Search results for: denaturing gradient gel electrophoresis

Authors: Manjula Weerasekera, Chris Sissons, Lisa Wong, Sally Anderson, Ann Holmes, Richard Cannon

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The aim of this study was to characterize bacterial population and yeasts in saliva by Polymerase chain reaction followed by denaturing gradient gel electrophoresis (PCR-DGGE) and measure yeast levels by culture. PCR-DGGE was performed to identify oral bacteria and yeasts in 24 saliva samples. DNA was extracted and used to generate DNA amplicons of the V2–V3 hypervariable region of the bacterial 16S rDNA gene using PCR. Further universal primers targeting the large subunit rDNA gene (25S-28S) of fungi were used to amplify yeasts present in human saliva. Resulting PCR products were subjected to denaturing gradient gel electrophoresis using Universal mutation detection system. DGGE bands were extracted and sequenced using Sanger method. A potential relationship was evaluated between groups of bacteria identified by cluster analysis of DGGE fingerprints with the yeast levels and with their diversity. Significant interpersonal variation of salivary microbiome was observed. Cluster and principal component analysis of the bacterial DGGE patterns yielded three significant major clusters, and outliers. Seventeen of the 24 (71%) saliva samples were yeast positive going up to 10³ cfu/mL. Predominately, C. albicans, and six other species of yeast were detected. The presence, amount and species of yeast showed no clear relationship to the bacterial clusters. Microbial community in saliva showed a significant variation between individuals. A lack of association between yeasts and the bacterial fingerprints in saliva suggests the significant ecological person-specific independence in highly complex oral biofilm systems under normal oral conditions.

Keywords: bacteria, denaturing gradient gel electrophoresis, oral biofilm, yeasts

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Authors: Meenakshi Srivastava, A. K. Mishra

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This study characterizes the metabolic versatility of denitrifying bacterial communities residing in the paddy soil using the GC-MS based Phospholipid Fatty Acid (PLFA) analyses simultaneously with nosZ gene based PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and real time Q-PCR analysis. We have analyzed the abundance of nitrous oxide reductase (nosZ) genes, which was subsequently related to soil PLFA profile and DGGE based denitrifier community structure. Soil denitrifying bacterial community comprised majority or dominance of Ochrobactrum sp. following Cupriavidus and uncultured bacteria strains in paddy soil of selected sites. Initially, we have analyzed the abundance of the nitrous oxide reductase gene (nosZ), which was found to be related with PLFA based lipid profile. Chandauli of Eastern UP, India represented greater amount of lipid content (C18-C20) and denitrifier’s diversity. This study suggests the positive co-relation between soil PLFA profiles, DGGE, and Q-PCR data. Thus, a close networking among metabolic abilities and taxonomic composition of soil microbial communities existed, and subsequently, such work at greater extent could be helpful in managing nutrient dynamics as well as microbial dynamics of paddy soil ecosystem.

Keywords: denaturing gradient gel electrophoresis, DGGE, nitrifying and denitrifying bacteria, PLFA, Q-PCR

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Authors: Mansur Abdulrasheed, Hussein I. Ibrahim, Ahmed F. Umar

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Nitrification, the microbial oxidation of ammonia to nitrate (NO3-) via nitrite (NO2-) is a vital process in the biogeochemical nitrogen cycle and is performed by two distinct functional groups; ammonia oxidisers (comprised of ammonia oxidising bacteria (AOB) and ammonia oxidising archaea (AOA)) and nitrite oxidising bacteria. Autotrophic nitrification is said to occur in acidic soils, even though most laboratory cultures of isolated ammonia and nitrite oxidising bacteria fail to grow below neutral pH. Published studies revealed that soil pH is a major driver for determining the distribution and abundance of AOB and AOA. To determine whether distinct populations of nitrite oxidising bacteria within the lineages of Nitrospira and Nitrobacter are adapted to a particular range of pH as observed in ammonia oxidising organisms, the community structure of Nitrospira-like and Nitrobacter-like NOB were examined across a pH gradient (4.5–7.5) by amplifying nitrite oxido-reductase (nxrA) and 16S rRNA genes followed by denaturing gradient gel electrophoresis (DGGE). The community structure of both Nitrospira and Nitrobacter changed with soil pH, with distinct populations observed in acidic and neutral soils. The abundance of Nitrospira-like 16S rRNA and Nitrobacter-like nxrA gene copies contrasted across the pH gradient. Nitrobacter-like nxrA gene abundance decreased with increasing soil pH, whereas Nitrospira-like 16S rRNA gene abundance increased with increasing pH. Findings indicated that abundance and distributions of soil NOB is influence by soil pH.

Keywords: nitrospira, nitrobacter, nitrite-oxidizing bacteria, nitrification, pH, soil

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Authors: Jian Peng, Wenhui Xiong, Zheng Lu

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An optimal recipe of amendment (nutrients and electron acceptors) was developed and dominant indigenous benzene-degrading microorganisms were characterized in this study. Lessons were learnt from the development of the optimal amendment recipe: (1) salinity and substantial initial concentration of benzene were detrimental for benzene biodegradation; (2) large dose of amendments can shorten the lag time for benzene biodegradation occurrence; (3) toluene was an essential co-substance for promoting benzene degradation activity. The stable isotope probing study identified incorporation 13C from 13C-benzene into microorganisms, which can be considered as a direct evidence of the occurrence of benzene biodegradation. The dominant mechanism for benzene removal was identified by quantitative polymerase chain reaction analysis to be nitrate reduction. Microbial analyses (denaturing gradient gel electrophoresis and 16S ribosomal RNA) demonstrated that members of genus Dokdonella spp., Pusillimonas spp., and Advenella spp. were predominant within the microbial community and involved in the anaerobic benzene bioremediation.

Keywords: benzene, enhanced anaerobic bioremediation, stable isotope probing, biosep biotrap

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Authors: Begüm Terzi, Özlem Ateş Sönmezoğlu, Kerime Özkay, Ahmet Yıldırım

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In plant biotechnology, electrophoresis is used to detect nucleic acids. Ethidium bromide (EtBr) is used as an intercalator dye to stain DNA in agarose gel electrophoresis, but this dye is mutagenic and carcinogenic. In this study, a visible, reliable and organic Ruthenium-based dye (N-719) for staining plant DNA in comparison to EtBr. When prestaining and post-staining for gel electrophoresis, N-719 stained both DNA and PCR product bands with the same clarity as EtBr. The organic dye N-719 stained DNA bands as sensitively and as clearly as EtBr. The organic dye was found to have staining activity suitable for the identification of DNA.Consequently, N-719 organic dye can be used to stain and visualize DNA during gel electrophoresis as alternatives to EtBr in plant biotechnology studies.

Keywords: agarose gel, DNA staining, organic dye, N-719

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Authors: Rupamoni Thakur, Madhusmita Dehingia, Narayan C. Talukdar, Mojibur R. Khan

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The human gut is an extremely active fermentation site and is inhabited by diverse bacterial species. Consumption of alcoholic beverages has been shown to substantially modulate the human gut bacterial profile (GBP) of an individual. Assam, a major north-eastern state of India, is home to a number of tribal populations of which the tea-tribes form a major community. These tea-tribal communities are known to prepare and consume a locally-prepared alcoholic beverage from fermented jaggery, whose chemical composition is unknown. In this study, we demonstrate the effect of daily intake of the locally-prepared alcoholic beverage on the GBP of the tea-tribal communities and correlate it with the changes in the biochemical biomarkers of the population. The fecal bacterial diversity of 40 drinkers and 35 non-drinking healthy individuals were analyzed by polymerase chain reaction (PCR)–denaturing gradient gel electrophoresis (DGGE). The results suggested that the GBP was significantly modulated in the fermented-beverage consuming subjects. Significant difference was also observed in the serum biochemical parameters such as triglyceride, total cholesterol and the liver marker enzymes (ASAT/ALAT and GGT). Further studies to identify the GBP of drinkers vs non-drinkers through Next-generation Sequencing (NGS) analysis and to correlate the changes with the biochemical biomarkers of the population is underway.

Keywords: alcoholic beverage, gut bacterial profile, PCR-DGGE analysis, tea-tribes of India

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Authors: Nadia Ben Youssef, Aicha Bouzid

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Gradient estimation is one of the most fundamental tasks in the field of image processing in general, and more particularly for color images since that the research in color image gradient remains limited. The widely used gradient method is Di Zenzo’s gradient operator, which is based on the measure of squared local contrast of color images. The proposed gradient mechanism, presented in this paper, is based on the principle of the Di Zenzo’s approach using quaternion representation. This edge detector is compared to a marginal approach based on multiscale product of wavelet transform and another vector approach based on quaternion convolution and vector gradient approach. The experimental results indicate that the proposed color gradient operator outperforms marginal approach, however, it is less efficient then the second vector approach.

Keywords: gradient, edge detection, color image, quaternion

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Authors: Y. T. Boon, M. N. Naim, R. Zakaria, N. F. Abu Bakar, N. Ahmad, I. W. Lenggoro

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In this study, encapsulation of agarwood oil with non-ionic surfactant, Tween 80 was prepared at critical micelle concentration of 0.0167 % v/v to produce the most stable nano-emulsion in aqueous. The encapsulation has minimized the bioactive compounds degradation in various pH conditions thus prolong their shelf life and maintained its initial oil grade. The oil grading of the prepared samples were conducted using the gel electrophoresis instead of using common analytical industrial grading such as gas chromatography- mass spectrometry (GC- MS). The grading method was chosen due to their unique zeta potential value after the encapsulation process. This paper demonstrates the feasibility of applying the electrophoresis principles to separate the encapsulated agarwood oil or grading of the emulsified agarwood oil. The results indicated that the grading process are potential to be further investigate based on their droplet size and zeta potential value at various pH condition when the droplet were migrate through polyacrylamide gel.

Keywords: electrophoretic mobility, essential oil, nanoemulsion, polyacrylamide gel electrophoresis, tween 80, zeta potential

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Authors: Danni Cong, Meiping Wu, Hua Mu, Xiaofeng He, Junxiang Lian, Juliang Cao, Shaokun Cai, Hao Qin

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Gravity field is of great significance in geoscience, national economy and national security, and gravitational gradient measurement has been extensively studied due to its higher accuracy than gravity measurement. Gravity gradient sensor, being one of core devices of the gravity gradient instrument, plays a key role in measuring accuracy. Therefore, this paper starts from analyzing the working principle of the gravity gradient sensor by Newton’s law, and then considers the relative motion between inertial and non-inertial systems to build a relatively adequate mathematical model, laying a foundation for the measurement error calibration, measurement accuracy improvement.

Keywords: gravity gradient, gravity gradient sensor, accelerometer, single-axis rotation modulation

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Authors: Sandeep Kaur

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Phycoerythrin (PE) from the mesophilic filamentous cyanobacterium Nostoc piscinale PUPCCC 405.17, a good producer of phycobiliproteins, has been characterized in terms of their unit assembly and stability. The phycoerythrin was extracted by freeze-thawing the cells in water, concentrated by ammonium sulphate fractionation and purified by anion exchange chromatography. The purification process resulted in 2.90 fold increase in phycoerythrin purity reaching to 1.54. Sodium Dodecyl Sulphate- Polyacrylamide Gel Electrophoresis of purified PE demonstrated three protein bands of 14.3, 27.54 and 39.81 kDa. The native PE also showed one band of 125.87 kDa, assumed to be a dimer (αβ)2γ based on results of non-denaturing PAGE. Lyophilized powder PE was more stable compared to phycoerythrin in the solution. The half-life of dry PE is 80 days when stored at 4 °C under dark. The phycoerythrin from this organism has potential applications in food as natural colour and as a fluorescent marker.

Keywords: characterization, Nostoc piscinale, phycoerythrin, purification

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Authors: Aldi Nel, Cliff L. W. Jones, Justin O. G. Kemp, Peter J. Britz

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Kelp Ecklonia maxima is included in formulated abalone feeds in South Africa, but its effect on abalone growth, feed utilisation efficiency and gut-bacterial communities has not previously been investigated. An eight-month on-farm growth trial with sub-adult Haliotis midae (~43 mm shell length) fed graded levels of kelp in formulated feeds was conducted. Kelp inclusion (0.44–3.54 % of pellet dry mass) promoted faster growth (65.7 – 74.5 % total mass gain), with better feed and protein conversions (FCR: 1.4 – 1.8; PER 2.3 – 2.7), compared to abalone fed the non-supplemented feed (52.3% total mass gain; FCR: 2.1; PER 1.9; p < 0.001). The gut-bacterial communities of abalone fed kelp-supplemented feed (0.88 % of pellet dry mass) were subsequently compared with that of abalone fed a non-supplemented control diet. Abalone gut-bacterial DNA was sequenced using 16S rRNA pyrosequencing and sequences were clustered into operational taxonomic units (OTUs) at a 97 % similarity level. A supplementary 16S rRNA denaturing gradient gel electrophoresis (DGGE) analysis was conducted. The dominant OTUs differed in terms of their relative abundances, with that of an autochthonous Mollicutes strain being significantly higher (p = 0.03) in the guts of abalone fed kelp-supplemented feed. The DGGE band patterns displayed a higher within-group variability of dominant bacterial strains for abalone fed the control diet, suggesting that dietary inclusion of kelp, which is rich in fermentable polysaccharides, promotes a balanced gut-bacterial community. This may contribute to the better feed utilisation and growth in abalone fed kelp-supplemented feeds.

Keywords: abfeed, digestion, macroalgae, mariculture

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Authors: Ahmad Alhawarat, Mustafa Mamat, Mohd Rivaie, Ismail Mohd

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Conjugate gradient method has been enormously used to solve large scale unconstrained optimization problems due to the number of iteration, memory, CPU time, and convergence property, in this paper we find a new class of nonlinear conjugate gradient coefficient with global convergence properties proved by exact line search. The numerical results for our new βK give a good result when it compared with well-known formulas.

Keywords: conjugate gradient method, conjugate gradient coefficient, global convergence

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Authors: Can Hu, Huixia Shi, Hongcheng Mei, Jun Zhu, Hongling Guo

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Textile fibers are important trace evidence and frequently encountered in criminal investigations. A significant aspect of fiber evidence examination is the determination of fiber dyes. Although several instrumental methods have been developed for dyes detection, the analysis speed is not fast enough yet. A rapid dye analysis method is still needed to further improve the efficiency of case handling. Capillary electrophoresis has the advantages of high separation speed and high separation efficiency and is an ideal method for the rapid analysis of fiber dyes. In this paper, acid dyes used for protein fiber dyeing were determined by a developed short-end injection capillary electrophoresis technique. Five acid red dyes with similar structures were successfully baseline separated within 5 min. The separation reproducibility is fairly good for the relative standard deviation of retention time is 0.51%. The established method is rapid and accurate which has great potential to be applied in forensic setting.

Keywords: acid dyes, capillary electrophoresis, fiber evidence, rapid determination

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Authors: O. Ubani, H. I. Atagana, M. S. Thantsha

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This study was conducted to measure the reduction in polycyclic aromatic hydrocarbons (PAHs) content in oil sludge by co-composting the sludge with pig, cow, horse and poultry manures under laboratory conditions. Four kilograms of soil spiked with 800 g of oil sludge was co-composted differently with each manure in a ratio of 2:1 (w/w) spiked soil:manure and wood-chips in a ratio of 2:1 (w/v) spiked soil:wood-chips. Control was set up similar as the one above but without manure. Mixtures were incubated for 10 months at room temperature. Compost piles were turned weekly and moisture level was maintained at between 50% and 70%. Moisture level, pH, temperature, CO2 evolution and oxygen consumption were measured monthly and the ash content at the end of experimentation. Bacteria capable of utilizing PAHs were isolated, purified and characterized by molecular techniques using polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), amplification of the 16S rDNA gene using the specific primers (16S-P1 PCR and 16S-P2 PCR) and the amplicons were sequenced. Extent of reduction of PAHs was measured using automated soxhlet extractor with dichloromethane as the extraction solvent coupled with gas chromatography/mass spectrometry (GC/MS). Temperature did not exceed 27.5O°C in all compost heaps, pH ranged from 5.5 to 7.8 and CO2 evolution was highest in poultry manure at 18.78 µg/dwt/day. Microbial growth and activities were enhanced. Bacteria identified were Bacillus, Arthrobacter and Staphylococcus species. Results from PAH measurements showed reduction between 77 and 99%. The results from the control experiments may be because it was invaded by fungi. Co-composting of spiked soils with animal manures enhanced the reduction in PAHs. Interestingly, all bacteria isolated and identified in this study were present in all treatments, including the control.

Keywords: bioremediation, co-composting, oil refinery sludge, PAHs, bacteria spp, animal manures, molecular techniques

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Authors: M. Yaqub Khan, Usman Shabbir

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History of plasma reveals that continuous struggle of experimentalists and theorists are not fruitful for confinement up to now. It needs a change to bring the research through entropy. Approximately, all the quantities like number density, temperature, electrostatic potential, etc. are connected to entropy. Therefore, it is better to change the way of research. In ion temperature gradient mode with the help of Braginskii model, Boltzmannian electrons, effect of velocity shear is studied inculcating entropy in the magnetoplasma. New dispersion relation is derived for ion temperature gradient mode, and dependence on entropy gradient drift is seen. It is also seen velocity shear enhances the instability but in anomalous transport, its role is not seen significantly but entropy. This work will be helpful to the next step of tokamak and space plasmas.

Keywords: entropy, velocity shear, ion temperature gradient mode, drift

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Authors: Belloufi Mohammed, Sellami Badreddine

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This paper deals with a new nonlinear modified three-term conjugate gradient algorithm for solving large-scale unstrained optimization problems. The search direction of the algorithms from this class has three terms and is computed as modifications of the classical conjugate gradient algorithms to satisfy both the descent and the conjugacy conditions. An example of three-term conjugate gradient algorithm from this class, as modifications of the classical and well known Hestenes and Stiefel or of the CG_DESCENT by Hager and Zhang conjugate gradient algorithms, satisfying both the descent and the conjugacy conditions is presented. Under mild conditions, we prove that the modified three-term conjugate gradient algorithm with Wolfe type line search is globally convergent. Preliminary numerical results show the proposed method is very promising.

Keywords: unconstrained optimization, three-term conjugate gradient, sufficient descent property, line search

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Authors: Mustafa Arda, Metin Aydogdu

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Carbon nanotubes (CNTs) have many possible application areas because of their superior physical properties. Nonlocal Theory, which unlike the classical theories, includes the size dependency. Nonlocal Stress and Strain Gradient approaches can be used in nanoscale static and dynamic analysis. In the present study, torsional vibration of CNTs was investigated according to nonlocal stress and strain gradient theories. Effects of the small scale parameters to the non-dimensional frequency were obtained. Results were compared with the Molecular Dynamics Simulation and Lattice Dynamics. Strain Gradient Theory has shown more weakening effect on CNT according to the Stress Gradient Theory. Combination of both theories gives more acceptable results rather than the classical and stress or strain gradient theory according to Lattice Dynamics.

Keywords: torsional vibration, carbon nanotubes, nonlocal gradient theory, stress, strain

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Authors: B. Sellami, Y. Laskri, M. Belloufi

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Conjugate gradient methods are an important class of methods for unconstrained optimization, especially for large-scale problems. Recently, they have been much studied. In this paper, a new family of conjugate gradient method is proposed for unconstrained optimization. This method includes the already existing two practical nonlinear conjugate gradient methods, which produces a descent search direction at every iteration and converges globally provided that the line search satisfies the Wolfe conditions. The numerical experiments are done to test the efficiency of the new method, which implies the new method is promising. In addition the methods related to this family are uniformly discussed.

Keywords: conjugate gradient method, global convergence, line search, unconstrained optimization

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Authors: B. Sellami, M. Belloufi

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Conjugate gradient methods are an important class of methods for unconstrained optimization, especially for large-scale problems. Recently, they have been much studied. In this paper, we propose a new two-parameter family of conjugate gradient methods for unconstrained optimization. The two-parameter family of methods not only includes the already existing three practical nonlinear conjugate gradient methods, but also has other family of conjugate gradient methods as subfamily. The two-parameter family of methods with the Wolfe line search is shown to ensure the descent property of each search direction. Some general convergence results are also established for the two-parameter family of methods. The numerical results show that this method is efficient for the given test problems. In addition, the methods related to this family are uniformly discussed.

Keywords: unconstrained optimization, conjugate gradient method, line search, global convergence

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Authors: A. Selmi, A. Bisharat

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Using Fourier transform and based on the Mindlin's 2^nd gradient model that involves two length scale parameters, the Green's function, the Eshelby tensor, and the Eshelby-like tensor for a spherical inclusion are derived. It is proved that the Eshelby tensor consists of two parts; the classical Eshelby tensor and a gradient part including the length scale parameters which enable the interpretation of the size effect. When the strain gradient is not taken into account, the obtained Green's function and Eshelby tensor reduce to its analogue based on the classical elasticity. The Eshelby tensor in and outside the inclusion, the volume average of the gradient part and the Eshelby-like tensor are explicitly obtained. Unlike the classical Eshelby tensor, the results show that the components of the new Eshelby tensor vary with the position and the inclusion dimensions. It is demonstrated that the contribution of the gradient part should not be neglected.

Keywords: Eshelby tensor, Eshelby-like tensor, Green’s function, Mindlin’s 2nd gradient model, spherical inclusion

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Authors: Changqiao Wu, Guoqing Ding, Xin Chen

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In this paper, ways of modeling dynamic measurement systems are discussed. Specially, for linear system with single-input single-output, it could be modeled with shallow neural network. Then, gradient based optimization algorithms are used for searching the proper coefficients. Besides, method with normal equation and second order gradient descent are proposed to accelerate the modeling process, and ways of better gradient estimation are discussed. It shows that the mathematical essence of the learning objective is maximum likelihood with noises under Gaussian distribution. For conventional gradient descent, the mini-batch learning and gradient with momentum contribute to faster convergence and enhance model ability. Lastly, experimental results proved the effectiveness of second order gradient descent algorithm, and indicated that optimization with normal equation was the most suitable for linear dynamic models.

Keywords: dynamic system modeling, neural network, normal equation, second order gradient descent

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Authors: Kai Pai Huang

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Background: There are several types of plasma cell neoplasms including multiple myeloma, plasmacytoma, lymphoplasmacytic lymphoma, and monoclonal gammopathy of undetermined significance (MGUS) are found in our lab. Today, we want to compare with two cases using the method of capillary electrophoresis. Method: Serum is prepared and electrophoresis is performed at alkaline PH in a capillary using the Sebia® Capillary 2. Albumin and globulins are detected by the detector which is located in the cathode of the capillary and the signals are transformed to peaks. Serum was treated with beta-mercaptoethanol which reducing the polymerized immunoglobulin to monomer immunoglobulin to clarify two M-protein are secreted from the same plasma cell clone in bone marrow. Result: Case 1: A 78-year-old female presenting dysuria, oliguria and leg edema for several months. Laboratory data showed proteinuria, leukocytosis, results of high serum IgA and lambda light chain. A renal biopsy found amyloid fibrils in the glomerular mesangial area. Serum protein electrophoresis shows a major monoclonal peak in the β region and minor small peak in gamma region, and the immunotyping studies for serum showed two IgA/λ type. Case 2: A 55-year-old male presenting abdominal distension and low back pain for more than one month. Laboratory data showed T12 T8 compression fracture, results of high serum IgM and kappa light chain. Bone marrow aspiration showed the cells from the bone marrow are B cells with monotypic kappa chain expression. Bone marrow biopsy found this is lymphoplasmacytic lymphoma (Waldenstrom macroglobulin). Serum protein electrophoresis shows a monoclonal peak in the β region and the immunotyping studies for serum showed IgM/κ type. Conclusion: Plasma cell neoplasm can be diagnosed by many examinations. Among them, using capillary electrophoresis by a lab can separate several types of gammopathy and the quantification of a monoclonal peak can be used to evaluate the patients’ prognosis or treatment.

Keywords: plasma cell neoplasm, capillary electrophoresis, serum protein electrophoresis, immunotyping

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Authors: Mantai Chen, Johnny Ching Ming Ho

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The stress-strain relationship of concrete under flexure is one of the essential parameters in assessing ultimate flexural strength capacity of RC beams. Currently, the concrete stress-strain curve in flexure is obtained by incorporating a constant scale-down factor of 0.85 in the uniaxial stress-strain curve. However, it was revealed that strain gradient would improve the maximum concrete stress under flexure and concrete stress-strain curve is strain gradient dependent. Based on the strain-gradient-dependent concrete stress-strain curve, the investigation of the combined effects of strain gradient and concrete strength on flexural strength of RC beams was extended to high strength concrete up to 100 MPa by theoretical analysis. As an extension and application of the authors’ previous study, a new flexural strength design method incorporating the combined effects of strain gradient and concrete strength is developed. A set of equivalent rectangular concrete stress block parameters is proposed and applied to produce a series of design charts showing that the flexural strength of RC beams are improved with strain gradient effect considered.

Keywords: beams, equivalent concrete stress block, flexural strength, strain gradient

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Authors: Meng Wu

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Motion planning is a common task required to be fulfilled by robots. A strategy combining Ant Colony Optimization (ACO) and gravity gradient inversion algorithm is proposed for motion planning of mobile robots. In this paper, in order to realize optimal motion planning strategy, the cost function in ACO is designed based on gravity gradient inversion algorithm. The obstacles around mobile robot can cause gravity gradient anomalies; the gradiometer is installed on the mobile robot to detect the gravity gradient anomalies. After obtaining the anomalies, gravity gradient inversion algorithm is employed to calculate relative distance and orientation between mobile robot and obstacles. The relative distance and orientation deduced from gravity gradient inversion algorithm is employed as cost function in ACO algorithm to realize motion planning. The proposed strategy is validated by the simulation and experiment results.

Keywords: motion planning, gravity gradient inversion algorithm, ant colony optimization

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Authors: Xiaobai Li, Li Li, Yujin Hu, Weiming Deng, Zhe Ding

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A size-dependent Euler–Bernoulli beam model, which accounts for nonlocal stress field, strain gradient field and higher order inertia force field, is derived based on the nonlocal strain gradient theory considering velocity gradient effect. The governing equations and boundary conditions are derived both in dimensional and dimensionless form by employed the Hamilton principle. The analytical solutions based on different continuum theories are compared. The effect of higher order inertia terms is extremely significant in high frequency range. It is found that there exists an asymptotic frequency for the proposed beam model, while for the nonlocal strain gradient theory the solutions diverge. The effect of strain gradient field in thickness direction is significant in low frequencies domain and it cannot be neglected when the material strain length scale parameter is considerable with beam thickness. The influence of each of three size effect parameters on the natural frequencies are investigated. The natural frequencies increase with the increasing material strain gradient length scale parameter or decreasing velocity gradient length scale parameter and nonlocal parameter.

Keywords: Euler-Bernoulli Beams, free vibration, higher order inertia, Nonlocal Strain Gradient Theory, velocity gradient

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Authors: Diana Puigserver Cuerda, Jofre Herrero Ferran, José M. Carmona Perez

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In the transition zone between aquifers and basal aquitards, DNAPL-pools of chlorinated solvents are more recalcitrant than at other depths in the aquifer. Although degradation of carbon tetrachloride (CT) and chloroform (CF) occurs in this zone, this is a slow process, which is why an adequate remediation strategy is necessary. The working hypothesis of this study is that the biostimulation of the transition zone of an aquifer contaminated by CT and CF can be an effective remediation strategy. This hypothesis has been tested in a site on an unconfined aquifer in which the major contaminants were CT and CF of industrial origin and where the hydrochemical background was rich in other compounds that can hinder natural attenuation of chloromethanes. Field studies and five laboratory microcosm experiments were carried out at the level of groundwater and sediments to identify: i) the degradation processes of CT and CF; ii) the structure of microbial communities; and iii) the microorganisms implicated on this degradation. For this, concentration of contaminants and co-contaminants (nitrate and sulfate), Compound Specific Isotope Analysis, molecular techniques (Denaturing Gradient Gel Electrophoresis) and clone library analysis were used. The main results were: i) degradation processes of CT and CF occurred in groundwater and in the lesser conductive sediments; ii) sulfate-reducing conditions in the transition zone were high and similar to those in the source of contamination; iii) two microorganisms (Azospira suillum and a bacterium of the Clostridiales order) were identified in the transition zone at the field and lab experiments that were compatible with the role of carrying out the reductive dechlorination of CT, CF and their degradation products (dichloromethane and chloromethane); iv) these two microorganisms were present at the high starting concentrations of the microcosm experiments (similar to those in the source of DNAPL) and continued being present until the last day of the lactate biostimulation; and v) the lactate biostimulation gave rise to the fastest and highest degradation rates and promoted the elimination of other electron acceptors (e.g. nitrate and sulfate). All these results are evidence that lactate biostimulation can be effective in remediating the source and plume, especially in the transition zone, and highlight the environmental relevance of the treatment of contaminated transition zones in industrial contexts similar to that studied.

Keywords: Azospira suillum, lactate biostimulation of carbon tetrachloride and chloroform, reductive dechlorination, transition zone between aquifer and aquitard

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Authors: Robert van Ling, Alexander Schwahn, Shanhua Lin, Ken Cook, Frank Steiner, Rowan Moore, Mauro de Pra

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Purpose: Demonstration of fast high resolution charge variant analysis for monoclonal antibody (mAb) therapeutics within 5 minutes. Methods: Three commercially available mAbs were used for all experiments. The charge variants of therapeutic mAbs (Bevacizumab, Cetuximab, Infliximab, and Trastuzumab) are analyzed on a strong cation exchange column with a linear pH gradient separation method. The linear gradient from pH 5.6 to pH 10.2 is generated over time by running a linear pump gradient from 100% Thermo Scientific™ CX-1 pH Gradient Buffer A (pH 5.6) to 100% CX-1 pH Gradient Buffer B (pH 10.2), using the Thermo Scientific™ Vanquish™ UHPLC system. Results: The pH gradient method is generally applicable to monoclonal antibody charge variant analysis. In conjunction with state-of-the-art column and UHPLC technology, ultra fast high-resolution separations are consistently achieved in under 5 minutes for all mAbs analyzed. Conclusion: The linear pH gradient method is a platform method for mAb charge variant analysis. The linear pH gradient method can be easily optimized to improve separations and shorten cycle times. Ultra-fast charge variant separation is facilitated with UHPLC that complements, and in some instances outperforms CE approaches in terms of both resolution and throughput.

Keywords: charge variants, ion exchange chromatography, monoclonal antibody, UHPLC

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Authors: Belloufi Mohammed, Sellami Badreddine

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Conjugate gradient methods have played a special role for solving large scale optimization problems due to the simplicity of their iteration, convergence properties and their low memory requirements. In this work, we propose a new class of conjugate gradient methods which ensures sufficient descent. Moreover, we propose a new search direction with the Wolfe line search technique for solving unconstrained optimization problems, a global convergence result for general functions is established provided that the line search satisfies the Wolfe conditions. Our numerical experiments indicate that our proposed methods are preferable and in general superior to the classical conjugate gradient methods in terms of efficiency and robustness.

Keywords: unconstrained optimization, conjugate gradient method, sufficient descent property, numerical comparisons

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Authors: Şeyma Özçirak Ergün, Ergün Şakalar, Emrah Yalazi̇, Nebahat Şahi̇n

Abstract:

Food irradiation is a usage of exposing food to ionising radiation (IR) such as gamma rays. IR has been used to decrease the number of harmful microorganisms in the food such as spices. Excessive usage of IR can cause damage to both food and people who consuming food. And also it causes to damages on food DNA. Generally, IR detection techniques were utilized in literature for spices are Electron Spin Resonance (ESR), Thermos Luminescence (TL). Storage creates negative effect on IR detection method then analyses of samples have been performed without storage in general. In the experimental part, red pepper (Capsicum annuum) and mint (Mentha piperita) as spices were exposed to 0, 0.272, 0.497, 1.06, 3.64, 8.82, and 17.42 kGy ionize radiation. ESR was applied to samples irradiated. DNA isolation from irradiated samples was performed using GIDAGEN Multi Fast DNA isolation kit. The DNA concentration was measured using a microplate reader spectrophotometer (Infinite® 200 PRO-Life Science–Tecan). The concentration of each DNA was adjusted to 50 ng/µL. Genomic DNA was imaged by UV transilluminator (Gel Doc XR System, Bio-Rad) for the estimation of genomic DNA bp-fragment size after IR. Thus, agarose gel profiles of irradiated spices were obtained to determine the change of band profiles. Besides, samples were examined at three different time periods (0, 3, 6 months storage) to show the feasibility of developed method. Results of gel electrophoresis showed especially degradation of DNA of irradiated samples. In conclusion, this study with gel electrophoresis can be used as a basis for the identification of the dose of irradiation by looking at degradation profiles at specific amounts of irradiation. Agarose gel results of irradiated samples were confirmed with ESR analysis. This method can be applied widely to not only food products but also all biological materials containing DNA to predict radiation-induced damage of DNA.

Keywords: DNA, electrophoresis, gel electrophoresis, ionizeradiation

Procedia PDF Downloads 228

Authors: Sudip Sudhir Godbole

Abstract:

In transmission line surface potential gradient is a critical design parameter for planning overhead line, as it determines the level of corona loss (CL), radio interference (RI) and audible noise (AN).With increase of transmission line voltage level bulk power transfer is possible, using bundle conductor configuration used, it is more complex to find accurate surface stress in bundle configuration. The majority of existing models for surface gradient calculations are based on analytical methods which restrict their application in simulating complex surface geometry. This paper proposes a novel technique which utilizes both analytical and numerical procedure to predict the surface gradient. One of 400 kV transmission line configurations has been selected as an example to compare the results for different methods. The different strand shapes are a key variable in determining.

Keywords: surface gradient, Maxwell potential coefficient method, market and Mengele’s method, successive images method, charge simulation method, finite element method

Procedia PDF Downloads 508