Search results for: target sequencing

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: Niamh Higgins, Dawn Howard

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The Irish agri-food sector is of major importance to Ireland’s manufacturing sector and to the Irish economy through employment and the exporting of animal products worldwide. Infectious diseases and parasites have an impact on farm animal health causing profitability and productivity to be affected. For the sustainability of Irish dairy farming, there must be the highest standard of animal health. There can be a lack of information in accounting for > 1% of complete microbial diversity in an environment. There is the tendency of culture-based methods of microbial identification to overestimate the prevalence of species which grow easily on an agar surface. There is a need for new technologies to address these issues to assist with animal health. Metagenomic approaches provide information on both the whole genome and transcriptome present through DNA sequencing of total DNA from environmental samples producing high determination of functional and taxonomic information. Nanopore Next Generation Technologies have the ability to be powerful sequencing technologies. They provide high throughput, low material requirements and produce ultra-long reads, simplifying the experimental process. The aim of this study is to use a metagenomics approach to analyze dairy cattle faecal samples using the Oxford Nanopore MinION Next Generation Sequencer and to establish an in-house pipeline for metagenomic characterization of complex samples. Faecal samples will be obtained from Irish dairy farms, DNA extracted and the MinION will be used for sequencing, followed by bioinformatics analysis. Of particular interest, will be the parasite Buxtonella sulcata, which there has been little research on and which there is no research on its presence on Irish dairy farms. Preliminary results have shown the ability of the MinION to produce hundreds of reads in a relatively short time frame of eight hours. The faecal samples were obtained from 90 dairy cows on a Galway farm. The results from Oxford Nanopore ‘What’s in my pot’ (WIMP) using the Epi2me workflow, show that from a total of 926 classified reads, 87% were from the Kingdom Bacteria, 10% were from the Kingdom Eukaryota, 3% were from the Kingdom Archaea and < 1% were from the Kingdom Viruses. The most prevalent bacteria were those from the Genus Acholeplasma (71 reads), Bacteroides (35 reads), Clostridium (33 reads), Acinetobacter (20 reads). The most prevalent species present were those from the Genus Acholeplasma and included Acholeplasma laidlawii (39 reads) and Acholeplasma brassicae (26 reads). The preliminary results show the ability of the MinION for the identification of microorganisms to species level coming from a complex sample. With ongoing optimization of the pipe-line, the number of classified reads are likely to increase. Metagenomics has the potential in animal health for diagnostics of microorganisms present on farms. This would support wprevention rather than a cure approach as is outlined in the DAFMs National Farmed Animal Health Strategy 2017-2022.

Keywords: animal health, buxtonella sulcata, infectious disease, irish dairy cattle, metagenomics, minION, next generation sequencing

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Authors: L. Salomon, P. Sklenar

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The Andes hold the highest plant species diversity in the world. How this occurred is one of the most intriguing questions in studies addressing the origin and patterning of plant diversity worldwide. Recently, the explosive adaptive radiations found in high Andean groups have been pointed as triggers to this spectacular diversity. The Andes is the species-richest area for the biggest genus from the Asteraceae family: Senecio. There, the genus presents an incredible diversity of species, striking growth form variation, and large niche span. Even when some studies tried to disentangle the evolutionary story for some Andean species in Senecio, they obtained partially resolved and low supported phylogenies, as expected for recently radiated groups. The high-throughput sequencing (HTS) approaches have proved to be a powerful tool answering phylogenetic questions in those groups whose evolutionary stories are recent and traditional techniques like Sanger sequencing are not informative enough. Although these tools have been used to understand the evolution of an increasing number of Andean groups, nowadays, their scope has not been applied for Senecio. This project aims to contribute to a better knowledge of the mechanisms shaping the hyper diversity of Senecio in the Andean region, using HTS focusing on Senecio ser. Culcitium (Asteraceae), recently recircumscribed. Firstly, reconstructing a highly resolved and supported phylogeny, and after assessing the role of allopatric differentiation, hybridization, and genome duplication in the diversification of the group. Using the Hyb-Seq approach, combining target enrichment using Asteraceae COS loci baits and genome skimming, more than 100 new accessions were generated. HybPhyloMaker and HybPiper pipelines were used for the phylogenetic analyses, and another pipeline in development (Paralogue Wizard) was used to deal with paralogues. RAxML was used to generate gene trees and Astral for species tree reconstruction. Phyparts were used to explore as first step of gene tree discordance along the clades. Fully resolved with moderated supported trees were obtained, showing Senecio ser. Culcitium as monophyletic. Within the group, some species formed well-supported clades with morphologically related species, while some species would not have exclusive ancestry, in concordance with previous studies using amplified fragment length polymorphism (AFLP) showing geographical differentiation. Discordance between gene trees was detected. Paralogues were detected for many loci, indicating possible genome duplications; ploidy level estimation using flow cytometry will be carried out during the next months in order to identify the role of this process in the diversification of the group. Likewise, TreeSetViz package for Mesquite, hierarchical likelihood ratio congruence test using Concaterpillar, and Procrustean Approach to Cophylogeny (PACo), will be used to evaluate the congruence among different inheritance patterns. In order to evaluate the influence of hybridization and Incomplete Lineage Sorting (ILS) in each resultant clade from the phylogeny, Joly et al.'s 2009 method in a coalescent scenario and Paterson’s D-statistic will be performed. Even when the main discordance sources between gene trees were not explored in detail yet, the data show that at least to some degree, processes such as genome duplication, hybridization, and/or ILS could be involved in the evolution of the group.

Keywords: adaptive radiations, Andes, genome duplication, hybridization, Senecio

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Authors: Koirala Abarodh, Maghaiya Ujjwal, Guragain Phani Raj

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This analysis is focused on defining the spectrum evaluation model for telecom operators in terms of the total cost of ownership (TCO). A quantitative approach for specific case analysis research methodology has been used for identifying the results. Specific input parameters like target user experience, year-on-year traffic growth, capacity site limit per year, target new spectrum type, bandwidth, spectrum efficiency, UE penetration have been used for the spectrum evaluation process and desired outputs in terms of a 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 new spectrums 700 and 2600 band have a better evaluation in terms of TCO and performance and it is recommended to use this band in terms of 5G rather than current expansion in current 1800 and 2100 band.

Keywords: spectrum, capex planning, 5G, case study methodology

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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: 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: Maryam Vaezjalali, Koroush Rahimian, Maryam Asli, Tahmineh Kandelouei, Foad Davoodbeglou, Amir H. Kashi

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Objectives: The present study was conducted to assess the HBV molecular profiles including genotypes, subgenotypes, subtypes & mutations in hepatitis B genes. Materials/Patients and Methods: This study was conducted on 229 intravenous drug users who referred to three Drop- in-Centers and a hospital in Tehran. HBV DNA was extracted from HBsAg positive serum samples and amplified by Nested PCR. HBV genotype, subgenotypes, subtype and genes mutation were determined by direct sequencing. Phylogenetic tree was constructed using neighbor- joining (NJ) method. Statistical analyses were carried out by SPSS 20. Results: HBV DNA was found in 3 HBsAg positive cases. Phylogenetic tree of derived HBV DNAs showed the existence of genotype D (subgenotype D1, subtype ayw2). Also immune escape mutations were determined in S gene. Conclusion: There were a few variations and genotypes and subtypes among infected intravenous drug users. This study showed the predominance of genotype D among intravenous drug users. Our study concurs with other reports from Iran, that all showing currently only genotype D is the only detectable genotype in Iran.

Keywords: drug users, genotype, HBV, phylogenetic tree

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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: Tanushree Jaitly, Shailendra Gupta, Leila Taher, Gerold Schuler, Julio Vera

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Genomics-based personalized medicine is a promising approach to fight aggressive tumors based on patient's specific tumor mutation and expression profiles. A remarkable case is, dendritic cell-based immunotherapy, in which tumor epitopes targeting patient's specific mutations are used to design a vaccine that helps in stimulating cytotoxic T cell mediated anticancer immunity. Here we present a computational pipeline for epitope-based personalized cancer vaccines using patient-specific haplotype and cancer mutation profiles. In the workflow proposed, we analyze Whole Exome Sequencing and RNA Sequencing patient data to detect patient-specific mutations and their expression level. Epitopes including the tumor mutations are computationally predicted using patient's haplotype and filtered based on their expression level, binding affinity, and immunogenicity. We calculate binding energy for each filtered major histocompatibility complex (MHC)-peptide complex using docking studies, and use this feature to select good epitope candidates further.

Keywords: cancer immunotherapy, epitope prediction, NGS data, personalized medicine

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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: 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: 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: 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: Lydia Tan, Philippe Lemey, Lieselot Houspie, Marco Viveen, Darren Martin, Frank Coenjaerts

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Introduction: Human respiratory syncytial virus (hRSV) is the leading cause of severe respiratory tract infections in infants under the age of two. Genomic substitutions and related evolutionary dynamics of hRSV are of great influence on virus transmission behavior. The evolutionary patterns formed are due to a precarious interplay between the host immune response and RSV, thereby selecting the most viable and less immunogenic strains. Studying genomic profiles can teach us which genes and consequent proteins play an important role in RSV survival and transmission dynamics. Study design: In this study, genetic diversity and evolutionary rate analysis were conducted on 36 RSV subgroup B whole genome sequences and 37 subgroup A genome sequences. Clinical RSV isolates were obtained from nasopharyngeal aspirates and swabs of children between 2 weeks and 5 years old of age. These strains, collected during epidemic seasons from 2001 to 2011 in the Netherlands and Belgium by either conventional or 454-sequencing. Sequences were analyzed for genetic diversity, recombination events, synonymous/non-synonymous substitution ratios, epistasis, and translational consequences of mutations were mapped to known 3D protein structures. We used Bayesian statistical inference to estimate the rate of RSV genome evolution and the rate of variability across the genome. Results: The A and B profiles were described in detail and compared to each other. Overall, the majority of the whole RSV genome is highly conserved among all strains. The attachment protein G was the most variable protein and its gene had, similar to the non-coding regions in RSV, more elevated (two-fold) substitution rates than other genes. In addition, the G gene has been identified as the major target for diversifying selection. Overall, less gene and protein variability was found within RSV-B compared to RSV-A and most protein variation between the subgroups was found in the F, G, SH and M2-2 proteins. For the F protein mutations and correlated amino acid changes are largely located in the F2 ligand-binding domain. The small hydrophobic phosphoprotein and nucleoprotein are the most conserved proteins. The evolutionary rates were similar in both subgroups (A: 6.47E-04, B: 7.76E-04 substitution/site/yr), but estimates of the time to the most recent common ancestor were much lower for RSV-B (B: 19, A: 46.8 yrs), indicating that there is more turnover in this subgroup. Conclusion: This study provides a detailed description of whole RSV genome mutations, the effect on translation products and the first estimate of the RSV genome evolution tempo. The immunogenic G protein seems to require high substitution rates in order to select less immunogenic strains and other conserved proteins are most likely essential to preserve RSV viability. The resulting G gene variability makes its protein a less interesting target for RSV intervention methods. The more conserved RSV F protein with less antigenic epitope shedding is, therefore, more suitable for developing therapeutic strategies or vaccines.

Keywords: drug target selection, epidemiology, respiratory syncytial virus, RSV

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Authors: Yousif Mohamed Y. Abdallah

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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

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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

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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: Christian Liebchen

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Both from an environmental perspective and with respect to road traffic flow quality, planning so-called green waves along major road axes is a well-established target for traffic engineers. For one-way road axes (e.g. the Avenues in Manhattan), this is a trivial downstream task. For bidirectional arterials, the well-known necessary condition for establishing a green wave in both directions is that the driving times between two subsequent crossings must be an integer multiple of half of the cycle time of the signal programs at the nodes. In this paper, we propose an integer linear optimization model to establish fixed-time green waves in both directions that are as long and as wide as possible, even in the situation where the driving time condition is not fulfilled. In particular, we are considering an arterial along whose nodes separate left-turn signal groups are realized. In our computational results, we show that scheduling left-turn phases before or after the straight phases can reduce waiting times along the arterial. Moreover, we show that there is always a solution with green waves in both directions that are as long and as wide as possible, where absolute priority is put on just one direction. Compared to optimizing both directions together, establishing an ideal green wave into one direction can only provide suboptimal quality when considering prioritized parts of a green band (e.g., first few seconds).

Keywords: traffic light coordination, synchronization, phase sequencing, green waves, integer programming

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Authors: Dalia. G. Aseel, E. E. Hafez, S. M. Hammad

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Viral RNAs of both potato leaf roll virus (PLRV) and potato virus Y (PVY) were extracted from infected potato leaves collected from different Egyptian regions. Differential Display Polymerase Chain Reaction (DD-PCR) using (Endogluconase, β-1,3-glucanases, Chitinase, Peroxidase and Polyphenol oxidase) primers (forward strand) for was performed. The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, a 58 up regulated and 19 down regulated genes were detected, while, 31 up regulated and 14 down regulated genes were observed in case of PVY. Based on the nucleotide sequencing, variable phylogenetic relationships were reported for the three sequenced genes coding for: Induced stolen tip protein, Disease resistance RPP-like protein and non-specific lipid-transfer protein. In a complementary approach, using the quantitative Real-time PCR, the expressions of PRs genes understudy were estimated in the infected leaves by PLRV and PVY of three potato cultivars (Spunta, Diamont and Cara). The infection with both viruses inhibited the expressions of the five PRs genes. On the contrary, infected leaves by PLRV or PVY elevated the expression of some defense genes. This interaction also may be enhanced and/or inhibited the expression of some genes responsible for the plant defense mechanisms.

Keywords: PLRV, PVY, PR genes, DD-PCR, qRT-PCR, sequencing

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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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Authors: Güldane Zengin

Abstract:

Advertisers often make use of humorous elements in advertisements they create. Advertisements that contain such elements play a great role in creating awareness and attaining positive attitudes. Caricature, which is an element of humour, is interesting, eye catching, entertaining and memorable by its very nature. Because of these characteristics of caricatures, they are being used for advertising purposes. Advertisements with caricatures are spreading rapidly and embraced by consumers easily. Especially in the last ten years, companies in different sectors use advertisements with caricatures to publicize their products and services. These companies have different target audiences with different characteristics. They all have differences in opinions, attitudes, perceptions and buying behaviours. Target audiences’ brand choices depend on many different factors. Advertising is an important factor in brand choice. Using attention grabbing methods like advertising with caricatures affects their buying behaviours. This study examines the use of caricatures in Sütaş advertisements. Target audiences’ opinions, perceptions and attitudes about advertisements with caricatures are examined in this descriptive study.

Keywords: advertising, advertisements with caricatures, caricature, communication, humour, Sütaş caricatures

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Authors: Young Ah Kim, Hyunsoo Kim, Eun-Jeong Yoon, Young Hee Seo, Kyungwon Lee

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Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli from food animals are considered as a reservoir for transmission of ESBL genes to human. The aim of this study is to assess the prevalence and molecular epidemiology of ESBL-producing E. coli colonization in pigs, farm workers, and farm environments to elucidate the transmission of multidrug-resistant clones from animal to human. Nineteen pig farms were enrolled across the country in Korea from August to December 2017. ESBL-producing E. coli isolates were detected in 190 pigs, 38 farm workers, and 112 sites of farm environments using ChromID ESBL (bioMerieux, Marcy l'Etoile, France), directly (stool or perirectal swab) or after enrichment (sewage). Antimicrobial susceptibility tests were done with disk diffusion methods and blaTEM, blaSHV, and blaCTX-M were detected with PCR and sequencing. The genomes of the four CTX-M-55-producing E. coli isolates from various sources in one farm were entirely sequenced to assess the relatedness of the strains. Whole genome sequencing (WGS) was performed with PacBio RS II system (Pacific Biosciences, Menlo Park, CA, USA). ESBL genotypes were 85 CTX-M-1 group (one CTX-M-3, 23 CTX-M-15, one CTX-M-28, 59 CTX-M-55, one CTX-M-69) and 60 CTX-M-9 group (41 CTX-M-14, one CTX-M-17, one CTX-M-27, 13 CTX-M-65, 4 CTX-M-102) in total 145 isolates. The rectal colonization rates were 53.2% (101/190) in pigs and 39.5% (15/38) in farm workers. In WGS, sequence types (STs) were determined as ST69 (E. coli PJFH115 isolate from a human carrier), ST457 (two E. coli isolates PJFE101 recovered from a fence and PJFA1104 from a pig) and ST5899 (E. coli PJFA173 isolate from the other pig). The four plasmids encoding CTX-M-55 (88,456 to 149, 674 base pair), whether it belonged to IncFIB or IncFIC-IncFIB type, shared IncF backbone furnishing the conjugal elements, suggesting of genes originated from same ancestor. In conclusion, the prevalence of ESBL-producing E. coli in swine farms was surprisingly high, and many of them shared common ESBL genotypes of clinical isolates such as CTX-M-14, 15, and 55 in Korea. It could spread by horizontal transfer between isolates from different reservoirs (human-animal-environment).

Keywords: Escherichia coli, extended-spectrum β-lactamase, prevalence, whole genome sequencing

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Authors: Yaqing Hu

Abstract:

This paper puts forward a syntactic analysis involving multidominance and rightward movement in Chinese bi-comparatives, as in 'Yuehan bi Mali gao (John is taller than Mary).' It is argued here that the predicate of comparison is a shared constituent in two small clauses, namely one for the target and one for the standard; and then it moves rightward to form a degree phrase with the comparative morpheme. This proposal comes from four aspects. First, the example above can also be expressed in this way, 'A: Yuehan he Mali, shui gao? (John and Mary, who is taller?) B: Yuehan gao./Yuehan geng gao. (John is taller).' This shows that the gradable adjective is predicated of the target. In addition, according to a constraint on Chinese bi-comparatives, namely the target and the standard must be arguments of the predicate simultaneously, it is not unreasonable to assume that the gradable adjective may also be predicated of the standard. Second, subcomparatives are totally disallowed in Chinese, as in '*zhe-zhang zhuozi bi zhe-zhang yizi kuan chang. (This table is longer than this chair is wide.)' In order to save it from ungrammaticality, the target and the standard should be compared along the same dimension denoted by the gradable adjective. It may follow that in Chinese comparatives, having equal roles in the same eventuality, the target and the standard bear the same thematic relationship with the predicate of comparison. Third, verb-copy can appear in Chinese bi-comparatives, as in 'Yuehan qi ma bi Mali qi ma qi de kuai. (John rides horses faster than Mary does.)' The predicate qi seems to form a small clause with both the target and the standard. This might be supporting evidence that both the target and the standard share the predicate of comparison. Fourth, Chinese comparatives do have comparative morphemes, as in 'Yuehan bi Mali geng gao. (John is taller than Mary)', which is semantically equivalent to the first example above. Thus, it follows that one feature of Chinese comparative morphemes is that they can remain overt or covert in the syntax, which will not affect semantics. This further shows that comparative morphemes in bi-comparatives may not be able to saturate the degree argument denoted by the predicate of comparison due to its optionality in the structure. These four aspects present a challenge to the Direct Analysis used in Chinese comparatives since this approach would presume that the target and the standard somehow show independency with the predicate in the syntax. Meanwhile, this study also rejects the previous analysis of multidomiance in bi-comparatives in which the degree phrase comprised of the comparative morpheme and the gradable adjective may be shared by the standard when the comparative morpheme is covert. This syntactic analysis proposed in this study will therefore offer a different perspective of how to treat degree phrase in Chinese comparatives and may offer evidence to argue whether there is degree phrase movement in bi-comparatives as in its English counterparts.

Keywords: Chinese comparatives, degree phrase, movement, multidominance, syntactic analysis

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Authors: Uzma Saqib, Mirza S. Baig

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Myeloid differentiation primary response protein 88 (MYD88) has long been considered a central player in the inflammatory pathway. Recent studies clearly suggest that it is an important therapeutic target in inflammation. On the other hand, a recent study on the interaction between the orphan nuclear receptor (Nur77) and p38α, leading to increased lipopolysaccharide-induced hyperinflammatory response, suggests this binary complex as a therapeutic target. In this study, we have designed inhibitors that can inhibit both MYD88 and Nur77 at the same time. Since both MYD88 and Nur77 are an integral part of the pathways involving lipopolysaccharide-induced activation of NF-κB-mediated inflammation, we tried to target both proteins with the same library in order to retrieve compounds having dual inhibitory properties. To perform this, we developed a homodimeric model of MYD88 and, along with the crystal structure of Nur77, screened a virtual library of compounds from the traditional Chinese medicine database containing ~61,000 compounds. We analyzed the resulting hits for their efficacy for dual binding and probed them for developing a common pharmacophore model that could be used as a prototype to screen compound libraries as well as to guide combinatorial library design to search for ideal dual-target inhibitors. Thus, our study explores the identification of novel leads having dual inhibiting effects due to binding to both MYD88 and Nur77 targets.

Keywords: drug design, Nur77, MYD88, inflammation

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Authors: Barsha Saha, Shouvik Chakravarty, Sukanta Ray, Kshaunish Das, Nidhan K. Biswas, Srikanta Goswami

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Pancreatic Ductal Adenocarcinoma is a well-recognised cause of cancer death with a five-year survival rate of about 9%, and its incidence in India has been found to be increased manifold in recent years. Due to delayed detection, this highly metastatic disease has a poor prognosis. Several molecular alterations happen during the progression of the disease from pre-cancerous conditions, and many such alterations could be investigated for their biomarker potential. MicroRNAs have been shown to be prognostic for PDAC patients in a variety of studies. We hereby used NGS technologies to evaluate the role of small RNA changes during pancreatic cancer development from chronic pancreatitis. Plasma samples were collected from pancreatic cancer patients (n=16), chronic pancreatitis patients (n=8), and also from normal individuals (n=16). Pancreatic tumour tissue (n=5) and adjacent normal tissue samples (n=5) were also collected. Sequencing of small RNAs was carried out after small RNAs were isolated from plasma samples and tissue samples. We find that certain microRNAs are highly deregulated in pancreatic cancer patients in comparison to normal samples. A combinatorial analysis of plasma and tissue microRNAs and subsequent exploration of their targets and altered molecular pathways could not only identify potential biomarkers for disease diagnosis but also help to understand the underlying mechanism.

Keywords: small RNA sequencing, pancreatic cancer, biomarkers, tissue sample

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Authors: Maximilian Cedzich, Ingo Dietz Von Bayer, Roland Jochem

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In order for industrial companies to continue to succeed in dynamic, globalized markets, they must be able to train their employees in an agile manner and at short notice in line with the exogenous conditions that arise. For this purpose, it is indispensable to operate a proactive competence management system for employees that recognizes qualification needs timely in order to be able to address them promptly through qualification measures. However, there are hardly any approaches to be found in the literature that includes systematic, proactive competence management. In order to help close this gap, this publication presents a process model that systematically develops bottom-up, future-oriented target competence profiles based on the tasks of the employees. Concretely, in the first step, the tasks of the individual employees are examined for assumed future conditions. In other words, qualitative scenarios are considered for the individual tasks to determine how they are likely to change. In a second step, these scenario-based future tasks are translated into individual future-related target competencies of the employee using a matrix of generic task properties. The final step pursues the goal of validating the target competence profiles formed in this way within the framework of a management workshop. This process model provides industrial companies with a tool that they can use to determine the competencies required by their own employees in the future and compare them with the actual prevailing competencies. If gaps are identified between the target and the actual, these qualification requirements can be closed in the short term by means of qualification measures.

Keywords: dynamic globalized markets, employee competence management, industrial companies, knowledge management

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