Search results for: molecular modelling

Authors: Sarocha Vivatvakin, Thanaporn Ratchataswan, Thiratest Leesutipornchai, Komkrit Ruangritchankul, Somboon Keelawat, Virachai Kerekhanjanarong, Patnarin Mahattanasakul, Saknan Bongsebandhu-Phubhakdi

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In this globalization era, much attention has been drawn to various molecular biomarkers, which may have the potential to predict the progression of cancer. Epidermal growth factor receptor (EGFR) is the classic member of the ErbB family of membrane-associated intrinsic tyrosine kinase receptors. EGFR expression was found in several organs throughout the body as its roles involve in the regulation of cell proliferation, survival, and differentiation in normal physiologic conditions. However, anomalous expression, whether over- or under-expression is believed to be the underlying mechanism of pathologic conditions, including carcinogenesis. Even though numerous discussions regarding the EGFR as a prognostic tool in head and neck cancer have been established, the consensus has not yet been met. The aims of the present study are to assess the correlation between the level of EGFR expression and demographic data as well as clinicopathological features and to evaluate the ability of EGFR as a reliable prognostic marker. Furthermore, another aim of this study is to investigate the probable pathophysiology that explains the finding results. This retrospective study included 30 squamous cell laryngeal carcinoma patients treated at King Chulalongkorn Memorial Hospital from January 1, 2000, to December 31, 2004. EGFR expression level was observed to be significantly downregulated with the progression of the laryngeal cancer stage. (one way ANOVA, p = 0.001) A statistically significant lower EGFR expression in the late stage of the disease compared to the early stage was recorded. (unpaired t-test, p = 0.041) EGFR overexpression also showed the tendency to increase recurrence of cancer (unpaired t-test, p = 0.128). A significant downregulation of EGFR expression was documented in advanced stage laryngeal cancer. The results indicated that EGFR level correlates to prognosis in term of stage progression. Thus, EGFR expression might be used as a prevailing biomarker for laryngeal squamous cell carcinoma prognostic prediction.

Keywords: downregulation, epidermal growth factor receptor, immunohistochemistry, laryngeal squamous cell carcinoma

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Authors: ALi Zaker, Zhi Chen

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Due to the concerns about the depletion of fossil fuel sources and the deteriorating environment, the attempt to investigate the production of renewable energy will play a crucial role as a potential to alleviate the dependency on mineral fuels. In this respect, biofuels are measured as a vital nominee for national energy security and energy sustainability. Sewage sludge (SS), as an alternative source of renewable energy with a complex composition, is a major waste generated during wastewater treatment. Stricter legislation is continuously refining the requirements for the level of removal of various pollutants in treated water, causing continuous growth of sludge production, which has become a global challenge. In general, there are two main procedures for dealing with SS: incineration and landfill. However, there are a variety of limitations in these options (e.g., production of greenhouse gases and restrictive environmental regulations) in regard to negative social and economic impacts. Pyrolysis is a feasible and cost-effective technology that can simultaneously tackle boundaries concerning the current disposal routes while retrieving bioenergy. Pyrolysis of SS has drawn vigorous interest in research due to the ability of high mass yield of pyrolytic liquid production. Nonetheless, the presence of high molecular weight hydrocarbons and oxygenated- and nitrogenated compounds poses a considerable challenge. In this context, catalytic pyrolysis is another attainable route in order to upgrade the bio-oil quality. Among different catalysts (i.e., zeolites) studied for sewage sludge pyrolysis, activated chars are eco-friendly and low-cost alternatives. The beneficial features comprise comparatively large surface area, long-term stability, and enriched surface functional groups. In light of these premises, this research attempts to investigate the catalytic pyrolysis of sewage sludge with a high-performance sludge-based activated char in contrast to HZSM5 from a theoretical and experimental point of view.

Keywords: catalytic pyrolysis, sewage sludge, char, HZSM5, bio-oil.

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Authors: Tugbanur Ozen Balaban, Gultekin Tarcan, Unsal Gemici, Mumtaz Colak, I. Hakki Karamanderesi

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Buyuk Menderes Graben is located in the Western Anatolia (Turkey). The graben has become the largest industrial and agricultural area with a total population exceeding 3.000.000. There are two big cities within the study areas from west to east as Aydın and Denizli. The study area is very rich with regard to cold ground waters and thermal waters. Electrical production using geothermal potential has become very popular in the last decades in this area. Buyuk Menderes Graben is a tectonically active extensional region and is undergoing a north–south extensional tectonic regime which commenced at the latest during Early Middle Miocene period. The basement of the study area consists of Menderes massif rocks that are made up of high-to low-grade metamorphics and they are aquifer for both cold ground waters and thermal waters depending on the location. Neogene terrestrial sediments, which are mainly composed by alluvium fan deposits unconformably cover the basement rocks in different facies have very low permeability and locally may act as cap rocks for the geothermal systems. The youngest unit is Quaternary alluvium which is the shallow regional aquifer consists of Holocene alluvial deposits in the study area. All the waters are of meteoric origin and reflect shallow or deep circulation according to the 8O, 2H and 3H contents. Meteoric waters move to deep zones by fractured system and rise to the surface along the faults. Water samples (drilling well, spring and surface waters) and local seawater were collected between 2010 and 2012 years. Geochemical modeling was calculated distribution of the aqueous species and exchange processes by using PHREEQCi speciation code. Geochemical analyses show that cold ground water types are evolving from Ca–Mg–HCO3 to Na–Cl–SO4 and geothermal aquifer waters reflect the water types of Na-Cl-HCO3 in Aydın. Water types of Denizli are Ca-Mg-HCO3 and Ca-Mg-HCO3-SO4. Thermal water types reflect generally Na-HCO3-SO4. The B versus Cl rates increase from east to west with the proportion of seawater introduced into the fresh water aquifers and geothermal reservoirs. Concentrations of some elements (As, B, Fe and Ni) are higher than the tolerance limit of the drinking water standard of Turkey (TS 266) and international drinking water standards (WHO, FAO etc).

Keywords: Buyuk Menderes, isotope chemistry, geochemical modelling, water quality

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Authors: Jasbir Singh, Devender Kumar, Davender Redhu, Surender Kumar, Vandana Bhardwaj

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Single Nucleotide polymorphism (SNP) of proteosomal gene complex is involved in the pathogenesis of hepatitis B Virus (HBV) infection. Some of such proteosomal gene complex are large multifunctional proteins (LMP) and antigen associated transporters that help in antigen presentation. Both are involved in intracellular processing and presentation of viral antigens in association with Major Histocompatability Complex (MHC) Class I molecules. A total of hundred each of hepatitis B virus infected and control samples from northern India were studied. Genomic DNA was extracted from all studied samples and PCR-RFLP method was used for genotyping at different positions of LMP genes. Genotypes at a given position were inferred from the pattern of bands and genotype frequencies and haplotype frequencies were also calculated. Homozygous SNP {A>C} was observed at codon 145 of LMP7 gene and having a protective role against HBV as there was statistically significant high distribution of this SNP among controls than cases. Heterozygous SNP {A>C} was observed at codon 145 of LMP7 gene and made individuals more susceptible to HBV infection as there was statistically significant high distribution of this SNP among cases than control. SNP {T>C} was observed at codon 60 of LMP2 gene but statistically significant differences were not observed among controls and cases. For codon 145 of LMP7 and codon 60 of LMP2 genes, four haplotypes were constructed. Haplotype I (LMP2 ‘C’ and LMP7 ‘A’) made individuals carrying it more susceptible to HBV infection as there was statistically significant high distribution of this haplotype among cases than control. Haplotype II (LMP2 ‘C’ and LMP7 ‘C’) made individuals carrying it more immune to HBV infection as there was statistically significant high distribution of this haplotype among control than cases. Thus it can be concluded that homozygous SNP {A>C} at codon 145 of LMP7 and Haplotype II (LMP2 ‘C’ and LMP7 ‘C’) has a protective role against HBV infection whereas heterozygous SNP {A>C} at codon 145 of LMP7 and Haplotype I (LMP2 ‘C’ and LMP7 ‘A’) made individuals more susceptible to HBV infection.

Keywords: Hepatitis B Virus, single nucleotide polymorphism, low molecular weight proteins, transporters associated with antigen presentation

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Authors: A. T. Toci, M. V. B. Zanoni

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The advanced oxidation processes have been defined as destructive technologies treatment of wastewater. These involve the formation of powerful oxidizing agents (usually hydroxyl radical .OH) capable of reacting with organic compounds present in wastewater, transforming damaging substances in CO2 and H2O (mineralization) or other innocuous products. However, the photochemical degradation with singlet oxygen has been little explored as oxidative pathway for the treatment of effluents containing food colorants. The molecular oxygen is an effective suppressor of organic molecules in the triplet excited state. One of the possible results of the physical withdrawal is the formation of singlet oxygen. Studies with singlet oxygen (1O2) show an high reactivity of the excited state of the molecule with olefins, aromatic hydrocarbons and a number of other organic and inorganic compounds. Its reactivity is about 2500 times larger than the oxygen in the ground state. Thus, in this work, it was studied the degradation of some dyes used in food industry (tartrazine, sunset yellow, erythrosine and carmoisine) by singlet oxygen. The sensitizer used for generating the 1O2 was methylene blue, which has a quantum yield generation of 0.50. Samples were prepared in water at a concentration of 5 ppm and irradiated with a sunlight simulator (Newport brand, model no. 67005) by consecutive 8h. The absorption spectra of UV-Vis molecules were made each hour irradiation. The degradation kinetics for each dye was determined using the maximum length of each dye absorption. The analysis by UV-Vis revealed that the processes were very efficient for the colorants sunset yellow and carmoisine. Both presented degradation kinetics of order zero with degradation constants 0.416 and 0.104, respectively. In the case of sunset yellow degradation reached 53% after 7h irradiation, Demonstrating the process efficiency. The erithrosine presented during the period irradiated a oscillating degradation kinetics, which requires further study. In the other hand, tartrazine was stable in the presence of 1O2. The investigation of the dyes degradation products owned degradation by 1O2 are underway, the techniques used for this are MS and NMR. The results of this study will enable the application of the cleanest methods for the treatment of industrial effluents, as there are other non-toxic and polluting molecules to generate 1O2.

Keywords: food colourants, singlet oxygen, degradation, wastewater, oxidative

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Authors: Kan Yu, Khui Hung Lee, Eben Afrifa-Yamoah, Jing Guo, Katrina Harrison, Jack Goldblatt, Nicholas Pachter, Jitian Xiao, Guicheng Brad Zhang

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Background and Significance of the Study: Congenital Heart Defects (CHDs) are the most common malformation at birth and one of the leading causes of infant death. Although the exact etiology remains a significant challenge, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of congenital heart defects. At present, no existing DNA methylation biomarkers are used for early detection of CHDs. The existing CHD diagnostic techniques are time-consuming and costly and can only be used to diagnose CHDs after an infant was born. The present study employed a machine learning technique to analyse genome-wide methylation data in children with and without CHDs with the aim to find methylation biomarkers for CHDs. Methods: The Illumina Human Methylation EPIC BeadChip was used to screen the genome‐wide DNA methylation profiles of 24 infants diagnosed with congenital heart defects and 24 healthy infants without congenital heart defects. Primary pre-processing was conducted by using RnBeads and limma packages. The methylation levels of top 600 genes with the lowest p-value were selected and further investigated by using a random forest approach. ROC curves were used to analyse the sensitivity and specificity of each biomarker in both training and test sample sets. The functionalities of selected genes with high sensitivity and specificity were then assessed in molecular processes. Major Findings of the Study: Three genes (MIR663, FGF3, and FAM64A) were identified from both training and validating data by random forests with an average sensitivity and specificity of 85% and 95%. GO analyses for the top 600 genes showed that these putative differentially methylated genes were primarily associated with regulation of lipid metabolic process, protein-containing complex localization, and Notch signalling pathway. The present findings highlight that aberrant DNA methylation may play a significant role in the pathogenesis of congenital heart defects.

Keywords: biomarker, congenital heart defects, DNA methylation, random forest

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Authors: Aqsa Kanwal, Min Zhang, Faisal Sharaf, Li Chengtao

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The globe is facing increasing challenges of plastic pollution due to single-use of plastic-based packaging material. The plastic material is continuously being dumped into the natural environment, which causes serious harm to the entire ecosystem. Polymer degradation in nature is very difficult, so the use of biodegradable polymers instead of conventional polymers can mitigate this issue. Due to the good mechanical properties and biodegradability, aliphatic-aromatic polymers are being widely commercialized. Due to the advancement in molecular biology, many studies have reported specific microbes that can effectively degrade PBAT. Aliphatic polyesters undergo hydrolytic cleavage of ester groups, so they can be easily degraded by microorganisms. In this study, we investigated the enzymatic degradation of poly (butylene adipate terephthalate) (PBAT) copolymer using lipase B from Candida Antarctica (CALB). Results of the study displayed approximately 5.16 % loss in PBAT mass after 2 days which significantly increased to approximately 15.7 % at the end of the experiment (12 days) as compared to blank. The pH of the degradation solution also displayed significant reduction and reached the minimum value of 6.85 at the end of the experiment. The structure and morphology of PBAT after degradation were characterized by FTIR, XRD, SEM, and TGA. FTIR analysis showed that after degradation many peaks become weaker and the peak at 2950 cm-1 almost disappeared after 12 days. The XRD results indicated that as the degradation time increases the intensity of diffraction peaks slightly increases as compared to the blank PBAT. TGA analysis also confirmed the successful degradation of PBAT with time. SEM micrographs further confirmed that degradation has occurred. Hence, biodegradable polymers can widely be used. The effect of PBAT biodegradation on plant growth was also studied and it was found that PBAT has no toxic effect on the growth of plants. Hence PBAT can be employed in a wide range of applications.

Keywords: aliphatic-aromatic co-polyesters, polybutylene adipate terephthalate, lipase (CALB), biodegradation, plant growth

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Authors: Sina Abadzadesahraei, Stephen Déry, John Rex

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Climate research has repeatedly identified strong associations between anthropogenic emissions of ‘greenhouses gases’ and observed increases of global mean surface air temperature over the past century. Studies have also demonstrated that the degree of warming varies regionally. Canada is not exempt from this situation, and evidence is mounting that climate change is beginning to cause diverse impacts in both environmental and socio-economic spheres of interest. For example, northeastern British Columbia (BC), whose climate is controlled by a combination of maritime, continental and arctic influences, is warming at a greater rate than the remainder of the province. There are indications that these changing conditions are already leading to shifting patterns in the region’s hydrological cycle, and thus its available water resources. Coincident with these changes, northeastern BC is undergoing rapid development for oil and gas extraction: This depends largely on subsurface hydraulic fracturing (‘fracking’), which uses enormous amounts of freshwater. While this industrial activity has made substantial contributions to regional and provincial economies, it is important to ensure that sufficient and sustainable water supplies are available for all those dependent on the resource, including ecological systems. In this turn demands a comprehensive understanding of how water in all its forms interacts with landscapes, the atmosphere, and of the potential impacts of changing climatic conditions on these processes. The aim of this study is therefore to characterize and quantify all components of the water budget in the small watershed of Coles Lake (141.8 km², 100 km north of Fort Nelson, BC), through a combination of field observations and numerical modelling. Baseline information will aid the assessment of the sustainability of current and future plans for freshwater extraction by the oil and gas industry, and will help to maintain the precarious balance between economic and environmental well-being. This project is a perfect example of interdisciplinary research, in that it not only examines the hydrology of the region but also investigates how natural gas operations and growth can affect water resources. Therefore, a fruitful collaboration between academia, government and industry has been established to fulfill the objectives of this research in a meaningful manner. This project aims to provide numerous benefits to BC communities. Further, the outcome and detailed information of this research can be a huge asset to researchers examining the effect of climate change on water resources worldwide.

Keywords: northeastern British Columbia, water resources, climate change, oil and gas extraction

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Authors: Eunsu Jang, Kang Park

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In developing an armored ground combat vehicle (AGCV), it is a very important step to analyze the vulnerability (or the survivability) of the AGCV against enemy’s attack. In the vulnerability analysis, the penetration equations are usually used to get the penetration depth and check whether a bullet can penetrate the armor of the AGCV, which causes the damage of internal components or crews. The penetration equations are derived from penetration experiments which require long time and great efforts. However, they usually hold only for the specific material of the target and the specific type of the bullet used in experiments. Thus, penetration simulation using ANSYS can be another option to calculate penetration depth. However, it is very important to model the targets and select the input parameters in order to get an accurate penetration depth. This paper performed a sensitivity analysis of input parameters of ANSYS on the accuracy of the calculated penetration depth. Two conflicting objectives need to be achieved in adopting ANSYS in penetration analysis: maximizing the accuracy of calculation and minimizing the calculation time. To maximize the calculation accuracy, the sensitivity analysis of the input parameters for ANSYS was performed and calculated the RMS error with the experimental data. The input parameters include mesh size, boundary condition, material properties, target diameter are tested and selected to minimize the error between the calculated result from simulation and the experiment data from the papers on the penetration equation. To minimize the calculation time, the parameter values obtained from accuracy analysis are adjusted to get optimized overall performance. As result of analysis, the followings were found: 1) As the mesh size gradually decreases from 0.9 mm to 0.5 mm, both the penetration depth and calculation time increase. 2) As diameters of the target decrease from 250mm to 60 mm, both the penetration depth and calculation time decrease. 3) As the yield stress which is one of the material property of the target decreases, the penetration depth increases. 4) The boundary condition with the fixed side surface of the target gives more penetration depth than that with the fixed side and rear surfaces. By using above finding, the input parameters can be tuned to minimize the error between simulation and experiments. By using simulation tool, ANSYS, with delicately tuned input parameters, penetration analysis can be done on computer without actual experiments. The data of penetration experiments are usually hard to get because of security reasons and only published papers provide them in the limited target material. The next step of this research is to generalize this approach to anticipate the penetration depth by interpolating the known penetration experiments. This result may not be accurate enough to be used to replace the penetration experiments, but those simulations can be used in the early stage of the design process of AGCV in modelling and simulation stage.

Keywords: ANSYS, input parameters, penetration depth, sensitivity analysis

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Authors: Uraib Sharaha, Guy Beck, Joseph Kapelushnik, Adam H. Agbaria, Itshak Lapidot, Shaul Mordechai, Ahmad Salman, Mahmoud Huleihel

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Infectious diseases cause a significant burden on the public health and the economic stability of societies all over the world for several centuries. A reliable detection of the causative agent of infection is not possible based on clinical features, since some of these infections have similar symptoms, including fever, sneezing, inflammation, vomiting, diarrhea, and fatigue. Moreover, physicians usually encounter difficulties in distinguishing between viral and bacterial infections based on symptoms. Therefore, there is an ongoing need for sensitive, specific, and rapid methods for identification of the etiology of the infection. This intricate issue perplex doctors and researchers since it has serious repercussions. In this study, we evaluated the potential of the mid-infrared spectroscopic method for rapid and reliable identification of bacterial and viral infections based on simple peripheral blood samples. Fourier transform infrared (FTIR) spectroscopy is considered a successful diagnostic method in the biological and medical fields. Many studies confirmed the great potential of the combination of FTIR spectroscopy and machine learning as a powerful diagnostic tool in medicine since it is a very sensitive method, which can detect and monitor the molecular and biochemical changes in biological samples. We believed that this method would play a major role in improving the health situation, raising the level of health in the community, and reducing the economic burdens in the health sector resulting from the indiscriminate use of antibiotics. We collected peripheral blood samples from young 364 patients, of which 93 were controls, 126 had bacterial infections, and 145 had viral infections, with ages lower than18 years old, limited to those who were diagnosed with fever-producing illness. Our preliminary results showed that it is possible to determine the infectious agent with high success rates of 82% for sensitivity and 80% for specificity, based on the WBC data.

Keywords: infectious diseases, (FTIR) spectroscopy, viral infections, bacterial infections.

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Authors: Sara A. Ben Lashihar

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The heritage building information modelling (HBIM) of the historical masonry buildings has expanded lately to meet the urgent needs for conservation and structural analysis. The masonry structures are unique features for ancient building architectures worldwide that have special cultural, spiritual, and historical significance. However, there is a research gap regarding the reliability of the HBIM modeling process of these structures. The HBIM modeling process of the masonry structures faces significant challenges due to the inherent complexity and uniqueness of their structural systems. Most of these processes are based on tracing the point clouds and rarely follow documents, archival records, or direct observation. The results of these techniques are highly abstracted models where the accuracy does not exceed LOD 200. The masonry assemblages, especially curved elements such as arches, vaults, and domes, are generally modeled with standard BIM components or in-place models, and the brick textures are graphically input. Hence, future investigation is necessary to establish a methodology to generate automatically parametric masonry components. These components are developed algorithmically according to mathematical and geometric accuracy and the validity of the survey data. The main aim of this paper is to provide a comprehensive review of the state of the art of the existing researches and papers that have been conducted on the HBIM modeling of the masonry structural elements and the latest approaches to achieve parametric models that have both the visual fidelity and high geometric accuracy. The paper reviewed more than 800 articles, proceedings papers, and book chapters focused on "HBIM and Masonry" keywords from 2017 to 2021. The studies were downloaded from well-known, trusted bibliographic databases such as Web of Science, Scopus, Dimensions, and Lens. As a starting point, a scientometric analysis was carried out using VOSViewer software. This software extracts the main keywords in these studies to retrieve the relevant works. It also calculates the strength of the relationships between these keywords. Subsequently, an in-depth qualitative review followed the studies with the highest frequency of occurrence and the strongest links with the topic, according to the VOSViewer's results. The qualitative review focused on the latest approaches and the future suggestions proposed in these researches. The findings of this paper can serve as a valuable reference for researchers, and BIM specialists, to make more accurate and reliable HBIM models for historic masonry buildings.

Keywords: HBIM, masonry, structure, modeling, automatic, approach, parametric

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Authors: Laribi-Habchi Hasiba, Bouanane-Darenfed Amel, Drouiche Nadjib, Pausse André, Mameri Nabil

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Chitin, a linear 1, 4-linked N-acetyl-d-glucosamine (GlcNAc) polysaccharide is the major structural component of fungal cell walls, insect exoskeletons and shells of crustaceans. It is one of the most abundant naturally occurring polysaccharides and has attracted tremendous attention in the fields of agriculture, pharmacology and biotechnology. Each year, a vast amount of chitin waste is released from the aquatic food industry, where crustaceans (prawn, crab, Shrimp and lobster) constitute one of the main agricultural products. This creates a serious environmental problem. This linear polymer can be hydrolyzed by bases, acids or enzymes such as chitinase. In this context an extracellular chitinase (ChiA-65) was produced and purified from a newly isolated LHH100. Pure protein was obtained after heat treatment and ammonium sulphate precipitation followed by Sephacryl S-200 chromatography. Based on matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) analysis, the purified enzyme is a monomer with a molecular mass of 65,195.13 Da. The sequence of the 27 N-terminal residues of the mature ChiA-65 showed high homology with family-18 chitinases. Optimal activity was achieved at pH 4 and 75◦C. Among the inhibitors and metals tested p-chloromercuribenzoic acid, N-ethylmaleimide, Hg2+ and Hg + completelyinhibited enzyme activity. Chitinase activity was high on colloidal chitin, glycol chitin, glycol chitosane, chitotriose and chitooligosaccharide. Chitinase activity towards synthetic substrates in the order of p-NP-(GlcNAc) n (n = 2–4) was p-NP-(GlcNAc)2> p-NP-(GlcNAc)4> p-NP-(GlcNAc)3. Our results suggest that ChiA-65 preferentially hydrolyzed the second glycosidic link from the non-reducing end of (GlcNAc) n. ChiA-65 obeyed Michaelis Menten kinetics the Km and kcat values being 0.385 mg, colloidal chitin/ml and5000 s−1, respectively. ChiA-65 exhibited remarkable biochemical properties suggesting that this enzyme is suitable for bioconversion of chitin waste.

Keywords: Bacillus licheniformis LHH100, characterization, extracellular chitinase, purification

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Authors: Melvin Sethobya, Sithule Xanga, Sechaba Lenong, Lunga Nolakana, Gbenga Adesola

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Mining has been the cornerstone of the South African economy for the last century. Most of the gold mining in South Africa was conducted within the Witwatersrand basin, which contributed to the rapid growth of the city of Johannesburg and capitulated the city to becoming the business and wealth capital of the country. But with gradual depletion of resources, a stoppage in the extraction of underground water from mines and other factors relating to survival of the mining operations over a lengthy period, most of the mines were abandoned and left to pollute the local waterways and groundwater with toxins, heavy metal residue and increased acid mine drainage ensued. The Department of Mineral Resources and Energy commissioned a project whose aim is to monitor, maintain, and mitigate the adverse environmental impacts of polluted water mine water flowing into local streams affecting local ecosystems and livelihoods downstream. As part of mitigation efforts, the diagnosis and monitoring of groundwater or surface water polluted sites has become important. Geophysical surveys, in particular, Resistivity and Magnetics surveys, were selected as some of most suitable techniques for investigation of local ingress points along of one the major streams cutting through the Witwatersrand basin, namely the Blesbokspruit, which is found in the eastern part of the basin. The aim of the surveys was to provide information that could be used to assist in determining possible water loss/ ingress from the Blesbokspriut stream. Modelling of geophysical surveys results offered an in-depth insight into the interaction and pathways of polluted water through mapping of possible ingress channels near the Blesbokspruit. The resistivity - depth profile of the surveyed site exhibit a three(3) layered model with low resistivity values (10 to 200 Ω.m) overburden, which is underlain by a moderate resistivity weathered layer (>300 Ω.m), which sits on a more resistive crystalline bedrock (>500 Ω.m). Two locations of potential ingress channels were mapped across the two traverses at the site. The magnetic survey conducted at the site mapped a major NE-SW trending regional linearment with a strong magnetic signature, which was modeled to depth beyond 100m, with the potential to act as a conduit for dispersion of stream water away from the stream, as it shared a similar orientation with the potential ingress channels as mapped using the resistivity method.

Keywords: eletrictrical resistivity, magnetics survey, blesbokspruit, ingress

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Authors: Mohd Khairul Bazli Mohd Aziz, Fadhilah Yusof, Zulkifli Yusop, Zalina Mohd Daud, Mohammad Afif Kasno

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Recent developed rainfall network design techniques have been discussed and compared by many researchers worldwide due to the demand of acquiring higher levels of accuracy from collected data. In many studies, rain-gauge networks are designed to provide good estimation for areal rainfall and for flood modelling and prediction. In a certain study, even using lumped models for flood forecasting, a proper gauge network can significantly improve the results. Therefore existing rainfall network in Johor must be optimized and redesigned in order to meet the required level of accuracy preset by rainfall data users. The well-known geostatistics method (variance-reduction method) that is combined with simulated annealing was used as an algorithm of optimization in this study to obtain the optimal number and locations of the rain gauges. Rain gauge network structure is not only dependent on the station density; station location also plays an important role in determining whether information is acquired accurately. The existing network of 84 rain gauges in Johor is optimized and redesigned by using rainfall, humidity, solar radiation, temperature and wind speed data during monsoon season (November – February) for the period of 1975 – 2008. Three different semivariogram models which are Spherical, Gaussian and Exponential were used and their performances were also compared in this study. Cross validation technique was applied to compute the errors and the result showed that exponential model is the best semivariogram. It was found that the proposed method was satisfied by a network of 64 rain gauges with the minimum estimated variance and 20 of the existing ones were removed and relocated. An existing network may consist of redundant stations that may make little or no contribution to the network performance for providing quality data. Therefore, two different cases were considered in this study. The first case considered the removed stations that were optimally relocated into new locations to investigate their influence in the calculated estimated variance and the second case explored the possibility to relocate all 84 existing stations into new locations to determine the optimal position. The relocations of the stations in both cases have shown that the new optimal locations have managed to reduce the estimated variance and it has proven that locations played an important role in determining the optimal network.

Keywords: geostatistics, simulated annealing, semivariogram, optimization

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Authors: A. Aslihan Gokaltun, Martin L. Yarmush, Ayse Asatekin, O. Berk Usta

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Poly(dimethylsiloxane) (PDMS) is one of the most widely used materials in the fabrication of microfluidic devices. It is easily patterned and can replicate features down to nanometers. Its flexibility, gas permeability that allows oxygenation, and low cost also drive its wide adoption. However, a major drawback of PDMS is its hydrophobicity and fast hydrophobic recovery after surface hydrophilization. This results in significant non-specific adsorption of proteins as well as small hydrophobic molecules such as therapeutic drugs limiting the utility of PDMS in biomedical microfluidic circuitry. While silicon, glass, and thermoplastics have been used, they come with problems of their own such as rigidity, high cost, and special tooling needs, which limit their use to a smaller user base. Many strategies to alleviate these common problems with PDMS are lack of general practical applicability, or have limited shelf lives in terms of the modifications they achieve. This restricts large scale implementation and adoption by industrial and research communities. Accordingly, we aim to tailor biocompatible PDMS surfaces by developing a simple and one step bulk modification approach with novel smart materials to reduce non-specific molecular adsorption and to stabilize long-term cell analysis with PDMS substrates. Smart polymers that blended with PDMS during device manufacture, spontaneously segregate to surfaces when in contact with aqueous solutions and create a < 1 nm layer that reduces non-specific adsorption of organic and biomolecules. Our methods are fully compatible with existing PDMS device manufacture protocols without any additional processing steps. We have demonstrated that our modified PDMS microfluidic system is effective at blocking the adsorption of proteins while retaining the viability of primary rat hepatocytes and preserving the biocompatibility, oxygen permeability, and transparency of the material. We expect this work will enable the development of fouling-resistant biomedical materials from microfluidics to hospital surfaces and tubing.

Keywords: cell culture, microfluidics, non-specific protein adsorption, PDMS, smart polymers

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Authors: Antti Lanki, Justiina Halonen, Juuso Punnonen, Emmi Rantavuo

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Marine oil spill response operation requires extensive vessel maneuvering and navigation skills. At-sea oil containment and recovery include both single vessel and multi-vessel operations. Towing long oil containment booms that are several hundreds of meters in length, is a challenge in itself. Boom deployment and towing in multi-vessel configurations is an added challenge that requires precise coordination and control of the vessels. Efficient communication, as a prerequisite for shared situational awareness, is needed in order to execute the response task effectively. To gain and maintain adequate maritime skills, practical training is needed. Field exercises are the most effective way of learning, but especially the related vessel operations are resource-intensive and costly. Field exercises may also be affected by environmental limitations such as high sea-state or other adverse weather conditions. In Finland, the seasonal ice-coverage also limits the training period to summer seasons only. In addition, environmental sensitiveness of the sea area restricts the use of real oil or other target substances. This paper examines, whether maritime simulator training can offer a complementary method to overcome the training challenges related to field exercises. The objective is to assess the efficiency and the learning impact of simulator training, and the specific skills that can be trained most effectively in simulators. This paper provides an overview of learning results from two oil spill response pilot courses, in which maritime navigational bridge simulators were used to train the oil spill response authorities. The simulators were equipped with an oil spill functionality module. The courses were targeted at coastal Fire and Rescue Services responsible for near shore oil spill response in Finland. The competence levels of the participants were surveyed before and after the course in order to measure potential shifts in competencies due to the simulator training. In addition to the quantitative analysis, the efficiency of the simulator training is evaluated qualitatively through feedback from the participants. The results indicate that simulator training is a valid and effective method for developing marine oil spill response competencies that complement traditional field exercises. Simulator training provides a safe environment for assessing various oil containment and recovery tactics. One of the main benefits of the simulator training was found to be the immediate feedback the spill modelling software provides on the oil spill behaviour as a reaction to response measures.

Keywords: maritime training, oil spill response, simulation, vessel manoeuvring

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Authors: Zeina Bourhane, Anders Lanzen, Christine Cagnon, Olfa Ben Said, Cristiana Cravo-Laureau, Robert Duran

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The anthropogenic pressure in coastal areas increases dramatically with the exploitation of environmental resources. Biomonitoring coastal areas are crucial to determine the impact of pollutants on bacterial communities in soils and sediments since they provide important ecosystem services. However, relevant biomonitoring tools allowing fast determination of the ecological status are yet to be defined. Microbial ecology approaches provide useful information for developing such microbial monitoring tools reporting on the effect of environmental stressors. Chemical and microbial molecular approaches were combined in order to determine microbial bioindicators for assessing the ecological status of soil and river ecosystems around the Ichkeul Lake (Tunisia), an area highly impacted by human activities. Samples were collected along soil/river/lake continuums in three stations around the Ichkeul Lake influenced by different human activities at two seasons (summer and winter). Contaminant pressure indexes (PI), including PAHs (Polycyclic aromatic hydrocarbons), alkanes, and OCPs (Organochlorine pesticides) contents, showed significant differences in the contamination level between the stations with seasonal variation. Bacterial communities were characterized by 16S ribosomal RNAs (rRNA) gene metabarcoding. Although microgAMBI indexes, determined from the sequencing data, were in accordance with contaminant contents, they were not sufficient to fully explain the PI. Therefore, further microbial indicators are still to be defined. The comparison of bacterial communities revealed the specific microbial assemblage for soil, river, and lake sediments, which were significantly correlated with contaminant contents and PI. Such observation offers the possibility to define a relevant set of bioindicators for reporting the effects of human activities on the microbial community structure. Such bioindicators might constitute useful monitoring tools for the management of microbial communities in coastal areas.

Keywords: bacterial communities, biomonitoring, contamination, human impacts, microbial bioindicators

Procedia PDF Downloads 144

Authors: Ogemdi Chinwendu Anika, Anna Strzelecka, Yadira Bajón-Fernández, Raffaella Villa

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Anaerobic digestion (AD) has been used since time in memorial to take care of organic wastes in the environment, especially for sewage and wastewater treatments. Recently, the rising demand/need to increase renewable energy from organic matter has caused the AD substrates spectrum to expand and include a wider variety of organic materials such as agricultural residues and farm manure which is annually generated at around 140 billion metric tons globally. The problem, however, is that agricultural wastes are composed of materials that are heterogeneous and too difficult to degrade -particularly lignin, that make up about 0–40% of the total lignocellulose content. This study aimed to evaluate the impact of varying concentrations of lignin on biogas yields and their subsequent response to a commercial yeast-based bioadditive in batch anaerobic digesters. The experiments were carried out in batches for a retention time of 56 days with different lignin concentrations (200 mg, 300 mg, 400 mg, 500 mg, and 600 mg) treated to different conditions to first determine the concentration of the bioadditive that was most optimal for overall process improvement and yields increase. The batch experiments were set up using 130 mL bottles with a working volume of 60mL, maintained at 38°C in an incubator shaker (150rpm). Digestate obtained from a local plant operating at mesophilic conditions was used as the starting inoculum, and commercial kraft lignin was used as feedstock. Biogas measurements were carried out using the displacement method and were corrected to standard temperature and pressure using standard gas equations. Furthermore, the modified Gompertz equation model was used to non-linearly regress the resulting data to estimate gas production potential, production rates, and the duration of lag phases as indicatives of degrees of lignin inhibition. The results showed that lignin had a strong inhibitory effect on the AD process, and the higher the lignin concentration, the more the inhibition. Also, the modelling showed that the rates of gas production were influenced by the concentrations of the lignin substrate added to the system – the higher the lignin concentrations in mg (0, 200, 300, 400, 500, and 600) the lower the respective rate of gas production in ml/gVS.day (3.3, 2.2, 2.3, 1.6, 1.3, and 1.1), although the 300 mg increased by 0.1 ml/gVS.day over that of the 200 mg. The impact of the yeast-based bioaddition on the rate of production was most significant in the 400 mg and 500 mg as the rate was improved by 0.1 ml/gVS.day and 0.2 ml/gVS.day respectively. This indicates that agricultural residues with higher lignin content may be more responsive to inhibition alleviation by yeast-based bioadditive; therefore, further study on its application to the AD of agricultural residues of high lignin content will be the next step in this research.

Keywords: anaerobic digestion, renewable energy, lignin valorisation, biogas

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Authors: Dangut Maren David, Skaf Zakwan

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Adequate monitoring of vehicle component in other to obtain high uptime is the goal of predictive maintenance, the major challenge faced by businesses in industries is the significant cost associated with a delay in service delivery due to system downtime. Most of those businesses are interested in predicting those problems and proactively prevent them in advance before it occurs, which is the core advantage of Prognostic Health Management (PHM) application. The recent emergence of industry 4.0 or industrial internet of things (IIoT) has led to the need for monitoring systems activities and enhancing system-to-system or component-to- component interactions, this has resulted to a large generation of data known as big data. Analysis of big data represents an increasingly important, however, due to complexity inherently in the dataset such as imbalance classification problems, it becomes extremely difficult to build a model with accurate high precision. Data-driven predictive modeling for condition-based maintenance (CBM) has recently drowned research interest with growing attention to both academics and industries. The large data generated from industrial process inherently comes with a different degree of complexity which posed a challenge for analytics. Thus, imbalance classification problem exists perversely in industrial datasets which can affect the performance of learning algorithms yielding to poor classifier accuracy in model development. Misclassification of faults can result in unplanned breakdown leading economic loss. In this paper, an advanced approach for handling imbalance classification problem is proposed and then a prognostic model for predicting aircraft component replacement is developed to predict component replacement in advanced by exploring aircraft historical data, the approached is based on hybrid ensemble-based method which improves the prediction of the minority class during learning, we also investigate the impact of our approach on multiclass imbalance problem. We validate the feasibility and effectiveness in terms of the performance of our approach using real-world aircraft operation and maintenance datasets, which spans over 7 years. Our approach shows better performance compared to other similar approaches. We also validate our approach strength for handling multiclass imbalanced dataset, our results also show good performance compared to other based classifiers.

Keywords: prognostics, data-driven, imbalance classification, deep learning

Procedia PDF Downloads 156

Authors: Fang Liu, JunShuai Xue, JiaJia Yao, GuanLin Wu, ZuMaoLi, XueYan Yang, HePeng Zhang, ZhiPeng Sun

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Terahertz spectra is in great demand since last two decades for many photonic and electronic applications. III-Nitride resonant tunneling diode is one of the promising candidates for portable and compact THz sources. Room temperature microwave oscillator based on GaN/AlN resonant tunneling diode was reported in this work. The devices, grown by plasma-assisted molecular-beam epitaxy on free-standing c-plane GaN substrates, exhibit highly repeatable and robust negative differential resistance (NDR) characteristics at room temperature. To improve the interface quality at the active region in RTD, indium surfactant assisted growth is adopted to enhance the surface mobility of metal atoms on growing film front. Thanks to the lowered valley current associated with the suppression of threading dislocation scattering on low dislocation GaN substrate, a positive peak current density of record-high 2.1 MA/cm2 in conjunction with a peak-to-valley current ratio (PVCR) of 1.2 are obtained, which is the best results reported in nitride-based RTDs up to now considering the peak current density and PVCR values simultaneously. When biased within the NDR region, microwave oscillations are measured with a fundamental frequency of 0.31 GHz, yielding an output power of 5.37 µW. Impedance mismatch results in the limited output power and oscillation frequency described above. The actual measured intrinsic capacitance is only 30fF. Using a small-signal equivalent circuit model, the maximum intrinsic frequency of oscillation for these diodes is estimated to be ~260GHz. This work demonstrates a microwave oscillator based on resonant tunneling effect, which can meet the demands of terahertz spectral devices, more importantly providing guidance for the fabrication of the complex nitride terahertz and quantum effect devices.

Keywords: GaN resonant tunneling diode, peak current density, microwave oscillation, intrinsic capacitance

Procedia PDF Downloads 117

Authors: Harika Atmaca, Emir Bozkurt, Latife Merve Oktay, Selim Uzunoglu, Ruchan Uslu, Burçak Karaca

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Microarrays have been developed for highly parallel enzyme-linked immunosorbent assay (ELISA) applications. The most common protein arrays are produced by using multiple monoclonal antibodies, since they are robust molecules which can be easily handled and immobilized by standard procedures without loss of activity. Protein expression profiling with protein array technology allows simultaneous analysis of the protein expression pattern of a large number of proteins. Trabectedin, a tetrahydroisoquinoline alkaloid derived from a Caribbean tunicate, Ecteinascidia turbinata, has been shown to have antitumor effects. Here, we used a novel proteomic approach to explore the mechanism of action of trabectedin in prostate cancer cell line PC-3 by apoptosis antibody microarray. XTT cell proliferation kit and Cell Death Detection Elisa Plus Kit (Roche) was used for measuring cytotoxicity and apoptosis. Human Apoptosis Protein Array (R&D Systems) which consists of 35 apoptosis related proteins was used to assess the omic protein expression pattern. Trabectedin induced cytotoxicity and apoptosis in prostate cancer cells in a time and concentration-dependent manner. The expression levels of the death receptor pathway molecules, TRAIL-R1/DR4, TRAIL R2/DR5, TNF R1/TNFRSF1A, FADD were significantly increased by 4.0-, 21.0-, 4.20- and 11.5-fold by trabectedin treatment in PC-3 cells. Moreover, mitochondrial pathway related pro-apoptotic proteins Bax, Bad, Cytochrome c, and Cleaved Caspase-3 expressions were induced by 2.68-, 2.07-, 2.8-, and 4.5-fold and the expression levels of anti-apoptotic proteins Bcl-2 and Bcl-XL were reduced by 3.5- and 5.2-fold in PC-3 cells. Proteomic (antibody microarray) analysis suggests that the mechanism of action of trabectedin may be exerted via the induction of both intrinsic and extrinsic apoptotic pathways. The antibody microarray platform can be utilised to explore the molecular mechanism of action of novel anticancer agents.

Keywords: trabectedin, prostate cancer, omic protein expression profile, apoptosis

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Authors: Priscilla Echeverria

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This paper addresses initial teacher formation as a formative space in which pedagogy students develop a pedagogical agency capacity to contribute to social justice, considering ethical, political, and epistemic dimensions. This paper is structured by discussing first the concepts of agency, pedagogical interaction, and social justice from a critical perspective; and continues offering preliminary results on the capacity of pedagogical agency in novice teachers after the analysis of critical incidents as a research methodology. This study is motivated by the concern that responding to the current neoliberal scenario, many initial teacher formation (ITF) programs have reduced the meaning of education to instruction, and pedagogy to methodology, favouring the formation of a technical professional over a reflective or critical one. From this concern, this study proposes that the restitution of the subject is an urgent task in teacher formation, so it is essential to enable him in his capacity for action and advance in eliminating institutionalized oppression insofar as it affects that capacity. Given that oppression takes place in human interaction, through this work, I propose that initial teacher formation develops sensitivity and educates the gaze to identify oppression and take action against it, both in pedagogical interactions -which configure political, ethical, and epistemic subjectivities- as in the hidden and official curriculum. All this from the premise that modelling democratic and dialogical interactions are basic for any program that seeks to contribute to a more just and empowered society. The contribution of this study lies in the fact that it opens a discussion in an area about which we know little: the impact of the type of interactions offered by university teaching at ITF on the capacity of future teachers to be pedagogical agents. For this reason, this study seeks to gather evidence of the result of this formation, analysing the capacity of pedagogical agency of novice teachers, or, in other words, how capable the graduates of secondary pedagogies are in their first pedagogical experiences to act and make decisions putting the formative purposes that they are capable of autonomously defining before technical or bureaucratic issues imposed by the curriculum or the official culture. This discussion is part of my doctoral research, "The importance of developing the capacity for ethical-political-epistemic agency in novice teachers during initial teacher formation to contribute to social justice", which I am currently developing in the Educational Research program of the University of Lancaster, United Kingdom, as a Conicyt fellow for the 2019 cohort.

Keywords: initial teacher formation, pedagogical agency, pedagogical interaction, social justice, hidden curriculum

Procedia PDF Downloads 75

Authors: A. Gilewska, J. Masternak, K. Kazimierczuk, L. Turlej, J. Wietrzyk, B. Barszcz

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Platinum-based drugs are now widely used as chemotherapeutic agents. However the platinum complexes show the toxic side-effects: i) the development of platinum resistance; ii) the occurrence of severe side effects, such as nephro-, neuro- and ototoxicity; iii) the high toxicity towards human fibroblast. Therefore the development of new anticancer drugs containing different transition-metal ions, for example, ruthenium, rhodium, iridium is a valid strategy in cancer treatment. In this paper, we reported the synthesis, spectroscopic, structural and biological properties of complexes of ruthenium, rhodium, and iridium containing N,N-chelating ligand (2,2’-bisimidazole). These complexes were characterized by elemental analysis, UV-Vis and IR spectroscopy, X-ray diffraction analysis. These complexes exhibit a typical pseudotetrahedral three-legged piano-stool geometry, in which the aromatic arene ring forms the seat of the piano-stool, while the bidentate 2,2’-bisimidazole (ligand) and the one chlorido ligand form the three legs of the stool. The spectroscopy data (IR, UV-Vis) and elemental analysis correlate very well with molecular structures. Moreover, the cytotoxic activity of the complexes was carried out on human cancer cell lines: LoVo (colorectal adenoma), MV-4-11 (myelomonocytic leukaemia), MCF-7 (breast adenocarcinoma) and normal healthy mouse fibroblast BALB/3T3 cell lines. To predict a binding mode, a potential interaction of metal complexes with calf thymus DNA (CT-DNA) and protein (BSA) has been explored using UV absorption and circular dichroism (CD). It is interesting to note that the investigated complexes show no cytotoxic effect towards the normal BALB/3T3 cell line, compared to cisplatin, which IC₅₀ values was determined as 2.20 µM. Importantly, Ru(II) displayed the highest activity against HL-60 (IC₅₀ 4.35 µM). The biological studies (UV-Vis and circular dichroism) suggest that arene-complexes could interact with calf thymus DNA probably via an outside binding mode and interact with protein (BSA).

Keywords: ruthenium(II) complex, rhodium(III) complex, iridium(III) complex, biological activity

Procedia PDF Downloads 117

Authors: Young Ah Kim, Hyunsoo Kim, Eun-Jeong Yoon, Young Hee Seo, Kyungwon Lee

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from food animals are considered as a reservoir for transmission of ESBL genes to human. The aim of this study is to assess the prevalence and molecular epidemiology of ESBL-producing E. coli colonization in pigs, farm workers, and farm environments to elucidate the transmission of multidrug-resistant clones from animal to human. Nineteen pig farms were enrolled across the country in Korea from August to December 2017. ESBL-producing E. coli isolates were detected in 190 pigs, 38 farm workers, and 112 sites of farm environments using ChromID ESBL (bioMerieux, Marcy l'Etoile, France), directly (stool or perirectal swab) or after enrichment (sewage). Antimicrobial susceptibility tests were done with disk diffusion methods and blaTEM, blaSHV, and blaCTX-M were detected with PCR and sequencing. The genomes of the four CTX-M-55-producing E. coli isolates from various sources in one farm were entirely sequenced to assess the relatedness of the strains. Whole genome sequencing (WGS) was performed with PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA). ESBL genotypes were 85 CTX-M-1 group (one CTX-M-3, 23 CTX-M-15, one CTX-M-28, 59 CTX-M-55, one CTX-M-69) and 60 CTX-M-9 group (41 CTX-M-14, one CTX-M-17, one CTX-M-27, 13 CTX-M-65, 4 CTX-M-102) in total 145 isolates. The rectal colonization rates were 53.2% (101/190) in pigs and 39.5% (15/38) in farm workers. In WGS, sequence types (STs) were determined as ST69 (E. coli PJFH115 isolate from a human carrier), ST457 (two E. coli isolates PJFE101 recovered from a fence and PJFA1104 from a pig) and ST5899 (E. coli PJFA173 isolate from the other pig). The four plasmids encoding CTX-M-55 (88,456 to 149, 674 base pair), whether it belonged to IncFIB or IncFIC-IncFIB type, shared IncF backbone furnishing the conjugal elements, suggesting of genes originated from same ancestor. In conclusion, the prevalence of ESBL-producing E. coli in swine farms was surprisingly high, and many of them shared common ESBL genotypes of clinical isolates such as CTX-M-14, 15, and 55 in Korea. It could spread by horizontal transfer between isolates from different reservoirs (human-animal-environment).

Keywords: Escherichia coli, extended-spectrum β-lactamase, prevalence, whole genome sequencing

Procedia PDF Downloads 194

Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Islam Nowisser, Noha Farag, Mohamed El Azizi

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Helicobacter pylori is a highly important human pathogen which inhabits about 50% of the population worldwide. Infection with this bacteria is very hard to treat, with high probability of recurrence. H. pylori causes severe gastric diseases, including peptic ulcer, gastritis, and gastric cancer, which has been linked to chronic inflammation. The infection has been reported to be associated with high levels of pro-inflammatory cytokines, especially IL-1β and TNF-α. The aim of the current study is to investigate the molecular mechanisms by which H. pylori activates NLRP3 inflammasome and its contribution to Il-1 β production in an innate cellular model. H. pylori PMSS1 and G27 standard strains, as well as the PMSS1 isogenic mutant strain PMSS1ΔVacA and G27ΔVacA, G27ΔCagA in addition to clinical isolates obtained from biopsy samples from the antrum and corpus mucosa of chronic gastritis patients, were used to establish infection in RAW-264.7 macrophages. The production levels of TNF-α and IL-1β was assessed using ELISA. Since expression of these cytokines is often regulated by the transcription factor complex, nuclear factor-kB (NF-kB), the activation of NF-κB in H. pylori infected cells was also evaluated by luciferase assay. Genomic DNA was extracted from bacterial cultures of H. pylori clinical isolates as well as the standard strains and their corresponding mutants, where they were evaluated for the cagA pathogenicity island and vacA expression. The correlation between these findings and expression of the cagA Pathogenicity Island and vacA in the bacteria was also investigated. The results showed IL-1β, and TNF-α production significantly increased in raw macrophages following H. pylori infection. The cagA+ and vacA+ H. pylori strains induced significant production of IL-1β compared to cagA- and vacA- strains. The activation pattern of NF-κB was correlated in the isolates to their cagA and vacA expression profiles. A similar finding could not be confirmed for TNF-α production. Our study shows the ability of H. pylori to activate NF-kB and induce significant IL-1β production as a possible mechanism for the augmented inflammatory response seen in subjects infected with cagA+ and vacA+ H. pylori strains that would lead to the progression to more severe form of the disease.

Keywords: Helicobacter pylori, IL-1β, inflammatory cytokines, nuclear factor KB, TNF-α

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Authors: Sudhakara Naidu Neppalli, Tejas S. Bhosale

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It is well known that the block copolymer (BCP) can form a complex molecule, through non-covalent bonds such as hydrogen bond, ionic bond and co-ordination bond, with low molecular weight compound as well as with macromolecules, which provide vast applications, includes the alteration of morphology and properties of polymers. Hence we covered the research that, the importance of non-covalent bonds in increasing the non-favourable segmental interactions of the blocks was well examined by attaching and detaching the bonds between the BCP and additive. We also monitored the phase transition of block copolymer and effective interaction parameter (χeff) for Li-doped polymers using small angle x-ray scattering and transmission electron microscopy. The effective interaction parameter (χeff) between two block components was evaluated using Leibler theory based on the incompressible random phase approximation (RPA) for ionized BCP in a disordered state. Furthermore, conductivity experiments demonstrate that the ionic conductivity in the samples quenched from the different structures is morphology-independent, while it increases with increasing ion salt concentration. Morphological transitions, interaction parameter, and thermal stability also examined in quarternized block copolymer. D-spacing was used to estimate effective interaction parameter (χeff) of block components in weak and strong segregation regimes of ordered phase. Metal-containing polymer has been the topic of great attention in recent years due to their wide range of potential application. Similarly, metal- ligand complex is used as a supramolecular linker between the polymers giving rise to a ‘Metallo-Supramolecule assembly. More precisely, functionalized polymer end capped with 2, 2’:6’, 2”- terpyridine ligand can be selectively complexed with wide range of transition metal ions and then subsequently attached to other terpyridine terminated polymer block. In compare to other supramolecular assembly, BCP involved metallo-supramolecule assembly offers vast applications such as optical activity, electrical conductivity, luminescence and photo refractivity.

Keywords: band gap, block copolymer, conductivity, interaction parameter, phase transition

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Authors: Yassir Adam Shuaib, Stefan Niemann, Eltahir Awad Khalil, Ulrich Schaible, Lothar Heinz Wieler, Mohammed Ahmed Bakhiet, Abbashar Osman Mohammed, Mohamed Abdelsalam Abdalla, Elvira Richter

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Tuberculosis (TB) is a chronic bacterial disease of humans and animals and it is characterized by the progressive development of specific granulomatous tubercle lesions in affected tissues. In a six-month study, from June to November 2014, a total of 2,304 carcasses of cattle, camel, sheep, and goats slaughtered at East and West Gaash slaughterhouses, Kassala, were investigated during postmortem, in parallel, 101 sputum samples from TB suspected patients at Kassala and El-Gadarif Teaching Hospitals were collected in order to investigate tuberculosis in animals and humans. Only 0.1% carcasses were found with suspected TB lesions in the liver and lung and peritoneal cavity of two sheep and no tuberculous lesions were found in the carcasses of cattle, goats or camels. All samples, tissue lesions and sputum, were decontaminated by the NALC-NaOH method and cultured for mycobacterial growth at the NRZ for Mycobacteria, Research Center Borstel, Germany. Genotyping and molecular characterization of the grown strains were done by line probe assay (GenoType CM and MTBC) and 16S rDNA, rpoB gene, and ITS sequencing, spoligotyping, MIRU-VNTR typing and next generation sequencing (NGS). Culture of the specimens revealed growth of organisms from 81.6% of all samples. Mycobacterium tuberculosis (76.2%), M. intracellulare (14.2%), mixed infection with M. tuberculosis and M. intracellulare (6.0%) and mixed infection with M. tuberculosis and M. fortuitum and with M. intracellulare and unknown species (1.2%) were detected in the sputum samples and unknown species (1.2%) were detected in the samples of one of the animals tissues. From the 69 M. tuberculosis strains, 25 (36.2%) were showing either mono-drug-resistant or multi-drug-resistant or poly-drug-resistant but none was extensively drug-resistant. In conclusion, the prevalence of TB in animals was very low while in humans M. tuberculosis-Delhi/CAS lineage was responsible for most cases and there was an evidence of MDR transmission and acquisition.

Keywords: animal, human, slaughterhouse, Sudan, tuberculosis

Procedia PDF Downloads 349

Authors: Tetyana Kendzerska, David T. Zhu, Michael Pugliese, Douglas Manuel, Mohsen Sadatsafavi, Marcus Povitz, Therese A. Stukel, Teresa To, Shawn D. Aaron, Sunita Mulpuru, Melanie Chin, Claire E. Kendall, Kednapa Thavorn, Rebecca Robillard, Andrea S. Gershon

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The impact of the COVID-19 pandemic on the management of ambulatory care sensitive conditions (ACSCs) remains unknown. To compare observed and expected (projected based on previous years) trends in all-cause mortality and healthcare use for ACSCs in the first year of the pandemic (March 2020 - March 2021). A population-based study using provincial health administrative data.General adult population (Ontario, Canada). Monthly all-cause mortality, and hospitalizations, emergency department (ED) and outpatient visit rates (per 100,000 people at-risk) for seven combined ACSCs (asthma, COPD, angina, congestive heart failure, hypertension, diabetes, and epilepsy) during the first year were compared with similar periods in previous years (2016-2019) by fitting monthly time series auto-regressive integrated moving-average models. Compared to previous years, all-cause mortality rates increased at the beginning of the pandemic (observed rate in March-May 2020 of 79.98 vs. projected of 71.24 [66.35-76.50]) and then returned to expected in June 2020—except among immigrants and people with mental health conditions where they remained elevated. Hospitalization and ED visit rates for ACSCs remained lower than projected throughout the first year: observed hospitalization rate of 37.29 vs. projected of 52.07 (47.84-56.68); observed ED visit rate of 92.55 vs. projected of 134.72 (124.89-145.33). ACSC outpatient visit rates decreased initially (observed rate of 4,299.57 vs. projected of 5,060.23 [4,712.64-5,433.46]) and then returned to expected in June 2020. Reductions in outpatient visits for ACSCs at the beginning of the pandemic combined with reduced hospital admissions may have been associated with temporally increased mortality—disproportionately experienced by immigrants and those with mental health conditions. The Ottawa Hospital Academic Medical Organization

Keywords: COVID-19, chronic disease, all-cause mortality, hospitalizations, emergency department visits, outpatient visits, modelling, population-based study, asthma, COPD, angina, heart failure, hypertension, diabetes, epilepsy

Procedia PDF Downloads 78

Authors: F. Murilo T. Luna, Vanessa F. Oliveira, Alysson Rocha, Expedito J. S. Parente, Andre V. Bueno, Matheus C. M. Farias, Celio L. Cavalcante Jr.

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Aviation jetfuel used in aircraft gas-turbine engines is customarily obtained from the kerosene distillation fraction of petroleum (150-275°C). Mineral jetfuel consists of a hydrocarbon mixture containing paraffins, naphthenes and aromatics, with low olefins content. In order to ensure their safety, several stringent requirements must be met by jetfuels, such as: high energy density, low risk of explosion, physicochemical stability and low pour point. In this context, aviation fuels eventually obtained from biofeedstocks (which have been coined as ‘biojetfuel’), must be used as ‘drop in’, since adaptations in aircraft engines are not desirable, to avoid problems with their operation reliability. Thus, potential aviation biofuels must present the same composition and physicochemical properties of conventional jetfuel. Among the potential feedtstocks for aviation biofuel, the babaçu oil, extracted from a palm tree extensively found in some regions of Brazil, contains expressive quantities of short chain saturated fatty acids and may be an interesting choice for biojetfuel production. In this study, biojetfuel was synthesized through homogeneous transesterification of babaçu oil using methanol and its properties were compared with petroleum-based jetfuel through measurements of oxidative stability, physicochemical properties and low temperature properties. The transesterification reactions were carried out using methanol and after decantation/wash procedures, the methyl esters were purified by molecular distillation under high vacuum at different temperatures. The results indicate significant improvement in oxidative stability and pour point of the products when compared to the fresh oil. After optimization of operational conditions, potential biojetfuel samples were obtained, consisting mainly of C8 esters, showing low pour point and high oxidative stability. Jet engine tests are being conducted in an automated test bed equipped with pollutant emissions analysers to study the operational performance of the biojetfuel that was obtained and compare with a mineral commercial jetfuel.

Keywords: biojetfuel, babaçu oil, oxidative stability, engine tests

Procedia PDF Downloads 245