Search results for: molecular imprinted polymers

Authors: Nadjib Melkemi, Salah Belaidi

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Quantitative Structure-Activity Relationship (QSAR) studies have been performed on nineteen molecules of 1,2-dithiole-3-thione analogues. The compounds used are the potent inducers of enzymes involved in the maintenance of reduced glutathione pools as well as phase-2 enzymes important to electrophile detoxication. A multiple linear regression (MLR) procedure was used to design the relationships between molecular descriptor and detoxication properties of the 1,2-dithiole-3-thione derivatives. The predictivity of the model was estimated by cross-validation with the leave-one-out method. Our results suggest a QSAR model based of the following descriptors: qS2, qC3, qC5, qS6, DM, Pol, log P, MV, SAG, HE and EHOMO for the specific activity of quinone reductase; qS1, qS2, qC3, qC4, qC5, qS6, DM, Pol, logP, MV, SAG, HE and EHOMO for the production of growth hormone. To confirm the predictive power of the models, an external set of molecules was used. High correlation between experimental and predicted activity values was observed, indicating the validation and the good quality of the derived QSAR models.

Keywords: QSAR, quinone reductase activity, production of growth hormone, MLR

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Authors: Yusuf, S. I., Saba, A., Olaoye, D. O., Ibrahim J. A., Yahaya H. M., Jatto A. O

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Nuclear Magnetic Resonance (NMR) technology has been applied in several ways to provide vital information about petro-physical properties of reservoirs. However, due to the need to study the molecular behaviours of particles of the fluids in different restricted media, diffusion magnetic resonance equation is hereby applied in spherical coordinates and solved analytically using the method of separation of variables and solution of Legendre equation by Frobenius method. The viscous fluid considered in this research work is unused oil while the non-viscous fluid is water. The results obtained show that water begins to manifest appreciable change at radial adjustment value of 10 and Magnetization of 2.31191995400015x1014 and relaxes finally at 2.30x1014 at radial adjustment value of 1. On the other hand, unused engine oil begins to manifest its changes at radial adjustment value of 40 and Magnetization of 1.466557018x1014and relaxes finally at 1.48x1014 at radial adjustment value of 5.

Keywords: viscous and non-viscous fluid, restricted medium, relaxation times, coefficient of diffusion

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Authors: Minjin Kim, Jihwan Kim, Bongsoo Kim, Junho Suh

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We demonstrate nanomechanical resonators constructed with synthetic nanowires (NWs) and study their electro-mechanical properties at millikelvin temperatures. Nanomechanical resonators are fabricated using single-crystalline Au NWs and InAs NWs. The mechanical resonance signals are acquired by either magnetomotive or capacitive detection methods. The Au NWs are synthesized by chemical vapor transport method at 1100 °C, and they exhibit clean surface and single-crystallinity with little defects. Due to pristine surface quality, these Au NW mechanical resonators could provide an ideal model system for studying surface-related effects on the mechanical systems. The InAs NWs are synthesized by molecular beam epitaxy or metal organic chemical vapor deposition method. The InAs NWs show electronic conductance modulation resembling Coulomb blockade, which also manifests in the mechanical resonance signals in the form of damping and resonance frequency shift. Our result provides an evidence of strong electro-mechanical coupling in synthetic NW nanomechanical resonators.

Keywords: Au nanowire, InAs nanowire, nanomechanical resonator, synthetic nanowires

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Authors: M. A. Ojo, E. O. Ogbole, A. O. Ojo

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This study analysed improved household solid waste management system in Minna metropolis, Niger state. Multi-staged sampling technique was used to administer 155 questionnaires to respondents, where Minna was divided into two income groups A and B based on the quality of the respondent’s houses. Primary data was collected with the aid of structured questionnaires and analysed using descriptive statistics to obtain results for the socioeconomic characteristics of respondents, types of waste generated and methods of disposing solid waste, the level of awareness and reliability of waste disposal methods as well as the willingness of households to pay for solid waste management in the area. The results revealed that majority of the household heads in the study area were male, 94.20% of the household heads fell between the ages of 21 and 50 and also that 96.80% of them had one form of formal education or the other. The results also revealed that 47.10% and 43.20% of the households generated food wastes and polymers respectively as a major constituent of waste disposed. The results of this study went further to reveal that 81.90% of the household heads were aware of the use of collection cans as a method of waste disposal while only 32.90% of them considered the method highly reliable. Multiple regression was used to determine the factors affecting the willingness of households to pay for waste disposal in the study area. The results showed that 76.10% of the respondents were willing to pay for solid waste management which indicates that households in Minna are concerned and willing to cater for their immediate environment. The multiple regression results revealed that age, income, environmental awareness and household expenditure have a positive and statistically significant relationship with the willingness of households to pay for waste disposal in the area while household size has a negative and statistically significant relationship with households’ willingness to pay. Based on these findings, it was recommended that more waste management services be made readily available to residents of Minna, waste collection service should be privatised to increase their effectiveness through increased competition and also that community participatory approach be used to create more environmental awareness amongst residents.

Keywords: household, solid waste, management, WTP

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Authors: D. M. Tshwane, R. R. Maphanga, P. E. Ngoepe

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Nanostructured materials are attractive candidates for efficient electrochemical energy storage devices because of their unique physicochemical properties. Nanotubes have drawn a continuous attention because of their unique electrical, optical and magnetic properties contrast to that of bulk system. They have potential application in the field of optical, electronics and energy storage device. Introducing nanotubes structures as electrode materials; represents one of the most attractive strategies that could dramatically enhance the battery performance. Spinel LiMn2O4 is the most promising cathode material for Li-ion batteries. In this work, computer simulation methods are used to generate and investigate properties of spinel LiMn2O4 nanotubes. Molecular dynamic simulation is used to probe the local structure of LiMn2O4 nanotubes and the effect of temperature on these systems. It is found that diameter, Miller indices and size have a direct control on nanotubes morphology. Furthermore, it is noted that stability depends on surface and wrapping of the nanotube. The nanotube structures are described using the radial distribution function and XRD patterns. There is a correlation between calculated XRD and experimentally reported results.

Keywords: LiMn2O4, li-ion batteries, nanotubes, nanostructures

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Authors: Sharmin Akhter, M. Salahuddin, Sukalyan Kumar Kundu, Mohammad Fahim Kadir

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Relatively insoluble candidate drug like carbamazepine (CBZ) often exhibit incomplete or erratic absorption; and hence wide consideration is given to improve aqueous solubility of such compound. Solid dispersions were formulated with an aim of improving aqueous solubility, oral bioavailability and the rate of dissolution of Carbamazepine using different hydrophyllic polymer like Polyethylene Glycol (PEG) 6000, Polyethylene Glycol (PEG) 4000, kollidon 30, HPMC 6 cps, poloxamer 407 and povidone k 30. Solid dispersions were prepared with different drug to polymer weight ratio by the solvent evaporation method where methanol was used as solvent. Drug-polymer physical mixtures were also prepared to compare the rate of dissolution. Effects of different polymer were studied for solid dispersion formulation as well as physical mixtures. These formulations were characterized in the solid state by Fourier Transform Infrared (FTIR) spectroscopy and Scanning Electron Microscopy (SEM). Solid state characterization indicated CBZ was present as fine particles and entrapped in carrier matrix of PEG 6000 and PVP K30 solid dispersions. Fourier Transform Infrared (FTIR) spectroscopic studies showed the stability of CBZ and absence of well-defined drug-polymer interactions. In contrast to the very slow dissolution rate of pure CBZ, dispersions of drug in polymers considerably improved the dissolution rate. This can be attributed to increased wettability and dispersibility, as well as decreased crystallinity and increase in amorphous fraction of drug. Solid dispersion formulations containing PEG 6000 and Povidone K 30 showed maximum drug release within one hour at the ratio of 1:1:1. Even physical mixtures of CBZ prepared with both carriers also showed better dissolution profiles than those of pure CBZ. In conclusions, solid dispersions could be a promising delivery of CBZ with improved oral bioavailability and immediate release profiles.

Keywords: carbamazepine, FTIR, kollidon 30, HPMC 6 CPS, PEG 6000, PEG 4000, poloxamer 407, water solubility, povidone k 30, SEM, solid dispersion

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Authors: Khaled Benyounes, Abderrahmane Mellak

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The rheology of aqueous solutions of polyelectrolyte (polyanionic cellulose, PAC) at high molecular weight was investigated using a controlled stress rheometer. Several rheological measurements; viscosity measurements, creep compliance tests at a constant low shear stress and oscillation experiments have been performed. The concentrations ranged by weight from 0.01 to 2.5% of PAC. It was found that the aqueous solutions of PAC do not exhibit a yield stress, the flow curves of PAC over a wide range of shear rate (0 to 1000 s-1) could be described by the cross model and the Williamson models. The critical concentrations of polymer c* and c** have been estimated. The dynamic moduli, i.e., storage modulus (G’) and loss modulus (G’’) of the polymer have been determined at frequency sweep from 0.01 to 10 Hz. At polymer concentration above 1%, the modulus G’ is superior to G’’. The relationships between the dynamic modulus and concentration of polymer have been established. The creep-recovery experiments demonstrated that polymer solutions show important viscoelastic properties of system water-PAC when the concentration of the polymer increases.

Keywords: polyanionic cellulose, viscosity, creep, oscillation, cross model

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Authors: Hayal Akyildirim Beğen, Özgür Emi̇nağaoğlu

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DNA barcoding is the method of description of species based on gene diversity. In current studies, registration, genetic identification and protection of especially endemic plants pecies are carried out by DNA barcoding techniques. Molecular studies are based on the amplification and sequencing of the barcode gene region by the PCR method. Endemic Campanula choruhensis Kit Tan & Sorger, Campanula troegera Damboldt and Campanula betulifolia K.Koch is widespread in Artvin, Erzurum and around Çoruh valley passing through it. Intense road and dam constructions are carried out in and around the distribution area of this species. This situation harms the habitat of the species and puts its extinction. In this study, the plastid matK barcode gene regions (650 bp) of three Campanula species were created. To make the identification of this species quickly and accurately, gene sequence compared with sequences of other Campanula L. species. As a result of phylogenetic analysis, C. choruhensis is close relative to C. betulifolia. Morphologically, these species were determined to be more similar to each other with flower and leaf characters. C. troegera formed a separate branch.

Keywords: campanula, DNA barcoding, endemic, türkiye, artvin

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Authors: Gabriela Borilova, Monika Petrakova, Petr Kralik

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Nowadays, European producers are increasingly interested in the production of halal meat products. Halal meat has been increasingly appearing in the EU's market network and meat products from European producers are being exported to Islamic countries. Halal criteria are mainly related to the origin of muscle used in production, and also to the way products are obtained and processed. Although the EU has legislatively addressed the question of food authenticity, the circumstances of previous years when products with undeclared horse or poultry meat content appeared on EU markets raised the question of the effectiveness of control mechanisms. Replacement of expensive or not-available types of meat for low-priced meat has been on a global scale for a long time. Likewise, halal products may be contaminated (falsified) by pork or food components obtained from pigs. These components include collagen, offal, pork fat, mechanically separated pork, emulsifier, blood, dried blood, dried blood plasma, gelatin, and others. These substances can influence sensory properties of the meat products - color, aroma, flavor, consistency and texture or they are added for preservation and stabilization. Food manufacturers sometimes access these substances mainly due to their dense availability and low prices. However, the use of these substances is not always declared on the product packaging. Verification of the presence of declared ingredients, including the detection of undeclared ingredients, are among the basic control procedures for determining the authenticity of food. Molecular biology methods, based on DNA analysis, offer rapid and sensitive testing. The PCR method and its modification can be successfully used to identify animal species in single- and multi-ingredient raw and processed foods and qPCR is the first choice for food analysis. Like all PCR-based methods, it is simple to implement and its greatest advantage is the absence of post-PCR visualization by electrophoresis. qPCR allows detection of trace amounts of nucleic acids, and by comparing an unknown sample with a calibration curve, it can also provide information on the absolute quantity of individual components in the sample. Our study addresses a problem that is related to the fact that the molecular biological approach of most of the work associated with the identification and quantification of animal species is based on the construction of specific primers amplifying the selected section of the mitochondrial genome. In addition, the sections amplified in conventional PCR are relatively long (hundreds of bp) and unsuitable for use in qPCR, because in DNA fragmentation, amplification of long target sequences is quite limited. Our study focuses on finding a suitable genomic DNA target and optimizing qPCR to reduce variability and distortion of results, which is necessary for the correct interpretation of quantification results. In halal products, the impact of falsification of meat products by the addition of components derived from pigs is all the greater that it is not just about the economic aspect but above all about the religious and social aspect. This work was supported by the Ministry of Agriculture of the Czech Republic (QJ1530107).

Keywords: food fraud, halal food, pork, qPCR

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Authors: Rania Abdulkareem Aboubakr Mahdaly Ammar

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The aortic valve (AV) is a complex mechanical environment that includes flexure, tension, pressure and shear stress forces to blood flow during cardiac cycle. This mechanical environment regulates AV tissue structure by constantly renewing and remodeling the phenotype. In vitro, ex vivo and in vivo studies have explained that pathological states such as hypertension and congenital defects like bicuspid AV ( BAV ) can potentially alter the AV’s mechanical environment, triggering a cascade of remodeling, inflammation and calcification activities in AV tissue. Changes in mechanical environments are first sent by the endothelium that induces changes in the extracellular matrix, and triggers cell differentiation and activation. However, the molecular mechanism of this process is not very well understood. Understanding these mechanisms is critical for the development of effective medical based therapies. Recently, there have been some interesting studies on characterizing the hemodynamics associated with AV, especially in pathologies like BAV, using different experimental and numerical methods. Here, we review the current knowledge of the local AV mechanical environment and its effect on valve biology, focusing on in vitro and ex vivo approaches.

Keywords: aortic valve mechanobiology, bicuspid calcification, pressure stretch, shear stress

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Authors: Furqan M. Kadhum, Asmaa A. Hussein, Maysaa Ch. Hatem

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Hyaluronidase enzyme was purified from the clinical isolate Staphyloccus aureus in three purification steps, first by precipitation with 90% saturated ammonium sulfate, ion exchange chromatography on DEAE-Cellulose, and gel filtration chromatography throughout Sephacryl S-300. Specific activity of the purified enzyme was reached 930 U/mg protein with 7.4 folds of purification and 46.5% recovery. The enzyme has an average molecular weight of about 69 kDa, with an optimum pH of enzyme activity and stability at pH 7, also the optimum temperature for activity was 37oC. The enzyme was stable with full activity at a temperature ranged between 30-40 oC. Metal ions showed variable inhibitory degree with the strongest effect for Fe+3, however, the chelating and reducing agents had no or little effects. Cytotoxic studies for purified and crude hyaluronidase against cancer cell Hep G2 type at different enzyme concentrations and exposure times showed that the inhibition effect of both crude and purified enzyme increased by increasing the enzyme concentration with no change was observed at 24hr, while at 48 and 72 hrs the same inhibition rate were observed for purified enzyme and differ for the crude filtrate.

Keywords: hyaluronidase, S. aureus, metal ions, cytotoxicity

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Authors: Hülya Kuru Mutlu, Mustafa Kulakcı, Uğur Serincan

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The sun is one of the latest developments in renewable energy sources, which has a variety of application. Solar energy is the most preferred renewable energy sources because it can be used directly, it protects the environment and it is economic. In this work, we investigated that important parameter of GaAs-based solar cells with respect to the growth temperature. The samples were grown on (100) oriented p-GaAs substrates by solid source Veeco GEN20MC MBE system equipped with Ga, In, Al, Si, Be effusion cells and an Arsenic cracker cell. The structures of the grown samples are presented. After initial oxide desorption, Sample 1 and Sample 2 were grown at about 585°C and 535°C, respectively. From the grown structures, devices were fabricated by using the standard photolithography procedure. Current-voltage measurements were performed at room temperature (RT). It is observed that Sample 1 which was grown at 585°C has higher efficiency and fill factor compared to Sample 2. Hence, it is concluded that the growth temperature of 585°C is more suitable to grow GaAs-based solar cells considering our samples used in this study.

Keywords: molecular beam epitaxy, solar cell, current-voltage measurement, Sun

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Authors: Benedict Ita, Peter Okoi

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In this work, the concept of the extended Nikiforov-Uvarov technique is discussed and employed to obtain the exact bound state energy eigenvalues and the corresponding normalized eigenfunctions of the inverse square root potential. With expressions for the exact energy eigenvalues and corresponding eigenfunctions, the expressions for the expectation values of the inverse separation-squared, kinetic energy, and the momentum-squared of the potential are presented using the Hellmann Feynman theorem. For visualization, algorithms written and implemented in Python language are used to generate tables and plots for l-states of the energy eigenvalues and some expectation values. The results obtained here may find suitable applications in areas like atomic and molecular physics, chemical physics, nuclear physics, and solid-state physics.

Keywords: Schrodinger equation, Nikoforov-Uvarov method, inverse square root potential, diatomic molecules, Python programming, Hellmann-Feynman theorem, second order differential equation, matrix algebra

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Authors: Warda Fatima, Hasnain Javed

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The emerging trend of Drug resistance in childhood Tuberculosis is increasing worldwide and now becoming a priority challenge for National TB Control Programs of the world. Childhood TB accounts for 10-15% of total TB burden across the globe and same proportion is quantified in case of drug resistant TB. One third population suffering from MDR TB dies annually because of non-diagnosis and unavailability of appropriate treatment. However, true Childhood MDR TB cannot be estimated due to non-confirmation. Diagnosis of Pediatric TB by sputum Smear Microscopy and Culture inoculation are limited due to paucibacillary nature and difficulties in obtaining adequate sputum specimens. Diagnosis becomes more difficult when it comes to HIV infected child. New molecular advancements for early case detection of TB and MDR TB in adults have not been endorsed in children. Multi centered trials are needed to design better diagnostic approaches and efficient and safer treatments for DR TB in high burden countries. The aim of the present study is to sketch out the current situation of the childhood Drug resistant TB especially in the developing world and to highlight the classic and novel methods that are to be implemented in high-burden resource-limited locations.

Keywords: drug resistant TB, childhood, diagnosis, novel methods

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Authors: Aleksandra BužArovska, Gordana Bogoeva Gaceva

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Biodegradable polymers have received significant scientific attention in tissue engineering (TE) application, in particular their composites consisting of inorganic nanoparticles. In the last 15 years, they are subject of intensive research by many groups, aiming to develop polymer scaffolds with defined biodegradability, porosity and adequate mechanical stability. The most important characteristic making these materials attractive for TE is their biodegradability, a process that could be time controlled and long enough to enable generation of a new tissue as a replacement for the degraded polymer scaffold. In this work poly(L-lactic acid) scaffolds, filled with TiO2 nanoparticles functionalized with oleic acid, have been prepared by thermally induced phase separation method (TIPS). The functionalization of TiO2 nanoparticles with oleic acid was performed in order to improve the nanoparticles dispersibility within the polymer matrix and at the same time to inhibit the cytotoxicity of the nanofiller. The oleic acid was chosen as amphiphilic molecule belonging to the fatty acid family because of its non-toxicity and possibility for mediation between the hydrophilic TiO2 nanoparticles and hydrophobic PLA matrix. The produced scaffolds were characterized with thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and mechanical compression measurements. The bioactivity for bone tissue engineering application was tested in supersaturated simulated body fluid. The degradation process was followed by Fourier transform infrared spectroscopy (FTIR). The results showed anisotropic morphology with elongated open pores (100 µm), high porosity (around 92%) and perfectly dispersed nanofiller. The compression moduli up to 10 MPa were identified independent on the nanofiller content. Functionalized TiO2 nanoparticles induced formation of hydroxyapatite clusters as much as unfunctionalized TiO2. The prepared scaffolds showed properties ideal for scaffold vascularization, cell attachment, growth and proliferation.

Keywords: biodegradation, bone tissue engineering, mineralization, PLA scaffolds

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and trans-membrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrin repeats and trans-membrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number of trans-membrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: alternative splicing, ankyrin repeats, trans-membrane domains, arabidopsis

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Authors: Feridun Demir, Pelin Okdem

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Polymers are versatile materials with many unique properties, such as low density, reasonable strength, flexibility, and easy processability. However, the mechanical properties of these materials are insufficient for many engineering applications. Therefore, there is a continuous search for new polymeric materials with improved properties. Polymeric nanocomposites are an advanced class of composite materials that have attracted great attention in both academic and industrial fields. Since nano-reinforcement materials are very small in size, they provide ultra-large interfacial area per volume between the nano-element and the polymer matrix. This allows the nano-reinforcement composites to exhibit enhanced toughness without compromising hardness or optical clarity. PPy and MWCNT/PPy nanocomposites were synthesized by the chemical oxidative polymerization method and the supercapacitor properties of the obtained nanocomposites were investigated. In addition, pure MWCNT was functionalized with acid (H₂SO₄/H₂O₂) and base (NH₄OH/H₂O₂) solutions at a ratio of 3:1 and a-MWCNT/d-PPy, and b-MWCNT/d-PPy nanocomposites were obtained. The homogeneous distribution of MWCNTs in the polypyrrole matrix and shell-core type morphological structures of the nanocomposites was observed with SEM images. It was observed with SEM, FTIR and XRD analyses that the functional groups formed by the functionalization of MWCNTs caused the MWCNTs to come together and partially agglomerate. It was found that the conductivity of the nanocomposites consisting of MWCNT and d-PPy was higher than that of pure d-PPy. CV, GCD and EIS results show that the use of a-MWCNT and b-MWCNTs in nanocomposites with low particle content positively affects the supercapacitor properties of the materials but negatively at high particle content. It was revealed that the functional MWCNT particles combined in nanocomposites with high particle content cause a decrease in the conductivity and distribution of ions in the electrodes and, thus, a decrease in their energy storage capacity.

Keywords: polypyrrole, multi-walled carbon nanotube (MWCNT), conducting polymer, chemical oxidative polymerization, nanocomposite, supercapacitor

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Authors: Massimiliano Biagini, Marco Spinsanti, Gabriella De Angelis, Sara Tomei, Ilaria Ferlenghi, Maria Scarselli, Alessia Biolchi, Alessandro Muzzi, Brunella Brunelli, Silvana Savino, Marzia M. Giuliani, Isabel Delany, Paolo Costantino, Rino Rappuoli, Vega Masignani, Nathalie Norais

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The gram-negative bacterium Neisseria meningitidis serogroup B (MenB) is an exclusively human pathogen representing the major cause of meningitides and severe sepsis in infants and children but also in young adults. This pathogen is usually present in the 30% of healthy population that act as a reservoir, spreading it through saliva and respiratory fluids during coughing, sneezing, kissing. Among surface-exposed protein components of this diplococcus, factor H binding protein is a lipoprotein proved to be a protective antigen used as a component of the recently licensed Bexsero vaccine. fHbp is a highly variable meningococcal protein: to reflect its remarkable sequence variability, it has been classified in three variants (or two subfamilies), and with poor cross-protection among the different variants. Furthermore, the level of fHbp expression varies significantly among strains, and this has also been considered an important factor for predicting MenB strain susceptibility to anti-fHbp antisera. Different methods have been used to assess fHbp expression on meningococcal strains, however, all these methods use anti-fHbp antibodies, and for this reason, the results are affected by the different affinity that antibodies can have to different antigenic variants. To overcome the limitations of an antibody-based quantification, we developed a quantitative Mass Spectrometry (MS) approach. Selected Reaction Monitoring (SRM) recently emerged as a powerful MS tool for detecting and quantifying proteins in complex mixtures. SRM is based on the targeted detection of ProteoTypicPeptides (PTPs), which are unique signatures of a protein that can be easily detected and quantified by MS. This approach, proven to be highly sensitive, quantitatively accurate and highly reproducible, was used to quantify the absolute amount of fHbp antigen in total extracts derived from 105 clinical isolates, evenly distributed among the three main variant groups and selected to be representative of the fHbp circulating subvariants around the world. We extended the study at the genetic level investigating the correlation between the differential level of expression and polymorphisms present within the genes and their promoter sequences. The implications of fHbp expression on the susceptibility of the strain to killing by anti-fHbp antisera are also presented. To date this is the first comprehensive fHbp expression profiling in a large panel of Neisseria meningitidis clinical isolates driven by an antibody-independent MS-based methodology, opening the door to new applications in vaccine coverage prediction and reinforcing the molecular understanding of released vaccines.

Keywords: quantitative mass spectrometry, Neisseria meningitidis, vaccines, bexsero, molecular epidemiology

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Authors: Mohd Adil, Rosina Khan, Asad U. Khan, Vasantha Rupasinghe HP

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The study examined the effects of Syzygium aromaticum extracts on the virulence properties of Streptococcus mutans. The activity of glucosyltransferases in the presence of crude and diethylether fraction was reduced to 80% at concentration 78.12μg/ml and 39.06μg/ml respectively. The glycolytic pH drop by S. mutans cells was also disrupted by these extracts without affecting the bacterial viability. Microscopic analysis revealed morphological changes of the S. mutans biofilms, indicating that these plant extracts at sub-MICs could significantly affect the ability of S. mutans to form biofilm with distorted extracellular matrix. Furthermore, with the help of quantitative RT-PCR, the expression of different genes involved in adherence, quorum sensing, in the presence of these extracts were down regulated. The crude and active fractions were found effective in preventing caries development in rats. The data showed that S. aromaticum holds promise as a naturally occurring source of compounds that may prevent biofilm-related oral diseases.

Keywords: biofilm, quorum sensing, Streptococcus mutans, Syzygium aromaticum extract

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Authors: M. Khalid Alamgir, Javed Ahsan Bhatti, M. Zafarullah Khan

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Thin film of amorphous carbon (DLC) was deposited on 316 steel using Nd: YAG laser having energy 300mJ. Pure graphite was used as a target. The vacuum in the deposition chamber was generated in the range of 10-6 mbar by turbo molecular pump. Ratio of sp3 to sp2 content shows amorphous nature of the film. This was confirmed by Raman spectra having two peaks around 1300 cm-1 i.e. D-band to 1700 cm-1 i.e. G-band. If sp3 bonding ratio is high, the films behave like diamond-like whereas, with high sp2, films are graphite-like. The ratio of sp3 and sp2 contents in the film depends upon the deposition method, hydrogen contents and system parameters. The structural study of the film was carried out by XRD. The hardness of the films as measured by Vickers hardness tester and was found to be 28 GPa. The EDX result shows the presence of carbon contents on the surface in high rate and optical microscopy result shows the smoothness of the film on substrate. The film possesses good adhesion and can be used to coat surgical instruments.

Keywords: DLC, thin film, Raman spectroscopy, XRD, EDX

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Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Methicillin-resistant Staphylococcus aureus, dihydroxyacetone kinase, essential genes, drug target, phosphoryl group donor

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Authors: Sema Şenoğlu, Sevgi Karakuş

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Hydrazone scaffold is important to design new drug groups and is found to possess numerous uses in pharmaceutical chemistry. Besides, hydrazone derivatives are also known for biological activities such as anticancer, antimicrobial, antiviral, and antifungal. Hydrazone derivatives are promising anticancer agents because they inhibit cancer proliferation and induce apoptosis. Human carbonic anhydrase IX has a high potential to be an antiproliferative drug target, and targeting this protein is also important for obtaining potential anticancer inhibitors. The protein construct was retrieved as a PDB file from the RCSB protein database. This binding interaction of proteins and ligands was performed using Discovery Studio Visualizer. In vitro inhibitory activity of hydrazone derivatives was tested against enzyme carbonic anhydrase IX on the PyRx programme. Most of these molecules showed remarkable human carbonic anhydrase IX inhibitory activity compared to the acetazolamide. As a result, these compounds appear to be a potential target in drug design against human carbonic anhydrase IX.

Keywords: cancer, carbonic anhydrase IX enzyme, docking, hydrazone

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Authors: Miroslava Markovic, Snezana Rajkovic, Ljubinko Rakonjac, Aleksandar Lucic

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Oak powdery mildew is a serious problem on seedlings in nurseries as well as on naturally and artificially introduced progeny. The experiments were set on oak seedlings in two nurseries located in Central Serbia, where control of oak powdery mildew Microsphaera alphitoides Griff. et Maubl. had been conducted through alternative protection measures by means of various dosages of AQ-10 biofungicide, with and without added polymer (which has so far never been used in this country for control of oak powdery mildew). Simultaneous testing was conducted on the efficiency of a chemical sulphur-based preparation (used in this area for many years as a measure of suppression of powdery mildews, without the possibility of developing resistance of the pathogen to the active matter). To date, the Republic of Serbia has registered no fungicides for suppression of pathogens in the forest ecosystems. In order to introduce proper use of new disease-fighting agents into a country, certain relevant principles, requirements and criteria prescribed by the Forest Stewardship Council (FSC) must be observed, primarily with respect to measures of assessment and mitigation of risks, the list of dangerous and highly dangerous pesticides with the possibility of alternative protection. One of the main goals of the research was adjustment of the protective measures to the FSC policy through selection of eco-toxicologically favourable fungicides, given the fact that only preparations named on the list of permitted active matters are approved for use in certified forests. The results of the research have demonstrated that AQ-10 biofungicide can be used as a part of integrated disease management programmes as an alternative, through application of several treatments during vegetation and combination with other active matters registered for these purposes, so as to curtail the use of standard fungicides for control of powdery mildews on oak seedlings in nurseries. The best results in suppression of oak powdery mildew were attained through use of AQ-10 biofungicide (dose 50 or 70g/ha) with added polymer Nu Film-17 (dose 1.0 or 1.5 l/ha). If the treatment is applied at the appropriate time, even fewer number of treatments and smaller doses will be just as efficient.

Keywords: oak powdery mildew, biofungicides, polymers, Microsphaera alphitoides

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Authors: Alexander Hudson, Shaogang Gong

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Structure determination is key to understanding protein function at a molecular level. Whilst significant advances have been made in predicting structure and function from amino acid sequence, researchers must still rely on expensive, time-consuming analytical methods to visualise detailed protein conformation. In this study, we demonstrate that it is possible to make accurate (≥80%) predictions of protein class and architecture from structures determined at low (>3A) resolution, using a deep convolutional neural network trained on high-resolution (≤3A) structures represented as 2D matrices. Thus, we provide proof of concept for high-speed, low-cost protein structure classification at low resolution, and a basis for extension to prediction of function. We investigate the impact of the input representation on classification performance, showing that side-chain information may not be necessary for fine-grained structure predictions. Finally, we confirm that high resolution, low-resolution and NMR-determined structures inhabit a common feature space, and thus provide a theoretical foundation for boosting with single-image super-resolution.

Keywords: transfer learning, protein distance maps, protein structure classification, neural networks

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Authors: Chen Niu, Xuesong Zhang, Dejiang Shang, Yongwei Liu

Abstract:

Fishes can secrete high molecular weight fluid on their body skin to enable their rapid movement in the water. In this work, we employ a hybrid method that combines Computational Fluid Dynamics (CFD) and Finite Element Method (FEM) to investigate the effects of different mucus viscosities and injection velocities on fluctuation pressure in the boundary layer and flow-induced structural vibration noise of a flat plate model. To accurately capture the transient flow distribution on the plate surface, we use Large Eddy Simulation (LES) while the mucus inlet is positioned at a sufficient distance from the model to ensure effective coverage. Mucus injection is modeled using the Volume of Fluid (VOF) method for multiphase flow calculations. The results demonstrate that mucus control of pulsating pressure effectively reduces flow-induced structural vibration noise, providing an approach for controlling flow-induced noise in underwater vehicles.

Keywords: mucus, flow control, noise control, flow-induced noise

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Authors: Georgeta Voicu, Cristina Daniela Ghitulica, Andreia Cucuruz, Cristina Busuioc

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In the field of tissue engineering, the compositional and microstructural features of the employed materials play an important role, with implications on the mechanical and biological behaviour of the medical devices. In this context, the development of apatite - natural biopolymer composites represents a choice of many scientific groups. Thus, hydroxyapatite powders were synthesized by a wet method, namely co-precipitation, starting from high purity reagents (CaO, MgO, and H3PO4). Moreover, the substitution of calcium with magnesium have been approached, in the 5 - 10 wt.% range. Afterward, the phosphate powders were integrated in two types of composites with chitosan, different from morphological point of view. First, 3D porous scaffolds were obtained by a freeze-drying procedure. Second, uniform, compact films were achieved by film casting. The influence of chitosan molecular weight (low, medium and high), as well as apatite powder to polymer ratio (1:1 and 1:2) on the morphological properties, were analysed in detail. In conclusion, the reported biocomposites, prepared by a straightforward route are suitable for bone substitution or repairing applications.

Keywords: bone reconstruction, chitosan, composite scaffolds, hydroxyapatite

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Authors: Pattaramon Pongjetpong

Abstract:

In recent years, infectious diseases have increased considerably, and they are amongst the most common leading causes of death all over the world. Several medicinal plants are well known to contain active constituents such as flavonoids, carotenoids, and phenolic compounds, which are plausible candidates for therapeutic purposes. This study aimed to examine the antimicrobial activities of M. cochinchinensis and P. kesiya extracts using the agar disk diffusion method and broth microdilution to determine the minimum inhibitory concentration (MIC) value. In this study, Momordica cochinchinensis and Pinus kesiya extracts are investigated for antibacterial activity against Staphylococcus aureus. The results showed that S. aureus was susceptible to P. kesiya extracts with an MIC value of 62.5 µg/ml, while M. cochinchinensis showed MIC against S. aureus was greater than 2000 µg/ml. In summary, P. kesiya extract showed potent antibacterial activity against S. aureus, which could greatly value developing as adjuvant therapy for infectious diseases. However, further investigation regarding purification of the active constituents as well as a determination of the mechanism of antimicrobial action of P. kesiya active compound should be performed to identify the molecular target of the active compounds.

Keywords: antimicrobial activity, Momordica cochinchinensis, Pinus kesiya, Staphylococcus aureus

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: synthetic gene network, network identification, optimization, nonlinear modeling

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Authors: Muhammad Umar Mushtaq, Muhammad Bilal Khan Niazi, Nouman Ahmad, Dooa Arif

Abstract:

Apart from organic dyes, heavy metals such as Pb, Ni, Cr, and Cu are present in textile effluent and pose a threat to humans and the environment. Many studies on removing heavy metallic ions from textile wastewater have been conducted in recent decades using metal-organic frameworks (MOFs). In this study new polyether sulfone ultrafiltration membrane, modified with Cu/Co and Cu/Zn-based bimetal-organic frameworks (MOFs), was produced. Phase inversion was used to produce the membrane, and atomic force microscopy (AFM), scanning electron microscopy (SEM) were used to characterize it. The bimetallic MOFs-based membrane structure is complex and can be comprehended using characterization techniques. The bimetallic MOF-based filtration membranes are designed to selectively adsorb specific contaminants while allowing the passage of water molecules, improving the ultrafiltration efficiency. MOFs' adsorption capacity and selectivity are enhanced by functionalizing them with particular chemical groups or incorporating them into composite membranes with other materials, such as polymers. The morphology and performance of the bimetallic MOF-based membrane were investigated regarding pure water flux and metal ion rejection. The advantages of developed bimetallic MOFs based membranes for wastewater treatment include enhanced adsorption capacity because of the presence of two metals in their structure, which provides additional binding sites for contaminants, leading to a higher adsorption capacity and more efficient removal of pollutants from wastewater. Based on the experimental findings, bimetallic MOF-based membranes are more capable of rejecting metal ions from industrial wastewater than conventional membranes that have already been developed. Furthermore, the difficulties associated with operational parameters, including pressure gradients and velocity profiles, are simulated using Ansys Fluent software. The simulation results obtained for the operating parameters are in complete agreement with the experimental results.

Keywords: bimetallic MOFs, heavy metal ions, industrial wastewater treatment, ultrafiltration.

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Authors: Federica Laface, Cristina Pedà, Francesco Longo, Francesca de Domenico, Riccardo Minichino, Pierpaolo Consoli, Pietro Battaglia, Silvestro Greco, Teresa Romeo

Abstract:

Plastics pollution represents one of the most important threats to marine biodiversity. In the last decades, different species are investigated to evaluate the extent of the plastic ingestion phenomenon. Even if the cephalopods play an important role in the food chain, they are still poorly studied. The aim of this research was to investigate the plastic ingestion in two commercial cephalopod species from the southern Tyrrhenian Sea: the common octopus, Octopus vulgaris (n=6; mean mantle length ML 10.7 ± 1.8) and the common cuttlefish, Sepia officinalis (n=13; mean ML 13.2 ± 1.7). Plastics were extracted from the filters obtained by the chemical digestion of cephalopods gastrointestinal tracts (GITs), using 10% potassium hydroxide (KOH) solution in a 1:5 (w/v) ratio. Once isolated, particles were photographed, measured, and their size class, shape and color were recorded. A total of 81 items was isolated from 16 of the 19 examined GITs, representing a total occurrence (%O) of 84.2% with a mean value of 4.3 ± 8.6 particles per individual. In particular, 62 plastics were found in 6 specimens of O. vulgaris (%O=100) and 19 particles in 10 S. officinalis (%O=94.7). In both species, the microplastics size class was the most abundant (93.8%). Plastic items found in O. vulgaris were mainly fibers (61%) while fragments were the most frequent in S. officinalis (53%). Transparent was the most common color in both species. The analysis will be completed by Fourier transform infrared (FT-IR) spectroscopy technique in order to identify polymers nature. This study reports preliminary data on plastic ingestion events in two cephalopods species and represents the first record of plastic ingestion by the common octopus. Microplastic items detected in both common octopus and common cuttlefish could derive from secondary and/or accidental ingestion events, probably due to their behavior, feeding habits and anatomical features. Further studies will be required to assess the effect of marine litter pollution in these ecologically and commercially important species.

Keywords: cephalopods, GIT analysis, marine pollution, Mediterranean sea, microplastics

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