Search results for: sequence alignment

Authors: Watcharapan Sukkerd, Teeradej Wuttipornpun

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This paper aims to present non-population search algorithms called tabu search (TS), simulated annealing (SA) and variable neighborhood search (VNS) to minimize the total cost of capacitated MRP problem in multi-stage assembly flow shop with two alternative machines. There are three main steps for the algorithm. Firstly, an initial sequence of orders is constructed by a simple due date-based dispatching rule. Secondly, the sequence of orders is repeatedly improved to reduce the total cost by applying TS, SA and VNS separately. Finally, the total cost is further reduced by optimizing the start time of each operation using the linear programming (LP) model. Parameters of the algorithm are tuned by using real data from automotive companies. The result shows that VNS significantly outperforms TS, SA and the existing algorithm.

Keywords: capacitated MRP, tabu search, simulated annealing, variable neighborhood search, linear programming, assembly flow shop, application in industry

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Authors: Eleanor Sweeney, Chunyuan Di

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The metaphors people use in everyday discourse do not arise randomly; rather, they develop from our physical experiences in our social and cultural environments. Conceptual Metaphor Theory (CMT) explains that through metaphor, we apply our embodied understanding of the physical world to non-material concepts to understand and express abstract concepts. Our most productive source domains derive from our embodied understanding and allow us to develop primary metaphors, and from primary metaphors, an elaborate, creative world of culturally constructed complex metaphors. Cognitive Linguistics researchers draw upon individual embodied experience for primary metaphors. Socioculturally embodied experience through music has long furnished linguistic expressions in diverse languages, as conceptual metaphors or everyday expressions.  Can a socially embodied experience function in the same way as an individually embodied experience in the creation of conceptual metaphors? The authors argue that since music is inherently social and embodied, musical experiences function as a richly motivated source domain. The focus of this study is socially embodied musical experience which is then reflected and expressed through metaphors. This cross-linguistic study explores music as a source domain for metaphors of social alignment in English, French, and Chinese. The authors explored two public discourse sites, Facebook and Linguée, in order to collect linguistic metaphors from three different languages. By conducting this cross-linguistic study, cross-cultural similarities and differences in metaphors for which music is the source domain can be examined. Different musical elements, such as melody, speed, rhythm and harmony, are analyzed for their possible metaphoric meanings of social alignment. Our findings suggest that the general metaphor cooperation is music is a productive metaphor with some subcases, and that correlated social behaviors can be metaphorically expressed with certain elements in music. For example, since performance is a subset of the category behavior, there is a natural mapping from performance in music to behavior in social settings: social alignment is musical performance. Musical performance entails a collective social expectation that exerts control over individual behavior.  When individual behavior does not align with the collective social expectation, music-related expressions are often used to express how the individual is violating social norms. Moreover, when individuals do align their behavior with social norms, similar musical expressions are used. Cooperation is a crucial social value in all cultures, indeed it is a key element of survival, and music provides a coherent, consistent, and rich source domain—one based upon a universal and definitive cultural practice.

Keywords: Chinese, Conceptual Metaphor Theory, cross-linguistic, culturally embodied experience, English, French, metaphor, music

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Authors: Adi Goldiner

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Historically, the social model of disability has played a pivotal role in bringing rights discourse into the disability debate. Against this backdrop, the paper explores the conceptual alignment between the social model’s account of disability and the nature of rights. Specifically, the paper examines the possibility that the social model conceptualizes disability in a way that aligns with the nature of rights and thus motivates the invocation of disability rights. Methodologically, the paper juxtaposes the literature on the social model of disability, primarily the work of the Union of the Physically Impaired Against Segregation in the UK and related scholarship, with theories of moral rights. By focusing on the interplay between the social model of disability and rights, the paper provides a conceptual explanation for the rise of disability rights. In addition, the paper sheds light on the nature of rights, their function and limitations, in the context of disability rights. The paper concludes that the social model’s conceptualization of disability is hospitable to rights, because it opens up the possibility that there are duties that correlate with disability rights. Under the social model, disability is a condition that can be eliminated by the removal of social, structural, and attitudinal barriers. Accordingly, the social model dispels the idea that the actions of others towards disabled people will have a marginal impact on their interests in not being disabled. Equally important, the social model refutes the idea that in order to significantly serve people's interest in not being disabled, it is necessary to cure bodily impairments, which is not always possible. As rights correlate with duties that are possible to comply with, as well as those that significantly serve the interests of the right holders, the social model’s conceptualization of disability invites the reframing of problems related to disability in terms of infringements of disability rights. A possible objection to the paper’s argument is raised, according to which the social model is at odds with the invocation of disability rights because disability rights are ineffective in realizing the social model's goal of improving the lives of disabled by eliminating disability. The paper responds to this objection by drawing a distinction between ‘moral rights,’ which, conceptually, are not subject to criticism of ineffectiveness, and ‘legal rights’ which are.

Keywords: disability rights, duties, moral rights, social model

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Authors: Rajkumar Ghosh

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Out-of-sequence thrusts (OOST) are reported at different geographic locations with various local names along Siwalik Himalaya (SH), Lesser Himalaya (LH), Higher Himalaya (HH) from Bhutan, India, Nepal, and Pakistan Himalayan range. Most of OOSTs have been identified within the upper LH, and the lower HH based on geochronological age jump across. These thrusts activated from Late Miocene to recent. The Chaura Thrust (CT) was deciphered from age jump of Apatite Fission Track (AFT) and considered as blind thrust base on variable exhumation rates in Chaura region, Satluj river valley, Himachal Pradesh. CT is located north of Jhakri Thrust (JhT) and is also differently identified as Sarahan thrust (ST). Structural documentation from the rocks near the OOST in Chaura was not so far done. Detail structural study of the Jeori Group of rocks was carried out in this study to understand the manifestation of the Chaura thrust and associated structures in meso- to micro-scale. Box fold, scar fold, kink fold, crenulation cleavages, and boudins are developed in the Chaura region. These structures usually do not indicate shear sense. When studied under an optical microscope, the Chaura samples reveal that the mica fish are usually lenticular with aspect ratio (R) varying from 6–11 and inclination angle (α) from 15–40°. According to ‘R’ and ‘α’, elongated sigmoid shaped mica fish and parallelogram shaped mica fish were also documented. Asymmetric mica fish demonstrate top-to-S/SW ductile shear, which is similar as that of Chaura thrust. Grain boundary migration (GBM) structures in quartzo-feldspathic grains from Jeori Group of rocks indicate deformation temperature ranging from 400 to 650°C. This can indicate that the OOST at Chaura, i.e., the Chaura Thrust, underwent thrusting in the ductile regime.

Keywords: out-of-sequence thrust, chaura thrust, sarahan thrust, jakhri thrust, higher himalaya, s/c- fabric

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Authors: Shibo Wei, Ting Jiang

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Convolutional-recurrent neural networks (CRN) have achieved much success recently in the speech enhancement field. The common processing method is to use the convolution layer to compress the feature space by multiple upsampling and then model the compressed features with the LSTM layer. At last, the enhanced speech is obtained by deconvolution operation to integrate the global information of the speech sequence. However, the feature space compression process may cause the loss of information, so we propose to model the upsampling result of each step with the residual LSTM layer, then join it with the output of the deconvolution layer and input them to the next deconvolution layer, by this way, we want to integrate the global information of speech sequence better. The experimental results show the network model (RES-CRN) we introduce can achieve better performance than LSTM without residual and overlaying LSTM simply in the original CRN in terms of scale-invariant signal-to-distortion ratio (SI-SNR), speech quality (PESQ), and intelligibility (STOI).

Keywords: convolutional-recurrent neural networks, speech enhancement, residual LSTM, SI-SNR

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Authors: Martina I. Reinhold, Theresa Bacon-Baguley

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Background: Medical knowledge continuously evolves and to help health care providers to stay up-to-date, evidence-based medicine (EBM) has emerged as a model. The practice of EBM requires new skills of the health care provider, including directed literature searches, the critical evaluation of research studies, and the direct application of the findings to patient care. This paper describes the integration and evaluation of an evidence-based medicine course sequence into a Physician Assistant curriculum. This course sequence teaches students to manage and use the best clinical research evidence to competently practice medicine. A survey was developed to assess the outcomes of the EBM course sequence. Methodology: The cornerstone of the three-semester sequence of EBM are interactive small group discussions that are designed to introduce students to the most clinically applicable skills to identify, manage and use the best clinical research evidence to improve the health of their patients. During the three-semester sequence, the students are assigned each semester to participate in small group discussions that are facilitated by faculty with varying background and expertise. Prior to the start of the first EBM course in the winter semester, PA students complete a knowledge-based survey that was developed by the authors to assess the effectiveness of the course series. The survey consists of 53 Likert scale questions that address the nine objectives for the course series. At the end of the three semester course series, the same survey was given to all students in the program and the results from before, and after the sequence of EBM courses are compared. Specific attention is paid to overall performance of students in the nine course objectives. Results: We find that students from the Class of 2016 and 2017 consistently improve (as measured by percent correct responses on the survey tool) after the EBM course series (Class of 2016: Pre- 62% Post- 75%; Class of 2017: Pre- 61 % Post-70%). The biggest increase in knowledge was observed in the areas of finding and evaluating the evidence, with asking concise clinical questions (Class of 2016: Pre- 61% Post- 81%; Class of 2017: Pre- 61 % Post-75%) and searching the medical database (Class of 2016: Pre- 24% Post- 65%; Class of 2017: Pre- 35 % Post-66 %). Questions requiring students to analyze, evaluate and report on the available clinical evidence regarding diagnosis showed improvement, but to a lesser extend (Class of 2016: Pre- 56% Post- 77%; Class of 2017: Pre- 56 % Post-61%). Conclusions: Outcomes identified that students did gain skills which will allow them to apply EBM principles. In addition, the outcomes of the knowledge-based survey allowed the faculty to focus on areas needing improvement, specifically the translation of best evidence into patient care. To address this area, the clinical faculty developed case scenarios that were incorporated into the lecture and discussion sessions, allowing students to better connect the research studies with patient care. Students commented that ‘class discussion and case examples’ contributed most to their learning and that ‘it was helpful to learn how to develop research questions and how to analyze studies and their significance to a potential client’. As evident by the outcomes, the EBM courses achieved the goals of the course and were well received by the students. 

Keywords: evidence-based medicine, clinical education, assessment tool, physician assistant

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Authors: Nikolaos Mamalis

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The work of the eminent architect and composer has undoubtedly been influenced both by his architecture and collaboration with Le Corbusier and by the conquests of the musical avant-garde of the 20th century (Schoenberg, Messian, Bartock, electroacoustic music). It is known that the golden mean and the Fibonacci sequence played a momentous role in the Architectural Avant-garde (Modulor) and expanded on musical pursuits. Especially in the 50s (serialism), it was a structural tool for composition. Xenakis' architectural and musical work (Sacrifice, Metastasis, Rebonds, etc.) received the influence of the Golden Section, as has been repeatedly demonstrated. However, the idea of this retrospective sequence and the reflection raised by the search for new proportions, both in the architectural and the musical work of Xenakis, was not limited to constituting a step, a workable formula that acted unifyingly with regard to the other parameters of the musical work, or as an aesthetic model that makes sense - philosophically and poetically - an anthropocentric dimension as in other composers (see Luigi Nono) ̇ triggered a qualitative leap, an opening of the composer to the assimilation of mathematical concepts and scientific types in music and the consolidation of new sound horizons of stochastic music.

Keywords: golden ratio, music, space, stochastic music

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Authors: E. L. Albuquerque, U. L. Fulco, G. S. Ourique

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The focus of this work is on the numerical investigation of the charge transport properties of the de novo-designed alpha3 polypeptide, as well as in its variants, all of them probed by gene engineering. The theoretical framework makes use of a tight-binding model Hamiltonian, together with ab-initio calculations within quantum chemistry simulation. The alpha3 polypeptide is a 21-residue with three repeats of the seven-residue amino acid sequence Leu-Glu-Thr-Leu-Ala-Lys-Ala, forming an alpha–helical bundle structure. Its variants are obtained by Ala→Gln substitution at the e (5th) and g (7th) position, respectively, of the alpha3 polypeptide amino acid sequence. Using transmission electron microscopy and atomic force microscopy, it was observed that the alpha3 polypeptide and one of its variant do have the ability to form fibrous assemblies, while the other does not. Our main aim is to investigate whether or not the biased alpha3 polypeptide and its variants can be also identified by quantum charge transport measurements through current-voltage (IxV) curves as a pattern to characterize their fibrous assemblies. It was observed that each peptide has a characteristic current pattern, which may be distinguished by charge transport measurements, suggesting that it might be a useful tool for the development of biosensors.

Keywords: charge transport properties, electronic transmittance, current-voltage characteristics, biological sensor

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Authors: Aishik Deb, Rituparna Sinha

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We have developed an algorithm to detect the abnormal segment/"structural variation in the genome across a number of samples. We have worked on simulated as well as real data from the BAM Files and have designed a segmentation algorithm where abnormal segments are detected. This algorithm aims to improve the accuracy and performance of the existing CNV-CH algorithm. The next-generation sequencing (NGS) approach is very fast and can generate large sequences in a reasonable time. So the huge volume of sequence information gives rise to the need for Big Data and parallel approaches of segmentation. Therefore, we have designed a map-reduce approach for the existing CNV-CH algorithm where a large amount of sequence data can be segmented and structural variations in the human genome can be detected. We have compared the efficiency of the traditional and map-reduce algorithms with respect to precision, sensitivity, and F-Score. The advantages of using our algorithm are that it is fast and has better accuracy. This algorithm can be applied to detect structural variations within a genome, which in turn can be used to detect various genetic disorders such as cancer, etc. The defects may be caused by new mutations or changes to the DNA and generally result in abnormally high or low base coverage and quantification values.

Keywords: cancer detection, convex hull segmentation, map reduce, next generation sequencing

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Authors: William Feng, Qingyu Gao

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Despite the extensive discussions about Hong Kong’s sentiments towards the Chinese Mainland since the sovereignty transfer in 1997, there has been no large-scale empirical analysis of the changing attitudes in the mainstream media, which both reflect and shape sentiments in the society. To address this gap, the present study uses an optimised semantic-based automatic sentiment analysis method to examine a corpus of news about China from 1997 to 2020 in three main Chinese-language newspapers in Hong Kong, namely Apple Daily, Ming Pao, and Oriental Daily News. The analysis shows that although the Hong Kong press had a positive emotional tone toward China in general, the overall trend of sentiment was becoming increasingly negative. Meanwhile, the alignment and antagonism toward China have both increased, providing empirical evidence of attitudinal polarisation in the Hong Kong society. Specifically, Apple Daily’s depictions of China have become increasingly negative, though with some positive turns before 2008, whilst Oriental Daily News has consistently expressed more favourable sentiments. Ming Pao maintained an impartial stance toward China through an increased but balanced representation of positive and negative sentiments, with its subjectivity and sentiment intensity growing to an industry-standard level. The results provide new insights into the complexity of sentiments towards China in the Hong Kong press and media attitudes in general in terms of the “us” and “them” positioning by explicating the cross-newspaper and cross-period variations using an enhanced sentiment analysis method which incorporates sentiment-oriented and semantic role analysis techniques.

Keywords: media attitude, sentiment analysis, Hong Kong press, one country two systems

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Authors: Mahdi Fakoor, Seyed Mohammad Navid Ghoreishi

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Composite patching is a common way for reinforcing the cracked pipes and cylinders. The effects of composite patch reinforcement on fracture parameters of a cracked pipe depend on a variety of parameters such as number of layers, angle, thickness, and material of each layer. Therefore, stacking sequence optimization of composite patch becomes crucial for the applications of cracked pipes. In this study, in order to obtain the optimal stacking sequence for a composite patch that has minimum weight and maximum resistance in propagation of cracks, a coupled Multi-Objective Genetic Algorithm (MOGA) and Finite Element Method (FEM) process is proposed. This optimization process has done for longitudinal and transverse semi-elliptical cracks and optimal stacking sequences and Pareto’s front for each kind of cracks are presented. The proposed algorithm is validated against collected results from the existing literature.

Keywords: multi objective optimization, pareto front, composite patch, cracked pipe

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Authors: Isabelle Snyder, Travis Smith

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Microgrid protection presents challenges to conventional protection techniques due to the low-induced fault current. Protection relays present in microgrid applications require a combination of settings groups to adjust based on the architecture of the microgrid in islanded and grid-connected modes. In a radial system where the microgrid is at the other end of the feeder, directional elements can be used to identify the direction of the fault current and switch settings groups accordingly (grid-connected or microgrid-connected). However, with multiple microgrid connections, this concept becomes more challenging, and the direction of the current alone is not sufficient to identify the source of the fault current contribution. ORNL has previously developed adaptive relaying schemes through other DOE-funded research projects that will be evaluated and used as a baseline for this research. The four protection techniques in this study are labeled as follows: (1) Adaptive Current only Protection System (ACPS), Intentional (2) Unbalanced Control for Protection Control (IUCPC), (3) Adaptive Protection System with Communication Controller (APSCC) (4) Adaptive Model-Driven Protective Relay (AMDPR).

Keywords: adaptive relaying, microgrid protection, sequence components, islanding detection

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Authors: Gurjit Kaur, Shashank Johri, Arpit Mehrotra

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In this paper we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension i.e. time slots whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for OCDMA system on a single platform. Results shows that 1D Extended Prime Code (EPC) can support more number of active users compared to other codes but at the expense of larger code length which further increases the complexity of the code. Modified Prime Code (MPC) supports lesser number of active users at λc=2 but it has a lesser code length as compared to 1D prime code. Analysis shows that 2D prime code supports lesser number of active users than 1D codes but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa

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Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

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Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

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Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

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The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson, and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence-based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation-prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: aggregation, amyloids, thermophilic proteins, amino acid residues, machine learning techniques

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Authors: Ovidiu Domşa, Nicolae Bold

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Using Information and Communication Technologies (ICT) notions in education and three basic processes of education (teaching, learning and assessment) can bring benefits to the pupils and the professional development of teachers. In this matter, we refer to these notions as concepts taken from the informatics area and apply them to the domain of education. These notions refer to genetic algorithms and arborescent structures, used in the specific process of assessment or evaluation. This paper uses these kinds of notions to generate subtrees from a main tree of tests related between them by their degree of difficulty. These subtrees must contain the highest number of connections between the nodes and the lowest number of missing edges (which are subtrees of the main tree) and, in the particular case of the non-existence of a subtree with no missing edges, the subtrees which have the lowest (minimal) number of missing edges between the nodes, where a node is a test and an edge is a direct connection between two tests which differs by one degree of difficulty. The subtrees are represented as sequences. The tests are the same (a number coding a test represents that test in every sequence) and they are reused for each sequence of tests.

Keywords: chromosome, genetic algorithm, subtree, test

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Authors: Harveen Kaur Tatla, Parisa Niknejad, Rajender Gupta, Bipro Ranjan Dhar, Mohd. Adana Khan

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Sewage sludge management presents a pressing challenge in the realm of wastewater treatment, calling for sustainable and efficient solutions. This study explores the integration of Hydrothermal Liquefaction (HTL) and Anaerobic Digestion (AD) as a promising approach to address the complexities associated with sewage sludge treatment. The integration of these two processes offers a complementary and synergistic framework, allowing for the mitigation of inherent limitations, thereby enhancing overall efficiency, product quality, and the comprehensive utilization of sewage sludge. In this research, we investigate the optimal sequencing of HTL and AD within the treatment framework, aiming to discern which sequence, whether HTL followed by AD or AD followed by HTL, yields superior results. We explore a range of HTL working temperatures, including 250°C, 300°C, and 350°C, coupled with residence times of 30 and 60 minutes. To evaluate the effectiveness of each sequence, a battery of tests is conducted on the resultant products, encompassing Total Ammonia Nitrogen (TAN), Chemical Oxygen Demand (COD), and Volatile Fatty Acids (VFA). Additionally, elemental analysis is employed to determine which sequence maximizes energy recovery. Our findings illuminate the intricate dynamics of HTL and AD integration for sewage sludge management, shedding light on the temperature-residence time interplay and its impact on treatment efficiency. This study not only contributes to the optimization of sewage sludge treatment but also underscores the potential of integrated processes in sustainable waste management strategies. The insights gleaned from this research hold promise for advancing the field of wastewater treatment and resource recovery, addressing critical environmental and energy challenges.

Keywords: Anaerobic Digestion (AD), aqueous phase, energy recovery, Hydrothermal Liquefaction (HTL), sewage sludge management, sustainability.

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Authors: Harsh Panchal, Saurabh Amrutkar

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Quality management is an essential part of any project that has directly related to the performance of a project. Quality management is depended on multiple factors at different stages in a project, right from time management to construction logistics. A project is a mixture of various components that include iternary management, health and safety, crew productivity, and many more. From the survey conducted, we came to the conclusion that advancement in technology and indigenous approach to any project will result in maximum quality standards and better project performance. In this paper, we discuss various components of the factors above that lead to compromise the quality of a project and how it can be controlled in order to achieve maximum quality assurance using quality planning and total quality management. The paper also focuses on limitations and problems faced in each factor responsible for quality management and to tackle them using techniques and processes based on activities and identifying the sequence, approaching critical path, and duration. The project management concept that deals with the sequence of scope cost time give us an overview regarding the ongoing quality management, in a nutshell, giving us hints to regulate the current procedure for maximum achievable quality. It also deals with the problems faced by engineers that make the mundane work process slow, reducing the quality outcome drastically.

Keywords: management, performance, project, quality

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Authors: Sabeen Alam, Mehboob Alam

Abstract:

The research work entitled “Effect of Bacillus pumilus strains on heavy metal accumulation in lettuce grown on contaminated soil” focused on functional role of Bacillus pumilus strains inoculated with lettuce seed in mitigating heavy metal in chromite mining soil. In this experiment, factor A was three Bacillus pumilus strains (sequence C-2PMW-8, C-1 SSK-8 and C-1 PWK-7) while soil used for this experiment was collected from Prang Ghar mining site and lettuce seeds were grown in three levels of chromite mining soil (2.27, 4.65 and 7.14 %). For mining soil minimum days to germinate noted in lettuce grown on garden soil inoculated with sequence. Maximum germination percentage noted was for C-1 SSK-8 grown on garden soil, maximum lettuce height for sequence C-2 PWM-8, fresh leaf weight for C-1 PWK-7 inoculated lettuce, dry weight of lettuce leaf for lettuce inoculated with C-1 SSK-8 and C-1 PWK-7 strains, number of leaves per plant for lettuce inoculated with C-1 SSK-8, leaf area for C-2 PMW-8 inoculated lettuce, survival percentage for C-1 SSK-8 treated lettuce and chlorophyll content for C-2 PMW-8. Results related to heavy metals accumulation showed that minimum chromium was in lettuce and in soil for all three sequences, cadmium (Cd) in lettuce and in soil for all three sequences, manganese (Mn) in lettuce and in soil for three sequences, lead (Pb) in lettuce and in soil for three sequences. It can be concluded that chromite mining soil significantly reduced the growth and survival of lettuce, but when lettuce was inoculated with Bacillus.pumilus strains, it enhances growth and survival. Similarly, minimum heavy metal accumulation in plant and soil, regardless of type of Bacillus pumilus used, all three sequences has same mitigating effect on heavy metal in both soil and lettuce. All the three Bacillus pumilus strains ensured reduction in heavy metals content (Mn, Cd, Cr) in lettuce, below the maximum permissible limits of WHO 2011.

Keywords: bacillus pumilus, heavy metals, permissible limits, lettuce, chromite mining soil, mitigating effect

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Authors: Isabelle Snyder

Abstract:

Microgrid protection presents challenges to conventional protection techniques due to the low induced fault current. Protection relays present in microgrid applications require a combination of settings groups to adjust based on the architecture of the microgrid in islanded and grid-connected mode. In a radial system where the microgrid is at the other end of the feeder, directional elements can be used to identify the direction of the fault current and switch settings groups accordingly (grid connected or microgrid connected). However, with multiple microgrid connections, this concept becomes more challenging, and the direction of the current alone is not sufficient to identify the source of the fault current contribution. ORNL has previously developed adaptive relaying schemes through other DOE-funded research projects that will be evaluated and used as a baseline for this research. The four protection techniques in this study are the following: (1) Adaptive Current only Protection System (ACPS), Intentional (2) Unbalanced Control for Protection Control (IUCPC), (3) Adaptive Protection System with Communication Controller (APSCC) (4) Adaptive Model-Driven Protective Relay (AMDPR). The first two methods focus on identifying the islanded mode without communication by monitoring the current sequence component generated by the system (ACPS) or induced with inverter control during islanded mode (IUCPC) to identify the islanding condition without communication at the relay to adjust the settings. These two methods are used as a backup to the APSCC, which relies on a communication network to communicate the islanded configuration to the system components. The fourth method relies on a short circuit model inside the relay that is used in conjunction with communication to adjust the system configuration and computes the fault current and adjusts the settings accordingly.

Keywords: adaptive relaying, microgrid protection, sequence components, islanding detection, communication controlled protection, integrated short circuit model

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Authors: Othman Maklouf, Ahmed Adwaib

Abstract:

This paper introduces a comparative study between the main GPS/INS coupling schemes, this will include the loosely coupled and tightly coupled configurations, several types of situations and operational conditions, in which the data fusion process is done using Kalman filtering. This will include the importance of sensors calibration as well as the alignment of the strap down inertial navigation system. The limitations of the inertial navigation systems are investigated.

Keywords: GPS, INS, Kalman filter, sensor calibration, navigation system

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Authors: Harsh Vikram Singh, Ankur Rai, Anand Mohan

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In this paper, we propose secure and robust data hiding algorithm based on DCT by Arnold transform and chaotic sequence. The watermark image is scrambled by Arnold cat map to increases its security and then the chaotic map is used for watermark signal spread in middle band of DCT coefficients of the cover image The chaotic map can be used as pseudo-random generator for digital data hiding, to increase security and robustness .Performance evaluation for robustness and imperceptibility of proposed algorithm has been made using bit error rate (BER), normalized correlation (NC), and peak signal to noise ratio (PSNR) value for different watermark and cover images such as Lena, Girl, Tank images and gain factor .We use a binary logo image and text image as watermark. The experimental results demonstrate that the proposed algorithm achieves higher security and robustness against JPEG compression as well as other attacks such as addition of noise, low pass filtering and cropping attacks compared to other existing algorithm using DCT coefficients. Moreover, to recover watermarks in proposed algorithm, there is no need to original cover image.

Keywords: data hiding, watermarking, DCT, chaotic sequence, arnold transforms

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Authors: Dieter Veldsman, Theo Heyns Veldsman

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The knowledge economy demands an organisation that is flexible, adaptable and able to navigate the ever-changing environment. This fast-paced environment has however resulted in an organizational landscape that battles to engage employees, retain top talent and create meaningful work for its members. In the knowledge economy, the concept of organizational identity has become an important consideration as organisations aim to create a compelling and inviting narrative for all stakeholders across the business value chain. Values are often seen as the behavioural framework that informs organisational culture, yet often values are perceived to be inauthentic and misaligned with the true character or identity of the organisation and how it is perceived by different role players. This paper focuses on exploring the relationship between organisational identity and value systems by focusing on a case study within a multi-national organisation within South Africa. The paper evaluates the implementation of mixed methods OD approach that gathered collaborative inputs of more than 4500 employees who participated in crafting the newly established values system post a retrenchment process. The paper will evaluate the relationship between the newly crafted value system and the identity of the organisation as described by various internal and external stakeholders in order to explore potential alignment, dissonance and key insights into understanding the relationship between organisational identity and values. The case study will be reported from the perspective of an OD consultant who supported the transformation process over a period of 8 months and aims to provide key insights into values and identity alignment within knowledge economy organisations. From a practical perspective, the paper provides insights into how values are created, perceived and lived within organisations and the impact on employee engagement and culture.

Keywords: culture, organisational development, organisational identity, values

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Authors: Moneesh Thakur, Hridayesh Prasad, Nikitasha Bora, Parimal Roy Choudhary, A. K. Samanta, Sanjeev Kumar

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Canine demodicosis is a common parasitic condition which involves dog skin. Demodicosis in dogs is due the prominent growth of Demodex. Out of various canine Demodex spp., Demodex canis is the most often involved species. Canine demodicosis can occur as either a localized or generalized form of demodicosis severely affect the dogs and in non-treated dogs may cause death. This study was planned with the aim to screen and characterize the 18S rRNA gene of isolated Demodex canis. A total of 1200 dogs were screened during this study period. The skin scrapings of all the suspected dogs were examined under a microscope at 100X magnification for the presence of Demodex canis. The skin scrapings positive for Demodex canis were examined using PCR for confirmation. A total of 35 dogs were confirmed a positive result for D. canis based on 18S rRNA gene amplification by PCR. Further, the 18S rRNA gene of isolated Demodex canis was cloned and sequenced for genome analysis. On the sequence analysis, it was found that isolated sequence (GenBank Accession No. MK177513) had close similarity (99.7%) to that of D. canis genotype of China (Accession No. MG372254).

Keywords: PCR, phylogenetic analysis, cloning and sequening, Demodex canis

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Authors: Girma Yohannis Bade, Olga Kolesnikova, Grigori Sidorov

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Named entity recognition (NER) is a building block for information extraction. Though the information extraction process has been automated using a variety of techniques to find and extract a piece of relevant information from unstructured documents, the discovery of targeted knowledge still poses a number of research difficulties because of the variability and lack of structure in Web data. NER, a subtask of information extraction (IE), came to exist to smooth such difficulty. It deals with finding the proper names (named entities), such as the name of the person, country, location, organization, dates, and event in a document, and categorizing them as predetermined labels, which is an initial step in IE tasks. This survey paper presents the roles and importance of NER to IE from the perspective of different algorithms and application area domains. Thus, this paper well summarizes how researchers implemented NER in particular application areas like finance, medicine, defense, business, food science, archeology, and so on. It also outlines the three types of sequence labeling algorithms for NER such as feature-based, neural network-based, and rule-based. Finally, the state-of-the-art and evaluation metrics of NER were presented.

Keywords: the role of NER, named entity recognition, information extraction, sequence labeling algorithms, named entity application area

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Authors: David de Oliveira Costa, Miguel Ângelo Lellis Moreira, Carlos Francisco Simões Gomes, Daniel Augusto de Moura Pereira, Marcos dos Santos

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Strategic management is a fundamental process for global companies that intend to remain competitive in an increasingly dynamic and complex market. To do so, it is necessary to maintain alignment with their principles and values. The Balanced Scorecard (BSC) proposes to ensure that the overall business performance is based on different perspectives (financial, customer, internal processes, and learning and growth). However, relying solely on the BSC may not be enough to ensure the success of strategic management. It is essential that companies also evaluate and prioritize strategic projects that need to be implemented to ensure they are aligned with the business vision and contribute to achieving established goals and objectives. In this context, the proposition involves the incorporation of the SAPEVO-M multicriteria method to indicate the degree of relevance between different perspectives. Thus, the strategic objectives linked to these perspectives have greater weight in the classification of structural projects. Additionally, it is proposed to apply the concept of the Impact & Probability Matrix (I&PM) to structure and ensure that strategic projects are evaluated according to their relevance and impact on the business. By structuring the business's strategic management in this way, alignment and prioritization of projects and actions related to strategic planning are ensured. This ensures that resources are directed towards the most relevant and impactful initiatives. Therefore, the objective of this article is to present the proposal for integrating the BSC methodology, the SAPEVO-M multicriteria method, and the prioritization matrix to establish a concrete weighting of strategic planning and obtain coherence in defining strategic projects aligned with the business vision. This ensures a robust decision-making support process.

Keywords: MCDA process, prioritization problematic, corporate strategy, multicriteria method

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

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The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Avent Grange, Frederic Bertrand, Jean-Baptiste Droin, Amandine Marrel, Jean-Henry Ferrasse, Olivier Boutin

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CEA and its industrial partners are designing a gas Power Conversion System (PCS) based on a Brayton cycle for the ASTRID Sodium-cooled Fast Reactor. Investigations of control and regulation requirements to operate this PCS during operating, incidental and accidental transients are necessary to adapt core heat removal. To this aim, we developed a methodology to optimize the thermal-hydraulic behavior of the reactor during normal operations, incidents and accidents. This methodology consists of a multi-objective optimization for a specific sequence, whose aim is to increase component lifetime by reducing simultaneously several thermal stresses and to bring the reactor into a stable state. Furthermore, the multi-objective optimization complies with safety and operating constraints. Operating, incidental and accidental sequences use specific regulations to control the thermal-hydraulic reactor behavior, each of them is defined by a setpoint, a controller and an actuator. In the multi-objective problem, the parameters used to solve the optimization are the setpoints and the settings of the controllers associated with the regulations included in the sequence. In this way, the methodology allows designers to define an optimized and specific control strategy of the plant for the studied sequence and hence to adapt PCS piloting at its best. The multi-objective optimization is performed by evolutionary algorithms coupled to surrogate models built on variables computed by the thermal-hydraulic system code, CATHARE2. The methodology is applied to a loss of off-site power sequence. Three variables are controlled: the sodium outlet temperature of the sodium-gas heat exchanger, turbomachine rotational speed and water flow through the heat sink. These regulations are chosen in order to minimize thermal stresses on the gas-gas heat exchanger, on the sodium-gas heat exchanger and on the vessel. The main results of this work are optimal setpoints for the three regulations. Moreover, Proportional-Integral-Derivative (PID) control setting is considered and efficient actuators used in controls are chosen through sensitivity analysis results. Finally, the optimized regulation system and the reactor control procedure, provided by the optimization process, are verified through a direct CATHARE2 calculation.

Keywords: gas power conversion system, loss of off-site power, multi-objective optimization, regulation, sodium fast reactor, surrogate model

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Authors: Rizka Ardhiyana, Liesbetini Haditjaroko, Sri Mulijani, Reki Ashadi Wicaksono, Raafqi Ranasasmita

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Designing a sensitive, specific and easy to use method to detect pork contamination in the food industry remains a major challenge. In the current study, we developed a sensitive thiol-bond AuNP-Probe biosensor that will change color when detecting pork DNA in the Cytochrome B region. The interaction between the biosensors and DNA sample is measured by spectrophotometer at 540 nm. The biosensor is made by reducing gold with trisodium citrate to produce gold nanoparticle with 39.05 nm diameter. The AuNP-Probe biosensor (gold nanoprobe) achieved 16.04 ng DNA/µl limit of detection and 53.48 ng DNA/µl limit of quantification. The linearity (R2) between color absorbance changes and DNA concentration is 0.9916. The biosensor has a good specificty as it does not cross-react with DNA of chicken and beef. To verify specificity towards the target sequence, PCR was tested to the target sequence and reacted to the PCR product with the biosensor. The PCR DNA isolate resulted in a 2.7 fold higher absorbance compared to pork-DNA isolate alone (without PCR). The sensitivity and specificity of the method show the promising application of the thiol-bond AuNP biosensor in pork-detection.

Keywords: biosensor, DNA probe, gold nanoparticle (AuNP), pork meat, qPCR

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Authors: Rita Lopa, Yukihiro Shimatani

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The focus of this research is 880m extension development along the Kamisaigo River. The river is flowing tributary of grade 2 rivers Fukutsu City, Fukuoka Prefecture. This river is a small-scale urban river and the river was formerly a straight concrete sea wall construction. The river runs through National Highway No. 3 from the confluence of Saigo River. The study covers the river basin about 326 ha with a catchment area of 20.63 ha and 4,700 m3 capacity regulating pond. The river is not wide, shallow, and has a straight alignment with active (un-vegetated) river channel sinuosity (ratio of river length to valley length) ranging between 1 and 1.3. However, the alignment of the low-flow river channel does have meandering or sinuous characteristics. Flooding is likely to occur. It has become difficult to live in the environment for organisms of the river. Hydrophilic is very low (children cannot play). There is little connection with the local community. Overall, the Kamisaigo River watershed is heavily urbanized and from a morphological, biological and habitat perspective, Kamisaigo River functions marginally not well. For river improvement and maintenance of the Kamisaigo River, the workshop was conducted in the form of planning for the proposed model is presented by the Watershed Management Laboratory. This workshop showed the relationship between citizens, City Government, and University of mutual trust has been established, that have been made landscape, environment, usage, etc.: retaining wall maintenance, hydrophilic zone, landscape zone, nature walks zone: adjacent medical facilities and adjacent to large commercial facilities. Propose of Nature walks zone with point of the design: provide slope that the wheelchair can access and walking paths to enjoy the scenery, and summary of the Kamisaigo River workshop: creating a multi-model study and creation of natural rivers.

Keywords: river restoration, river improvement, natural rivers, Saigo River

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