Search results for: shotgun metagenomic sequence analysis

Authors: Wilailak Siripornadulsil, Siriyanapat Tasaku, Jutamas Buahorm, Surasak Siripornadulsil

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The objectives of this study were to isolate LAB from various sources, dietary supplement, Thai traditional fermented food, and freshwater fish and to characterize their potential as probiotic cultures. Out of 1,558 isolates, 730 were identified as LAB based on isolation on MRS agar supplemented with a bromocresol purple indicator and CaCO3 and gram-positive, catalase and oxidase negative characteristics. Eight isolates showed the potential probiotic properties including tolerance to acid, bile salt and heat, proteolytic, amylolytic and lipolytic activities and oxalate-degrading capability. They all showed the antimicrobial activity against some Gram-negative and Gram-positive pathogenic bacteria. Based on 16S rDNA sequence analysis, they were identified as Enterococcus faecalis BT2 and MG30, Leconostoc mesenteroides SW64 and Pediococcus pentosaceous BD33, CF32, NP6, PS34 and SW5. The health beneficial effects and food safety will be further investigated and developed as a probiotic or protective culture used in Nile tilapia belly flap meat fermentation.

Keywords: probiotic, lactic acid bacteria, pathogen, protective culture

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Authors: Gargi Prasad, Ashiho A. Mao, Deepu Vijayan, S. Mandal

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The main objective of the present study was to optimize and develop an efficient protocol for in vitro propagation of a medicinally important orchid Cephalantheropsis obcordata (Lindl.) Ormerod along with genetic stability analysis of regenerated plants. This plant has been traditionally used in Chinese folk medicine and the decoction of whole plant is known to possess anticancer activity. Nodal segments used as explants were inoculated on Murashige and Skoog (MS) medium supplemented with various concentrations of isopentenyl adenine (2iP). The rooted plants were successfully acclimatized in the greenhouse with 100% survival rate. Inter-simple sequence repeats (ISSR) markers were used to assess the genetic fidelity of in vitro raised plants and the mother plant. It was revealed that monomorphic bands showing the absence of polymorphism in all in vitro raised plantlets analyzed, confirming the genetic uniformity among the regenerants. Phytochemical analysis was done to compare the antioxidant activities and HPLC fingerprinting assay of 80% aqueous ethanol extract of the leaves and stem of in vitro and in vivo grown C. obcordata. The extracts of the plants were examined for their antioxidant activities by using free radical 1, 1-diphenyl-2-picryl hydrazyl (DPPH) scavenging method, 2,2’-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical scavenging ability, reducing power capacity, estimation of total phenolic content, flavonoid content and flavonol content. A simplified method for the detection of ascorbic acid, phenolic acids and flavonoids content was also developed by using reversed phase high-performance liquid chromatography (HPLC). This is the first report on the micropropagation, genetic integrity study and quantitative phytochemical analysis of in vitro regenerated plants of C. obcordata.

Keywords: Cephalantheropsis obcordata, genetic fidelity, ISSR markers, HPLC

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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: Yasmeen A. S. Essawy, Khaled Nassar

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With the rapid increase of complexity in the building industry, professionals in the A/E/C industry were forced to adopt Building Information Modeling (BIM) in order to enhance the communication between the different project stakeholders throughout the project life cycle and create a semantic object-oriented building model that can support geometric-topological analysis of building elements during design and construction. This paper presents a model that extracts topological relationships and geometrical properties of building elements from an existing fully designed BIM, and maps this information into a directed acyclic Elemental Graph Data Model (EGDM). The model incorporates BIM-based search algorithms for automatic deduction of geometrical data and topological relationships for each building element type. Using graph search algorithms, such as Depth First Search (DFS) and topological sortings, all possible construction sequences can be generated and compared against production and construction rules to generate an optimized construction sequence and its associated schedule. The model is implemented in a C# platform.

Keywords: building information modeling (BIM), elemental graph data model (EGDM), geometric and topological data models, graph theory

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Authors: Lela Mirtskhulava, Mariam Khunjgurua, Nino Lomineishvili, Koba Bakuria

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Software reliability prediction gives a great opportunity to measure the software failure rate at any point throughout system test. A software reliability prediction model provides with the technique for improving reliability. Software reliability is very important factor for estimating overall system reliability, which depends on the individual component reliabilities. It differs from hardware reliability in that it reflects the design perfection. Main reason of software reliability problems is high complexity of software. Various approaches can be used to improve the reliability of software. We focus on software reliability model in this article, assuming that there is a time redundancy, the value of which (the number of repeated transmission of basic blocks) can be an optimization parameter. We consider given mathematical model in the assumption that in the system may occur not only irreversible failures, but also a failure that can be taken as self-repairing failures that significantly affect the reliability and accuracy of information transfer. Main task of the given paper is to find a time distribution function (DF) of instructions sequence transmission, which consists of random number of basic blocks. We consider the system software unreliable; the time between adjacent failures has exponential distribution.

Keywords: exponential distribution, conditional mean time to failure, distribution function, mathematical model, software reliability

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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: Hojjat Mohammadi, Randall Divito, Gary J. E. Kramer

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Tunnelling and pipe jacking in very soft soils (fat clays), even with an Earth Pressure Balance tunnel boring machine (EPBM), can cause large ground displacements. In this study, the short-term and long-term ground and tunnel response is predicted for twin, pipe-jacked EPBM 3 meter diameter tunnels with a narrow pillar width. Initial modelling indicated complete closure of the annulus gap at the tail shield onto the centrifugally cast, glass-fiber-reinforced, polymer mortar jacking pipe (FRP). Numerical modelling was employed to simulate the excavation and support installation sequence, examine the ground response during excavation, confirm the adequacy of the pillar width and check the structural adequacy of the installed pipe. In the numerical models, Mohr-Coulomb constitutive model with the effect of unloading was adopted for the fat clays, while for the bedrock layer, the generalized Hoek-Brown was employed. The numerical models considered explicit excavation sequences and different levels of ground convergence prior to support installation. The well-studied excavation sequences made the analysis possible for this study on a very soft clay, otherwise, obtaining the convergency in the numerical analysis would be impossible. The predicted results indicate that the ground displacements around the tunnel and its effect on the pipe would be acceptable despite predictions of large zones of plastic behaviour around the tunnels and within the entire pillar between them due to excavation-induced ground movements.

Keywords: finite element modeling (FEM), pipe-jacked tunneling, very soft clay, EPBM

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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: Suikinai Nobre Santos, Ranko Gacesa, Paul F. Long, Itamar Soares de Melo

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Extremophilic microorganism are adapted to biotopes combining several stress factors (temperature, pressure, radiation, salinity and pH), which indicate the richness valuable resource for the exploitation of novel biotechnological processes and constitute unique models for investigations their biomolecules (1, 2). The above information encourages us investigate bioprospecting synthesized compounds by a noval actinomycete, designated thermotolerant Streptomyces caatingaensis CMAA 1322, isolated from sample soil tropical dry forest (Caatinga) in the Brazilian semiarid region (3-17°S and 35-45°W). This set of constrating physical and climatic factores provide the unique conditions and a diversity of well adapted species, interesting site for biotechnological purposes. Preliminary studies have shown the great potential in the production of cytotoxic, pesticidal and antimicrobial molecules (3). Thus, to extend knowledge of the genes clusters responsible for producing biosynthetic pathways of natural products in strain CMAA1322, whole-genome shotgun (WGS) DNA sequencing was performed using paired-end long sequencing with PacBio RS (Pacific Biosciences). Genomic DNA was extracted from a pure culture grown overnight on LB medium using the PureLink genomic DNA kit (Life Technologies). An approximately 3- to 20-kb-insert PacBio library was constructed and sequenced on an 8 single-molecule real-time (SMRT) cell, yielding 116,269 reads (average length, 7,446 bp), which were allocated into 18 contigs, with 142.11x coverage and N50 value of 20.548 bp (BioProject number PRJNA288757). The assembled data were analyzed by Rapid Annotations using Subsystems Technology (RAST) (4) the genome size was found to be 7.055.077 bp, comprising 6167 open reading frames (ORFs) and 413 subsystems. The G+C content was estimated to be 72 mol%. The closest-neighbors tool, available in RAST through functional comparison of the genome, revealed that strain CMAA1322 is more closely related to Streptomyces hygroscopicus ATCC 53653 (similarity score value, 537), S. violaceusniger Tu 4113 (score value, 483), S. avermitilis MA-4680 (score value, 475), S. albus J1074 (score value, 447). The Streptomyces sp. CMAA1322 genome contains 98 tRNA genes and 135 genes copies related to stress response, mainly osmotic stress (14), heat shock (16), oxidative stress (49). Functional annotation by antiSMASH version 3.0 (5) identified 41 clusters for secondary metabolites (including two clusters for lanthipeptides, ten clusters for nonribosomal peptide synthetases [NRPS], three clusters for siderophores, fourteen for polyketide synthetase [PKS], six clusters encoding a terpene, two clusters encoding a bacteriocin, and one cluster encoding a phenazine). Our work provide in comparative analyse of genome and extract produced (data no published) by lineage CMAA1322, revealing the potential of microorganisms accessed from extreme environments as Caatinga” to produce a wide range of biotechnological relevant compounds.

Keywords: caatinga, streptomyces, environmental stresses, biosynthetic pathways

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Authors: Fu Lin

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We consider the worst-case load-shedding problem in electric power networks where a number of transmission lines are to be taken out of service. The objective is to identify a prespecified number of line outages that lead to the maximum interruption of power generation and load at the transmission level, subject to the active power-flow model, the load and generation capacity of the buses, and the phase-angle limit across the transmission lines. For this nonlinear model with binary constraints, we show that all decision variables are separable except for the nonlinear power-flow equations. We develop an iterative decomposition algorithm, which converts the worst-case load shedding problem into a sequence of small subproblems. We show that the subproblems are either convex problems that can be solved efficiently or nonconvex problems that have closed-form solutions. Consequently, our approach is scalable for large networks. Furthermore, we prove the convergence of our algorithm to a critical point, and the objective value is guaranteed to decrease throughout the iterations. Numerical experiments with IEEE test cases demonstrate the effectiveness of the developed approach.

Keywords: load shedding, power system, proximal alternating linearization method, vulnerability analysis

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Authors: Stephan Printz, Kristina Lahl, René Vossen, Sabina Jeschke

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Strategic investment decisions are characterized by high innovation potential and long-term effects on the competitiveness of enterprises. Due to the uncertainty and risks involved in this complex decision making process, the need arises for well-structured support activities. A method that considers cost and the long-term added value is the cost-benefit effectiveness estimation. One of those methods is the “profitability estimation focused on benefits – PEFB”-method developed at the Institute of Management Cybernetics at RWTH Aachen University. The method copes with the challenges associated with strategic investment decisions by integrating long-term non-monetary aspects whilst also mapping the chronological sequence of an investment within the organization’s target system. Thus, this method is characterized as a holistic approach for the evaluation of costs and benefits of an investment. This participation-oriented method was applied to business environments in many workshops. The results of the workshops are a library of more than 96 cost aspects, as well as 122 benefit aspects. These aspects are preprocessed and comparatively analyzed with regards to their alignment to a series of risk levels. For the first time, an accumulation and a distribution of cost and benefit aspects regarding their impact and probability of occurrence are given. The results give evidence that the PEFB-method combines precise measures of financial accounting with the incorporation of benefits. Finally, the results constitute the basics for using information technology and data science for decision support when applying within the PEFB-method.

Keywords: cost-benefit analysis, multi-criteria decision, profitability estimation focused on benefits, risk and uncertainty analysis

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Authors: Patience Orobosa Olajide

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Five hydrocarbon degrading bacterial strains isolated from contaminated environment were investigated with respect to polyhydroxybutyrate (PHB) biosynthesis. Screening for bioplastic production was done on assay mineral salts agar medium containing 0.2% poly (3-hydroxybutyrate) as the sole carbon source. Two of the test bacteria were positive for PHB biosynthesis and were identified based on gram staining, biochemical tests, 16S rRNA gene sequence analysis as Pseudomonas aeruginosa and Bacillus licheniformis which grew at 37 and up to 65 °C respectively, thus suggesting the later to be thermotolerant. In this study, the effects of different carbon and nitrogen sources on PHB production in these strains were investigated. Maximum PHB production was obtained in 48 hr for the two strains and amounted to yields of 72.86 and 62.22 percentages for Bacillus licheniformis and Pseudomonas aeruginosa respectively. In these strains, glycine was the most efficient carbon sources for the production of PHB compared with other carbon (glucose, lactose, sucrose, Arabinose) and nitrogen (L- glycine, L-cysteine, DL-Tryptophan, and Potassium Nitrate) sources. The screening of microbial strains for industrial PHB production should be based on several factors including the cell’s capability to mineralize an inexpensive substrate, rate of growth and the extent of polymer accumulation.

Keywords: bacteria, poly-3-hydroxybutyrate (PHB), hydrocarbon, thermotolerant

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Authors: Stephanie Khater, Ali Chehade, Lamis Chalak

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The progressive replacement of the Lebanese autochthonous grapevine cultivars during the last decade by the imported foreign varieties almost resulted in the genetic erosion of the local germplasm and the confusion with cultivars' names. Hence there is a need to characterize these local cultivars and to assess the possible existing variability at the cultivar level. This work was conducted in an attempt to evaluate the intra-varietal diversity within Lebanese traditional cultivars 'Aswad', 'Maghdoushe', 'Maryame', 'Merweh', 'Meksese' and 'Obeide'. A total of 50 accessions distributed over five main geographical areas in Lebanon were collected and submitted to both ampelographic description and ISSR DNA analysis. A set of 35 ampelographic descriptors previously established by the International Office of Vine and Wine and related to leaf, bunch, berry, and phenological stages, were examined. Variability was observed between accessions within cultivars for blade shape, density of prostrate and erect hairs, teeth shape, berry shape, size and color, cluster shape and size, and flesh juiciness. At the molecular level, nine ISSR (inter-simple sequence repeat) primers, previously developed for grapevine, were used in this study. These primers generated a total of 35 bands, of which 30 (85.7%) were polymorphic. Totally, 29 genetic profiles were differentiated, of which 9 revealed within 'Obeide', 6 for 'Maghdoushe', 5 for 'Merweh', 4 within 'Maryame', 3 for 'Aswad' and 2 within 'Meksese'. Findings of this study indicate the existence of several genotypes that form the basis of the main indigenous cultivars grown in Lebanon and which should be further considered in the establishment of new vineyards and selection programs.

Keywords: ampelography, autochthonous cultivars, ISSR markers, Lebanon, Vitis vinifera L.

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Authors: Zhenfeng Xie

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Acute gastroenteritis (AGE) is a common cause of morbidity and mortality in infants and young children worldwide, especially in developing countries. Enterovirus(EVs) have been identified in patients with AGE in many countries around the world, and some studies have revealed that EV infection is associated with gastrointestinal symptoms and plays a role in AGE. As a potential causative pathogen of AGE in humans, continuous detection and identification of EVs in pediatric patients with AGE is needed. In this study, we aimed to investigate the prevalence, seasonal distribution, and molecular characteristics of EVs circulating in pediatric patients with AGE in Thailand from 2019 to 2022. A total of 1422 stool specimens were collected for this study. RT-PCR amplification of the 5'UTR was used to screen for EV positive samples. EV genotyping was determined based on nucleotide sequence and phylogenetic analysis of the VP1 sequences. EV prevalence in pediatric AGE patients was 8.3% (118 out of 1,422). Among these, 35.6% of EV infection cases were caused by species A, followed by species C and B (33.1% and 30.5%, respectively). A total of 26 EV genotypes were identified in this study. Poliovirus 3 and coxsackievirus A2 were the predominant genotypes detected(14% and 13%, respectively). EV was detected all year round with higher prevalence between July and December. In summary, this study reports EV's prevalence and genotype diversity in pediatric patients with AGE in Thailand during 2019-2022.

Keywords: enterovirus, epidemiology, acute gastroenteritis, genotype

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Authors: Prittesh Patel, Rushabh Shah, Krishnamurthy Ramar, Vakulbhushan Bhaskar

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The present research work aims at finding genetic differences in the genomes of sugarcane red rot isolates Colletotrichum falcatum Went using Random Amplified Polymorphic DNA (RAPD) and interspersed simple sequence repeat (ISSR) molecular markers. Ten isolates of C. falcatum isolated from different red rot infected sugarcane cultivars stalk were used in present study. The amplified bands were scored across the lanes obtained in 15 RAPD primes and 21 ISSR primes successfully. The data were analysed using NTSYSpc 2.2 software. The results showed 80.6% and 68.07% polymorphism in RPAD and ISSR analysis respectively. Based on the RAPD analysis, ten genotypes were grouped into two major clusters at a cut-off value of 0.75. Geographically distant C. falcatum isolate cfGAN from south Gujarat had a level of similarity with Coimbatore isolate cf8436 presented on separate clade of bootstrapped dendrograms. First and second cluster consisted of five and three isolates respectively, indicating the close relation among them. The 21 ISSR primers produced 119 distinct and scorable loci in that 38 were monomorphic. The number of scorable loci for each primer varied from 2 (ISSR822) to 8 (ISSR807, ISSR823 and ISSR15) with an average of 5.66 loci per primer. Primer ISSR835 amplified the highest number of bands (57), while only 16 bands were obtained by primers ISSR822. Four primers namely ISSR830, ISSR845, ISSR4 and ISSR15 showed the highest value of percentage of polymorphism (100%). The results indicated that both of the marker systems RAPD and ISSR, individually can be effectively used in determination of genetic relationship among C falcatum accessions collected from different parts of south Gujarat.

Keywords: Colletotrichum falcatum, ISSR, RAPD, Red Rot

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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: Antoaneta Stefanova, Rositsa Gencheva, Pavlin Groudev

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This paper presents the modeling approach in SBO sequence for VVER 1000 reactors and describes the reactor core behavior at late in-vessel phase in case of late reflooding by HPIS and gives preliminary results for the ASTECv2 validation. The work is focused on investigation of plant behavior during total loss of power and the operator actions. The main goal of these analyses is to assess the phenomena arising during the Station blackout (SBO) followed by primary side high pressure injection system (HPIS) reflooding of already damaged reactor core at very late ‘in-vessel’ phase. The purpose of the analysis is to define how the later HPIS switching on can delay the time of vessel failure or possibly avoid vessel failure. For this purpose has been simulated an SBO scenario with injection of cold water by a high pressure pump (HPP) in cold leg at different stages of core degradation. The times for HPP injection were chosen based on previously performed investigations.

Keywords: VVER, operator action validation, reflooding of overheated reactor core, ASTEC computer code

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Authors: Ravinder Singh, Ankita Gurao, Saroj Bandhan, Sudhir Kumar Kashyap

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The Bos taurus Beta defensin 3 is a defensin peptide secreted by neutrophils and epithelial that exhibits anti-microbial activity. It is one of the crucial components forming an innate defense against intra mammary infections in livestock. The beta defensin 3 by virtue of its anti-microbial activity inhibits major mastitis pathogens including Staphylococcus aureus and Pseudomonas aeruginosa etc, which are also responsible for biofilm formation leading to antibiotic resistance phenomenon. Therefore, the defensin may prove as a non-conventional option to treat mastitis. In this study, computational analysis has been performed including sequence comparison among species and homology modeling of Bos taurus beta defensin 3 protein. The assessments of protein structure were done using the protein structure and model assessment tools integrated in Swiss Model server, which employs various local and global quality evaluation parameters. Further, molecular docking was also carried out between the defensin peptide and the components of biofilm to gain insight into various interactions and structural differences crucial for functionality of this protein.

Keywords: beta defensin 3, bos taurus, docking, homology modeling

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Authors: Christine Odinga, Fred Otieno, Josiah Adeyemo

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A study was done to establish the effectiveness of wetland plants: Echinocloa pyramidalis (L) and Cyperus papyrus (L) in purifying wastewater from sugar factory stabilization pond effluent. A pilot-scale Free Water Surface Wetland (FWSCW) system was constructed in Chemelil sugar factory, Kenya for the study. The wetland was divided into 8 sections (cells) and planted with C. papyrus and E. pyramidalis in alternating sequence. Water samples and plant specimen were taken fortnightly at inlets and outlets of the cells and analysed for total phosphates and total nitrates. The data was analysed by use of Microsoft excel and SPSS computer packages. Water analysis recorded a reduction in the nutrient levels between the inlet pond nine and the final outlet channel to River Nyando. The plants grown in the wetland experienced varied increases and reductions in the level of total foliar nitrogen and phosphorous, indicating that though the nutrients were being removed from the wetland, the same were not those assimilated by the plants either. The control plants had higher folia phosphorous and nitrogen, an indication that the system of the constructed wetland was able to eliminate the nutrients effectively from the plants.

Keywords: wetlands, constructed, plants, nutrients, wastewater, industrial

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Authors: Mike-Franck Mienlam Essi, Joseph Quentin Yene Atangana, Mbida Yem

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The Kribi-Campo sub-basin belongs to the southern domain of the Cameroon Atlantic Margin in the Gulf of Guinea. It is the African homologous segment of the Sergipe-Alagoas Basin, located at the northeast side of the Brazil margin. The onset of the seafloor spreading period in the Southwest African Margin in general and the study area particularly remains controversial. Various studies locate this event during the Cretaceous times (Early Aptian to Late Albian), while others suggested that this event occurred during Pre-Cretaceous period (Palaeozoic or Jurassic). This work analyses 02 Cameroon Span seismic lines to re-examine the Early marine incursion period of the study area for a better understanding of the margin evolution. The methodology of analysis in this study is based on the delineation of the first seismic sequence, using the reflector’s terminations tracking and the analysis of its internal reflections associated to the external configuration of the package. The results obtained indicate from the bottom upwards that the first deposits overlie a first seismic horizon (H1) associated to “onlap” terminations at its top and underlie a second horizon which shows “Downlap” terminations at its top (H2). The external configuration of this package features a prograded fill pattern, and it is observed within the depocenter area with discontinuous reflections that pinch out against the basement. From east to west, this sequence shows two seismic facies (SF1 and SF2). SF1 has parallel to subparallel reflections, characterized by high amplitude, and SF2 shows parallel and stratified reflections, characterized by low amplitude. The distribution of these seismic facies reveals a lateral facies variation observed. According to the fundamentals works on seismic stratigraphy and the literature review of the geological context of the study area, particularly, the stratigraphical natures of the identified horizons and seismic facies have been highlighted. The seismic horizons H1 and H2 correspond to Top basement and “Downlap Surface,” respectively. SF1 indicates continental sediments (Sands/Sandstone) and SF2 marine deposits (shales, clays). Then, the prograding configuration observed suggests a marine regression. The correlation of these results with the lithochronostratigraphic chart of Sergipe-Alagoas Basin reveals that the first marine deposits through the study area are dated from Pre-Cretaceous times (Palaeozoic or Jurassic). The first deposits onto the basement represents the end of a cycle of sedimentation. The hypothesis of Mike.F. Mienlam Essi is with the Earth Sciences Department of the Faculty of Science of the University of Yaoundé I, P.O. BOX 812 CAMEROON (e-mail: [email protected]). Joseph.Q. Yene Atangana is with the Earth Sciences Department of the Faculty of Science of the University of Yaoundé I, P.O. BOX 812 CAMEROON (e-mail: [email protected]). Mbida Yem is with the Earth Sciences Department of the Faculty of Science of the University of Yaoundé I, P.O. BOX 812 CAMEROON (e-mail: [email protected]). Cretaceous seafloor spreading through the study area is the onset of another cycle of sedimentation. Furthermore, the presence of marine sediments into the first deposits implies that this package could contain marine source rocks. The spatial tracking of these deposits reveals that they could be found in some onshore parts of the Kribi-Campo area or even in the northern side.

Keywords: cameroon span seismic, early marine incursion, kribi-campo sub-basin, pre-cretaceous period, sergipe-alagoas basin

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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: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Mahmoud al-Ashiriy

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This paper begins from the idea that the real history of literature is the history of its style. And since the rhyme –as known- is not merely the last letter, that have received a lot of analysis and investigation, but it is a collection of other values in addition to its different markings. This paper will explore the work of the connecting ha’ and its effectiveness in shaping the text of poetry, since it establishes vocal rhythms in addition to its role in indicating references through the pronoun, vertically through the poem through the sequence of its verses, also horizontally through what environs the one verse of sentences. If the scientific formation of prosody stopped at the possibilities and prohibitions; literary criticism and poetry studies should explore what is above the rule of aesthetic horizon of poetic effectiveness that varies from a text to another, a poet to another, a literary period to another, or from a poetic taste to another. Then the paper will explore this poetic essence in the texts of the famous Andalusian Poet Al-Husari Al-Qayrawani through his well-known Daliyya (a poem that its verses end with the letter D), and the role of the connecting ha’ in fulfilling its text and the accomplishment of its poetics, departing from this to the diwan (the big collection of poems) also as a higher text that surpasses the text/poem, and through what it represents of effectiveness the work of the phenomenon in accomplishing the poetics of the poem of Al-Husari Al-Qayrawani who is one of the pillars of Arabic poetics in Andalusia.

Keywords: Al-Husari Al-Qayrawni, poetics, rhyme, stylistics, science of the text

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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: Saira Khalid, Imran Hashmi

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Agrochemical industries produce huge amount of wastewater containing pesticides and other harmful residues. Environmental regulations make it compulsory to bring pesticides to a minimum level before releasing wastewater from industrial units.The present study was designed with the objective to investigate biodegradation of CP in real wastewater using bacterial cells immobilized in calcium alginate. Bacterial strain identified as Acromobacter xylosoxidans SRK5 (KT013092) using 16S rRNA nucleotide sequence analysis was used. SRK5 was immobilized in calcium alginate to make calcium alginate microspheres (CAMs). Real wastewater from industry having 50 mg L⁻¹ of CP was inoculated with free cells or CAMs and incubated for 96 h at 37˚C. CP removal efficiency with CAMs was 98% after 72 h of incubation, and no lag phase was observed. With free cells, 12h of lag phase was observed. After 96 h of incubation 87% of CP removal was observed when inoculated with free cells. No adsorption was observed on vacant CAMs. Phytotoxicity assay demonstrated considerable loss in toxicity. Almost complete COD removal was achieved at 96 h with CAMs. Study suggests the use of immobilized cells of SRK5 for bioaugmentation of industrial wastewater for CP degradation instead of free cells.

Keywords: biodegradation, chlorpyrifos, immobilization, wastewater

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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: M. Gogniashvili, I. Maisaia, A. Kotorashvili, N. Kotaria, T. Beridze

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Three types of plasmon (A, B and G) is typical for genus Triticum. In polyploid species - Triticum turgidum L. and Triticum aestivum L. plasmon B is detected. In the forthcoming paper, complete nucleotide sequence of chloroplast DNA of 11 representatives of Georgian wheat polyploid species, carrying plasmon B was determined. Sequencing of chloroplast DNA was performed on an Illumina MiSeq platform. Chloroplast DNA molecules were assembled using the SOAPdenovo computer program. All contigs were aligned to the reference chloroplast genome sequence using BLASTN. For detection of SNPs and Indels and phylogeny tree construction computer programs Mafft and Blast were used. Using Triticum aestivum L. subsp. macha (Dekapr. & Menabde) Mackey var. paleocolchicum Dekapr. et Menabde as a reference, 5 SNPs can be identified in chloroplast DNA of Georgian endemic polyploid wheat. The number of noncoding substitutions is 2, coding substitutions - 3. In comparison with reference DNA two - 38 bp and 56 bp inversions were observed in paleocolchicum subspecies. There were six 1 bp indels detected in Georgian polyploid wheats, all of them at microsatellite stretches. The phylogeny tree shows that subspecies macha, carthlicum and paleocolchicum occupy different positions. According to the simplified scheme based on SNP and indel data, the ancestral, female parent of the all studied polyploid wheat is unknown X predecesor, from which four lines were formed. 1 SNP and two inversions (38 bp and 56 bp) caused the formation of subsp. paleocolchicum. Three other lines are macha, durum and carthlicum lines. Macha line is further divided into two sublines (M_1 and M_4). Carthlicum line includes subsp.carthlicum and T.aestivum - C_1 - C_2 - A_1. One of the central question of wheat domestication is which people(s) participated in wheat domestication? It is proposed that the predecessors of Georgian peoples (Proto-Kartvelians) must be placed, on the evidence of archaic lexical and toponymic data, in the mountainous regions of the western and central part of the Little Caucasus (the Transcaucasian foothills) at least 4,000 years ago. One of the possibility to explain the ‘wheat puzzle’ is that Kartvelian speakers brought domesticated wheat species and subspecis from Fertile Crescent further north to South Caucasus.

Keywords: chloroplast DNA, sequencing, SNP, triticum

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