Search results for: phylogenetic analysis

Authors: M. Tassi, E. Dotsika, P. Karalis, A. Trantalidou, A. Mazarakis Ainian

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The Kythnos Island in Greece is of particular archaeological interest, as it has been inhabited from the 12th BC until the 7th AD. From island excavations, numerous faunal and human skeletal remains have been recovered. This work is the first attempt at the paleoenvironmental reconstruction of the island via stable isotope analysis. Specifically, we perform 13C and 18O isotope analysis in faunal bone apatite in order to investigate the climate conditions that prevailed in the area. Additionally, we conduct 13C and 15N isotope analysis in faunal bone collagen, which will constitute the baseline for the subsequent diet reconstruction of the ancient Kythnos population.

Keywords: stable isotopes analysis, bone collagen stable isotope analysis, bone apatite stable isotope analysis, paleodiet, palaeoclimate

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Authors: A. B. Bolkhir, A. Elshafie, T. K. Yousif

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This paper highlights the methods of error estimation in finite element analysis (FEA) results. It indicates that the modeling error could be eliminated by performing finite element analysis with successively finer meshes or by extrapolating response predictions from an orderly sequence of relatively low degree of freedom analysis results. In addition, the paper eliminates the round-off error by running the code at a higher precision. The paper provides application in finite element analysis results. It draws a conclusion based on results of application of methods of error estimation.

Keywords: finite element analysis (FEA), discretization error, round-off error, mesh refinement, richardson extrapolation, monotonic convergence

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Authors: Austyn Snowden

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Aim: To examine the construct validity of the Trait Emotional Intelligence Questionnaire Short form. Background: Emotional intelligence involves the identification and regulation of our own emotions and the emotions of others. It is therefore a potentially useful construct in the investigation of recruitment and retention in nursing and many questionnaires have been constructed to measure it. Design: Secondary analysis of existing dataset of responses to TEIQue-SF using concurrent application of Rasch analysis and confirmatory factor analysis. Method: First year undergraduate nursing and computing students completed Trait Emotional Intelligence Questionnaire-Short Form. Responses were analysed by synthesising results of Rasch analysis and confirmatory factor analysis.

Keywords: emotional intelligence, rasch analysis, factor analysis, nurse recruiters

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Authors: Kalangi Rodrigo

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The term Neuroecology elucidates the study of customizable variation in cognition and the brain. Subject marked the birth since 1980s, when researches began to apply methods of comparative evolutionary biology to cognitive processes and the underlying neural mechanisms of cognition. In Archaeology and Anthropology, we observe behaviors such as social learning skills, innovative feeding and foraging, tool use and social manipulation to determine the cognitive processes of ancient mankind. Depending on the brainstem size was used as a control variable, and phylogeny was controlled using independent contrasts. Both disciplines need to enriched with comparative literature and neurological experimental, behavioral studies among tribal peoples as well as primate groups which will lead the research to a potential end. Neuroecology examines the relations between ecological selection pressure and mankind or sex differences in cognition and the brain. The goal of neuroecology is to understand how natural law acts on perception and its neural apparatus. Furthermore, neuroecology will eventually lead both principal disciplines to Ethology, where human behaviors and social management studies from a biological perspective. It can be either ethnoarchaeological or prehistoric. Archaeology should adopt general approach of neuroecology, phylogenetic comparative methods can be used in the field, and new findings on the cognitive mechanisms and brain structures involved mating systems, social organization, communication and foraging. The contribution of neuroecology to archaeology and anthropology is the information it provides on the selective pressures that have influenced the evolution of cognition and brain structure of the mankind. It will shed a new light to the path of evolutionary studies including behavioral ecology, primate archaeology and cognitive archaeology.

Keywords: Neuroecology, Archaeology, Brain Evolution, Cognitive Archaeology

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Authors: Pingping Lin, Xudong Luo

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Natural language often conveys emotions of speakers. Therefore, sentiment analysis on what people say is prevalent in the field of natural language process and has great application value in many practical problems. Thus, to help people understand its application value, in this paper, we survey various applications of sentiment analysis, including the ones in online business and offline business as well as other types of its applications. In particular, we give some application examples in intelligent customer service systems in China. Besides, we compare the applications of sentiment analysis on Twitter, Weibo, Taobao and Facebook, and discuss some challenges. Finally, we point out the challenges faced in the applications of sentiment analysis and the work that is worth being studied in the future.

Keywords: application, natural language processing, online comments, sentiment analysis

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Authors: Irina M. Kolesnikova, Andrey M. Gaponov, Sergey A. Roumiantsev, Tatiana V. Grigoryeva, Dilyara R. Khusnutdinova, Dilyara R. Kamaldinova, Alexander V. Shestopalov

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Background. Obese patients have unequal risks of metabolic disorders. It is accepted to distinguish between metabolically healthy obesity (MHO) and metabolically unhealthy obesity (MUHO). MUHO patients have a high risk of metabolic disorders, insulin resistance, and diabetes mellitus. Among the other things, the gut microbiota also contributes to the development of metabolic disorders in obesity. Obesity is accompanied by significant changes in the gut microbial community. In turn, bacterial translocation from the intestine is the basis for the blood microbiome formation. The aim was to study the features of the blood microbiome in patients with various metabolic types of obesity. Patients, materials, methods. The study included 116 healthy donors and 101 obese patients. Depending on the metabolic type of obesity, the obese patients were divided into subgroups with MHO (n=36) and MUHO (n=53). Quantitative and qualitative assessment of the blood microbiome was based on metagenomic analysis. Blood samples were used to isolate DNA and perform sequencing of the variable v3-v4 region of the 16S rRNA gene. Alpha diversity indices (Simpson index, Shannon index, Chao1 index, phylogenetic diversity, the number of observed operational taxonomic units) were calculated. Moreover, we compared taxa (phyla, classes, orders, and families) in terms of isolation frequency and the taxon share in the total bacterial DNA pool between different patient groups. Results. In patients with MHO, the characteristics of the alpha-diversity of the blood microbiome were like those of healthy donors. However, MUHO was associated with an increase in all diversity indices. The main phyla of the blood microbiome were Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Cyanobacteria, TM7, Thermi, Verrucomicrobia, Chloroflexi, Acidobacteria, Planctomycetes, Gemmatimonadetes, and Tenericutes were found to be less significant phyla of the blood microbiome. Phyla Acidobacteria, TM7, and Verrucomicrobia were more often isolated in blood samples of patients with MUHO compared with healthy donors. Obese patients had a decrease in some taxonomic ranks (Bacilli, Caulobacteraceae, Barnesiellaceae, Rikenellaceae, Williamsiaceae). These changes appear to be related to the increased diversity of the blood microbiome observed in obesity. An increase of Lachnospiraceae, Succinivibrionaceae, Prevotellaceae, and S24-7 was noted for MUHO patients, which, apparently, is explained by a magnification in intestinal permeability. Conclusion. Blood microbiome differs in obese patients and healthy donors at class, order, and family levels. Moreover, the nature of the changes is determined by the metabolic type of obesity. MUHO linked to increased diversity of the blood microbiome. This appears to be due to increased microbial translocation from the intestine and non-intestinal sources.

Keywords: blood microbiome, blood bacterial DNA, obesity, metabolically healthy obesity, metabolically unhealthy obesity

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Authors: V. Cesaroni, C. Girometta, A. Bernicchia, M. Brusoni, F. Corana, R. M. Baiguera, C. M. Cusaro, M. L. Guglielminetti, B. Mannucci, H. Kawagishi, C. Perini, A. M. Picco, P. Rossi, E. Salerni, E. Savino

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Fungi of the genus Hericium contain various compounds with antibacterial activity, cytotoxic effect on cancer cells and bioactive molecules. Some of the active metabolites stimulate the synthesis of the Nerve Growth Factor (NGF). Recently, the effect of dietary supplement based on Hericium erinaceus on recognition memory and on hippocampal mossy fiber-CA3 neurotransmission was published. The aim of this study was to investigate the presence of Hericium species on Italian territory in order to isolate the strains for further studies and applications. The first step was to collect Hericium sporophores in Tuscany: H. alpestre Pers., H. coralloides (Scop.) Pers. and H. erinaceus (Bull.) Pers. were the species present. The strains of H. alpestre (H.a.1), H. coralloides (H.c.1) and H. erinaceus (H.e.1 & H.e.2) have been isolated in pure culture and preserved in the collection of the University of Pavia (MicUNIPV). The DNA sequences obtained from the strains were compared to other sequences found in international databases. Therefore, it was possible to construct a phylogenetic tree that highlights the clear separation in clades of the sequences and the molecular identification of our strains with the species of Hericium considered. The second step was to cultivate indoor and outdoor H. erinaceus in order to obtain as many sporophores as possible for further chemical analysis. All the procedures for H. erinaceus cultivation have been followed. Among the available recipes for indoor H. erinaceus cultivation, it was used a substrate formulation contained 70% oak sawdust, 20% rice bran, 10% wheat straw, 1% CaCO3 and 1% sucrose. The bioactive compounds present in the mycelia and in the sporophores of H. erinaceus were chemically analyzed in collaboration with the Centro Grandi Strumenti of the University of Pavia using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). The materials to be analyzed were previously freeze-dried and then extracted with an alcoholic procedure. Preliminary chromatographic analysis revealed the presence of potentially bioactive and structurally different secondary metabolites such as polysaccharides, erinacins, ericenones, steroids and other terpenoids. Ericenones C and D (in sporophores) and erinacin A (in mycelium) have been identified by comparison with the respective standards. These molecules are known to have effects on the Central Nervous System (CNS) cells, which is the main objective of our studies. Thanks to the high sensitivity in the detection of bioactive compounds of H. erinaceus, it will be possible to use the To obtain lyophilized mycelium and the respective culture broth, 4 small pieces (about 5 mm2) of the respective H.e.1 or H.c.1 strains, taken from the margin of growing cultures (MEA), were inoculated into 1 liter of 2% ME (malt extract, Biokar Diagnostics). The static liquid cultures were kept at 24 °C in the dark chamber and fungi grew for one month. 10 replicates for each strain have been done. The method proposed as an analytical screening protocol to determine the optimal growth conditions of the fungus and to improve the production chain of H. erinaceus. These results encourage to carry out chemical analyzes also on H. alpestre and H. coralloides in order to evaluate the presence of bioactive compounds in these two species.

Keywords: Hericium species, Hercium erinaceus bioactive compounds, medicinal mushrooms, mushroom cultivation

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Authors: Pallavi Roe

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Violent crime is a significant public safety concern in urban areas across the United States, and Washington, DC, is no exception. This research discusses the prevalence and types of crime, particularly violent crime, in Washington, DC, along with the factors contributing to the high rate of violent crime in the city, including poverty, inequality, access to guns, and racial disparities. The organizations working towards ensuring safety in neighborhoods are also listed. The proposal to perform spatial and temporal analysis on violent crime and the use of guns in crime analysis is presented to identify patterns and trends to inform evidence-based interventions to reduce violent crime and improve public safety in Washington, DC. The stakeholders for crime analysis are also discussed, including law enforcement agencies, prosecutors, judges, policymakers, and the public. The anticipated result of the spatial and temporal analysis is to provide stakeholders with valuable information to make informed decisions about preventing and responding to violent crimes.

Keywords: crime analysis, spatial analysis, temporal analysis, violent crime

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Authors: Jie Liu, Xudong Luo, Pingping Lin, Yifan Fan

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Facebook, Twitter, Weibo, and other social media and significant e-commerce sites generate a massive amount of online texts, which can be used to analyse people’s opinions or sentiments for better decision-making. So, sentiment analysis, especially fine-grained sentiment analysis, is a very active research topic. In this paper, we survey various methods for fine-grained sentiment analysis, including traditional sentiment lexicon-based methods, machine learning-based methods, and deep learning-based methods in aspect/target/attribute-based sentiment analysis tasks. Besides, we discuss their advantages and problems worthy of careful studies in the future.

Keywords: sentiment analysis, fine-grained, machine learning, deep learning

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Authors: A. B. Robert, Adam Pramadia, Calvin Andika

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The main purpose of this study is to explore consumer loyalty characteristic of mobile phone category in Indonesia. Second, this research attempts to identify consumer segment and to explore their profile in each segment as the basis of marketing strategy formulation. This study used some tools of multivariate analysis such as discriminant analysis and cluster analysis. Discriminate analysis used to discriminate consumer loyal and not loyal by using particular variables. Cluster analysis used to reveal various segment in mobile phone category. In addition to having better customer understanding in each segment, this study used descriptive analysis and cross tab analysis in each segment defined by cluster analysis. This study expected several findings. First, consumer can be divided into two large group of loyal versus not loyal by set of variables. Second, this study identifies customer segment in mobile phone category. Third, exploring customer profile in each segment that has been identified. This study answer a call for additional empirical research into different product categories. Therefore, a replication research is advisable. By knowing the customer loyalty characteristic, and deep analysis of their consumption behavior and profile for each segment, this study is very advisable for high impact marketing strategy development. This study contributes body of knowledge by adding empirical study of consumer loyalty, segmentation analysis in mobile phone category by multiple brand analysis.

Keywords: customer loyalty, segmentation, marketing strategy, discriminant analysis, cluster analysis, mobile phone

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Authors: Anish Shah, Steve A. Wakelin, Derrick Moot, Aurélie Laugraud, Hayley J. Ridgway

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A mixed pasture system of ryegrass-clover is used in New Zealand, where clovers are generally inoculated with commercially available strains of rhizobia. The community of rhizobia living in the soil and the way in which they interact with the plant are affected by different biotic and abiotic factors. In general, bacterial richness and diversity in soil varies by soil pH. pH also affects cell physiology and acts as a master variable that controls the wider soil physiochemical conditions such as P availability, Al release and micronutrient availability. As such, pH can have both primary and secondary effects on soil biology and processes. The aim of this work was to investigate the effect of soil pH on the genetic diversity and metabolic profile of Rhizobium leguminosarum strains nodulating clover. Soils were collected from 12 farms across New Zealand which had a pH(water) range of between 4.9 and 7.5, with four acidic (pH 4.9 – 5.5), four ‘neutral’ (5.8 – 6.1) and four alkaline (6.5 – 7.5) soils. Bacteria were recovered from nodules of Trifolium repens (white clover) and T. subterraneum (subterranean clover) grown in the soils. The strains were cultured and screened against a range of pH-amended media to demonstrate whether they were adapted to pH levels similar to their native soils. The strains which showed high relative growth at a given pH (~20% of those isolated) were selected for metabolic and taxonomic profiling. The Omnilog (Biolog Inc., Hayward, CA) phenotype array was used to perform assays on carbon (C) utilisation for selected strains. DNA was extracted from the strains which had differing C utilisation profiles and PCR products for both forward and reverse primers were sequenced for the following genes: 16S rRNA, recA, nodC, nodD and nifH (symbiotic).

Keywords: bacterial diversity, clover, metabolic and taxonomic profiling, pH adaptation, rhizobia

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Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: Chothmal, Basant Agarwal

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Sentiment analysis means to classify a given review document into positive or negative polar document. Sentiment analysis research has been increased tremendously in recent times due to its large number of applications in the industry and academia. Sentiment analysis models can be used to determine the opinion of the user towards any entity or product. E-commerce companies can use sentiment analysis model to improve their products on the basis of users’ opinion. In this paper, we propose a new One-class Support Vector Machine (One-class SVM) based sentiment analysis model for movie review documents. In the proposed approach, we initially extract features from one class of documents, and further test the given documents with the one-class SVM model if a given new test document lies in the model or it is an outlier. Experimental results show the effectiveness of the proposed sentiment analysis model.

Keywords: feature selection methods, machine learning, NB, one-class SVM, sentiment analysis, support vector machine

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Authors: Otuwose E. Agyeno, Adeniyi A. Jayeola, Bashir A. Ajala

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P. esculentus is indigenous to Nigeria yet no wild relation has been encountered or reported. This has made it difficult to establish proper lineages between the varieties and landraces under cultivation. The present work is the first to determine the apormophy of 135 morphoanatomical characters in organs of 46 accessions drawn from 23 populations of this species based on dicta. The character states were coded in accession x character-state matrices and only 83 were informative and utilised for neighbour joining clustering based on euclidean values, and heuristic search in parsimony analysis using PAST ver. 3.15 software. Compatibility and evolutionary trends between accessions were then explored from values and diagrams produced. The low consistency indices (CI) recorded support monophyly and low homoplasy in this taxon. Agglomerative schedules based on character type and source data sets divided the accessions into mainly 3 clades, each of complexes of accessions. Solenostemon rotundifolius (Poir) J.K Morton was the outgroup (OG) used, and it occurred within the largest clades except when the characters were combined in a data set. The OG showed better compatibility with accessions of populations of landrace Isci, and varieties Riyum and Long’at. Otherwise, its aerial parts are more consistent with those of accessions of variety Bebot. The highly polytomous clades produced due to anatomical data set may be an indication of how stable such characters are in this species. Strict consensus trees with more than 60 nodes outputted showed that the basal nodes were strongly supported by 3 to 17 characters across the data sets, suggesting that populations of this species are more alike. The OG was clearly the first diverging lineage and closely related to accessions of landrace Gwe and variety Bebot morphologically, but different from them anatomically. It was also distantly related to landrace Fina and variety Long’at in terms of root, stem and leaf structural attributes. There were at least 5 other clades with each comprising of complexes of accessions from different localities and terrains within the study area. Spherical stem in cross section, size of vascular bundles at the stem corners as well as the alternate and whorl phyllotaxy are attributes which may have facilitated each other’s evolution in all accessions of the landrace Gwe, and they may be innovative since such states are not characteristic of the larger Lamiaceae, and Plectranthus L’Her in particular. In conclusion, this study has provided valuable information about infraspecific diversity in this taxon. It supports recognition of the varietal statuses accorded to populations of P. esculentus, as well as the hypothesis that the wild gene might have been distributed on the Jos Plateau. However, molecular characterisation of accessions of populations of this species would resolve this problem better.

Keywords: clustering, lineage, morphoanatomical characters, Nigeria, phylogenetics, Plectranthus esculentus, population

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Authors: Hasan Fatih Ertuğrul, Beytullah Okur, Huseyin Üvet, Kadir Erkan

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The objective of this paper is to analyze a 4-pole hybrid magnetic levitation system by using 3D finite element and analytical methods. The magnetostatic analysis of the system is carried out by using ANSYS MAXWELL-3D package. An analytical model is derived by magnetic equivalent circuit (MEC) method. The purpose of magnetostatic analysis is to determine the characteristics of attractive force and rotational torques by the change of air gap clearances, inclination angles and current excitations. The comparison between 3D finite element analysis and analytical results are presented at the rest of the paper.

Keywords: yoke hybrid electromagnet, 3D finite element analysis, magnetic levitation system, magnetostatic analysis

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Authors: Debjit Ray

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Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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Authors: Ju-Young Hwang, Hyo-Gyoung Kwak

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This paper introduces a numerical analysis method for reinforced-concrete (RC) structures exposed to fire and compares the result with experimental results. The proposed analysis method for RC structure under the high temperature consists of two procedures. First step is to decide the temperature distribution across the section through the heat transfer analysis by using the time-temperature curve. After determination of the temperature distribution, the nonlinear analysis is followed. By considering material and geometrical nonlinearity with the temperature distribution, nonlinear analysis predicts the behavior of RC structure under the fire by the exposed time. The proposed method is validated by the comparison with the experimental results. Finally, prediction model to describe the status of after-cooling concrete can also be introduced based on the results of additional experiment. The product of this study is expected to be embedded for smart structure monitoring system against fire in u-City.

Keywords: RC, high temperature, after-cooling analysis, nonlinear analysis

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Authors: Syed Ahzam Tariq, Atharva Modi

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This paper presents a probabilistic analysis of the safety of water tube boilers using fault tree analysis (FTA). A fault tree has been constructed by considering all possible areas where a malfunction could lead to a boiler accident. Boiler accidents are relatively rare, causing a scarcity of data. The fuzzy approach is employed to perform a quantitative analysis, wherein theories of fuzzy logic are employed in conjunction with expert elicitation to calculate failure probabilities. The Fuzzy Fault Tree Analysis (FFTA) provides a scientific and contingent method to forecast and prevent accidents.

Keywords: fault tree analysis water tube boiler, fuzzy probability score, failure probability

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Authors: S. D. N. K. Bathige, G. I. Godahewa, Navaneethaiyer Umasuthan, Jehee Lee

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Kunitz-type serine protease inhibitors (KTIs) are identified in various organisms including animals, plants and microbes. These proteins shared single or multiple Kunitz inhibitory domains link together or associated with other types of domains. Characteristic Kunitz type domain composed of around 60 amino acid residues with six conserved cysteine residues to stabilize by three disulfide bridges. KTIs are involved in various physiological processes, such as ion channel blocking, blood coagulation, fibrinolysis and inflammation. In this study, two Kunitz-type domain containing protein was identified from rock bream database and designated as RbKunitz. The coding sequence of RbKunitz encoded for 507 amino acids with 56.2 kDa theoretical molecular mass and 5.7 isoelectric point (pI). There are several functional domains including MANEC superfamily domain, PKD superfamily domain, and LDLa domain were predicted in addition to the two characteristic Kunitz domain. Moreover, trypsin interaction sites were also identified in Kunitz domain. Homology analysis revealed that RbKunitz shared highest identity (77.6%) with Takifugu rubripes. Completely conserved 28 cysteine residues were recognized, when comparison of RbKunitz with other orthologs from different taxonomical groups. These structural evidences indicate the rigidity of RbKunitz folding structure to achieve the proper function. The phylogenetic tree was constructed using neighbor-joining method and exhibited that the KTIs from fish and non-fish has been evolved in separately. Rock bream was clustered with Takifugu rubripes. The SYBR Green qPCR was performed to quantify the RbKunitz transcripts in different tissues and challenged tissues. The mRNA transcripts of RbKunitz were detected in all tissues (muscle, spleen, head kidney, blood, heart, skin, liver, intestine, kidney and gills) analyzed and highest transcripts level was detected in gill tissues. Temporal transcription profile of RbKunitz in rock bream blood tissues was analyzed upon LPS (lipopolysaccharide), Poly I:C (Polyinosinic:polycytidylic acid) and Edwardsiella tarda challenge to understand the immune responses of this gene. Compare to the unchallenged control RbKunitz exhibited strong up-regulation at 24 h post injection (p.i.) after LPS and E. tarda injection. Comparatively robust expression of RbKunits was observed at 3 h p.i. upon Poly I:C challenge. Taken together all these data indicate that RbKunitz may involve into to immune responses upon pathogenic stress, in order to protect the rock bream.

Keywords: Kunitz-type, rock bream, immune response, serine protease inhibitor

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Authors: Thanthrige Thiunuwan Priyathilaka, Don Anushka Sandaruwan Elvitigala, Bong-Soo Lim, Hyung-Bok Jeong, Jehee Lee

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Toll like receptors (TLRs) are a phylogeneticaly conserved family of pattern recognition receptors, which participates in the host immune responses against various pathogens and pathogen derived mitogen. TLR21, a non-mammalian type, is almost restricted to the fish species even though those can be identified rarely in avians and amphibians. Herein, this study was carried out to identify and characterize TLR21 from rock bream (Oplegnathus fasciatus) designated as RbTLR21, at transcriptional and genomic level. In this study, the full length cDNA and genomic sequence of RbTLR21 was identified using previously constructed cDNA sequence database and BAC library, respectively. Identified RbTLR21 sequence was characterized using several bioinformatics tools. The quantitative real time PCR (qPCR) experiment was conducted to determine tissue specific expressional distribution of RbTLR21. Further, transcriptional modulation of RbTLR21 upon the stimulation with Streptococcus iniae (S. iniae), rock bream iridovirus (RBIV) and Edwardsiella tarda (E. tarda) was analyzed in spleen tissues. The complete coding sequence of RbTLR21 was 2919 bp in length which can encode a protein consisting of 973 amino acid residues with molecular mass of 112 kDa and theoretical isoelectric point of 8.6. The anticipated protein sequence resembled a typical TLR domain architecture including C-terminal ectodomain with 16 leucine rich repeats, a transmembrane domain, cytoplasmic TIR domain and signal peptide with 23 amino acid residues. Moreover, protein folding pattern prediction of RbTLR21 exhibited well-structured and folded ectodomain, transmembrane domain and cytoplasmc TIR domain. According to the pair wise sequence analysis data, RbTLR21 showed closest homology with orange-spotted grouper (Epinephelus coioides) TLR21with 76.9% amino acid identity. Furthermore, our phylogenetic analysis revealed that RbTLR21 shows a close evolutionary relationship with its ortholog from Danio rerio. Genomic structure of RbTLR21 consisted of single exon similar to its ortholog of zebra fish. Sevaral putative transcription factor binding sites were also identified in 5ʹ flanking region of RbTLR21. The RBTLR 21 was ubiquitously expressed in all the tissues we tested. Relatively, high expression levels were found in spleen, liver and blood tissues. Upon induction with rock bream iridovirus, RbTLR21 expression was upregulated at the early phase of post induction period even though RbTLR21 expression level was fluctuated at the latter phase of post induction period. Post Edwardsiella tarda injection, RbTLR transcripts were upregulated throughout the experiment. Similarly, Streptococcus iniae induction exhibited significant upregulations of RbTLR21 mRNA expression in the spleen tissues. Collectively, our findings suggest that RbTLR21 is indeed a homolog of TLR21 family members and RbTLR21 may be involved in host immune responses against bacterial and DNA viral infections.

Keywords: rock bream, toll like receptor 21 (TLR21), pattern recognition receptor, genomic characterization

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Authors: Samaneh Nadali, Masrah Azrifah Azmi Murad, Nurfadhlina Mohammad Sharef

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Sarcasm is a common phenomenon in social media which is a nuanced form of language for stating the opposite of what is implied. Due to the intentional ambiguity, analysis of sarcasm is a difficult task not only for a machine but even for a human. Although sarcasm detection has an important effect on sentiment, it is usually ignored in social media analysis because sarcasm analysis is too complicated. While there is a few systems exist which can detect sarcasm, almost no work has been carried out on a study and the review of the existing work in this area. This survey presents a nearly full image of sarcasm detection techniques and the related fields with brief details. The main contributions of this paper include the illustration of the recent trend of research in the sarcasm analysis and we highlight the gaps and propose a new framework that can be explored.

Keywords: sarcasm detection, sentiment analysis, social media, sarcasm analysis

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Authors: Shuai Liu

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In corporate social responsibility (CSR) reporting, companies are expected to present both the positive and negative parts of the social and environmental impacts of their performance. This study investigates how the companies that listed in fortune 500 respond to this challenge by analyzing the representations of negative part especially the safety performance. It has found that in the level of genre analysis, it presented 3 major moves and 11 steps in terms of the interdiscursivity analysis. It was made up of three dominant discourse.. The study calls for greater focus on the internal and external analysis of the negative aspect of aspects of companies’ self-disclosure.

Keywords: CSR reports, negative parts, critical genre analysis, interdiscursivity

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Authors: Quan Gu, Daniel Dimitrov

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BingleSeq was developed as a shiny-based, intuitive, and comprehensive application that enables the analysis of single-Cell RNA-Sequencing count data. This was achieved via incorporating three state-of-the-art software packages for each type of RNA sequencing analysis, alongside functional annotation analysis and a way to assess the overlap of differential expression method results. At its current state, the functionality implemented within BingleSeq is comparable to that of other applications, also developed with the purpose of lowering the entry requirements to RNA Sequencing analyses. BingleSeq is available on GitHub and will be submitted to R/Bioconductor.

Keywords: bioinformatics, functional annotation analysis, single-cell RNA-sequencing, transcriptomics

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Authors: Juliza Hidayati, Sawarni Hasibuan

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PT. XYZ is a manufacturing company that produces Crude Palm Oil (CPO). The fierce competition in the global markets not only between companies but also a competition between supply chains. This research aims to analyze the supply chain and value chain of Crude Palm Oil (CPO) in the company. Data analysis method used is qualitative analysis and quantitative analysis. The qualitative analysis describes supply chain and value chain, while the quantitative analysis is used to find out value added and the establishment of the value chain. Based on the analysis, the value chain of crude palm oil (CPO) in the company consists of four main actors that are suppliers of raw materials, processing, distributor, and customer. The value chain analysis consists of two actors; those are palm oil plantation and palm oil processing plant. The palm oil plantation activities include nurseries, planting, plant maintenance, harvesting, and shipping. The palm oil processing plant activities include reception, sterilizing, thressing, pressing, and oil classification. The value added of palm oil plantations was 72.42% and the palm oil processing plant was 10.13%.

Keywords: palm oil, value chain, value added, supply chain

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Authors: Alexiou Dimitra, Fragkaki Maria

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The objective of the paper is the study of geographic, economic and educational variables and their contribution to determine the position of each member-state among the EU-28 countries based on the values of seven variables as given by Eurostat. The Data Analysis methods of Multiple Factorial Correspondence Analysis (MFCA) Principal Component Analysis and Factor Analysis have been used. The cross tabulation tables of data consist of the values of seven variables for the 28 countries for 2014. The data are manipulated using the CHIC Analysis V 1.1 software package. The results of this program using MFCA and Ascending Hierarchical Classification are given in arithmetic and graphical form. For comparison reasons with the same data the Factor procedure of Statistical package IBM SPSS 20 has been used. The numerical and graphical results presented with tables and graphs, demonstrate the agreement between the two methods. The most important result is the study of the relation between the 28 countries and the position of each country in groups or clouds, which are formed according to the values of the corresponding variables.

Keywords: Multiple Factorial Correspondence Analysis, Principal Component Analysis, Factor Analysis, E.U.-28 countries, Statistical package IBM SPSS 20, CHIC Analysis V 1.1 Software, Eurostat.eu Statistics

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Authors: J. R. Wang, W. Y. Cheng, J. S. Yeh, S. W. Chen, Y. M. Ferng, J. H. Yang, W. S. Hsu, C. Shih

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To understand the risk for dry storage concrete casks in the cask loading, transfer, and storage phase, the purpose of this research is to establish the probabilistic risk assessment (PRA) analysis methodology for dry storage concrete casks by using SAPHIRE 8 code. This analysis methodology is used to perform the study of Taiwan nuclear power plants (NPPs) dry storage system. The process of research has three steps. First, the data of the concrete casks and Taiwan NPPs are collected. Second, the PRA analysis methodology is developed by using SAPHIRE 8. Third, the PRA analysis is performed by using this methodology. According to the analysis results, the maximum risk is the multipurpose canister (MPC) drop case.

Keywords: PRA, dry storage, concrete cask, SAPHIRE

Procedia PDF Downloads 181

Authors: A. S. Vidyashree, C. M. Kalleshwaraswamy, R. Asokan, H. M. Mahadevaswamy

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Termites are very vital ecological thespians in tropical ecosystem, having been designated as “ecosystem engineers”, due to their significant role in providing soil ecosystem services. Despite their importance, our understanding of a number of their basic biological processes in termites is extremely limited. Developing a better understanding of termite biology is closely dependent upon consistent species identification. At present, identification of termites is relied on soldier castes. But for many species, soldier caste is not reported, that creates confusion in identification. The use of molecular markers may be helpful in estimating phylogenetic relatedness between the termite species and estimating genetic differentiation among local populations within each species. To understand this, termites samples were collected from various places of Western Ghats covering four states namely Karnataka, Kerala, Tamil Nadu, Maharashtra during 2013-15. Termite samples were identified based on their morphological characteristics, molecular characteristics, or both. Survey on the termite fauna in Karnataka, Kerala, Maharashtra and Tamil Nadu indicated the presence of a 16 species belongs to 4 subfamilies under two families viz., Rhinotermitidae and Termitidae. Termititidae was the dominant family which was belonging to 4 genera and four subfamilies viz., Macrotermitinae, Amitermitinae, Nasutitermitinae and Termitinae. Amitermitinae had three species namely, Microcerotermes fletcheri, M. pakistanicus and Speculitermes sinhalensis. Macrotermitinae had the highest number of species belonging two genera, namely Microtermes and Odontotermes. Microtermes genus was with only one species i.e., Microtermes obesi. The genus Odontotermes was represented by the highest number of species (07), namely, O. obesus was the dominant (41 per cent) and the most widely distributed species in Karnataka, Karala, Maharashtra and Tamil nadu followed by O. feae (19 per cent), O.assmuthi (11 per cent) and others like O. bellahunisensis O. horni O. redemanni, O. yadevi. Nasutitermitinae was represented by two genera namely Nasutitermes anamalaiensis and Trinervitermes biformis. Termitinae subfamily was represented by Labiocapritermes distortus. Rhinotermitidae was represented by single subfamily Heterotermetinae. In Heterotermetinae, two species namely Heterotermes balwanthi and H. malabaricus were recorded. Genetic relationship among termites collected from various locations of Western Ghats of India was characterized based on mitochondrial DNA sequences (12S, 16S, and COII). Sequence analysis and divergence among the species was assessed. These results suggest that the use of both molecular and morphological approaches is crucial in ensuring accurate species identification. Efforts were made to understand their evolution and to address the ambiguities in morphological taxonomy. The implication of the study in revising the taxonomy of Indian termites, their characterization and molecular comparisons between the sequences are discussed.

Keywords: isoptera, mitochondrial DNA sequences, rhinotermitidae, termitidae, Western ghats

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Authors: Abdullah Alaklabi, Ibrahim A. Arif, Sameera O. Bafeel, Ahmad H. Alfarhan, Anis Ahamed, Jacob Thomas, Mohammad A. Bakir

Abstract:

Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. The close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (≥99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana. The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Keywords: Diospyros mespiliformis, endangered plant, identification partial rbcL

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Authors: Jeong-Hyun Park, Young-Sik Park, Hyo-Teag Jung

Abstract:

This paper presents static analysis deployment model for code quality on R&D Projects of SW Development. The proposed model includes the scope of R&D projects and index for static analysis of source code, operation model and execution process, environments and infrastructure system for R&D projects of SW development. There is the static analysis result of pilot project as case study based on the proposed deployment model and environment, and strategic considerations for success operation of the proposed static analysis deployment model for R&D Projects of SW Development. The proposed static analysis deployment model in this paper will be adapted and improved continuously for quality upgrade of R&D projects, and customer satisfaction of developed source codes and products.

Keywords: static analysis, code quality, coding rules, automation tool

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Authors: Ju-young Hwang, Hyo-Gyoung Kwak, Hong Jae Yim

Abstract:

This paper introduces a numerical analysis method for reinforced-concrete (RC) structures exposed to fire and compares the result with experimental results. The proposed analysis method for RC structure under the high temperature consists of two procedures. First step is to decide the temperature distribution across the section through the heat transfer analysis by using the time-temperature curve. After determination of the temperature distribution, the nonlinear analysis is followed. By considering material and geometrical non-linearity with the temperature distribution, nonlinear analysis predicts the behavior of RC structure under the fire by the exposed time. The proposed method is validated by the comparison with the experimental results. Finally, Prediction model to describe the status of after-cooling concrete can also be introduced based on the results of additional experiment. The product of this study is expected to be embedded for smart structure monitoring system against fire in u-City.

Keywords: RC structures, heat transfer analysis, nonlinear analysis, after-cooling concrete model

Procedia PDF Downloads 329