Search results for: genome sequence

Authors: Deboraj Muchahary, Amlan Deep Borah Abir J. Mondal, Alak Majumder

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A discrete cosine transform (DCT) is described and a technique to compute it using fast Fourier transform (FFT) is developed. In this work, DCT of a finite length sequence is obtained by incorporating CORDIC methodology in radix-2 FFT algorithm. The proposed methodology is simple to comprehend and maintains a regular structure, thereby reducing computational complexity. DCTs are used extensively in the area of digital processing for the purpose of pattern recognition. So the efficient computation of DCT maintaining a transparent design flow is highly solicited.

Keywords: DCT, DFT, CORDIC, FFT

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Authors: Bandana Saikia, Ashok Bhattacharyya

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Endophytic microbes and their metabolites positively impact overall plant health, which may have a potential implication in agriculture. In the present study, 177 bacterial endophytes and 57 fungal endophytes were isolated, with the highest recovery rate from tomato roots. A maximum of 112 endophytes were isolated during monsoon, followed by 64 isolates and 58 isolates isolated during pre-monsoon and post-monsoon periods, respectively, indicating the rich diversity in bacterial and fungal endophytes of tomato crops from different locations of Assam, India. Further, the endophytes were evaluated for their antagonistic potential against Fusarium oxysporum f. sp. lycopersici. Fungal endophytic isolate AAUTLF (Endophytic Fungi of Tomato Leaf from Assam Agricultural University, Assam, India area) and bacterial endophyte D1B (Endophytic bacteria of tomato from Dhemiji, India district) showed the highest antifungal activity against the pathogen both in vitro and in vivo. Based on 5.8 rDNA sequence analysis of fungal and 16S rDNA sequence of bacteria endophytes, the most effective fungal and bacterial isolates against FOL were identified as Trichoderma asperellum AAUTLF and Stenotrophomonas maltophilia D1B, respectively. The isolates showed an antagonistic effect against Fusarium oxysporum f.sp. lycopersici in-vitro and reduced the disease index of Fusarium wilt in tomatoes by 64.4% under pot conditions. Trichoderma asperellum AAUTLF produced an antifungal compound viz., 6-pentyl-2H-pyran-2-one, which also possesses growth-promoting characteristics. The bacteria Stenotrophomonas maltophilia D1B produced antifungal compounds, including benzothiazole, oleic acid, phenylacetic acid, and 3-(Hydroxy-phenyl-methyl)-2,3-dimethyl-octan-4-one. This would be of high importance for the source of antagonistic strains and biocontrol of tomato Fusarium wilt, as well as other plant fungal diseases.

Keywords: root endophytes, Stemotrophomonas, Trichoderma, benzothiazole, 6-pentyl-2H-pyran-2-one

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Authors: Vikrant Gupta, Amrit Goswami

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The fixed income market forms the basis of the modern financial market. All other assets in financial markets derive their value from the bond market. Owing to its over-the-counter nature, corporate bonds have relatively less data publicly available and thus is researched upon far less compared to Equities. Bond price prediction is a complex financial time series forecasting problem and is considered very crucial in the domain of finance. The bond prices are highly volatile and full of noise which makes it very difficult for traditional statistical time-series models to capture the complexity in series patterns which leads to inefficient forecasts. To overcome the inefficiencies of statistical models, various machine learning techniques were initially used in the literature for more accurate forecasting of time-series. However, simple machine learning methods such as linear regression, support vectors, random forests fail to provide efficient results when tested on highly complex sequences such as stock prices and bond prices. hence to capture these intricate sequence patterns, various deep learning-based methodologies have been discussed in the literature. In this study, a recurrent neural network-based deep learning model using long short term networks for prediction of corporate bond prices has been discussed. Long Short Term networks (LSTM) have been widely used in the literature for various sequence learning tasks in various domains such as machine translation, speech recognition, etc. In recent years, various studies have discussed the effectiveness of LSTMs in forecasting complex time-series sequences and have shown promising results when compared to other methodologies. LSTMs are a special kind of recurrent neural networks which are capable of learning long term dependencies due to its memory function which traditional neural networks fail to capture. In this study, a simple LSTM, Stacked LSTM and a Masked LSTM based model has been discussed with respect to varying input sequences (three days, seven days and 14 days). In order to facilitate faster learning and to gradually decompose the complexity of bond price sequence, an Empirical Mode Decomposition (EMD) has been used, which has resulted in accuracy improvement of the standalone LSTM model. With a variety of Technical Indicators and EMD decomposed time series, Masked LSTM outperformed the other two counterparts in terms of prediction accuracy. To benchmark the proposed model, the results have been compared with traditional time series models (ARIMA), shallow neural networks and above discussed three different LSTM models. In summary, our results show that the use of LSTM models provide more accurate results and should be explored more within the asset management industry.

Keywords: bond prices, long short-term memory, time series forecasting, empirical mode decomposition

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Authors: Maryam Moosavi, Hadi Khatibzadeh

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The main purpose of this paper is to study the proximal point algorithm for quasi-nonexpansive mappings in Hadamard spaces. △-convergence and strong convergence of cyclic resolvents for a finite family of quasi-nonexpansive mappings one to a fixed point of the mappings are established

Keywords: Fixed point, Hadamard space, Proximal point algorithm, Quasi-nonexpansive sequence of mappings, Resolvent

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Authors: Radoslaw Lukasz Staniszewski

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The aim of the research was to verify lateral extent and thickness variability of individual limestone layers within early-Jurassic medium- and thick-bedded limestone interbedded with marlstones. Location: The main research area is located in the south-central part of Poland in the south-western part of Permo-Mesozoic margin of the Holy Cross Mountains. It includes outcroppings located on the line between Mieczyn and Wola Morawicka. The analyses were carried out on six profiles (Mieczyn, Gniezdziska, Tokarnia, Wola Morawicka, Morawica and Wolica) representing three early-Jurassic links: Jasna Gora layers, grey limestone, Morawica limestone. Additionally, an attempt was made to correlate the thickness sequence from the Holy Cross Mountains to the profile from the quarry in Zawodzie located 3 km east of Czestochowa. The distance between the outermost profiles is 122 km in a straight line. Methodology of research: The Callovian-Oxfordian border was taken as the reference point during the correlation. At the same time, ammonite-based stratigraphic studies were carried out, which allowed to identify individual packages in the remote outcroppings. The analysis of data collected during fieldwork was mainly devoted to the correlation of thickness sequences of limestone layers in subsequent profiles. In order to check the objectivity of the subsequent outcroppings, the profiles have been presented in the form of the thickness functions of the subsequent layers. The generated functions were auto-correlated, and the Pearson correlation coefficient was calculated. The next step in the research was to statistically determine the percentage increment of the individual layers thickness in the subsequent profiles, and on this basis to plot the function of relative carbonate productivity. Results: The result of the above-mentioned procedures consists in illustrating the extent of 34 rock layers across the examined area in demonstrating the repeatability of their success in subsequent outcroppings. It can also be observed that the thickness of individual layers in the Holy Cross Mountains is increasing from north-west towards south-east. Despite changes in the thickness of the layers in the profiles, their relations within the sequence remain constant. The lowest matching ratio of thickness sequence calculated using the Pearson correlation coefficient formula is 0.67, while the highest is 0.84. The thickness of individual layers changes between 4% and 230% over the examined area. Interpretation: Layers in the outcroppings covered by the research show continuity throughout the examined area and it is possible to precisely correlate them, which means that the process determining the formation of the layers was regional and probably included both the fringe of the Holy Cross Mountains and the north-eastern part of the Krakow-Czestochowa Jura Upland. Local changes in the sedimentation environment affecting the productivity of the subtidal carbonate factory only cause the thickness of the layers to change without altering the thickness proportions of the profiles. Based on the percentage of changes in the thickness of individual layers in the subsequent profiles, it can be concluded that the local productivity of the subtidal carbonate factory is increasing logarithmically.

Keywords: Oxfordian, Holy Cross Mountains, carbonate factory, Limestone

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Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule

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Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.

Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity

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Authors: Parveen Kumar

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This article discusses institute information resources. Information, in its most restricted technical sense, is a sequence of symbols that can be interpreted as message information can be recorded as signs, or transmitted as signals. Information is any kind of event that affects the state of a dynamic system. Conceptually, information is the message being conveyed. This concept has numerous other meanings in different contexts. Moreover, the concept of information is closely related to notions of constraint, communication, control, data, form, instruction, knowledge, meaning, mental stimulus, pattern, perception, representation, and especially entropy.

Keywords: institutions, information institutions, information services for mission-oriented institute, pattern

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Authors: Omaima A. Sharaf, Wafaa M. Abd El-Rahim, Hassan Moawad, Michael J. Sadowsky

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Textile industry is one of the important industries in the worldwide. It is known that the eco-friendly industrial and agricultural activities are significant for socio-economic stability of all countries. The absence of appropriate industrial waste water treatments is essential barrier for sustainable development in food and agricultural sectors especially in developing country like Egypt. Thus, the development of enzymatic bioremediation technology for textile dye removal will enhance the collaboration between scientists who develop the technology and industry where this technology will be implemented towards the safe disposal of the textile dye wastes. Highly efficient microorganisms are of most importance in developing and using highly effective biological treatment processes. Bacterial degradation of azo dyes is generally initiated by an enzymatic step that involves cleavage of azo linkages, usually with the aid of an azoreductase as electron donor. Thus, expanding the spectrum of microorganisms with high enzymatic activities as azoreductases and discovering novel azo-dye degrading enzymes, with enhanced stability and superior catalytic properties, are necessary for many environmental and industrial applications. Consequently, the use of molecular tools has become increasingly integrated into the understanding of enzyme properties and characterization. Researchers have utilized a gene cloning and expression methods as a tool to produce recombinant protein for decolorizing dyes more efficiently. Thus, presumptive evidence for the presence of genes encoding azoreductases in the genomes of selected local, and most potent azo-degrading strains were obtained by using specific oligonucleotides primers. These potent strains have been isolated from textile industrial wastewater in Egypt and identified using 16S rRNA sequence analysis as 'Lysinibacillus macrolidesB8, Brevibacillus parabrevisB11, Bacillus coagulansB7, and B. cereusB5'. PCR products of two full length genes designated as (AZO1;621bp and AZO2;534bp) were detected. BLASTx results indicated that AZO1 gene was corresponding to predicted azoreductase from of Bacillus sp. ABP14, complete genome, multispecies azoreductase [Bacillus], It was submitted to the gene bank by an accession no., BankIt2085371 AZO1 MG923210 (621bp; 207 amino acids). AZO1 was generated from the DNA of our identified strains Lysinibacillus macrolidesB8. On the other hand, AZO2 gene was corresponding to a predicted azoreductase from Bacillus cereus strain S2-8. Gene bank accession no. was BankIt2085839 AZO2 MG932081 (534bp;178 amino acids) and it was amplified from our Bacillus coagulansB7. Both genes were successfully cloned into pCR2.1TOPO (Invitrogen) and in pET28b+ vectors, then they transformed into E. coli DH5α and BL21(DE3) cells for heterologous expression studies. Our recombinant azoreductases (AZO1&AZO2) exhibited potential enzyme activity and efficiently decolorized an azo dye (Direct violet). They exhibited pH stability between 6 and 8 with optimum temperature up to 60°C and 37 °C after induction by 1mM and 1.5mM IPTG, for both AZO1 &AZO2, respectively. These results suggested that further optimization and purification of these recombinant proteins by using different heterologous expression systems will give great potential for the sustainable utilization of these recombinant enzymes in several industrial applications especially in wastewater treatments.

Keywords: azoreductases, decolorization, enzyme activity, gene cloning and expression

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Authors: Sa’adu Mafara Abubakar, Muhammad Nuraddeen Danjuma, Adewole Tomiwa Adetunji, Richard Mundembe, Salisu Mohammed, Francis Bayo Lewu, Joseph I. Kiok

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Pearl millet is the most drought tolerant of all domesticated cereals, is cultivated extensively to feed millions of people who mainly live in hash agroclimatic zones. It serves as a major source of food for more than 40 million smallholder farmers living in the marginal agricultural lands of Northern Nigeria. Pearl millet grain is more nutritious than other cereals like maize, is also a principal source of energy, protein, vitamins, and minerals for millions of poorest people in the regions where it is cultivated. Pearl millet has recorded relatively little research attention compared with other crops and no sufficient work has analyzed its genetic diversity in north-western Nigeria. Therefore, this study was undertaken with the objectives to analyze the genetic diversity of pearl millet accessions using SSR marker and to analyze the extent of evolutionary relationship among pearl millet accessions at the molecular level. The result of the present study confirmed diversity among accessions of pearl millet in the study area. Simple Sequence Repeats (SSR) markers were used for genetic analysis and evolutionary relationship of the accessions of pearl millet. To analyze the level of genetic diversity, 8 polymorphic SSR markers were used to screen 69 accessions collected based on three maturity periods. SSR markers result reveal relationships among the accessions in terms of genetic similarities, evolutionary and ancestral origin, it also reveals a total of 53 alleles recorded with 8 microsatellites and an average of 6.875 per microsatellite, the range was from 3 to 9 alleles in PSMP2248 and PSMP2080 respectively. Moreover, both the factorial analysis and the dendrogram of phylogeny tree grouping patterns and cluster analysis were almost in agreement with each other that diversity is not clustering according to geographical patterns but, according to similarity, the result showed maximum similarity among clusters with few numbers of accessions. It has been recommended that other molecular markers should be tested in the same study area.

Keywords: pearl millet, genetic diversity, simple sequence repeat (SSR)

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Authors: Monika Soni, Shovonlal Bhowmick, Chandra Bhattacharya, Jitendra Sharma, Prafulla Dutta, Jagadish Mahanta

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Aedes aegypti and Aedes albopictus are considered as two major vectors to transmit dengue virus. In North-east India, two states viz. Assam and Arunachal Pradesh are known to be high endemic zone for dengue and Chikungunya viral infection. The taxonomical classification of medically important vectors are important for mapping of actual evolutionary trends and epidemiological studies. However, misidentification of mosquito species in field-collected mosquito specimens could have a negative impact which may affect vector-borne disease control policy. DNA barcoding is a prominent method to record available species, differentiate from new addition and change of population structure. In this study, a combined approach of a morphological and molecular technique of DNA barcoding was adopted to explore sequence variation in mitochondrial cytochrome c oxidase subunit I (COI) gene within dengue vectors. The study has revealed the map distribution of the dengue vector from two states i.e. Assam and Arunachal Pradesh, India. Approximate five hundred mosquito specimens were collected from different parts of two states, and their morphological features were compared with the taxonomic keys. The analysis of detailed taxonomic study revealed identification of two species Aedes aegypti and Aedes albopictus. The species aegypti comprised of 66.6% of the specimen and represented as dominant dengue vector species. The sequences obtained through standard DNA barcoding protocol were compared with public databases, viz. GenBank and BOLD. The sequences of all Aedes albopictus have shown 100% similarity whereas sequence of Aedes aegypti has shown 99.77 - 100% similarity of COI gene with that of different geographically located same species based on BOLD database search. From dengue prevalent different geographical regions fifty-nine sequences were retrieved from NCBI and BOLD databases of the same and related taxa to determine the evolutionary distance model based on the phylogenetic analysis. Neighbor-Joining (NJ) and Maximum Likelihood (ML) phylogenetic tree was constructed in MEGA6.06 software with 1000 bootstrap replicates using Kimura-2-Parameter model. Data were analyzed for sequence divergence and found that intraspecific divergence ranged from 0.0 to 2.0% and interspecific divergence ranged from 11.0 to 12.0%. The transitional and transversional substitutions were tested individually. The sequences were deposited in NCBI: GenBank database. This observation claimed the first DNA barcoding analysis of Aedes mosquitoes from North-eastern states in India and also confirmed the range expansion of two important mosquito species. Overall, this study insight into the molecular ecology of the dengue vectors from North-eastern India which will enhance the understanding to improve the existing entomological surveillance and vector incrimination program.

Keywords: COI, dengue vectors, DNA barcoding, molecular identification, North-east India, phylogenetics

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Authors: O. O. Fola-Matthews, O. O. Soyinka, D. N. Bitalo

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Nigeria is one of the major shark fishing nations in Africa, but its fisheries managers still record catch data in aggregates ‘sharks’ with no species-specific details. This is because most of the shark specimens look identical in morphology, and field identification of some closely related species is tricky. This study uses DNA barcoding as a method to identify shark species from five different landing areas off the Nigerian Coast. 100 dorsal fins were sampled in order to provide a Chondrichthyan sequence that would be matched to reference specimens in a DNA barcode database

Keywords: BOLD, DNA barcoding, nigeria, sharks

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Authors: Nwogiji Cletus Olando, Oselebe Happiness Ogba, Enoch Achigan-Dako

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Digitaria iburua, commonly known as black fonio, is a cereal crop native to Africa and extensively cultivated by smallholder farmers in Northern Benin, Togo, and Nigeria. This crop holds immense nutritional and socio-cultural value. Unfortunately, limited knowledge about its genetic diversity exists due to a lack of scientific attention. As a result, its potential for improvement in food and agriculture remains largely untapped. To address this gap, a study was conducted using 41 accessions of D. iburua stored in the genebank of the Laboratory of Genetics, Biotechnology, and Seed Science at Abomey-Calavi University, Benin. The study employed both morphological and simple sequence repeat (SSR) markers to evaluate the genetic variability of the accessions. Agro-morphological assessments were carried out during the 2020 cropping season, utilizing an alpha lattice design with three replications. The collected data encompassed qualitative and quantitative traits. Additionally, molecular variability was assessed using eleven SSR markers. The results revealed significant phenotypic variability among the evaluated accessions, leading to their classification into three main clusters. Furthermore, the eleven SSR markers identified a total of 50 alleles, averaging 4.55 alleles per locus. The primers exhibited an average polymorphic information content value of 0.43, with the DE-ARC019 primer displaying the highest value (0.59). These findings suggest a substantial degree of genetic heterogeneity within the evaluated accessions, and the SSR markers employed in the study proved highly effective in detecting and characterizing this genetic variability. In conclusion, this study highlights the presence of significant genetic diversity in black fonio and provides valuable insights for future efforts aimed at its genetic improvement and conservation.

Keywords: genetic diversity, digitaria iburua, genetic improvement, simple sequence repeat markers, Nigeria, conservation

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Authors: Iftikhar Tayubi, Tabrej Khan, Rayan Alsulmi, Abdulrahman Labban

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Spider produces a special kind of substance. This special kind of substance is called a toxin. The toxin is composed of many types of protein, which differs from species to species. Spider toxin consists of several proteins and non-proteins that include various categories of toxins like myotoxin, neurotoxin, cardiotoxin, dendrotoxin, haemorrhagins, and fibrinolytic enzyme. Protein Sequence information with references of toxins was derived from literature and public databases. From the previous findings, the Spider toxin would be the best choice to treat different types of tumors and cancer. There are many therapeutic regimes, which causes more side effects than treatment hence a different approach must be adopted for the treatment of cancer. The combinations of drugs are being encouraged, and dramatic outcomes are reported. Spider toxin is one of the natural cytotoxic compounds. Hence, it is being used to treat different types of tumors; especially its positive effect on breast cancer is being reported during the last few decades. The efficacy of this database is that it can provide a user-friendly interface for users to retrieve the information about Spiders, toxin and toxin protein of different Spiders species. SPIDTOXD provides a single source information about spider toxins, which will be useful for pharmacologists, neuroscientists, toxicologists, medicinal chemists. The well-ordered and accessible web interface allows users to explore the detail information of Spider and toxin proteins. It includes common name, scientific name, entry id, entry name, protein name and length of the protein sequence. The utility of this database is that it can provide a user-friendly interface for users to retrieve the information about Spider, toxin and toxin protein of different Spider species. The database interfaces will satisfy the demands of the scientific community by providing in-depth knowledge about Spider and its toxin. We have adopted the methodology by using A MySQL and PHP and for designing, we used the Smart Draw. The users can thus navigate from one section to another, depending on the field of interest of the user. This database contains a wealth of information on species, toxins, and clinical data, etc. This database will be useful for the scientific community, basic researchers and those interested in potential pharmaceutical Industry.

Keywords: siptoxd, php, mysql, toxin

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Authors: Nora Geczy

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In today’s architectural practice, during the process of designing public, educational, healthcare and cultural space, human-centered architectural designs helping spatial orientation, safe space usage and the appropriate spatial sequence of actions are gaining increasing importance. Related to the methodology of designing public buildings, several scientific experiments in spatial recognition, spatial analysis and spatial psychology with regard to the components of space producing mental and physiological effects have been going on at the Department of Architectural Design and the Interdisciplinary Student Workshop (IDM) at the Széchenyi István University, Győr since 2013. Defining the creation of preventive, anticipated spatial design and the architectural tools of spatial comfort of public buildings and their practical usability are in the limelight of our research. In the experiments applying eye-tracking cameras, we studied the way public spaces are used, especially concentrating on the characteristics of spatial behaviour, orientation, recognition, the sequence of actions, and space usage. Along with the role of mental maps, human perception, and interaction problems in public spaces (at railway stations, galleries, and educational institutions), we analyzed the spatial situations influencing psychological and ergonomic factors. We also analyzed the eye movements of the experimental subjects in dynamic situations, in spatial procession, using stairs and corridors. We monitored both the consequences and the distorting effects of the ocular dominance of the right eye on spatial orientation; we analyzed the gender-based differences of women and men’s orientation, stress-inducing spaces, spaces affecting concentration and the spatial situation influencing territorial behaviour. Based on these observations, we collected the components of creating public interior spaces, which -according to our theory- contribute to the optimal usability of public spaces. We summed up our research in criteria for design, including 10 points. Our further goals are testing design principles needed for optimizing orientation and space usage, their discussion, refinement, and practical usage.

Keywords: architecture, eye-tracking, human-centered spatial design, public interior spaces, visual perception

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Authors: Hwang Ho Kim, Do Gyun Kim, Jin Young Choi, Sang Chul Park

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Since tire production process is very complicated, company-wide management of it is very difficult, necessitating considerable amounts of capital and labors. Thus, productivity should be enhanced and maintained competitive by developing and applying effective production plans. Among major processes for tire manufacturing, consisting of mixing component preparation, building and curing, the mixing process is an essential and important step because the main component of tire, called compound, is formed at this step. Compound as a rubber synthesis with various characteristics plays its own role required for a tire as a finished product. Meanwhile, scheduling tire mixing process is similar to flexible job shop scheduling problem (FJSSP) because various kinds of compounds have their unique orders of operations, and a set of alternative machines can be used to process each operation. In addition, setup time required for different operations may differ due to alteration of additives. In other words, each operation of mixing processes requires different setup time depending on the previous one, and this kind of feature, called sequence dependent setup time (SDST), is a very important issue in traditional scheduling problems such as flexible job shop scheduling problems. However, despite of its importance, there exist few research works dealing with the tire mixing process. Thus, in this paper, we consider the scheduling problem for tire mixing process and suggest an efficient particle swarm optimization (PSO) algorithm to minimize the makespan for completing all the required jobs belonging to the process. Specifically, we design a particle encoding scheme for the considered scheduling problem, including a processing sequence for compounds and machine allocation information for each job operation, and a method for generating a tire mixing schedule from a given particle. At each iteration, the coordination and velocity of particles are updated, and the current solution is compared with new solution. This procedure is repeated until a stopping condition is satisfied. The performance of the proposed algorithm is validated through a numerical experiment by using some small-sized problem instances expressing the tire mixing process. Furthermore, we compare the solution of the proposed algorithm with it obtained by solving a mixed integer linear programming (MILP) model developed in previous research work. As for performance measure, we define an error rate which can evaluate the difference between two solutions. As a result, we show that PSO algorithm proposed in this paper outperforms MILP model with respect to the effectiveness and efficiency. As the direction for future work, we plan to consider scheduling problems in other processes such as building, curing. We can also extend our current work by considering other performance measures such as weighted makespan or processing times affected by aging or learning effects.

Keywords: compound, error rate, flexible job shop scheduling problem, makespan, particle encoding scheme, particle swarm optimization, sequence dependent setup time, tire mixing process

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Authors: A. Kyprianou, A. Tjirkallis

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Condition monitoring of structures in service is very important as it provides information about the risk of damage development. One of the essential constituents of structural condition monitoring is the damage detection methodology. In the context of condition monitoring of in service structures a damage detection methodology analyses data obtained from the structure while it is in operation. Usually, this means that the data could be affected by operational and environmental conditions in a way that could mask the effects of a possible damage on the data. This, depending on the damage detection methodology, could lead to either false alarms or miss existing damages. In this article a damage detection methodology that is based on the Spatio-temporal continuous wavelet transform (SPT-CWT) analysis of a sequence of experimental time responses of a cantilever beam is proposed. The cantilever is subjected to white and pink noise excitation to simulate different operating conditions. In addition, in order to simulate changing environmental conditions, the cantilever is subjected to heating by a heat gun. The response of the cantilever beam is measured by a high-speed camera. Edges are extracted from the series of images of the beam response captured by the camera. Subsequent processing of the edges gives a series of time responses on 439 points on the beam. This sequence is then analyzed using the SPT-CWT to identify damage. The algorithm proposed was able to clearly identify damage under any condition when the structure was excited by white noise force. In addition, in the case of white noise excitation, the analysis could also reveal the position of the heat gun when it was used to heat the structure. The analysis could identify the different operating conditions i.e. between responses due to white noise excitation and responses due to pink noise excitation. During the pink noise excitation whereas damage and changing temperature were identified it was not possible to clearly identify the effect of damage from that of temperature. The methodology proposed in this article for damage detection enables the separation the damage effect from that due to temperature and excitation on data obtained from measurements of a cantilever beam. This methodology does not require information about the apriori state of the structure.

Keywords: spatiotemporal continuous wavelet transform, damage detection, data normalization, varying temperature

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Authors: Salman Akrokayan

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Synthetic cDNA (ScDNA) of granulocyte colony-stimulating factor (G-CSF) was constructed using a DNA synthesizer with the aim to increase its expression level. 5' end of the ScDNA of G-CSF coding region was modified by decreasing the GC content without altering the predicted amino acids sequence. The identity of the resulting protein from ScDNA was confirmed by the highly specific enzyme-linked immunosorbent assay. In conclusion, a synthetic G-CSF cDNA in combination with the recombinant DNA protocol offers a rapid and reliable strategy for synthesizing the target protein. However, the commercial utilization of this methodology requires rigorous validation and quality control.

Keywords: synthetic cDNA, recombinant G-CSF, cloning, gene expression

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: Benjamin Lee Warren

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Many problems exist in additive number theory which is essential to determine the primes that are the sum of two elements from a given single-variable polynomial sequence, and most of them are unattackable in the present day. Here, we determine solutions for this problem to a few certain sequences (certain binomial coefficients and power sums) using only elementary algebra and some algebraic factoring methods (as well as Euclid’s Lemma and Faulhaber’s Formula). In particular, we show that there are finitely many primes as sums of two of these types of elements. Several cases are fully illustrated, and bounds are presented for the cases not fully illustrated.

Keywords: binomial coefficients, power sums, primes, algebra

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: globular protein, modulating function, white noise, winding probability

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Authors: Rajkumar Ghosh

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Jhakri Thrust (JT), Sarahan Thrust (ST), and Chaura Thrust (CT) are the three OOST along Jakhri-Chaura segment along the Sutlej river valley in Himachal Pradesh. CT is deciphered only by Apatite Fission Track dating. Such geochronological information is not currently accessible for the Jhakri and Sarahan thrusts. JT was additionally validated as OOST without any dating. The described rock types include ductile sheared gneisses and upper greenschist-amphibolite facies metamorphosed schists. Locally, the Munsiari (Jutogh) Thrust is referred to as the JT. Brittle shear, the JT, borders the research area's southern and ductile shear, the CT, and its northern margins. The JT has a 50° western dip and is south-westward verging. It is 15–17 km deep. A progressive rise in strain towards the JT zone based on microstructural tests was observed by previous researchers. The high-temperature ranges of the MCT root zone are cited in the current work as supportive evidence for the ductile nature of the OOST. In Himachal Pradesh, the lithological boundaries for OOST are not set. In contrast, the Sarahan thrust is NW-SE striking and 50-80 m wide. ST and CT are probably equivalent and marked by a sheared biotite-chlorite matrix with a top-to-SE kinematic indicator. It is inferred from cross-section balancing that the CT is folded with this anticlinorium. These thrust systems consist of several branches, some of which are still active. The thrust system exhibits complex internal geometry consisting of box folds, boudins, scar folds, crenulation cleavages, kink folds, and tension gashes. Box folds are observed on the hanging wall of the Chaura thrust. The ductile signature of CT represents steepen downward of the thrust. After the STDSU stopped deformation, out-of-sequence thrust was initiated in some sections of the Higher Himalaya. A part of GHC and part of the LH is thrust southwestward along the Jutogh Thrust/Munsiari Thrust/JT as also the Jutogh Nappe. The CT is concealed beneath Jutogh Thrust sheet hence the basal part of GHC is unexposed to the surface in Sutlej River section. Fieldwork and micro-structural studies of the Greater Himalayan Crystalline (GHC) along the Sutlej section reveal (a) initial top-to-SW sense of ductile shearing (CT); (b) brittle-ductile extension (ST); and (c) uniform top-to-SW sense of brittle shearing (JT). A group of samples of schistose rock from Jutogh Group of Greater Himalayan Crystalline and Quartzite from Rampur Group of Lesser Himalayan Crystalline were analyzed. No such physiographic transition in that area is to determine a break in the landscape due to OOST. OOSTs from GHC are interpreted mainly from geochronological studies to date, but proper field evidence is missing. Apart from minimal documentation in geological mapping for OOST, there exists a lack of suitable exposure of rock to generalize the features of OOST in the field in NW Higher Himalaya. Multiple sets of thrust planes may be activated within this zone or a zone along which OOST is engaged.

Keywords: out-of-sequence thrust, main central thrust, grain boundary migration, South Tibetan detachment system, Jakhri Thrust, Sarahan Thrust, Chaura Thrust, higher Himalaya, greater Himalayan crystalline

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Authors: Rosa Figueroa, Christopher Flores

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Text categorization is the problem of assigning a new document to a set of predetermined categories, on the basis of a training set of free-text data that contains documents whose category membership is known. To train a classification model, it is necessary to extract characteristics in the form of tokens that facilitate the learning and classification process. In text categorization, the feature extraction process involves the use of word sequences also known as N-grams. In general, it is expected that documents belonging to the same category share similar features. The Smith-Waterman (SW) algorithm is a dynamic programming algorithm that performs a local sequence alignment in order to determine similar regions between two strings or protein sequences. This work explores the use of SW algorithm as an alternative to feature extraction in text categorization. The dataset used for this purpose, contains 2,610 annotated documents with the classes Obese/Non-Obese. This dataset was represented in a matrix form using the Bag of Word approach. The score selected to represent the occurrence of the tokens in each document was the term frequency-inverse document frequency (TF-IDF). In order to extract features for classification, four experiments were conducted: the first experiment used SW to extract features, the second one used unigrams (single word), the third one used bigrams (two word sequence) and the last experiment used a combination of unigrams and bigrams to extract features for classification. To test the effectiveness of the extracted feature set for the four experiments, a Support Vector Machine (SVM) classifier was tuned using 20% of the dataset. The remaining 80% of the dataset together with 5-Fold Cross Validation were used to evaluate and compare the performance of the four experiments of feature extraction. Results from the tuning process suggest that SW performs better than the N-gram based feature extraction. These results were confirmed by using the remaining 80% of the dataset, where SW performed the best (accuracy = 97.10%, weighted average F-measure = 97.07%). The second best was obtained by the combination of unigrams-bigrams (accuracy = 96.04, weighted average F-measure = 95.97) closely followed by the bigrams (accuracy = 94.56%, weighted average F-measure = 94.46%) and finally unigrams (accuracy = 92.96%, weighted average F-measure = 92.90%).

Keywords: comorbidities, machine learning, obesity, Smith-Waterman algorithm

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Authors: Krishnendra Shekhawat

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Given a graph G = (V, E), a rectangular dual of G represents the vertices of G by a set of interior-disjoint rectangles such that two rectangles touch if and only if there is an edge between the two corresponding vertices in G. Rectangular duals do not exist for every graph, so we can define maximal rectangular duals. A maximal rectangular dual is a rectangular dual of a graph G such that there exists no graph G ′ with a rectangular dual where G is a subgraph of G ′. In this paper, we enumerate all maximal rectangular duals (or, to be precise, the corresponding planar graphs) up to six nodes and presents a necessary condition for the existence of a rectangular dual. This work allegedly has applications in integrated circuit design and architectural floor plans.

Keywords: adjacency, degree sequence, dual graph, rectangular dual

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Authors: Narayan Moger, Divya B., Preethi Jambagi, Krishnaveni C. K., Apsana M. R., B. R. Patil, Basvaraj Bagewadi

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Salinity is one of the major threats to world food security. Considering the requirement for salt tolerant crop plants in the present study was undertaken to clone and transferred the salt tolerant ectA gene from marine ecosystem into agriculture crop system to impart salinity tolerance. Ectoine is the compatible solute which accumulates in the cell membrane, is known to be involved in salt tolerance activity in most of the Halophiles. The present situation is insisting to development of salt tolerant transgenic lines to combat abiotic stress. In this background, the investigation was conducted to develop transgenic tomato lines by cloning and transferring of ectA gene is an ectoine derivative capable of enzymatic action for the production of acetyl-diaminobutyric acid. The gene ectA is involved in maintaining the osmotic balance of plants. The PCR amplified ectA gene (579bp) was cloned into T/A cloning vector (pTZ57R/T). The construct pDBJ26 containing ectA gene was sequenced by using gene specific forward and reverse primers. Sequence was analyzed using BLAST algorithm to check similarity of ectA gene with other isolates. Highest homology of 99.66 per cent was found with ectA gene sequences of isolates Halomonas elongata with the available sequence information in NCBI database. The ectA gene was further sub cloned into pRI101-AN plant expression vector and transferred into E. coli DH5α for its maintenance. Further pDNM27 was mobilized into A. tumefaciens LBA4404 through tri-parental mating system. The recombinant Agrobacterium containing pDNM27 was transferred into tomato plants through In planta plant transformation method. Out of 300 seedlings, co-cultivated only twenty-seven plants were able to well establish under the greenhouse condition. Among twenty-seven transformants only twelve plants showed amplification with gene specific primers. Further work must be extended to evaluate the transformants at T1 and T2 generations for ectoine accumulation, salinity tolerance, plant growth and development and yield.

Keywords: salinity, computable solutes, ectA, transgenic, in planta transformation

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Authors: Cristian Chacha, David Asiain, Jesús Ponce de León, José Ramón Beltrán

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This work explores and characterizes the behavior of the AFE AD5941 in impedance measurement using an embedded algorithm with a constant current AC source. The main aim of this research is to improve the exact measurement of impedance values for their application in EDA-focused wearable devices. Through comprehensive study and characterization, it has been observed that employing a measurement sequence with a constant current source produces results with increased dispersion but higher accuracy. As a result, this approach leads to a more accurate system for impedance measurement.

Keywords: EDA, constant current AC source, wearable, precision, accuracy, impedance

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Authors: Camilla Trevor, Matthew K. Higgins, Andrea Gonzalez-Munoz, Mark Carrington

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Trypanosomiasis is a devastating disease affecting both humans and livestock in sub-Saharan Africa. The diseases are caused by infection with African trypanosomes, protozoa transmitted by tsetse flies. Treatment currently relies on the use of chemotherapeutics with ghastly side effects. Here, we describe the development of effective antibody-drug conjugates that target the T. brucei transferrin receptor. The receptor is essential for trypanosome growth in a mammalian host but there are approximately 12 variants of the transferrin receptor in the genome. Two of the most divergent variants were used to generate recombinant monoclonal immunoglobulin G using phage display and we identified cross-reactive antibodies that bind both variants using phage ELISA, fluorescence resonance energy transfer assays and surface plasmon resonance. Fluorescent antibodies were used to demonstrate uptake into trypanosomes in culture. Toxin-conjugated antibodies were effective at killing trypanosomes at sub-nanomolar concentrations. The approach of using antibody-drug conjugates has proven highly effective.

Keywords: antibody-drug conjugates, phage display, transferrin receptor, trypanosomes

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Authors: Rowan Moore, Kai Scheffler, Eugen Damoc, Jennifer Sutton, Aaron Bailey, Stephane Houel, Simon Cubbon, Jonathan Josephs

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Purpose: MS analysis of monoclonal antibodies (mAbs) at the protein and peptide levels is critical during development and production of biopharmaceuticals. The compositions of current generation therapeutic proteins are often complex due to various modifications which may affect efficacy. Intact proteins analyzed by MS are detected in higher charge states that also provide more complexity in mass spectra. Protein analysis in native or native-like conditions with zero or minimal organic solvent and neutral or weakly acidic pH decreases charge state value resulting in mAb detection at higher m/z ranges with more spatial resolution. Methods: Three commercially available mAbs were used for all experiments. Intact proteins were desalted online using size exclusion chromatography (SEC) or reversed phase chromatography coupled on-line with a mass spectrometer. For streamlined use of the LC- MS platform we used a single SEC column and alternately selected specific mobile phases to perform separations in either denaturing or native-like conditions: buffer A (20 % ACN, 0.1 % FA) with Buffer B (100 mM ammonium acetate). For peptide analysis mAbs were proteolytically digested with and without prior reduction and alkylation. The mass spectrometer used for all experiments was a commercially available Thermo Scientific™ hybrid Quadrupole-Orbitrap™ mass spectrometer, equipped with the new BioPharma option which includes a new High Mass Range (HMR) mode that allows for improved high mass transmission and mass detection up to 8000 m/z. Results: We have analyzed the profiles of three mAbs under reducing and native conditions by direct infusion with offline desalting and with on-line desalting via size exclusion and reversed phase type columns. The presence of high salt under denaturing conditions was found to influence the observed charge state envelope and impact mass accuracy after spectral deconvolution. The significantly lower charge states observed under native conditions improves the spatial resolution of protein signals and has significant benefits for the analysis of antibody mixtures, e.g. lysine variants, degradants or sequence variants. This type of analysis requires the detection of masses beyond the standard mass range ranging up to 6000 m/z requiring the extended capabilities available in the new HMR mode. We have compared each antibody sample that was analyzed individually with mixtures in various relative concentrations. For this type of analysis, we observed that apparent native structures persist and ESI is benefited by the addition of low amounts of acetonitrile and formic acid in combination with the ammonium acetate-buffered mobile phase. For analyses on the peptide level we analyzed reduced/alkylated, and non-reduced proteolytic digests of the individual antibodies separated via reversed phase chromatography aiming to retrieve as much information as possible regarding sequence coverage, disulfide bridges, post-translational modifications such as various glycans, sequence variants, and their relative quantification. All data acquired were submitted to a single software package for analysis aiming to obtain a complete picture of the molecules analyzed. Here we demonstrate the capabilities of the mass spectrometer to fully characterize homogeneous and heterogeneous therapeutic proteins on one single platform. Conclusion: Full characterization of heterogeneous intact protein mixtures by improved mass separation on a quadrupole-Orbitrap™ mass spectrometer with extended capabilities has been demonstrated.

Keywords: disulfide bond analysis, intact analysis, native analysis, mass spectrometry, monoclonal antibodies, peptide mapping, post-translational modifications, sequence variants, size exclusion chromatography, therapeutic protein analysis, UHPLC

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Authors: Hui Li, Xueying Zhao, Ke Ma, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

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Soil can often link a person or item to a crime scene, which makes it a valuable evidence in forensic casework. Several techniques have been utilized in forensic soil discrimination in previous studies. Because soil contains a vast number of microbiomes, the analyse of soil microbiomes is expected to be a potential way to characterise soil evidence. In this study, we applied massively parallel sequencing (MPS) to soil bacterial profiling on the Ion Torrent Personal Genome Machine (PGM). Soils from different regions were collected repeatedly. V-region 3 and 4 of Bacterial 16S rRNA gene were detected by MPS. Operational taxonomic units (OTU, 97%) were used to analyse soil bacteria. Several bioinformatics methods (PCoA, NMDS, Metastats, LEfse, and Heatmap) were applied in bacterial profiles. Our results demonstrate that MPS can provide a more detailed picture of the soil microbiomes and the composition of soil bacterial components from different region was individualistic. In conclusion, the utility of soil bacterial profiling via MPS of the 16S rRNA gene has potential value in characterising soil evidences and associating them with their place of origin, which can play an important role in forensic science in the future.

Keywords: bacterial profiling, forensic, massively parallel sequencing, soil evidence

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Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

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Authors: Lara Dutil-Fafard, Caroline Rhéaume, Patrick Archambault, Daniel Lafond, Neal W. Pollock

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Improving resources for medical autonomy of astronauts in prolonged space missions, such as a Mars mission, requires not only technology development, but also decision-making support systems. The Advanced Crew Medical System - Medical Condition Requirements study, funded by the Canadian Space Agency, aimed to create knowledge content and a scenario-based query capability to support medical autonomy of astronauts. The key objective of this study was to create a prototype tool for identifying medical infrastructure requirements in terms of medical knowledge, skills and materials. A multicriteria decision-making method was used to prioritize the highest risk medical events anticipated in a long-term space mission. Starting with those medical conditions, event sequence diagrams (ESDs) were created in the form of decision trees where the entry point is the diagnosis and the end points are the predicted outcomes (full recovery, partial recovery, or death/severe incapacitation). The ESD formalism was adapted to characterize and compare possible outcomes of medical conditions as a function of available medical knowledge, skills, and supplies in a given mission scenario. An extensive literature review was performed and summarized in a medical condition database. A PostgreSQL relational database was created to allow query-based evaluation of health outcome metrics with different medical infrastructure scenarios. Critical decision points, skill and medical supply requirements, and probable health outcomes were compared across chosen scenarios. The three medical conditions with the highest risk rank were acute coronary syndrome, sepsis, and stroke. Our efforts demonstrate the utility of this approach and provide insight into the effort required to develop appropriate content for the range of medical conditions that may arise.

Keywords: decision support system, event-sequence diagram, exploration mission, medical autonomy, scenario-based queries, space medicine

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