Search results for: sequence analysis

Authors: Alireza Dantism

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Presently, describing the function of a protein sequence is one of the most common problems in biology. Usually, this problem can be facilitated by studying the three-dimensional structure of proteins. In the absence of a protein structure, comparative modeling often provides a useful three-dimensional model of the protein that is dependent on at least one known protein structure. Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) mainly based on its alignment with one or more proteins of known structure (templates). Comparative modeling consists of four main steps 1. Similarity between the target sequence and at least one known template structure 2. Alignment of target sequence and template(s) 3. Build a model based on alignment with the selected template(s). 4. Prediction of model errors 5. Optimization of the built model There are many computer programs and web servers that automate the comparative modeling process. One of the most important advantages of these servers is that it makes comparative modeling available to both experts and non-experts, and they can easily do their own modeling without the need for programming knowledge, but some other experts prefer using programming knowledge and do their modeling manually because by doing this they can maximize the accuracy of their modeling. In this study, a web-based tool has been designed to predict the tertiary structure of proteins using PHP and Python programming languages. This tool is called EasyModel. EasyModel can receive, according to the user's inputs, the desired unknown sequence (which we know as the target) in this study, the protein sequence file (template), etc., which also has a percentage of similarity with the primary sequence, and its third structure Predict the unknown sequence and present the results in the form of graphs and constructed protein files.

Keywords: structural bioinformatics, protein tertiary structure prediction, modeling, comparative modeling, modeller

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Authors: Balamurali Gunji, B. B. V. L. Deepak, B. B. Biswal, Amrutha Rout, Golak Bihari Mohanta

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Robots play an important role in the operations like pick and place, assembly, spot welding and much more in manufacturing industries. Out of those, assembly is a very important process in manufacturing, where 20% of manufacturing cost is wholly occupied by the assembly process. To do the assembly task effectively, Assembly Sequences Planning (ASP) is required. ASP is one of the multi-objective non-deterministic optimization problems, achieving the optimal assembly sequence involves huge search space and highly complex in nature. Many researchers have followed different algorithms to solve ASP problem, which they have several limitations like the local optimal solution, huge search space, and execution time is more, complexity in applying the algorithm, etc. By keeping the above limitations in mind, in this paper, a new automated optimal robotic assembly sequence planning using Artificial Bee Colony (ABC) Algorithm is proposed. In this algorithm, automatic extraction of assembly predicates is done using Computer Aided Design (CAD) interface instead of extracting the assembly predicates manually. Due to this, the time of extraction of assembly predicates to obtain the feasible assembly sequence is reduced. The fitness evaluation of the obtained feasible sequence is carried out using ABC algorithm to generate the optimal assembly sequence. The proposed methodology is applied to different industrial products and compared the results with past literature.

Keywords: assembly sequence planning, CAD, artificial Bee colony algorithm, assembly predicates

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Authors: Sanjay Kumar Parjapati, Ajai Jain

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This paper presents optimization of makespan for ‘n’ jobs and ‘m’ machines flexible job shop scheduling problem with sequence dependent setup time using genetic algorithm (GA) approach. A restart scheme has also been applied to prevent the premature convergence. Two case studies are taken into consideration. Results are obtained by considering crossover probability (pc = 0.85) and mutation probability (pm = 0.15). Five simulation runs for each case study are taken and minimum value among them is taken as optimal makespan. Results indicate that optimal makespan can be achieved with more than one sequence of jobs in a production order.

Keywords: flexible job shop, genetic algorithm, makespan, sequence dependent setup times

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Authors: S. H. Borghei, E. Teymourian, M. Mobin, G. M. Komaki, S. Sheikh

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Imperialist competitive algorithm (ICA) is a recent meta-heuristic method that is inspired by the social evolutions for solving NP-Hard problems. The ICA is a population based algorithm which has achieved a great performance in comparison to other meta-heuristics. This study is about developing enhanced ICA approach to solve the cell formation problem (CFP) using sequence data. In addition to the conventional ICA, an enhanced version of ICA, namely EICA, applies local search techniques to add more intensification aptitude and embed the features of exploration and intensification more successfully. Suitable performance measures are used to compare the proposed algorithms with some other powerful solution approaches in the literature. In the same way, for checking the proficiency of algorithms, forty test problems are presented. Five benchmark problems have sequence data, and other ones are based on 0-1 matrices modified to sequence based problems. Computational results elucidate the efficiency of the EICA in solving CFP problems.

Keywords: cell formation problem, group technology, imperialist competitive algorithm, sequence data

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Authors: G. Tamilpavai, C. Vishnuppriya

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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.

Keywords: bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM

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Authors: Himanshu Kumar Gupta

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The Jaisalmer Basin is one of the parts of the Rajasthan basin in northwestern India. The presence of five major unconformities/hiatuses of varying span i.e. at the top of Archean basement, Cambrian, Jurassic, Cretaceous, and Eocene have created the foundation for constructing a sequence stratigraphic framework. Based on basin formative tectonic events and their impact on sedimentation processes three first-order sequences have been identified in Rajasthan Basin. These are Proterozoic-Early Cambrian rift sequence, Permian to Middle-Late Eocene shelf sequence and Pleistocene - Recent sequence related to Himalayan Orogeny. The Permian to Middle Eocene I order sequence is further subdivided into three-second order sequences i.e. Permian to Late Jurassic II order sequence, Early to Late Cretaceous II order sequence and Paleocene to Middle-Late Eocene II order sequence. In this study, Late Jurassic to Early Cretaceous sequence was identified and log-based interpretation of smaller order T-R cycles have been carried out. A log profile from eastern margin to western margin (up to Shahgarh depression) has been taken. The depositional environment penetrated by the wells interpreted from log signatures gave three major facies association. The blocky and coarsening upward (funnel shape), the blocky and fining upward (bell shape) and the erratic (zig-zag) facies representing distributary mouth bar, distributary channel and marine mud facies respectively. Late Jurassic Formation (Baisakhi-Bhadasar) and Early Cretaceous Formation (Pariwar) shows a lesser number of T-R cycles in shallower and higher number of T-R cycles in deeper bathymetry. Shallowest well has 3 T-R cycles in Baisakhi-Bhadasar and 2 T-R cycles in Pariwar, whereas deeper well has 4 T-R cycles in Baisakhi-Bhadasar and 8 T-R cycles in Pariwar Formation. The Maximum Flooding surfaces observed from the stratigraphy analysis indicate major shale break (high shale content). The study area is dominated by the alternation of shale and sand lithologies, which occurs in an approximate ratio of 70:30. A seismo-geological cross section has been prepared to understand the stratigraphic thickness variation and structural disposition of the strata. The formations are quite thick to the west, the thickness of which reduces as we traverse towards the east. The folded and the faulted strata indicated the compressional tectonics followed by the extensional tectonics. Our interpretation is supported with seismic up to second order sequence indicates - Late Jurassic sequence is a Highstand Systems Tract (Baisakhi - Bhadasar formations), and the Early Cretaceous sequence is Regressive to Lowstand System Tract (Pariwar Formation).

Keywords: Jaisalmer Basin, sequence stratigraphy, system tract, T-R cycle

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Authors: James Jr. Mashiyane, Risuna Nkolele, Stephanie J. Müller, Gciniwe S. Dlamini, Rebone L. Meraba, Darlington S. Mapiye

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When performing language tasks in natural language processing (NLP), the dimensionality of word embeddings is chosen either ad-hoc or is calculated by optimizing the Pairwise Inner Product (PIP) loss. The PIP loss is a metric that measures the dissimilarity between word embeddings, and it is obtained through matrix perturbation theory by utilizing the unitary invariance of word embeddings. Unlike in natural language, in genomics, especially in genome sequence processing, unlike in natural language processing, there is no notion of a “word,” but rather, there are sequence substrings of length k called k-mers. K-mers sizes matter, and they vary depending on the goal of the task at hand. The dimensionality of word embeddings in NLP has been studied using the matrix perturbation theory and the PIP loss. In this paper, the sufficiency and reliability of applying word-embedding algorithms to various genomic sequence datasets are investigated to understand the relationship between the k-mer size and their embedding dimension. This is completed by studying the scaling capability of three embedding algorithms, namely Latent Semantic analysis (LSA), Word2Vec, and Global Vectors (GloVe), with respect to the k-mer size. Utilising the PIP loss as a metric to train embeddings on different datasets, we also show that Word2Vec outperforms LSA and GloVe in accurate computing embeddings as both the k-mer size and vocabulary increase. Finally, the shortcomings of natural language processing embedding algorithms in performing genomic tasks are discussed.

Keywords: word embeddings, k-mer embedding, dimensionality reduction

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Authors: G. B. Manjunatha

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Natural fibers have been considerable demand in recent years due to their ecofriendly and renewable nature. The advantages of low density, acceptable specific properties, better thermal and insulate properties with low cost.In the present study, hybrid composite associating Sheep wool fiber and glass fiber reinforced with epoxy were developed and investigated the effect of stacking sequence on physical and chemical properties. The hybrid composite was designed for engineering applications as an alternative material to glass fiber composites. The hybrid composite laminates were fabricated by using hand lay-up technique at total fiber volume fraction of 60% (Sheep wool fiber 30% and Glass fiber 30%) and 40% reinforcement. The specimen preparation and testing were conducted as per American Society for Testing and Materials (ASTM) standards. Three different stacking are used. The result shows that tensile and bending tests of sequence of glass fiber between sheep wool fiber have high strength and maximum bending compared to other sequence of composites. At the same time better moisture and chemical absorption were observed.

Keywords: hybrid composites, mechanical properties, polymer composites, stacking sequence

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Authors: Ahmad Helman Hamdani, Diana Putri Hamdiana

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The Sajau coal measures of Berau Basin, northeastern Kalimantan were deposited within a range of facies associations spanning a spectrum of settings from fluvial to marine. The transitional to terrestrial coal measures are dominated by siliciclastics, but they also contain three laterally extensive marine bands (mudstone). These bands act as marker horizons that enable correlation between fully marine and terrestrial facies. Examination of this range of facies and their sedimentology has enabled the development of a high-resolution sequence stratigraphic framework. Set against the established backdrop of third-order Sajau transgression, nine fourth-order sequences are recognized. Results show that, in the composite sequences, peat accumulation predominantly correlates in transitional areas with early transgressive sequence sets (TSS) and highstand sequence set (HSS), while in more landward areas it correlates with the middle TSS to late highstand sequence sets (HSS). Differences in peat accumulation regimes within the sequence stratigraphic framework are attributed to variations in subsidence and background siliciclastic input rates in different depositional settings, with these combining to produce differences in the rate of accommodation change. The preservation of coal resources in the middle to late HSS in this area was most likely related to the rise of the regional base level throughout the Sajau.

Keywords: sequence stratigraphy, coal, Pliocene, Berau basin

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Authors: Faisal A. Aburub

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Organizations today need to invest in software in order to run their businesses, and to the organizations’ objectives, the software should be in line with the business process. This research presents an approach for linking process models and system models. Particularly, the new approach aims to synthesize sequence diagram based on role activity diagram (RAD) model. The approach includes four steps namely: Create business process model using RAD, identify computerized activities, identify entities in sequence diagram and identify messages in sequence diagram. The new approach has been validated using the process of student registration in University of Petra as a case study. Further research is required to validate the new approach using different domains.

Keywords: business process modelling, system models, role activity diagrams, sequence diagrams

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Authors: Bin Liu

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Prokaryotic promoter, consisted of two short DNA sequences located at in -35 and -10 positions, is responsible for controlling the initiation and expression of gene expression. Different types of promoters have different functions, and their consensus sequences are similar. In addition, their consensus sequences may be different for the same type of promoter, which poses difficulties for promoter identification. Unfortunately, all existing computational methods treat promoter identification as a binary classification task and can only identify whether a query sequence belongs to a specific promoter type. It is desired to develop computational methods for effectively identifying promoters and their types. Here, a two-layer predictor is proposed to try to deal with the problem. The first layer is designed to predict whether a given sequence is a promoter and the second layer predicts the type of promoter that is judged as a promoter. Meanwhile, we also analyze the importance of feature and sequence conversation in two aspects: promoter identification and promoter type identification. To the best knowledge of ours, it is the first computational predictor to detect promoters and their types.

Keywords: promoter, promoter type, random forest, sequence information

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Authors: Bilal Wajid, Erchin Serpedin

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The health industry is aiming towards personalized medicine. If the patient’s genome needs to be sequenced it is important that the entire analysis be completed quickly. This paper explores use of parallel computing to analyze very large sequences. Two cases have been considered. In the first case, the sequence is kept constant and the effect of increasing the number of MPI-based processes is evaluated in terms of execution time, speed and efficiency. In the second case the number of MPI-based processes have been kept constant whereas, the length of the sequence was increased.

Keywords: parallel computing, alignment, genome assembly, alignment

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Authors: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Anjan Hazra, Nirjhar Dasgupta, Chandan Sengupta, Sauren Das

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Tea (Camellia sinensis) has received substantial attention from the scientific world time to time, not only for its commercial importance, but also for its demand to the health-conscious people across the world for its extensive use as potential sources of antioxidant supplement. These health-benefit traits primarily rely on some regulatory networks of different metabolic pathways. Development of microsatellite markers from the conserved genomic regions is being worthwhile for studying the genetic diversity of closely related species or self-pollinated species. Although several SSR markers have been reported, in tea the trait-specific Simple Sequence Repeats (SSRs) are yet to be identified, which can be used for marker assisted breeding technique. MicroRNAs are endogenous, noncoding, short RNAs directly involved in regulating gene expressions at the post-transcriptional level. It has been found that diversity in miRNA gene interferes the formation of its characteristic hair pin structure and the subsequent function. In the present study, the precursors of small regulatory RNAs (microRNAs) has been fished out from tea Expressed Sequence Tag (EST) database. Furthermore, the simple sequence repeat motifs within the putative miRNA precursor genes are also identified in order to experimentally validate their existence and function. It is already known that genic-SSR markers are very adept and breeder-friendly source for genetic diversity analysis. So, the potential outcome of this in-silico study would provide some novel clues in understanding the miRNA-triggered polymorphic genic expression controlling specific metabolic pathways, accountable for tea quality.

Keywords: micro RNA, simple sequence repeats, tea quality, trait specific marker

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Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

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Authors: Marian Dragomir, Alin Dragomir

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In the paper, two fault location algorithms are presented for transmission lines which use the line parameters to estimate the distance to the fault. The first algorithm uses only the measurements from one end of the line and the positive and zero sequence parameters of the line, while the second one uses the measurements from both ends of the line and only the positive sequence parameters of the line. The algorithms were tested using a transmission grid transposed in MATLAB. In a first stage it was established a fault location base line, where the algorithms mentioned above estimate the fault locations using the exact line parameters. After that, the positive and zero sequence resistance and reactance of the line were calculated again for different ground resistivity values and then the fault locations were estimated again in order to compare the results with the base line results. The results show that the algorithm which uses the zero sequence impedance of the line is the most sensitive to the line parameters modifications. The other algorithm is less sensitive to the line parameters modification.

Keywords: estimation algorithms, fault location, line parameters, simulation tool

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Authors: Muhammad Tarmidzi, Reza M. G. Gani, Andri Luthfi

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The purpose of this study is to identify rock zone containing hydrocarbons with calculating rock property includes volume shale, total porosity, effective porosity and water saturation. Identification method rock property based on GR log, resistivity log, neutron log and density rock. Zoning is based on sequence stratigraphic markers that are sequence boundary (SB), transgressive surface (TS) and flooding surface (FS) which correlating ten well log in blok “M”. The results of sequence stratigraphic correlation consist of eight zone that are two LST zone, three TST zone and three HST zone. The result of rock property calculation in each zone is showing two LST zone containing hydrocarbons. LST-1 zone has average volume shale (Vsh) 25%, average total porosity (PHIT) 14%, average effective porosity (PHIE) 11% and average water saturation 0,83. LST-2 zone has average volume shale (Vsh) 19%, average total porosity (PHIT) 21%, average effective porosity (PHIE) 17% and average water saturation 0,82.

Keywords: hydrocarbons zone, petrophysic, rock property, sequence stratigraphic

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Authors: Lamiche Chaabane

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In this study, a new method for solving sequence alignment problem is proposed, which is named ITS (Improved Tabu Search). This algorithm is based on the classical Tabu Search (TS). ITS is implemented in order to obtain results of multiple sequence alignment. Several ideas concerning neighbourhood generation, move selection mechanisms and intensification/diversification strategies for our proposed ITS is investigated. ITS have generated high-quality results in terms of measure of scores in comparison with the classical TS and simple iterative search algorithm.

Keywords: multiple sequence alignment, tabu search, improved tabu search, neighbourhood generation, selection mechanisms

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Authors: Ernesto Linan, Linda Cruz, Lucero Becerra

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In this paper, a new hybridized algorithm based on Chemical Reaction Optimization and Simulated Annealing is proposed to solve the alignment sequence Problem. The Chemical Reaction Optimization is a population-based meta-heuristic algorithm based on the principles of a chemical reaction. Simulated Annealing is applied to solve a large number of combinatorial optimization problems of general-purpose. In this paper, we propose hybridization between Chemical Reaction Optimization algorithm and Simulated Annealing in order to solve the Sequence Alignment Problem. An initial population of molecules is defined at beginning of the proposed algorithm, where each molecule represents a sequence alignment problem. In order to simulate inter-molecule collisions, the process of Chemical Reaction is placed inside the Metropolis Cycle at certain values of temperature. Inside this cycle, change of molecules is done due to collisions; some molecules are accepted by applying Boltzmann probability. The results with the hybrid scheme are better than the results obtained separately.

Keywords: chemical reaction optimization, sequence alignment problem, simulated annealing algorithm, metaheuristics

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Authors: Mona Alwhibi, Najat Bukhary

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Heliotropium digynum, a member of Boraginaceae family, the growth of the plant, as well as its size, length of inflorescence, and speed of development depends on the amount of rain in its habitat. In this study, we studied the applicability of inter-simple sequence repeat (ISSR) polymorphism in Heliotropium digynum in a different region of Saudi Arabia. We found that. ISSR analysis using 15 primers were used for ISSR-PCR optimization trials, five primers (UBC810, UBC811, UBC818, UBC834, and UBC849) which gave the best amplification results produced a total of 43 polymorphic bands. The number of polymorphic loci was 20 and the percentage of polymorphism was 90.47%. The similarity result indicates the presence of a high-level genetic diversity between populations and a dendrogram constructed by UPGMA method.

Keywords: genetic differentiation, genetic diversity, Heliotropium digynum, ISSR

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Authors: Dalia G. Aseel

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The potato (Solanum tubersum, L.) has become one of the major vegetable crops in Egypt and all over the world. Potato leafroll virus(PLRV) was observed on potato plants collected from different governorates in Egypt. Three cultivars, Spunta, Diamont, and Cara, infected with PLRV were collected; RNA was extracted and subjected to Real-Time PCR using the coat protein gene primers. The results showed that the expression of the coat protein was 39.6-fold, 12.45-fold, and 47.43-fold, respectively, for Spunta, Diamont, and Cara cultivars. Differential Display Polymerase Chain Reaction (DD-PCR) using pathogenesis-related protein 1 (PR-1), β-1,3-glucanases (PR-2), chitinase (PR-3), peroxidase (POD), and polyphenol oxidase (PPO) forward primers for pathogenesis-related proteins (PR). The obtained data revealed different banding patterns depending on the viral type and the region of infection. Regarding PLRV, 58 up-regulated and 19 down-regulated genes were detected. Sequence analysis of the up-and down-regulated genes revealed that infected plants were observed in comparison with the healthy control. Sequence analysis of the up-regulated gene was performed, and the encoding sequence analysis showed that the obtained genes include: induced stolen tip protein. On the other hand, two down-regulated genes were identified: disease resistance RPP-like protein and non-specific lipid-transfer protein. In this study, the expressions of PR-1, PR-2, PR-3, POD, and PPO genes in the infected leaves of three potato cultivars were estimated by quantitative real-time PCR. We can conclude that the PLRV-infection of potato plants inhibited the expression of the five PR genes. On the contrary, infected leaves by PLRV elevated the expression of some defense genes. This interaction may also induce and/or suppress the expression of some genes responsible for the plant's defense mechanisms.

Keywords: PLRV, pathogenesis-related proteins (PRs), DD-PCR, sequence, real-time PCR

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Authors: Jung Ho Yang, Yong Soo Kim

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Electrical units are operated by electrical and electronic components. An environmental test sequence is useful for testing electrical units to reduce reliability issues. This study introduces test sequence guidelines based on relevant principles and considerations for electronic testing according to international standard IEC-60068-1 and the United States military standard MIL-STD-810G. Then, test sequences were proposed based on the descriptions for each test. Finally, General Motors (GM) specification GMW3172 was interpreted and compared to IEC-60068-1 and MIL-STD-810G.

Keywords: reliability, environmental test sequence, electrical units, IEC 60068-1, MIL-STD-810G

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Authors: Rajkumar Ghosh

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Earthquakes are natural disasters that pose a significant risk to human life and infrastructure. Effective earthquake mitigation measures require a thorough understanding of the dynamics of seismic occurrences, including thrust movement. Traditionally, estimating thrust movement has relied on typical techniques that may not capture the full complexity of these events. Therefore, investigating alternative approaches, such as incorporating out-of-sequence thrust movement data, could enhance earthquake mitigation strategies. This review aims to provide an overview of the applications of out-of-sequence thrust movement in earthquake mitigation. By examining existing research and studies, the objective is to understand how precise estimation of thrust movement can contribute to improving structural design, analyzing infrastructure risk, and developing early warning systems. The study demonstrates how to estimate out-of-sequence thrust movement using multiple data sources, including GPS measurements, satellite imagery, and seismic recordings. By analyzing and synthesizing these diverse datasets, researchers can gain a more comprehensive understanding of thrust movement dynamics during seismic occurrences. The review identifies potential advantages of incorporating out-of-sequence data in earthquake mitigation techniques. These include improving the efficiency of structural design, enhancing infrastructure risk analysis, and developing more accurate early warning systems. By considering out-of-sequence thrust movement estimates, researchers and policymakers can make informed decisions to mitigate the impact of earthquakes. This study contributes to the field of seismic monitoring and earthquake risk assessment by highlighting the benefits of incorporating out-of-sequence thrust movement data. By broadening the scope of analysis beyond traditional techniques, researchers can enhance their knowledge of earthquake dynamics and improve the effectiveness of mitigation measures. The study collects data from various sources, including GPS measurements, satellite imagery, and seismic recordings. These datasets are then analyzed using appropriate statistical and computational techniques to estimate out-of-sequence thrust movement. The review integrates findings from multiple studies to provide a comprehensive assessment of the topic. The study concludes that incorporating out-of-sequence thrust movement data can significantly enhance earthquake mitigation measures. By utilizing diverse data sources, researchers and policymakers can gain a more comprehensive understanding of seismic dynamics and make informed decisions. However, challenges exist, such as data quality difficulties, modelling uncertainties, and computational complications. To address these obstacles and improve the accuracy of estimates, further research and advancements in methodology are recommended. Overall, this review serves as a valuable resource for researchers, engineers, and policymakers involved in earthquake mitigation, as it encourages the development of innovative strategies based on a better understanding of thrust movement dynamics.

Keywords: earthquake, out-of-sequence thrust, disaster, human life

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Authors: Bin Liu

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Protein remote homology detection and fold recognition are two most important tasks in protein sequence analysis, which is critical for protein structure and function studies. In this study, we combined the profile-based features with various string kernels, and constructed several computational predictors for protein remote homology detection and fold recognition. Experimental results on two widely used benchmark datasets showed that these methods outperformed the competing methods, indicating that these predictors are useful computational tools for protein sequence analysis. By analyzing the discriminative features of the training models, some interesting patterns were discovered, reflecting the characteristics of protein superfamilies and folds, which are important for the researchers who are interested in finding the patterns of protein folds.

Keywords: protein remote homology detection, protein fold recognition, profile-based features, Support Vector Machines (SVMs)

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Abu Hasan, Rochmadi, Hary Sulistyo, Suharto Honggokusumo

Abstract:

This research purpose is to study the effect of Ingredients mixing sequence in rubber compounding onto the formation of bound rubber and cross link density of natural rubber and also the relationship of bound rubber and cross link density. Analysis of bound rubber formation of rubber compound and cross link density of rubber vulcanizates were carried out on a natural rubber formula having masticated and mixing, followed by curing. There were four methods of mixing and each mixing process was followed by four mixing sequence methods of carbon black into the rubber. In the first method of mixing sequence, rubber was masticated for 5 min and then rubber chemicals and carbon black N 330 were added simultaneously. In the second one, rubber was masticated for 1 min and followed by addition of rubber chemicals and carbon black N 330 simultaneously using the different method of mixing then the first one. In the third one, carbon black N 660 was used for the same mixing procedure of the second one, and in the last one, rubber was masticated for 3 min, carbon black N 330 and rubber chemicals were added subsequently. The addition of rubber chemicals and carbon black into masticated rubber was distinguished by the sequence and time allocated for each mixing process. Carbon black was added into two stages. In the first stage, 10 phr was added first and the remaining 40 phr was added later along with oil. In the second one to the fourth one, the addition of carbon black in the first and the second stage was added in the phr ratio 20:30, 30:20, and 40:10. The results showed that the ingredients mixing process influenced bound rubber formation and cross link density. In the three methods of mixing, the bound rubber formation was proportional with crosslink density. In contrast in the fourth one, bound rubber formation and cross link density had contradictive relation. Regardless of the mixing method operated, bound rubber had non linear relationship with cross link density. The high cross link density was formed when low bound rubber formation. The cross link density became constant at high bound rubber content.

Keywords: bound-rubber, cross-link density, natural rubber, rubber mixing process

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Authors: Vidhu Mitha Goutham, Ruma Mukherjee

Abstract:

The low availability of well-trained, unlimited, dynamic-access models for specific languages makes it hard for corporate users to adopt quick translation techniques and incorporate them into product solutions. As translation tasks increasingly require a dynamic sequence learning curve; stable, cost-free opensource models are scarce. We survey and compare current translation techniques and propose a modified sequence to sequence model repurposed with attention techniques. Sequence learning using an encoder-decoder model is now paving the path for higher precision levels in translation. Using a Convolutional Neural Network (CNN) encoder and a Recurrent Neural Network (RNN) decoder background, we use Fairseq tools to produce an end-to-end bilingually trained Spanish-English machine translation model including source language detection. We acquire competitive results using a duo-lingo-corpus trained model to provide for prospective, ready-made plug-in use for compound sentences and document translations. Our model serves a decent system for large, organizational data translation needs. While acknowledging its shortcomings and future scope, it also identifies itself as a well-optimized deep neural network model and solution.

Keywords: attention, encoder-decoder, Fairseq, Seq2Seq, Spanish, translation

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Authors: Nahed Al-Hajeri

Abstract:

There are several reasons which lead to a delay in project completion, out of all, one main reason is the delay in deliverable processing, i.e. submission and review of documents. Most of the project cycles start with a list of deliverables but without a sequence of submission of the same, means without a direction to move, leading to overlapping of activities and more interdependencies. Hence Project Design Deliverables (PDD) is developed as a solution to Organize Transmittals (Documents/Drawings) received from contractors/consultants during different phases of an EPC (Engineering, Procurement, and Construction) projects, which gives proper direction to the stakeholders from the beginning, to reduce inter-discipline dependency, avoid overlapping of activities, provide a list of deliverables, sequence of activities, etc. PDD attempts to provide a list and sequencing of the engineering documents/drawings required during different phases of a Project which will benefit both client and Contractor in performing planned activities through timely submission and review of deliverables. This helps in ensuring improved quality and completion of Project in time. The successful implementation begins with a detailed understanding the specific challenges and requirements of the project. PDD will help to learn about vendor document submissions including general workflow, sequence and monitor the submission and review of the deliverables from the early stages of Project. This will provide an overview for the Submission of deliverables by the concerned during the projects in proper sequence. The goal of PDD is also to hold responsible and accountability of all stakeholders during complete project cycle. We believe that successful implementation of PDD with a detailed list of documents and their sequence will help organizations to achieve the project target.

Keywords: EPC (Engineering, Procurement, and Construction), project design deliverables (PDD), econometrics sciences, management sciences

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Authors: H. Imad, Y. Cheah, O. Aamera

Abstract:

The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

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Authors: Syeda Qamarunnisa, Ishrat Jamil, Abid Azhar, Zabta K. Shinwari, Syed Irtifaq Ali

Abstract:

A phylogenetic analysis of family Solanaceae was conducted using sequence data from the chloroplast intergenic atpB-rbcL spacer. Sequence data was generated from 17 species representing 09 out of 14 genera of Solanaceae from Pakistan. Cladogram was constructed using maximum parsimony method and results indicate that Solanaceae is mainly divided into two subfamilies; Solanoideae and Cestroideae. Four major clades within Solanoideae represent tribes; Physaleae, Capsiceae, Datureae and Solaneae are supported by high bootstrap value and the relationships among them are not corroborating with the previous studies. The findings established that subfamily Cestroideae comprised of three genera; Cestrum, Lycium, and Nicotiana with high bootstrap support. Position of Nicotiana inferred with atpB-rbcL sequence is congruent with traditional classification, which placed the taxa in Cestroideae. In the current study Lycium unexpectedly nested with Nicotiana with 100% bootstrap support and identified as a member of tribe Nicotianeae. Expanded sampling of other genera from Pakistan could be valuable towards improving our understanding of intrafamilial relationships within Solanaceae.

Keywords: systematics, solanaceae, phylogenetics, intergenic spacer, tribes

Procedia PDF Downloads 437