Search results for: sequencing strategies

Authors: Kanokrat Kunasaraphan

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The purpose of the study was to identify whether English language learning strategies commonly used by the first year students at International College, Suan Sunandha Rajabhat University include six direct and indirect strategies. The study served to explore whether there was a difference in these students’ use of six direct and indirect English learning strategies between the different levels of their English proficiency. The questionnaire used as a research instrument was comprised of two parts: General information of participants and the Strategy Inventory for Language Learning (SILL). The researcher employed descriptive statistics and one-way ANOVA (F-test) to analyze the data. The results of the analysis revealed that English learning strategies commonly used by the first year students include six direct and indirect strategies, including differences in strategy use of the students with different levels of English proficiency. Recommendations for future research include the study of language learning strategy use with other research methods focusing on other languages, specific language skills, and/or the relationship of language learning strategy use and other factors in other programs and/or institutions.

Keywords: English learning strategies, direct strategies, indirect strategies, proficiency level

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Authors: Michal Levy

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Despite the emotional impact students' misbehavior and aggression has on teacher's emotional wellbeing, teachers frequently use suppressive strategies in the classroom, which maintain a discordance between felt and expressed emotions. The current study sought to gain a deeper insight into teachers' utilization of discordant emotional labor strategies (i.e., expressive suppression, surface acting and emotional dissonance) and their motives to using these strategies in student aggression. A qualitative study was conducted on 16 special education Jewish Israeli teachers. Thematic analysis of the in-depth semi-structured interviews revealed novice teachers were inclined to use expressive suppression, while experienced teachers used emotional dissonance. The teacher's motives for using discordant emotional labor strategies included both instrumental and hedonic goals. Implications for policymakers and professionals in practice are discussed to improve teachers' emotional wellbeing.

Keywords: discordant strategies, emotional labor, student aggression, teachers

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Authors: Elisabeth Eder

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Memorizing music plays an important role for instrumentalists and has been researched very little so far. Almost every musician is confronted with memorizing music in the course of their musical career. For numerous competitions, examinations (e.g., at universities, music schools), solo performances, and the like, memorization is a requirement. Learners are often required to learn a piece by heart but are rarely given guidance on how to proceed. This was also confirmed by Eder's preliminary study to examine the topicality and relevance of the topic, in which 111 instrumentalists took part. The preliminary study revealed a great desire for more knowledge or information about learning strategies as well as a greater sense of security when performing by heart on stage through the use of learning strategies by those musicians who use learning strategies. Eder’s research focuses on learning strategies for memorizing music. As part of a large-scale empirical study – an online questionnaire translated into 10 languages was used to conduct the study – 1091 musicians from 64 different countries described how they memorize. The participants in the study also evaluated their learning strategies and justified their choice in terms of their degree of effectiveness. Based on the study and pedagogical literature, 100 learning strategies were identified and categorized; the strategies were examined with regard to their effectiveness, and instrument-specific, age-specific, country-specific, gender-specific, and education-related differences and similarities concerning the choice of learning strategies were investigated. Her research also deals with forms and models of memory and how music-related information can be stored and retrieved and also forgotten again. A further part is devoted to the possibilities that teachers and learners have to support the process of memorization independently of learning strategies. The findings resulting from Elisabeth Eder's research should enable musicians and instrumental students to memorize faster and more confidently.

Keywords: memorizing music, learning strategies, empirical study, effectiveness of strategies

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Authors: Kanlaya Ratanasuphakarn, Suttipong Boonphadung

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The research on the development of ability in reading comprehension based on metacognitive strategies aimed to (1) improve the students’development of ability in reading comprehension based on metacognitive strategies, (2) evaluate the students’ satisfaction on using metacognitive strategies in learning as a tool developing the ability in reading comprehension. Forty-eight of Mattayom 3 students who have enrolled in the subject of research for learning development of semester 2 in 2013 were purposively selected as the research cohort. The research tools were lesson plans for reading comprehension, pre-posttest and satisfaction questionnaire that were approved as content validity and reliability (IOC=.66-1.00,0.967). The research found that the development of ability in reading comprehension of the research samples before using metacognitive strategies in learning activities was in the normal high level. Additionally, the research discovered that the students’ satisfaction of the research cohort after applying model in learning activities appeared to be high level of satisfaction on using metacognitive strategies in learning as a tool for the development of ability in reading comprehension.

Keywords: development of ability, metacognitive strategies, satisfaction, reading comprehension

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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

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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: Hui Wang, Huan Zhang

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This study uses systematic review and qualitative comparative analysis methods to comprehensively inquire about the recent street-level policy entrepreneurship research, to identify the characteristics and lessons we can learn from 20 years of street-level policy entrepreneurship literature, and the relations between political contexts and street-level policy entrepreneurs’ strategies. Using data from a systematic review of street-level policy entrepreneurship literature, we identify the sub-components of different political contexts and core strategies of street-level policy entrepreneurs and estimate the configurational relations between different political settings and street-level policy entrepreneurs’ strategies. Our results show that street-level policy entrepreneurs display social acuity, define the problem, and build team strategies when policy or political streams dominate. Street-level policy entrepreneurs will use lead-by-example strategies when both policy and political streams dominate. Furthermore, street-level policy entrepreneurs will use bureaucratic strategies, even if no stream dominates in the political context.

Keywords: policy entrepreneurs, qualitative comparative analysis, street-level bureaucracy, systematic review

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Authors: Swarkar Sharma, Ekta Rai, Ankit Mahajan, Parvinder Kumar, Manoj K Dhar, Sushil Razdan, Kumarasamy Thangaraj, Carol Wise, Shiro Ikegawa M.D., K.K. Pandita M.D.

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Rare disorders are poorly understood hence, remain uncharacterized or patients are misdiagnosed and get poor medical attention. A rare mysterious skeletal disorder that remained unidentified for decades and rendered many people physically challenged and disabled for life has been reported in an isolated remote village ‘Arai’ of Poonch district of Jammu and Kashmir. This village is located deep in mountains and the population residing in the region is highly consanguineous. In our survey of the region, 70 affected people were reported, showing similar phenotype, in the village with a population of approximately 5000 individuals. We were able to collect samples from two multi generational extended families from the village. Through Whole Exome sequencing (WES), we identified a rare variation NM_003880.3:c.156C>A NP_003871.1:p.Cys52Ter, which results in introduction of premature stop codon in WISP3 gene. We found this variation perfectly segregating with the disease in one of the family. However, this variation was absent in other family. Interestingly, a novel splice site mutation at position c.643+1G>A of WISP3 gene, perfectly segregating with the disease was observed in the second family. Thus, exploiting WES and putting different evidences together (familial histories and genetic data, clinical features, radiological and biochemical tests and findings), the disease has finally been diagnosed as a very rare recessive hereditary skeletal disease “Progressive Pseudorheumatoid Arthropathy of Childhood” (PPAC) also known as “Spondyloepiphyseal Dysplasia Tarda with Progressive Arthropathy” (SEDT-PA). This genetic characterization and identification of the disease causing mutations will aid in genetic counseling, critically required to curb this rare disorder and to prevent its appearance in future generations in the population. Further, understanding of the role of WISP3 gene the biological pathways should help in developing treatment for the disorder.

Keywords: whole exome sequencing, Next Generation Sequencing, rare disorders

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Authors: Ayman K. El Essawy, Amal M. Hosny, Hala M. Abu Shady

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The rapid detection of TB and drug resistance, both optimizes treatment and improves outcomes. In the current study, respiratory specimens were collected from 155 patients. Conventional susceptibility testing and MIC determination were performed for rifampicin (RIF) and isoniazid (INH). Genotype MTBDRplus assay, which is a molecular genetic assay based on the DNA-STRIP technology and specific gene sequencing with primers for rpoB, KatG, and mab-inhA genes were used to detect mutations associated with resistance to rifampicin and isoniazid. In comparison to other categories, most of rifampicin resistant (61.5%) and isoniazid resistant isolates (47.1%) were from patients relapsed in treatment. The genotypic profile (using Genotype MTBDRplus assay) of multi-drug resistant (MDR) isolates showed missing of katG wild type 1 (WT1) band and appearance of mutation band katG MUT2. For isoniazid mono-resistant isolates, 80% showed katG MUT1, 20% showed katG MUT1, and inhA MUT1, 20% showed only inhA MUT1. Accordingly, 100% of isoniazid resistant strains were detected by this assay. Out of 17 resistant strains, 16 had mutation bands for katG distinguished high resistance to isoniazid. The assay could clearly detect rifampicin resistance among 66.7% of MDR isolates that showed mutation band rpoB MUT3 while 33.3% of them were considered as unknown. One mono-resistant rifampicin isolate did not show rifampicin mutation bands by Genotype MTBDRplus assay, but it showed an unexpected mutation in Codon 531 of rpoB by DNA sequence analysis. Rifampicin resistance in this strain could be associated with a mutation in codon 531 of rpoB (based on molecular sequencing), and Genotype MTBDRplus assay could not detect the associated mutation. If the results of Genotype MTBDRplus assay and sequencing were combined, this strain shows hetero-resistance pattern. Gene sequencing of eight selected isolates, previously tested by Genotype MTBDRplus assay, could detect resistance mutations mainly in codon 315 (katG gene), position -15 in inhA promotes gene for isoniazid resistance and codon 531 (rpoB gene) for rifampicin resistance. Genotyping techniques allow distinguishing between recurrent cases of reinfection or reactivation and supports epidemiological studies.

Keywords: M. tuberculosis, rpoB, KatG, inhA, genotype MTBDRplus

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Authors: Mohammed Hassan Alshaikhi

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Teaching vocabulary is a fundamental step in helping students to develop a good grasp of language. Exploring new strategies is an essential part of improving the teaching of vocabulary. The study aimed to explore the teaching vocabulary strategies in Saudi primary classrooms (aged 11 and 12 years old) in Jeddah, Saudi Arabia. The study was based on qualitative data collected from a large-scale case study, which utilised observations at eight male state and private primary schools during the academic year 2016-2017. The observations were transcribed, coded and entered into Nvivo software to be organised and analysed. Varying teaching vocabulary strategies were explored, and then they were circulated to many English teachers to be used in their classes.

Keywords: case study, English language, Saudi teachers, teaching vocabulary strategies

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Authors: Lata Kumari Dhanesh Tiwary, Pradeep Kumar Mishra

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The effluent coming from various industries such as textile, carpet, food, pharmaceutical and many other industries is big challenge due to its recalcitrant and xenobiotiocs in nature. Recently, biodegradation of dye wastewater through biological means was widely used due to eco-friendly and cost effective with the higher percentage of removal of dye from wastewater. The present study deals with the biodegradation and decolourization of Direct Red 23 dye using indigenously isolated bacterial consortium. The bacterial consortium was isolated from soil sample from dye contaminated site near a cluster of Carpet industries of Bhadohi, Uttar Pradesh, India. The bacterial strain formed consortia were identified and characterized by morphological, biochemical and 16S rRNA gene sequence analysis. The bacterial strain mainly Staphylococcus saprophyticus strain BHUSS X3 (KJ439576), Microbacterium sp. BHUMSp X4 (KJ740222) and Staphylococcus saprophyticus strain BHUSS X5 (KJ439576) were used as consortia for further studies of dye decolorization. Experimental investigations were made in a Sequencing Air- lift bioreactor using the synthetic solution of Direct Red 23 dye by optimizing various parameters for efficient degradation of dye. The effect of several operating parameters such as flow rate, pH, temperature, initial dye concentration and inoculums size on removal of dye was investigated. The efficiency of isolated bacterial consortia from dye contaminated area in Sequencing Air- lift Bioreactor with different concentration of dye between 100-1200 mg/l at different hydraulic rate (HRTs) 26h and 10h. The maximum percentage of dye decolourization 98% was achieved when operated at HRT of 26h. The percentage of decolourization of dye was confirmed by using UV-Vis spectrophotometer and HPLC.

Keywords: carpet industry, bacterial consortia, sequencing air-lift bioreactor

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

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Authors: Nemat Sokhandan Bashir

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Threats from viruses to agricultural crops could be even larger than the losses caused by the other pathogens because, in many cases, the viral infection is latent but crucial from an epidemic point of view. Wild vegetation can be a source of many viruses that eventually find their destiny in crop plants. Although often asymptomatic in wild plants due to adaptation, they can potentially cause serious losses in crops. Therefore, exploring viruses in wild vegetation is very important. Recently, omics have been quite useful for exploring plant viruses from various plant sources, especially wild vegetation. For instance, we have discovered viruses such as Ambrossia asymptomatic virus I (AAV-1) through the application of metagenomics from Oklahoma Prairie Reserve. Accordingly, extracts from randomly-sampled plants are subjected to high speed and ultracentrifugation to separated virus-like particles (VLP), then nucleic acids in the form of DNA or RNA are extracted from such VLPs by treatment with phenol—chloroform and subsequent precipitation by ethanol. The nucleic acid preparations are separately treated with RNAse or DNAse in order to determine the genome component of VLPs. In the case of RNAs, the complementary cDNAs are synthesized before submitting to DNA sequencing. However, for VLPs with DNA contents, the procedure would be relatively straightforward without making cDNA. Because the length of the nucleic acid content of VPLs can be different, various strategies are employed to achieve sequencing. Techniques similar to so-called "chromosome walking" may be used to achieve sequences of long segments. When the nucleotide sequence data were obtained, they were subjected to BLAST analysis to determine the most related previously reported virus sequences. In one case, we determined that the novel virus was AAV-l because the sequence comparison and analysis revealed that the reads were the closest to the Indian citrus ringspot virus (ICRSV). AAV—l had an RNA genome with 7408 nucleotides in length and contained six open reading frames (ORFs). Based on phylogenies inferred from the replicase and coat protein ORFs of the virus, it was placed in the genus Mandarivirus.

Keywords: wild, plant, novel, metagenomics

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Authors: Jihan Albayati, Kim Abdullah

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This poster focuses on the significance of active learning strategies and their usage in the ESL classroom. Active learning is a big shift from traditional lecturing to active student engagement which can enhance and enrich student learning; therefore, engaging students is the core of this approach. Students learn more when they participate in the process of learning such as discussions, debates, analysis, synthesis, or any form of activity that requires student involvement. In order to achieve active learning, teachers can use different instructional strategies that are conducive to learning and the selection of these strategies depends on student learning outcomes. Active learning techniques must be carefully designed and integrated into the classroom to increase critical thinking and student participation. This poster provides a concise definition of active learning and its importance, instructional strategies, active learning techniques and their impact on student engagement. Also, it demonstrates the differences between passive and active learners.

Keywords: active learning, learner engagement, student-centered, teaching strategies

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Authors: L. Lamola, E. Manolas, A. Krause

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Background: The incidence of childhood cancer incidence is increasing gradually in low-middle income countries, such as South Africa. Globally, there is an extensive range of familial- and hereditary-cancer syndromes, where underlying germline variants increase the likelihood of developing cancer in childhood. Next-Generation Sequencing (NGS) technologies have been key in determining the occurrence and genetic contribution of germline variants to paediatric cancer development. We aimed to design and evaluate a candidate gene panel specific to inherited cancer-predisposing genes to provide a comprehensive insight into the contribution of germline variants to childhood cancer. Methods: 32 paediatric patients (aged 0-18 years) diagnosed with a malignant tumour were recruited, and biological samples were obtained. After quality control, DNA was sequenced using an ion Ampliseq 50 candidate gene panel design and Ion Torrent S5 technologies. Sequencing variants were called using Ion Torrent Suite software and were subsequently annotated using Ion Reporter and Ensembl's VEP. High priority variants were manually analysed using tools such as MutationTaster, SIFT-INDEL and VarSome. Putative identified candidates were validated via Sanger Sequencing. Results: The patients studied had a variety of cancers, the most common being nephroblastoma (13), followed by osteosarcoma (4) and astrocytoma (3). We identified 10 pathogenic / likely pathogenic variants in 10 patients, most of which were novel. Conclusions: According to the literature, we expected ~10% of our patient population to harbour pathogenic or likely pathogenic germline variants, however, we reported about 3 times (~30%) more than we expected. Majority of the identified variants are novel; this may be because this is the first study of its kind in an understudied South African population.

Keywords: Africa, genetics, germline-variants, paediatric-cancer

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Authors: Temitayo Ogunsanwo

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Problem-solving is an important way of learning way of learning because it propels children to use previous experiences to deal with new situations. The purpose of this study is to find out the attitude of pre-service teachers to problem-solving as a strategy for promoting early mathematics learning in children. This qualitative study employed a descriptive design to investigate the experiences of twenty second-year undergraduate early childhood education Pre-service teachers in a teaching practice and their attitude towards five-year-old children’s problem-solving strategies in mathematics. Pre-service teachers were exposed to different strategies for teaching children how to solve problems in mathematics. They were taken through a micro teaching in class using different strategies to teach problem-solving in different topics in the five-year-old mathematics curriculum. The students were then made to teach five-year-olds in neighbouring schools for three weeks, working in pairs, observing and recording children’s problem-solving activities and strategies. After the three weeks exercise, their experiences and attitude towards children’s problem-solving strategies were collected using open-ended questions and analysed in themes. Findings were discussed.

Keywords: attitude, early mathematics learning, experience, pre-service teachers, problem-solving, strategies

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Authors: Khalid Alasim

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This study investigated Saudi Arabian elementary school teachers’ knowledge of strategies to teach reading components to hard-of-hearing students. The study focused on four of the five reading components the National Reading Panel (NPR, 2000) identified: phonemic awareness; phonics; vocabulary, and reading comprehension, and explored the relationship between teachers’ demographic characteristics and their knowledge of the strategies as well. An explanatory sequential mixed methods design was used that included two phases. The quantitative phase examined the knowledge of these Arabic reading components among 89 elementary school teachers of hard-of-hearing students, and the qualitative phase consisted of interviews with 10 teachers. The results indicated that the teachers have a great deal of knowledge (above the mean score) of strategies to teach reading components. Specifically, teachers’ knowledge of strategies to teach the vocabulary component was the highest. The results also showed no significant association between teachers’ demographic characteristics and their knowledge of strategies to teach reading components. The qualitative analysis revealed two themes: 1) teachers’ lack of basic knowledge of strategies to teach reading components, and 2) the absence of in-service courses and training programs in reading for teachers.

Keywords: knowledge, reading, components, hard-of-hearing, phonology, vocabulary

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Authors: Elifcan Oztekin

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Compliment response strategies in cross-linguistic contexts have received a considerable amount of interest in sociolinguistic research in various language settings. In this respect, a common finding of these studies indicates that speakers of different languages employ different patterns in strategies to respond to compliments. This has triggered varying theoretical approaches to compliment responses within theories of politeness and the universality of speech acts. In the light of previous studies, the present study investigates compliment response strategies that Turkish-English bilingual university students use in English and Turkish response conditions through a cross-linguistic discourse completion task and interviews. Data were analyzed using Holmes’ (1988) taxonomy and the results indicate a similar pattern to what has been observed in Turkish compliments responses in previous research. Turkish-English comparisons also display noticeable similarities in macro-level strategies, while subtle differences in micro-level strategies were also observed.

Keywords: compliment response strategies, cross-cultural differences, bilingualism, sociolinguistics

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Authors: A. Seham A. Elgamal, Reham H. Saleh

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Chronic kidney disease became a global health problem worldwide. Therefore, in order to maintain a patient’s life and improve the survival rate, hemodialysis is essential to replace the function of their kidneys. However, those patients may complain about multiple physical and psychological stressors due to the nature of the disease and the need for frequent hemodialysis sessions. So, those patients use various strategies to cope with the stressors related to their disease and the treatment procedures. Cross-sectional, descriptive study was carried out to achieve the aim of the study. A convenient sample including all adult patients was recruited for this study. Hemodialysis Stressors Scale (HSS) and Jalowiec Coping Scale (JCS) were used to investigate the stressors and coping strategies of 89 hemodialysis patients, at a governmental hospital (King Khalid Hospital-Jeddah). Results of the study revealed that 50.7% experienced physiological stressors and 38% experienced psychosocial stressors. Also, optimistic, fatalistic, and supportive coping strategies were the most common coping strategies used by the patients with mean scores (2.88 + 0.75, 2.87 + 0.75, and 1.82 + 0.71), respectively. In conclusion, being familiar with the types of stressors and the effective coping strategies of hemodialysis patients and their families are important in order to enhance their adaptation with chronic kidney diseases.

Keywords: copying strategies, hemodialysis, physiological stressors, psychological stressors

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Authors: Hazem Hasan Hushayish

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Motivation and teaching strategies are commonly believed to improve students’ communicative competence in English as a foreign language; still, there is not much empirical evidence to support this claim. The present study is intended to focus on the effects of motivational factors and teaching strategies on the communicative competence among the Palestinian undergraduates. In the first phase, one hundred and eighty participants, who are studying English language in three Palestinian universities, answered a questionnaire. The questionnaire included items derived from Gardner’s 2001, 2004, 2006, 2007 Attitude/Motivation Test Battery AMTB and items from Dörnyei 2007 and Guilloteaux and Dörnyei 2008 teaching strategies framework for foreign language classrooms. In the second phase, 6 participants, from the same universities, were interviewed. The quantitative results indicated that participants’ communicative competence is significantly affected by motivation and teaching strategies. Also, the qualitative results indicated that teaching strategies do not directly affect students’ communicative competence, but rather affect their motivation. Consequently, the current study will add substantively to the literature concerning the effects of motivation and teaching strategies in communicative competencies among EFL learners in the Palestinian context, and some suggested procedures and suggestions that help improve learners’ communicative competences.

Keywords: communicative competence, motivation, teaching strategies, Palestinian undergraduates

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Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

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As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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Authors: Zubana Afzal, Afsheen Massod

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This quantitative study was carried out in order to explore the role of coping strategies as an explanatory mechanism in the relationship between self-determination needs and quality of life. A cross-sectional survey research design was conducted using scales such as the Basic Psychological Needs Scale (Deci&Ryan, 2000) to measure self-determination-based needs, Pain Coping Strategies Questionnaire (Harland &Georgieff, 2003), and Quality of Life Brief (The WHOQOL Group, 1998), in translated form in addition to a demographic information sheet. The sample comprised 120 (Women=63, Men=57), taken from different hospitals in Lahore, Multan, and Gojra. Descriptive and Inferential analyses were executed through SPSS version 23.00. All self-determination needs were found in result to be significantly and positively correlated with diversion and cognitive pain coping strategies, physical, psychological, social, and environmental quality of life, and significantly negatively correlated with catastrophizing and reinterpreting pain coping strategies. Cognitive and diversion pain coping strategies were found to be significantly and positively associated with all physical, psychological, social, and environmental quality of life. The regression analyses revealed that the strongest predictors were autonomy, cognitive and diversion pain coping strategies in predicting quality of life. All coping strategies except reinterpreting played a mediating role between self-determination needs and quality of life. The findings can lead to a better understanding of the role of self-determination needs and pain coping strategies in determining the quality of life among chronic non-specific lower back pain patients.

Keywords: quality of life, chronic lower back pain, coping strategies, self determination needs

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Authors: Richard K. Jolley, Jonathan A. Coffman

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Since Enterococci has been implicated in oral disease, we hypothesized the transmission of avian Enterococci to humans via fecal-oral transmission facilitated by adherence to dental plaque. To demonstrate the capability of Enterococci to bind to a dental plaque we filtered avian excreta and incubated the filtrate on a sucrose-induced, Streptococcus mutans biofilm. The biofilm was washed several times with a detergent to remove bacteria binding non-specifically to the biofilm, DNA was isolated from the biofilm, 16S rDNA was amplified, sequenced by Ion Torrent DNA sequencing and analyzed with bioinformatics. Enterococci and other known bacterial pathogens were shown to adhere to the biofilm. Culturing the washed biofilm with Bile Esculin Azide (BEA) agar also confirmed the presence of Enterococci as verified with Sanger sequencing. The results suggest that Enteroccoci in avian excreta has the ability to adhere to human dental plaque and may be a mechanism of entry when humans encounter contaminated aerosols, water or food.

Keywords: Enterococci, avian excreta, dental plaque, NGS

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Authors: Inuusah Mahama

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The study focused on the importance of diversity and the use of evidence-based practices and strategies in teaching learners with ASD. The study employed a mixed-methods design, including surveys, interviews, and observations. A total of 500 K-12 practitioners participated in the study, including teachers, administrators, and support staff. The study sought to investigate the current understanding and knowledge level of K-12 practitioners regarding diversity, evidence-based practices, and strategies for teaching learners with ASD. The study also examined the challenges that K-12 practitioners face in preparing learners with ASD and the resources they require to improve their practice. The results indicated that K-12 practitioners in Ghana have limited knowledge and skills in teaching learners with ASD, particularly in using evidence-based practices and strategies. Therefore, there is a need for providing training and professional development opportunities for K-12 practitioners, developing and implementing evidence-based practices and strategies, and increasing awareness of ASD and the need for effective teaching strategies. This would go a long way to improve the quality of education for learners with ASD in Ghana and ultimately lead to better outcomes for these students.

Keywords: autism, practitioners, diversity, evidence-based practises

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Authors: Erdinc Ozturk, Gizem Akcan

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Although there are several advantages of information and communication technologies, they cause some problems like cyber bullying and cyber victimization. Cyber bullying and cyber victimization have lots of negative effects on people. There are lots of different strategies to prevent cyber bullying and victimization. This study was conducted to provide information about the strategies that are used to prevent cyber bullying and cyber victimization. 120 (60 women, 60 men) university students whose ages are between 18 and 35 participated this study. According to findings of this study, men are more prone to cyber bullying than women. Moreover, men are also more prone to cyber victimization than women.

Keywords: cyber bullying, cyber victimization, coping strategies, sex

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Authors: Jaco Oosthuizen, Nerina C. Van Der Merwe

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The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency.

Keywords: familial breast cancer, multiplex ligation-dependent probe amplification, next generation sequencing, South Africa

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Authors: Deni Stincer Gomez, Zuraya Monroy Nasr, Luis Pérez Alvarez

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The preparation of academic documents such as thesis, articles and research projects is one of the requirements of the higher educational level. These documents demand the implementation of logical argumentative thinking which is experienced and executed with difficulty. To mitigate the effect of these difficulties this study designed a thesis seminar, with which the authors have seven years of experience. It is taught in a graduate program in Psychology at the National Autonomous University of Mexico. In this study the authors use the Toulmin model as a mental heuristic and for the application of a set of psychodidactic strategies that facilitate the elaboration of the plot and culmination of the thesis. The efficiency in obtaining the degree in the groups exposed to the seminar has increased by 94% compared to the 10% that existed in the generations that were not exposed to the seminar. In this article the authors will emphasize the psychodidactic strategies used. The Toulmin model alone does not guarantee the success achieved. A set of actions of a psychological nature (almost psychotherapeutic) and didactics of the teacher also seem to contribute. These are actions that derive from an understanding of the psychological, epistemological and ontogenetic obstacles and the most frequent errors in which thought tends to fall when it is demanded a logical course. The authors have grouped the strategies into three groups: 1) strategies to facilitate logical thinking, 2) strategies to strengthen the scientific self and 3) strategies to facilitate the act of writing the text. In this work the authors delve into each of them.

Keywords: psychodidactic strategies, logical thinking, academic documents, Toulmin model

Procedia PDF Downloads 158

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: Vyacheslav Furtak, Merja Roivainen, Olga Mirochnichenko, Majid Laassri, Bella Bidzhieva, Tatiana Zagorodnyaya, Vladimir Chizhikov, Konstantin Chumakov

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Molecular epidemiology and environmental surveillance are parts of a rational strategy to control infectious diseases. They have been widely used in the worldwide campaign to eradicate poliomyelitis, which otherwise would be complicated by the inability to rapidly respond to outbreaks and determine sources of the infection. The conventional scheme involves isolation of viruses from patients and the environment, followed by their identification by nucleotide sequences analysis to determine phylogenetic relationships. This is a tedious and time-consuming process that yields definitive results when it may be too late to implement countermeasures. Because of the difficulty of high-throughput full-genome sequencing, most such studies are conducted by sequencing only capsid genes or their parts. Therefore the important information about the contribution of other parts of the genome and inter- and intra-species recombination to viral evolution is not captured. Here we propose a new approach based on the rapid concentration of sewage samples with tangential flow filtration followed by deep sequencing and reconstruction of nucleotide sequences of viruses present in the samples. The entire nucleic acids content of each sample is sequenced, thus preserving in digital format the complete spectrum of viruses. A set of rapid algorithms was developed to separate deep sequence reads into discrete populations corresponding to each virus and assemble them into full-length consensus contigs, as well as to generate a complete profile of sequence heterogeneities in each of them. This provides an effective approach to study molecular epidemiology and evolution of natural viral populations.

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

Procedia PDF Downloads 254

Authors: Yi-Lin Chen, Sheng-Jou Hung, Tsunglin Liu

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Adaptive immune system recognizes a wide range of antigens via expressing a large number of structurally distinct T cell and B cell receptor genes. The distinct receptor genes arise from complex rearrangements called V(D)J recombination, and constitute the immune repertoire. A common method of profiling immune repertoire is via amplifying recombined receptor genes using multiple primers and high-throughput sequencing. This multiplex-PCR approach is efficient; however, the resulting repertoire can be distorted because of primer bias. To eliminate primer bias, 5’ RACE is an alternative amplification approach. However, the application of RACE approach is limited by its low efficiency (i.e., the majority of data are non-regular receptor sequences, e.g., containing intronic segments) and lack of the convenient tool for analysis. We propose a computational tool that can correctly identify non-regular receptor sequences in RACE data via aligning receptor sequences against the whole gene instead of only the exon regions as done in all other tools. Using our tool, the remaining regular data allow for an accurate profiling of immune repertoire. In addition, a RACE approach is improved to yield a higher fraction of regular T-cell receptor sequences. Finally, we quantify the degree of primer bias of a multiplex-PCR approach via comparing it to the RACE approach. The results reveal significant differences in frequency of VJ combination by the two approaches. Together, we provide a new experimental and computation pipeline for an unbiased profiling of immune repertoire. As immune repertoire profiling has many applications, e.g., tracing bacterial and viral infection, detection of T cell lymphoma and minimal residual disease, monitoring cancer immunotherapy, etc., our work should benefit scientists who are interested in the applications.

Keywords: immune repertoire, T-cell receptor, 5' RACE, high-throughput sequencing, sequence alignment

Procedia PDF Downloads 169