight that the L-disallowed conformation of glycyls is selected to facilitate native folding and prevent inter-molecular aggregations. The findings may also have implications for designing more stable proteins and prioritizing the genetic lesions implicated in diseases.

Keywords: Ramachandran plot, β-sheet, protein stability, protein aggregation

Procedia PDF Downloads 72