Search results for: genome characterization

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

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

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

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Authors: I. Slim, H. Akkari, A. Ben Abdallah, I. Bhouri, M. Hedi Bedoui

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Osteoporosis is a common disease characterized by low bone mass and deterioration of micro-architectural bone tissue, which provokes an increased risk of fracture. This work treats the texture characterization of trabecular bone radiographs. The aim was to analyze according to clinical research a group of 174 subjects: 87 osteoporotic patients (OP) with various bone fracture types and 87 control cases (CC). To characterize osteoporosis, Fractal and MultiFractal (MF) methods were applied to images for features (attributes) extraction. In order to improve the results, a new method of MF spectrum based on the q-stucture function calculation was proposed and a combination of Fractal and MF attributes was used. The Support Vector Machines (SVM) was applied as a classifier to distinguish between OP patients and CC subjects. The features fusion (fractal and MF) allowed a good discrimination between the two groups with an accuracy rate of 96.22%.

Keywords: fractal, micro-architecture analysis, multifractal, osteoporosis, SVM

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Authors: Guillaume Linassier, Morgan Balland, Hugo Pervier, Marie Pervier, David Hammond

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Atmospheric icing for turbojet is caused by ingestion of super-cooled water droplets. To prevent operability risks, manufacturer can implement ice protection systems. Thermal systems are commonly used for this purpose, but their activation can cause the formation of a water liquid film, that can freeze downstream the heated surface or even on other components. In the framework of STORM, a European project dedicated to icing physics in turbojet engines, a cascade rig representative of engine inlet blades was built and tested in an icing wind tunnel. This mock-up integrates two rows of blades, the upstream one being anti-iced using an electro-thermal device the downstream one being unheated. Under icing conditions, the anti-icing system is activated and set at power level to observe a liquid film on the surface and droplet re-emission at the trailing edge. These re-emitted droplets will impinge on the downstream row and contribute to ice accretion. A complete experimental database was generated, including the characterization of ice accretion shapes, and the characterization of electro-thermal anti-icing system (power limit for apparition of the runback water or ice accretion). These data will be used for validation of numerical tools for modeling thermal anti-icing systems in the scope of engine application, as well as validation of re-emission droplets model for stator parts.

Keywords: turbomachine, anti-icing, cascade rig, runback water

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Authors: Ewelina Wisnik, Zsolt Regdon, Kinga Chmielewska, Laszlo Virag, Agnieszka Robaszkiewicz

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Apart from protecting genome, PARP1 has been documented to regulate many intracellular processes inter alia gene transcription by physically interacting with chromatin bound proteins and by their ADP-ribosylation. Our recent findings indicate that expression of PARP1 decreases during the differentiation of human CD34+ hematopoietic stem cells to monocytes as a consequence of differentiation-associated cell growth arrest and formation of E2F4-RBL2-HDAC1-SWI/SNF repressive complex at the promoter of this gene. Since the RBL2 complexes repress genes in a E2F-dependent manner and are widespread in the genome in G0 arrested cells, we asked (a) if RBL2 directly contributes to defining monocyte phenotype and function by targeting gene promoters and (b) if RBL2 controls gene transcription indirectly by repressing PARP1. For identification of genes controlled by RBL2 and/or PARP1,we used primer libraries for surface receptors and TLR signaling mediators, genes were silenced by siRNA or shRNA, analysis of gene promoter occupation by selected proteins was carried out by ChIP-qPCR, while statistical analysis in GraphPad Prism 5 and STATISTICA, ChIP-Seq data were analysed in Galaxy 2.5.0.0. On the list of 28 genes regulated by RBL2, we identified only four solely repressed by RBL2-E2F4-HDAC1-BRM complex. Surprisingly, 24 out of 28 emerged genes controlled by RBL2 were co-regulated by PARP1 in six different manners. In one mode of RBL2/PARP1 co-operation, represented by MAP2K6 and MAPK3, PARP1 was found to associate with gene promoters upon RBL2 silencing, which was previously shown to restore PARP1 expression in monocytes. PARP1 effect on gene transcription was observed only in the presence of active EP300, which acetylated gene promoters and activated transcription. Further analysis revealed that PARP1 binding to MA2K6 and MAPK3 promoters enabled recruitment of EP300 in monocytes, while in proliferating cancer cell lines, which actively transcribe PARP1, this protein maintained EP300 at the promoters of MA2K6 and MAPK3. Genome-wide analysis revealed a similar distribution of PARP1 and EP300 around transcription start sites and the co-occupancy of some gene promoters by PARP1 and EP300 in cancer cells. Here, we described a new RBL2/PARP1/EP300 axis which controls gene transcription regardless of the cell type. In this model cell, cycle-dependent transcription of PARP1 regulates expression of some genes repressed by RBL2 upon cell cycle limitation. Thus, RBL2 may indirectly regulate transcription of some genes by controlling the expression of EP300-recruiting PARP1. Acknowledgement: This work was financed by Polish National Science Centre grants nr DEC-2013/11/D/NZ2/00033 and DEC-2015/19/N/NZ2/01735. L.V. is funded by the National Research, Development and Innovation Office grants GINOP-2.3.2-15-2016-00020 TUMORDNS, GINOP-2.3.2-15-2016-00048-STAYALIVE and OTKA K112336. AR is supported by Polish Ministry of Science and Higher Education 776/STYP/11/2016.

Keywords: retinoblastoma transcriptional co-repressor like 2 (RBL2), poly(ADP-ribose) polymerase 1 (PARP1), E1A binding protein p300 (EP300), monocytes

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Authors: Dayo Samuel Banjo, Connice Trimmingham, Niloofar Yousefi, Nitin Agarwal

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Technological advancement and its omnipresent connection have pushed humans past the boundaries and limitations of a computer screen, physical state, or geographical location. It has provided a depth of avenues that facilitate human-computer interaction that was once inconceivable such as audio and body language detection. Given the complex modularities of emotions, it becomes vital to study human-computer interaction, as it is the commencement of a thorough understanding of the emotional state of users and, in the context of social networks, the producers of multimodal information. This study first acknowledges the accuracy of classification found within multimodal emotion detection systems compared to unimodal solutions. Second, it explores the characterization of multimedia content produced based on their emotions and the coherence of emotion in different modalities by utilizing deep learning models to classify emotion across different modalities.

Keywords: affective computing, deep learning, emotion recognition, multimodal

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Authors: Mohammad Salah Abdullatif, Salam Hajjar, Paul Khanna

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The development of instrument grade mmWave transceivers comes with many challenges. A general rule of thumb is that the performance of the instrument must be higher than the performance of the unit under test in terms of accuracy and stability. The calibration and characterizing of mmWave transceivers are important pillars for testing commercial products. Using a Vector Network Analyzer (VNA) with a mixer option has proven a high performance as an approach to calibrate mmWave transceivers. However, this approach comes with a high cost. In this work, a reduced-cost method to calibrate mmWave transceivers is proposed. A comparison between the proposed method and the VNA technology is provided. A demonstration of significant challenges is discussed, and an approach to meet the requirements is proposed.

Keywords: mmWave transceiver, scalar characterization, coupler connection, magic tee connection, calibration, VNA, vector network analyzer

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Authors: Sarra Sobti, Baelhadj Hamdi-Aïssa

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The bacteria of the soil, usually called rhizobium, have a considerable importance in agriculture because of their capacity to fix the atmospheric nitrogen in symbiosis with the plants of the family of legumes. The present work was to study the effect of the salinity on growth and nodulation of alfalfa-rhizobia symbiosis at different agricultural experimental sites in Ouargla. The experiment was conducted in 3 steps. The first one was the isolation and characterization of the Rhizobia; next, the evolution of the isolates tolerance to salinity at three levels of NaCl (6, 8,12 and 16 g/L); and the last step was the evolution of the tolerance on symbiotic characteristics. The results showed that the phenotypic characterizations behave practically as Rhizobia spp, and the effects of salinity affect the symbiotic process. The tolerance to high levels of salinity and the survival and persistence in severe and harsh desert conditions make these rhizobia highly valuable inoculums to improve productivity of the leguminous plants cultivated under extreme environments.

Keywords: rhizobia, symbiosis, salinity, tolerance, nodulation, soil, Medicago sativa L.

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Authors: R. Meier, M. Pander

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In accordance with the industry 4.0 concept, manufacturing process steps as well as the materials themselves are going to be more and more digitalized within the next years. The “digital twin” representing the simulated and measured dataset of the (semi-finished) product can be used to control and optimize the individual processing steps and help to reduce costs and expenditure of time in product development, manufacturing, and recycling. In the present work, two material characterization methods based on Lamb waves were evaluated and compared. For demonstration purpose, both methods were shown at a standard industrial product - copper ribbons, often used in photovoltaic modules as well as in high-current microelectronic devices. By numerical approximation of the Rayleigh-Lamb dispersion model on measured phase velocities second order elastic constants (Young’s modulus, Poisson’s ratio) were determined. Furthermore, the effective third order elastic constants were evaluated by applying elastic, “non-destructive”, mechanical stress on the samples. In this way, small microstructural variations due to mechanical preconditioning could be detected for the first time. Both methods were compared with respect to precision and inline application capabilities. Microstructure of the samples was systematically varied by mechanical loading and annealing. Changes in the elastic ultrasound transport properties were correlated with results from microstructural analysis and mechanical testing. In summary, monitoring the elastic material properties of plate-like structures using Lamb waves is valuable for inline and non-destructive material characterization and manufacturing process control. Second order elastic constants analysis is robust over wide environmental and sample conditions, whereas the effective third order elastic constants highly increase the sensitivity with respect to small microstructural changes. Both Lamb wave based characterization methods are fitting perfectly into the industry 4.0 concept.

Keywords: lamb waves, industry 4.0, process control, elasticity, acoustoelasticity, microstructure

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Authors: Hamza Zidoum

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This paper investigates the impact of human genetic variation on the function of human proteins using machine-learning algorithms. Single-Nucleotide Polymorphism represents the most common form of human genome variation. We focus on the single amino-acid polymorphism located in the coding region as they can affect the protein function leading to pathologic phenotypic change. We use several supervised Machine Learning methods to identify structural properties correlated with increased risk of the missense mutation being damaging. SVM associated with Principal Component Analysis give the best performance.

Keywords: single-nucleotide polymorphism, machine learning, feature selection, SVM

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Authors: Eriberto R. Astorga Jr., Herbert D. Vertucio, Evelyn M. Polison

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This study was conducted in order to determine the analysis with regards to the Characterization of Self-Esteem of EARIST Students according to their origin of self-esteem and low self-esteem as well as its causes. The respondents of this study are three thousand three hundred twenty three (3,323) randomly selected students from eight colleges of EARIST such as Arts and Sciences, Education, Public Administration and Criminology, Business Administration, Hospitality Management, Architecture and Fine Arts, Engineering, and Industrial Technology. A survey was conducted by using a validated questionnaire for information gathering about respondents profile and different factors relating to self-esteem of students such as self-origin, familial and social relationship, financial situation and education. Frequency, percentage, ranking and standards deviation, standard t-test and ANOVA were applied to investigate the differences of the answers of the respondents to the origin of their self-esteem and the reasons for low self-esteem. The results revealed that there are no significant differences in the origin of their self-esteem and the reasons of low esteem as to the eight group of respondent’s. Moreover, most causes of low esteem are caused by hearing a comment or experiencing an incident that has a negative impact student mentally and emotionally, poor health, being bullied, lack of support from family, friends, and job loss, experiencing verbal and sexual abuse and are in a violent relationship, feelings of isolation, divorce, dysfunctional family, death and lack of achievement at work and at school, trying to conform to stereotypes and prove our independence from our parents.

Keywords: characterization, plan of action, profile, self-esteem

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Authors: Arpit Kumar Shrivastava, Subrat Kumar, Rajani Kanta Mohapatra, Priyadarshi Soumyaranjan Sahu

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Computational approaches to predict structure, function and other biological characteristics of proteins are becoming more common in comparison to the traditional methods in drug discovery. Cryptosporidiosis is a major zoonotic diarrheal disease particularly in children, which is caused primarily by Cryptosporidium hominis and Cryptosporidium parvum. Currently, there are no vaccines for cryptosporidiosis and recommended drugs are not effective. With the availability of complete genome sequence of C. hominis, new targets have been recognized for the development of effective and better drugs and/or vaccines. We identified a unique hypothetical epitopic protein in C. hominis genome through BLASTP analysis. A 3D model of the hypothetical protein was generated using I-Tasser server through threading methodology. The quality of the model was validated through Ramachandran plot by PROCHECK server. The functional annotation of the hypothetical protein through DALI server revealed structural similarity with human Transportin 3. Phylogenetic analysis for this hypothetical protein also showed C. hominis hypothetical protein (CUV04613) was the closely related to human transportin 3 protein. The 3D protein model is further subjected to virtual screening study with inhibitors from the Zinc Database by using Dock Blaster software. Docking study reported N-(3-chlorobenzyl) ethane-1,2-diamine as the best inhibitor in terms of docking score. Docking analysis elucidated that Leu 525, Ile 526, Glu 528, Glu 529 are critical residues for ligand–receptor interactions. The molecular dynamic simulation was done to access the reliability of the binding pose of inhibitor and protein complex using GROMACS software at 10ns time point. Trajectories were analyzed at each 2.5 ns time interval, among which, H-bond with LEU-525 and GLY- 530 are significantly present in MD trajectories. Furthermore, antigenic determinants of the protein were determined with the help of DNA Star software. Our study findings showed a great potential in order to provide insights in the development of new drug(s) or vaccine(s) for control as well as prevention of cryptosporidiosis among humans and animals.

Keywords: cryptosporidium hominis, hypothetical protein, molecular docking, molecular dynamics simulation

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Authors: Nougrara Zineb

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The unique structure of the blood vessels in the retina has been used for biometric identification. The retina blood vessel pattern is a unique pattern in each individual and it is almost impossible to forge that pattern in a false individual. The retina biometrics’ advantages include high distinctiveness, universality, and stability overtime of the blood vessel pattern. Once the creases have been extracted from the images, a registration stage is necessary, since the position of the retinal vessel structure could change between acquisitions due to the movements of the eye. Image registration consists of following steps: Feature detection, feature matching, transform model estimation and image resembling and transformation. In this paper, we present an algorithm of registration; it is based on the characterization of retinal feature points. For experiments, retinal images from the DRIVE database have been tested. The proposed methodology achieves good results for registration in general.

Keywords: fovea, optic disc, registration, retinal images

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Authors: Houcine Ammar

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Chromenederivatives are an important class of heterocycles that are found in a wide range of natural products. Chromenes are commonly used as cosmetics, food additives, and possibly biodegradable agrochemicals. Recently, the synthesis of chromene derivatives has drawn more attention due to their pharmacological and biological applications. In the present work, we are interested in the synthesis and characterization of chromeno [2,3-b] pyridin-4-yl) formimidate, carried out in 4 steps: (i) the synthesis of 3-cyanoiminocoumarins is realized first by Knœvenagel reaction by reacting malonitrile with variously substituted o-phenolic benzaldehydes. In order to undergo reduction by sodium tetraborohydride NaBH4 to lead to new 2-amino-3-cyano-4H-chromenes, these compounds were easily transformed by the action of malonitrile leading to 2,4-diamino-5H-chromeno [2,3-b] pyridine-3-carbonitrile under microwave activation. For the final step, the action of triethylorthoformate on 2,4-diamino-5H-chromeno [2,3-b] pyridine-3-carbonitrile leads to new chromeno [2,3-b] pyridinheterocycles. -4-yl) formimidate. The synthesized compounds have been characterized by different spectroscopic techniques 1 H-NMR, 13 C-NMR, and IRTF.

Keywords: chromene, microwave, knovenagel condensation, chromeno [2, 3-b] pyridine

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Authors: Hacina Abchiche, Mounir Mellal, Imene Bouchelkia

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The knowledge of the rheological behavior of the used products in different fields is essential, both in digital simulation and the understanding of phenomenon involved during the flow of these products. The fluids presenting a nonlinear behavior represent an important category of materials used in the process of food-processing, chemical, pharmaceutical and oil industries. The issue is that the rheological characterization by classical rheometer cannot simulate, or take into consideration, the different parameters affecting the characterization of a complex fluid flow during real-time. The main objective of this study is to investigate the influence of the diameter of the flow conducts or pipe on the rheological behavior of a non-Newtonian fluid and Propose a mathematical model linking the rheologic parameters and the diameter of the conduits of flow. For this purpose, we have developed an experimental system based on the principal of a capillary rheometer.

Keywords: rhéologie, non-Newtonian fluids, experimental stady, mathematical model, cylindrical conducts

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Authors: D. S. Malatesh, K. J. Ananda, C. Ansar Kamran, K. Ganesh Udupa

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Dirofilaria repens is a mosquito-borne filarioid nematode of dogs and other carnivores and accidentally affects humans. D. repens is reported in many countries, including India. Subcutaneous dirofilariosis caused by D. repens is a zoonotic disease, widely distributed throughout Europe, Asia, and Africa, with higher prevalence reported in dogs from Sri Lanka (30-60%), Iran (61%) and Italy (21-25%). Dirofilariasis in dogs was diagnosed by detection of microfilariae in blood. Identification of different Dirofilaria species was done by using molecular methods like polymerase chain reaction (PCR). Even though many researchers reported molecular evidence of D. repens across India, to our best knowledge there is no data available on molecular diagnosis of D. repens in dogs and its zoonotic implication in Karnataka state a southern state in India. The aim of the present study was to identify the Dirofilaria species occurring in dogs from Karnataka, India. Out of 310 samples screened for the presence of microfilariae using traditional diagnostic methods, 99 (31.93%) were positive for the presence of microfilariae. Based on the morphometry, the microfilariae were identified as D. repens. For confirmation of species, the samples were subjected to PCR using pan filarial primers (DIDR-F1, DIDR-R1) for amplification of internal transcribed spacer region 2 (ITS2) of the ribosomal DNA. The PCR product of 484 base pairs on agarose gel was indicative of D. repens. Hence, a single PCR reaction using pan filarial primers can be used to differentiate filarial species found in dogs. The present study confirms that dirofilarial species occurring in dogs from Karnataka is D. repens and further sequencing studies are needed for genotypic characterization of D. repens.

Keywords: Dirofilaria repens, molecular characterization, polymerase chain reaction, Karnataka, India

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Authors: Djamal Atlaoui, Youcef Bouafia

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This work deals with the experimental study of the mechanical behavior, by shear tests (fracture shear), elements of concrete beams reinforced with fibers in chips. These fibers come from the machining waste of the steel parts. The shear tests are carried out on prismatic specimens of dimensions 10 x 20 x 120 cm³. The fibers are characterized by mechanical resistance and tearing. The optimal composition of the concrete was determined by the workability test. Two fiber contents are selected for this study (W = 0.6% and W = 0.8%) and a BT control concrete (W = 0%) of the same composition as the matrix is developed to serve as a reference with a sand-to-gravel ratio (S/G) of concrete matrix equal to 1. The comparison of the different results obtained shows that the chips fibers confer a significant ductility to the material after cracking of the concrete. Also, the fibers used limit diagonal cracks in shear and improve strength and rigidity.

Keywords: characterization, chips fibers, cracking mode, ductility, undulation, shear

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Authors: Solomon Tilahun Desisa, Muktar Seid Hussen

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Hibiscus macranthus is one of family Malvaceae and genus Hibiscus plant which grows mainly in western part of Ethiopia. Hibiscus macranthus is the most adaptable and abundant plant in the nation, which are used as an ornamental plant often a hedge or fence plant, and used as a firewood after harvesting the stem together with the bark, and used also as a fiber for trying different kinds of things by forming the rope. However, Hibiscus macranthus plant fibre has not been commercially exploited and extracted properly. This study of work describes the possibility of mechanical and retting methods of Hibiscus macranthus fibre extraction and characterization. Hibiscus macranthus fibre is a bast fibre which obtained naturally from the stem or stalks of the dicotyledonous plant since it is a natural cellulose plant fiber. And the fibre characterized by studying its physical and chemical properties. The physical characteristics were investigated as follows, including the length of 100-190mm, fineness of 1.0-1.2Tex, diameter under X100 microscopic view 16-21 microns, the moisture content of 12.46% and dry tenacity of 48-57cN/Tex along with breaking extension of 0.9-1.6%. Hibiscus macranthus fiber productivity was observed that 12-18% of the stem out of which more than 65% is primary long fibers. The fiber separation methods prove to decrease of non-cellulose ingredients in the order of mechanical, water and chemical methods. The color measurement also shows the raw Hibiscus macranthus fiber has a natural golden color according to YID1925 and paler look under both retting methods than mechanical separation. Finally, it is suggested that Hibiscus macranthus fibre can be used for manufacturing of natural and organic crop and coffee packages as well as super absorbent, fine and high tenacity textile products.

Keywords: Hibiscus macranthus, bast fiber, extraction, characterization

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Authors: Iyabode A. Kehinde, Joshua O. Oyekanmi, Jumoke T. Abimbola, Olajumoke E. Ayanda

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African yam bean (AYB), (Sphenostylis stenocarpa) is a leguminous crop that provides nutritionally rich seeds, tubers and leaves for human consumption. AYB potentials as an important food security crop is yet to be realized and thus classified as underutilized crop. Underutilization of the crop has been partly associated with scarce information on the incidence and characterization of fungal endophytes infecting vascular parts of AYB. Accurate and robust detection of these endophytic fungi is essential for diagnosis, modeling, surveillance and protection of germplasm (seed) health. This work aimed at isolating and identifying fungal endophytes associated with leaves, stems and roots of AYB in Ogun State, Nigeria. This study investigated both cultural and molecular properties of endophytic fungi in AYB for its characterization and diversity. Fungal endophytes were isolated and culturally identified. DNA extraction, PCR amplification using ITS primers and analyses of nucleotide sequences of ribosomal DNA fragments were conducted on selected isolates. BLAST analysis was conducted on consensus nucleotide sequences of 28 out of 30 isolates and results showed similar homology with genera of Rhizopus, Cunninghamella, Fusarium, Aspergillus, Penicillium, Alternaria, Diaporthe, Nigrospora, Purpureocillium, Corynespora, Magnaporthe, Macrophomina, Curvularia, Acrocalymma, Talaromyces and Simplicillium. Slight similarity was found with endophytes associated with soybean. Phylogenetic analysis by maximum likelihood method showed high diversity among the general. These organisms have high economic importance in crop improvement. For an instance, Purpureocillium lilacinum showed high potential in control of root rot caused by nematodes in tomatoes. Though some can be pathogens, but many of the fungal endophytes have beneficial attributes to plant in host health, uptake of nutrients, disease suppression, and host immunity.

Keywords: molecular characterization, African Yam Bean, fungal endophyte, plant parts

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Authors: Zakaria Boual, Abdellah Kemassi, Toufik Chouana, Philippe Michaud, Mohammed Didi Ould El Hadj

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In order to investigate the prebiotic potential of oligosaccharides prepared by chemical hydrolysis of water-soluble polysaccharides (WSP) from Zizyphus lotus leaves, the effect of oligosaccharides on bacterial growth was studied. The chemical composition of WSP was evaluated by colorimetric assays revealed the average values: 7.05±0.73% proteins and 86.21±0.74% carbohydrates, among them 64.81±0.42% are neutral sugar and the rest 16.25±1.62% are uronic acids. The characterization of monosaccharides was determined by high performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) was found to be composed of galactose (23.95%), glucose (21.30%), rhamnose (20.28%), arabinose (9.55%), and glucuronic acid (22.95%). The effects of oligosaccharides on the growth of lactic acid bacteria were compared with those of fructo-oligosaccharide (RP95). The oligosaccharides concentration was 1g/L of man rogosa sharpe broth. Bacterial growth was assessed during 2, 4.5, 6.5, 9, 12, 16 and 24 h by measuring the optical density of the cultures at 600 nm (OD600) and pH values. During fermentation, pH in broth cultures decreased from 6.7 to 5.87±0.15. The enumeration of lactic acid bacteria indicated that oligosaccharides led to a significant increase in bacteria (P≤0.05) compared to the control. The fermentative metabolism appeared to be faster on RP95 than on oligosaccharides from Zizyphus lotus leaves. Both RP95 and oligosaccharides showed clear prebiotic effects, but had differences in fermentation kinetics because of to the different degree of polymerization. This study shows the prebiotic effectiveness of oligosaccharides, and provides proof for the selection of leaves of Zizyphus lotus for use as functional food ingredients.

Keywords: Zizyphus lotus, polysaccharides, characterization, prebiotic effects

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Authors: Goban Kumar Panneer Selvam

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In past years, there is lots of death caused due to harmful gases. So its very important to monitor harmful gases for human safety, and semiconductor material play important role in producing effective gas sensors.A novel solvothermal synthesis method based on sol-gel processing was prepared to deposit tin oxide thin films on glass substrate at high temperature for gas sensing application. The structure and morphology of tin oxide were analyzed by X-ray diffraction (XRD), Fourier transforms infrared spectroscopy (FTIR) and scanning electron microscopy (SEM). The SEM analysis of how spheres shape in tin oxide nanoparticles. The structure characterization of tin oxide studied by X-ray diffraction shows 8.95 nm (calculated by sheers equation). The UV visible spectroscopy indicated a maximum absorption band shown at 390 nm. Further dope tin oxide with selected metals to attain maximum sensitivity using dip coating technique with different immersion and sensing characterization are measured.

Keywords: tin oxide, gas sensor, chlorine free, sensitivity, crystalline size

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Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Moomen Chaari, Wolfgang Ecker, Thomas Kruse, Bogdan-Andrei Tabacaru

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In our daily life, we frequently interact with complex systems which facilitate our mobility, enhance our access to information, and sometimes help us recover from illnesses or diseases. The reliance on these systems is motivated by the established evaluation and assessment procedures which are performed during the different phases of the design and manufacturing flow. Such procedures are aimed to qualify the system’s delivered services with respect to their availability, reliability, safety, and other properties generally referred to as dependability attributes. In this paper, we propose a metamodel based generic characterization of dependability concepts and describe an automation methodology to customize this characterization to different standards and contexts. When integrated in concrete design and verification environments, the proposed methodology promotes the reuse of already available dependability assessment tools and reduces the costs and the efforts required to create consistent and efficient artefacts for fault injection or error simulation.

Keywords: dependability analysis, model-driven development, metamodeling, code generation

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Authors: Adithya Nadig

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In the field of production, characterization of surface roughness plays a vital role in assessing the quality of a manufactured product. The defined parameters for this assessment, each, have their own drawbacks in describing a profile surface. From the purview of small-scale and medium-scale industries, an increase in time spent for manual inspection of a product for various parameters adds to the cost of the product. In order to reduce this, a uniform and established standard is necessary for quantifying a profile of a manufactured product. The inspection procedure in the small and medium-scale manufacturing units at Jigani Industrial area, Bangalore, was observed. The parameters currently in use in those industries are described in the paper and a change in the inspection method is proposed.

Keywords: efficiency of quality assessment, manual areal profiling technique, manufacturing in small and medium-scale industries product-oriented inspection, standardization of manual inspection, surface roughness characterization

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Authors: G. Çelik Gül, F. Kurtuluş

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Rare earths containing complex metal oxides have drawn much attention due to physical, chemical and optical properties which make them feasible in so many areas such as non-linear optical materials and ion exchanger. We have researched a systematic study to obtain rare earth containing zirconium molybdate compound, characterization, investigation of crystal system and calculation of unit cell parameters.  After a successful synthesis of Nd₂Zr₃(MoO₄)₉ which is a member of rare earth metal containing complex oxides family, X-ray diffraction (XRD), High Score Plus/Rietveld refinement analysis, and Fourier Transform Infrared Spectroscopy (FTIR) were completed to determine the crystal structure. Morphological properties and elemental composition were determined by scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) analysis. Thermal properties were observed via Thermogravimetric-differential thermal analysis (TG/DTA).

Keywords: Nd₂Zr₃(MoO₄)₉, powder x-ray diffraction, solid state synthesis, zirconium molybdates

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Authors: M. P. Joshi, F. Deganello, L. F. Liotta, V. La Parola, G. Pantaleo

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For the first time, commercial iron nitrate was replaced by rust wastes, as a source of Iron for the preparation of LaFeO₃ powders by solution combustion synthesis (SCS). A detailed comparison with a reference powder obtained by SCS, starting from a commercial iron nitrate, was also performed. Several techniques such as X-ray diffraction combined with Rietveld refinement, mass plasma atomic emission spectroscopy, nitrogen adsorption measurements, temperature programmed reduction, X-ray photoelectron spectroscopy, Fourier transform analysis and scanning electron microscopy were used for the characterization of the rust wastes as well as of the perovskite powders. The performance of this ecofriendly material was evaluated by testing the activity and selectivity in the propylene oxidation, in order to use it for the benefit of the environment. Characterization and performance results clearly evidenced limitations and peculiarities of this new approach.

Keywords: perovskite type catalysts, solution combustion synthesis, X-ray diffraction, rust wastes

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Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu

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Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.

Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence

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Authors: C. L Popa, C.S. Ciobanu, S. L. Iconaru, P. Chapon, A. Costescu, P. Le Coustumer, D. Predoi

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In this paper, the preparation and characterization of silver doped hydroxyapatite thin films and their antimicrobial activity characterized is reported. The resultant Ag: HAp films coated on commercially pure Si disks substrates were systematically characterized by Scanning Electron Microscopy (SEM) coupled with X-ray Energy Dispersive Spectroscopy detector (X-EDS), Glow Discharge Optical Emission Spectroscopy (GDOES) and Fourier Transform Infrared spectroscopy (FT-IR). GDOES measurements show that a substantial Ag content has been deposited in the films. The X-EDS and GDOES spectra revealed the presence of a material composed mainly of phosphate, calcium, oxygen, hydrogen and silver. The antimicrobial efficiency of Ag:HAp thin films against Escherichia coli and Staphylococcus aureus bacteria was demonstrated. Ag:HAp thin films could lead to a decrease of infections especially in the case of bone and dental implants by surface modification of implantable medical devices.

Keywords: silver, hydroxyapatite, thin films, GDOES, SEM, FTIR, antimicrobial effect

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Authors: Farnoosh Attar

Abstract:

Nowadays, buffalo’s milk due to has highly nutritional properties, has a special place among consumers and its application for the production of dairy products due to the high technological properties is increasing day by day. In the present study, the physicochemical characteristics of Iranian buffalo’s milk were compared with cow's milk. According to chemical analysis, the amount of fat, protein, and total solid was higher in buffalo milk than cow's milk (respectively, 8.2%, 4.73%, and 15.92% compared with 3.5%, 3.25%, and 12.5%). Also, the percentage of cholesterol buffalo’s milk was less than in cow's milk. In contrast, no significant difference between the pH, acidity, and specific gravity was observed. The size of buffalo milk fat globules was larger than cow's milk. In addition, the profile of buffalo free fatty acids milk showed the relatively high distribution of long chain saturated fatty acids. The presence of four major bands related to αs casein, β casein, β-lactoglobulin, and α-lactalbumin with quite higher intensity than cow’s milk was also observed. The results obtained will provide a reference investigation to improve the developing of buffalo milk standard.

Keywords: buffalo milk, physicochemical characterization, standardization, dairy products

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Authors: Fengmei Li, Li Xu, Guoliang Xia

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Lysozyme is a catalytic enzyme that performs bacterial cell lysis by cleaving the β-1,4-glycosidic bond between N-acetylmuramic acid and N-acetylglucosamine of peptidoglycan in cell walls. In the present study, an invertebrate-type (i-type) lysozyme gene was cloned from Chinese mitten crab Eriocheir sinensis (designated as EsLysozyme) based on PCR-based rapid amplification of cDNA ends (RACE) technology. The full-length cDNA of EsLysozyme was of 831 bp. SMART and SIGNALP 3.0 program analysis revealed that EsLysozyme contained a signal peptide and a destabilase domain. The five amino acid residues (Tyr63, Trp64, Tyr91, His110, Pro114) and the conserved motif GSLSCG(P/Y)FQI and CL(E/L/R/H)C(I/M)C in i-type lysozymes were also found in EsLysozyme. The high similarity of EsLysozyme with L. vannamei lysozymes and phylogenetic analysis suggested that EsLysozyme should be a new member of i-type lysozyme family.

Keywords: i-type lysozyme, Eriocheir sinensis, cloning, characterization

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Authors: Satwik Majumder, Dongyun Jung, Jennifer Ronholm, Saji George

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Bovine mastitis is the most common infectious disease in dairy cattle, with major economic implications for the dairy industry worldwide. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from dairy farms is vital not only for animal husbandry but also for public health. In this study, the prevalence of AMR in 113 Escherichia coli isolates from cases of bovine clinical mastitis in Canada was investigated. Kirby-Bauer disk diffusion test with 18 antibiotics and microdilution method with three heavy metals (copper, zinc, and silver) was performed to determine the antibiotic and heavy-metal susceptibility. Resistant strains were assessed for efflux and ß-lactamase activities besides assessing biofilm formation and hemolysis. Whole-genome sequences for each of the isolates were examined to detect the presence of genes corresponding to the observed AMR and virulence factors. Phenotypic analysis revealed that 32 isolates were resistant to one or more antibiotics, and 107 showed resistance against at least one heavy metal. Quinolones and silver were the most efficient against the tested isolates. Among the AMR isolates, AcrAB-TolC efflux activity and ß-lactamase enzyme activities were detected in 13 and 14 isolates, respectively. All isolates produced biofilm but with different capacities, and 33 isolates showed α-hemolysin activity. A positive correlation (Pearson r = +0.89) between efflux pump activity and quantity of biofilm was observed. Genes associated with aggregation, adhesion, cyclic di-GMP, quorum sensing were detected in the AMR isolates, corroborating phenotype observations. This investigation showed the prevalence of AMR in E. coli isolates from bovine clinical mastitis. The results also suggest the inadequacy of antimicrobials with a single mode of action to curtail AMR bacteria with multiple mechanisms of resistance and virulence factors. Therefore, it calls for combinatorial therapy for the effective management of AMR infections in dairy farms and combats its potential transmission to the food supply chain through milk and dairy products.

Keywords: antimicrobial resistance, E. coli, bovine mastitis, antibiotics, heavy-metals, efflux pump, ß-lactamase enzyme, biofilm, whole-genome sequencing

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