Search results for: target specificity

Authors: Hyeongbok Kim, Lingling Zhao, Xiaohong Su, Junjie Wang

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The Bernoulli filter is a precise Bayesian filter for single target tracking based on the random finite set theory. The standard Bernoulli filter often underestimates the number of targets. This study proposes a Gaussian particle flow (GPF) Bernoulli filter employing particle flow to migrate particles from prior to posterior positions to improve the performance of the standard Bernoulli filter. By employing the particle flow filter, the computational speed of the Bernoulli filters is significantly improved. In addition, the GPF Bernoulli filter provides a more accurate estimation compared with that of the standard Bernoulli filter. Simulation results confirm the improved tracking performance and computational speed in two- and three-dimensional scenarios compared with other algorithms.

Keywords: Bernoulli filter, particle filter, particle flow filter, random finite sets, target tracking

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Authors: Olena Mayboroda, Angel Gonzalez Benito, Jonathan Sabate Del Rio, Marketa Svobodova, Sandra Julich, Herbert Tomaso, Ciara K. O'Sullivan, Ioanis Katakis

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DNA amplification is required for most molecular diagnostic applications but conventional PCR has disadvantages for field testing. Isothermal amplification techniques are being developed to respond to this problem. One of them is the Recombinase Polymerase Amplification (RPA) that operates at isothermal conditions without sacrificing specificity and sensitivity in easy-to-use formats. In this work RPA was used for the optical detection of solid-phase amplification of the potential biowarfare agent Yersinia pestis. Thiolated forward primers were immobilized on the surface of maleimide-activated microtitre plates for the quantitative detection of synthetic and genomic DNA, with elongation occurring only in the presence of the specific template DNA and solution phase reverse primers. Quantitative detection was achieved via the use of biotinylated reverse primers and post-amplification addition of streptavidin-HRP conjugate. The overall time of amplification and detection was less than 1 hour at a constant temperature of 37oC. Single-stranded and double-stranded DNA sequences were detected achieving detection limits of 4.04*10-13 M and 3.14*10-16 M, respectively. The system demonstrated high specificity with negligible responses to non-specific targets.

Keywords: recombinase polymerase amplification, Yersinia pestis, solid-phase detection, ELONA

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Authors: Khue Nguyen Dinh, Loi Nguyen Van, Thanh Nguyen Nhu

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In this paper, we propose an adaptive method to resolve ambiguities and a ghost target removal process to extract targets detected by a ground-based pulse-Doppler radar using medium pulse repetition frequency (PRF) waveforms. The ambiguity resolution method is an adaptive implementation of the coincidence algorithm, which is implemented on a two-dimensional (2D) range-velocity matrix to resolve range and velocity ambiguities simultaneously, with a proposed clustering filter to enhance the anti-error ability of the system. Here we consider the scenario of multiple target environments. The ghost target removal process, which is based on the power after Doppler processing, is proposed to mitigate ghosting detections to enhance the performance of ground-based radars using a short PRF schedule in multiple target environments. Simulation results on a ground-based pulsed Doppler radar model will be presented to show the effectiveness of the proposed approach.

Keywords: ambiguity resolution, coincidence algorithm, medium PRF, ghosting removal

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Authors: Mona Hamdy, Iman Shaheen, Hadeel Seif Eldin, Basma Ali, Omnia Abdeldayem

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Summary: Bone involvement of sickle cell disease (SCD) patients varies from acute clinical manifestations of painful vaso-occlusive crises or osteomyelitis to more chronic affection of bone mineral density (BMD) and debilitating osteonecrosis and osteoporosis. Secreted klotho protein is involved in calcium (Ca) reabsorption in the kidney. This study aimed to measure serum klotho levels in children with SCD to determine the possibility of using it as a marker of low BMD in children with SCD in correlation with a dual-energy radiograph absorptiometry scan. This study included 60 sickle disease patients and 30 age-matched and sex-matched control participants without SCD. A highly statistically significant difference was found between patients with normal BMD and those with low BMD, with serum Ca and klotho levels being lower in the latter group. Klotho serum level correlated positively with both serum Ca and BMD. Serum klotho level showed 94.9% sensitivity and 95.2% specificity in the detection of low BMD. Both serum Ca and klotho serum levels may be useful markers for detection of low BMD related to SCD with high sensitivity and specificity; however, klotho may be a better indicator as it is less affected by the nutritional and endocrinal status of patients or by intake of Ca supplements.

Keywords: sickle cell disease, BMD, osteoporosis, DEXA, klotho

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Authors: Mohammed Alasel, Michael Keusgen

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Gold is a noble metal; in its nano-scale level (e.g. spherical nanoparticles), the conduction electrons are triggered to collectively oscillate with a resonant frequency when certain wavelengths of electromagnetic radiation interact with its surface; this phenomenon is known as surface plasmon resonance (SPR). SPR is responsible for giving the gold nanoparticles its intense red color depending mainly on its size, shape and distance between nanoparticles. A decreased distance between gold nanoparticles results in aggregation of them causing a change in color from red to blue. This aggregation enables gold nanoparticles to serve as a sensitive biosensoric indicator. In the proposed work, gold nanoparticles were modified with two proteins: i) Borrelia antigen, variable lipoprotein surface-exposed protein (VlsE), and ii) protein A. VlsE antigen induces a strong antibody response against Lyme disease and can be detected from early to late phase during the disease in humans infected with Borrelia. In addition, it shows low cross-reaction with the other non-pathogenic Borrelia strains. The high specificity of VlsE antigen to anti-Borrelia antibodies, combined simultaneously with the high specificity of protein A to the Fc region of all IgG human antibodies, was utilized to develop a rapid test for serological point of care diagnosis of borreliosis in human serum. Only in the presence of anti-Borrelia antibodies in the serum probe, an aggregation of gold nanoparticles can be observed, which is visible by a concentration-dependent colour shift from red (low IgG) to blue (high IgG). Experiments showed it is clearly possible to distinguish between positive and negative sera samples using a simple suspension of the two-protein modified gold nanoparticles in a very short time (30 minutes). The proposed work showed the potential of using such modified gold nanoparticles generally for serological diagnosis. Improved specificity and reduced assay time can be archived in applying increased salt concentrations combined with decreased pH values (pH 5).

Keywords: gold nanoparticles, gold aggregation, serological diagnosis, protein A, lyme borreliosis

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Authors: Dawit Gebreegzabher Hagos, Yazezew Kebede Kiro, Mahmud Abdulkader, Henk H. D. F. Schallig, Dawit Wolday

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Rapid and accurate visceral leishmaniasis (VL) diagnosis is needed to initiate prompt treatment to reduce morbidity and mortality. Here, we evaluated the performance of loop-mediated isothermal amplification (LAMP) assay for the diagnosis of VL from blood in an endemic area in Ethiopia. LAMP was positive in 117/122 confirmed VL cases and negative in 149/152 controls, resulting in a sensitivity of 95.9% (95% CI: 90.69–98.66) and a specificity of 98.0% (95% CI: 94.34–99.59), respectively. The sensitivity of the LAMP assay was 95.0% (95% CI: 88.61–98.34) in HIV-negatives and 100% (95% CI: 85.18–100.0) in HIV-positives. Compared with microscopy, LAMP detected 82/87 (94.3%, 95% CI: 87.10–98.11) of the microscopy1 cases and was negative in 11/27 (40.7%, 95% CI: 22.39–61.20) of the microscopy2 cases. Compared with the rK39 serology, LAMP detected 113/120 (94.2%, 95% CI: 88.35–97.62) of the rK391 cases and was negative in 149/154 (96.8%, 95% CI: 92.59–98.94) of the rK392 cases. However, when compared with microscopy only, rK39 detected 83/87 (95.4%, 95% CI: 88.64–98.73) of the microscopy1 cases and negative in only 12/27 (44.4%, 95% CI: 25.48–64.67) of the microscopy– cases. There was an excellent agreement between rK39 and LAMP (Kappa 5 0.91, 95% CI: 0.86–0.96). Furthermore, an algorithm using rK39 followed by LAMP would yield a sensitivity of 99.2% (95%CI: 95.52–99.89) and a specificity of 98.0% (95% CI: 94.34–99.59). The findings demonstrate that the LAMP assay is an accurate and rapid molecular assay for VL diagnosis, including in HIV-1 co-infected patients, in an endemic setting.

Keywords: visceral leishmaniasis, HIV, diagnosis, LAMP, Ethiopia

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Authors: Yu-Jia Jian, Emily Chia-Yu Su, Hui-Ling Hsu, Jian-Jhih Chen

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Coronary artery is the major supplier of myocardial blood flow. When fat and cholesterol are deposit in the coronary arterial wall, narrowing and stenosis of the artery occurs, which may lead to myocardial ischemia and eventually infarction. According to the World Health Organization (WHO), estimated 740 million people have died of coronary heart disease in 2015. According to Statistics from Ministry of Health and Welfare in Taiwan, heart disease (except for hypertensive diseases) ranked the second among the top 10 causes of death from 2013 to 2016, and it still shows a growing trend. According to American Heart Association (AHA), the risk factors for coronary heart disease including: age (> 65 years), sex (men to women with 2:1 ratio), obesity, diabetes, hypertension, hyperlipidemia, smoking, family history, lack of exercise and more. We have collected a dataset of 421 patients from a hospital located in northern Taiwan who received coronary computed tomography (CT) angiography. There were 300 males (71.26%) and 121 females (28.74%), with age ranging from 24 to 92 years, and a mean age of 56.3 years. Prior to coronary CT angiography, basic data of the patients, including age, gender, obesity index (BMI), diastolic blood pressure, systolic blood pressure, diabetes, hypertension, hyperlipidemia, smoking, family history of coronary heart disease and exercise habits, were collected and used as input variables. The output variable of the prediction module is the degree of coronary artery stenosis. The output variable of the prediction module is the narrow constriction of the coronary artery. In this study, the dataset was randomly divided into 80% as training set and 20% as test set. Four machine learning algorithms, including logistic regression, stepwise regression, neural network and decision tree, were incorporated to generate prediction results. We used area under curve (AUC) / accuracy (Acc.) to compare the four models, the best model is neural network, followed by stepwise logistic regression, decision tree, and logistic regression, with 0.68 / 79 %, 0.68 / 74%, 0.65 / 78%, and 0.65 / 74%, respectively. Sensitivity of neural network was 27.3%, specificity was 90.8%, stepwise Logistic regression sensitivity was 18.2%, specificity was 92.3%, decision tree sensitivity was 13.6%, specificity was 100%, logistic regression sensitivity was 27.3%, specificity 89.2%. From the result of this study, we hope to improve the accuracy by improving the module parameters or other methods in the future and we hope to solve the problem of low sensitivity by adjusting the imbalanced proportion of positive and negative data.

Keywords: decision support, computed tomography, coronary artery, machine learning

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Authors: Tong He, Long Chen, Irag Mantegh, Wen-Fang Xie

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This paper proposes an image-based obstacle avoidance and tracking target identification strategy in GPS-degraded or GPS-denied environment for an Unmanned Aerial Vehicle (UAV). The traditional force algorithm for obstacle avoidance could produce local minima area, in which UAV cannot get away obstacle effectively. In order to eliminate it, an artificial potential approach based on harmonic potential is proposed to guide the UAV to avoid the obstacle by using the vision system. And image-based visual servoing scheme (IBVS) has been adopted to implement the proposed obstacle avoidance approach. In IBVS, the pixel accuracy is a key factor to realize the obstacle avoidance. In this paper, the deep reinforcement learning framework has been applied by reducing pixel errors through constant interaction between the environment and the agent. In addition, the combination of OpenTLD and Tensorflow based on neural network is used to identify the type of tracking target. Numerical simulation in Matlab and ROS GAZEBO show the satisfactory result in target identification and obstacle avoidance.

Keywords: image-based visual servoing, obstacle avoidance, tracking target identification, deep reinforcement learning, artificial potential approach, neural network

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Authors: Haythem H. Abdullah, Hesham Elkady

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With the fast increase in radio frequency identification (RFID) applications such as medical recording, library management, etc., the limitation of active tags stems from its need to external batteries as well as passive or active chips. The chipless RFID tag reduces the cost to a large extent but at the expense of utilizing the spectrum. The reduction of the cost of chipless RFID is due to the absence of the chip itself. The identification is done by utilizing the spectrum in such a way that the frequency response of the tags consists of some resonance frequencies that represent the bits. The system capacity is decided by the number of resonators within the pre-specified band. It is important to find a solution to enhance the spectrum utilization when using chipless RFID. Target identification is a process that results in a decision that a specific target is present or not. Several target identification schemes are present, but one of the most successful techniques in radar target identification in the oscillatory region is the extinction pulse technique (E-Pulse). The E-Pulse technique is used to identify targets via its characteristics (natural) modes. By introducing an innovative solution for chipless RFID reader and tag designs, the spectrum utilization goes to the optimum case. In this paper, a novel capacity enhancement scheme based on the E-pulse technique is introduced to improve the performance of the chipless RFID system.

Keywords: chipless RFID, E-pulse, natural modes, resonators

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Authors: Anh Duc Dang, Joachim Horn

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This paper presents a new approach to control robots, which can quickly find their swarm while tracking a moving target through the obstacles of the environment. In this approach, an artificial potential field is generated between each free-robot and the virtual attractive point of the swarm. This artificial potential field will lead free-robots to their swarm. The swarm-finding of these free-robots dose not influence the general motion of their swarm and nor other robots. When one singular robot approaches the swarm then its swarm-search will finish, and it will further participate with its swarm to reach the position of the target. The connections between member-robots with their neighbours are controlled by the artificial attractive/repulsive force field between them to avoid collisions and keep the constant distances between them in ordered formation. The effectiveness of the proposed approach has been verified in simulations.

Keywords: formation control, potential field method, obstacle avoidance, swarm intelligence, multi-agent systems

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Authors: Jagannath Singh, Durga Prasad Mohapatra

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Software refactoring is very essential for maintaining the software quality. It is an usual practice that we first design the software and then go for coding. But after coding is completed, if the requirement changes slightly or our expected output is not achieved, then we change the codes. For each small code change, we cannot change the design. In course of time, due to these small changes made to the code, the software design decays. Software refactoring is used to restructure the code in order to improve the design and quality of the software. In this paper, we propose an approach for performing code refactoring. We use slice-based cohesion metrics to identify the target methods which requires refactoring. After identifying the target methods, we use program slicing to divide the target method into two parts. Finally, we have used the concepts of Aspects to adjust the code structure so that the external behaviour of the original module does not change.

Keywords: software refactoring, program slicing, AOP, cohesion metrics, code restructure, AspectJ

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Authors: Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho, Tzu-Hao Chang, Cheng-Wei Chang

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Background: Human cytomegalovirus (HCMV) infects much people around the world, and there were many researches mention that many diseases were caused by HCMV. To understand the mechanism of HCMV lead to diseases during infection. We observe a microRNA (miRNA) – miRNA interaction between HCMV and host during infection. We found HCMV miRNA sequence component complementary with host miRNA precursors, and we also found that the host miRNA abundances were decrease in HCMV infection. Hence, we focus on the host miRNA which may target by the other HCMV miRNA to find theirs target mRNAs expression and analysis these mRNAs affect what kind of signaling pathway. Interestingly, we found the affected mRNA play an important role in some diseases related pathways, and these diseases had been annotated by HCMV infection. Results: From our analysis procedure, we found 464 human miRNAs might be targeted by 26 HCMV miRNAs and there were 291 human miRNAs shows the concordant decrease trend during HCMV infection. For case study, we found hcmv-miR-US22-5p may regulate hsa-mir-877 and we analysis the KEGG pathway which built by hsa-mir-877 validate target mRNA. Additionally, through survey KEGG Disease database found that these mRNA co-regulate some disease related pathway for instance cancer, nerve disease. However, there were studies annotated that HCMV infection casuse cancer and Alzheimer. Conclusions: This work supply a different scenario of miRNA target interactions(MTIs). In previous study assume miRNA only target to other mRNA. Here we wonder there is possibility that miRNAs might regulate non-mRNA targets, like other miRNAs. In this study, we not only consider the sequence similarity with HCMV miRNAs and human miRNA precursors but also the expression trend of these miRNAs. Then we analysis the human miRNAs validate target mRNAs and its associated KEGG pathway. Finally, we survey related works to validate our investigation.

Keywords: human cytomegalovirus, HCMV, microRNA, miRNA

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Authors: Hao Yuan, Yongjian Shen, Xiangjun He, Yuheng Li, Zhouzhou Zhang, Pengyu Zhang, Minkang Cai

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Remote sensing data can provide support for decision-making in disaster assessment or disaster relief. The traditional processing methods of sensitive targets in remote sensing mapping are mainly based on manual retrieval and image editing tools, which are inefficient. Methods based on deep learning for sensitive target hiding are faster and more flexible. But these methods have disadvantages in training time and cost of calculation. This paper proposed a target hiding model Self Attention (SA) Deepfill, which used self-attention modules to replace part of gated convolution layers in image inpainting. By this operation, the calculation amount of the model becomes smaller, and the performance is improved. And this paper adds free-form masks to the model’s training to enhance the model’s universal. The experiment on an open remote sensing dataset proved the efficiency of our method. Moreover, through experimental comparison, the proposed method can train for a longer time without over-fitting. Finally, compared with the existing methods, the proposed model has lower computational weight and better performance.

Keywords: remote sensing mapping, image inpainting, self-attention mechanism, target hiding

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Authors: Koirala Abarodh, Maghaiya Ujjwal, Guragain Phani Raj

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This analysis focuses on defining the spectrum evaluation model for telecom operators in terms of total cost of ownership (TCO). A quantitative approach for specific case analysis research methodology was used for identifying the results. Specific input parameters like target User experience, year on year traffic growth, capacity site limit per year, target additional spectrum type, bandwidth, spectrum efficiency, UE penetration have been used for the spectrum evaluation process and desired outputs in terms of the number of sites, capex in USD and required spectrum bandwidth have been calculated. Furthermore, this study gives a comparison of capex investment for target growth with and without addition spectrum. As a result, the combination of additional spectrum bands of 700 and 2600 MHz has a better evaluation in terms of TCO and performance. It is our recommendation to use these bands for expansion rather than expansion in the current 1800 and 2100 bands.

Keywords: spectrum, capex planning, case study methodology, TCO

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Authors: Jean Berger, Nassirou Lo, Martin Noel

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Perfectly suited for natural or man-made emergency and disaster management situations such as flood, earthquakes, tornadoes, or tsunami, multi-target search path planning for a team of rescue agents is known to be computationally hard, and most techniques developed so far come short to successfully estimate optimality gap. A novel mixed-integer linear programming (MIP) formulation is proposed to optimally solve the multi-target multi-agent discrete search and rescue (SAR) path planning problem. Aimed at maximizing cumulative probability of successful target detection, it captures anticipated feedback information associated with possible observation outcomes resulting from projected path execution, while modeling agent discrete actions over all possible moving directions. Problem modeling further takes advantage of network representation to encompass decision variables, expedite compact constraint specification, and lead to substantial problem-solving speed-up. The proposed MIP approach uses CPLEX optimization machinery, efficiently computing near-optimal solutions for practical size problems, while giving a robust upper bound obtained from Lagrangean integrality constraint relaxation. Should eventually a target be positively detected during plan execution, a new problem instance would simply be reformulated from the current state, and then solved over the next decision cycle. A computational experiment shows the feasibility and the value of the proposed approach.

Keywords: search path planning, search and rescue, multi-agent, mixed-integer linear programming, optimization

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Authors: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Ahlam Inayatullah Badrul Munir, M. Husaini A. Rahman, Mohd Sukri Hassan

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Real-time PCR is a molecular biology technique that is currently being widely used for halal services to differentiating between porcine and bovine DNA. The useful of technique become very important for student or workers (who works in the laboratory) to learn how the technique could be run smoothly without fail. Same concept with conventional PCR, real-time PCR also needed DNA template, primer, enzyme polymerase, dNTP, and buffer. The difference is in real-time PCR, have additional component namely fluorescent dye. The most common use of fluorescent dye in real-time PCR is SYBR green. The purpose of this study was to find out how sensitive, specific and efficient real-time PCR technique was combined with SYBR green method and specific primers of CYT b. The results showed that real-time PCR technique using SYBR Green, capable of detecting porcine and bovine DNA concentrations up to 0.0001 µl/ng. The level of efficiency for both types of DNA was 91% (90-110). Not only that in specific primer CYT b bovine primer could detect only bovine DNA, and porcine primer could detect only porcine primer. So, from the study could be concluded that real-time PCR technique that was combined with specific primer CYT b and SYBR green method, was sensitive, specific and efficient to detect porcine and bovine DNA.

Keywords: sensitivity, specificity, efficiency, real-time PCR, SYBR green, Cytochrome b, porcine DNA, bovine DNA

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Authors: Giorgio Visentin, Inna S. Kalinina, Alexei A. Buchachenko

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In the ambit of intermolecular interactions, a combination rule is defined as a relation linking a potential parameter for the interaction of two unlike species with the same parameters for interaction pairs of like species. Some of their most exemplificative applications cover the construction of molecular dynamics force fields and dispersion-corrected density functionals. Here, an extended combination rule is proposed, relating the dipole-dipole dispersion coefficients for the interaction of like target species to the same coefficients for the interaction of the target and a set of partner species. The rule can be devised in two different ways, either by uniform discretization of the Casimir-Polder integral on a Gauss-Legendre quadrature or by relating the dynamic polarizabilities of the target and the partner species. Both methods return the same system of linear equations, which requires the knowledge of the dispersion coefficients for interaction between the partner species to be solved. The test examples show a high accuracy for dispersion coefficients (better than 1% in the pristine test for the interaction of Yb atom with rare gases and alkaline-earth metal atoms). In contrast, the rule does not ensure correct monotonic behavior of the dynamic polarizability of the target species. Acknowledgment: The work is supported by Russian Science Foundation grant # 17-13-01466.

Keywords: combination rule, dipole-dipole dispersion coefficient, Casimir-Polder integral, Gauss-Legendre quadrature

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Authors: Musatafa Abbas Abbood Albadr, Masri Ayob, Sabrina Tiun, Fahad Taha Al-Dhief, Mohammad Kamrul Hasan

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Breast Cancer (BC) is considered one of the most frequent reasons of cancer death in women between 40 to 55 ages. The BC is diagnosed by using digital images of the FNA (Fine Needle Aspirate) for both benign and malignant tumors of the breast mass. Therefore, this work proposes the Online Sequential Extreme Learning Machine (OSELM) algorithm for diagnosing BC by using the tumor features of the breast mass. The current work has used the Wisconsin Diagnosis Breast Cancer (WDBC) dataset, which contains 569 samples (i.e., 357 samples for benign class and 212 samples for malignant class). Further, numerous measurements of assessment were used in order to evaluate the proposed OSELM algorithm, such as specificity, precision, F-measure, accuracy, G-mean, MCC, and recall. According to the outcomes of the experiment, the highest performance of the proposed OSELM was accomplished with 97.66% accuracy, 98.39% recall, 95.31% precision, 97.25% specificity, 96.83% F-measure, 95.00% MCC, and 96.84% G-Mean. The proposed OSELM algorithm demonstrates promising results in diagnosing BC. Besides, the performance of the proposed OSELM algorithm was superior to all its comparatives with respect to the rate of classification.

Keywords: breast cancer, machine learning, online sequential extreme learning machine, artificial intelligence

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Authors: Kan Yu, Khui Hung Lee, Eben Afrifa-Yamoah, Jing Guo, Katrina Harrison, Jack Goldblatt, Nicholas Pachter, Jitian Xiao, Guicheng Brad Zhang

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Background and Significance of the Study: Congenital Heart Defects (CHDs) are the most common malformation at birth and one of the leading causes of infant death. Although the exact etiology remains a significant challenge, epigenetic modifications, such as DNA methylation, are thought to contribute to the pathogenesis of congenital heart defects. At present, no existing DNA methylation biomarkers are used for early detection of CHDs. The existing CHD diagnostic techniques are time-consuming and costly and can only be used to diagnose CHDs after an infant was born. The present study employed a machine learning technique to analyse genome-wide methylation data in children with and without CHDs with the aim to find methylation biomarkers for CHDs. Methods: The Illumina Human Methylation EPIC BeadChip was used to screen the genome‐wide DNA methylation profiles of 24 infants diagnosed with congenital heart defects and 24 healthy infants without congenital heart defects. Primary pre-processing was conducted by using RnBeads and limma packages. The methylation levels of top 600 genes with the lowest p-value were selected and further investigated by using a random forest approach. ROC curves were used to analyse the sensitivity and specificity of each biomarker in both training and test sample sets. The functionalities of selected genes with high sensitivity and specificity were then assessed in molecular processes. Major Findings of the Study: Three genes (MIR663, FGF3, and FAM64A) were identified from both training and validating data by random forests with an average sensitivity and specificity of 85% and 95%. GO analyses for the top 600 genes showed that these putative differentially methylated genes were primarily associated with regulation of lipid metabolic process, protein-containing complex localization, and Notch signalling pathway. The present findings highlight that aberrant DNA methylation may play a significant role in the pathogenesis of congenital heart defects.

Keywords: biomarker, congenital heart defects, DNA methylation, random forest

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Authors: Michael Ayomoh, Adriaan Roux, Oyindamola Omotuyi

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This paper presents an efficient robot navigation model in a multi-target domain amidst static and dynamic workspace obstacles. The problem is that of developing an optimal algorithm to minimize the total travel time of a robot as it visits all target points within its task domain amidst unknown workspace obstacles and finally return to its initial position. In solving this problem, a classical algorithm was first developed to compute the optimal number of paths to be travelled by the robot amidst the network of paths. The principle of shortest distance between robot and targets was used to compute the target point visitation order amidst workspace obstacles. Algorithm premised on the standard polar coordinate system was developed to determine the length of obstacles encountered by the robot hence giving room for a geometrical estimation of the total surface area occupied by the obstacle especially when classified as a relevant obstacle i.e. obstacle that lies in between a robot and its potential visitation point. A stochastic model was developed and used to estimate the likelihood of a dynamic obstacle bumping into the robot’s navigation path and finally, the navigation/obstacle avoidance algorithm was hinged on the hybrid virtual force field (HVFF) method. Significant modelling constraints herein include the choice of navigation path to selected target points, the possible presence of static obstacles along a desired navigation path and the likelihood of encountering a dynamic obstacle along the robot’s path and the chances of it remaining at this position as a static obstacle hence resulting in a case of re-routing after routing. The proposed algorithm demonstrated a high potential for optimal solution in terms of efficiency and effectiveness.

Keywords: multi-target, mobile robot, optimal path, static obstacles, dynamic obstacles

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Authors: Anika Chebrolu

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Mono-targeted drugs can be of limited efficacy against complex diseases. Recently, multi-target drug design has been approached as a promising tool to fight against these challenging diseases. However, the scope of current computational approaches for multi-target drug design is limited. DeepLig presents a de-novo drug discovery platform that uses reinforcement learning to generate and optimize novel, potent, and multitargeted drug candidates against protein targets. DeepLig’s model consists of two networks in interplay: a generative network and a predictive network. The generative network, a Stack- Augmented Recurrent Neural Network, utilizes a stack memory unit to remember and recognize molecular patterns when generating novel ligands from scratch. The generative network passes each newly created ligand to the predictive network, which then uses multiple Graph Attention Networks simultaneously to forecast the average binding affinity of the generated ligand towards multiple target proteins. With each iteration, given feedback from the predictive network, the generative network learns to optimize itself to create molecules with a higher average binding affinity towards multiple proteins. DeepLig was evaluated based on its ability to generate multi-target ligands against two distinct proteins, multi-target ligands against three distinct proteins, and multi-target ligands against two distinct binding pockets on the same protein. With each test case, DeepLig was able to create a library of valid, synthetically accessible, and novel molecules with optimal and equipotent binding energies. We propose that DeepLig provides an effective approach to design multi-targeted drug therapies that can potentially show higher success rates during in-vitro trials.

Keywords: drug design, multitargeticity, de-novo, reinforcement learning

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Authors: N. Haj Salem, M. Belhadj, S. Ben Jomâa, R. Dhouieb, S. Saadi, M. A. Mesrati, A. Chadly

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Introduction: The hyoid bone is considered as one of many bones used to identify a missed person. There is a specificity of each population group in human identifications. Objective: To analyze the relationship between age, sex and metric parameters of hyoid bone in Tunisian population sample, using CT-scan. Materials and Methods: A prospective study was conducted in the Department of Forensic Medicine of FattoumaBourguiba Hospital of Monastir-Tunisia during 4 years. A total of 240 samples of hyoid bone were studied. The age of cases ranged from 18 days to 81 years. The specimens were collected only from the deceased of known age. Once dried, each hyoid bone was scanned using CT scan. For each specimen, 10 measurements were taken using a computer program. The measurements consisted of 6 lengths and 4 widths. A regression analysis was used to estimate the relationship between age, sex, and different measurements. For age estimation, a multiple logistic regression was carried out for samples ≤ 35 years. For sex determination, ROC curve was performed. Discriminant value finally retained was based on the best specificity with the best sensitivity. Results: The correlation between real age and estimated age was good (r²=0.72) for samples aged 35 years or less. The unstandardised canonical function equation was estimated using three variables: maximum length of the right greater cornua, length from the middle of the left joint space to the middle of the right joint space and perpendicular length from the centre point of a line between the distal ends of the right and left greater cornua to the centre point of the anterior view of the body of the hyoid bone. For sex determination, the ROC curve analysis reveals that the area under curve was at 81.8%. Discriminant value was 0.451 with a specificity of 73% and sensibility of 79%. The equation function was estimated based on two variables: maximum length of the greater cornua and maximum length of the hyoid bone. Conclusion: The findings of the current study suggest that metric analysis of the hyoid bone may predict the age ≤ 35 years. Sex estimation seems to be more reliable. Further studies dealing with the fusion of the hyoid bone and the current study could help to achieve more accurate age estimation rates.

Keywords: anthropology, age estimation, CT scan, sex determination, Tunisia

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Authors: Yousif Mohamed Y. Abdallah

Abstract:

This is an experimental study deals with detection, measurement and analysis of the periodic physiological organ motion during external beam radiotherapy; to improve the accuracy of the radiation field placement, and to reduce the exposure of healthy tissue during radiation treatments. The importance of this study is to detect the maximum path of the mobile structures during radiotherapy delivery, to define the planning target volume (PTV) and irradiated volume during both inspiration and expiration period and to verify the target volume. In addition to its role to highlight the importance of the application of Intense Guided Radiotherapy (IGRT) methods in the field of radiotherapy. The results showed (body contour was equally (3.17 + 0.23 mm), for left lung displacement reading (2.56 + 0.99 mm) and right lung is (2.42 + 0.77 mm) which the radiation oncologist to take suitable countermeasures in case of significant errors. In addition, the use of the image registration technique for automatic position control is predicted potential motion. The motion ranged between 2.13 mm and 12.2 mm (low and high). In conclusion, individualized assessment of tumor mobility can improve the accuracy of target areas definition in patients undergo Sterostatic RT for stage I, II and III lung cancer (NSCLC). Definition of the target volume based on a single CT scan with a margin of 10 mm is clearly inappropriate.

Keywords: respiratory motion, external beam radiotherapy, image processing, lung

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Authors: Nipun Manirajan, Heeralal Gargama, Sushil Guhe, Manoj Prabhakaran

Abstract:

In railway industry, train sets are designed based on contractual requirements (mission profile), where reliability targets are measured in terms of mean distance between failures (MDBF). However, during the beginning of revenue services, trains do not achieve the designed mission profile distance (mileage) within the timeframe due to infrastructure constraints, scarcity of commuters or other operational challenges thereby not respecting the original design inputs. Since trains do not run sufficiently and do not achieve the designed mileage within the specified time, car builder has a risk of not achieving the contractual MDBF target. This paper proposes a constant failure rate based model to deal with the situations where mileage accumulation is not a part of the design mission profile. The model provides appropriate MDBF target to be demonstrated based on actual accumulated mileage. A case study of rolling stock running in the field is undertaken to analyze the failure data and MDBF target demonstration during low mileage accumulation. The results of case study prove that with the proposed method, reliability targets are achieved under low mileage accumulation.

Keywords: mean distance between failures, mileage-based reliability, reliability target appropriations, rolling stock reliability

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Authors: Maaly Jarrah

Abstract:

Oral fluency in the target language is what many second language learners hope to achieve by living abroad. Research in the past has demonstrated the role informal environments play in improving L2 learners' oral fluency. However, living in the target country and being part of its community does not ensure the development of oral fluency skills. L2 learners' desire to communicate and access to speaking opportunities in the host community are key in achieving oral fluency in the target language. This study attempts to identify differences in oral fluency, specifically speech rate, between learners who communicate in the L2 outside the classroom and those who do not. In addition, as the desire to communicate is a crucial factor in developing oral fluency, this study investigates whether or not learners' desire to speak the L2 outside the classroom plays a role in their frequency of L2 use outside the classroom. Finally, given the importance of the availability of speaking opportunities for L2 learners in order to practice their speaking skills, this study reports on the participants' perceptions of the speaking opportunities accessible to them in the target community while probing whether or not their perceptions differed based on their oral fluency level and their desire to communicate. The results suggest that exposure to the target language and daily communication with the native speakers is strongly related to the development of learners' oral fluency. Moreover, the findings suggest that learners' desire to communicate affects their frequency of communication in their L2 outside the classroom. At the same time, all participants, regardless of their oral fluency level and their desire to communicate, asserted that speaking opportunities beyond the classroom are very limited. Finally, the study finds there are marked differences in the perceptions learners have regarding opportunities for learning offered by the same language program. After reporting these results, the study concludes with recommendations for ESL programs that serve international students.

Keywords: ESL programs, L2 Learners, oral fluency, second language

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Authors: Mohamad Ammar Ayass, Natalya Griko, Victor Pashkov, Wanying Cao, Kevin Zhu, Jin Zhang, Lina Abi Mosleh

Abstract:

Respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for coronavirus disease 2019 (COVID-19). Early evidence pointed at the angiotensin-converting enzyme 2 (ACE-2) expressed on the epithelial cells of the lung as the main entry point of SARS-CoV-2 into the cells. The viral entry is mediated by the binding of the Receptor Binding Domain (RBD) of the spike protein that is expressed on the surface of the virus to the ACE-2 receptor. As the number of SARS-CoV-2 variants continues to increase, mutations arising in the RBD of SARS-CoV-2 may lead to the ineffectiveness of RBD targeted neutralizing antibodies. To address this limitation, the objective of this study is to develop a combination of aptamers that target different regions of the RBD, preventing the binding of the spike protein to ACE-2 receptor and subsequent viral entry and replication. A safe and innovative biomedical tool was developed to inhibit viral infection and reduce the harms of COVID-19. In the present study, DNA aptamers were developed against a recombinant trimer S protein using the Systematic Evolution of Ligands by Exponential enrichment (SELEX). Negative selection was introduced at round number 7 to select for aptamers that bind specifically to the RBD domain. A series of 9 aptamers (ADI2010, ADI2011, ADI201L, ADI203L, ADI205L, ADIR68, ADIR74, ADIR80, ADIR83) were selected and characterized with high binding affinity and specificity to the RBD of the spike protein. Aptamers (ADI25, ADI2009, ADI203L) were able to bind and pull down endogenous spike protein expressed on the surface of SARS-CoV-2 virus in COVID-19 positive patient samples and determined by liquid chromatography- tandem mass spectrometry analysis (LC-MS/MS). LC-MS/MS data confirmed that aptamers can bind to the RBD of the spike protein. Furthermore, results indicated that the combination of the 9 best aptamers inhibited the binding of the purified trimer spike protein to the ACE-2 receptor found on the surface of Vero E6 cells. In the same experiment, the combined aptamers displayed a better neutralizing effect than antibodies. The data suggests that the selected aptamers could be used in therapy to neutralize the effect of the SARS-CoV-2 virus by inhibiting the interaction between the RBD and ACE-2 receptor, preventing viral entry into target cells and therefore blocking viral replication.

Keywords: aptamer, ACE-2 receptor, binding inhibitor, COVID-19, spike protein, SARS-CoV-2, treatment

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Authors: Tanwarat Kajsongkram, Saowalux Rotamporn, Sirinat Limbunruang, Sirinan Thubthimthed.

Abstract:

High-Performance Liquid Chromatography (HPLC) method was developed and validated for simultaneous estimation of 6-Gingerol(6G) and 6-Shogaol(6S) in joint pain relief gel containing ginger extract. The chromatographic separation was achieved by using C18 column, 150 x 4.6mm i.d., 5μ Luna, mobile phase containing acetonitrile and water (gradient elution). The flow rate was 1.0 ml/min and the absorbance was monitored at 282 nm. The proposed method was validated in terms of the analytical parameters such as specificity, accuracy, precision, linearity, range, limit of detection (LOD), limit of quantification (LOQ), and determined based on the International Conference on Harmonization (ICH) guidelines. The linearity ranges of 6G and 6S were obtained over 20-60 and 6-18 µg/ml respectively. Good linearity was observed over the above-mentioned range with linear regression equation Y= 11016x- 23778 for 6G and Y = 19276x-19604 for 6S (x is concentration of analytes in μg/ml and Y is peak area). The value of correlation coefficient was found to be 0.9994 for both markers. The limit of detection (LOD) and limit of quantification (LOQ) for 6G were 0.8567 and 2.8555 µg/ml and for 6S were 0.3672 and 1.2238 µg/ml respectively. The recovery range for 6G and 6S were found to be 91.57 to 102.36 % and 84.73 to 92.85 % for all three spiked levels. The RSD values from repeated extractions for 6G and 6S were 3.43 and 3.09% respectively. The validation of developed method on precision, accuracy, specificity, linearity, and range were also performed with well-accepted results.

Keywords: ginger, 6-gingerol, HPLC, 6-shogaol

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Authors: Manjunath A. P., Al-Ajmi G. M., Al Shukri M., Girija S

Abstract:

Introduction: This study aimed to compare the ability of hysteroscopy and ultrasonography to diagnose uterine polyps. To correlate the ultrasonography and hystroscopic findings with various clinical factors and histopathology of uterine polyps. Methods: This is a retrospective study conducted at the Department of Obstetrics and Gynaecology at Sultan Qaboos University Hospital from 2014 to 2019. All women undergoing hysteroscopy for suspected uterine polyps were included. All relevant data were obtained from the electronic patient record and analysed using SPSS. Results: A total of 77 eligible women were analysed. The mean age of the patients was 40 years. The clinical risk factors; obesity, hypertension, and diabetes mellitus, showed no significant statistical association with the presence of uterine polyps (p-value>0.005). Although 20 women (52.6%) with uterine polyps had thickened endometrium (>11 mm), however, there is no statistical association (p-value>0.005). The sensitivity and specificity of ultrasonography in the detection of uterine polyp were 39% and 65%, respectively. Whereas for hysteroscopy, it was 89% and 20%, respectively. The prevalence of malignant and premalignant lesions were 1.85% and 7.4%, respectively. Conclusion: This study found that obesity, hypertension, and diabetes mellitus were not associated with the presence of uterine polyps. There was no association between thick endometrium and uterine polyps. The sensitivity is higher for hysteroscopy, whereas the specificity is higher for sonography in detecting uterine polyps. The prevalence of malignancy was very low in uterine polyps.

Keywords: endometrial polyps, hysteroscopy, ultrasonography, premalignant, malignant

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Authors: Bingqing Xu, Wenxing Shuai

Abstract:

This study investigates the priming effects of different Chinese compound words by native Mandarin speakers. There are lots of homonym, polysemy, and synonym in Chinese. However, it is unclear which kind of words have the biggest priming effect. Native Mandarin speakers were tested in a visual-word lexical decision experiment. The stimuli, which are all two-character compound words, consisted of two parts: primes and targets. Five types of relationships were used in all stimuli: morphologically related condition, in which the prime and the target contain the same morpheme; orthographically related condition, in which the target and the prime contain the different morpheme with the same form; phonologically related condition, in which the target and the prime contain the different morpheme with the same phonology; semantically related condition, in which the target and the prime contain the different morpheme with similar meanings; totally unrelated condition. The time since participants saw the target to respond was recorded. Analyses on reaction time showed that the average reaction time of morphologically related targets was much shorter than others, suggesting the morphological priming effect is the biggest. However, the reaction time of the phonologically related conditions was the longest, even longer than unrelated conditions. According to scatter plots analyses, 86.7% of participants had priming effects in morphologically related conditions, only 20% of participants had priming effects in phonologically related conditions. These results suggested that morphologically related conditions had the biggest priming effect. The orthographically and semantically related conditions also had priming effects, whereas the phonologically related conditions had few priming effects.

Keywords: priming effect, morphology, phonology, semantics, orthography

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