Search results for: binding constant

Authors: Davender Kumar

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Aim: It is important for the orthodontist to be familiar with the sliding resistance (SR) generated by the ligation method used during the space closure phase with sliding mechanics. To determine new, experimental non-conventional (slide) ligature demonstrates less friction in vitro when compared other ligatures on the market. Methods: Experimental in vitro were carried out to test the performance of the low-friction system with regard to assess the forces released by different bracket–ligature systems with bonded in iron plate mounted on an Instron machine. Results: The outcomes of experimental testing showed that the combination of the low-friction ligatures with the super elastic nickel-titanium and SS wires produced a significantly smaller amount of binding at the bracket/arch wire/ligature unit when compared to conventional elastomeric ligatures. Conclusion: The biomechanical consequences of the use of low-friction ligatures were shorter duration of orthodontic treatment during the levelling and aligning phase, concurrent dentoalveolar expansion of the dental arch, and the possibility of using biologically adequate orthodontic forces.

Keywords: archwire, bracket, friction, ligation

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Authors: Ved Vrat Verma, Rani Gupta, Manisha Goel

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γ-glutamyltranspeptidase (GGT: EC 2.3.2.2) is an N-terminal nucleophile hydrolase conserved in all three domains of life. GGT plays a key role in glutathione metabolism where it catalyzes the breakage of the γ-glutamyl bonds and transfer of γ-glutamyl group to water (hydrolytic activity) or amino acids or short peptides (transpeptidase activity). GGTs from bacteria, archaea, and eukaryotes (human, rat and mouse) are homologous proteins sharing >50% sequence similarity and conserved four layered αββα sandwich like three dimensional structural fold. These proteins though similar in their structure to each other, are quite diverse in their enzyme activity: some GGTs are better at hydrolysis reactions but poor in transpeptidase activity, whereas many others may show opposite behaviour. GGT is known to be involved in various diseases like asthma, parkinson, arthritis, and gastric cancer. Its inhibition prior to chemotherapy treatments has been shown to sensitize tumours to the treatment. Microbial GGT is known to be a virulence factor too, important for the colonization of bacteria in host. However, all known inhibitors (mimics of its native substrate, glutamate) are highly toxic because they interfere with other enzyme pathways. However, a few successful efforts have been reported previously in designing species specific inhibitors. We aim to leverage the diversity seen in GGT family (pathogen vs. eukaryotes) for designing specific inhibitors. Thus, in the present study, we have used DIVERGE software to identify sites in GGT proteins, which are crucial for the functional and structural divergence of these proteins. Since, type II divergence sites vary in clade specific manner, so type II divergent sites were our focus of interest throughout the study. Type II divergent sites were identified for pathogen vs. eukaryotes clusters and sites were marked on clade specific representative structures HpGGT (2QM6) and HmGGT (4ZCG) of pathogen and eukaryotes clade respectively. The crucial divergent sites within 15 A radii of the binding cavity were highlighted, and in-silico mutations were performed on these sites to delineate the role of these sites on the mechanism of catalysis and protein folding. Further, the amino acid network (AAN) analysis was also performed by Cytoscape to delineate assortative mixing for cavity divergent sites which could strengthen our hypothesis. Additionally, molecular dynamics simulations were performed for wild complexes and mutant complexes close to physiological conditions (pH 7.0, 0.1 M ionic strength and 1 atm pressure) and the role of putative divergence sites and structural integrities of the homologous proteins have been analysed. The dynamics data were scrutinized in terms of RMSD, RMSF, non-native H-bonds and salt bridges. The RMSD, RMSF fluctuations of proteins complexes are compared, and the changes at protein ligand binding sites were highlighted. The outcomes of our study highlighted some crucial divergent sites which could be used for novel inhibitors designing in a species-specific manner. Since, for drug development, it is challenging to design novel drug by targeting similar protein which exists in eukaryotes, so this study could set up an initial platform to overcome this challenge and help to deduce the more effective targets for novel drug discovery.

Keywords: γ-glutamyltranspeptidase, divergence, species-specific, drug design

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Authors: L. L. Tundisi, A. Pessoa Jr., E. B. Tambourgi, E. Silveira, P. G. Mazzola

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L-asparaginase (L-ASNase) is the gold standard treatment for acute lymphoblastic leukemia that mainly affects pediatric patients; treatment increases survival from 20% to 90%. The characterization of other L-Asparaginases, apart from the most used from Escherichia coli and Erwinia chrysanthemi, has been reported, but the choice of the most appropriate is still under debate. This choice should be based on its pharmacokinetics, immune hypersensitivity, doses, prices, pharmacodynamics. The main factors influencing the antileukemic activity of ASNase are enzymatic activity, Km, glutaminase activity, clearance of the enzyme and development of resistance. However, most of the commercialized enzyme present an intrinsic glutaminase activity, which is responsible for some side effects. In this study, glutaminase free asparaginase produced from Aspergillus oryzae was precipitated in different percentages of ethanol (0–80%), until optimum ethanol concentration of 60% (w/w) was found. Following, precipitation of crude L-ASNase was performed in a single step, using 60% (w/w) ethanol, under constant agitation and temperature. It presented activity of 135.45 U/mg and after gel filtration chromatography with Sephadex G-the enzymatic activity was 322.02 U/mg. The apparent molecular mass of the purified L-ASNase fraction was estimated by 10% SDS-PAGE. Proteins were stained with Coomassie Brilliant Blue R-250. The molar mass range was from 10 kDa to 250 kDa. L-ASNase from Aspergillus oryzae was characterized aiming possible therapeutic use. Four different buffers (phosphate-citrate buffer pH 2.6 to 5.8; phosphate buffer pH 5.8 to 7.4; Tris - HCl pH 7.4 to 9.0; and carbonate buffer pH 9.8 to 10.6) were used to measure the optimum pH for L-ASNase activity. The optimum temperature for enzyme activity was measured at optimal pH conditions (Tris-HCl and phosphate buffer, pH 7.4) at different temperatures ranging from 5 to 55°C. All activities were calculated by quantifying the free ammonia, using the Nessler reagent. The kinetic parameters calculation, e.g. Michaelis-Menten constant (Km), maximum velocity (Vmax) and Hills coefficient (n), were performed by incubating the enzyme in different concentrations of the substrate at optimum conditions of pH and fitted on Hill’s equation. This glutaminase free asparaginase showed a low Km (3.39 mM and 3.81 mM) and enzymatic activity of 135.45 U/mg after precipitation with ethanol. After gel filtration chromatography it rose to 322.02 U/mg. Optimum activity was found between pH 5.8 - 9.0, best activity results with phosphate buffer pH 7.4 and Tris-HCl pH 7.4 and showed activity from 5°C to 55°C. These results indicate that L-ASNase from A. oryzae has the potential for human use.

Keywords: biopharmaceuticals, bioprocessing, bioproducts, biotechnology, enzyme activity, ethanol precipitation

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: Pouneh Soleimaninejadian, Chengyu Yang

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In this paper, we use data on Household Income and Expenditure survey of Statistics Centre of Iran, conducted from 2005-2014, to calculate several inequality measures and to estimate the effects of Iran’s targeted subsidy reform act on consumption and income inequality. We first calculate Gini coefficients for income and consumption in order to study the relation between the two and also the effects of subsidy reform. Results show that consumption inequality has not been always mirroring changes in income inequality. However, both Gini coefficients indicate that subsidy reform caused improvement in inequality. Then we calculate Generalized Entropy Index based on consumption and income for years before and after the Subsidy Reform Act of 2010 in order to have a closer look into the changes in internal structure of inequality after subsidy reforms. We find that the improvement in income inequality is mostly caused by the decrease in inequality of lower income individuals. At the same time consumption inequality has been decreased as a result of more equal consumption in both lower and higher income groups. Moreover, the increase in Engle coefficient after the subsidy reform shows that a bigger portion of income is allocated to consumption on food which is a sign of lower living standard in general. This increase in Engle coefficient is due to rise in inflation rate and relative increase in price of food which partially is another consequence of subsidy reform. We have conducted some experiments on effect of subsidy payments and possible effects of change on distribution pattern and amount of cash subsidy payments on income inequality. Result of the effect of cash payments on income inequality shows that it leads to a definite decrease in income inequality and had a bigger share in improvement of rural areas compared to those of urban households. We also examine the possible effect of constant payments on the increasing income inequality for years after 2011. We conclude that reduction in value of payments as a result of inflation plays an important role regardless of the fact that there may be other reasons. We finally experiment with alternative allocations of transfers while keeping the total amount of cash transfers constant or make it smaller through eliminating three higher deciles from the cash payment program, the result shows that income equality would be improved significantly.

Keywords: consumption inequality, generalized entropy index, income inequality, Irans subsidy reform

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Authors: Evan Lowhorn, Rocio Alba-Flores

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The purpose of this work is to develop a method for classifying hand signals and using the output in a drone control algorithm. To achieve this, methods based on Convolutional Neural Networks (CNN) were applied. CNN's are a subset of deep learning, which allows grid-like inputs to be processed and passed through a neural network to be trained for classification. This type of neural network allows for classification via imaging, which is less intrusive than previous methods using biosensors, such as EMG sensors. Classification CNN's operate purely from the pixel values in an image; therefore they can be used without additional exteroceptive sensors. A development bench was constructed using a desktop computer connected to a high-definition webcam mounted on a scissor arm. This allowed the camera to be pointed downwards at the desk to provide a constant solid background for the dataset and a clear detection area for the user. A MATLAB script was created to automate dataset image capture at the development bench and save the images to the desktop. This allowed the user to create their own dataset of 12,000 images within three hours. These images were evenly distributed among seven classes. The defined classes include forward, backward, left, right, idle, and land. The drone has a popular flip function which was also included as an additional class. To simplify control, the corresponding hand signals chosen were the numerical hand signs for one through five for movements, a fist for land, and the universal “ok” sign for the flip command. Transfer learning with PyTorch (Python) was performed using a pre-trained 18-layer residual learning network (ResNet-18) to retrain the network for custom classification. An algorithm was created to interpret the classification and send encoded messages to a Ryze Tello drone over its 2.4 GHz Wi-Fi connection. The drone’s movements were performed in half-meter distance increments at a constant speed. When combined with the drone control algorithm, the classification performed as desired with negligible latency when compared to the delay in the drone’s movement commands.

Keywords: classification, computer vision, convolutional neural networks, drone control

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Authors: Qing Liu, Jean-fabien Capsal, Claude Richard

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In this current contribution, authors are dedicated to investigate influence of the crystal lamellae orientation on electromechanical behaviors of relaxor ferroelectric Poly (vinylidene fluoride –trifluoroethylene -chlorotrifluoroethylene) (P(VDF-TrFE-CTFE)) films by control of polymer microstructure, aiming to picture the full map of structure-property relationship. In order to define their crystal orientation films, terpolymer films were fabricated by solution-casting, stretching and hot-pressing process. Differential scanning calorimetry, impedance analyzer, and tensile strength techniques were employed to characterize crystallographic parameters, dielectric permittivity, and elastic Young’s modulus respectively. In addition, large electrical induced out-of-plane electrostrictive strain was obtained by cantilever beam mode. Consequently, as-casted pristine films exhibited surprisingly high electrostrictive strain 0.1774% due to considerably small value of elastic Young’s modulus although relatively low dielectric permittivity. Such reasons contributed to large mechanical elastic energy density. Instead, due to 2 folds increase of elastic Young’s modulus and less than 50% augmentation of dielectric constant, fully-crystallized film showed weak electrostrictive behavior and mechanical energy density as well. And subjected to mechanical stretching process, Film C exhibited stronger dielectric constant and out-performed electrostrictive strain over Film B because edge-on crystal lamellae orientation induced by uniaxially mechanical stretch. Hot-press films were compared in term of cooling rate. Rather large electrostrictive strain of 0.2788% for hot-pressed Film D in quenching process was observed although its dielectric permittivity equivalent to that of pristine as-casted Film A, showing highest mechanical elastic energy density value of 359.5 J/m^3. In hot-press cooling process, dielectric permittivity of Film E saw values at 48.8 concomitant with ca.100% increase of Young’s modulus. Films with intermediate mechanical energy density were obtained.

Keywords: crystal orientation, electrostroctive strain, mechanical energy density, permittivity, relaxor ferroelectric

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Authors: M. Khaing, A. V. Tkacheva

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The work is devoted to solving the problem of temperature stresses, caused by the heating point of the round plate. The plate is made of elastoplastic material, so the Prandtl-Reis model is used. A piecewise-linear condition of the Ishlinsky-Ivlev flow is taken as the loading surface, in which the yield stress depends on the temperature. Piecewise-linear conditions (Treska or Ishlinsky-Ivlev), in contrast to the Mises condition, make it possible to obtain solutions of the equilibrium equation in an analytical form. In the problem under consideration, using the conditions of Tresca, it is impossible to obtain a solution. This is due to the fact that the equation of equilibrium ceases to be satisfied when the two Tresca conditions are fulfilled at once. Using the conditions of plastic flow Ishlinsky-Ivlev allows one to solve the problem. At the same time, there are also no solutions on the edge of the Ishlinsky-Ivlev hexagon in the plane-stressed state. Therefore, the authors of the article propose to jump from the edge to the edge of the mine edge, which gives an opportunity to obtain an analytical solution. At the same time, there is also no solution on the edge of the Ishlinsky-Ivlev hexagon in a plane stressed state; therefore, in this paper, the authors of the article propose to jump from the side to the side of the mine edge, which gives an opportunity to receive an analytical solution. The paper compares solutions of the problem of plate thermal deformation. One of the solutions was obtained under the condition that the elastic moduli (Young's modulus, Poisson's ratio) which depend on temperature. The yield point is assumed to be parabolically temperature dependent. The main results of the comparisons are that the region of irreversible deformation is larger in the calculations obtained for solving the problem with constant elastic moduli. There is no repeated plastic flow in the solution of the problem with elastic moduli depending on temperature. The absolute value of the irreversible deformations is higher for the solution of the problem in which the elastic moduli are constant; there are also insignificant differences in the distribution of the residual stresses.

Keywords: temperature stresses, elasticity, plasticity, Ishlinsky-Ivlev condition, plate, annular heating, elastic moduli

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Authors: Michal Štros, Eva Polanská, Šárka Pospíšilová

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HMGB1 is an architectural protein in chromatin, acting also as a signaling molecule outside the cell. Recent reports from several laboratories provided evidence that a number of both the intracellular and extracellular functions of HMGB1 may depend on redox-sensitive cysteine residues of the protein. MALDI-TOF analysis revealed that mild oxidization of HMGB1 resulted in a conformational change of the protein due to formation of an intramolecular disulphide bond by opposing Cys23 and Cys45 residues. We have demonstrated that redox state of HMGB1 could significantly modulate the ability of the protein to bind and bend DNA. We have also shown that reduced HMGB1 could easily displace histone H1 from DNA, while oxidized HMGB1 had limited capacity for H1 displacement. Using microscale thermophoresis (MST) we have further studied mechanism of HMGB1 interaction with histone H1 in free solution or when histone H1 was bound to DNA. Our MST analysis indicated that reduced HMGB1 exhibited in free solution > 1000 higher affinity of for H1 (KD ~ 4.5 nM) than oxidized HMGB1 (KD <10 M). Finally, we present a novel mechanism for the HMGB1-mediated modulation of histone H1 binding to DNA.

Keywords: HMGB1, histone H1, redox state, interaction, cross-linking, DNA bending, DNA end-joining, microscale thermophoresis

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Authors: I. Sinnarasa, Y. Thimont, L. Presmanes, A. Barnabé

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The thermoelectricity is a promising technique to overcome the issues in recovering waste heat to electricity without using moving parts. In fact, the thermoelectric (TE) effect defines as the conversion of a temperature gradient directly into electricity and vice versa. To optimize TE materials, the power factor (PF = σS² where σ is electrical conductivity and S is Seebeck coefficient) must be increased by adjusting the carrier concentration, and/or the lattice thermal conductivity Kₜₕ must be reduced by introducing scattering centers with point defects, interfaces, and nanostructuration. The PF does not show the advantages of the thin film because it does not take into account the thermal conductivity. In general, the thermal conductivity of the thin film is lower than the bulk material due to their microstructure and increasing scattering effects with decreasing thickness. Delafossite type oxides CuᴵMᴵᴵᴵO₂ received main attention for their optoelectronic properties as a p-type semiconductor they exhibit also interesting thermoelectric (TE) properties due to their high electrical conductivity and their stability in room atmosphere. As there are few proper studies on the TE properties of Mg-doped CuCrO₂ thin films, we have investigated, the influence of the annealing temperature on the electrical conductivity and the Seebeck coefficient of Mg-doped CuCrO₂ thin films and calculated the PF in the temperature range from 40 °C to 220 °C. For it, we have deposited Mg-doped CuCrO₂ thin films on fused silica substrates by RF magnetron sputtering. This study was carried out on 300 nm thin films. The as-deposited Mg doped CuCrO₂ thin films have been annealed at different temperatures (from 450 to 650 °C) under primary vacuum. Electrical conductivity and Seebeck coefficient of the thin films have been measured from 40 to 220 °C. The highest electrical conductivity of 0.60 S.cm⁻¹ with a Seebeck coefficient of +329 µV.K⁻¹ at 40 °C have been obtained for the sample annealed at 550 °C. The calculated power factor of optimized CuCrO₂:Mg thin film was 6 µW.m⁻¹K⁻² at 40 °C. Due to the constant Seebeck coefficient and the increasing electrical conductivity with temperature it reached 38 µW.m⁻¹K⁻² at 220 °C that was a quite good result for an oxide thin film. Moreover, the degenerate behavior and the hopping mechanism of CuCrO₂:Mg thin film were elucidated. Their high and constant Seebeck coefficient in temperature and their stability in room atmosphere could be a great advantage for an application of this material in a high accuracy temperature measurement devices.

Keywords: thermoelectric, oxides, delafossite, thin film, power factor, degenerated semiconductor, hopping mode

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Authors: Babak Darvish Rouhani, Mohd Nazri Mahrin, Fatemeh Nikpay, Pourya Nikfard, Maryam Khanian Najafabadi

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Enterprise Architecture (EA) is a strategy that is employed by enterprises in order to align their business and Information Technology (IT). EA is managed, developed, and maintained through Enterprise Architecture Implementation Methodology (EAIM). The effectiveness of EA implementation is the degree in which EA helps to achieve the collective goals of the organization. This paper analyzes the results of a survey that aims to explore the factors that affect the effectiveness of EAIM and specifically the relationship between factors and effectiveness of the output and functionality of EA project. The exploratory factor analysis highlights a specific set of five factors: alignment, adaptiveness, support, binding, and innovation. The regression analysis shows that there is a statistically significant and positive relationship between each of the five factors and the effectiveness of EAIM. Consistent with theory and practice, the most prominent factor for developing an effective EAIM is innovation. The findings contribute to the measuring the effectiveness of EA implementation project by providing an indication of the measurement implementation approaches which is used by the Enterprise Architects, and developing an effective EAIM.

Keywords: enterprise architecture, enterprise architecture implementation methodology, implementation methodology, factors, EA, effectiveness

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Authors: Jaco Oosthuizen, Nerina C. Van Der Merwe

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The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency.

Keywords: familial breast cancer, multiplex ligation-dependent probe amplification, next generation sequencing, South Africa

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Authors: K. P. Valdés García, E. I. Rodríguez Fonseca, L. G. Juárez Cantú

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Suicide is a global, multidimensional and dynamic problem of mental health, which requires a constant study for its understanding and prevention. When research of this phenomenon is done, it is necessary to consider the different characteristics it may have because of the individual and sociocultural variables, the importance of this consideration is related to the generation of effective treatments and interventions. Adolescents are a vulnerable population due to the characteristics of the development stage. The investigation was carried out with the objective of identifying and describing the conceptualization of adolescents of suicide, and in this process, we find possible differences between men and women. The study was carried out in Saltillo, Coahuila, Mexico. The sample was composed of 418 volunteer students aged between 11 and 18 years. The ethical aspects of the research were reviewed and considered in all the processes of the investigation with the participants, their parents and the schools to which they belonged, psychological attention was offered to the participants and preventive workshops were carried in the educational institutions. Natural semantic networks were the instrument used, since this hybrid method allows to find and analyze the social concept of a phenomenon; in this case, the word suicide was used as an evocative stimulus and participants were asked to evoke at least five words and a maximum 10 that they thought were related to suicide, and then hierarchize them according to the closeness with the construct. The subsequent analysis was carried with Excel, yielding the semantic weights, affective loads and the distances between each of the semantic fields established according to the words reported by the subjects. The results showed similarities in the conceptualization of suicide in adolescents, men and women. Seven semantic fields were generated; the words were related in the discourse analysis: 1) death, 2) possible triggering factors, 3) associated moods, 4) methods used to carry it out, 5) psychological symptomatology that could affect, 6) words associated with a rejection of suicide, and finally, 7) specific objects to carry it out. One of the necessary aspects to consider in the investigations of complex issues such as suicide is to have a diversity of instruments and techniques that adjust to the characteristics of the population and that allow to understand the phenomena from the social constructs and not only theoretical. The constant study of suicide is a pressing need, the loss of a life from emotional difficulties that can be solved through psychiatry and psychological methods requires governments and professionals to pay attention and work with the risk population.

Keywords: adolescents, psychological construct, semantic networks, suicide

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Authors: Gulcan Sahal, Isil Seyis Bilkay

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Candida species which often exist as commensal microorganisms in healthy individuals are major causes of important infections, especially in AIDS and immunocompromised patients, by means of their biofilm formation abilities. Therefore, in this study, determination of biofilm formation in different clinical strains of Candida species, investigation of strong biofilm forming Candida strains, examination of clinical information of each strong and weak biofilm forming Candida strains and investigation of some plant substances’ effects on biofilm formation of strong biofilm forming strains were aimed. In this respect, biofilm formation of Candida strains was analyzed via crystal violet binding assay. According to our results, biofilm levels of strains belong to different Candida species were different from each other. Additionally, it is also found that some plant substances effect biofilm formation. All these results indicate that, as well as C. albicans strains, other non-albicans Candida species also emerge as causative agents of infections and have biofilm formation abilities. In addition, usage of some plant substances in different concentrations may provide a new treatment against biofilm related Candida infections.

Keywords: anti-biofilm, biofilm formation, Candida species, biosystems engineering

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Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

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Authors: K. Karuppasamy

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In this paper analysis of an infinite beam resting on multilayer tensionless extensible geosynthetic reinforced granular fill - poor soil system overlying soft soil strata under moving the load with constant velocity is presented. The beam is subjected to a concentrated load moving with constant velocity. The upper reinforced granular bed is modeled by a rough membrane embedded in Pasternak shear layer overlying a series of compressible nonlinear Winkler springs representing the underlying the very poor soil. The multilayer tensionless extensible geosynthetic layer has been assumed to deform such that at the interface the geosynthetic and the soil have some deformation. Nonlinear behavior of granular fill and the very poor soil has been considered in the analysis by means of hyperbolic constitutive relationships. Governing differential equations of the soil foundation system have been obtained and solved with the help of appropriate boundary conditions. The solution has been obtained by employing finite difference method by means of Gauss-Siedel iterative scheme. Detailed parametric study has been conducted to study the influence of various parameters on the response of soil – foundation system under consideration by means of deflection and bending moment in the beam and tension mobilized in the geosynthetic layer. These parameters include the magnitude of applied load, the velocity of the load, damping, the ultimate resistance of the poor soil and granular fill layer. The range of values of parameters has been considered as per Indian Railways conditions. This study clearly observed that the comparisons of multilayer tensionless extensible geosynthetic reinforcement with poor foundation soil and magnitude of applied load, relative compressibility of granular fill and ultimate resistance of poor soil has significant influence on the response of soil – foundation system. However, for the considered range of velocity, the response has been found to be insensitive towards velocity. The ultimate resistance of granular fill layer has also been found to have no significant influence on the response of the system.

Keywords: infinite beams, multilayer tensionless extensible geosynthetic, granular layer, moving load and nonlinear behavior of poor soil

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Authors: Adenike Adesanya, Nonthaphat Wong, Xiang-Yun Lan, Shea Ping Yip, Chien-Ling Huang

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Background: The most challenging mutation of the oncokinase BCR-ABL protein T315I, which is commonly known as the “gatekeeper” mutation and is notorious for its strong resistance to almost all tyrosine kinase inhibitors (TKIs), especially imatinib. Therefore, this study aims to identify T315I-dependent downstream microRNA (miRNA) pathways associated with drug resistance in chronic myeloid leukemia (CML) for prognostic and therapeutic purposes. Methods: T315I-carrying K562 cell clones (K562-T315I) were generated by the CRISPR-Cas9 system. Imatinib-treated K562-T315I cells were subjected to small RNA library preparation and next-generation sequencing. Putative lncRNA-miRNA-mRNA networks were analyzed with (i) DESeq2 to extract differentially expressed miRNAs, using Padj value of 0.05 as cut-off, (ii) STarMir to obtain potential miRNA response element (MRE) binding sites of selected miRNAs on lncRNA H19, (iii) miRDB, miRTarbase, and TargetScan to predict mRNA targets of selected miRNAs, (iv) IntaRNA to obtain putative interactions between H19 and the predicted mRNAs, (v) Cytoscape to visualize putative networks, and (vi) several pathway analysis platforms – Enrichr, PANTHER and ShinyGO for pathway enrichment analysis. Moreover, mitochondria isolation and transcript quantification were adopted to determine the new mechanism involved in T315I-mediated resistance of CML treatment. Results: Verification of the CRISPR-mediated mutagenesis with digital droplet PCR detected the mutation abundance of ≥80%. Further validation showed the viability of ≥90% by cell viability assay, and intense phosphorylated CRKL protein band being detected with no observable change for BCR-ABL and c-ABL protein expressions by Western blot. As reported by several investigations into hematological malignancies, we determined a 7-fold increase of H19 expression in K562-T315I cells. After imatinib treatment, a 9-fold increment was observed. DESeq2 revealed 171 miRNAs were differentially expressed K562-T315I, 112 out of these miRNAs were identified to have MRE binding regions on H19, and 26 out of the 112 miRNAs were significantly downregulated. Adopting the seed-sequence analysis of these identified miRNAs, we obtained 167 mRNAs. 6 hub miRNAs (hsa-let-7b-5p, hsa-let-7e-5p, hsa-miR-125a-5p, hsa-miR-129-5p, and hsa-miR-372-3p) and 25 predicted genes were identified after constructing hub miRNA-target gene network. These targets demonstrated putative interactions with H19 lncRNA and were mostly enriched in pathways related to cell proliferation, senescence, gene silencing, and pluripotency of stem cells. Further experimental findings have also shown the up-regulation of mitochondrial transcript and lncRNA MALAT1 contributing to the lncRNA-miRNA-mRNA networks induced by BCR-ABL T315I mutation. Conclusions: Our results have indicated that lncRNA-miRNA regulators play a crucial role not only in leukemogenesis but also in drug resistance, considering the significant dysregulation and interactions in the K562-T315I cell model generated by CRISPR-Cas9. In silico analysis has further shown that lncRNAs H19 and MALAT1 bear several complementary miRNA sites. This implies that they could serve as a sponge, hence sequestering the activity of the target miRNAs.

Keywords: chronic myeloid leukemia, imatinib resistance, lncRNA-miRNA-mRNA, T315I mutation

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Authors: Jayanthi Sivaraman

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Claudins are the important components of the tight junctions that play a key role in paracellular permeability. Among various members of Claudin family, Claudin 4 (CLDN4) is found to be overexpressed in ovarian, pancreatic carcinomas and other epithelial malignancies. Therefore, in this study, an attempt has been made to identify potent inhibitors for CLDN4 from the ZINC database using virtual screening, molecular docking and molecular dynamics simulations. A well refined molecular model of CLDN4 was built using Prime of Schrodinger v10.2(Template- PDB ID: 4P79). Approximately, 6 million compounds from ZINC database are subjected to high-throughput virtual screening (HTVS) against the active site of CLDN4. Molecular docking using GLIDE predicted ARG31, ASN142, ASP146 and ARG158 as critically important residues. Furthermore, three compounds from ZINC database (ZINC96331839, ZINC36533519 and ZINC75819394) showed highly promising ADME properties and binding affinity with stable conformation. The therapeutic efficiency of these lead compounds is evaluated and confirmed by in-vitro and in-vivo studies which leads to the development of novel anti-cancer drugs.

Keywords: ADME property, inhibitors, molecular docking, virtual screening

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Authors: Azila Adnan, Giridhar R. Nair, Mark C. Lay, Janis E. Swan

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The effect of aeration on bacterial cellulose (BC) production by Gluconacetobacter xylinus DSM46604 was studied in 5-L bioreactor. Four aeration rates were applied (0.3, 0.6, 1.0 and 1.5 vvm) in the fermentation media at constant agitation rate, 150 rpm. One vvm enhanced BC concentration (4.4 g/L) and productivity (0.44 g/L/day) while greater agitation rate (1.5 vvm) decreased BC concentration (4.0 g/L) and productivity (0.40 g/L/day).

Keywords: aeration, bacterial cellulose, fermentation, gluconacetobacter xylinus

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Authors: Aurelio Palacardo, Giulio Mangano, Alberto De Marco

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Nowadays, the global economic framework is extremely competitive, and it consequently requires an efficient deployment of the resources provided by EU. In this context, Project management practices are intended to be one of the levers for increasing such an efficiency. The objective of this work is to explore the usage of Project Management methodologies and good practices in the European-wide research program “Horizon2020” and establish whether their maturity might impact the project's success. This allows to identify strengths in terms of application of PM methodologies and good practices and, in turn, to provide feedback and opportunities for improvements to be implemented in future programs. In order to achieve this objective, the present research makes use of a survey-based data retrieval and correlation analysis to investigate the level of perceived PM maturity in H2020 projects and the correlation of maturity with project success. The results show the Project Managers involved in H2020 to hold a high level of PM maturity, confirming PM standards, which are imposed by the EU commission as a binding process, are effectively enforced.

Keywords: project management, project management maturity, maturity models, project success

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Authors: Vijayendra Anil Menon, Ashwath Narayan Murali

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The present day vehicles do not reuse the energy expelled in running the vehicle. The energy used to run the vehicle is expelled immediately.This has remained a constant for many decades. With all the vehicles running on non-renewable resources like fossil fuels, there is an urgent need to improve efficiency of the vehicles until a reliable replacement for fossil fuels is found.Our design is based on the concept of Kinetic energy recovery systems. Though our design lies in principle with the KERS, our design can be used in day-to-day driving. With our design, efficiency of vehicles increases and fuel conservation is possible thereby reducing the carbon footprint.

Keywords: KERS, Battery, Wheels, Efficiency.

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Authors: L. Richter, J. Lübkemann, P. Nyhuis

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In order to remain competitive in what is a turbulent environment; businesses must be able to react rapidly to change. The past response to volatile market conditions was to introduce an element of flexibility to production. Nowadays, what is often required is a redesign of factory structures in order to cope with the state of constant flux. The Institute of Production Systems and Logistics is currently developing a descriptive and causal model for the redesign of plant structures as part of an ongoing research project. This article presents the first research findings attained in devising this model.

Keywords: change driven factory redesign, factory planning, plant structure, flexibility

Procedia PDF Downloads 271

Authors: Anita Kushwaha

Abstract:

We propose a new evolutionary computational model called Artificial Reproduction System which is based on the complex process of meiotic reproduction occurring between male and female cells of the living organisms. Artificial Reproduction System is an attempt towards a new computational intelligence approach inspired by the theoretical reproduction mechanism, observed reproduction functions, principles and mechanisms. A reproductive organism is programmed by genes and can be viewed as an automaton, mapping and reducing so as to create copies of those genes in its off springs. In Artificial Reproduction System, the binding mechanism between male and female cells is studied, parameters are chosen and a network is constructed also a feedback system for self regularization is established. The model then applies Mendel’s law of inheritance, allele-allele associations and can be used to perform data analysis of imbalanced data, multivariate, multiclass and big data. In the experimental study Artificial Reproduction System is compared with other state of the art classifiers like SVM, Radial Basis Function, neural networks, K-Nearest Neighbor for some benchmark datasets and comparison results indicates a good performance.

Keywords: bio-inspired computation, nature- inspired computation, natural computing, data mining

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Authors: H. Oudira, A. Saifi

Abstract:

The therapeutic utility of certain Auger emitters such as iodine-125 depends on their position within the cell nucleus . Or diagnostically, and to maintain as low as possible cell damage, it is preferable to have radionuclide localized outside the cell or at least the core. One solution to this problem is to consider markers capable of conveying anticancer drugs to the tumor site regardless of their location within the human body. The objective of this study is to simulate the impact of a complex such as bleomycin on single and double strand breaks in the DNA molecule. Indeed, this simulation consists of the following transactions: - Construction of BLM -Fe- DNA complex. - Simulation of the electron’s transport from the metastable state excitation of Fe 57 by the Monte Carlo method. - Treatment of chemical reactions in the considered environment by the diffusion equation. For physical, physico-chemical and finally chemical steps, the geometry of the complex is considered as a sphere of 50 nm centered on the binding site , and the mathematical method used is called step by step based on Monte Carlo codes.

Keywords: concentration, yield, radical species, bleomycin, excitation, DNA

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Authors: Kei Kamada, Rikito Murakami, Masahiko Ito, Mototaka Arakawa, Yasuhiro Shoji, Toshiyuki Ueno, Masao Yoshino, Akihiro Yamaji, Shunsuke Kurosawa, Yuui Yokota, Yuji Ohashi, Akira Yoshikawa

Abstract:

Techniques of energy harvesting y have been widely developed in recent years, due to high demand on the power supply for ‘Internet of things’ devices such as wireless sensor nodes. In these applications, conversion technique of mechanical vibration energy into electrical energy using magnetostrictive materials n have been brought to attention. Among the magnetostrictive materials, Fe-Ga and Fe-Al alloys are attractive materials due to the figure of merits such price, mechanical strength, high magnetostrictive constant. Up to now, bulk crystals of these alloys are produced by the Bridgman–Stockbarger method or the Czochralski method. Using these method big bulk crystal up to 2~3 inch diameter can be grown. However, non-uniformity of chemical composition along to the crystal growth direction cannot be avoid, which results in non-uniformity of magnetostriction constant and reduction of the production yield. The micro-pulling down (μ-PD) method has been developed as a shaped crystal growth technique. Our group have reported shaped crystal growth of oxide, fluoride single crystals with different shape such rod, plate tube, thin fiber, etc. Advantages of this method is low segregation due to high growth rate and small diffusion of melt at the solid-liquid interface, and small kerf loss due to near net shape crystal. In this presentation, we report the shaped long plate crystal growth of Fe-Ga and Fe-Al alloys using the μ-PD method. Alloy crystals were grown by the μ-PD method using calcium oxide crucible and induction heating system under the nitrogen atmosphere. The bottom hole of crucibles was 5 x 1mm² size. A <100> oriented iron-based alloy was used as a seed crystal. 5 x 1 x 320 mm³ alloy crystal plates were successfully grown. The results of crystal growth, chemical composition analysis, magnetostrictive properties and a prototype vibration energy harvester are reported. Furthermore, continuous crystal growth using powder supply system will be reported to minimize the chemical composition non-uniformity along the growth direction.

Keywords: crystal growth, micro-pulling-down method, Fe-Ga, Fe-Al

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Authors: Siddharth Vishwakarma, Danie Shajie A., Mishra H. N.

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Milk powder becomes very useful in the low milk supply area but the exact amount to add for one glass of milk and the handling is difficult. So, the idea of instant soluble milk tablet comes into existence for its high solubility and easy handling. The moisture content of milk tablets is increased by the direct addition of water with no additives for binding. The variation of the tensile strength of instant soluble milk tablets and the flowability of milk powder with the moisture content is analyzed and optimized for the highest tensile strength of instant soluble milk tablets and flowability, above a particular value of milk powder using response surface methodology. The flowability value is necessary for ease in quantifying the milk powder, as a feed, in the designed tablet making machine. The instant soluble nature of milk tablets purely depends upon the disintegration characteristic of tablets in water whose study is under progress. Conclusions: The optimization results are very useful in the commercialization of milk tablets.

Keywords: flowability, milk powder, response surface methodology, tablet making machine, tensile strength

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Authors: Meriem Boukais, B. Dennai, A. Ould- Abbas

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The efficiency of SiGe solar cells might be improved by a wide-band-gap window layer. In this work we were simulated using the one dimensional simulation program called analysis of microelectronic and photonic structures (AMPS-1D). In the modeling, the thickness of silicon window was varied from 80 to 150 nm. The rest of layer’s thicknesses were kept constant, by varying thickness of window layer the simulated device performance was demonstrate in the form of current-voltage (I-V) characteristics and quantum efficiency (QE).

Keywords: modeling, SiGe, AMPS-1D, quantum efficiency, conversion, efficiency

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Authors: Shri Krishna Mishra, Badri Yadav

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Proficient persons should be involved in formulation of the structure of the textbooks so that the topics selected in the Hindi textbooks for Class VII should contribute towards linguistic and literary development of the child and the language of the textbook matches the comprehension level of the student.The topics of tile textbooks should provide good illustrations and suitable exercises. Topics of variety of taste can be included in the textbook to satisfy the inquisitive children. There could be abstracts/hints at the beginning of each lesson. Meanings for difficult words must be given at the end of each topic for convenience of the parents and children as most of them find it difficult and time consuming to use Hindi dictionary. Exercises should be relevant covering the whole topic and the difficulty level should match the maturity level of the students in respect of CBSE Board. The stitching and binding of CBSE prescribed books may be improved to increase durability.

Keywords: comparative study of CBSE and BSEMPB, Central Secondary Education, Board of Secondry Education, BHOPAL

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Authors: Hui-Ling Huang, Tamara Vasylenko, Phasit Charoenkwan, Shih-Hsiang Chiu, Shinn-Ying Ho

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The knowledge of the human transporters is still limited due to technically demanding procedure of crystallization for the structural characterization of transporters by spectroscopic methods. It is desirable to develop bioinformatics tools for effective analysis of available sequences in order to identify human transmembrane transporter proteins (HMTPs). This study proposes a scoring card method (SCM) based method for predicting HMTPs. We estimated a set of propensity scores of dipeptides to be HMTPs using SCM from the training dataset (HTS732) consisting of 366 HMTPs and 366 non-HMTPs. SCM using the estimated propensity scores of 20 amino acids and 400 dipeptides -as HMTPs, has a training accuracy of 87.63% and a test accuracy of 66.46%. The five top-ranked dipeptides include LD, NV, LI, KY, and MN with scores 996, 992, 989, 987, and 985, respectively. Five amino acids with the highest propensity scores are Ile, Phe, Met, Gly, and Leu, that hydrophobic residues are mostly highly-scored. Furthermore, obtained propensity scores were used to analyze physicochemical properties of human transporters.

Keywords: dipeptide composition, physicochemical property, human transmembrane transporter proteins, human transmembrane transporters binding propensity, scoring card method

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Authors: M. Hosseinnezhad, K. Gharanjig

Abstract:

Natural dyes, extracted from black carrot and bramble, were utilized as photosensitizers to prepare dye-sensitized solar cells (DSSCs). Spectrophotometric studies of the natural dyes in solution and on a titanium dioxide substrate were carried out in order to assess changes in the status of the dyes. The results show that the bathochromic shift is seen on the photo-electrode substrate. The chemical binding of the natural dyes at the surface photo-electrode were increased by the chelating effect of the Ti(IV) ions. The cyclic voltammetry results showed that all extracts are suitable to be performed in DSSCs. Finally, photochemical performance and stability of DSSCs based on natural dyes were studied. The DSSCs sensitized by black carrot extract have been reported to achieve up to Jsc=1.17 mAcm^-2, Voc= 0.55 V, FF= 0.52, η=0.34%, whereas Bramble extract can obtain up to Jsc=2.24 mAcm^-2, Voc= 0.54 V, FF= 0.57, η=0.71%. The power conversion efficiency was obtained from the mixed dyes in DSSCs. The power conversion efficiency of dye-sensitized solar cells using mixed Black carrot and Bramble dye is the average of the their efficiency in single DSSCs.

Keywords: anthocyanin, dye-sensitized solar cells, green energy, optical materials

Procedia PDF Downloads 245