Search results for: molecular identification

Authors: Hyo-In Koh, Anders Nordborg, Alex Sievi, Chun-Kwon Park

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The noise source for the interior room of the high speed train is constituted by the rolling contact between the wheel and the rail, aerodynamic noise and structure-borne sound generated through the vibrations of bogie, connection points to the carbody. Air-borne sound is radiated through the panels and structures into the interior room of the trains. The high-speed lines are constructed with slab track systems and many tunnels. The interior noise level and the frequency characteristics vary according to types of the track structure and the infrastructure. In this paper the main sound sources and the transfer paths are studied to find out the contribution characteristics of the sources to the interior noise of a high-speed rail vehicle. For the identification of the acoustic power of each parts of the rolling noise sources a calculation model of wheel/rail noise is developed and used. For the analysis of the transmission of the sources to the interior noise noise and vibration are measured during the operation of the vehicle. According to operation speeds, the mainly contributed sources and the paths could be analyzed. Results of the calculations on the source generation and the results of the measurement with a high-speed train are shown and discussed.

Keywords: rail vehicle, high-speed, interior noise, noise source

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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: Kishor Chandra Kandpal, Amit Kumar

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The Indian Himalaya region harbours approximately 1748 plants of medicinal importance, and as per International Union for Conservation of Nature (IUCN), the 112 plant species among these are threatened and endangered. To ease the pressure on these plants, the government of India is encouraging its in-situ cultivation. The Saussurea costus, Valeriana jatamansi, and Picrorhiza kurroa have also been prioritized for large scale cultivation owing to their market demand, conservation value and medicinal properties. These species are found from 1000 m to 4000 m elevation ranges in the Indian Himalaya. Identification of these plants in the field requires taxonomic skills, which is one of the major bottleneck in the conservation and management of these plants. In recent years, Hyperspectral remote sensing techniques have been precisely used for the discrimination of plant species with the help of their unique spectral signatures. In this background, a spectral library of the above 03 medicinal plants was prepared by collecting the spectral data using a handheld spectroradiometer (325 to 1075 nm) from farmer’s fields of Himachal Pradesh and Uttarakhand states of Indian Himalaya. The Random forest (RF) model was implied on the spectral data for the classification of the medicinal plants. The 80:20 standard split ratio was followed for training and validation of the RF model, which resulted in training accuracy of 84.39 % (kappa coefficient = 0.72) and testing accuracy of 85.29 % (kappa coefficient = 0.77). This RF classifier has identified green (555 to 598 nm), red (605 nm), and near-infrared (725 to 840 nm) wavelength regions suitable for the discrimination of these species. The findings of this study have provided a technique for rapid and onsite identification of the above medicinal plants in the field. This will also be a key input for the classification of hyperspectral remote sensing images for mapping of these species in farmer’s field on a regional scale. This is a pioneer study in the Indian Himalaya region for medicinal plants in which the applicability of hyperspectral remote sensing has been explored.

Keywords: himalaya, hyperspectral remote sensing, machine learning; medicinal plants, random forests

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Authors: W. A. Gonçalves, E. P. Souza, C. R. Alcântara

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The ISCCP-Tracking database offers an opportunity to study physical and morphological characteristics of Convective Systems based on geostationary meteorological satellites. This database contains 26 years of tracking of Convective Systems for the entire globe. Then, Tropical Squall Lines which occur in Brazil are certainly within the database. In this study, we propose a methodology for identification of these systems based on the ISCCP-Tracking database. A physical and morphological characterization of these systems is also shown. The proposed methodology is firstly based on the year of 2007. The Squall Lines were subjectively identified by visually analyzing infrared images from GOES-12. Based on this identification, the same systems were identified within the ISCCP-Tracking database. It is known, and it was also observed that the Squall Lines which occur on the north coast of Brazil develop parallel to the coast, influenced by the sea breeze. In addition, it was also observed that the eccentricity of the identified systems was greater than 0.7. Then, a methodology based on the inclination (based on the coast) and eccentricity (greater than 0.7) of the Convective Systems was applied in order to identify and characterize Tropical Squall Lines in Brazil. These thresholds were applied back in the ISCCP-Tracking database for the year of 2007. It was observed that other systems, which were not Squall Lines, were also identified. Then, we decided to call all systems identified by the inclination and eccentricity thresholds as Linear Convective Systems, instead of Squall Lines. After this step, the Linear Convective Systems were identified and characterized for the entire database, from 1983 to 2008. The physical and morphological characteristics of these systems were compared to those systems which did not have the required inclination and eccentricity to be called Linear Convective Systems. The results showed that the convection associated with the Linear Convective Systems seems to be more intense and organized than in the other systems. This affirmation is based on all ISCCP-Tracking variables analyzed. This type of methodology, which explores 26 years of satellite data by an objective analysis, was not previously explored in the literature. The physical and morphological characterization of the Linear Convective Systems based on 26 years of data is of a great importance and should be used in many branches of atmospheric sciences.

Keywords: squall lines, convective systems, linear convective systems, ISCCP-Tracking

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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: 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: 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: A. I. Alajtal, H. G. M. Edwards, M. A. Elbagermi

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Raman spectroscopy is currently a part of the instrumentation suite of the ESA ExoMars mission for the remote detection of life signatures in the Martian surface and subsurface. Terrestrial analogues of Martian sites have been identified and the biogeological modifications incurred as a result of extremophilic activity have been studied. Analytical instrumentation protocols for the unequivocal detection of biomarkers in suitable geological matrices are critical for future unmanned explorations, including the forthcoming ESA ExoMars mission to search for life on Mars scheduled for 2018 and Raman spectroscopy is currently a part of the Pasteur instrumentation suite of this mission. Here, Raman spectroscopy using 785nm excitation was evaluated for determining various concentrations of beta-carotene in admixture with polyaromatic hydrocarbons and usnic acid have been investigated by Raman microspectrometry to determine the lowest levels detectable in simulation of their potential identification remotely in geobiological conditions in Martian scenarios. Information from this study will be important for the development of a miniaturized Raman instrument for targetting Martian sites where the biosignatures of relict or extant life could remain in the geological record.

Keywords: raman spectroscopy, mars-analog, beta-carotene, PAHs

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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: Mani Venkatesh, Catarina Delgado, Purvishkumar Patel

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The sustainable supply chain is gaining popularity among practitioners because of increased environmental degradation and stakeholder awareness. On the other hand supply chain, risk management is very crucial for the practitioners as it potentially disrupts supply chain operations. Prediction and addressing the risk caused by social issues in the supply chain is paramount importance to the sustainable enterprise. More recently, the usage of Big data analytics for forecasting business trends has been gaining momentum among professionals. The aim of the research is to explore the application of big data, predictive analytics in successfully mitigating supply chain social risk and demonstrate how such mitigation can help in achieving sustainability (environmental, economic & social). The method involves the identification and validation of social issues in the supply chain by an expert panel and survey. Later, we used a case study to illustrate the application of big data in the successful identification and mitigation of social issues in the supply chain. Our result shows that the company can predict various social issues through big data, predictive analytics and mitigate the social risk. We also discuss the implication of this research to the body of knowledge and practice.

Keywords: big data, sustainability, supply chain social sustainability, social risk, case study

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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: Noura Al Akkari, Aurélie Foucquier, Sylvain Lespinats

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Load monitoring is a management process for energy consumption towards energy savings and energy efficiency. Non Intrusive Load Monitoring (NILM) is one method of load monitoring used for disaggregation purposes. NILM is a technique for identifying individual appliances based on the analysis of the whole residence data retrieved from the main power meter of the house. Our NILM framework starts with data acquisition, followed by data preprocessing, then event detection, feature extraction, then general appliance modeling and identification at the final stage. The event detection stage is a core component of NILM process since event detection techniques lead to the extraction of appliance features. Appliance features are required for the accurate identification of the household devices. In this research work, we aim at developing a new event detection methodology with accurate load disaggregation to extract appliance features. Time-domain features extracted are used for tuning general appliance models for appliance identification and classification steps. We use unsupervised algorithms such as Dynamic Time Warping (DTW). The proposed method relies on detecting areas of operation of each residential appliance based on the power demand. Then, detecting the time at which each selected appliance changes its states. In order to fit with practical existing smart meters capabilities, we work on low sampling data with a frequency of (1/60) Hz. The data is simulated on Load Profile Generator software (LPG), which was not previously taken into consideration for NILM purposes in the literature. LPG is a numerical software that uses behaviour simulation of people inside the house to generate residential energy consumption data. The proposed event detection method targets low consumption loads that are difficult to detect. Also, it facilitates the extraction of specific features used for general appliance modeling. In addition to this, the identification process includes unsupervised techniques such as DTW. To our best knowledge, there exist few unsupervised techniques employed with low sampling data in comparison to the many supervised techniques used for such cases. We extract a power interval at which falls the operation of the selected appliance along with a time vector for the values delimiting the state transitions of the appliance. After this, appliance signatures are formed from extracted power, geometrical and statistical features. Afterwards, those formed signatures are used to tune general model types for appliances identification using unsupervised algorithms. This method is evaluated using both simulated data on LPG and real-time Reference Energy Disaggregation Dataset (REDD). For that, we compute performance metrics using confusion matrix based metrics, considering accuracy, precision, recall and error-rate. The performance analysis of our methodology is then compared with other detection techniques previously used in the literature review, such as detection techniques based on statistical variations and abrupt changes (Variance Sliding Window and Cumulative Sum).

Keywords: general appliance model, non intrusive load monitoring, events detection, unsupervised techniques;

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Authors: Mohammad Javad Seddighi, Avar Almukhtar

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Sustainable urban planning and design (SUPD) play a critical role in achieving the United Nations Sustainable Development Goals (UN SDGs). While there are many rating systems and standards available to assess the sustainability of the built environment, there is still a lack of a comprehensive framework that can assess the quality of SUPD in a specific context. In this paper, we present a framework for assessing the quality of SUPD in Iranian cities, considering their unique cultural, social, and environmental contexts. The aim of this study is to develop a framework for assessing the quality of SUPD in Iranian cities. To achieve this aim, the following objectives are pursued review and synthesis of relevant literature on SUPD, identification of key indicators and criteria for assessing the quality of SUPD in Iranian cities application of the framework to case studies of Iranian cities and evaluation and refinement of the framework based on the results of the case studies. The framework is developed based on a review and synthesis of relevant literature on SUPD, and the identification of key indicators and criteria for assessing the quality of SUPD in Iranian cities. The framework is then applied to case studies of Iranian cities and the results are evaluated and refined. The data for this study are collected through a review of relevant literature on SUPD, including academic journals, conference proceedings, and books. The case studies of Iranian cities are selected based on their relevance and availability of data. The data are collected through interviews, site visits, and document analysis. This paper presents a framework for assessing the quality of SUPD in Iranian cities. The framework is developed based on a review and synthesis of relevant literature, identification of key indicators and criteria, application to case studies, and evaluation and refinement. The framework provides a comprehensive and context-specific approach to assessing the quality of SUPD in Iranian cities. It can be used by urban planners, designers, and policymakers to improve the sustainability and liveability of Iranian cities, and it can be adapted for use in other contexts.

Keywords: sustainable urban planning and design, framework, quality assessment, Iranian cities, case studies

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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: Lola Brasseur, Guillaume Caulier, Marie Demeyer, Pascal Gerbaux, Igor Eeckhaut

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Seawater being an ideal dispersing agent, chemical communication stays predominant in marine ecosystems. However, if many molecules acting in chemical heterospecific communication have already been well described in terrestrial ecosystems, only three of these molecules were identified in marine ecosystems. Echinoderms and their symbiotic organisms constitute very good models to study heterospecific chemical communication because each class synthesizes a specific type of molecules and symbioses with echinoderms as hosts are very usual. In this study, the chemical communication that allows the commensal shrimps Tuleariocaris holthuisi Hipeau-Jacquotte, 1965 to live with their host Echinometra mathaei (Blainville, 1825) was investigated. The chemoreception of the shrimp was characterized using olfactometers and it was demonstrated that hosts and synthetic hydroxynaphthoquinones are attractive to the symbiotic shrimps. Hydroxynaphthoquinonic pigments also known as spinochromes are by the way synthesized by sea urchin and involved in all probability in a lot of mechanisms. To our knowledge, this study is the first highlighting the ecological function of naphthoquinones as kairomones. Chemical extractions were also performed on sea urchins in order to analyze and identify their specific hydroxynaphthoquinones using HPLC-ESI-MS. Accurate mass identification and elemental composition have been performed on various organs (gonads, coelomic liquid, digestive system and test) in different morphotypes of Echinometra mathaei for a better understanding of the molecular diversity of these semiochemicals. Moreover, some experiments were performed to investigate the dependence of T. holthuisi for their host. First, the analyses showed that the molecules involved in shrimp pigmentation are the same that the ones involved in E. mathaei, suggesting a potential feeding on the host. Secondly, a substantial shrimp depigmentation and an increase of the mortality rate were demonstrated after the symbionts-host separation which could mean a potential implication of spinochromes in the shrimp metabolism.

Keywords: crustacean, sea urchin, spinochrome, symbiosis

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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: J. Bernasovská, R. Lohajová Behulová, E. Petrejčiková, I. Boroňová, I. Bernasovský

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Y chromosome microdeletions are the most common genetic cause of male infertility and screening for these microdeletions in azoospermic or severely oligospermic men is now standard practice. Analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions in the euchromatic part of the long arm of the human Y chromosome (Yq11) that are frequently deleted in men with otherwise unexplained spermatogenic failure. PCR analysis of microdeletions in the AZFa, AZFb and AZFc regions of the human Y chromosome is an important screening tool. The aim of this study was to analyse the type of microdeletions in men with fertility disorders in Slovakia. We evaluated 227 patients with azoospermia and with normal karyotype. All patient samples were analyzed cytogenetically. For PCR amplification of sequence-tagged sites (STS) of the AZFa, AZFb and AZFc regions of the Y chromosome was used Devyser AZF set. Fluorescently labeled primers for all markers in one multiplex PCR reaction were used and for automated visualization and identification of the STS markers we used genetic analyzer ABi 3500xl (Life Technologies). We reported 13 cases of deletions in the AZF region 5,73%. Particular types of deletions were recorded in each region AZFa,b,c .The presence of microdeletions in the AZFc region was the most frequent. The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.

Keywords: AZF, male infertility, microdeletions, Y chromosome

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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

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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

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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: 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

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Authors: Samiyah Tasleem, Muhammad Abdul Haq, Syed Baqir Shyum Naqvi, Muhammad Abid Husnain, Sajjad Haider Naqvi

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The objective of the present study was: a) to investigate the antimicrobial activity of honey samples of different floral sources of Pakistan, b) to recover the phenolic acids in them as a possible contributing factor of antimicrobial activity. Six honey samples from different floral sources, namely: Trachysperm copticum, Acacia species, Helianthus annuus, Carissa opaca, Zizyphus and Magnifera indica were used. The antimicrobial activity was investigated by the disc diffusion method against eight freshly isolated clinical isolates (Staphylococci aureus, Staphylococci epidermidis, Streptococcus faecalis, Pseudomonas aeruginosa, Klebsiella pneumonia, Escherichia coli, Proteus vulgaris and Candida albicans). Antimicrobial activity of honey was compared with five commercial antibiotics, namely: doxycycline (DO-30ug/mL), oxytetracycline (OT-30ug/mL), clarithromycin (CLR–15ug/mL), moxifloxacin (MXF-5ug/mL) and nystatin (NT – 100 UT). The fractions responsible for antimicrobial activity were extracted using ethyl acetate. Solid phase extraction (SPE) was used to recover the phenolic acids of honey samples. Identification was carried out via High-Performance Liquid Chromatography (HPLC). The results indicated that antimicrobial activity was present in all honey samples and found comparable to the antibiotics used in the study. In the microbiological assay, the ethyl acetate honey extract was found to exhibit a very promising antimicrobial activity against all the microorganisms tested, indicating the existence of phenolic compounds. Six phenolic acids, namely: gallic, caffeic, ferulic, vanillic, benzoic and cinnamic acids were identified besides some unknown substance by HPLC. In conclusion, Pakistani honey samples showed a broad spectrum antibacterial and promising antifungal activity. Identification of six different phenolic acids showed that Pakistani honey samples are rich sources of phenolic compounds that could be the contributing factor of antimicrobial activity.

Keywords: Pakistani honey, antimicrobial activity, Phenolic acids eg.gallic, caffeic, ferulic, vanillic, benzoic and cinnamic acids

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Authors: Adjebli Ahmed, Messis Abdelaziz, Ayeche Riad, Tighilet Karim, Talbi Melissa, Smaili Yanis, Lehri Mokrane, Louardiane Mustapha

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Colorectal cancer is one of the most common types of cancer worldwide, and its incidence has been increasing in recent years. Data and fecal samples from colorectal cancer patients were collected at the Amizour Public Hospital's oncology department (Bejaia, Algeria). Microbiological and cohort study were conducted at the Biological Engineering of Cancers laboratory at the Faculty of Medicine of the University of Bejaia. All the data showed that patients aged between 50 and 70 years were the most affected by colorectal cancer, while the age categories of [30-40] and [40-50] were the least affected. Males were more likely to be at risk of contracting colorectal cancer than females. The most common types of colorectal cancer among the studied population were sigmoid cancer, rectal cancer, transverse colon cancer, and ascending colon cancer. The hereditary factor was found to be more dominant than other risk factors. Bacterial identification revealed the presence of certain pathogenic and opportunistic bacterial genera, such as E. coli, K. pneumoniae, Shigella sp, and Streptococcus group D. These results led us to conclude that dysbiosis of the intestinal microbiome is strongly present in colorectal cancer patients at the EPH of Amizour.

Keywords: microbiome, colorectal cancer, risk factors, bacterial identification

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Authors: Ming-Yen Chang, Sheng-Hung Ke

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This research focuses on the development of a speed bump identification system for real-time control of adjustable shock absorbers in vehicular suspension systems. The study initially involved the collection of images of various speed bumps, and rubber speed bump profiles found on roadways. These images were utilized for training and recognition purposes through the deep learning object detection algorithm YOLOv5. Subsequently, the trained speed bump identification program was integrated with an in-vehicle camera system for live image capture during driving. These images were instantly transmitted to a computer for processing. Using the principles of monocular vision ranging, the distance between the vehicle and an approaching speed bump was determined. The appropriate control distance was established through both practical vehicle measurements and theoretical calculations. Collaboratively, with the electronically adjustable shock absorbers equipped in the vehicle, a shock absorber control system was devised to dynamically adapt the damping force just prior to encountering a speed bump. This system effectively mitigates passenger discomfort and enhances ride quality.

Keywords: adjustable shock absorbers, image recognition, monocular vision ranging, ride

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Authors: Rimeyah H. S. Almutairi, Alaa Eldin A. Ayoub

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The aim of this study was to identify empirical and theoretical studies that explored giftedness theories and identification. In order to assess and synthesize the mechanisms, outcomes, and impacts of gifted identification models. Thus, we sought to provide an evidence-informed answer to how does current giftedness theories work and effectiveness. In order to develop a model that incorporates the advantages of existing models and avoids their disadvantages as much as possible. We conducted a systematic literature review (SLR). The disciplined analysis resulted in a final sample consisting of 30 appropriate searches. The results indicated that: (a) there is no uniform and consistent definition of Giftedness; (b) researchers are using several non-consistent criteria to detect gifted, and (d) The detection of talent is largely limited to early ages, and there is obvious neglect of adults. This study contributes to the development of Giftedness Cloud Model (GCM) which defined as a model that attempts to interpretation giftedness within an interactive psychological and ecological framework. GCM aims to help a talented to reach giftedness core and manifestation talent in creative productivity or invention. Besides that, GCM suggests classifying giftedness into four levels of mastery, excellence, creative productivity, and manifestation. In addition, GCM presents an idea to distinguish between talent and giftedness.

Keywords: giftedness cloud model, talent, systematic literature review, giftedness concept

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Authors: Ebenezer O. Olaniyi, Oyebade K. Oyedotun, Khashman Adnan

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In the food industry high quality production is required within a limited time to meet up with the demand in the society. In this research work, we have developed a model which can be used to replace the human operator due to their low output in production and slow in making decisions as a result of an individual differences in deciding the defective and healthy banana. This model can perform the vision attributes of human operators in deciding if the banana is defective or healthy for food production based. This research work is divided into two phase, the first phase is the image processing where several image processing techniques such as colour conversion, edge detection, thresholding and morphological operation were employed to extract features for training and testing the network in the second phase. These features extracted in the first phase were used in the second phase; the classification system phase where the multilayer perceptron using backpropagation neural network was employed to train the network. After the network has learned and converges, the network was tested with feedforward neural network to determine the performance of the network. From this experiment, a recognition rate of 97% was obtained and the time taken for this experiment was limited which makes the system accurate for use in the food industry.

Keywords: banana, food processing, identification system, neural network

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Authors: Sara Seyfi

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DDT and petroleum contamination in coastal sand alters the physical and mechanical properties of contaminated soils. This article aims to understand the effects of DDT pollution on the geotechnical characteristics of sand groups, including sand, silty sand, and clay sand. First, the studies conducted on the topic of the article will be reviewed. In the initial stage of the tests, this article deals with the identification of the used sands (sand, silty sand, clay sand) by FTIR, µ-XRF and SEM methods. Then, the geotechnical characteristics of these sand groups, including density, permeability, shear strength, compaction, and plasticity, are investigated using a sand cone, head permeability test, Vane shear test, strain gauge penetrometer, and plastic limit test. Sand groups are artificially contaminated with petroleum substances with 1, 2, 4, 8, 10, 12% by weight. In a separate experiment, amounts of 2, 4, 8, 12, 16, 20 mg/liter of DDT were added to the sand groups. Geotechnical characteristics and identification analysis are performed on the contaminated samples. In the final tests, the mentioned amounts of oil pollution and DDT are simultaneously added to the sand groups, and identification and measurement processes are carried out. The results of the tests showed that petroleum contamination had reduced the optimal moisture content, permeability, and plasticity of all samples. Except silty sand’s plasticity, which petroleum increased it by 1-4% and decreased it by 8-12%. The dry density of sand and clay sand increased, but that of silty sand decreased. Also, the shear strength of sand and silty sand increased, but that of clay sand decreased. DDT contamination increased the maximum dry density and decreased the permeability of all samples. It also reduced the optimum moisture content of the sand. The shear resistance of silty sand and clayey sand decreased, and plasticity of clayey sand increased, and silty sand decreased. The simultaneous effect of petroleum and DDT pollution on the maximum dry density of sand and clayey sand has been synergistic, on the plasticity of clayey sand and silty sand, there has been antagonism. This process has caused antagonism of optimal sand content, shear strength of silty sand and clay sand. In other cases, the effect of synergy or antagonism is not observed.

Keywords: DDT contamination, geotechnical characteristics, petroleum contamination, sand

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Authors: Yasser Gaber, Mohamed Ismail, Serena Bisagni, Mohamad Takwa, Rajni Hatti-Kaul

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Enzymes are safe and selective catalysts. They skillfully catalyze chemical reactions; however, the native form is not usually suitable for industrial applications. Enzymes are therefore engineered by several techniques to meet the required catalytic task. Clopidogrel is recorded among the five best selling pharmaceutical in 2010 under the brand name Plavix. The commonly used route for production of the drug on an industrial scale is the synthesis of the racemic mixture followed by diastereomeric resolution to obtain the pure S isomer. The process consumes a lot of solvents and chemicals. We have evaluated a biocatalytic cleaner approach for asymmetric hydrolysis of racemic clopidogrel. Initial screening of a selected number of hydrolases showed only one enzyme EST to exhibit activity and selectivity towards the desired stereoisomer. As the crude EST is a mixture of several isoenzymes, a homology model of EST-1 was used in molecular dynamic simulations to study the interaction of the enzyme with R and S isomers of clopidogrel. Analysis of the geometric hindrances of the tetrahedral intermediates revealed a potential site for mutagenesis in order to improve the activity and the selectivity. Single point mutation showed dramatic increase in activity and inversion of the enantioselectivity (400 fold change in E value).

Keywords: biocatalysis, biotechnology, enzyme, protein engineering, molecular modeling

Procedia PDF Downloads 427