Search results for: genome scale metabolic model

Authors: Jan Masak, Eva Kvasnickova, Vladimir Scholtz, Olga Matatkova, Marketa Valkova, Alena Cejkova

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Microbial colonization of medical instruments, catheters, implants, etc. is a serious problem in the spread of nosocomial infections. Biofilms exhibit enormous resistance to environment. The resistance of biofilm populations to antibiotic or biocides often increases by two to three orders of magnitude in comparison with suspension populations. Subjects of interests are substances or physical processes that primarily cause the destruction of biofilm, while the released cells can be killed by existing antibiotics. In addition, agents that do not have a strong lethal effect do not cause such a significant selection pressure to further enhance resistance. Non-thermal plasma (NTP) is defined as neutral, ionized gas composed of particles (photons, electrons, positive and negative ions, free radicals and excited or non-excited molecules) which are in permanent interaction. In this work, the effect of NTP generated by the cometary corona with a metallic grid on the formation and stability of biofilm and metabolic activity of cells in biofilm was studied. NTP was applied on biofilm populations of Staphylococcus epidermidis DBM 3179, Pseudomonas aeruginosa DBM 3081, DBM 3777, ATCC 15442 and ATCC 10145, Escherichia coli DBM 3125 and Candida albicans DBM 2164 grown on solid media on Petri dishes and on the titanium alloy (Ti6Al4V) surface used for the production joint replacements. Erythromycin (for S. epidermidis), polymyxin B (for E. coli and P. aeruginosa), amphotericin B (for C. albicans) and ceftazidime (for P. aeruginosa) were used to study the combined effect of NTP and antibiotics. Biofilms were quantified by crystal violet assay. Metabolic activity of the cells in biofilm was measured using MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) colorimetric test based on the reduction of MTT into formazan by the dehydrogenase system of living cells. Fluorescence microscopy was applied to visualize the biofilm on the surface of the titanium alloy; SYTO 13 was used as a fluorescence probe to stain cells in the biofilm. It has been shown that biofilm populations of all studied microorganisms are very sensitive to the type of used NTP. The inhibition zone of biofilm recorded after 60 minutes exposure to NTP exceeded 20 cm², except P. aeruginosa DBM 3777 and ATCC 10145, where it was about 9 cm². Also metabolic activity of cells in biofilm differed for individual microbial strains. High sensitivity to NTP was observed in S. epidermidis, in which the metabolic activity of biofilm decreased after 30 minutes of NTP exposure to 15% and after 60 minutes to 1%. Conversely, the metabolic activity of cells of C. albicans decreased to 53% after 30 minutes of NTP exposure. Nevertheless, this result can be considered very good. Suitable combinations of exposure time of NTP and the concentration of antibiotic achieved in most cases a remarkable synergic effect on the reduction of the metabolic activity of the cells of the biofilm. For example, in the case of P. aeruginosa DBM 3777, a combination of 30 minutes of NTP with 1 mg/l of ceftazidime resulted in a decrease metabolic activity below 4%.

Keywords: anti-biofilm activity, antibiotic, non-thermal plasma, opportunistic pathogens

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Authors: Ahmet Diken, Tahsin Karabulut

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The factor which developing countries are in need is capital. Such countries make an effort to increase their income in order to meet their expenses for employment, infrastructure, superstructure investments, education, health and defense. The sole income of the countries is taxes collected from businesses. The businesses should drive profit and return in order to be able to toll. In a world where competition exists, different strategies may be followed by business in developing countries and they must specify their target markets. İn order to minimize cost and maximize profit, SMEs have to concentrate on target markets and select cost oriented strategy. In this study, a theoretical model is suggested that SME firms have to act as cluster between each other, and also must be optimal provider for large scale firms. SMEs’ policy must be supported by public. This relationship can benefit large scale firms to have brand over the world, and this organization increases value added for developing countries.

Keywords: competitiveness, countries, SMEs developing, sustainability

Procedia PDF Downloads 291

Authors: Henok Hailemariam, Frank Wuttke

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Collapsible soils are weak soils that appear to be stable in their natural state, normally dry condition, but rapidly deform under saturation (wetting), thus generating large and unexpected settlements which often yield disastrous consequences for structures unwittingly built on such deposits. In this study, a prediction model for the relative subsidence of stressed collapsible soils based on dielectric permittivity measurement is presented. Unlike most existing methods for soil subsidence prediction, this model does not require moisture content as an input parameter, thus providing the opportunity to obtain accurate estimation of the relative subsidence of collapsible soils using dielectric measurement only. The prediction model is developed based on an existing relative subsidence prediction model (which is dependent on soil moisture condition) and an advanced theoretical frequency and temperature-dependent electromagnetic mixing equation (which effectively removes the moisture content dependence of the original relative subsidence prediction model). For large scale sub-surface soil exploration purposes, the spatial sub-surface soil dielectric data over wide areas and high depths of weak (collapsible) soil deposits can be obtained using non-destructive high frequency electromagnetic (HF-EM) measurement techniques such as ground penetrating radar (GPR). For laboratory or small scale in-situ measurements, techniques such as an open-ended coaxial line with widely applicable time domain reflectometry (TDR) or vector network analysers (VNAs) are usually employed to obtain the soil dielectric data. By using soil dielectric data obtained from small or large scale non-destructive HF-EM investigations, the new model can effectively predict the relative subsidence of weak soils without the need to extract samples for moisture content measurement. Some of the resulting benefits are the preservation of the undisturbed nature of the soil as well as a reduction in the investigation costs and analysis time in the identification of weak (problematic) soils. The accuracy of prediction of the presented model is assessed by conducting relative subsidence tests on a collapsible soil at various initial soil conditions and a good match between the model prediction and experimental results is obtained.

Keywords: collapsible soil, dielectric permittivity, moisture content, relative subsidence

Procedia PDF Downloads 334

Authors: Ante Turudic, Filip Varga, Zlatko Liber, Jernej Jakse, Zlatko Satovic, Ivan Radosavljevic, Martina Grdisa

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Microsatellites (SSRs) are highly informative repetitive sequences of 2-6 base pairs, which are the most used molecular markers in assessing the genetic diversity of plant species. Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip) is an outcrossing diploid (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repetitiveness and large size of the genome (haploid genome size of 9,58 pg), previous attempts to develop microsatellite markers using the standard methods were unsuccessful. A next-generation sequencing (NGS) approach was applied on genomic DNA extracted from fresh leaves of Dalmatian pyrethrum. The sequencing was conducted using NovaSeq6000 Illumina sequencer, after which almost 400 million high-quality paired-end reads were obtained, with a read length of 150 base pairs. Short reads were assembled by combining two approaches; (1) de-novo assembly and (2) joining of overlapped pair-end reads. In total, 6.909.675 contigs were obtained, with the contig average length of 249 base pairs. Of the resulting contigs, 31.380 contained one or multiple microsatellite sequences, in total 35.556 microsatellite loci were identified. Out of detected microsatellites, dinucleotide repeats were the most frequent, accounting for more than half of all microsatellites identifies (21,212; 59.7%), followed by trinucleotide repeats (9,204; 25.9%). Tetra-, penta- and hexanucleotides had similar frequency of 1,822 (5.1%), 1,472 (4.1%), and 1,846 (5.2%), respectively. Contigs containing microsatellites were further filtered by SSR pattern type, transposon occurrences, assembly characteristics, GC content, and the number of occurrences against the draft genome of T. cinerariifolium published previously. After the selection process, 50 microsatellite loci were used for primer design. Designed primers were tested on samples from five distinct populations, and 25 of them showed a high degree of polymorphism. The selected loci were then genotyped on 20 samples belonging to one population resulting in 17 microsatellite markers. Availability of codominant SSR markers will significantly improve the knowledge on population genetic diversity and structure as well as complex genetics and biochemistry of this species. Acknowledgment: This work has been fully supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir/ Sch. Bip.) insecticidal potential’ - (PyrDiv) (IP-06-2016-9034).

Keywords: genome assembly, NGS, SSR, Tanacetum cinerariifolium

Procedia PDF Downloads 107

Authors: Shenlun Chen, Leonard Wee

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Tumor grading is an essential reference for colorectal cancer (CRC) staging and survival prognostication. The widely used World Health Organization (WHO) grading system defines histological grade of CRC adenocarcinoma based on the density of glandular formation on whole slide images (WSI). Tumors are classified as well-, moderately-, poorly- or un-differentiated depending on the percentage of the tumor that is gland forming; >95%, 50-95%, 5-50% and <5%, respectively. However, manually grading WSIs is a time-consuming process and can cause observer error due to subjective judgment and unnoticed regions. Furthermore, pathologists’ grading is usually coarse while a finer and continuous differentiation grade may help to stratifying CRC patients better. In this study, a deep learning based automatic differentiation grading algorithm was developed and evaluated by survival analysis. Firstly, a gland segmentation model was developed for segmenting gland structures. Gland regions of WSIs were delineated and used for differentiation annotating. Tumor regions were annotated by experienced pathologists into high-, medium-, low-differentiation and normal tissue, which correspond to tumor with clear-, unclear-, no-gland structure and non-tumor, respectively. Then a differentiation prediction model was developed on these human annotations. Finally, all enrolled WSIs were processed by gland segmentation model and differentiation prediction model. The differentiation grade can be calculated by deep learning models’ prediction of tumor regions and tumor differentiation status according to WHO’s defines. If multiple WSIs were possessed by a patient, the highest differentiation grade was chosen. Additionally, the differentiation grade was normalized into scale between 0 to 1. The Cancer Genome Atlas, project COAD (TCGA-COAD) project was enrolled into this study. For the gland segmentation model, receiver operating characteristic (ROC) reached 0.981 and accuracy reached 0.932 in validation set. For the differentiation prediction model, ROC reached 0.983, 0.963, 0.963, 0.981 and accuracy reached 0.880, 0.923, 0.668, 0.881 for groups of low-, medium-, high-differentiation and normal tissue in validation set. Four hundred and one patients were selected after removing WSIs without gland regions and patients without follow up data. The concordance index reached to 0.609. Optimized cut off point of 51% was found by “Maxstat” method which was almost the same as WHO system’s cut off point of 50%. Both WHO system’s cut off point and optimized cut off point performed impressively in Kaplan-Meier curves and both p value of logrank test were below 0.005. In this study, gland structure of WSIs and differentiation status of tumor regions were proven to be predictable through deep leaning method. A finer and continuous differentiation grade can also be automatically calculated through above models. The differentiation grade was proven to stratify CAC patients well in survival analysis, whose optimized cut off point was almost the same as WHO tumor grading system. The tool of automatically calculating differentiation grade may show potential in field of therapy decision making and personalized treatment.

Keywords: colorectal cancer, differentiation, survival analysis, tumor grading

Procedia PDF Downloads 117

Authors: Theo Ndereyimana, Yann Dufresne, Micael Boulet, Stephane Moreau

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The DEM (Discrete Element Method) is used a lot in the industry to simulate large-scale flows of particles; for instance, in a fluidized bed, it allows to predict of the trajectory of every particle. One of the main limits of the DEM is the computational time. The CGM (Coarse-Graining Method) has been developed to tackle this issue. The goal is to increase the size of the particle and, by this means, decrease the number of particles. The method leads to a reduction of the collision frequency due to the reduction of the number of particles. Multiple characteristics of the particle movement and the fluid flow - when there is a coupling between DEM and CFD (Computational Fluid Dynamics). The main characteristic that is impacted is the energy dissipation of the system, to regain the dissipation, an ADM (Additional Dissipative Mechanism) can be added to the model. The objective of this current work is to observe the influence of the choice of the ADM and the factor of coarse-graining on the numerical results. These results will be compared with experimental results of a fluidized bed and with a numerical model of the same fluidized bed without using the CGM. The numerical model is one of a 3D cylindrical fluidized bed with 9.6M Geldart B-type particles in a bubbling regime.

Keywords: additive dissipative mechanism, coarse-graining, discrete element method, fluidized bed

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Authors: Nitish Kumar Vaja, Oumar Barry, Brian DeJong

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Aeolian vibrations are the major cause for the failure of conductor cables. Using a Stockbridge damper reduces these vibrations and increases the life span of the conductor cable. Designing an efficient Stockbridge damper that suits the conductor cable requires a robust mathematical model with minimum assumptions. However it is not easy to analytically model the complex geometry of the messenger. Therefore an equivalent stiffness must be determined so that it can be used in the analytical model. This paper examines the bending stiffness of the cable and discusses the effect of this stiffness on the natural frequencies. The obtained equivalent stiffness compensates for the assumption of modeling the messenger as a rod. The results from the free vibration analysis of the analytical model with the equivalent stiffness is validated using the full scale finite element model of the Stockbridge damper.

Keywords: equivalent stiffness, finite element model, free vibration response, Stockbridge damper

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Authors: Anand K. Patel

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Background: Patients with COPD have decreased pulmonary functions, which in turn reflect on their day-to-day activities. Objectives: To assess the correlation between functional vital capacity (FVC) and forced expiratory volume in one second (FEV1) with 6 minutes walk test (6MWT). To correlate the Borg rating for perceived exertion scale (Borg scale) and Modified medical research council (MMRC) dyspnea scale with the 6MWT, FVC and FEV1. Method: In this prospective study total 72 patients with COPD diagnosed by the GOLD guidelines were enrolled after taking written consent. They were first asked to rate physical exertion on the Borg scale as well as the modified medical research council dyspnea scale and then were subjected to perform pre and post bronchodilator spirometry followed by 6 minute walk test. The findings were correlated by calculating the Pearson coefficient for each set and obtaining the p-values, with a p < 0.05 being clinically significant. Result: There was a significant correlation between spirometry and 6MWT suggesting that patients with lower measurements were unable to walk for longer distances. However, FVC had the stronger correlation than FEV1. MMRC scale had a stronger correlation with 6MWT as compared to the Borg scale. Conclusion: The study suggests that 6MWT is a better test for monitoring the patients of COPD. In spirometry, FVC should be used in monitoring patients with COPD, instead of FEV1. MMRC scale shows a stronger correlation than the Borg scale, and we should use it more often.

Keywords: spirometry, 6 minute walk test, MMRC, Borg scale

Procedia PDF Downloads 173

Authors: Münevver Başman, Deniz Gülleroğlu

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The purpose of this study is to develop a scale to determine the attitudes towards social networking sites. 45 tryout items, prepared for this aim, were applied to 342 students studying at Marmara University, Faculty of Education. The reliability and the validity of the scale were conducted with the help of these students. As a result of exploratory factor analysis with Varimax rotation, 41 items grouped according to the structure with three factors (interest, reality and negative effects) is obtained. While alpha reliability of the scale is obtained as .899; the reliability of factors is obtained as .899, .799, .775, respectively.

Keywords: Attitude, reliability, social networking sites, validity.

Procedia PDF Downloads 355

Authors: Soultana Konstantinidou, Tiziana Schmidt, Elena Landi, Alessandro De Carli, Giovanni Maltinti, Darius Witt, Alicja Dziadosz, Agnieszka Lindstaedt, Michele Lai, Mauro Pistello, Valentina Cappello, Luciana Dente, Chiara Gabellini, Piotr Barski, Vittoria Raffa

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CRISPR/Cas9 technology has gained the interest of researchers in the field of biotechnology for genome editing. Since its discovery as a microbial adaptive immune defense, this system has been widely adopted and is acknowledged for having a variety of applications. However, critical barriers related to safety and delivery are persisting. Here, we propose a new concept of genome engineering, which is based on a nano-formulation of Cas9. The Cas9 enzyme was conjugated to a gold nanoparticle (AuNP-Cas9). The AuNP-Cas9 maintained its cleavage efficiency in vitro, to the same extent as the ribonucleoprotein, including non-conjugated Cas9 enzyme, and showed high gene editing efficiency in vivo in zebrafish embryos. Since CRISPR/Cas9 technology is extensively used in cancer research, melanoma was selected as a validation target. Cell studies were performed in A375 human melanoma cells. Particles per se had no impact on cell metabolism and proliferation. Intriguingly, the AuNP-Cas9 internalized spontaneously in cells and localized as a single particle in the cytoplasm and organelles. More importantly, the AuNP-Cas9 showed a high nuclear localization signal. The AuNP-Cas9, overcoming the delivery difficulties of Cas9, could be used in cellular biology and localization studies. Taking advantage of the plasmonic properties of gold nanoparticles, this technology could potentially be a bio-tool for combining gene editing and photothermal therapy in cancer cells. Further work will be focused on intracellular interactions of the nano-formulation and characterization of the optical properties.

Keywords: CRISPR/Cas9, gene editing, gold nanoparticles, nanotechnology

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Authors: Xin Chen, Moxiao Li, Xuechao Sun, Fei Ti, Shaobao Liu, Feng Xu, Tian Jian Lu

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The composite materials with pores have the characteristics of light weight, sound insulation, and heat insulation, and have broad prospects in many fields, including aerospace. In general, the stiffness of such composite is less than the stiffness of the matrix material, limiting their applications. In this paper, we establish a theoretical model to analyze the deformation mechanism of a nano-pore. The interface between the pores and matrix material is described by the Gurtin-Murdoch model. By considering scale effect related with current deformation, we estimate the effective mechanical properties (e.g., effective shear modulus and bulk modulus) of a composite with nano-pores. Due to the scale effect, the elastic field in the composite was changed and local hardening was observed around the nano-pore, and the effective shear modulus and effective bulk modulus were found to be a function of the surface energy. The effective shear modulus increase with the surface energy and decrease with the size of the nano-pores, and the effective bulk modulus decrease with the surface energy and increase with the size of the nano-pores. These results have potential applications in the nanocomposite mechanics and aerospace field.

Keywords: composite mechanics, nano-inhomogeneity, nano-pores, scale effect

Procedia PDF Downloads 118

Authors: Lin Li, P. G. R. N. I. Pussella

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When representing spatial data and their attributes on different types of maps, the scale plays a key role in the process of map generalization. The process is consisted with two main operators such as selection and omission. Once some data were selected, they would undergo of several geometrical changing processes such as elimination, simplification, smoothing, exaggeration, displacement, aggregation and size reduction. As a result of these operations at different levels of data, the geometry of the spatial features such as length, sinuosity, orientation, perimeter and area would be altered. This would be worst in the case of preparation of small scale maps, since the cartographer has not enough space to represent all the features on the map. What the GIS users do is when they wanted to analyze a set of spatial data; they retrieve a data set and does the analysis part without considering very important characteristics such as the scale, the purpose of the map and the degree of generalization. Further, the GIS users use and compare different maps with different degrees of generalization. Sometimes, GIS users are going beyond the scale of the source map using zoom in facility and violate the basic cartographic rule 'it is not suitable to create a larger scale map using a smaller scale map'. In the study, the effect of map generalization for GIS analysis would be discussed as the main objective. It was used three digital maps with different scales such as 1:10000, 1:50000 and 1:250000 which were prepared by the Survey Department of Sri Lanka, the National Mapping Agency of Sri Lanka. It was used common features which were on above three maps and an overlay analysis was done by repeating the data with different combinations. Road data, River data and Land use data sets were used for the study. A simple model, to find the best place for a wild life park, was used to identify the effects. The results show remarkable effects on different degrees of generalization processes. It can see that different locations with different geometries were received as the outputs from this analysis. The study suggests that there should be reasonable methods to overcome this effect. It can be recommended that, as a solution, it would be very reasonable to take all the data sets into a common scale and do the analysis part.

Keywords: generalization, GIS, scales, spatial analysis

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Authors: Shrikant Chavan, Vikas Minchekar

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The present study examined the self-efficacy, emotional intelligence and social maturity of High school boys and girls. Furthermore, study aimed at to foster the self-efficacy, emotional intelligence and social maturity of high school students. The study was conducted on 100 high school students, out of which 50 boys and 50 girls were selected through simple random sampling method from the Sangli city of Maharashtra state, India. The age range of the sample is 14 to 16 years. Self-efficacy scale developed by Jesusalem Schwarzer, Emotional intelligence scale developed by Hyde, Pethe and Dhar and social maturity scale developed by Rao were administered to the sample. Data was analyzed using mean, SD and ‘t’ test further Karl Pearson’s product moment, correlation of coefficient was used to know the correlation between emotional intelligence, self-efficacy, and social maturity. Results revealed that boys and girls did not differ significantly in their self-efficacy and social maturity. Further, the analysis revealed that girls are having high emotional intelligence compared to boys, which is significant at 0.01 level. It is also found that there is a significant and positive correlation between self-efficacy and emotional intelligence, self-efficacy and social maturity and emotional intelligence and social maturity. Some developmental strategies to strengthen the self-efficacy, emotional intelligence and social maturity of high school students are suggested in the study.

Keywords: self-efficacy, emotional intelligence, social maturity, developmental model and high school students

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Authors: Young-Kwang Lee, Eun-Gu Ji, Min-Joo Kim, Seung-Jae Oh

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The purpose of this study is to develop a social participation activity scale for the elderly. As a result of exploratory factor analysis, confirmatory factor analysis was conducted using maximum likelihood method using bundled items. In conclusion, thirteen items of social participation activity scale seemed appropriate. Finally, convergent validity and discriminant validity were verified on the scale with the fit. The convergent validity was based on the variance extracted value. In other words, the hypothesis that the variables are the same is rejected and the validity is confirmed. This study extensively considered the measurement items of the social participation activity scale used to measure social participation activities of the elderly. In the future, it will be meaningful that it can be used as a tool to verify the effectiveness of services in organizations that provide social welfare services to elderly people such as comprehensive social welfare centers and the elderly comprehensive social welfare centers.

Keywords: elderly, social participation, scale development, validity

Procedia PDF Downloads 158

Authors: Marco Antonio Lara De la Calleja, María Catalina Ovando Chico, Eduardo Lopez Ruiz

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Community empowerment has been proved to be a key element in the solution of the food security problem. As a result of a conceptual analysis, it was found that agricultural production, economic development and governance, are the traditional basis of food security models. Although the literature points to social inclusion as an important factor for food security, no model has considered it as the basis of it. The aim of this research is to identify different dimensions that make an integral model for food security, with emphasis on community empowerment. A diagnosis was made in the study community (Tatoxcac, Zacapoaxtla, Puebla), to know the aspects that impact the level of food insecurity. With a statistical sample integrated by 200 families, the Latin American and Caribbean Food Security Scale (ELCSA) was applied, finding that: in households composed by adults and children, have moderated food insecurity, (ELCSA scale has three levels, low, moderated and high); that result is produced mainly by the economic income capacity and the diversity of the diet on its food. With that being said, a model was developed to promote food security through five dimensions: 1. Regional context of the community; 2. Structure and system of local food; 3. Health and nutrition; 4. Information and technology access; and 5. Self-awareness and empowerment. The specific actions on each axis of the model, allowed a systemic approach needed to attend food security in the community, through the empowerment of society. It is concluded that the self-awareness of local communities is an area of extreme importance, which must be taken into account for participatory schemes to improve food security. In the long term, the model requires the integrated participation of different actors, such as government, companies and universities, to solve something such vital as food security.

Keywords: community empowerment, food security, model, systemic approach

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Authors: Tolulope Babawarun, Harry Ngwangwa

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The wind turbine blade may sustain structural damage from external loads such as high winds or collisions, which could compromise its aerodynamic efficiency. The wind turbine blade vibrates at significant intensities and amplitudes under these conditions. The effect of these vibrations on the dynamic flow field surrounding the blade changes the forces operating on it. The structural dynamic analysis of a small wind turbine blade is considered in this study. It entails creating a finite element model, validating the model, and doing structural analysis on the verified finite element model. The analysis is based on the structural reaction of a small-scale wind turbine blade to various loading sources. Although there are many small-scale off-shore wind turbine systems in use, only preliminary structural analysis is performed during design phases; these systems' performance under various loading conditions as they are encountered in real-world situations has not been properly researched. This will allow us to record the same Equivalent von Mises stress and deformation that the blade underwent. A higher stress contour was found to be more concentrated near the middle span of the blade under the various loading scenarios studied. The highest stress that the blade in this study underwent is within the range of the maximum stress that blade material can withstand. The maximum allowable stress of the blade material is 1,770 MPa. The deformation of the blade was highest at the blade tip. The critical speed of the blade was determined to be 4.3 Rpm with a rotor speed range of 0 to 608 Rpm. The blade's mode form under loading conditions indicates a bending mode, the most prevalent of which is flapwise bending.

Keywords: ANSYS, finite element analysis, static loading, dynamic analysis

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Authors: Parag Katira, Frederika Rentzeperis, Zuzanna Nowicka, Giada Fiandaca, Thomas Veith, Jack Farinhas, Noemi Andor

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Resource limitations shape the outcome of competitions between genetically heterogeneous pre-malignant cells. One example of such heterogeneity is in the ploidy (DNA content) of pre-malignant cells. A whole-genome duplication (WGD) transforms a diploid cell into a tetraploid one and has been detected in 28-56% of human cancers. If a tetraploid subclone expands, it consistently does so early in tumor evolution, when cell density is still low, and competition for nutrients is comparatively weak – an observation confirmed for several tumor types. WGD+ cells need more resources to synthesize increasing amounts of DNA, RNA, and proteins. To quantify resource limitations and how they relate to ploidy, we performed a PAN cancer analysis of WGD, PET/CT, and MRI scans. Segmentation of >20 different organs from >900 PET/CT scans were performed with MOOSE. We observed a strong correlation between organ-wide population-average estimates of Oxygen and the average ploidy of cancers growing in the respective organ (Pearson R = 0.66; P= 0.001). In-vitro experiments using near-diploid and near-tetraploid lineages derived from a breast cancer cell line supported the hypothesis that DNA content influences Glucose- and Oxygen-dependent proliferation-, death- and migration rates. To model how subpopulations with variable DNA content compete in the resource-limited environment of the human brain, we developed a stochastic state-space model of the brain (S3MB). The model discretizes the brain into voxels, whereby the state of each voxel is defined by 8+ variables that are updated over time: stiffness, Oxygen, phosphate, glucose, vasculature, dead cells, migrating cells and proliferating cells of various DNA content, and treat conditions such as radiotherapy and chemotherapy. Well-established Fokker-Planck partial differential equations govern the distribution of resources and cells across voxels. We applied S3MB on sequencing and imaging data obtained from a primary GBM patient. We performed whole genome sequencing (WGS) of four surgical specimens collected during the 1ˢᵗ and 2ⁿᵈ surgeries of the GBM and used HATCHET to quantify its clonal composition and how it changes between the two surgeries. HATCHET identified two aneuploid subpopulations of ploidy 1.98 and 2.29, respectively. The low-ploidy clone was dominant at the time of the first surgery and became even more dominant upon recurrence. MRI images were available before and after each surgery and registered to MNI space. The S3MB domain was initiated from 4mm³ voxels of the MNI space. T1 post and T2 flair scan acquired after the 1ˢᵗ surgery informed tumor cell densities per voxel. Magnetic Resonance Elastography scans and PET/CT scans informed stiffness and Glucose access per voxel. We performed a parameter search to recapitulate the GBM’s tumor cell density and ploidy composition before the 2ⁿᵈ surgery. Results suggest that the high-ploidy subpopulation had a higher Glucose-dependent proliferation rate (0.70 vs. 0.49), but a lower Glucose-dependent death rate (0.47 vs. 1.42). These differences resulted in spatial differences in the distribution of the two subpopulations. Our results contribute to a better understanding of how genomics and microenvironments interact to shape cell fate decisions and could help pave the way to therapeutic strategies that mimic prognostically favorable environments.

Keywords: tumor evolution, intra-tumor heterogeneity, whole-genome doubling, mathematical modeling

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Authors: Alex Fedoseyev

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This study investigates a generalized hydrodynamic equation (GHE) simplified model for the simulation of turbulent flow over a two-dimensional backward-facing step (BFS) at Reynolds number Re=132000. The GHE were derived from the generalized Boltzmann equation (GBE). GBE was obtained by first principles from the chain of Bogolubov kinetic equations and considers particles of finite dimensions. The GHE has additional terms, temporal and spatial fluctuations, compared to the Navier-Stokes equations (NSE). These terms have a timescale multiplier τ, and the GHE becomes the NSE when $\tau$ is zero. The nondimensional τ is a product of the Reynolds number and the squared length scale ratio, τ=Re*(l/L)², where l is the apparent Kolmogorov length scale, and L is a hydrodynamic length scale. The BFS flow modeling results obtained by 2D calculations cannot match the experimental data for Re>450. One or two additional equations are required for the turbulence model to be added to the NSE, which typically has two to five parameters to be tuned for specific problems. It is shown that the GHE does not require an additional turbulence model, whereas the turbulent velocity results are in good agreement with the experimental results. A review of several studies on the simulation of flow over the BFS from 1980 to 2023 is provided. Most of these studies used different turbulence models when Re>1000. In this study, the 2D turbulent flow over a BFS with height H=L/3 (where L is the channel height) at Reynolds number Re=132000 was investigated using numerical solutions of the GHE (by a finite-element method) and compared to the solutions from the Navier-Stokes equations, k–ε turbulence model, and experimental results. The comparison included the velocity profiles at X/L=5.33 (near the end of the recirculation zone, available from the experiment), recirculation zone length, and velocity flow field. The mean velocity of NSE was obtained by averaging the solution over the number of time steps. The solution with a standard k −ε model shows a velocity profile at X/L=5.33, which has no backward flow. A standard k−ε model underpredicts the experimental recirculation zone length X/L=7.0∓0.5 by a substantial amount of 20-25%, and a more sophisticated turbulence model is needed for this problem. The obtained data confirm that the GHE results are in good agreement with the experimental results for turbulent flow over two-dimensional BFS. A turbulence model was not required in this case. The computations were stable. The solution time for the GHE is the same or less than that for the NSE and significantly less than that for the NSE with the turbulence model. The proposed approach was limited to 2D and only one Reynolds number. Further work will extend this approach to 3D flow and a higher Re.

Keywords: backward-facing step, comparison with experimental data, generalized hydrodynamic equations, separation, reattachment, turbulent flow

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Authors: Anila Xhahysa, Migena Ceyhan, Neki Kuka, Klajdi Qoshi, Damiano Koxhaj

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The seismic event catalog has been updated in the framework of a bilateral project supported by the Central European Investment Fund and with the extensive support of Global Earthquake Model Foundation to update Albania's national seismic hazard model. The earthquake catalogue prepared within this project covers the Western Balkan area limited by 38.0° - 48°N, 12.5° - 24.5°E and includes 41,806 earthquakes that occurred in the region between 510 BC and 2022. Since the moment magnitude characterizes the earthquake size accurately and the selected ground motion prediction equations for the seismic hazard assessment employ this scale, it was chosen as the uniform magnitude scale for the catalogue. Therefore, proxy values of moment magnitude had to be obtained by using new magnitude conversion equations between the local and other magnitude types to this unified scale. The Global Centroid Moment Tensor Catalogue was considered the most authoritative for moderate to large earthquakes for moment magnitude reports; hence it was used as a reference for calibrating other sources. The best fit was observed when compared to some regional agencies, whereas, with reports of moment magnitudes from Italy, Greece and Turkey, differences were observed in all magnitude ranges. For teleseismic magnitudes, to account for the non-linearity of the relationships, we used the exponential model for the derivation of the regression equations. The obtained regressions for the surface wave magnitude and short-period body-wave magnitude show considerable differences with Global Earthquake Model regression curves, especially for low magnitude ranges. Moreover, a conversion relation was obtained between the local magnitude of Albania and the corresponding moment magnitude as reported by the global and regional agencies. As errors were present in both variables, the Deming regression was used.

Keywords: regression, seismic catalogue, local magnitude, tele-seismic magnitude, moment magnitude

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Authors: Saba Harati, Nasrin Arian Parsa

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The current research was an attempt to investigate the effect of resilience on mental health and life satisfaction. In one Cross Sectional research, 287 (173 females and 114 males) students of Tehran University were participated their average age was 23.17 years old (SD=4.9). The instruments used for assessing the research variables included: Cutter and Davidson resilience scale (CD-RISC), the short form of the depression-anxiety-stress scale, and life satisfaction scale. The data analysis was done in the form of structural equation model. The results of Simultaneous Hierarchical Multiple Regression Analysis indicated that there was a significant mediating role of the negative emotions (depression, anxiety, and stress), in the relationship between the family resilience (p < 0.001) and satisfaction with life (p < 0.001). Resilience results in life satisfaction by reducing the emotional problems (or increasing the mental health level). The effect of the resilience variable on life satisfaction was indirect.

Keywords: resilience, negative emotion, mental health, life satisfaction

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Authors: Junwon Seo, Bipin Adhikari, Euiseok Jeong

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This paper is intended to evaluate the structural performance of welded electronic road signs under various damage scenarios (DSs) using a finite element (FE) model calibrated with full-scale ultimate load testing results. The tested electronic road sign specimen was built with a back skin made of 5052 aluminum and two channels and a frame made of 6061 aluminum, where the back skin was connected to the frame by welding. The size of the tested specimen was 1.52 m long, 1.43 m wide, and 0.28 m deep. An actuator applied vertical loads at the center of the back skin of the specimen, resulting in a displacement of 158.7 mm and an ultimate load of 153.46 kN. Using these testing data, generation and calibration of a FE model of the tested specimen were executed in ABAQUS, indicating that the difference in the ultimate load between the calibrated model simulation and full-scale testing was only 3.32%. Then, six different DSs were simulated where the areas of the welded connection in the calibrated model were diminished for the DSs. It was found that the corners at the back skin-frame joint were prone to connection failure for all the DSs, and failure of the back skin-frame connection occurred remarkably from the distant edges.

Keywords: computational analysis, damage scenarios, electronic road signs, finite element, welded connections

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Authors: R. Monteiro, A. Abarca

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Large scale seismic risk assessment has become increasingly popular to evaluate the physical vulnerability of a given region to seismic events, by putting together hazard, exposure and vulnerability components. This study, developed within the scope of the EU-funded project ITERATE (Improved Tools for Disaster Risk Mitigation in Algeria), explains the steps and expected results for the development of an integrated seismic risk model for assessment of the vulnerability of residential buildings in Northern Algeria. For this purpose, the model foresees the consideration of an updated seismic hazard model, as well as ad-hoc exposure and physical vulnerability models for local residential buildings. The first results of this endeavor, such as the hazard model and a specific taxonomy to be used for the exposure and fragility components of the model are presented, using as starting point the province of Blida, in Algeria. Specific remarks and conclusions regarding the characteristics of the Northern Algerian in-built are then made based on these results.

Keywords: Northern Algeria, risk, seismic hazard, vulnerability

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Authors: Prasanjit Das, M .M. K. Khan, M. G. Rasul, Jie Wu, I. Youn

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Crystallisation scale occurs when dissolved minerals precipitate from an aqueous solution. To investigate the crystallisation scale growth of normal solubility salt, a lab-scale agitation tank with and without baffles were used as a benchmark using potassium nitrate as the test fluid. Potassium nitrate (KNO3) solution in this test leads to crystallisation scale on heat transfer surfaces. This experimental investigation has focused on the effect of surface crystallisation of potassium nitrate on the low-temperature heat exchange surfaces on the wall of the agitation tank. The impeller agitation rate affects the scaling rate at the low-temperature agitation wall and it shows a decreasing scaling rate with an increasing agitation rate. It was observed that there was a significant variation of heat transfer coefficients and scaling resistance coefficients with different agitation rate as well as with varying impeller size, tank with and without baffles and solution concentration.

Keywords: crystallisation, heat transfer coefficient, scale, resistance

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Authors: Sumeet Rai, Anuj Tyagi, B. T. Naveen Kumar, Shubhkaramjeet Kaur, Niraj K. Singh

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Since their discovery, indiscriminate use of antibiotics in human, veterinary and aquaculture systems has resulted in global emergence/spread of multidrug-resistant bacterial pathogens. Thus, the need for alternative approaches to control bacterial infections has become utmost important. High selectivity/specificity of bacteriophages (phages) permits the targeting of specific bacteria without affecting the desirable flora. In this study, a lytic phage (Ahp1) specific to Aeromonas hydrophila subsp. hydrophila was isolated from finfish aquaculture pond. The host range of Ahp1 range was tested against 10 isolates of A. hydrophila, 7 isolates of A. veronii, 25 Vibrio cholerae isolates, 4 V. parahaemolyticus isolates and one isolate each of V. harveyi and Salmonella enterica collected previously. Except the host A. hydrophila subsp. hydrophila strain, no lytic activity against any other bacterial was detected. During the adsorption rate and one-step growth curve analysis, 69.7% of phage particles were able to get adsorbed on host cell followed by the release of 93 ± 6 phage progenies per host cell after a latent period of ~30 min. Phage nucleic acid was extracted by column purification methods. After determining the nature of phage nucleic acid as dsDNA, phage genome was subjected to next-generation sequencing by generating paired-end (PE, 2 x 300bp) reads on Illumina MiSeq system. De novo assembly of sequencing reads generated circular phage genome of 42,439 bp with G+C content of 58.95%. During open read frame (ORF) prediction and annotation, 22 ORFs (out of 49 total predicted ORFs) were functionally annotated and rest encoded for hypothetical proteins. Proteins involved in major functions such as phage structure formation and packaging, DNA replication and repair, DNA transcription and host cell lysis were encoded by the phage genome. The complete genome sequence of Ahp1 along with gene annotation was submitted to NCBI GenBank (accession number MF683623). Stability of Ahp1 preparations at storage temperatures of 4 °C, 30 °C, and 40 °C was studied over a period of 9 months. At 40 °C storage, phage counts declined by 4 log units within one month; with a total loss of viability after 2 months. At 30 °C temperature, phage preparation was stable for < 5 months. On the other hand, phage counts decreased by only 2 log units over a period of 9 during storage at 4 °C. As some of the phages have also been reported as glycerol sensitive, the stability of Ahp1 preparations in (0%, 15%, 30% and 45%) glycerol stocks were also studied during storage at -80 °C over a period of 9 months. The phage counts decreased only by 2 log units during storage, and no significant difference in phage counts was observed at different concentrations of glycerol. The Ahp1 phage discovered in our study had a very narrow host range and it may be useful for phage typing applications. Moreover, the endolysin and holin genes in Ahp1 genome could be ideal candidates for recombinant cloning and expression of antimicrobial proteins.

Keywords: Aeromonas hydrophila, endolysin, phage, narrow host range

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Authors: Yoshimoto Kurihara, Tad Gonsalves

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Currently, in the field of object posture estimation, there is research on estimating the position and angle of an object by storing a 3D model of the object to be estimated in advance in a computer and matching it with the model. However, in this research, we have succeeded in creating a module that is much simpler, smaller in scale, and faster in operation. Our 6D pose estimation model consists of two different networks – a classification network and a regression network. From a single RGB image, the trained model estimates the class of the object in the image, the coordinates of the object, and its rotation angle in 3D space. In addition, we compared the estimation accuracy of each camera position, i.e., the angle from which the object was captured. The highest accuracy was recorded when the camera position was 75°, the accuracy of the classification was about 87.3%, and that of regression was about 98.9%.

Keywords: 6D posture estimation, image recognition, deep learning, AlexNet

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Authors: Xulu Yao, Moi Hoon Yap, Yanlong Zhang

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As a branch of artificial neural network, deep learning is widely used in the field of image recognition, but the lack of its dataset leads to imperfect model learning. By analysing the data scale requirements of deep learning and aiming at the application in GUI generation, it is found that the collection of GUI dataset is a time-consuming and labor-consuming project, which is difficult to meet the needs of current deep learning network. To solve this problem, this paper proposes a semi-supervised deep learning model that relies on the original small-scale datasets to produce a large number of reliable data sets. By combining the cyclic neural network with the generated countermeasure network, the cyclic neural network can learn the sequence relationship and characteristics of data, make the generated countermeasure network generate reasonable data, and then expand the Rico dataset. Relying on the network structure, the characteristics of collected data can be well analysed, and a large number of reasonable data can be generated according to these characteristics. After data processing, a reliable dataset for model training can be formed, which alleviates the problem of dataset shortage in deep learning.

Keywords: GUI, deep learning, GAN, data augmentation

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Authors: Yung-Feng Yen, Yun-Ju Lai

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Background: Metabolic syndrome (MetS) is reversible; however, the effect of changes in MetS status on the risk of incident cancer has not been extensively studied. We aimed to investigate the effects of changes in MetS status on incident cancer risk. Methods: This prospective, longitudinal study used data from Taiwan’s MJ cohort of 157,915 adults recruited from 2002–2016 who had repeated MetS measurements 5.2 (±3.5) years apart and were followed up for the new onset of cancer over 8.2 (±4.5) years. A new diagnosis of incident cancer in study individuals was confirmed by their pathohistological reports. The participants’ MetS status included MetS-free (n=119,331), MetS-developed (n=14,272), MetS-recovered (n=7,914), and MetS-persistent (n=16,398). We used the Fine-Gray sub-distribution method, with death as the competing risk, to determine the association between MetS changes and the risk of incident cancer. Results: During the follow-up period, 7,486 individuals had new development of cancer. Compared with the MetS-free group, MetS-persistent individuals had a significantly higher risk of incident cancer (adjusted hazard ratio [aHR], 1.10; 95% confidence interval [CI], 1.03-1.18). Considering the effect of dynamic changes in MetS status on the risk of specific cancer types, MetS persistence was significantly associated with a higher risk of incident colon and rectum, kidney, pancreas, uterus, and thyroid cancer. The risk of kidney, uterus, and thyroid cancer in MetS-recovered individuals was higher than in those who remained MetS but lower than MetS-persistent individuals. Conclusions: Persistent MetS is associated with a higher risk of incident cancer, and recovery from MetS may reduce the risk. The findings of our study suggest that it is imperative for individuals with pre-existing MetS to seek treatment for this condition to reduce the cancer risk.

Keywords: metabolic syndrome change, cancer, risk factor, cohort study

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Authors: Abdullah Eqal Al Mazrooei

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In this work, a new nonlinear model will be introduced. The model is in the state-space form. The nonlinearity of this model is in the state equation where the state vector is multiplied by its self. This technique makes our model generalizes many famous models as Lotka-Volterra model and Lorenz model which have many applications in the real life. We will apply our new model to estimate the wind speed by using a new nonlinear estimator which suitable to work with our model.

Keywords: nonlinear systems, state-space model, Kronecker product, nonlinear estimator

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Authors: Deepa Shokeen, Bani Tamber Aeri

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Food choice is a complex process influenced by the interplay of multiple factors, including physical, socio-cultural and economic factors comprising macro or micro level food environments. While a clear understanding of the relationship between what we eat and the environmental context in which these food choices are made is still needed; it has however now been shown that food environments do play a significant role in the obesity epidemic and increasing cardio-metabolic risk factors. Evidence in other countries indicates that the food environment may strongly influence the prevalence of obesity and cardio-metabolic risk factors among young adults. Although in the Indian context, data does indicate the associations between sedentary lifestyle, stress, faulty diets but very little evidence supports the role of food environment in influencing cardio-metabolic health among employed adults. Thus, this research is required to establish how different environments affect different individuals as individuals interact with the environment on a number of levels. Methodology: The objective of the present study is to assess the effect of selected food and nutrition environments with emphasis on worksite environment and to analyse its impact on the food choices and dietary behaviour of the employees (25-45 years of age) of the organizations under study. In the proposed study an attempt will be made to randomly select various worksite environments from Delhi and NCR. The study will be conducted in two phases. In phase I, Information will be obtained on their socio-demographic profile and various factors influencing their food choices including most commonly consumed foods and most frequently visited eating outlets in and around the work place. Data will also be gathered on anthropometry (height, weight, waist circumference), biochemical parameters (lipid profile and fasting glucose), blood pressure and dietary intake. Based on the findings of phase I, a list of the most frequently visited eating outlets in and around the workplace will be prepared in Phase II. These outlets will then be subjected to nutrition environment assessment survey (NEMS). On the basis of the information gathered from phase I and phase II, influence of selected food and nutrition environments on food choice, dietary behaviour and prevalence of cardio-metabolic risk factors among employed adults will be assessed. Expected outcomes: The proposed study will try to ascertain the impact of selected food and nutrition environments on food choice and dietary intake of the working adults as it is important to learn how these food environments influence the eating perceptions and health behavior of the adults. In addition to this, anthropometry blood pressure and biochemical assessment of the subjects will be done to assess the prevalence of cardio-metabolic risk factors. If the findings indicate that the work environment, where most of these young adults spend their productive hours of the day, influence their health, than perhaps steps maybe needed to make these environments more conducive to health.

Keywords: food and nutrition environment, cardio-metabolic risk factors, India, worksite environment

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Authors: Shama, Asif Mahmood, Wen Zhang

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Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to library construction, which were then sequenced on the Illumina MiSeq platform. The sequenced reads were analyzed using a viral metagenomic analysis pipeline. A cardiovirus from the feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on the P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats, which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

Keywords: cardioviruses, viral metagenomics, novel viruses, virus-host interaction

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