Search results for: normalized Laplacian eigenvalue

Authors: Abobaker Mohammed Qasem Farhan, Shangming Yang, Mohammed Al-Nehari

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Pneumonia is a kind of lung disease that creates congestion in the chest. Such pneumonic conditions lead to loss of life due to the severity of high congestion. Pneumonic lung disease is caused by viral pneumonia, bacterial pneumonia, or COVID-19 induced pneumonia. The early prediction and classification of such lung diseases help reduce the mortality rate. We propose the automatic Computer-Aided Diagnosis (CAD) system in this paper using the deep learning approach. The proposed CAD system takes input from raw computerized tomography (CT) scans of the patient's chest and automatically predicts disease classification. We designed the Hybrid Deep Learning Algorithm (HDLA) to improve accuracy and reduce processing requirements. The raw CT scans are pre-processed first to enhance their quality for further analysis. We then applied a hybrid model that consists of automatic feature extraction and classification. We propose the robust 2D Convolutional Neural Network (CNN) model to extract the automatic features from the pre-processed CT image. This CNN model assures feature learning with extremely effective 1D feature extraction for each input CT image. The outcome of the 2D CNN model is then normalized using the Min-Max technique. The second step of the proposed hybrid model is related to training and classification using different classifiers. The simulation outcomes using the publicly available dataset prove the robustness and efficiency of the proposed model compared to state-of-art algorithms.

Keywords: CT scans, COVID-19, deep learning, image processing, pneumonia, lung disease.

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Authors: Xi Gu, Guan Heng Yeoh, Victoria Timchenko

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In the current work, a three-dimensional geometry of a 75% stenosed blood vessel is analyzed. Large eddy simulation (LES) with the help of a dynamic subgrid scale Smagorinsky model is applied to model the turbulent pulsatile flow. The geometry, the transmural pressure and the properties of the blood and the elastic boundary were based on clinical measurement data. For the flexible wall model, a thin solid region is constructed around the 75% stenosed blood vessel. The deformation of this solid region was modelled as a deforming boundary to reduce the computational cost of the solid model. Fluid-structure interaction is realized via a twoway coupling between the blood flow modelled via LES and the deforming vessel. The information of the flow pressure and the wall motion was exchanged continually during the cycle by an arbitrary Lagrangian-Eulerian method. The boundary condition of current time step depended on previous solutions. The fluctuation of the velocity in the post-stenotic region was analyzed in the study. The axial velocity at normalized position Z=0.5 shows a negative value near the vessel wall. The displacement of the elastic boundary was concerned in this study. In particular, the wall displacement at the systole and the diastole were compared. The negative displacement at the stenosis indicates a collapse at the maximum velocity and the deceleration phase.

Keywords: Large Eddy Simulation, Fluid Structural Interaction, Constricted Artery, Computational Fluid Dynamics.

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Authors: H. W. Xiao, F. H. Lee

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Cement stabilization has been widely used for improving the strength and stiffness of soft clayey soils. Cement treated soil specimens used to investigate the stress-strain behaviour in the laboratory study are usually cured for 7 days. This paper examines the effects of curing time on the strength and stress strain behaviour of cement treated marine clay under triaxial loading condition. Laboratory-prepared cement treated Singapore marine clay with different mix proportion S-C-W (soil solid-cement solid-water) and curing time (7 days to 180 days) was investigated through conducting unconfined compressive strength test and triaxial test. The results show that the curing time has a significant effect on the unconfined compressive strength u q , isotropic compression behaviour and stress strain behaviour. Although the primary yield loci of the cement treated soil specimens with the same mix proportion expand with curing time, they are very narrowly banded and have nearly the same shape after being normalized by isotropic compression primary stress ' py p . The isotropic compression primary yield stress ' py p was shown to be linearly related to unconfined compressive strength u q for specimens with different curing time and mix proportion. The effect of curing time on the hardening behaviour will diminish with consolidation stress higher than isotropic compression primary yield stress but its damping rate is dependent on the cement content.

Keywords: Cement treated soil, curing time effect, hardening behaviour, isotropic compression primary yield stress, unconfined compressive strength.

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, Slovakia, sports performance.

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Authors: Jagadish H. Pujar, Pallavi S. Gurjal, Shambhavi D. S, Kiran S. Kunnur

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Medical image segmentation based on image smoothing followed by edge detection assumes a great degree of importance in the field of Image Processing. In this regard, this paper proposes a novel algorithm for medical image segmentation based on vigorous smoothening by identifying the type of noise and edge diction ideology which seems to be a boom in medical image diagnosis. The main objective of this algorithm is to consider a particular medical image as input and make the preprocessing to remove the noise content by employing suitable filter after identifying the type of noise and finally carrying out edge detection for image segmentation. The algorithm consists of three parts. First, identifying the type of noise present in the medical image as additive, multiplicative or impulsive by analysis of local histograms and denoising it by employing Median, Gaussian or Frost filter. Second, edge detection of the filtered medical image is carried out using Canny edge detection technique. And third part is about the segmentation of edge detected medical image by the method of Normalized Cut Eigen Vectors. The method is validated through experiments on real images. The proposed algorithm has been simulated on MATLAB platform. The results obtained by the simulation shows that the proposed algorithm is very effective which can deal with low quality or marginal vague images which has high spatial redundancy, low contrast and biggish noise, and has a potential of certain practical use of medical image diagnosis.

Keywords: Image Segmentation, Image smoothing, Edge Detection, Impulsive noise, Gaussian noise, Median filter, Canny edge, Eigen values, Eigen vector.

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Authors: Meenal Surawar, Rajashree Kotharkar

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Urban Heat Island (UHI) is found more pronounced as a prominent urban environmental concern in developing cities. To study the UHI effect in the Indian context, the Nagpur urban area has been explored in this paper using Landsat 7 ETM+ satellite images through Remote Sensing and GIS techniques. This paper intends to study the effect of LU/LC pattern on daytime Land Surface Temperature (LST) variation, contributing UHI formation within the Nagpur Urban area. Supervised LU/LC area classification was carried to study urban Change detection using ENVI 5. Change detection has been studied by carrying Normalized Difference Vegetation Index (NDVI) to understand the proportion of vegetative cover with respect to built-up ratio. Detection of spectral radiance from the thermal band of satellite images was processed to calibrate LST. Specific representative areas on the basis of urban built-up and vegetation classification were selected for observation of point LST. The entire Nagpur urban area shows that, as building density increases with decrease in vegetation cover, LST increases, thereby causing the UHI effect. UHI intensity has gradually increased by 0.7°C from 2000 to 2006; however, a drastic increase has been observed with difference of 1.8°C during the period 2006 to 2013. Within the Nagpur urban area, the UHI effect was formed due to increase in building density and decrease in vegetative cover.

Keywords: Land use, land cover, land surface temperature, remote sensing, urban heat island.

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Authors: Muhammad Imran, Iqra Basit, Mobushir Riaz Khan, Sajid Rasheed Ahmad

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The present study investigates the space-time impact of climate change on the rice crop calendar in tropical Gujranwala, Pakistan. The climate change impact was quantified through the climatic variables, whereas the existing calendar of the rice crop was compared with the phonological stages of the crop, depicted through the time series of the Normalized Difference Vegetation Index (NDVI) derived from Landsat data for the decade 2005-2015. Local maxima were applied on the time series of NDVI to compute the rice phonological stages. Panel models with fixed and cross-section fixed effects were used to establish the relation between the climatic parameters and the time-series of NDVI across villages and across rice growing periods. Results show that the climatic parameters have significant impact on the rice crop calendar. Moreover, the fixed effect model is a significant improvement over cross-sectional fixed effect models (R-squared equal to 0.673 vs. 0.0338). We conclude that high inter-annual variability of climatic variables cause high variability of NDVI, and thus, a shift in the rice crop calendar. Moreover, inter-annual (temporal) variability of the rice crop calendar is high compared to the inter-village (spatial) variability. We suggest the local rice farmers to adapt this change in the rice crop calendar.

Keywords: Landsat NDVI, panel models, temperature, rainfall.

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Authors: Wehash, F. E., Ismail I. Abo-Ghanema, Rasha Mohamed Saleh

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This study was conducted to evaluate the anti-diabetic properties of ethanolic extract of two plants commonly used in folk medicine, Mormodica charantia (bitter melon) and Trigonella foenum-graecum (fenugreek). The study was performed on STZinduced diabetic rats (DM type-I). Plant extracts of these two plants were given to STZ diabetic rats at the concentration of 500 mg/kg body weight ,50 mg/kg body weight respectively. Cidophage® (metformin HCl) were administered to another group to support the results at a dose of 500 mg/kg body weight, the ethanolic extracts and Cidophage administered orally once a day for four weeks using a stomach tube and; serum samples were obtained for biochemical analysis. The extracts caused significant decreases in glucose levels compared with diabetic control rats. Insulin secretions were increased after 4 weeks of treatment with Cidophage® compared with the control non-diabetic rats. Levels of AST and ALT liver enzymes were normalized by all treatments. Decreases in liver cholesterol, triglycerides, and LDL in diabetic rats were observed with all treatments. HDL levels were increased by the treatments in the following order: bitter melon, Cidophage®, and fenugreek. Creatinine levels were reduced by all treatments. Serum nitric oxide and malonaldehyde levels were reduced by all extracts. GSH levels were increased by all extracts. Extravasation as measured by the Evans Blue test increased significantly in STZ-induced diabetic animals. This effect was reversed by ethanolic extracts of bitter melon or fenugreek.

Keywords: Cidophage®, Diabetic rats, Mormodica charantia, Trigonella foenum-graecum

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Authors: Souvik Bhattacharyya, Gautam Sanyal

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Recent years have witnessed the rapid development of the Internet and telecommunication techniques. Information security is becoming more and more important. Applications such as covert communication, copyright protection, etc, stimulate the research of information hiding techniques. Traditionally, encryption is used to realize the communication security. However, important information is not protected once decoded. Steganography is the art and science of communicating in a way which hides the existence of the communication. Important information is firstly hidden in a host data, such as digital image, video or audio, etc, and then transmitted secretly to the receiver.In this paper a data hiding model with high security features combining both cryptography using finite state sequential machine and image based steganography technique for communicating information more securely between two locations is proposed. The authors incorporated the idea of secret key for authentication at both ends in order to achieve high level of security. Before the embedding operation the secret information has been encrypted with the help of finite-state sequential machine and segmented in different parts. The cover image is also segmented in different objects through normalized cut.Each part of the encoded secret information has been embedded with the help of a novel image steganographic method (PMM) on different cuts of the cover image to form different stego objects. Finally stego image is formed by combining different stego objects and transmit to the receiver side. At the receiving end different opposite processes should run to get the back the original secret message.

Keywords: Cover Image, Finite state sequential machine, Melaymachine, Pixel Mapping Method (PMM), Stego Image, NCUT.

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Authors: Yanping Liao, Zenan Wu, Ruigang Zhao

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Frequency diverse array (FDA) beamforming is a technology developed in recent years, and its antenna pattern has a unique angle-distance-dependent characteristic. However, the beam is always required to have strong concentration, high resolution and low sidelobe level to form the point-to-point interference in the concentrated set. In order to eliminate the angle-distance coupling of the traditional FDA and to make the beam energy more concentrated, this paper adopts a multi-carrier FDA structure based on proposed power exponential frequency offset to improve the array structure and frequency offset of the traditional FDA. The simulation results show that the beam pattern of the array can form a dot-shape beam with more concentrated energy, and its resolution and sidelobe level performance are improved. However, the covariance matrix of the signal in the traditional adaptive beamforming algorithm is estimated by the finite-time snapshot data. When the number of snapshots is limited, the algorithm has an underestimation problem, which leads to the estimation error of the covariance matrix to cause beam distortion, so that the output pattern cannot form a dot-shape beam. And it also has main lobe deviation and high sidelobe level problems in the case of limited snapshot. Aiming at these problems, an adaptive beamforming technique based on exponential correction for multi-carrier FDA is proposed to improve beamforming robustness. The steps are as follows: first, the beamforming of the multi-carrier FDA is formed under linear constrained minimum variance (LCMV) criteria. Then the eigenvalue decomposition of the covariance matrix is ​​performed to obtain the diagonal matrix composed of the interference subspace, the noise subspace and the corresponding eigenvalues. Finally, the correction index is introduced to exponentially correct the small eigenvalues ​​of the noise subspace, improve the divergence of small eigenvalues ​​in the noise subspace, and improve the performance of beamforming. The theoretical analysis and simulation results show that the proposed algorithm can make the multi-carrier FDA form a dot-shape beam at limited snapshots, reduce the sidelobe level, improve the robustness of beamforming, and have better performance.

Keywords: Multi-carrier frequency diverse array, adaptive beamforming, correction index, limited snapshot, robust.

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Authors: Vishnu Raj, Chockalingam Prathap

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The objective of this study was to explore the impact of variation in the exit annular area on the local flow field features and the flame stability of an annular premixed swirl burner (unconfined) operated with a premixed n-butane air mixture at an equivalence ratio (Φ) = 1, 1 bar, and 300K. A swirl burner with an axial swirl generator having a swirl number of 1.5 was used. Three different burner heads were chosen to have the exit area increased from 100%, 160%, and 220% resulting in inner and outer diameters and cross-sectional areas as (1) 10 mm & 15 mm, 98 mm2 (2) 17.5 mm & 22.5 mm, 157 mm2 and (3) 25 mm & 30 mm, 216 mm2. The bulk velocity and Reynolds number based on the hydraulic diameter and unburned gas properties were kept constant at 12 m/s and 4000. (i) Planar Particle Image Velocimetry (PIV) with TiO2 seeding particles and (ii) CH* chemiluminescence was used to measure the velocity fields and reaction zones of the swirl flames at 5 Hz, respectively. Velocity fields and the jet spreading rates measured at the isothermal and reactive conditions revealed that the presence of a flame significantly altered the flow field in the radial direction due to the gas expansion. Important observations from the flame measurements were: the height and maximum width of the recirculation bubbles normalized by the hydraulic diameter, and the jet spreading angles for the flames for the three exit area cases were: (a) 4.52, 1.95, 34◦, (b) 6.78, 2.37, 26◦, and (c) 8.73, 2.32, 22◦. The lean blowout (LBO) was also measured, and the respective equivalence ratios were: 0.80, 0.92, and 0.82. LBO was relatively narrow for the 157 mm2 case. For this case, PIV measurements showed that Turbulent Kinetic Energy and turbulent intensity were relatively high compared to the other two cases, resulting in higher stretch rates and narrower LBO.

Keywords: Chemiluminescence, jet spreading rate, lean blow out, swirl flow.

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Authors: Saba Gachpaz, Hamid Reza Heidari

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The sharp increase in population growth leads to more pressure on agricultural areas to satisfy the food supply. This necessitates increased resource consumption and underscores the importance of addressing sustainable agriculture development along with other environmental considerations. Land-use management is a crucial factor in obtaining optimum productivity. Machine learning is a widely used technique in the agricultural sector, from yield prediction to customer behavior. This method focuses on learning and provides patterns and correlations from our data set. In this study, nine physical control factors, namely, soil classification, electrical conductivity, normalized difference water index (NDWI), groundwater level, elevation, annual precipitation, pH of water, annual mean temperature, and slope in the alluvial plain in Khuzestan (an agricultural hotspot in Iran) are used to decide the best agricultural land use for both rainfed and irrigated agriculture for 10 different crops. For this purpose, each variable was imported into Arc GIS, and a raster layer was obtained. In the next level, by using training samples, all layers were imported into the python environment. A random forest model was applied, and the weight of each variable was specified. In the final step, results were visualized using a digital elevation model, and the importance of all factors for each one of the crops was obtained. Our results show that despite 62% of the study area being allocated to agricultural purposes, only 42.9% of these areas can be defined as a suitable class for cultivation purposes.

Keywords: Land suitability, machine learning, random forest, sustainable agriculture.

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Authors: Jiahua Zhang, Qing Chang, Fengmei Yao

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Studying on the response of vegetation phenology to climate change at different temporal and spatial scales is important for understanding and predicting future terrestrial ecosystem dynamics and the adaptation of ecosystems to global change. In this study, the Moderate Resolution Imaging Spectroradiometer (MODIS) Normalized Difference Vegetation Index (NDVI) dataset and climate data were used to analyze the dynamics of grassland phenology as well as their correlation with climatic factors in different eco-geographic regions and elevation units across the Tibetan Plateau. The results showed that during 2003–2012, the start of the grassland greening season (SOS) appeared later while the end of the growing season (EOS) appeared earlier following the plateau’s precipitation and heat gradients from southeast to northwest. The multi-year mean value of SOS showed differences between various eco-geographic regions and was significantly impacted by average elevation and regional average precipitation during spring. Regional mean differences for EOS were mainly regulated by mean temperature during autumn. Changes in trends of SOS in the central and eastern eco-geographic regions were coupled to the mean temperature during spring, advancing by about 7d/°C. However, in the two southwestern eco-geographic regions, SOS was delayed significantly due to the impact of spring precipitation. The results also showed that the SOS occurred later with increasing elevation, as expected, with a delay rate of 0.66 d/100m. For 2003–2012, SOS showed an advancing trend in low-elevation areas, but a delayed trend in high-elevation areas, while EOS was delayed in low-elevation areas, but advanced in high-elevation areas. Grassland SOS and EOS changes may be influenced by a variety of other environmental factors in each eco-geographic region.

Keywords: Grassland, phenology, MODIS, eco-geographic regions, elevation, climatic factors, Tibetan Plateau.

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Authors: Mohammad R. Kavian Nezhad, Carlos F. Lange, Brian A. Fleck

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This research presents the validation study of a computational fluid dynamics (CFD) model developed to simulate the scalar dispersion emitted from rooftop sources around the buildings at the University of Alberta North Campus. The ANSYS CFX code was used to perform the numerical simulation of the wind regime and pollutant dispersion by solving the 3D steady Reynolds-averaged Navier-Stokes (RANS) equations on a building-scale high-resolution grid. The validation study was performed in two steps. First, the CFD model performance in 24 cases (eight wind directions and three wind speeds) was evaluated by comparing the predicted flow fields with the available data from the previous measurement campaign designed at the North Campus, using the standard deviation method (SDM), while the estimated results of the numerical model showed maximum average percent errors of approximately 53% and 37% for wind incidents from the North and Northwest, respectively. Good agreement with the measurements was observed for the other six directions, with an average error of less than 30%. In the second step, the reliability of the implemented turbulence model, numerical algorithm, modeling techniques, and the grid generation scheme was further evaluated using the Mock Urban Setting Test (MUST) dispersion dataset. Different statistical measures, including the fractional bias (FB), the mean geometric bias (MG), and the normalized mean square error (NMSE), were used to assess the accuracy of the predicted dispersion field. Our CFD results are in very good agreement with the field measurements.

Keywords: CFD, plume dispersion, complex urban geometry, validation study, wind flow.

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Authors: U. Waqas, M. F. Ahmed, A. Mehmood, M. A. Rashid

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In geophysical exploration surveys, the quality of acquired data holds significant importance before executing the data processing and interpretation phases. In this study, 2D seismic reflection survey data of Fort Abbas area, Cholistan Desert, Pakistan was taken as test case in order to assess its quality on statistical bases by using normalized root mean square error (NRMSE), Cronbach’s alpha test (α) and null hypothesis tests (t-test and F-test). The analysis challenged the quality of the acquired data and highlighted the significant errors in the acquired database. It is proven that the study area is plain, tectonically least affected and rich in oil and gas reserves. However, subsurface 3D modeling and contouring by using acquired database revealed high degrees of structural complexities and intense folding. The NRMSE had highest percentage of residuals between the estimated and predicted cases. The outcomes of hypothesis testing also proved the biasness and erraticness of the acquired database. Low estimated value of alpha (α) in Cronbach’s alpha test confirmed poor reliability of acquired database. A very low quality of acquired database needs excessive static correction or in some cases, reacquisition of data is also suggested which is most of the time not feasible on economic grounds. The outcomes of this study could be used to assess the quality of large databases and to further utilize as a guideline to establish database quality assessment models to make much more informed decisions in hydrocarbon exploration field.

Keywords: Data quality, null hypothesis, seismic lines, seismic reflection survey.

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Authors: S. Sadhu, M. Ramgopal, S. Bhattacharyya

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Natural circulation loops (NCLs) are buoyancy driven flow systems without any moving components. NCLs have vast applications in geothermal, solar and nuclear power industry where reliability and safety are of foremost concern. Due to certain favorable thermophysical properties, especially near supercritical regions, carbon dioxide can be considered as an ideal loop fluid in many applications. In the present work, a high temperature NCL that uses supercritical carbon dioxide as loop fluid is analysed. The effects of relevant design and operating variables on loop performance are studied. The system operating under steady state is modelled taking into account the axial conduction through loop fluid and loop wall, and heat transfer with surroundings. The heat source is considered to be a heater with controlled heat flux and heat sink is modelled as an end heat exchanger with water as the external cold fluid. The governing equations for mass, momentum and energy conservation are normalized and are solved numerically using finite volume method. Results are obtained for a loop pressure of 90 bar with the power input varying from 0.5 kW to 6.0 kW. The numerical results are validated against the experimental results reported in the literature in terms of the modified Grashof number (Gr_m) and Reynolds number (Re). Based on the results, buoyancy and friction dominated regions are identified for a given loop. Parametric analysis has been done to show the effect of loop diameter, loop height, ambient temperature and insulation. The results show that for the high temperature loop, heat loss to surroundings affects the loop performance significantly. Hence this conjugate heat transfer between the loop and surroundings has to be considered in the analysis of high temperature NCLs.

Keywords: Conjugate heat transfer, heat loss, natural circulation loop, supercritical carbon dioxide.

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Authors: Mohamed K. Shahin, Ahmed M. Badawi, Mohamed E. M. Rasmy

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Prior research evidenced that unimodal biometric systems have several tradeoffs like noisy data, intra-class variations, restricted degrees of freedom, non-universality, spoof attacks, and unacceptable error rates. In order for the biometric system to be more secure and to provide high performance accuracy, more than one form of biometrics are required. Hence, the need arise for multimodal biometrics using combinations of different biometric modalities. This paper introduces a multimodal biometric system (MMBS) based on fusion of whole dorsal hand geometry and fingerprints that acquires right and left (Rt/Lt) near-infra-red (NIR) dorsal hand geometry (HG) shape and (Rt/Lt) index and ring fingerprints (FP). Database of 100 volunteers were acquired using the designed prototype. The acquired images were found to have good quality for all features and patterns extraction to all modalities. HG features based on the hand shape anatomical landmarks were extracted. Robust and fast algorithms for FP minutia points feature extraction and matching were used. Feature vectors that belong to similar biometric traits were fused using feature fusion methodologies. Scores obtained from different biometric trait matchers were fused using the Min-Max transformation-based score fusion technique. Final normalized scores were merged using the sum of scores method to obtain a single decision about the personal identity based on multiple independent sources. High individuality of the fused traits and user acceptability of the designed system along with its experimental high performance biometric measures showed that this MMBS can be considered for med-high security levels biometric identification purposes.

Keywords: Unimodal, Multi-Modal, Biometric System, NIR Imaging, Dorsal Hand Geometry, Fingerprint, Whole Hands, Feature Extraction, Feature Fusion, Score Fusion

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Authors: Aditya Arya, Hairin Taha, Ataul Karim Khan, Nayiar Shahid, Hapipah Mohd Ali, Mustafa Ali Mohd

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This study has investigated the antidiabetic and antioxidant potential of Pseudovaria macrophylla bark extract on streptozotocin–nicotinamide induced type 2 diabetic rats. LCMSQTOF and NMR experiments were done to determine the chemical composition in the methanolic bark extract. For in vivo experiments, the STZ (60 mg/kg/b.w, 15 min after 120 mg/kg/1 nicotinamide, i.p.) induced diabetic rats were treated with methanolic extract of Pseuduvaria macrophylla (200 and 400 mg/kg·bw) and glibenclamide (2.5 mg/kg) as positive control respectively. Biochemical parameters were assayed in the blood samples of all groups of rats. The pro-inflammatory cytokines, antioxidant status and plasma transforming growth factor βeta-1 (TGF-β1) were evaluated. The histological study of the pancreas was examined and its expression level of insulin was observed by immunohistochemistry. In addition, the expression of glucose transporters (GLUT 1, 2 and 4) were assessed in pancreas tissue by western blot analysis. The outcomes of the study displayed that the bark methanol extract of Pseuduvaria macrophylla has potentially normalized the elevated blood glucose levels and improved serum insulin and C-peptide levels with significant increase in the antioxidant enzyme, reduced glutathione (GSH) and decrease in the level of lipid peroxidation (LPO). Additionally, the extract has markedly decreased the levels of serum pro-inflammatory cytokines and transforming growth factor beta-1 (TGF-β1). Histopathology analysis demonstrated that Pseuduvaria macrophylla has the potential to protect the pancreas of diabetic rats against peroxidation damage by downregulating oxidative stress and elevated hyperglycaemia. Furthermore, the expression of insulin protein, GLUT-1, GLUT-2 and GLUT-4 in pancreatic cells was enhanced. The findings of this study support the anti-diabetic claims of Pseudovaria macrophylla bark.

Keywords: Diabetes mellitus, Pseuduvaria macrophylla, alkaloids, caffeic acid.

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Authors: Caixia Gao, Chuanrong Li, Lingli Tang, Lingling Ma, Yaokai Liu, Xinhong Wang, Yongsheng Zhou

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Performances analysis of remote sensing sensor is required to pursue a range of scientific research and application objectives. Laboratory analysis of any remote sensing instrument is essential, but not sufficient to establish a valid inflight one. In this study, with the aid of the in situ measurements and corresponding image of three-gray scale permanent artificial target, the in-flight radiometric performances analyses (in-flight radiometric calibration, dynamic range and response linearity, signal-noise-ratio (SNR), radiometric resolution) of self-developed short-wave infrared (SWIR) camera are performed. To acquire the inflight calibration coefficients of the SWIR camera, the at-sensor radiances (L_i) for the artificial targets are firstly simulated with in situ measurements (atmosphere parameter and spectral reflectance of the target) and viewing geometries using MODTRAN model. With these radiances and the corresponding digital numbers (DN) in the image, a straight line with a formulation of L = G × DN + B is fitted by a minimization regression method, and the fitted coefficients, G and B, are inflight calibration coefficients. And then the high point (L_H) and the low point (L_L) of dynamic range can be described as L_H= (G × DN_H + B) and L_L= B, respectively, where DN_H is equal to 2ⁿ − 1 (n is the quantization number of the payload). Meanwhile, the sensor’s response linearity (δ) is described as the correlation coefficient of the regressed line. The results show that the calibration coefficients (G and B) are 0.0083 W·sr⁻¹m⁻²µm⁻¹ and −3.5 W·sr⁻¹m⁻²µm⁻¹; the low point of dynamic range is −3.5 W·sr⁻¹m⁻²µm⁻¹ and the high point is 30.5 W·sr⁻¹m⁻²µm⁻¹; the response linearity is approximately 99%. Furthermore, a SNR normalization method is used to assess the sensor’s SNR, and the normalized SNR is about 59.6 when the mean value of radiance is equal to 11.0 W·sr⁻¹m⁻²µm⁻¹; subsequently, the radiometric resolution is calculated about 0.1845 W•sr^-1m^-2μm^-1. Moreover, in order to validate the result, a comparison of the measured radiance with a radiative-transfer-code-predicted over four portable artificial targets with reflectance of 20%, 30%, 40%, 50% respectively, is performed. It is noted that relative error for the calibration is within 6.6%.

Keywords: Calibration, dynamic range, radiometric resolution, SNR.

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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Authors: Hayder H. Kareem, Shunqi Pan

Abstract:

Groundwater is a vital water resource in many areas in the world, particularly in the Middle-East region where the water resources become scarce and depleting. Sustainable management and planning of the groundwater resources become essential and urgent given the impact of the global climate change. In the recent years, numerical models have been widely used to predict the flow pattern and assess the water resources security, as well as the groundwater quality affected by the contaminants transported. In this study, MODFLOW is used to study the current status of groundwater resources and the risk of water resource security in the region centred at Al-Najaf City, which is located in the mid-west of Iraq and adjacent to the Euphrates River. In this study, a conceptual model is built using the geologic and hydrogeologic collected for the region, together with the Digital Elevation Model (DEM) data obtained from the "Global Land Cover Facility" (GLCF) and "United State Geological Survey" (USGS) for the study area. The computer model is also implemented with the distributions of 69 wells in the area with the steady pro-defined hydraulic head along its boundaries. The model is then applied with the recharge rate (from precipitation) of 7.55 mm/year, given from the analysis of the field data in the study area for the period of 1980-2014. The hydraulic conductivity from the measurements at the locations of wells is interpolated for model use. The model is calibrated with the measured hydraulic heads at the locations of 50 of 69 wells in the domain and results show a good agreement. The standard-error-of-estimate (SEE), root-mean-square errors (RMSE), Normalized RMSE and correlation coefficient are 0.297 m, 2.087 m, 6.899% and 0.971 respectively. Sensitivity analysis is also carried out, and it is found that the model is sensitive to recharge, particularly when the rate is greater than (15mm/year). Hydraulic conductivity is found to be another parameter which can affect the results significantly, therefore it requires high quality field data. The results show that there is a general flow pattern from the west to east of the study area, which agrees well with the observations and the gradient of the ground surface. It is found that with the current operational pumping rates of the wells in the area, a dry area is resulted in Al-Najaf City due to the large quantity of groundwater withdrawn. The computed water balance with the current operational pumping quantity shows that the Euphrates River supplies water into the groundwater of approximately 11759 m³/day, instead of gaining water of 11178 m³/day from the groundwater if no pumping from the wells. It is expected that the results obtained from the study can provide important information for the sustainable and effective planning and management of the regional groundwater resources for Al-Najaf City.

Keywords: Al-Najaf city, conceptual modelling, groundwater, unconfined aquifer, visual MODFLOW.

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