Search results for: structure guided saturation mutagenesis

Authors: Sarah Gaßmeyer, Nadine Hülsemann, Raphael Stoll, Kenji Miyamoto, Robert Kourist

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Enzymatic racemization allows the smooth interconversion of stereocenters under very mild reaction conditions. Racemases find frequent applications in deracemization and dynamic kinetic resolutions. Arylmalonate decarboxylase (AMDase) from Bordetella Bronchiseptica has high structural similarity to amino acid racemases. These cofactor-free racemases are able to break chemically strong CH-bonds under mild conditions. The racemase-like catalytic machinery of mutant G74C conveys it a unique activity in the racemisation of pharmacologically relevant derivates of 2-phenylpropionic acid (profenes), which makes AMDase G74C an interesting object for the mechanistic investigation of cofactor-independent racemases. Structure-guided protein engineering achieved a variant of this unique racemase with 40-fold increased activity in the racemisation of several arylaliphatic carboxylic acids. By saturation–transfer–difference NMR spectroscopy (STD-NMR), substrate binding during catalysis was investigated. All atoms of the substrate showed interactions with the enzyme. STD-NMR measurements revealed distinct nuclear Overhauser effects in experiments with and without molecular conversion. The spectroscopic analysis led to the identification of several amino acid residues whose variation increased the activity of G74C. While single-amino acid exchanges increased the activity moderately, structure-guided saturation mutagenesis yielded a quadruple mutant with a 40 times higher reaction rate. This study presents STD-NMR as versatile tool for the analysis of enzyme-substrate interactions in catalytically competent systems and for the guidance of protein engineering.

Keywords: racemase, rational protein design, STD-NMR, structure guided saturation mutagenesis

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Authors: Mark-Adam Kellerman

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Proteins are capable of exploring vast mutational spaces. This makes it difficult for protein engineers to devise rational methods to improve stability and function via mutagenesis. Deciding which residues to mutate requires knowledge of the characteristics they elicit. We probed the characteristics of residues in granulocyte-colony stimulating factor (G-CSF) using a thermal melt (from 295K to 323K) to denature it in a 700 MHz Bruker spectrometer. These characteristics included dynamics, micro-environmental changes experienced/ induced during denaturing and structure-function relationships. 15N-1H HSQC experiments were performed at 2K increments along with this thermal melt. We observed that dynamic residues that also undergo a lot of change in their microenvironment were predominantly in unstructured regions. Moreover, we were able to identify four residues (G4, A6, T133 and Q134) that we class as high priority targets for mutagenesis, given that they all appear in both the top 10% of measures for environmental changes and dynamics (∑Δ and ∆PI). We were also able to probe these NMR observables and combine them with molecular dynamics (MD) to elucidate what appears to be an opening motion of G-CSFs binding site III. V48 appears to be pivotal to this opening motion, which also seemingly distorts the loop region between helices A and B. This observation is in agreement with previous findings that the conformation of this loop region becomes altered in an aggregation-prone state of G-CSF. Hence, we present here an approach to profile the characteristics of residues in order to highlight their potential as rational mutagenesis targets and their roles in important conformational changes. These findings present not only an opportunity to effectively make biobetters, but also open up the possibility to further understand epistasis and machine learn residue behaviours.

Keywords: protein engineering, rational mutagenesis, NMR, molecular dynamics

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Authors: Khulud M. Rahuma, Ibrahim B. Younis

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Assessment of petrophysical parameters are very essential for reservoir engineer. Three techniques can be used to predict reservoir properties: well logging, well testing, and core analysis. Cementation factor and saturation exponent are very required for calculation, and their values role a great effect on water saturation estimation. In this study a sensitive analysis was performed to investigate the influence of cementation factor and saturation exponent variation applying logs, and core analysis. Measurements of water saturation resulted in a maximum difference around fifteen percent.

Keywords: porosity, cementation factor, saturation exponent, formation factor, water saturation

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Authors: Yakup Ulusu, Numan Eczacıoğlu, İsa Gökçe, Helen Waller, Jeremy H. Lakey

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Besides having the appropriate amino acid sequence to perform the function of proteins, it is important to have correct conformation after this sequence to process. To consist of this conformation depends on the amino acid sequence at the primary structure, hydrophobic interaction, chaperones and enzymes in charge of folding etc. Misfolded proteins are not functional and tend to be aggregated. Cysteine originating disulfide cross-links make stable this conformation of functional proteins. When two of the cysteine amino acids come side by side, disulfide bond is established that forms a cystine bridge. Due to this feature cysteine plays an important role on the formation of three-dimensional structure of many proteins. There are two cysteine amino acids (C44, C69) in the Tol-A-III protein. Unlike protein disulfide bonds from within his own, any non-specific cystine bridge causes a change in the three dimensional structure of the protein. Proteins can be expressed in various host cells as directly or fusion (chimeric). As a result of overproduction of the recombinant proteins, aggregation of insoluble proteins in the host cell can occur by forming a crystal structure called inclusion body. In general fusion proteins are produced for provide affinity tags to make proteins more soluble and production of some toxic proteins via fusion protein expression system like pTolT. Proteins can be modified by using a site-directed mutagenesis. By this way, creation of non-specific disulfide crosslinks can be prevented at fusion protein expression system via the present cysteine replaced by another amino acid such as serine, glycine or etc. To do this, we need; a DNA molecule that contains the gene that encodes for the target protein, required primers for mutation to be designed according to site directed mutagenesis reaction. This study was aimed to be replaced cysteine encoding codon TGT with serine encoding codon AGT. For this sense and reverse primers designed (given below) and used site-directed mutagenesis reaction. Several new copy of the template plasmid DNA has been formed with above mentioned mutagenic primers via polymerase chain reaction (PCR). PCR product consists of both the master template DNA (wild type) and the new DNA sequences containing mutations. Dpn-l endonuclease restriction enzyme which is specific for methylated DNA and cuts them to the elimination of the master template DNA. E. coli cells obtained after transformation were incubated LB medium with antibiotic. After purification of plasmid DNA from E. coli, the presence of the mutation was determined by DNA sequence analysis. Developed this new plasmid is called PtolT-δ.

Keywords: site directed mutagenesis, Escherichia coli, pTolT, protein expression

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Authors: Ramesh Chandra Majhi

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Saturation flow is a very important input variable for the design of signalized intersections. Saturation flow measurement is well established for homogeneous traffic. However, saturation flow measurement and modeling is a challenging task in heterogeneous characterized by multiple vehicle types and non-lane based movement. Present study focuses on proposing a field procedure for Saturation flow measurement and the effect of typical mixed traffic behavior at the signal as far as non-lane based traffic movement is concerned. Data collected during peak and off-peak hour from five intersections with varying approach width is used for validating the saturation flow model. The insights from the study can be used for modeling saturation flow and delay at signalized intersection in heterogeneous traffic conditions.

Keywords: optimization, passenger car unit, saturation flow, signalized intersection

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Authors: Nan Tang, Bin Wu, Cunfu He

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The trapezoid rods are widely used in civil engineering as load –carrying members. Ultrasonic guided wave is one of the most popular techniques in analyzing the propagation of elastic guided wave. The goal of this paper is to investigate the propagation of elastic waves in the isotropic bar with trapezoid cross-section. Dispersion curves that describe the relationship between the frequency and velocity provide the fundamental information to describe the propagation of elastic waves through a structure. Based on the SAFE (semi-analytical finite element) a linear algebraic system of equations is obtained. By using numerical methods, dispersion curves solved for the rods with the trapezoid cross-section. These fundamental information plays an important role in applying ultrasonic guided waves to NTD for structures with trapezoid cross section.

Keywords: guided wave, dispersion, finite element method, trapezoid rod

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Authors: L. Giraudet, O. Simonetti, G. de Tournadre, N. Dumelié, B. Clarenc, F. Reisdorffer

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In this paper we intend to give a comprehensive view of the saturation misbehavior of thin film transistors (TFTs) based on disordered semiconductors, such as most organic TFTs, and its link to the field activation of the mobility. Experimental evidence of the field activation of the mobility is given for disordered semiconductor based TFTs, when reducing the gate length. Saturation misbehavior is observed simultaneously. Advanced transport models have been implemented in a quasi-2D numerical TFT simulation software. From the numerical simulations it is clearly established that field activation of the mobility alone cannot explain the saturation misbehavior. Evidence is given that high longitudinal field gradient at the drain end of the channel is responsible for an excess charge accumulation, preventing saturation. The two combined effects allow reproducing the experimental output characteristics of short channel TFTs, with S-shaped characteristics and saturation failure.

Keywords: mobility field activation, numerical simulation, OTFT, saturation failure

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Authors: Myoung Ah Kim, Dong Ho Sin, Chul Gyu Song

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Blood oxygen saturation system is a well-established, noninvasive photoplethysmographic method to monitor vital signs. Conventional blood oxygen saturation measurements for the two LED light source is the ambiguity of the oxygen saturation measurement principle and the measurement results greatly influenced and heat and motion artifact. A high accuracy in order to solve these problems blood oxygen saturation measuring method has been proposed using a broadband light source that can be easily understood by the algorithm. The measurement of blood oxygen saturation based on broad-band light source has advantage of simple testing facility and easy understanding. Broadband light source based on blood oxygen saturation measuring program proposed in this paper is a combination of LabVIEW and MATLAB. Using the wavelength range of 450 nm-750 nm using a floating light absorption of oxyhemoglobin and deoxyhemoglobin to measure the blood oxygen saturation. Hand movement is to fix the probe to the motor stage in order to prevent oxygen saturation measurement that affect the sample and probe kept constant interval. Experimental results show that the proposed method noticeably increases the accuracy and saves time compared with the conventional methods.

Keywords: oxygen saturation, broad-band light source, CCD, light reflectance theory

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Authors: Noreddin Mousa

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The main objective of this study is to estimate which type of clay minerals that more effect on saturation exponent using Global Hydraulic Elements (GHEs) approach to estimating the distribution of saturation exponent factor. Two wells and seven core samples have been selected from various (GHEs) for detailed study. There are many factors affecting saturation exponent such as wettability, grain pattern pressure of certain authigenic clays, which may promote oil wet characteristics of history of fluid displacement. The saturation exponent is related to the texture and affected by wettability and clay minerals. Capillary pressure (mercury injection) has been used to confirm GHEs which are selected to define rock types; the porous plate method is used to derive the saturation exponent in the laboratory. The petrography is very important in order to study the mineralogy and texture. In this study the results showing excellent relation between saturation exponent and the type of clay minerals which was observed that the Global Hydraulic Elements GHE-2 and GHE-5 which are containing Chlorite is more affect on saturation exponent comparing with the other GHE’s.

Keywords: GHEs, wettability, global hydraulic elements, petrography

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Authors: Arpita Saha, Apoorv Jain, Satish Chandra, Indrajit Ghosh

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Level of service at a signal controlled intersection is directly measured from the delay. Similarly, saturation flow rate is a fundamental parameter to measure the intersection capacity. The present study calculates vehicle arrival rate, departure rate, and queue length for every five seconds interval in each cycle. Based on the queue lengths, the total delay of the cycle has been calculated using Simpson’s 1/3rd rule. Saturation flow has been estimated in terms of veh/hr of green/lane for every five seconds interval of the green period until at least three vehicles are left to cross the stop line. Vehicle composition shows an immense effect on total delay and saturation flow rate. The increase in two-wheeler proportion increases the saturation flow rate and reduces the total delay per vehicle significantly. Additionally, an increase in the heavy vehicle proportion reduces the saturation flow rate and increases the total delay for each vehicle.

Keywords: delay, saturation flow, signalised intersection, vehicle composition

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Authors: Fatima Mehmood, Khalid Farooq, Rabeea Bakhtawer

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For geotechnical engineers, one of the most important properties of soil to consider in various stability analyses is its shear strength which is governed by a number of factors. The objective of this research is to ascertain the effect of compaction and degree of saturation on the shear strength of fine-grained soil. For this purpose, three different dry densities such as in-situ, maximum standard proctor, and maximum modified proctor, were determined for the sandy clay soil. The soil samples were then prepared to keep dry density constant and varying degrees of saturation. These samples were tested for (UU) unconsolidated undrained shear strength in triaxial compression tests. The decrease in shear strength was observed with the decrease in density and increase in the saturation. The values of the angle of internal friction followed the same trend. However, the change in cohesion with the increase in saturation showed a different behavior, analogous to the compaction curve.

Keywords: compaction, degree of saturation, dry density, geotechnical investigation, laboratory testing, shear strength

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Authors: Narin Salehiyan

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The three iodothyronine selenodeiodinases catalyze the start and end of thyroid hormone impacts in vertebrates. Auxiliary examinations of these proteins have been prevented by their indispensably film nature and the wasteful eukaryotic-specific pathway for selenoprotein blend. Hydrophobic cluster examination utilized in combination with Position-specific Iterated Impact uncovers that their extramembrane parcel has a place to the thioredoxin-fold superfamily for which test structure data exists. Besides, a expansive deiodinase locale imbedded within the thioredoxin overlay offers solid similitudes with the dynamic location of iduronidase, a part of the clan GH-A-fold of glycoside hydrolases. This show can clarify a number of comes about from past mutagenesis examinations and grants unused irrefutable experiences into the auxiliary and utilitarian properties of these proteins.

Keywords: glycoside, hydrolase, GH-A-like structure, catalyze

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Authors: G. M. Hamada, A. A. Al-Gathe, A. M. Al-Khudafi

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Determination of water saturation in sandstone is a vital question to determine the initial oil or gas in place in reservoir rocks. Water saturation determination using electrical measurements is mainly on Archie’s formula. Consequently accuracy of Archie’s formula parameters affects water saturation values rigorously. Determination of Archie’s parameters a, m, and n is proceeded by three conventional techniques, Core Archie-Parameter Estimation (CAPE) and 3-D. This work introduces the hybrid system of parallel self-organizing neural network (PSONN) targeting accepted values of Archie’s parameters and, consequently, reliable water saturation values. This work focuses on Archie’s parameters determination techniques; conventional technique, CAPE technique, and 3-D technique, and then the calculation of water saturation using current. Using the same data, a hybrid parallel self-organizing neural network (PSONN) algorithm is used to estimate Archie’s parameters and predict water saturation. Results have shown that estimated Arche’s parameters m, a, and n are highly accepted with statistical analysis, indicating that the PSONN model has a lower statistical error and higher correlation coefficient. This study was conducted using a high number of measurement points for 144 core plugs from a sandstone reservoir. PSONN algorithm can provide reliable water saturation values, and it can supplement or even replace the conventional techniques to determine Archie’s parameters and thereby calculate water saturation profiles.

Keywords: water saturation, Archie’s parameters, artificial intelligence, PSONN, sandstone reservoir

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Authors: P. N. Salini, B. Anish Kini, R. Ashalatha

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At signalized intersections with heterogeneous traffic, the percentage share of different vehicle categories have a bearing on the inter-vehicle space utilization, which eventually impacts the saturation flow. This paper analyzed the impact of the percentage share of various vehicle categories in the traffic stream on the saturation flow at signalized intersections by video graphing major intersections with varying geometry in Kerala, India. It was found that as the percentage share of two-wheelers increases, the saturation flow at signalized intersections increases and vice-versa for the percentage share of cars. The effect of bus blockage and parking maneuvers on the saturation flow were also studied. As the distance of bus blockage increases from the stop line, the effect on the saturation flow decreases, while with more buses stopping at the same bus stop, the saturation flow reduces further. The study revealed that with higher kerbside parking maneuvers on the upstream, the saturation flow reduces, and with an increase in the distance of the parking maneuver from the stop line, the effect on the saturation flow decreases. The adjustment factors for bus blockage due to bus stops within 75m downstream and parking maneuvers within 75m upstream of the intersection have been established for mixed traffic conditions. These adjustment factors could empower the urban planners, enforcement personnel and decision-makers to estimate the reduction in the capacity of signalized intersections for suggesting improvements in the form of parking restrictions/ bus stop relocation for existing intersections or make design changes for planned intersections.

Keywords: signalized intersection, saturation flow, adjustment factors, capacity

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Authors: D. K. Soni

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A study of engineering properties of stones, i.e. compressive strength, tensile strength, modulus of elasticity, density, hardness were carried out to explore the possibility of optimum utilization of stone. The laboratory test results on equally dimensioned discs of the stone show a considerable variation in computed split tensile strength with varied rates of deformation. Hence, the effect of strain rate on the tensile strength of a sand stone and lime stone under wet and dry conditions has been studied experimentally using the split tensile strength test technique. It has been observed that the tensile strength of these stone is very much dependent on the rate of deformation particularly in a dry state. On saturation the value of split tensile strength reduced considerably depending upon the structure of rock and amount of water absorption.

Keywords: sedimentary rocks, split tensile test, deformation rate, saturation rate, sand stone, lime stone

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Authors: G. Ultanbekova, Zh. Suleimenova, Zh. Rakhmetova, G. Mombekova, S. Mantieva

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Plant Growth Promoting Rhizobacteria (PGPR) are a group of free-living bacteria that colonize the rhizosphere, enhance plant growth of many cereals and other important agricultural crops and protect plants from disease and abiotic stresses through a wide variety of mechanisms. The use of PGPR has been proven to be an environmentally sound way of increasing crop yields by facilitating plant growth. In the present study, strain improvement of PGPR isolates were carried out by chemical mutagenesis for the improvement of growth and yield of lima bean. Induced mutagenesis is widely used for the selection of microorganisms producing biologically active substances and further improving their activities. Strain improvement is usually done by classical mutagenesis which involves exposing the microbes to chemical or physical mutagens. The strains of Pseudomonas putida 4/1, Azotobacter chroococcum Р-29 and Bacillus subtilis were subjected to mutation process for strain improvement by treatment with a chemical agent (sodium nitrite) to cause mutation and were observed for its consequent action on the seeds germination and plant growth of lima bean (Phaseolus lunatus). Bacterial mutant strains of Pseudomonas putida M-1, Azotobacter chroococcum M-1 and Bacillus subtilis M-1, treated with sodium nitrite in the concentration of 5 mg/ml for 120 min, were found effective to enhance the germination of lima bean seeds compared to parent strains. Moreover, treatment of the lima bean seeds with a mutant strain of Bacillus subtilis M-1 had a significant stimulation effect on plant growth. The length of the stems and roots of lima bean treated with Bacillus subtilis M-1 increased significantly in comparison with parent strain in 1.6 and 1.3 times, respectively.

Keywords: chemical mutagenesis, germination, kidney bean, plant growth promoting rhizobacteria (PGPR)

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Authors: Evgeny Pokushalov, Claire Garcia, Andrey Ponomarenko, John Smith, Michael Johnson, Inessa Pak, Evgenya Shrainer, Dmitry Kudlay, Leila Kasimova, Richard Miller

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This study evaluated the efficacy of an AI-guided dietary supplement regimen compared to a standard physician-guided regimen in managing Type 2 diabetes (T2D). A total of 160 patients were randomly assigned to either the AI-guided group (n=80) or the physician-guided group (n=80) and followed over 90 days. The AI-guided group received 5.3 ± 1.2 supplements per patient, while the physician-guided group received 2.7 ± 0.6 supplements per patient. The AI system personalized supplement types and dosages based on individual genetic and metabolic profiles. The AI-guided group showed a significant reduction in HbA1c levels from 7.5 ± 0.8% to 7.1 ± 0.7%, compared to a reduction from 7.6 ± 0.9% to 7.4 ± 0.8% in the physician-guided group (mean difference: -0.3%, 95% CI: -0.5% to -0.1%; p < 0.01). Secondary outcomes, including fasting plasma glucose, HOMA-IR, and insulin levels, also improved more in the AI-guided group. Subgroup analyses revealed that the AI-guided regimen was particularly effective in patients with specific genetic polymorphisms and elevated metabolic markers. Safety profiles were comparable between both groups, with no serious adverse events reported. In conclusion, the AI-guided dietary supplement regimen significantly improved glycemic control and metabolic health in T2D patients compared to the standard physician-guided approach, demonstrating the potential of personalized AI-driven interventions in diabetes management.

Keywords: Type 2 diabetes, AI-guided supplementation, personalized medicine, glycemic control, metabolic health, genetic polymorphisms, dietary supplements, HbA1c, fasting plasma glucose, HOMA-IR, personalized nutrition

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Authors: A. J. Nazari, S. Honma

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This paper evaluates oil displacement by water in Hauterivian sandstone reservoir of Kashkari oil field in North of Afghanistan. The core samples of this oil field were taken out from well No-21^st, and the relative permeability and fractional flow are analyzed. Steady state flow laboratory experiments are performed to empirically obtain the fractional flow curves and relative permeability in different water saturation ratio. The relative permeability represents the simultaneous flow behavior in the reservoir. The fractional flow approach describes the individual phases as fractional of the total flow. The fractional flow curve interprets oil displacement by water, and from the tangent of fractional flow curve can find out the average saturation behind the water front flow saturation. Therefore, relative permeability and fractional flow curves are suitable for describing the displacement of oil by water in a petroleum reservoir. The effects of irreducible water saturation, residual oil saturation on the displaceable amount of oil are investigated through Buckley-Leveret analysis.

Keywords: fractional flow, oil displacement, relative permeability, simultaneously flow

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Authors: Abdelghafour Galadi

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In this paper, accurate power MOSFET models including quasi-saturation effect are presented. These models have no internal node voltages determined by the circuit simulator and use one JFET or one depletion mode MOSFET transistors controlled by an “effective” gate voltage taking into account the quasi-saturation effect. The proposed models achieve accurate simulation results with an average error percentage less than 9%, which is an improvement of 21 percentage points compared to the commonly used standard power MOSFET model. In addition, the models can be integrated in any available commercial circuit simulators by using their analytical equations. A description of the models will be provided along with the parameter extraction procedure.

Keywords: power MOSFET, drift layer, quasi-saturation effect, SPICE model

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Authors: E. Ateia, L. M. Salah, A. H. El-Bassuony

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Physical properties of nanocrystalline Ni1-xZnxCryFe2-yO4, (x=0.3, 0.5 and y=0.0, 0.1) with estimated crystallite size of 16.4 nm have been studied. XRD pattern of all prepared systems shows that, the nanosamples without Cr3+ have a cubic spinel structure with the appearance of small peaks designated as a secondary phase. Magnetic constants such as saturation magnetization, (MS) remanent magnetization (Mr) and coercive field (Hc) were obtained and reported. The obtained data shows that, the addition of Cr3+ (0.1mol) decreases the saturation magnetization. This is due to the decrease of magnetic moment of Cr3+ ion (3.0 μB) with respect to Fe3+ ion (5.85 μB). The electrical properties of the investigated samples were also investigated.

Keywords: electrical conductivity, ferrites, grain size, sintering

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Authors: Tabassum Husain, Shen Peng Li, Zhaolin Chen

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This paper evaluates the usability of 3D Guided Image Filtering to enhance the quality of short-time binned dynamic PET images by using MRI images. Guided image filtering is an edge-preserving filter proposed to enhance 2D images. The 3D filter is applied on 1 and 5-minute binned images. The results are compared with 15-minute binned images and the Gaussian filtering. The guided image filter enhances the quality of dynamic PET images while also preserving important information of the voxels.

Keywords: dynamic PET images, guided image filter, image enhancement, information preservation filtering

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Authors: Mohamed Arbi Khlifi, Badr M. Alshammari

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This paper discusses the general methods to saturation in the steady-state, two axis (d & q) frame models of synchronous machines. In particular, the important role of the magnetic coupling between the d-q axes (cross-magnetizing phenomenon), is demonstrated. For that purpose, distinct methods of saturation modeling of dumper synchronous machine with cross-saturation are identified, and detailed models synthesis in d-q axes. A number of models are given in the final developed form. The procedure and the novel models are verified by a critical application to prove the validity of the method and the equivalence between all developed models is reported. Advantages of some of the models over the existing ones and their applicability are discussed.

Keywords: cross-magnetizing, models synthesis, synchronous machine, saturated modeling, state-space vectors

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Authors: Caje F. Pinto, Jivan S. Parab, Gourish M. Naik

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This paper is about the development of non-invasive heart rate and oxygen saturation in human blood using Altera NIOS II soft-core processor system. In today's world, monitoring oxygen saturation and heart rate is very important in hospitals to keep track of low oxygen levels in blood. We have designed an Embedded System On Peripheral Chip (SOPC) reconfigurable system by interfacing two LED’s of different wavelengths (660 nm/940 nm) with a single photo-detector to measure the absorptions of hemoglobin species at different wavelengths. The implementation of the interface with Finger Probe and Liquid Crystal Display (LCD) was carried out using NIOS II soft-core system running on Altera NANO DE0 board having target as Cyclone IVE. This designed system is used to monitor oxygen saturation in blood and heart rate for different test subjects. The designed NIOS II processor based non-invasive heart rate and oxygen saturation was verified with another Operon Pulse oximeter for 50 measurements on 10 different subjects. It was found that the readings taken were very close to the Operon Pulse oximeter.

Keywords: heart rate, NIOS II, oxygen saturation, photoplethysmography, soft-core, SOPC

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Authors: Sakura Yoshii, Masakazu Abe, Akihiro Iijima

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Nitrogen saturation has become one of the serious issues in the field of forest environment. The watershed protection forests located in the downwind hinterland of Tokyo Metropolitan Area are believed to be facing nitrogen saturation. In this study, we carefully focus on the balance of nitrogen between load and runoff. Annual nitrogen load via atmospheric deposition was estimated to 461.1 t-N/year in the upper reaches of the Kanna River. Annual nitrogen runoff to the forested headwater stream of the Kanna River was determined to 184.9 t-N/year, corresponding to 40.1% of the total nitrogen load. Clear seasonal change in NO3-N concentration was still observed. Therefore, watershed protection forest of the Kanna River is most likely to be in Stage-1 on the status of nitrogen saturation.

Keywords: atmospheric deposition, nitrogen accumulation, denitrification, forest ecosystems

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Authors: Yea-Mei Leou, Shiu-Hsung Huang, T. C. Shen, Chin-Ya Fang

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The purposes of this study were to explore how to establish a professional learning community for English teachers at a junior high school, and to explore how teachers and students think about the guided reading program. The participants were three experienced English teachers and their ESL seventh-grade students from three classes in a junior high school. Leveled picture books and worksheets were used in the program. Questionnaires and interviews were used for gathering information. The findings were as follows: First, most students enjoyed this guided reading program. Second, the teachers thought the guided reading program was helpful to students’ learning and the discussions in the professional learning community refreshed their ideas, but the preparation for the teaching was time-consuming. Suggestions based on the findings were provided.

Keywords: ESL students, guided reading, leveled books, professional learning community

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Authors: Hassan Sbiga

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

Keywords: part of thesis, cementation, wettability, resistivity

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Authors: Wong Ka Fai

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Introduction: Many students are worried before an examination; that is a common picture worldwide. Health problems from stress before examination were insomnia, tiredness, isolation, stomach upset, and anxiety. Nursing students experienced high stress from the examination. Guided imagery is a healing process of applying imagination to help the body heal, survive, or live well. It can bring about significant physiological and biochemical changes, which can trigger the recovery process. A study of nursing students improving their anxiety before examination with guided imagery was proposed. Aim: The aim of this study was to explore the outcome of guided imagery on nursing students’ anxiety before examination in Hong Kong. Method: The qualitative study method was used. 16 first-year students studying nursing programme were invited to practice guided imagery to improve their anxiety before the examination period. One week before the examination, the semi-structured interviews with these students were carried out by the researcher. Result: From the content analysis of interview data, these nursing students showed considerable similarities in their anxiety perception. Nursing students’ perceived improved anxiety was evidenced by a reduction of stressful feelings, improved physical health, satisfaction with daily activities, and enhanced skills for solving problems and upcoming situations. Conclusion: This study indicated that guided imagery can be used as an alternative measure to improve students’ anxiety and psychological problems.

Keywords: nursing students, perception, anxiety, guided imagery

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Authors: Iman Farasat, Howard M. Salis

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The CRISPR/Cas9 system has revolutionized genome engineering by enabling site-directed and high-throughput genome editing, genome insertion, and gene knockdowns in several species, including bacteria, yeast, flies, worms, and human cell lines. This technology has the potential to enable human gene therapy to treat genetic diseases and cancer at the molecular level; however, the current CRISPR/Cas9 system suffers from seemingly sporadic off-target genome mutagenesis that prevents its use in gene therapy. A comprehensive mechanistic model that explains how the CRISPR/Cas9 functions would enable the rational design of the guide-RNAs responsible for target site selection while minimizing unexpected genome mutagenesis. Here, we present the first quantitative model of the CRISPR/Cas9 genome mutagenesis system that predicts how guide-RNA sequences (crRNAs) control target site selection and cleavage activity. We used statistical thermodynamics and law of mass action to develop a five-step biophysical model of cas9 cleavage, and examined it in vivo and in vitro. To predict a crRNA's binding specificities and cleavage rates, we then compiled a nearest neighbor (NN) energy model that accounts for all possible base pairings and mismatches between the crRNA and the possible genomic DNA sites. These calculations correctly predicted crRNA specificity across 5518 sites. Our analysis reveals that cas9 activity and specificity are anti-correlated, and, the trade-off between them is the determining factor in performing an RNA-mediated cleavage with minimal off-targets. To find an optimal solution, we first created a scheme of safe-design criteria for Cas9 target selection by systematic analysis of available high throughput measurements. We then used our biophysical model to determine the optimal Cas9 expression levels and timing that maximizes on-target cleavage and minimizes off-target activity. We successfully applied this approach in bacterial and mammalian cell lines to reduce off-target activity to near background mutagenesis level while maintaining high on-target cleavage rate.

Keywords: biophysical model, CRISPR, Cas9, genome editing

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Authors: hassan gheisari

Abstract:

Ferro silicate calcium nano particles are prepared through the sol-gel method using polyvinyl alcohol (PVA) as a chelating agent. The powder, as prepared, is annealed at three different temperatures (900 ºC, 1000 ºC, and 1100 ºC) for 3 h. The XRD patterns of the samples indicate broad peaks, and the full width at half maximum decreased with increasing annealing temperature. FTIR spectra of the samples confirm the presence of metal - oxygen complexes within the structure. The average particle size obtained from PSA curve demonstrates ultrafine particles. SEM micrographs indicate the particles synthesized have spherical morphology. The saturation magnetization (Ms) and remnant magnetization (Mr) of the samples show dependence on particle size and crystallinity of the samples. The highest saturation magnetization is achieved for the sample annealed at 1100 ºC having maximum average particle size. The high saturation magnetization of the samples suggests the present method is suitable for obtaining nano particles magnetic ferro bioceramic, which is desirable for practical applications such as hyperthermia bone cancer therapy.

Keywords: hyperthermia, bone cancer, bio ceramic; magnetic materials; sol– gel, silicate calcium

Procedia PDF Downloads 74

Authors: Hassan Gheisari

Abstract:

Ferro silicate calcium nano particles are prepared through the sol-gel method using polyvinyl alcohol (PVA) as a chelating agent. The powder as prepared is annealed at three different temperatures (900 ºC, 1000 ºC and 1100 ºC) for 3 h. The XRD patterns of the samples indicate broad peaks and the full width at half maximum decreased with increasing annealing temperature. FTIR spectra of the samples confirm the presence of metal - oxygen complexes within the structure. The average particle size obtained from PSA curve demonstrates ultrafine particles. SEM micrographs indicate the particles synthesized have spherical morphology. The saturation magnetization (Ms) and remnant magnetization (Mr) of the samples show dependence on particle size and crystallinity of the samples. The highest saturation magnetization is achieved for the sample annealed at 1100 ºC having maximum average particle size. The high saturation magnetization of the samples suggests the present method is suitable for obtaining nano particles magnetic ferro bioceramic which is desirable for practical applications such as hyperthermia bone cancer therapy.

Keywords: hyperthermia, bone cancer, bio ceramic, magnetic materials, sol– gel, silicate calcium

Procedia PDF Downloads 309