Search results for: laboratory molecular diagnostics

Authors: S. J. Matlan, M. Mukhlisin, M. R. Taha

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Characterization of the engineering behavior of unsaturated soil is dependent on the soil-water characteristic curve (SWCC), a graphical representation of the relationship between water content or degree of saturation and soil suction. A reasonable description of the SWCC is thus important for the accurate prediction of unsaturated soil parameters. The measurement procedures for determining the SWCC, however, are difficult, expensive, and time-consuming. During the past few decades, researchers have laid a major focus on developing empirical equations for predicting the SWCC, with a large number of empirical models suggested. One of the most crucial questions is how precisely existing equations can represent the SWCC. As different models have different ranges of capability, it is essential to evaluate the precision of the SWCC models used for each particular soil type for better SWCC estimation. It is expected that better estimation of SWCC would be achieved via a thorough statistical analysis of its distribution within a particular soil class. With this in view, a statistical analysis was conducted in order to evaluate the reliability of the SWCC prediction models against laboratory measurement. Optimization techniques were used to obtain the best-fit of the model parameters in four forms of SWCC equation, using laboratory data for relatively coarse-textured (i.e., sandy) soil. The four most prominent SWCCs were evaluated and computed for each sample. The result shows that the Brooks and Corey model is the most consistent in describing the SWCC for sand soil type. The Brooks and Corey model prediction also exhibit compatibility with samples ranging from low to high soil water content in which subjected to the samples that evaluated in this study.

Keywords: soil-water characteristic curve (SWCC), statistical analysis, unsaturated soil, geotechnical engineering

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Authors: Florin Leon, Silvia Curteanu

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Developing complete mechanistic models for polymerization reactors is not easy, because complex reactions occur simultaneously; there is a large number of kinetic parameters involved and sometimes the chemical and physical phenomena for mixtures involving polymers are poorly understood. To overcome these difficulties, empirical models based on sampled data can be used instead, namely regression methods typical of machine learning field. They have the ability to learn the trends of a process without any knowledge about its particular physical and chemical laws. Therefore, they are useful for modeling complex processes, such as the free radical polymerization of methyl methacrylate achieved in a batch bulk process. The goal is to generate accurate predictions of monomer conversion, numerical average molecular weight and gravimetrical average molecular weight. This process is associated with non-linear gel and glass effects. For this purpose, an adaptive sampling technique is presented, which can select more samples around the regions where the values have a higher variation. Several machine learning methods are used for the modeling and their performance is compared: support vector machines, k-nearest neighbor, k-nearest neighbor and random forest, as well as an original algorithm, large margin nearest neighbor regression. The suggested method provides very good results compared to the other well-known regression algorithms.

Keywords: batch bulk methyl methacrylate polymerization, adaptive sampling, machine learning, large margin nearest neighbor regression

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Authors: Leila Noori, Rosario Barone, Francesca Rappa, Antonella Marino Gammazza, Alessandra Maria Vitale, Giuseppe Donato Mangano, Giusy Sentiero, Filippo Macaluso, Kathryn H. Myburgh, Francesco Cappello, Federica Scalia

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The neuromuscular system controls, directs, and allows movement of the body through the action of neural circuits, which include motor neurons, sensory neurons, and skeletal muscle fibers. Protein homeostasis of the involved cytotypes appears crucial to maintain the correct and prolonged functions of the neuromuscular system, and both neuronal cells and skeletal muscle fibers express significant quantities of protein chaperones, the molecular machinery responsible to maintain the protein turnover. Genetic mutations or defective post-translational modifications of molecular chaperones (i.e., genetic or acquired chaperonopathies) may lead to neuromuscular disorders called as neurochaperonopathies. The limited knowledge of the effects of the defective chaperones on skeletal muscle fibers and neurons impedes the progression of therapeutic approaches. A distinct genetic variation of CCT5 gene encoding for the subunit 5 of the chaperonin CCT (Chaperonin Containing TCP1; also known as TRiC, TCP1 Ring Complex) was recently described associated with severe distal motor neuropathy by our team. In this study, we investigated the histopathological abnormalities of the skeletal muscle biopsy of the pediatric patient affected by the mutation Leu224Val in the CCT5 subunit. We provide molecular and structural features of the diseased skeletal muscle tissue that we believe may be useful to identify undiagnosed cases of this rare genetic disorder. We investigated the histological abnormalities of the affected tissue via hematoxylin and eosin staining. Then we used immunofluorescence and qPCR techniques to explore the expression and distribution of CCT5 in diseased and healthy skeletal muscle tissue. Immunofluorescence and immunohistochemistry assays were performed to study the sarcomeric and structural proteins of skeletal muscle, including actin, myosin, tubulin, troponin-T, telethonin, and titin. We performed Western blot to examine the protein expression of CCT5 and some heat shock proteins, Hsp90, Hsp60, Hsp27, and α-B crystallin, along with the main client proteins of the CCT5, actin, and tubulin. Our findings revealed muscular atrophy, abnormal morphology, and different sizes of muscle fibers in affected tissue. The swollen nuclei and wide interfiber spaces were seen. Expression of CCT5 had been decreased and showed a different distribution pattern in the affected tissue. Altered expression, distribution, and bandage pattern were detected by confocal microscopy for the interested muscular proteins in tissue from the patient compared to the healthy control. Protein levels of the studied Hsps normally located at the Z-disk were reduced. Western blot results showed increased levels of the actin and tubulin proteins in the diseased skeletal muscle biopsy compared to healthy tissue. Chaperones must be expressed at high levels in skeletal muscle to counteract various stressors such as mechanical, oxidative, and thermal crises; therefore, it seems relevant that defects of molecular chaperones may result in damaged skeletal muscle fibers. So far, several chaperones or cochaperones involved in neuromuscular disorders have been defined. Our study shows that alteration of the CCT5 subunit is associated with the damaged structure of skeletal muscle fibers and alterations of chaperone system components and paves the way to explore possible alternative substrates of chaperonin CCT. However, further studies are underway to investigate the CCT mechanisms of action to design applicable therapeutic strategies.

Keywords: molecular chaperones, neurochaperonopathy, neuromuscular system, protein homeostasis

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Authors: Ya-Ting Liao, Chien-Chang Huang

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Green diesel is a renewable biofuel obtained from plant oil or fatty acid deoxygenation. Because the molecular structure of green diesel is similar to that of fossil fuel, green diesel can be directly used in present vehicle engines without blending with fossil fuel. In this study, mesoporous carbon-based catalysts with doped metal ions, such as Mg, Ni, or Fe, were prepared using co-polymers and gallic acid as molecular templates and carbon sources, respectively. The prepared catalysts were then applied to carry out the deoxygenation of fatty acid and waste cooking oil. To obtain the highest net energy from the produced green diesel, the catalyzed deoxygenation reaction and catalyst preparation processes were carried out under ambient conditions, respectively, to avoid using H₂ as a reagent and reducing agent. XRD, BET, SEM, EDS, FT-IR, and pyridine-IR characterized the composition and configuration of the prepared catalyst. The results display that the doped metal ions were well-dispersed in the carbon-based catalyst and the surface of the catalysts was rich in Lewis acid sites after the catalysts were calcined at the proper temperature. The pore size present on the catalyst was 9-11 nm. To catalyze the deoxygenation of fatty acid by the prepared catalysts at 320℃ under H₂-free conditions, high fatty acid conversion (99%) and high selectivity for hydrocarbons (78%) were obtained when the ratio of doped Ni to doped Mg was optimized.

Keywords: ordered mesoporous carbon, catalysts, hydrocarbons, deoxygenation

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Authors: Jefto Terzovic, Ana Kontic, Isidora Ilic

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In the proposed design concept, laminated glass and laminated plexiglass, as ”unconventional materials”, are considered as a filling in a steel frame on which they overlap by the intermediate rubber layer, thereby forming a composite assembly. In this way vertical elements of stiffening are formed, capable for reception of seismic force and integrated into the structural system of the building. The applicability of such a system was verified by experiments in laboratory conditions where the experimental models based on laminated glass and laminated plexiglass had been exposed to the cyclic loads that simulate the seismic force. In this way the load capacity of composite assemblies was tested for the effects of dynamic load that was parallel to assembly plane. Thus, the stress intensity to which composite systems might be exposed was determined as well as the range of the structure stiffening referring to the expressed deformation along with the advantages of a particular type of filling compared to the other one. Using specialized software whose operation is based on the finite element method, a computer model of the structure was created and processed in the case study; the same computer model was used for analyzing the problem in the first phase of the design process. The stiffening system based on composite assemblies tested in laboratories is implemented in the computer model. The results of the modal analysis and seismic calculation from the computer model with stiffeners applied showed an efficacy of such a solution, thus rounding the design procedures for aseismic stiffening by using unconventional materials.

Keywords: laminated glass, laminated plexiglass, aseismic stiffening, experiment, laboratory testing, computer model, finite element method

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Authors: Soukaina Motia, Nadia El Alami El Hassani, Alassane Diouf, Benachir Bouchikhi, Nezha El Bari

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Parabens are the antimicrobial molecules largely used in cosmetic products as a preservative agent. Among them, the methylparaben (MP) is the most frequently used ingredient in cosmetic preparations. Nevertheless, their potential dangers led to the development of sensible and reliable methods for their determination in environmental samples. Firstly, a sensitive and selective molecular imprinted polymer (MIP) based on screen-printed gold electrode (Au-SPE), assembled on a polymeric layer of carboxylated poly(vinyl-chloride) (PVC-COOH), was developed. After the template removal, the obtained material was able to rebind MP and discriminate it among other interfering species such as glucose, sucrose, and citric acid. The behavior of molecular imprinted sensor was characterized by Cyclic Voltammetry (CV), Differential Pulse Voltammetry (DPV) and Electrochemical Impedance Spectroscopy (EIS) techniques. Then, the biosensor was found to have a linear detection range from 0.1 pg.mL^-1 to 1 ng.mL^-1 and a low limit of detection of 0.12 fg.mL^-1 and 5.18 pg.mL^-1 by DPV and EIS, respectively. For applications, this biosensor was employed to determine MP content in four wastewaters in Meknes city and two cosmetic products (shower gel and shampoo). The operational reproducibility and stability of this biosensor were also studied. Secondly, another MIP biosensor based on tungsten trioxide (WO₃) functionalized by gold nanoparticles (Au-NPs) assembled on a polymeric layer of PVC-COOH was developed. The main goal was to increase the sensitivity of the biosensor. The developed MIP biosensor was successfully applied for the MP determination in wastewater samples and cosmetic products.

Keywords: cosmetic products, methylparaben, molecularly imprinted polymer, wastewater

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Authors: Weirong Wang, Shenghong Huang, Xisheng Luo, Zhenyu Li

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Material mixing process and related dynamic issues at extreme compressing conditions have gained more and more concerns in last ten years because of the engineering appealings in inertial confinement fusion (ICF) and hypervelocity aircraft developments. However, there lacks models and methods that can handle fully coupled turbulent material mixing and complex fluid evolution under conditions of high energy density regime up to now. In aspects of macro hydrodynamics, three numerical methods such as direct numerical simulation (DNS), large eddy simulation (LES) and Reynolds-averaged Navier–Stokes equations (RANS) has obtained relative acceptable consensus under the conditions of low energy density regime. However, under the conditions of high energy density regime, they can not be applied directly due to occurrence of dissociation, ionization, dramatic change of equation of state, thermodynamic properties etc., which may make the governing equations invalid in some coupled situations. However, in view of micro/meso scale regime, the methods based on Molecular Dynamics (MD) as well as Monte Carlo (MC) model are proved to be promising and effective ways to investigate such issues. In this study, both classical MD and first-principle based electron force field MD (eFF-MD) methods are applied to investigate Richtmyer-Meshkov Instability of metal Lithium and gas Hydrogen (Li-H2) interface mixing at different shock loading speed ranging from 3 km/s to 30 km/s. It is found that: 1) Classical MD method based on predefined potential functions has some limits in application to extreme conditions, since it cannot simulate the ionization process and its potential functions are not suitable to all conditions, while the eFF-MD method can correctly simulate the ionization process due to its ‘ab initio’ feature; 2) Due to computational cost, the eFF-MD results are also influenced by simulation domain dimensions, boundary conditions and relaxation time choices, etc., in computations. Series of tests have been conducted to determine the optimized parameters. 3) Ionization induced by strong shock compression has important effects on Li-H2 interface evolutions of RMI, indicating a new micromechanism of RMI under conditions of high energy density regime.

Keywords: first-principle, ionization, molecular dynamics, material mixture, Richtmyer-Meshkov instability

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Authors: Keaghan Brown

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The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Nuha Mansour Alhazmi, Magda Mohamed Aly, Fardus M. Bokhari, Ahmed Bahieldin, Sherif Edris

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Out of 30 fungal isolates, 2 new isolates were proven to degrade poly-β-hydroxybutyrate (PHB). Enzyme assay for these isolates indicated the optimal environmental conditions required for depolymerase enzyme to induce the highest level of biopolymer degradation. The two isolates were basically characterized at the morphological level as Trichoderma asperellum (isolate S1), and Aspergillus fumigates (isolate S2) using standard approaches. The aim of the present study was to characterize these two isolates at the molecular level based on the highly diverged rRNA gene(s). Within this gene, two domains of the ribosome large subunit (LSU) namely internal transcribed spacer (ITS) and 26S were utilized in the analysis. The first domain comprises the ITS1/5.8S/ITS2 regions ( > 500 bp), while the second domain comprises the D1/D2/D3 regions ( > 1200 bp). Sanger sequencing was conducted at Macrogen (Inc.) for the two isolates using primers ITS1/ITS4 for the first domain, while primers LROR/LR7 for the second domain. Sizes of the first domain ranged between 594-602 bp for S1 isolate and 581-594 bp for S2 isolate, while those of the second domain ranged between 1228-1238 bp for S1 isolate and 1156-1291 for S2 isolate. BLAST analysis indicated 99% identities of the first domain of S1 isolate with T. asperellum isolates XP22 (ID: KX664456.1), CTCCSJ-G-HB40564 (ID: KY750349.1), CTCCSJ-F-ZY40590 (ID: KY750362.1) and TV (ID: KU341015.1). BLAST of the first domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other T. asperellum and A. fumigatus isolates and strains showed high level of identities with S1 and S2 isolates, respectively, based on the diversity of the first domain. BLAST of the second domain of S1 isolate indicated 99 and 100% identities with only two strains of T. asperellum namely TR 3 (ID: HM466685.1) and G (ID: KF723005.1), respectively. However, other T. species (ex., atroviride, hamatum, deliquescens, harzianum, etc.) also showed high level of identities. BLAST of the second domain of S2 isolate indicated 100% identities with A. fumigatus isolate YNCA0338 (ID: KP068684.1) and strain MEF-Cr-6 (ID: KU597198.1), while 99% identities with A. fumigatus isolate CCA101 (ID: KT877346.1) and strain CD1621 (ID: JX092088.1). Large numbers of other A. fumigatus isolates and strains showed high level of identities with S2 isolate. Overall, the results of molecular characterization based on rRNA diversity for the two isolates of T. asperellum and A. fumigatus matched those obtained by morphological characterization. In addition, ITS domain proved to be more sensitive than 26S domain in diversity profiling of fungi at the species level.

Keywords: Aspergillus fumigates, Trichoderma asperellum, PHB, degradation, BLAST, ITS, 26S, rRNA

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Authors: Shahriar Sepahvand, Mohammad Ali Davarpanah

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Infections caused by Acinetobacter baumannii are among the common hospital-acquired infections that have seen an increase in antibiotic resistance in recent years. Colistin is the last treatment option against this pathogen. The aim of this study is to investigate the histopathology of BALB/C mice receiving sensitive and resistant strains of Acinetobacter baumannii to colistin. A total of 68 female laboratory mice weighing 30 to 40 grams of the BALB/C breed were studied in this research for three weeks under appropriate laboratory conditions in terms of food and environment. The experimental groups included: control group, second group, third group, fourth group. Lung, liver, spleen, and kidney tissues were removed from anesthetized mice and, after washing in physiological serum, were fixed in 10% formalin for 14 days. For dehydration, alcohol with ascending degrees of 70, 80, 90, and 100 was used. After clearing and soaking in paraffin, the samples were embedded in paraffin. Then, sections with a thickness of 5 microns were prepared and, after staining by hematoxylin-eosin, the samples were ready for study with a light microscope. In liver, spleen, lung, and kidney tissues of mice receiving the colistin-sensitive strain of Acinetobacter baumannii, infiltration of inflammatory cells and hyperemia were observed compared to control group mice. Liver and lung tissues of mice receiving strains of Acinetobacter baumannii resistant to colistin showed tissue destruction in addition to infiltration of inflammatory cells and hyperemia, with more destruction observed in lung tissue.

Keywords: acinetobacter baumannii, colistin antibiotic, histopathological examination, resistant

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Authors: Dylan Treger, Lujia Zhang, Xiaoxiao Jia, Jessica H. Hui, Munkh-Amgalan Gantumur, Mizhou Hui, Li Liu

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Hyaluronic acid (HA) is involved in wound healing via inflammation, granulation, and re-epithelialization mechanisms. The poor physical properties of natural high-molecular-weight polymers limit their direct use in the medical field. In this clinical study, we investigated whether the local injection of a tissue-permeable 35 kDa HA fragment (HA35) could favor the healing process in patients with chronic wounds accompanied by neuropathic pain. The HA35 fragments were freshly manufactured by degradation of high-molecular-weight HA with bovine testis-derived hyaluronidase PH20. Twenty patients in this study had nonhealing wounds and wound-related pain for more than 3 months. Freshly produced HA35 was locally injected into healthy skin immediately surrounding chronic wounds once a day for 10 days. Wound-associated pain and the degree of wound healing were evaluated. The injection of HA35 relieved the pain associated with chronic wounds in 24 hours. HA35 treatment significantly promoted the healing of chronic wounds, including expanded fresh granulation tissue on the wounds; reduced darkness or redness, dryness, and damaged areas on the surface of the skin surrounding the wounds; and decreased the size of the wound area. It can be concluded that the topical injection of tissue-permeable HA35 around chronic wounds has great potential to promote wound healing.

Keywords: 35 kDa hyaluronan fragment HA35, chronic wound, wound healing, tissue permeability

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Authors: Sara Torabi, Sadegh Khazalpour, Mahdi Jamshidi

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Nitro aromatic compounds are valuable materials because of their applications in the preparation of chemical intermediates for the synthesis of dyes, plastics, perfumes, energetic materials, and pharmaceuticals. Chemical and electrochemical procedures are reported for nitration of aromatic compounds. Flavonoid derivatives are present in many vegetables and fruits and are constituent of many common pharmaceuticals and dietary supplements. Electrochemistry provides very versatile means for the electrosynthesis, mechanistic and kinetic studies. To the best of our knowledge, and despite the importance of these compounds in numerous scientific fields, there are no reports on the electrochemical nitration of Quercetin derivatives. Herein, we describe a green electrochemical synthesis of a nitro compound. In this work, electrochemical oxidation of Quercetin has been studied in the presence of nitrite ion as a nucleophile in acetate buffer solution (c = 0.2 M, pH = 6.0), by means of cyclic voltammetry and controlled-potential coulometry. The results indicate the participation of produced o-benzoquinones in Michael reaction with nitrite ion (in the divided cell) to form the corresponding nitro diol (EC mechanism). The purity of product and characterization was done using ¹H NMR, ¹³C NMR, FTIR spectroscopic techniques. The presented strategies use a water/ethanol mixture as solvent. Ethanol as cosolvent was also used in the previous studies because of its low cost, safety, easy availability, recyclability, bioproductability, and biodegradability. These strategies represent a one-pot and facile process for the synthesis of nitro compound in high yield and purity under green conditions.

Keywords: electrochemical synthesis, green chemistry, cyclic voltammetry, molecular docking

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Authors: Mohammad Ghiasvand, Babak Khorsandi, Morteza Kolahdoozan

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Under the influence of waves, oil in the sea is subject to vertical scattering in the water column. Scientists' knowledge of how oil is dispersed in the water column is one of the lowest levels of knowledge among other processes affecting oil in the marine environment, which highlights the need for research and study in this field. Therefore, this study investigates the distribution of oil in the water column in a turbulent environment with zero velocity characteristics. Lack of laboratory results to analyze the distribution of petroleum pollutants in deep water for information Phenomenon physics on the one hand and using them to calibrate numerical models on the other hand led to the development of laboratory models in research. According to the aim of the present study, which is to investigate the distribution of oil in homogeneous and isotropic turbulence caused by the oscillating Grid, after reaching the ideal conditions, the crude oil flow was poured onto the water surface and oil was distributed in deep water due to turbulence was investigated. In this study, all experimental processes have been implemented and used for the first time in Iran, and the study of oil diffusion in the water column was considered one of the key aspects of pollutant diffusion in the oscillating Grid environment. Finally, the required oscillation velocities were taken at depths of 10, 15, 20, and 25 cm from the water surface and used in the analysis of oil diffusion due to turbulence parameters. The results showed that with the characteristics of the present system in two static modes and network motion with a frequency of 0.8 Hz, the results of oil diffusion in the four mentioned depths at a frequency of 0.8 Hz compared to the static mode from top to bottom at 26.18, 57 31.5, 37.5 and 50% more. Also, after 2.5 minutes of the oil spill at a frequency of 0.8 Hz, oil distribution at the mentioned depths increased by 49, 61.5, 85, and 146.1%, respectively, compared to the base (static) state.

Keywords: homogeneous and isotropic turbulence, oil distribution, oscillating grid, oil spill

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Authors: Salah Brahim Belakhdar, Tari Mohammed Amin, Rafai Abderrahmen, Amalsi Bilal

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Shear strength of sandy soils has been considered as the important parameter to study the stability of different civil engineering structures when subjected to monotonic, cyclic, and earthquake loading conditions. The proposed research investigated the effect of grading characteristics on the shear strength and mechanical behaviour of granular classes of sands mixed with salt in loose and dense states (Dr=15% and 90%). The laboratory investigation aimed at understanding the extent or degree at which shear strength of sand-silt mixture soil is affected by its gradation under static loading conditions. For the purpose of clarifying and evaluating the shear strength characteristics of sandy soils, a series of Casagrande shear box tests were carried out on different reconstituted samples of sand-silt mixtures with various gradations. The soil samples were tested under different normal stresses (100, 200, and 300 kPa). The results from this laboratory investigation were used to develop insight into the shear strength response of sand and sand-silt mixtures under monotonic loading conditions. The analysis of the obtained data revealed that the grading characteristics (D10, D50, Cu, ESR, and MGSR) have a significant influence on the shear strength response. It was found that shear strength can be correlated to the grading characteristics for the sand-silt mixture. The effective size ratio (ESR) and mean grain size ratio (MGSR) appear as pertinent parameters to predict the shear strength response of the sand-silt mixtures for soil gradation under study.

Keywords: mechanical behavior, silty sand, friction angle, cohesion, fines content

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Authors: Deepika Saini, Sandeep Jain, Ajay Kumar

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The quinoline scaffold is one of the most widely studied in the discovery of derivatives with various heterocyclic moieties due to its potential antimalarial activities. In the present study, a chalcone series of quinoline derivatives clubbed with pyrazole were synthesized to evaluate their antimalarial property by in vitro schizont maturation inhibition assay against both chloroquine sensitive, 3D7 and chloroquine resistant, RKL9 strain of Plasmodium falciparum. Further, top five compounds were studied for in vivo preclinical study for antimalarial potential against P. berghei in Swiss albino mice. To understand the mechanism of synthesized analogues, they were screened computationally by molecular docking techniques. Compounds were docked into the active site of a protein receptor, Plasmodium falciparum Cysteine Protease Falcipain-2. The compounds were successfully synthesized, and structural confirmation was performed by FTIR, 1H-NMR, mass spectrometry and elemental analysis. In vitro study suggested that the compounds 5b, 5g, 5l, 5s and 5u possessed best antimalarial activity and further tested for in vivo screening. Compound 5u (CH₃ on both rings) with EC₅₀ 0.313 & 0.801 µg/ml against CQ-S & CQ-R strains of P. falciparum respectively and 78.01% suppression of parasitemia. The molecular docking studies of the compounds helped in understanding the mechanism of action against falcipain-2. The present study reveals the binding signatures of the synthesized ligands within the active site of the protein, and it explains the results from in vitro study in their EC₅₀ values and percentage parasitemia.

Keywords: antimalarial activity, chalcone, docking, quinoline

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Authors: Camille Perréard, Yoann Ladner, Fanny D'Orlyé, Stéphanie Descroix, Vélan Taniga, Anne Varenne, Cédric Guyon, Michael. Tatoulian, Frédéric Kanoufi, Cyrine Slim, Sophie Griveau, Fethi Bedioui

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The development of micro total analysis systems is of major interest for contaminant and biomarker analysis. As a lab-on-chip integrates all steps of an analysis procedure in a single device, analysis can be performed in an automated format with reduced time and cost, while maintaining performances comparable to those of conventional chromatographic systems. Moreover, these miniaturized systems are either compatible with field work or glovebox manipulations. This work is aimed at developing an analytical microsystem for trace and ultra trace quantitation in complex matrices. The strategy consists in the integration of a sample pretreatment step within the lab-on-chip by a confinement zone where selective ligands are immobilized for target extraction and preconcentration. Aptamers were chosen as selective ligands, because of their high affinity for all types of targets (from small ions to viruses and cells) and their ease of synthesis and functionalization. This integrated target extraction and concentration step will be followed in the microdevice by an electrokinetic separation step and an on-line detection. Polymers consisting of cyclic olefin copolymer (COC) or fluoropolymer (Dyneon THV) were selected as they are easy to mold, transparent in UV-visible and have high resistance towards solvents and extreme pH conditions. However, because of their low chemical reactivity, surface treatments are necessary. For the design of this miniaturized diagnostics, we aimed at modifying the microfluidic system at two scales : (1) on the entire surface of the microsystem to control the surface hydrophobicity (so as to avoid any sample wall adsorption) and the fluid flows during electrokinetic separation, or (2) locally so as to immobilize selective ligands (aptamers) on restricted areas for target extraction and preconcentration. We developed different novel strategies for the surface functionalization of COC and Dyneon, based on plasma, chemical and /or electrochemical approaches. In a first approach, a plasma-induced immobilization of brominated derivatives was performed on the entire surface. Further substitution of the bromine by an azide functional group led to covalent immobilization of ligands through “click” chemistry reaction between azides and terminal alkynes. COC and Dyneon materials were characterized at each step of the surface functionalization procedure by various complementary techniques to evaluate the quality and homogeneity of the functionalization (contact angle, XPS, ATR). With the objective of local (micrometric scale) aptamer immobilization, we developed an original electrochemical strategy on engraved Dyneon THV microchannel. Through local electrochemical carbonization followed by adsorption of azide-bearing diazonium moieties and covalent linkage of alkyne-bearing aptamers through click chemistry reaction, typical dimensions of immobilization zones reached the 50 µm range. Other functionalization strategies, such as sol-gel encapsulation of aptamers, are currently investigated and may also be suitable for the development of the analytical microdevice. The development of these functionalization strategies is the first crucial step in the design of the entire microdevice. These strategies allow the grafting of a large number of molecules for the development of new analytical tools in various domains like environment or healthcare.

Keywords: alkyne-azide click chemistry (CuAAC), electrochemical modification, microsystem, plasma bromination, surface functionalization, thermoplastic polymers

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Authors: Udayakumar Vee, Franck Quero

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Zwitterionic polymers generally have been viewed as a new class of antimicrobial and non-fouling materials. They offer a broad versatility for chemical modification and hence great freedom for accurate molecular design, which bear an equimolar number of homogenously distributed anionic and cationic groups along their polymer chains. This study explores the effectiveness of the auxetic zwitterion carboxylate/sulfonate hydrogel in the diabetic-induced mouse model. A series of silver metal-doped auxetic zwitterion carboxylate/sulfonate/vinylaniline copolymer hydrogels is designed via a 3D printer. Zwitterion monomers have been characterized by FT-IR and NMR techniques. The effect of changing the monomers and different loading ratios of Ag over zwitterion on the final hydrogel materials' antimicrobial properties and biocompatibility will be investigated in detail. The synthesized auxetic hydrogel has been characterized using a wide range of techniques to help establish the relationship between molecular level and macroscopic properties of these materials, including mechanical and antibacterial and biocompatibility and wound healing ability. This work's comparative studies and results provide new insights and guide us in choosing a better auxetic structured material for a broad spectrum of wound healing applications in the animal model. We expect this approach to provide a versatile and robust platform for biomaterial design that could lead to promising treatments for wound healing applications.

Keywords: auxetic, zwitterion, carboxylate, sulfonate, polymer, wound healing

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Authors: Toufik Bensana, Medkour Mihoub, Slimane Mekhilef

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The use of vibration analysis has been established as the most common and reliable method of analysis in the field of condition monitoring and diagnostics of rotating machinery. Rolling bearings cover a broad range of rotary machines and plays a crucial role in the modern manufacturing industry. Unfortunately, the vibration signals collected from a faulty bearing are generally nonstationary, nonlinear and with strong noise interference, so it is essential to obtain the fault features correctly. In this paper, a novel numerical analysis method based on local mean decomposition (LMD) is proposed. LMD decompose the signal into a series of product functions (PFs), each of which is the product of an envelope signal and a purely frequency modulated FM signal. The envelope of a PF is the instantaneous amplitude (IA), and the derivative of the unwrapped phase of a purely flat frequency demodulated (FM) signal is the IF. After that, the fault characteristic frequency of the roller bearing can be extracted by performing spectrum analysis to the instantaneous amplitude of PF component containing dominant fault information. The results show the effectiveness of the proposed technique in fault detection and diagnosis of rolling element bearing.

Keywords: fault diagnosis, rolling element bearing, local mean decomposition, condition monitoring

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Authors: Udayakumar Veerabagu, Franck Quero

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Zwitterion carboxylate and sulfonate polymers generally have been viewed as a new class of antimicrobial and non-fouling materials. They offer a broad versatility for chemical modification and hence great freedom for accurate molecular design, which bear an equimolar number of homogenously distributed anionic and cationic groups along their polymer chains. This study explores the effectiveness of the auxetic zwitterion carboxylate/sulfonate hydrogel in the diabetic-induced mouse model. A series of silver metal-doped auxetic zwitterion carboxylate/sulfonate/vinylaniline copolymer hydrogels is designed via a 3D printer. Zwitterion monomers have been characterized by FT-IR and NMR techniques. The effect of changing the monomers and different loading ratios of Ag over zwitterion on the final hydrogel materials' antimicrobial properties and biocompatibility will be investigated in detail. The synthesized auxetic hydrogel has been characterized using a wide range of techniques to help establish the relationship between molecular level and macroscopic properties of these materials, including mechanical and antibacterial and biocompatibility and wound healing ability. This work's comparative studies and results provide new insights and guide us in choosing a better auxetic structured material for a broad spectrum of wound healing applications in the animal model. We expect this approach to provide a versatile and robust platform for biomaterial design that could lead to promising treatments for wound healing applications.

Keywords: auxetic, zwitterion, carboxylate, sulfonate, polymer, wound healing

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Authors: Hassan Sbiga

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Laboratory measurements methods were undertaken on core samples selected from three different fields (A, B, and C) from the Nubian Sandstone Formation of the central graben reservoirs in Libya. These measurements were conducted in order to determine the factors which affect resistivity parameters, and to investigate the effect of rock heterogeneity and wettability on these parameters. This included determining the saturation exponent (n) in the laboratory at two stages. The first stage was before wettability measurements were conducted on the samples, and the second stage was after the wettability measurements in order to find any effect on the saturation exponent. Another objective of this work was to quantify experimentally pores and porosity types (macro- and micro-porosity), which have an affect on the electrical properties, by integrating capillary pressure curves with other routine and special core analysis. These experiments were made for the first time to obtain a relation between pore size distribution and saturation exponent n. Changes were observed in the formation resistivity factor and cementation exponent due to ambient conditions and changes of overburden pressure. The cementation exponent also decreased from GHE-5 to GHE-8. Changes were also observed in the saturation exponent (n) and water saturation (Sw) before and after wettability measurement. Samples with an oil-wet tendency have higher irreducible brine saturation and higher Archie saturation exponent values than samples with an uniform water-wet surface. The experimental results indicate that there is a good relation between resistivity and pore type depending on the pore size. When oil begins to penetrate micro-pore systems in measurements of resistivity index versus brine saturation (after wettability measurement), a significant change in slope of the resistivity index relationship occurs.

Keywords: part of thesis, cementation, wettability, resistivity

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Authors: Turban Kar, Maitree Bhattacharyya

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Curcumin, a dietary antioxidant has been identified as a wonder molecule to possess therapeutic properties protecting the cellular macromolecules from oxidative damage. In our experimental study, we have explored the effectiveness of curcumin in protecting the structural paradigm of Human Serum Albumin (HSA) when exposed to gamma irradiation. HSA, being an important transport protein of the circulatory system, is involved in binding of variety of metabolites, drugs, dyes and fatty acids due to the presence of hydrophobic pockets inside the structure. HSA is also actively involved in the transportation of drugs and metabolites to their targets, because of its long half-life and regulation of osmotic blood pressure. Gamma rays, in its increasing concentration, results in structural alteration of the protein and superoxide radical generation. Curcumin, on the other hand, mitigates the damage, which has been evidenced in the following experiments. Our study explores the possibility for protection by curcumin during the molecular and conformational changes of HSA when exposed to gamma irradiation. We used a combination of spectroscopic methods to probe the conformational ensemble of the irradiated HSA and finally evaluated the extent of restoration by curcumin. SDS - PAGE indicated the formation of cross linked aggregates as a consequence of increasing exposure of gamma radiation. CD and FTIR spectroscopy inferred significant decrease in alpha helix content of HSA from 57% to 15% with increasing radiation doses. Steady state and time resolved fluorescence studies complemented the spectroscopic measurements when lifetime decay was significantly reduced from 6.35 ns to 0.37 ns. Hydrophobic and bityrosine study showed the effectiveness of curcumin for protection against radiation induced free radical generation. Moreover, bityrosine and hydrophobic profiling of gamma irradiated HSA in presence and absence of curcumin provided light on the formation of ROS species generation and the protective (magical) role of curcumin. The molecular mechanism of curcumin protection to HSA from gamma irradiation is yet unknown, though a possible explanation has been proposed in this work using Thioflavin T assay. It was elucidated, that when HSA is irradiated at low dose of gamma radiation in presence of curcumin, it is capable of retaining the native characteristic properties to a greater extent indicating stabilization of molecular structure. Thus, curcumin may be utilized as a therapeutic strategy to protect cellular proteins.

Keywords: Bityrosine content, conformational change, curcumin, gamma radiation, human serum albumin

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Authors: Maturin Désiré Sop Sop, Didien Njumba Besende, Samuel Fosso Wamba

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This study seeks to examine the nexus between drinking water sources in the Kumba municipality and its related health implications vis-à-vis the recurrent incidences of waterborne diseases such as Typhoid, Cholera, Diarrhea, Dysentery, Hepatitis A and malaria. The study adopted a purposive sampling technique in which surveys were conducted between the months of June to December 2022. 150 questionnaires were retrieved from the 210 administered to the affected population of Kosala, Buea Road and Mambanda. Information for the study was collected using surveys, questionnaires, key informant interviews, the laboratory analysis of collected drinking water samples, the researcher’s direct observation as well and hospital reports on the prevalence of waterborne diseases. Water samples from the nearby streams and wells, which were communally used by the local population for drinking, and five slaughterhouses within the affected areas were laboratory tested to determine alterations in their chemical, physical and microbiological characteristics. The collected water samples from all the streams and wells used for drinking were tested for changes in properties such as temperature, turbidity, EC, pH, TDS, TSS, Cl, SO42-, PO43-, NO3-, Fe, Na, BOD, COD, DO, E.coli and total coliform concentration. These results were then compared with the WHO regulations for water quality. The results from the laboratory analysis of drinking water sources, which were at the same time used by the surrounding abattoirs revealed significant alterations in the water quality parameters such as temperature, turbidity, EC, pH, TDS, TSS, Cl, SO42-, PO43-, NO3-, Fe, Na, BOD, COD, DO, E.coli and total coliform concentration. This is due to the channeling of untreated wastes into the different drinking water points as well as the inter-use of dirty utensils such as buckets from slaughterhouses to fetch water from the streams and wells that serve as drinking water sources for the local population. On the human health aspect, the results were later compared with hospital data, and they revealed that the consumption of such contaminated water in the localities of Kosala, Mambanda, and Buea road negatively affected the local population because of the high incidences of Typhoid Cholera, Diarrhea, Dysentery, Hepatitis A and malaria. The poor management of drinking water sources pollutes streams and significantly exposes the local population to lots of waterborne diseases. Efforts should be made to provide clean pipe-borne water to the affected localities of Kumba as well as to ensure the proper management of wastes.

Keywords: drinking water, diseases, Kumba, municipality

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Authors: Milica Karadzic, Lidija Jevric, Sanja Podunavac-Kuzmanovic, Strahinja Kovacevic, Anamarija Mandic, Katarina Penov Gasi, Marija Sakac, Aleksandar Okljesa, Andrea Nikolic

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The present paper deals with chromatographic lipophilicity prediction of newly synthesized steroid derivatives. The prediction was achieved using in silico generated molecular descriptors and quantitative structure-retention relationship (QSRR) methodology with the artificial neural networks (ANN) approach. Chromatographic lipophilicity of the investigated compounds was expressed as retention factor value logk. For QSRR modeling, a feedforward back-propagation ANN with gradient descent learning algorithm was applied. Using the novel sum of ranking differences (SRD) method generated ANN models were ranked. The aim was to distinguish the most consistent QSRR model that can be found, and similarity or dissimilarity between the models that could be noticed. In this study, SRD was performed with average values of retention factor value logk as reference values. An excellent correlation between experimentally observed retention factor value logk and values predicted by the ANN was obtained with a correlation coefficient higher than 0.9890. Statistical results show that the established ANN models can be applied for required purpose. This article is based upon work from COST Action (TD1305), supported by COST (European Cooperation in Science and Technology).

Keywords: artificial neural networks, liquid chromatography, molecular descriptors, steroids, sum of ranking differences

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Authors: Biruhi Tesfaye, Avinash M. Potdar

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The laboratory test process to determine the California bearing ratio (CBR) of black cotton soils is not only overpriced but also time-consuming as well. Hence advanced prediction of CBR plays a significant role as it is applicable In pavement design. The prediction of CBR of treated soil was executed by Artificial Neural Networks (ANNs) which is a Computational tool based on the properties of the biological neural system. To observe CBR values, combined eggshell and waste glass was added to soil as 4, 8, 12, and 16 % of the weights of the soil samples. Accordingly, the laboratory related tests were conducted to get the required best model. The maximum CBR value found at 5.8 at 8 % of eggshell waste glass powder addition. The model was developed using CBR as an output layer variable. CBR was considered as a function of the joint effect of liquid limit, plastic limit, and plastic index, optimum moisture content and maximum dry density. The best model that has been found was ANN with 5, 6 and 1 neurons in the input, hidden and output layer correspondingly. The performance of selected ANN has been 0.99996, 4.44E-05, 0.00353 and 0.0067 which are correlation coefficient (R), mean square error (MSE), mean absolute error (MAE) and root mean square error (RMSE) respectively. The research presented or summarized above throws light on future scope on stabilization with waste glass combined with different percentages of eggshell that leads to the economical design of CBR acceptable to pavement sub-base or base, as desired.

Keywords: CBR, artificial neural network, liquid limit, plastic limit, maximum dry density, OMC

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Authors: R. Shrestha, D. P. Subedi, R. B. Tyata, C. S. Wong,

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In this paper, a technique for the determination of electron temperatures and electron densities in atmospheric pressure Argon/air discharge by the analysis of optical emission spectra (OES) is reported. The discharge was produced using a high voltage (0-20) kV power supply operating at a frequency of 27 kHz in parallel electrode system, with glass as dielectric. The dielectric layers covering the electrodes act as current limiters and prevent the transition to an arc discharge. Optical emission spectra in the range of (300nm-850nm) were recorded for the discharge with different inter electrode gap keeping electric field constant. Electron temperature (Te) and electron density (ne) are estimated from electrical and optical methods. Electron density was calculated using power balance method. The optical methods are related with line intensity ratio from the relative intensities of Ar-I and Ar-II lines in Argon plasma. The electron density calculated by using line intensity ratio method was compared with the electron density calculated by stark broadening method. The effect of dielectric thickness on plasma parameters (Te and ne) have also been studied and found that Te and ne increases as thickness of dielectric decrease for same inter electrode distance and applied voltage.

Keywords: electron density, electron temperature, optical emission spectra,

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Authors: Juan Carlos Baena, Zhongxiao Peng

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Ultra-high molecular weight polyethylene (UHMWPE) is extensively used in industrial and biomedical fields. The slippery nature of UHMWPE makes this material suitable for surface bearing applications, however, the operational conditions limit the lubrication efficiency, inducing boundary and mixed lubrication in the tribological system. The lack of lubrication in a tribological system intensifies friction, contact stress and consequently, operating temperature. With temperature increase, the material’s mechanical properties are affected, and the lifespan of the component is reduced. The understanding of how mechanical properties and wear performance of UHMWPE change when the temperature is increased has not been clearly identified. The understanding of the wear and mechanical performance of UHMWPE at different temperature is important to predict and further improve the lifespan of these components. This study evaluates the effects of temperature variation in a range of 20 °C to 60 °C on the hardness and the wear resistance of UHMWPE. A reduction of the hardness and wear resistance was observed with the increase in temperature. The variation of the wear rate increased 94.8% when the temperature changed from 20 °C to 50 °C. Although hardness is regarded to be an indicator of the material wear resistance, this study found that wear resistance decreased more rapidly than hardness with the temperature increase, evidencing a low material stability of this component in a short temperature interval. The reduction of the hardness was reflected by the plastic deformation and abrasion intensity, resulting in a significant wear rate increase.

Keywords: hardness, surface bearing, tribological system, UHMWPE, wear

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Authors: K. A. Mistry, I. B. Patel, A. H. Prajapati

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In the present work, the alloy of Bismuth-lead is prepared on the basis of percentage of molecular weight 9:1, 5:5 and 1:9 ratios and grown by Zone- Refining Technique under a vacuum atmosphere. The EDAX of these samples are done and the results are reported. Micro hardness test has been used as an alternative test for measuring material’s tensile properties. The effect of temperature and load on the hardness of the grown alloy has been studied. Further the comparative studies of work hardening coefficients are reported. In the present work, the alloy of Bismuth-lead is prepared on the basis of percentage of molecular weight 9:1, 5:5 and 1:9 ratios and grown by Zone- Refining Technique under a vacuum atmosphere. The EDAX of these samples are done and the results are reported. Micro hardness test has been used as an alternative test for measuring material’s tensile properties. The effect of temperature and load on the hardness of the grown alloy has been studied. Further the comparative studies of work hardening coefficients are reported.

Keywords: EDAX, hardening coefficient, micro hardness, Bi-Pb alloy

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Authors: Narsimhulu Sanke, D. N. Reddy

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The purpose of the paper is to discuss the biomass as a renewable source of energy for power generation. The setup is designed and fabricated in the Centre for Energy Technology (CET) and four different fuels are tested in the laboratory, but here the focus is on wood blocks (fuel) combustion with temperature, gas composition percentage by volume and the heating values.

Keywords: biomass, downdraft gasifier, power generation, renewable energy sources

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Authors: K. Thiel, P. Patrikainen, C. Nagy, D. Fitzpatrick, E.-M. Aro, P. Kallio

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Photosynthetic cyanobacteria have been recognized as potential future biotechnological hosts for the direct conversion of CO₂ into chemicals of interest using sunlight as the solar energy source. However, in order to develop commercially viable systems, the flux of electrons from the photosynthetic light reactions towards specified target chemicals must be significantly improved. The objective of the study was to investigate whether the autotrophic production efficiency of specified end-metabolites can be improved in engineered cyanobacterial cells by rescuing excited electrons that are normally lost to molecular oxygen due to the cyanobacterial flavodiiron protein Flv1/3. Natively Flv1/3 dissipates excess electrons in the photosynthetic electron transfer chain by directing them to molecular oxygen in Mehler-like reaction to protect photosystem I. To evaluate the effect of flavodiiron inactivation on autotrophic production efficiency in the cyanobacterial host Synechocystis sp. PCC 6803 (Synechocystis), sucrose was selected as the quantitative reporter and a representative of a potential end-product of interest. The concept is based on the native property of Synechocystis to produce sucrose as an intracellular osmoprotectant when exposed to high external ion concentrations, in combination with the introduction of a heterologous sucrose permease (CscB from Escherichia coli), which transports the sucrose out from the cell. In addition, cell growth, photosynthetic gas fluxes using membrane inlet mass spectrometry and endogenous storage compounds were analysed to illustrate the consequent effects of flv deletion on pathway flux distributions. The results indicate that a significant proportion of the electrons can be lost to molecular oxygen via Flv1/3 even when the cells are grown under high CO₂ and that the inactivation of flavodiiron activity can enhance the photosynthetic electron flux towards optionally available sinks. The flux distribution is dependent on the light conditions and the genetic context of the Δflv mutants, and favors the production of either sucrose or one of the two storage compounds, glycogen or polyhydroxybutyrate. As a conclusion, elimination of the native Flv1/3 reaction and concomitant introduction of an engineered product pathway as an alternative sink for excited electrons could enhance the photosynthetic electron flux towards the target endproduct without compromising the fitness of the host.

Keywords: cyanobacterial engineering, flavodiiron proteins, redirecting electron flux, sucrose

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Authors: Ian N. Robertson

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Alkali Silica Reaction (ASR) occurs in concrete when the alkali hydroxides (Na, K and OH) from the cement react with unstable silica, SiO2, in some types of aggregate. The gel that forms during this reaction will expand when it absorbs water, potentially leading to cracking and overall expansion of the concrete. ASR has resulted in accelerated deterioration of concrete highways, dams and other structures that are exposed to moisture during their service life. Concrete aggregates available in Hawaii have not demonstrated a history of ASR, however, accelerated laboratory tests using ASTM 1260 indicated a potential for ASR with some aggregates. Certain clients are now requiring import of aggregates from the US mainland at great expense. In order to assess the accuracy of the laboratory test results, a long-term field study of the potential for ASR in concretes made with Hawaiian aggregates was initiated in 2011 with funding from the US Federal Highway Administration and Hawaii Department of Transportation. Thirty concrete specimens were constructed of various concrete mixtures using aggregates from all Hawaiian aggregate sources, and some US mainland aggregates known to exhibit ASR expansion. The specimens are located in an open field site in Manoa valley on the Hawaiian Island of Oahu, exposed to relatively high humidity and frequent rainfall. A weather station at the site records the ambient conditions on a continual basis. After two years of monitoring, only one of the Hawaiian aggregates showed any sign of expansion. Ten additional specimens were fabricated with this aggregate to confirm the earlier observations. Admixtures known to mitigate ASR, such as fly ash and lithium, were included in some specimens to evaluate their effect on the concrete expansion. This paper describes the field evaluation program and presents the results for all forty specimens after four years of monitoring.

Keywords: aggregate, alkali silica reaction, concrete durability, field exposure

Procedia PDF Downloads 247