Search results for: biosynthetic gene clusters

Authors: Katarzyna Lubecka, Kirsty Flower, Megan Beetch, Lucinda Kurzava, Hannah Buvala, Samer Gawrieh, Suthat Liangpunsakul, Tracy Gonzalez, George McCabe, Naga Chalasani, James M. Flanagan, Barbara Stefanska

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Hepatocellular carcinoma (HCC), the most prevalent type of primary liver cancer, is the second leading cause of cancer death worldwide. Late onset of clinical symptoms in HCC results in late diagnosis and poor disease outcome. Approximately 85% of individuals with HCC have underlying liver cirrhosis. However, not all cirrhotic patients develop cancer. Reliable early detection biomarkers that can distinguish cirrhotic patients who will develop cancer from those who will not are urgently needed and could increase the cure rate from 5% to 80%. We used Illumina-450K microarray to test whether blood DNA, an easily accessible source of DNA, bear site-specific changes in DNA methylation in response to HCC before diagnosis with conventional tools (pre-diagnostic). Top 11 differentially methylated sites were selected for validation by pyrosequencing. The diagnostic potential of the 11 pyrosequenced probes was tested in blood samples from a prospective cohort of cirrhotic patients. We identified 971 differentially methylated CpG sites in pre-diagnostic HCC cases as compared with healthy controls (P < 0.05, paired Wilcoxon test, ICC ≥ 0.5). Nearly 76% of differentially methylated CpG sites showed lower levels of methylation in cases vs. controls (P = 2.973E-11, Wilcoxon test). Classification of the CpG sites according to their location relative to CpG islands and transcription start site revealed that those hypomethylated loci are located in regulatory regions important for gene transcription such as CpG island shores, promoters, and 5’UTR at higher frequency than hypermethylated sites. Among 735 CpG sites hypomethylated in cases vs. controls, 482 sites were assigned to gene coding regions whereas 236 hypermethylated sites corresponded to 160 genes. Bioinformatics analysis using GO, KEGG and DAVID knowledgebase indicate that differentially methylated CpG sites are located in genes associated with functions that are essential for gene transcription, cell adhesion, cell migration, and regulation of signal transduction pathways. Taking into account the magnitude of the difference, statistical significance, location, and consistency across the majority of matched pairs case-control, we selected 11 CpG loci corresponding to 10 genes for further validation by pyrosequencing. We established that methylation of CpG sites within 5 out of those 10 genes distinguish cirrhotic patients who subsequently developed HCC from those who stayed cancer free (cirrhotic controls), demonstrating potential as biomarkers of early detection in populations at risk. The best predictive value was detected for CpGs located within BARD1 (AUC=0.70, asymptotic significance ˂0.01). Using an additive logistic regression model, we further showed that 9 CpG loci within those 5 genes, that were covered in pyrosequenced probes, constitute a panel with high diagnostic accuracy (AUC=0.887; 95% CI:0.80-0.98). The panel was able to distinguish pre-diagnostic cases from cirrhotic controls free of cancer with 88% sensitivity at 70% specificity. Using blood as a minimally invasive material and pyrosequencing as a straightforward quantitative method, the established biomarker panel has high potential to be developed into a routine clinical test after validation in larger cohorts. This study was supported by Showalter Trust, American Cancer Society (IRG#14-190-56), and Purdue Center for Cancer Research (P30 CA023168) granted to BS.

Keywords: biomarker, DNA methylation, early detection, hepatocellular carcinoma

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Authors: Sonia Bedhiaf-Romdhani

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The sheep (Ovis aries) was domesticated, approximately 11,000 years ago (YBP), in the Fertile Crescent from Asian Mouflon (Ovis Orientalis). The Northern African (NA) sheep is 7,000 years old, represents a remarkable diversity of sheep populations reared under traditional and low input farming systems (LIFS) over millennia. The majority of small ruminants in developing countries are encountered in low input production systems and the resilience of local communities in rural areas is often linked to the wellbeing of small ruminants. Regardless of the rich biodiversity encountered in sheep ecotypes there are four main sheep breeds in the country with 61,6 and 35.4 percents of Barbarine (fat tail breed) and Queue Fine de l’Ouest (thin tail breed), respectively. Phoenicians introduced the Barbarine sheep from the steppes of Central Asia in the Carthaginian period, 3000 years ago. The Queue Fine de l’Ouest is a thin-tailed meat breed heavily concentrated in the Western and the central semi-arid regions. The Noire de Thibar breed, involving mutton-fine wool producing animals, has been on the verge of extinction, it’s a composite black coated sheep breed found in the northern sub-humid region because of its higher nutritional requirements and non-tolerance of the prevailing harsher condition. The D'Man breed, originated from Morocco, is mainly located in the southern oases of the extreme arid ecosystem. A genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. Genetic analysis of relationship between breeds highlighted the genetic differentiation of Noire de Thibar breed from the other local breeds, reflecting the effect of past events of introgression of European gene pool. The Queue Fine de l’Ouest breed showed a genetic heterogeneity and was close to Barbarine. The D'Man breed shared a considerable gene flow with the thin-tailed Queue Fine de l'Ouest breed. Native small ruminants breeds, are capable to be efficiently productive if essential ingredients and coherent breeding schemes are implemented and followed. Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources.

Keywords: sheep, farming systems, diversity, SNPs.

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Authors: Nam-Kuk Kim, Jin Kim, Soomin Park, Changhee Lee, Mijin Chu, Seong-Hun Lee

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In this study, we conducted whole genome re-sequencing of 10 cultivars originated from five countries including Korea, China, India, Pakistan and Ethiopia with Sesamum indicum (Zhongzho No. 13) genome as a reference. Almost 80% of the whole genome sequences of the reference genome could be covered by sequenced reads. Numerous SNP and InDel were detected by bioinformatic analysis. Among these variants, 266,051 SNPs were identified as unique to countries. Pakistan and Ethiopia had high densities of SNPs compared to other countries. Three main clusters (cluster 1: Korea, cluster 2: Pakistan and India, cluster 3: Ethiopia and China) were recovered by neighbor-joining analysis using all variants. Interestingly, some variants were detected in DGAT1 (diacylglycerol O-acyltransferase 1) and FADS (fatty acid desaturase) genes, which are known to be related with fatty acid synthesis and metabolism. These results can provide useful information to understand the regional characteristics and develop DNA markers for origin discrimination of sesame.

Keywords: Sesamum indicum, NGS, SNP, DNA marker

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Authors: Ouafek Nora, Keghouche Nassira, Dehdouh Heider, Untidt Carlos

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A lot of knowledge has been accumulated on the metal clusters supported on oxide surfaces because of their multiple applications in microelectronics, heterogeneous catalysis, and magnetic devices. In this work, the surface state of Ni / MgO has been studied by XPS (X-ray Photoemission Spectroscopy). The samples were prepared by impregnation with ion exchange Ni²⁺ / MgO, followed by either a thermal treatment in air (T = 100 -350 ° C) or a gamma irradiation (dose 100 kGy, 25 kGy dose rate h -1). The obtained samples are named after impregnation NMI, NMR after irradiation, and finally NMC(T) after calcination at the temperature T (T = 100-600 °C). A structural study by XRD and HRTEM reveals the presence of nanoscaled Ni-Mg intermetallic phases (Mg₂Ni, MgNi₂, and Mg₆Ni) and magnesium hydroxide. Mg(OH)₂ in nanometric range (2- 4 nm). Mg-Ni compounds are of great interest in energy fields (hydrogen storage…). XPS spectra show two Ni2p peaks at energies of about 856.1 and 861.9 eV, indicating that the nickel is primarily in an oxidized state on the surface. The shift of the main peak relative to the pure NiO (856.1 instead of 854.0 eV) suggests that in addition to oxygen, nickel is engaged in another link with magnesium. This is in agreement with the O1s spectra which present an overlap of peaks corresponds to NiO and MgO, at a calcination temperature T ≤ 300 °C.

Keywords: XPS, XRD, nanoparticules, Ni-MgO

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Authors: Lip Vui Tshin

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Sabah, one of the thirteen Malaysian states, is located in the northern part of Malaysian Borneo. It is a melting pot of many different cultures and traditions, being home to about 2.9 million people with more than 30 ethic groups. It is also known as one of the twelve mega-diversity sites in the world with its rich living heritage; ethnic makes it ideal for the ecotourism industry. Sabah enjoys a steady flow of eco tourists from domestic and international markets with a gradual increase in the number of visitor arrival each year. Sabah’s ecotourism is categorized by its natural attraction, wildlife and wilderness habitats. This paper sets out to interpret and develop the indicators for success ecotourism sites in Sabah and measures its development stage. The long-term viability of tourism can be assured only when the limitations and favorable opportunities of the overall environment for tourism development are understood and ways to measure changes induced by tourism are identified and applied. This is a literature review of ecotourism site success indicators, and the outcome of this review is the identification of existing clusters and categorization of indicators and charting the way forward to develop a better understanding in ecotourism site success.

Keywords: ecotourism, ecotourism indicators, ecotourism success, Sabah

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Authors: M. Acin-Albiac, P. Filannino, R. Coda, Carlo G. Rizzello, M. Gobbetti, R. Di Cagno

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Demand for smart management of large amounts of agro-food by-products has become an area of major environmental and economic importance worldwide. Brewers' spent grain (BSG), the most abundant by-product generated in the beer-brewing process, represents an example of valuable raw material and source of health-promoting compounds. To the date, the valorization of BSG as a food ingredient has been limited due to poor technological and sensory properties. Tailored bioprocessing through lactic acid bacteria (LAB) fermentation is a versatile and sustainable means for the exploitation of food industry by-products. Indigestible carbohydrates (e.g., hemicelluloses and celluloses), high phenolic content, and mostly lignin make of BSG a hostile environment for microbial survival. Hence, the selection of tailored starters is required for successful fermentation. Our study investigated the metabolic strategies of Leuconostoc pseudomesenteroides and Lactobacillus plantarum strains to exploit BSG as a food ingredient. Two distinctive BSG samples from different breweries (Italian IT- and Finish FL-BSG) were microbially and chemically characterized. Growth kinetics, organic acid profiles, and the evolution of phenolic profiles during the fermentation in two BSG model media were determined. The results were further complemented with gene expression targeting genes involved in the degradation cellulose, hemicelluloses building blocks, and the metabolism of anti-nutritional factors. Overall, the results were LAB genus dependent showing distinctive metabolic capabilities. Leuc. pseudomesenteroides DSM 20193 may degrade BSG xylans while sucrose metabolism could be furtherly exploited for extracellular polymeric substances (EPS) production to enhance BSG pro-technological properties. Although L. plantarum strains may follow the same metabolic strategies during BSG fermentation, the mode of action to pursue such strategies was strain-dependent. L. plantarum PU1 showed a great preference for β-galactans compared to strain WCFS1, while the preference for arabinose occurred at different metabolic phases. Phenolic compounds profiling highlighted a novel metabolic route for lignin metabolism. These findings will allow an improvement of understanding of how lactic acid bacteria transform BSG into economically valuable food ingredients.

Keywords: brewery by-product valorization, metabolism of plant phenolics, metabolism of lactic acid bacteria, gene expression

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Authors: Hamid R. Lashgarian Azad, Seyed N. Shetab Boushehri

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Wireless sensor networks (WSN) have become progressively popular due to their wide range of applications. Wireless Sensor Network is made of numerous tiny sensor nodes that are battery-powered. It is a very significant problem to maximize the lifetime of wireless sensor networks. In this paper, we propose a two-stage protocol based on an imperialist competitive algorithm (2S-ICA) to solve a sensor network optimization problem. The energy of the sensors can be greatly reduced and the lifetime of the network reduced by long communication distances between the sensors and the sink. We can minimize the overall communication distance considerably, thereby extending the lifetime of the network lifetime through connecting sensors into a series of independent clusters using 2SICA. Comparison results of the proposed protocol and LEACH protocol, which is common to solving WSN problems, show that our protocol has a better performance in terms of improving network life and increasing the number of transmitted data.

Keywords: wireless sensor network, imperialist competitive algorithm, LEACH protocol, k-means clustering

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Authors: Muhammad Haroon, LI Xiangju

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C. communis L. is an important weed of many crop, but very little information about the adaptation strategies of C. communis L. biotypes under drought stress. We investigated five biotypes of C. communis L under drought stress to identify the adaptation mechanism. The expression of drought stress related genes (DRS1, EREB and HRB1) was up-regulated in biotypes, while in some biotypes their expression was down regulated. All five biotypes can thus regulate water balance to consume less water to maintain their status under drought stress condition. This result concluded that C. communis L. biotypes can survive longer under drought stress condition. Weed scientist should seek more effective management strategies to deal with C. communis L.

Keywords: C. communis, biotypes, drought stress, gene expression

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Authors: Kaiyuan Chena, Senentxu Lanceros-Méndeza, Laijun Liub, Qi Zhanga

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0.6Bi(Mg1/2Ti1/2)O3-0.4Ba0.8Ca0.2(Nb0.125Ti0.875)O3 (0.6BMT-0.4BCNT) ceramics with a pseudo-cubic structure and re-entrant dipole glass behavior have been investigated via X-ray diffraction and dielectric permittivity-temperature spectra. It shows an excellent dielectric-temperature stability with small variations of dielectric permittivity (± 5%, 420 - 802 K) and dielectric loss tangent (tanδ < 2.5%, 441 - 647 K) in a wide temperature range. Three dielectric anomalies are observed from 290 K to 1050 K. The low-temperature weakly coupled re-entrant relaxor behavior was described using Vogel-Fulcher law and the new glass model. The mid- and high-temperature dielectric anomalies are characterized by isothermal impedance and electrical modulus. The activation energy of both dielectric relaxation and conductivity follows the Arrhenius law in the temperature ranges of 633 - 753 K and 833 - 973 K, respectively. The ultrahigh thermal stability of the dielectric permittivity is attributed to the weakly coupling of polar clusters, the formation of diffuse phase transition (DPT) and the local phase transition of calcium-containing perovskite.

Keywords: permittivity, relaxor, electronic ceramics, activation energy

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Authors: Angel Champion

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Chemotherapy and radiation use an acidified approach to induce apoptosis, which only kills mature cancer cells while resulting in gene and cell damage with significant levels of toxicity in tumor-affected tissues and organs. The acid approach, where the cells exterminated are not differentiated, induces the disappearance of white blood cells from the blood. This increases susceptibility to infection in severe forms of cancer spread. However, chemotherapy and radiation cannot kill cancer stem cells that metastasize, being the leading cause of 98% of cancer fatalities. With over 12 million new cancer cases symptomatic each year, including common malignancies such as Hepatocellular Carcinoma (HCC), this study aims to assess the bioactive constituents and phytochemical composition of Taraxacum Officinale (Dandelion). This analysis enables pharmaceutical quality and potency to be applied to studies on cancer cell proliferation and apoptosis. A phytochemical screening is carried out to identify the antioxidant components of Dandelion root, stem, and flower extract. The constituents tested for are phlorotannins, carbohydrates, glycosides, saponins, flavonoids, alkaloids, sterols, triterpenes, and anthraquinone glycosides. To conserve the existing phenolic compounds, a portion of the constituent tests will be examined with an acid, alcohol, or aqueous solvent. As a result, the qualitative and quantitative variations within the Dandelion extract that measure uniform effective potency are vital to the conformity for producing medicinal products. These medicines will be constructed with a consistent, uniform composition that physicians can use to control and effectively eradicate malignant diseases safely. Taraxacum Officinale's phytochemical composition comprises a highly-graded potency due to present bioactive contents that will essentially drive out malignant disease within the human body. Its high potency rate is powerful enough to eliminate both mature cancer cells and cancer stem cells without the cell and gene damage induced by chemotherapy and radiation. Correspondingly, the high margins of cancer mortality on a global scale are mitigated. This remarkable contribution to modern therapeutics will essentially optimize the margins of natural products and their derivatives, which account for 50% of pharmaceuticals in modern therapeutics, while preventing the adverse effects of radiation and chemotherapy drugs.

Keywords: antioxidant, apoptosis, metastasize, phytochemical, proliferation, potency

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Authors: M. Sakthivel, A. Devaki, D. Balasubramanyam, P. Kumarasamy, A. Raja, R. Anilkumar, H. Gopi

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The New Zealand White breed of rabbit is one of the most commonly used, well adapted exotic breeds in India. Earlier studies were limited only to analyze the environmental factors affecting the growth and reproductive performance. In the present study, the population of the New Zealand White rabbits in a closed herd was evaluated for its genetic structure. Data on pedigree information (n=2508) for 18 years (1995-2012) were utilized for the study. Pedigree analysis and the estimates of population genetic parameters based on gene origin probabilities were performed using the software program ENDOG (version 4.8). The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.489 years, 13.233 percent and 17.585 percent, respectively. The proportion of population inbred was 100 percent. The estimated mean values of average relatedness and the individual increase in inbreeding were 22.727 and 3.004 percent, respectively. The percent increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations, and complete generations, respectively. The number of ancestors contributing the most of 50% genes (fₐ₅₀) to the gene pool of reference population was 4 which might have led to the reduction in genetic variability and increased amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fₑ) and the effective number of ancestors (fₐ), as expressed by the fₑ/fₐ ratio was 1.1 which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29 percent pedigree was complete reflecting the well-maintained pedigree records. The maximum known generations were 15 with an average of 7.9 and the average equivalent generations traced were 5.6 indicating of a fairly good depth in pedigree. The realized effective population size was 14.93 which is very critical, and with the increasing trend of inbreeding, the situation has been assessed to be worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10 percent which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred with very high inbreeding coefficient and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve the genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Keywords: effective population size, genetic structure, pedigree analysis, rabbit genetics

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Authors: M. Novak, J. Dufourmount, D. Wildi, A. Sutherland, L. Sosa, J. Zimmer, E. Szabo

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The circular economy has grounded itself amongst scholars and practitioners operating across governments and enterprises. The aim of this paper is to augment the circular economy concept by identifying common core and enabling circular business models. To this aim, we have analysed over 150 papers regarding circular activities and identified 8 clusters of business models and enablers. We have mapped and harmonised the most prominent frameworks conceptualising the circular economy. Our findings indicate that circular economy core business models include regenerative in addition to reduce, reuse and recycle activities. We further find enabling activities in design, digital technologies, knowledge development and sharing, multistakeholder collaborations, and extended corporate responsibility initiatives in various forms. We critically contrast the application of these business models across the European and African contexts. Overall, we find that seemingly varied circular economy definitions distill the same conceptual business models. We hope to contribute towards the coherence of the circular economy concept, and the continuous development of practical guidance to select and implement circular strategies.

Keywords: Circular economy, content analysis, business models, definitions, enablers, frameworks

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Amine Ganibardi, Cherif Arab Ali

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This paper addresses the data cleaning issue as a part of web usage data preprocessing within the scope of Web Usage Mining. Weblog data recorded by web servers within log files reflect usage activity, i.e., End-users’ clicks and underlying user-agents’ hits. As Web Usage Mining is interested in End-users’ behavior, user-agents’ hits are referred to as noise to be cleaned-off before mining. Filtering hits from clicks is not trivial for two reasons, i.e., a server records requests interlaced in sequential order regardless of their source or type, website resources may be set up as requestable interchangeably by end-users and user-agents. The current methods are content-centric based on filtering heuristics of relevant/irrelevant items in terms of some cleaning attributes, i.e., website’s resources filetype extensions, website’s resources pointed by hyperlinks/URIs, http methods, user-agents, etc. These methods need exhaustive extra-weblog data and prior knowledge on the relevant and/or irrelevant items to be assumed as clicks or hits within the filtering heuristics. Such methods are not appropriate for dynamic/responsive Web for three reasons, i.e., resources may be set up to as clickable by end-users regardless of their type, website’s resources are indexed by frame names without filetype extensions, web contents are generated and cancelled differently from an end-user to another. In order to overcome these constraints, a clustering-based cleaning method centered on the logging structure is proposed. This method focuses on the statistical properties of the logging structure at the requested and referring resources attributes levels. It is insensitive to logging content and does not need extra-weblog data. The used statistical property takes on the structure of the generated logging feature by webpage requests in terms of clicks and hits. Since a webpage consists of its single URI and several components, these feature results in a single click to multiple hits ratio in terms of the requested and referring resources. Thus, the clustering-based method is meant to identify two clusters based on the application of the appropriate distance to the frequency matrix of the requested and referring resources levels. As the ratio clicks to hits is single to multiple, the clicks’ cluster is the smallest one in requests number. Hierarchical Agglomerative Clustering based on a pairwise distance (Gower) and average linkage has been applied to four logfiles of dynamic/responsive websites whose click to hits ratio range from 1/2 to 1/15. The optimal clustering set on the basis of average linkage and maximum inter-cluster inertia results always in two clusters. The evaluation of the smallest cluster referred to as clicks cluster under the terms of confusion matrix indicators results in 97% of true positive rate. The content-centric cleaning methods, i.e., conventional and advanced cleaning, resulted in a lower rate 91%. Thus, the proposed clustering-based cleaning outperforms the content-centric methods within dynamic and responsive web design without the need of any extra-weblog. Such an improvement in cleaning quality is likely to refine dependent analysis.

Keywords: clustering approach, data cleaning, data preprocessing, weblog data, web usage data

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Authors: T. Sadunishvili, L. Kutateladze, T. Urushadze, R. Khvedelidze, N. Zakariashvili, M. Jobava, G. Kvesitadze

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Multiple repeated soil-climatic zones in Georgia determines the diversity of microorganisms. Hundreds of microscopic fungi of different genera have been isolated from different ecological niches, including some extreme environments. Biosynthetic ability of microscopic fungi has been studied. Trichoderma ressei, representative of the Ascomycetes secrete cellulolytic and xylanolytic enzymes that act in synergy to hydrolyze polysaccharide polymers to glucose, xylose and arabinose, which can be fermented to biofuels. The other mesophilic strains producing cellulases are Allesheria terrestris, Chaetomium thermophile, Fusarium oxysporium, Piptoporus betulinus, Penicillium echinulatum, P. purpurogenum, Aspergillus niger, A. wentii, A. versicolor, A. fumigatus etc. In the majority of the cases the cellulases produced by strains of genus Aspergillus usually have high β-glucosidase activity and average endoglucanases levels (with some exceptions), whereas strains representing Trichoderma have high endo enzyme and low β-glucosidase, and hence has limited efficiency in cellulose hydrolysis. Six producers of stable cellulases and xylanases from mesophilic and thermophilic fungi have been selected. By optimization of submerged cultivation conditions, high activities of cellulases and xylanases were obtained. For enzymes purification, their sedimentation by organic solvents such as ethyl alcohol, acetone, isopropanol and by ammonium sulphate in different ratios have been carried out. Best results were obtained with precipitation by ethyl alcohol (1:3.5) and ammonium sulphate. The yields of enzyme according to cellulase activities were 80-85% in both cases. Cellulase activity of enzyme preparation obtained from the strain Trichoderma viride X 33 is 126 U/g, from the strain Penicillium canescence D 85–185U/g and from the strain Sporotrichum pulverulentum T 5-0 110 U/g. Cellulase activity of enzyme preparation obtained from the strain Aspergillus sp. Av10 is 120 U/g, xylanase activity of enzyme preparation obtained from the strain Aspergillus niger A 7-5–1155U/g and from the strain Aspergillus niger Aj 38-1250 U/g. Optimum pH and temperature of operation and thermostability, of the enzyme preparations, were established. The efficiency of hydrolyses of different agricultural residues by the microscopic fungi cellulases has been studied. The glucose yield from the residues as a result of enzymatic hydrolysis is highly determined by the ratio of enzyme to substrate, pH, temperature, and duration of the process. Hydrolysis efficiency was significantly increased as a result of different pretreatment of the residues by different methods. Acknowledgement: The Study was supported by the ISTC project G-2117, funded by Korea.

Keywords: cellulase, xylanase, microscopic fungi, enzymatic hydrolysis

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Authors: Zelikha Labbani

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The in vitro isolated microspore culture is the most powerful androgenic pathway to produce doubled haploid plants in the short time. To deviate a microspore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the microspore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of microspore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. As haploid single cells, microspore became a strategy to achieve various objectives particularly in genetic engineering. In this communication we would show the most recent advances in the producing haploid embryos via in vitro isolated microspore culture.

Keywords: in vitro isolated microspore culture, success, haploid cells, bioinformatics, biomedicine

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Authors: Amarjit S Tanda

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Integrated Pest Management Technology (IPMT) offers a crop protection model with sustainable agriculture production with minimum damage to the environment and human health. A concept of agro-ecological crop protection seems unsuitable under dynamic environmental systems. To remedy this, we are proposing Genetically Engineered Crop Protection System (GECPS), as an alternate concept in IPMT that suggests how GE cultivars can be optimally put to the service of crop protection. Genetically engineered cultivars which are developed by gene editing biotechnology may provide a preventive defense against the insect pests and plant diseases, a suitable alternative crop system for blending in IPMT program, in the future agro-industry.

Keywords: integrated, pest, management, technology

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Authors: Nasrine Olson

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With over 70,000 scholarly publications on the topic of biosensors, an overview of the field has become a challenge. To facilitate, there are currently over 700 expert-reviews of publications on biosensors and related topics. This study focuses on these review papers in order to provide a Meta-Review of the area. This paper provides a statistical analysis and overview of biosensor-related review papers. Comprehensive searches are conducted in the Web of Science, and PubMed databases and the resulting empirical material are analyzed using bibliometric methods and tools. The study finds that the biosensor-related review papers can be categorized in five related subgroups, broadly denoted by (i) properties of materials and particles, (ii) analysis and indicators, (iii) diagnostics, (iv) pollutant and analytical devices, and (v) treatment/ application. For an easy and clear access to the findings visualization of clusters and networks of connections are presented. The study includes a temporal dimension and identifies the trends over the years with an emphasis on the most recent developments. This paper provides useful insights for those who wish to form a better understanding of the research trends in the area of biosensors.

Keywords: bibliometrics, biosensors, meta-review, statistical analysis, trends visualization

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Authors: Phenphak Horadee, Rodchares Hanrinth, Saithip Suttiruksa

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Inappropriate use of antibiotics has happened in several hospitals, Thailand. Drug use evaluation (DUE) is one strategy to overcome this difficulty. However, most community hospitals still encounter incomplete evaluation resulting overuse of antibiotics with high cost. Consequently, drug-resistant bacteria have been rising due to inappropriate antibiotic use. The aim of this study was to involve stakeholders in conceptualizing, developing, and prioritizing a feasible intervention strategy to promote and support appropriate antibiotic prescribing in a community hospital, Thailand. Study antibiotics included four antibiotics such as Meropenem, Piperacillin/tazobactam, Amoxicillin/clavulanic acid, and Vancomycin. The study was conducted for the 1-year period between March 1, 2018, and March 31, 2019, in a community hospital in the northeastern part of Thailand. Concept mapping was used in a purposive sample, including doctors (one was an administrator), pharmacists, and nurses who involving drug use evaluation of antibiotics. In-depth interviews for each participant and survey research were conducted to seek the problems for inappropriate use of antibiotics based on drug use evaluation system. Seventy-seven percent of DUE reported appropriate antibiotic prescribing, which still did not reach the goal of 80 percent appropriateness. Meropenem led other antibiotics for inappropriate prescribing. The causes of the unsuccessful DUE program were classified into three themes such as personnel, lack of public relation and communication, and unsupported policy and impractical regulations. During the first meeting, stakeholders (n = 21) expressed the generation of interventions. During the second meeting, participants who were almost the same group of people in the first meeting (n = 21) were requested to independently rate the feasibility and importance of each idea and to categorize them into relevant clusters to facilitate multidimensional scaling and hierarchical cluster analysis. The outputs of analysis included the idealist, cluster list, point map, point rating map, cluster map, and cluster rating map. All of these were distributed to participants (n = 21) during the third meeting to reach consensus on an intervention model. The final proposed intervention strategy included 29 feasible and crucial interventions in seven clusters: development of information technology system, establishing policy and taking it into the action plan, proactive public relations of the policy, action plan and workflow, in cooperation of multidisciplinary teams in drug use evaluation, work review and evaluation with performance reporting, promoting and developing professional and clinical skill for staff with training programs, and developing practical drug use evaluation guideline for antibiotics. These interventions are relevant and fit to several intervention strategies for antibiotic stewardship program in many international organizations such as participation of the multidisciplinary team, developing information technology to support antibiotic smart use, and communication. These interventions were prioritized for implementation over a 1-year period. Once the possibility of each activity or plan is set up, the proposed program could be applied and integrated into hospital policy after evaluating plans. Effectiveness of each intervention could be promoted to other community hospitals to promote and support antibiotic smart use.

Keywords: antibiotic, concept mapping, drug use evaluation, multidisciplinary teams

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Authors: Judit Perjessy, Zsolt Zalan, Ferenc Hegyi, Eniko Horvath-Szanics, Krisztina Takacs, Andras Nagy, Adel Klupacs, Erika Koppany-Szabo, Zhirong Wang, Kaituo Wang, Muying Du, Jianquan Kan

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The post-harvest diseases cause great economic losses in the fruit and vegetables; the prevention of these deterioration has great importance. Against the fungi, which cause most of the diseases, are extensively used the fungicides. However, there are increasing consumer concerns over the presence of pesticide residues in food. An alternative and in recent years, increasingly studied method for the prevention of the diseases is biocontrol, where antagonistic microorganisms are used for the control of fungi. The genera of Lactobacillus is well known and extensively studied, but its applicability as biocontrol agents in post-harvest preservation of fruit and vegetables is poorly investigated. However these bacteria can be found on the surface of the plants and have great antimicrobial activity. In our study we have investigated the chitinase activity, the antifungal effect and the applicability of several Lactobacillus strains to select potential biocontrol agents. We investigated the determination of the environmental parameters of a gene (encoding chitinase) expression and we also investigated the relationship between actual antifungal activity and potential chitinase activity. Mixed cultures were also developed to enhance the antifungal activity and determined the optimal mold spore and bacteria concentration ratio for the appropriate efficacy. Five Lactobacillus strains (L. acidophilus N2, L. delbrueckii subsp. bulgaricus B397, L. sp. 2231, L. sake subsp. sake 2471, L. buchneri 1145) possess chitinase-coding gene from the 43 investigated Lactobacillus strains. Proteins with similar molecular weight and separation properties like bacterial chitinases were detected from these strains, which also possess chitin-binding property. Nevertheless, they were inactive, lacks the chitinolytic activity. In point of the cumulative activity of inhibition, our results showed that certain strains were statistically significant in a positive direction compared to other strains, e.g., L. rhamnosus VT1 and L. Casey 154 have shown great general antifungal effect against 11 molds from the genera Penicillium and Botrytis and isolated from spoiled fruit and vegetables. Also, some mixed cultures (L. rhamnosus VT1 - L. Plantarum 299v) showed significant antifungal effects against the indigenous molds on the surface of apple fruit during the industrial storage experiment. Thus, they could be promising for post-harvest biopreservation.

Keywords: biocontrol, chitinase, Lactobacillus, post-harvest

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Authors: Amel Hannech, Mehdi Adda, Hamid Mcheick

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In this paper, we propose a generic model of user profile integrating several elements that may positively impact the research process. We exploit the classical behavior of users and integrate a delimitation process of their research activities into several research sessions enriched with contextual and temporal information, which allows reflecting the current interests of these users in every period of time and infer data freshness. We argue that the annotation of resources gives more transparency on users' needs. It also strengthens social links among resources and users, and can so increase the scope of the user profile. Based on this idea, we integrate the social tagging practice in order to exploit the social users' behavior to enrich their profiles. These profiles are then integrated into a recommendation system in order to predict the interesting personalized items of users allowing to assist them in their researches and further enrich their profiles. In this recommendation, we provide users new research experiences.

Keywords: user profiles, topical ontology, contextual information, folksonomies, tags' clusters, data freshness, association rules, data recommendation

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Authors: Virupakshi Hiremata, Ratnakar M. Shet, Raghavendra Gunnaiah, Prashantha A.

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Muskmelon is a health-beneficial and refreshing dessert vegetable with a low shelf life. Mangalore melon, a genetic homeologue of muskmelon, has a shelf life of more than six months and is mostly used for culinary purposes. Understanding the genetics of shelf life, yield and yield-related traits and identification of markers linked to such traits is helpful in transfer of extended shelf life from Mangalore melon to the muskmelon through intra-specific hybridization. For QTL mapping, 276 F2 mapping population derived from the cross Arka Siri × SS-17 was genotyped with 40 polymorphic markers distributed across 12 chromosomes. The same population was also phenotyped for yield, shelf life and fruit quality traits. One major QTL (R2 >10) and fourteen minor QTLs (R2 <10) localized on four linkage groups, governing different traits were mapped in F2 mapping population developed from the intraspecific cross with a LOD > 5.5. The phenotypic varience explained by each locus varied from 3.63 to 10.97 %. One QTL was linked to shelf-life (qSHL-3-1), five QTLs were linked to TSS (qTSS-1-1, qTSS-3-3, qTSS-3-1, qTSS-3-2 and qTSS-1-2), two QTLs for flesh thickness (qFT-3-1, and qFT-3-2) and seven QTLs for fruit yield per vine (qFYV-3-1, qFYV-1-1, qFYV-3-1, qFYV1-1, qFYV-1-3, qFYV2-1 and qFYV6-1). QTL flanking markers may be used for marker assisted introgression of shelf life into muskmelon. Important QTL will be further fine-mapped for identifying candidate genes by QTLseq and RNAseq analysis. Fine-mapping of Important Quantitative Trait Loci (QTL) holds immense promise in elucidating the genetic basis of complex traits. Leveraging advanced techniques like QTLseq and RNA sequencing (RNA seq) is crucial for this endeavor. QTLseq combines next-generation sequencing with traditional QTL mapping, enabling precise identification of genomic regions associated with traits of interest. Through high-throughput sequencing, QTLseq provides a detailed map of genetic variations linked to phenotypic variations, facilitating targeted investigations. Moreover, RNA seq analysis offers a comprehensive view of gene expression patterns in response to specific traits or conditions. By comparing transcriptomes between contrasting phenotypes, RNA seq aids in pinpointing candidate genes underlying QTL regions. Integrating QTLseq with RNA seq allows for a multi-dimensional approach, coupling genetic variation with gene expression dynamics.

Keywords: QTL, shelf life, TSS, muskmelon and Mangalore melon

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Authors: Abdelaziz Fellah, Allaoua Maamir

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We propose a domain-independent merging-cluster filter approach complemented with a set of algorithms for identifying approximate duplicate entities efficiently and accurately within a single and across multiple data sources. The near-optimal merging-cluster filter (MCF) approach is based on the Monge-Elkan well-tuned algorithm and extended with an affine variant of the Smith-Waterman similarity measure. Then we present constant, variable, and function threshold algorithms that work conceptually in a divide-merge filtering fashion for detecting near duplicates as hierarchical clusters along with their corresponding representatives. The algorithms take recursive refinement approaches in the spirit of filtering, merging, and updating, cluster representatives to detect approximate duplicates at each level of the cluster tree. Experiments show a high effectiveness and accuracy of the MCF approach in detecting approximate duplicates by outperforming the seminal Monge-Elkan’s algorithm on several real-world benchmarks and generated datasets.

Keywords: data mining, data cleaning, approximate duplicates, near-duplicates detection, data mining applications and discovery

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Authors: Elene Zhuravliova, Tamar Barbakadze, Irina Kalandadze, Elnari Zaalishvili, Lali Shanshiashvili, David Mikeladze

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Background: Multiple sclerosis (MS) is an inflammatory, neurodegenerative disease, which is accompanied by demyelination and autoimmune response to myelin proteins. Among post-translational modifications, which mediate the modulation of inflammatory pathways during MS, methylation is the main one. The methylation of DNA, also amino acids lysine and arginine, occurs in the cell. It was found that decreased trans-methylation is associated with neuroinflammatory diseases. Therefore, abnormal regulation of the methyl cycle could induce demyelination through the action on PAD (peptidyl-arginine-deiminase) gene promoter. PAD takes part in protein citrullination and targets myelin basic protein (MBP), which is affected during demyelination. To determine whether MBP charge isomers are changing the methyl cycle, we have estimated the concentrations of methyl cycle metabolites in MBP-activated primary astrocytes and oligodendrocytes. For this purpose, the action of the citrullinated MBP- C8 and the most cationic MBP-C1 isomers on the primary cells were investigated. Methods: Primary oligodendrocyte and astrocyte cell cultures were prepared from whole brains of 2-day-old Wistar rats. The methyl cycle metabolites, including homocysteine, S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH), were estimated by HPLC analysis using fluorescence detection and prior derivatization. Results: We found that the action of MBP-C8 and MBP-C1 induces a decrease in the concentration of both methyl cycle metabolites, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), in astrocytes compared to the control cells. As for oligodendrocytes, the concentration of SAM was increased by the addition of MBP-C1, while MBP-C8 has no significant effect. As for SAH, its concentration was increased compared to the control cells by the action of both MBP-C1 and MBP-C8. A significant increase in homocysteine concentration was observed by the action of the MBP-C8 isomer in both oligodendrocytes and astrocytes. Conclusion: These data suggest that MBP charge isomers change the concentration of methyl cycle metabolites. MBP-C8 citrullinated isomer causes elevation of homocysteine in astrocytes and oligodendrocytes, which may be the reason for decreased astrocyte proliferation and increased oligodendrocyte cell death which takes place in neurodegenerative processes. Elevated homocysteine levels and subsequent abnormal regulation of methyl cycles in oligodendrocytes possibly change the methylation of DNA that activates PAD gene promoter and induces the synthesis of PAD, which in turn provokes the process of citrullination, which is the accompanying process of demyelination. Acknowledgment: This research was supported by the SRNSF Georgia RF17_534 grant.

Keywords: myelin basic protein, astrocytes, methyl cycle metabolites, homocysteine, oligodendrocytes

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Authors: Lei Qin

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As shared accommodation has become one of the most important market developments in the tourism industry, numerous contributions have emerged on travelers’ motivations to choose shared accommodation. A debated question, however, resides in the heterogeneity of travelers based on motivations. This paper aims to reconcile opposing perspectives by comparing motivation segmentation at two distinct phases of innovation adoption of this new hospitality option: (i) before the first travel – potential users showing interest (n=420) and (ii) after the first travel – users (n=420). Interestingly, we find that travelers (including pre-and-post adopters) have a stronger agreement in experiential motivations than practical motivations. However, the heterogeneity of motivations among travelers is significantly higher in users, increasing from two to six clusters, which means travelers cluster into more and distinct motivation groups after adoption. Rather than invalidating specific assumptions used in the literature in terms of motivation heterogeneity, this paper reconciles opposing findings by putting them along with one another in the process of innovation adoption. A subsequent tourists’ segmentation based on motivations were conducted according to their innovation adoption stages.

Keywords: motivation, pre-and-post adoption, shared accommodation, segmentation

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Authors: Noury Bakrim

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When dealing with motivation/arbitrariness, forming form (Forma Formans) and morphodynamics are to be grasped as relevant implications of enunciation/enactment, schematization within the specificity of language as sound/meaning articulation. Thus, the fact that a language is a form does not contradict stasis/dynamic enunciation (reflexivity vs double articulation). Moreover, some languages exemplify the role of the forming form, uttering, and schematization (roots in Semitic languages, the Chinese case). Beyond the evolutionary biosemiotic process (form/substance bifurcation, the split between realization/representation), non-isomorphism/asymmetry between linguistic form/norm and linguistic realization (phonetics for instance) opens up a new horizon problematizing the role of Brain – sensorimotor contribution in the continuous forming form. Therefore, we hypothesize biotization as both process/trace co-constructing motivation/forming form. Henceforth, referring to our findings concerning distribution and motivation patterns within Berber written texts (pulse based obstruents and nasal-lateral levels in poetry) and oral storytelling (consonant intensity clustering in quantitative and semantic/prosodic motivation), we understand consonant clustering, motivation and schematization as a complex phenomenon partaking in patterns of oral/written iconic prosody and reflexive metalinguistic representation opening the stable form. We focus our inquiry on both Amazigh and English clusters (/spl/, /spr/) and iconic consonant iteration in [gnunnuy] (to roll/tumble), [smummuy] (to moan sadly or crankily). For instance, the syllabic structures of /splaeʃ/ and /splaet/ imply an anamorphic representation of the state of the world: splash, impact on aquatic surfaces/splat impact on the ground. The pair has stridency and distribution as distinctive features which specify its phonetic realization (and a part of its meaning) /ʃ/ is [+ strident] and /t/ is [+ distributed] on the vocal tract. Schematization is then a process relating both physiology/code as an arthron vocal/bodily, vocal/practical shaping of the motor-articulatory system, leading to syntactic/semantic thematization (agent/patient roles in /spl/, /sm/ and other clusters or the tense uvular /qq/ at the initial position in Berber). Furthermore, the productivity of serial syllable sequencing in Berber points out different expressivity forms. We postulate two Components of motivated formalization: i) the process of memory paradigmatization relating to sequence modeling under sensorimotor/verbal specific categories (production/perception), ii) the process of phonotactic selection - prosodic unconscious/subconscious distribution by virtue of iconicity. Basing on multiple tests including a questionnaire, phonotactic/visual recognition and oral/written reproduction, we aim at patterning/conceptualizing consonant schematization and motivation among EFL and Amazigh (Berber) learners and speakers integrating biolinguistic hypotheses.

Keywords: consonant motivation and prosody, language and order of life, anamorphic representation, represented representation, biotization, sensori-motor and brain representation, form, formalization and schematization

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Authors: Lakmini Wijesooriya, Vicki Chalker, Jessica Day, Priyantha Perera, N. P. Sunil-Chandra

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M. pneumoniae has been identified as an etiology for exacerbation of asthma (EQA), although viruses play a major role in EOA. M. pneumoniae infection is treated empirically with macrolides, and its antibiotic sensitivity is not detected routinely. Characterization of the organism by genotyping and determination of macrolide resistance is important epidemiologically as it guides the empiric antibiotic treatment. To date, there is no such characterization of M. pneumoniae performed in Sri Lanka. The present study describes the characterization of M. pneumoniae detected from a child with EOA following a screening of 100 children with EOA. Of the hundred children with EOA, M. pneumoniae was identified only in one child by Real-Time polymerase chain reaction (PCR) test for identifying the community-acquired respiratory distress syndrome (CARDS) toxin nucleotide sequences. The M. pneumoniae identified from this patient underwent detection of macrolide resistance via conventional PCR, amplifying and sequencing the region of the 23S rDNA gene that contains single nucleotide polymorphisms that confer resistance. Genotyping of the isolate was performed via nested Multilocus Sequence Typing (MLST) in which eight (8) housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC, and adk) were amplified via nested PCR followed by gene sequencing and analysis. As per MLST analysis, the M. pneumoniae was identified as sequence type 14 (ST14), and no mutations that confer resistance were detected. Resistance to macrolides in M. pneumoniae is an increasing problem globally. Establishing surveillance systems is the key to informing local prescriptions. In the absence of local surveillance data, antibiotics are started empirically. If the relevant microbiological samples are not obtained before antibiotic therapy, as in most occasions in children, the course of antibiotic is completed without a microbiological diagnosis. This happens more frequently in therapy for M. pneumoniae which is treated with a macrolide in most patients. Hence, it is important to understand the macrolide sensitivity of M. pneumoniae in the setting. The M. pneumoniae detected in the present study was macrolide sensitive. Further studies are needed to examine a larger dataset in Sri Lanka to determine macrolide resistance levels to inform the use of macrolides in children with EOA. The MLST type varies in different geographical settings, and it also provides a clue to the existence of macrolide resistance. The present study enhances the database of the global distribution of different genotypes of M. pneumoniae as this is the first such characterization performed with the increased number of samples to determine macrolide resistance level in Sri Lanka. M. pneumoniae detected from a child with exacerbation of asthma in Sri Lanka was characterized as ST14 by MLST and no mutations that confer resistance were detected.

Keywords: mycoplasma pneumoniae, Sri Lanka, characterization, macrolide resistance

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Authors: Fayyaz Rasool, Naureen Aziz Qureshi, Shakeela Parveen

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Labeo rohita populations from five geographical locations from the hatchery and riverine system of Punjab-Pakistan were studied for the clustering on the basis of similarities and differences based on morphometric parameters within the species. Agglomerative Hierarchical Clustering (AHC) was done by using Pearson Correlation Coefficient and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) as Agglomeration method by XLSTAT 2012 version 1.02. A dendrogram with the data on the morphometrics of the representative samples of each site divided the populations of Labeo rohita in to five major clusters or classes. The variance decomposition for the optimal classification values remained as 19.24% for within class variation, while 80.76% for the between class differences. The representative central objects of the each class, the distances between the class centroids and also the distance between the central objects of the classes were generated by the analysis. A measurable distinction between the classes of the populations of the Labeo rohita was indicated in this study which determined the impacts of changing environment and other possible factors influencing the variation level among the populations of the same species.

Keywords: AHC, Labeo rohita, hatchery, riverine, morphometric

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Authors: Gail Louw, Helena Boshoff, Taeksun Song, Clifton Barry

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Drug resistance in Mycobacterium tuberculosis is primarily attributed to mutations in target genes. These mutations incur a fitness cost and result in bacterial generations that are less fit, which subsequently acquire compensatory mutations to restore fitness. We hypothesize that mutations in specific drug target genes influence bacterial metabolism and cellular function, which affects its ability to develop subsequent resistance to additional agents. We aim to determine whether the sequential acquisition of drug resistance and specific mutations in a well-defined clinical M. tuberculosis strain promotes or limits the development of additional resistance. In vitro mutants resistant to pretomanid, linezolid, moxifloxacin, rifampicin and kanamycin were generated from a pan-susceptible clinical strain from the Beijing lineage. The resistant phenotypes to the anti-TB agents were confirmed by the broth microdilution assay and genetic mutations were identified by targeted gene sequencing. Growth of mono-resistant mutants was done in enriched medium for 14 days to assess in vitro fitness. Double resistant mutants were generated against anti-TB drug combinations at concentrations 5x and 10x the minimum inhibitory concentration. Subsequently, mutation frequencies for these anti-TB drugs in the different mono-resistant backgrounds were determined. The initial level of resistance and the mutation frequencies observed for the mono-resistant mutants were comparable to those previously reported. Targeted gene sequencing revealed the presence of known and clinically relevant mutations in the mutants resistant to linezolid, rifampicin, kanamycin and moxifloxacin. Significant growth defects were observed for mutants grown under in vitro conditions compared to the sensitive progenitor. Mutation frequencies determination in the mono-resistant mutants revealed a significant increase in mutation frequency against rifampicin and kanamycin, but a significant decrease in mutation frequency against linezolid and sutezolid. This suggests that these mono-resistant mutants are more prone to develop resistance to rifampicin and kanamycin, but less prone to develop resistance against linezolid and sutezolid. Even though kanamycin and linezolid both inhibit protein synthesis, these compounds target different subunits of the ribosome, thereby leading to different outcomes in terms of fitness in the mutants with impaired cellular function. These observations showed that oxazolidinone treatment is instrumental in limiting the development of multi-drug resistance in M. tuberculosis in vitro.

Keywords: oxazolidinones, mutations, resistance, tuberculosis

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Authors: Boutheina Ben Abdelmoumen Mardassi, Salim Chibani, Safa Boujemaa, Amaury Vaysse, Julien Guglielmini, Elhem Yacoub

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Background and aim: Mycoplasma hominis (MH) is a pathogenic bacterium belonging to the Mollicutes class. It causes a wide range of gynecological infections and infertility among adults. Recently, we have explored for the first time the phylodistribution of Tunisian M. hominis clinical strains using an expanded MLST. We have demonstrated their distinction into two pure lineages, which each corresponding to a specific pathotype: genital infections and infertility. The aim of this project is to gain further insight into the evolutionary dynamics and the specific genetic factors that distinguish MH pathotypes Methods: Whole genome sequencing of Mycoplasma hominis clinical strains was performed using illumina Miseq. Denovo assembly was performed using a publicly available in-house pipeline. We used prokka to annotate the genomes, panaroo to generate the gene presence matrix and Jolytree to establish the phylogenetic tree. We used treeWAS to identify genetic loci associated with the pathothype of interest from the presence matrix and phylogenetic tree. Results: Our results revealed a clear categorization of the 62 MH clinical strains into two distinct genetic lineages, with each corresponding to a specific pathotype.; gynecological infections and infertility[AV1] . Genome annotation showed that GC content is ranging between 26 and 27%, which is a known characteristic of Mycoplasma genome. Housekeeping genes belonging to the core genome are highly conserved among our strains. TreeWas identified 4 virulence genes associated with the pathotype gynecological infection. encoding for asparagine--tRNA ligase, restriction endonuclease subunit S, Eco47II restriction endonuclease, and transcription regulator XRE (involved in tolerance to oxidative stress). Five genes have been identified that have a statistical association with infertility, tow lipoprotein, one hypothetical protein, a glycosyl transferase involved in capsule synthesis, and pyruvate kinase involved in biofilm formation. All strains harbored an efflux pomp that belongs to the family of multidrug resistance ABC transporter, which confers resistance to a wide range of antibiotics. Indeed many adhesion factors and lipoproteins (p120, p120', p60, p80, Vaa) have been checked and confirmed in our strains with a relatively 99 % to 96 % conserved domain and hypervariable domain that represent 1 to 4 % of the reference sequence extracted from gene bank. Conclusion: In summary, this study led to the identification of specific genetic loci associated with distinct pathotypes in M hominis.

Keywords: mycoplasma hominis, infertility, gynecological infections, virulence genes, antibiotic resistance

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