Search results for: genome rearrangement distance

Authors: Vinod Kumar Gupta, Narendrakumar M. Chaudhari, Suchismitha Iskepalli, Chitra Dutta

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Background-The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference draft genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium. Results-The analysis reveals the exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from the human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. The pan-genome for Prevotella remains “open”. Distribution of various functional COG categories differs appreciably among the habitat-specific genes, within Prevotella pan-genome and between the GIT-derived Bacteroides and Prevotella. The skin and GIT isolates of Prevotella are enriched in singletons involved in Signal transduction mechanisms, while the UGT and oral isolates show higher representation of the Defense mechanisms category. No niche-specific variations could be observed in the distribution of KEGG pathways. Conclusion-Prevotella may have developed distinct genetic strategies for adaptation to different anatomical habitats through selective, niche-specific acquisition and elimination of suitable gene-families. In addition, individual microorganisms tend to develop their own distinctive adaptive stratagems through large repertoires of singletons. Such in situ, habitat-driven refurbishment of the genetic makeup can impart substantial intra-lineage genome diversity within the microbes without perturbing their general taxonomic heritage.

Keywords: body niche adaptation, human microbiome, pangenome, Prevotella

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Authors: Lei Qin

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Culture has long been recognized as a possible reason to influence travelers’ decisions, which explains why travelers in different countries make distinct decisions. Cultural distance is a concept illustrating how much difference there is between travelers’ home culture and that of the destination, but the research in distinguishing short-and-long haul travel destinations is limited. This study explored the research gap by examining the impact of cultural distance on Chinese travelers’ intentions to visit short-haul and long-haul destinations, respectively. Six cultural distance measurements, including five measurements calculated from secondary database (Kogut & Singh, Developed Kogut & Singh, Euclidean distance Index (EDI), world value survey index (WVS), social axioms measurement (SAM)) and perceived cultural distance (PCD) collected from the primary survey. Of the six measurements, culture distance has the opposite impact on Chinese outbound travelers’ intentions in the short-haul and long haul. For short-haul travel, travelers’ intentions for traveling can be positive influenced by cultural distance; a possible reason is that travelers’ novelty-seeking satisfaction is greater than the strangeness obtained from overseas regions. For long-haul travel, travelers’ intentions for traveling can be negative influenced by cultural distance, a possible explanation is that travelers’ uncertainty, risk, and language concerns of farther destinations.

Keywords: cultural distance, intention, outbound travel, short-long haul

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Authors: Adel M. Zakri, Mohammed A. Al-Saleh, Judith. K. Brown, Ali M. Idris

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Betasatellites are small circular single stranded DNA molecules found associated with begomoviruses on field symptomatic plants. Their genome size is about half that of the helper begomovirus, ranging between 1.3 and 1.4 kb. The helper begomoviruses are usually members of the family Geminiviridae. Okra leaves showing vein thickening were collected from okra plants growing in Jazan, Saudi Arabia. Total DNA was extracted from leaves and used as a template to amplify circular DNA using rolling circle amplification (RCA) technology. Products were digested with PstI to linearize the helper viral genome(s), and associated DNA satellite(s), yielding a 2.8kbp and 1.4kbp fragment, respectively. The linearized fragments were cloned into the pGEM-5Zf (+) vector and subjected to DNA sequencing. The 2.8 kb fragment was identified as Cotton leaf curl Gezira virus genome, at 2780bp, an isolate closely related to strains reported previously from Saudi Arabia. A clone obtained from the 1.4 kb fragments he 1.4kb was blasted to GeneBank database found to be a betasatellite. The genome of betasatellite was 1357-bp in size. It was found to be a recombinant containing one fragment (877-bp) that shared 91% nt identity with Cotton leaf curl Gezira betasatellite [KM279620], and a smaller fragment [133--bp) that shared 86% nt identity with Tomato leaf curl Sudan virus [JX483708]. This satellite is thus a recombinant between a malvaceous-infecting satellite and a solanaceous-infecting begomovirus.

Keywords: begomovirus, betasatellites, cotton leaf curl Gezira virus, okra plants

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Authors: Leila Goosen, Toppie N. Mukasa-Lwanga

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The purpose of this paper relates to exploring academics’ use of distance education technologies for empowerment and equity in an Information Technology environment. Literature was studied on academics’ technology use towards effective teaching and meaningful learning in a distance education Information Technology environment. Main arguments presented center on formulating and situating significant concepts within an appropriate theoretical and conceptual framework, including those related to distance education, throughput and other measures of academic efficiency. The research design, sampling, data collection instrument and the validity and reliability thereof, as well as the data analysis method used is described. The paper discusses results related to academics’ use of technology towards effective teaching and meaningful learning in a distance education Information Technology environment. Conclusions are finally presented on the way in which this paper makes a significant and original contribution regarding academics’ use of technology towards effective teaching and meaningful learning in a distance education Information Technology environment.

Keywords: distance, education, technologies, Information Technology Environment

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Authors: Boris Melnikov, Ye Zhang, Dmitrii Chaikovskii

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We continue to consider one of the cybernetic methods in computational biology related to the study of DNA chains. Namely, we are considering the problem of reconstructing the not fully filled distance matrix of DNA chains. When applied in a programming context, it is revealed that with a modern computer of average capabilities, creating even a small-sized distance matrix for mitochondrial DNA sequences is quite time-consuming with standard algorithms. As the size of the matrix grows larger, the computational effort required increases significantly, potentially spanning several weeks to months of non-stop computer processing. Hence, calculating the distance matrix on conventional computers is hardly feasible, and supercomputers are usually not available. Therefore, we started publishing our variants of the algorithms for calculating the distance between two DNA chains; then, we published algorithms for restoring partially filled matrices, i.e., the inverse problem of matrix processing. In this paper, we propose an algorithm for restoring the distance matrix for DNA chains, and the primary focus is on enhancing the algorithms that shape the greedy function within the branches and boundaries method framework.

Keywords: DNA chains, distance matrix, optimization problem, restoring algorithm, greedy algorithm, heuristics

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Authors: Sayed-Mahdi Hashemi-Dehkordi, Ian Baker

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This paper investigates the benefits of implementing distance learning in training courses for the oil and gas industries to reduce lean. Due to the remote locations of many oil and gas operations, scheduling and organizing in-person training classes for employees in these sectors is challenging. Furthermore, considering that employees often work in periodic shifts such as day, night, and resting periods, arranging in-class training courses requires significant time and transportation. To explore the effectiveness of distance learning compared to in-class learning, a set of questionnaires was administered to employees of a far on-shore refinery unit in Iran, where both in-class and distance classes were conducted. The survey results revealed that over 72% of the participants agreed that distance learning saved them a significant amount of time by rating it 4 to 5 points out of 5 on a Likert scale. Additionally, nearly 67% of the participants acknowledged that distance learning considerably reduced transportation requirements, while approximately 64% agreed that it helped in resolving scheduling issues. Introducing and encouraging the use of distance learning in the training environments of oil and gas industries can lead to notable time and transportation savings for employees, ultimately reducing lean in a positive manner.

Keywords: distance learning, in-class learning, lean, oil and gas, scheduling, time, training programs, transportation

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Authors: Abu S. Mustafa, Mohammad W. Khan, Faraz Shaheed Khan, Nazima Habibi

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Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13.

Keywords: brucella, bioinformatics, comparative genomics, whole genome sequencing

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Authors: Guesh Mulaw, Haile Beruhulay, Anteneh Tesfaye, Tesfaye Sisay Diriba Muleta

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Probiotics are live microorganisms that, when administered in adequate amounts, promote the health of a consumer. The present work aims to study the whole genome sequence of probiotic strains of lactic acid bacteria (LAB) isolated from traditional Ethiopian fermented kocho for bacteriocin production and to evaluate their probiotic properties. LAB were isolated from traditionally fermented kocho samples and characterized following standard methods. Accordingly, a total of 150 LAB were isolated, of which 7 (4.67%) isolates showed 50.52-74.05% and 33.33-62.40% survival rates at pH 2 for 3 and 6 h, respectively. The 7 acid-tolerant isolates were also tolerated 0.3% bile salt for 24 h with 88.96 to 98.10% survival. The acid and bile salt-tolerant LAB isolates also inhibited some reference foodborne pathogenic bacteria to varying degrees. All 7 acid- and bile salt-tolerant isolates were susceptible to ampicillin, tetracycline and erythromycin. However, the potent isolates showed remarkable resistance to kanamycin. Likewise, four of the 7 isolates were resistant to streptomycin, but three of the 7 isolates were sensitive to streptomycin. The identification of the seven selected probiotic LAB isolates and their genetic relatedness was performed based on whole-genome sequence comparisons. Consequently, these isolates belonged to Lactobacillus species, including 6 Lb. plantarum, 1 Lb. brevis. Among the 7 potential probiotic LAB strains, BAGEL predicted 2 bacteriocin for class II in the genome of 7 strains. The 7 Lactobacillus strains were found to be potentially useful for producing functional products and could be suitable probiotic candidates for food processing industries

Keywords: ferneted foods, kocho, probiotics, lactic acid bacteria

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Authors: Yan Wang, Yasushi Asami, Yukio Sadahiro

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In urban area, several landmarks may affect housing price and rents, hedonic analysis should employ distance variables corresponding to each landmarks. Unfortunately, the effects of distances to landmarks on housing prices are generally not consistent with the true price. These distance variables may cause magnitude error in regression, pointing a problem of spatial multicollinearity. In this paper, we provided some approaches for getting the samples with less bias and method on locating the specific sampling area to avoid the multicollinerity problem in two specific landmarks case.

Keywords: landmarks, hedonic regression, distance variables, collinearity, multicollinerity

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Authors: Yan Wang, Yasushi Asami, Yukio Sadahiro

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In urban context, urban nodes such as amenity or hazard will certainly affect house price, while classic hedonic analysis will employ distance variables measured from each urban nodes. However, effects from distances to facilities on house prices generally do not represent the true price of the property. Distance variables measured on the same surface are suffering a problem called multicollinearity, which is usually presented as magnitude variance and mean value in regression, errors caused by instability. In this paper, we provided a theoretical framework to identify and gather the data with less bias, and also provided specific sampling method on locating the sample region to avoid the spatial multicollinerity problem in three distance variable’s case.

Keywords: hedonic regression, urban node, distance variables, multicollinerity, collinearity

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Authors: Edu Marcelina, Sule Sheidu A., Nsor Eunice

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As open and distance education is gradually becoming an acceptable means of solving the problem of access in higher education, quality has now become one of the main concerns among institutions and stakeholders of open and distance learning (ODL) and the education sector in general. This study assessed the challenges of academic quality in the open and distance learning (ODL) education in Nigeria using Distance Learning Institute (DLI), University of Lagos and National Open University of Nigeria as a case. In carrying out the study, a descriptive survey research design was employed. A researcher-designed and validated questionnaire was used to elicit responses that translated to the quantitative data for this study. The sample comprised 665 students of the Distance Learning Institute (DLI), and National Open University of Nigeria (NOUN), carefully selected through the method of simple random sampling. Data collected from the study were analyzed using Chi-Square (X2) at 0.05 Level of significance. The results of the analysis revealed that; the use of ICT tools is a factor in ensuring quality in the Open and Distance Learning (ODL) operations; the quality of the materials made available to ODL students will determine the quality of education that will be received by the students; and the time scheduled for students for self-study, online lecturing/interaction and face to face study and the quality of education in Open and Distance Learning Institutions has a lot of impact on the quality of education the students receive. Based on the findings, a number of recommendations were made.

Keywords: open and distance learning, quality, ICT, face-to-face interaction

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Authors: Atefeh Abedini, Pegah Soltani, Arda Kiani

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Background: Sarcoidosis and Tuberculosis are both considered granulomatous chronic diseases with some similar pulmonary and extra-pulmonary manifestations. It is hypothesized that given these morphological similarities, the genome of mycobacterium could have an impact on the development of Sarcoidosis. Identifying the potential correlation of these diseases may assist in the management of sarcoidosis. Herein, we aimed to inspect the lymph node biopsy of sarcoidosis patients for the existence of the HSP-65 mycobacterium DNA sequence. Methods: This cross-sectional survey was conducted on 1188 Sarcoidosis patients without active/latent tuberculosis infection who were diagnosed in Masih Daneshvari Hospital in Tehran, Iran, from January 2020 to January 2022. Trans-bronchial needle aspiration (TBNA) was performed due to bilateral hilar lymphadenopathy to take a specimen. Results: The under-evaluated patients were mainly women (N=815 (68.6%)), none-smoker (N=1016 (85.5%)), and middle-aged (50.1 (SD=4.22)) with average angiotensin-converting enzyme (ACE) index of 75.6 (SD=6.42). Dyslipidemias (n=314 (26.4%), Hypertension (n=295 (24.8%)), Diabetes mellitus (n=131 (11.0%)), and chronic heart diseases (n=97 (8.2%)) had the highest prevalence between comorbidities. Skin lesions (n= 655 (55.1%)), ophthalmic (n=341 (28.7%)), and cardiac involvement (n=229 (19.3%)) were obtained as the most common extra-pulmonary characteristics of the patients. Amongst 1188 enrolled patients who were not afflicted with Mycobacterium tuberculosis based on smear/culture essay, clinical symptoms, and Chest x-ray screening, 121 (10.2%) cases had detectable amplified DNA for Mycobacterium Tuberculosis extracted from mediastinal lung lymph nodes. Conclusion: In this survey, the mycobacterium genome was detected in almost 1 per 10 case biopsies of sarcoidosis. The remarkable number of cases (n=1188) evaluated in this study was the strength of this study which supported the hypothesis regarding sarcoidosis and mycobacterium genome correlation. Further investigation, such as case-control surveys, is required to better clarify this association.

Keywords: mycobacterium tuberculosis, sarcoidosis, genome, DNA, trans-bronchial needle aspiration

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Authors: Joshua Bradley, Matthew Buns

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This study aimed to identify the effect of concurrent nutritional supplementation on soccer performance as players ingested either carbohydrate CHO (52 g of Cytocarb Maltodextrin) or a combined carbohydrate and protein PRO (Muscle Milk Pro Series 17g CHO + 50 g PRO liquid) supplement. Twelve male, junior college soccer players (age: 18 ± 6 years, wt. 73.3 ± 8.6 kg) completed three trials wearing global positioning systems (GPS) to measure total running distance and sprinting distance during soccer simulation games. The first match simulation was a baseline match with no supplementation. One hour prior to the second match, simulation players were randomly assigned to one of two supplemental groups CHO or CHO + PRO. A repeated measures ANOVA with a Greenhouse-Geisser correction revealed a statistically significant increase in the total distance run for the CHO supplementation group in comparison to the CHO + PRO group (10.19 ± .200 km vs. 9.77± .194km, p = .035). Although the total running distance was meaningfully influenced by the supplementation, the pattern of response for total sprinting distance was not influenced by supplementation. There was a decline in sprinting distance and total running distance from first half to second half, both for the control (M = -0.01 km, SD = 0.17) and CHO supplementation group (-0.04 km, SD = .19), although these differences were not statistically meaningful. There was a positive correlation between sprinting distance and total distance, which was statistically significant (r = -.514, n = 36, p = .01) In conclusion, supplementation influenced the pattern of activity and demonstrated between-trial differences.

Keywords: GPS, nutrition, simulation, supplementation

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Authors: Petchpong Mayukhachot

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The purposes of this research were (1) to develop a distance training package on topic of Production of Handbook and Report writing for innovative learning and teaching for Vocational Teachers of Office of The Vocational Education Commission; (2) to study the effects of using the distance training package on topic Production of Handbook and Report writing for innovative learning and teaching for Vocational Teachers of Office of The Vocational Education Commission. and (3) to study the samples’ opinion on the distance training package on topic Production of Handbook and Report writing for innovative learning and teaching for Vocational Teachers of Office of The Vocational Education Commission Research and Development was used in this research. The purposive sampling group of this research was 39 Vocational Teachers of Office of The Vocational Education Commission. Instruments were; (1) the distance training package, (2) achievement tests on understanding of Production of Handbook and Report writing for innovative learning and teaching and learning activities to develop practical skills, and (3) a questionnaire for sample’s opinion on the distance training package. Percent, Mean, Standard Deviation, the E1/E2 efficiency index and t-test were used for data analysis. The findings of the research were as follows: (1) The efficiency of the distance training package was established as 80.90 / 81.90. The distance training package composed of the distance training package document and a manual for the distance training package. The distance training package document consisted of the name of the distance training package, direction for studying the distance training package, content’s structure, concepts, objectives, and activities after studying the distance training package. The manual for the distance training package consisted of the explanation of the distance training package and objectives, direction for using the distance training package, training schedule, documents as a manual of speech, and evaluations. (2) The effects of using the distance training package on topic Production of Handbook and Report writing for innovative learning and teaching for Vocational Teachers of Office of The Vocational Education Commission were the posttest average scores of achievement on understanding of Technology and Occupations teaching for development of critical thinking of the sample group were higher than the pretest average scores. (3) The most appropriate of trainees’ opinion were contents of the distance training package is beneficial to performance. That can be utilized in Teaching or operations. Due to the content of the two units is consistent and activities assigned to the appropriate content.

Keywords: distance training package, handbook writing for innovative learning, teaching report writing for innovative learning, teaching

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Authors: E. C. du Plessis

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Teaching practice is a major component of teacher education and the preparation of teachers for the real-life classroom throughout the world. Learning is seen as a constructive process, whether it is classroom based or takes place by means of distance education. Blending theory and practice with effective education in distance context as part of situated learning is crucial. Therefore, the aim of this research was to determine distance education student teachers' classroom readiness on completion of the teaching practice modules of their Postgraduate Certificate in Education (PGCE) course. A qualitative research approach was used for the collection, analysis, and interpretation of data. A total of 15 student teachers enrolled at the College of Education of an ODL (Open and Distance Learning) institution were selected and volunteered to participate in the research. In the light of the results of the research, it is recommended that more attention is given to the interaction between mentor teachers, academic lecturers, and student teachers, as well as the expectations and responsibilities of these role-players.

Keywords: communities of practice, mentor teachers, open and distance learning, practicum, professional development, student teachers, teaching practice

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Authors: Daniel Ecler

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This paper aims to compare the data obtained using semi-structured questionnaires and find some connections between them, which could help to understand what factors affect the perception of the advantages and disadvantages of distance learning compared to conventional education. The data collected came from respondents from Czech and Chinese university students, and expectations were such that the different cultural environments from which the two groups come would have an impact on different experiences of distance education. With the help of variation-finding comparison, it turned out that Chinese students did not have such difficulties with the transition to distance learning as students from the Czech Republic, as most of them came into contact with some form of distance education in the past. In addition, it has also been shown that Chinese students use modern technology to a much greater extent, which has also made it easier for them to become accustomed to another form of teaching. In conclusion, Chinese students have greater preconditions for easier management of distance learning, while Czech students prefer more personal contact, and thus full-time teaching. It is obvious that both approaches have their pros and cons; now, it is necessary to find out how to use them for maximum efficiency of the educational process.

Keywords: Chinese college students, cultural background, Czech college students, distance learning, full-time teaching

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Authors: Muhammad Afzal Malik

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Traditional Learning & Distance based learning are the two systems prevailing in Pakistan. These systems affect the level of education standard. The purpose of this study was to compare the traditional classroom learning and distance learning in Pakistan: (a) To explore the effectiveness of the traditional to Distance learning in Pakistan; (b) To identify the factors that affect traditional and distance learning. This review found that, on average, students in traditional classroom conditions performed better than those receiving education in and distance learning. The difference between student outcomes for traditional Classroom and distance learning classes —measured as the difference between treatment and control means, divided by the pooled standard deviation— was larger in those studies contrasting conditions that blended elements of online and face-to-face instruction with conditions taught entirely face-to-face. This research was conducted to highlight the impact of distance learning education system on education standard. The education standards were institutional support, course development, learning process, student support, faculty support, evaluation and assessment. A well developed questionnaire was administered and distributed among 26 faculty members of GCET, H-9 and Virtual University of Pakistan from each. Data was analyzed through correlation and regression analysis. Results confirmed that there is a significant relationship and impact of DLE system on education standards. This will also provide baseline for future research. It will add value to the existing body of knowledge.

Keywords: distance learning education, higher education, education standards, student performance

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Authors: Agostinho Antunes

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The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles.

Keywords: adaptation, animals, evolution, genomics

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Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.

Keywords: genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation

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Authors: Mohammad Ahangari

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Schizophrenia is a psychiatric disorder with symptoms that include cognitive deficits and nicotine has been suggested to have an effect on cognition. In recent years, the advents of Genome-Wide Association Studies(GWAS) has evolved our understanding about the genetic causes of complex disorders such as schizophrenia and studying the role of genome-wide significant genes could potentially lead to the development of new therapeutic agents for treatment of cognitive deficits in schizophrenia. The current study identified six Single Nucleotide Polymorphisms (SNP) from schizophrenia and smoking GWAS that are located on or in close proximity to the nicotinic receptor gene cluster (CHRN) and studied their association with cognition in an Irish sample of 1297 cases and controls using linear regression analysis. Further on, the interaction between CHRN gene cluster and Dopamine receptor D2 gene (DRD2) during working memory was investigated. The effect of these polymorphisms on nicotinic and dopaminergic neurotransmission, which is disrupted in schizophrenia, have been characterized in terms of their effects on memory, attention, social cognition and IQ as measured by a neuropsychological test battery and significant effects in two polymorphisms were found across global IQ domain of the test battery.

Keywords: cognition, dopamine, GWAS, nicotine, schizophrenia, SNPs

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Authors: Jamal Laaouine, Mohammed Elhassani Charkani

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Let p be a prime and let b be an integer. MDS b-symbol codes are a direct generalization of MDS codes. The γ-constacyclic codes of length pˢ over the finite commutative chain ring Fₚm [u]/ < u² > had been classified into four distinct types, where is a nonzero element of the field Fₚm. Let C₃ be a code of Type 3. In this paper, we obtain the b-symbol distance db(C₃) of the code C₃. Using this result, necessary and sufficient conditions under which C₃ is an MDS b-symbol code are given.

Keywords: constacyclic code, repeated-root code, maximum distance separable, MDS codes, b-symbol distance, finite chain rings

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Fumio Kasai, Noriko Hirayama, Jorge Pereira, Azusa Ohtani, Masashi Iemura, Malcolm A. Ferguson Smith, Arihiro Kohara

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The VERO cell line was established in 1962 from normal tissue of an African green monkey, Chlorocebus aethiops (2n=60), and has been commonly used worldwide for screening for toxins or as a cell substrate for the production of viral vaccines. The VERO genome was sequenced in 2014; however, its cytogenetic features have not been fully characterized as it contains several chromosome abnormalities and different karyotypes coexist in the cell line. In this study, the VERO cell line (JCRB0111) was compared with one of the sublines. In contrast to 59 chromosomes as the modal chromosome number in the VERO cell line, the subline had two peaks of 56 and 58 chromosomes. M-FISH analysis using human probes revealed that the VERO cell line was characterized by a translocation t(2;25) found in all metaphases, which was absent in the subline. Different abnormalities detected only in the subline show that the cell line is heterogeneous, indicating that the subline has the potential to change its genomic characteristics during cell culture. The various alterations in the two independent lineages suggest that genomic changes in both VERO cells can be accounted for by progressive rearrangements during their evolution in culture. Both t(5;X) and t(8;14) observed in all metaphases of the two cell lines might have a key role in VERO cells and could be used as genetic markers to identify VERO cells. The flow karyotype shows distinct differences from normal. Further analysis of sorted abnormal chromosomes may uncover other characteristics of VERO cells. Because of the absence of STR data, cytogenetic data are important in characterizing animal cell lines and can be an indicator of their quality control.

Keywords: VERO, cell culture passage, chromosome rearrangement, heterogeneous cells

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Authors: A. Abdul-Ameer

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The equations governing the distance, pressure- volume flow relationships for the pipeline transportation of gaseous mixtures, are considered. A derivation based on differential calculus, for an element of this system model, is addressed. Solutions, yielding the input- output response following pressure changes, are reviewed. The technical problems associated with these analytical results are identified. Procedures resolving these difficulties providing thereby an attractive, simple, analysis route are outlined. Computed responses, validating thereby calculated predictions, are presented.

Keywords: pressure, distance, flow, dissipation, models

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Authors: Chen Chan Wei

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The purpose of this study was to investigate the impact of swim 1500m, 10000m run, VO2 max, and body fat on Olympic distance triathlon competition performance. The subjects were thirteen college triathletes with endurance training, with an average age, height and weight of 20.61±1.04 years (mean ± SD), 171.76±8.54 cm and 65.32±8.14 kg respectively. All subjects were required to take the tests of swim 1500m, run 10000m, VO2 max, body fat, and participate in the Olympic distance triathlon competition. First, the swim 1500m test was taken in the standardized 50m pool, with a depth of 2m, and the 10000m run test on the standardized 400m track. After three days, VO2 max was tested with the MetaMax 3B and body fat was measured with the DEXA machine. After two weeks, all 13 subjects joined the Olympic distance triathlon competition at the 2016 New Taipei City Asian Cup. The relationships between swim 1500m, 10000m run, VO2 max, body fat test, and Olympic distance triathlon competition performance were evaluated using Pearson's product-moment correlation. The results show that 10000m run and body fat had a significant positive correlation with Olympic distance triathlon performance (r=.830, .768), but VO2 max has a significant negative correlation with Olympic distance triathlon performance (r=-.735). In conclusion, for improved non-draft Olympic distance triathlon performance, triathletes should focus on running than swimming training and can be measure VO2 max to prediction triathlon performance. Also, managing body fat can improve Olympic distance triathlon performance. In addition, swimming performance was not significantly correlated to Olympic distance triathlon performance, possibly because the 2016 New Taipei City Asian Cup age group was not a drafting competition. The swimming race is the shortest component of Olympic distance triathlons. Therefore, in a non-draft competition, swimming ability is not significantly correlated with overall performance.

Keywords: triathletes, olympic, non-drafting, correlation

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Authors: Bogdan Walek, Vladimir Bradac, Radim Farana

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Distance learning systems offer useful methods of learning and usually contain final course test or another form of test. The paper proposes web application for evaluating tests using expert system in distance learning systems. Proposed web application is appropriate for didactic tests or tests with results for subsequent studying follow-up courses. Web application works with test questions and uses expert system and LFLC tool for test evaluation. After test evaluation the results are visualized and shown to student.

Keywords: distance learning, test, uncertainty, fuzzy, expert system, student

Procedia PDF Downloads 486

Authors: Guna Raj Dhungana, Roshan Nepal, Apshara Parajuli, , Archana Maharjan, Shyam K. Mishra, Pramod Aryal, Rajani Malla

Abstract:

Introduction: Klebsiella pneumoniae is a well-known opportunistic human pathogen, primarily causing healthcare-associated infections. The global emergence of carbapenemase-producing K. pneumoniaeis a major public health burden, which is often extensively multidrug resistant.Thus, because of the difficulty to treat these ‘superbug’ and menace and some term as ‘apocalypse’ of post antibiotics era, an alternative approach to controlling this pathogen is prudent and one of the approaches is phage mediated control and/or treatment. Objective: In this study, we aimed to isolate novel bacteriophage against carbapenemase-producing K. pneumoniaeand characterize for potential use inphage therapy. Material and Methods: Twenty lytic phages were isolated from river water using double layer agar assay and purified. Biological features, physiochemical characters, burst size, host specificity and activity spectrum of phages were determined. One most potent phage: Phage TU_Kle10O was selected and characterized by electron microscopy. Whole genome sequences of the phage were analyzed for presence/absence of virulent factors, and other lysin genes. Results: Novel phage TU_Kle10O showed multiple host range within own genus and did not induce any BIM up to 5th generation of host’s life cycle. Electron microscopy confirmed that the phage was tailed and belonged to Caudovirales family. Next generation sequencing revealed its genome to be 166.2 Kb. bioinformatical analysis further confirmed that the phage genome ‘did not’ contain any ‘bacterial genes’ within phage genome, which ruled out the concern for transfer of virulent genes. Specific 'lysin’ enzyme was identified phages which could be used as 'antibiotics'. Conclusion: Extensively multidrug resistant bacteria like carbapenemase-producing K. pneumoniaecould be treated efficiently by phages.Absence of ‘virulent’ genes of bacterial origin and presence of lysin proteins within phage genome makes phages an excellent candidate for therapeutics.

Keywords: bacteriophage, Klebsiella pneumoniae, MDR, phage therapy, carbapenemase,

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Authors: Eleni Giouli

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Distance learning provides a flexible approach to education, enabling busy learners to complete their coursework at their own pace, on their own schedule, and from a convenient location. This flexibility combined with a series of other issues; make the benefits of lifelong distance learning numerous. The purpose of the paper is to investigate whether distance education can contribute to the improvement of adult skills in Greece, highlighting in this way the necessity of the lifelong distance learning. To investigate this goal, a questionnaire is constructed and analyzed based on responses from 3,016 attendees of lifelong distance learning programs in the e-learning of the National and Kapodistrian University of Athens in Greece. In order to do so, a series of relationships is examined including the effects of a) the gender, b) the previous educational level, c) the current employment status, and d) the method used in the distance learning program, on the development of new general, technical, administrative, social, cultural, entrepreneurial and green skills. The basic conclusions that emerge after using a binary logistic framework are that the following factors are critical in order to develop new skills: the gender, the education level and the educational method used in the lifelong distance learning program. The skills more significantly affected by those factors are the acquiring new skills in general, as well as acquiring general, language and cultural, entrepreneurial and green skills, while for technical and social skills only gender and educational method play a crucial role. Moreover, routine skills and social skills are not affected by the four factors included in the analysis.

Keywords: adult skills, distance learning, education, lifelong learning

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

Abstract:

The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

Procedia PDF Downloads 388