Search results for: simple sequence repeat markers

Authors: Sinarwati Mohamad Suhaili, Naomie Salim, Mohamad Nazim Jambli

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Sequence-to-sequence (seq2seq) models augmented with attention mechanisms are playing an increasingly important role in automated customer service. These models, which are able to recognize complex relationships between input and output sequences, are crucial for optimizing chatbot responses. Central to these mechanisms are neural attention weights that determine the focus of the model during sequence generation. Despite their widespread use, there remains a gap in the comparative analysis of different attention weighting functions within seq2seq models, particularly in the domain of chatbots using the Customer Support Twitter (CST) dataset. This study addresses this gap by evaluating four distinct attention-scoring functions—dot, multiplicative/general, additive, and an extended multiplicative function with a tanh activation parameter — in neural generative seq2seq models. Utilizing the CST dataset, these models were trained and evaluated over 10 epochs with the AdamW optimizer. Evaluation criteria included validation loss and BLEU scores implemented under both greedy and beam search strategies with a beam size of k=3. Results indicate that the model with the tanh-augmented multiplicative function significantly outperforms its counterparts, achieving the lowest validation loss (1.136484) and the highest BLEU scores (0.438926 under greedy search, 0.443000 under beam search, k=3). These results emphasize the crucial influence of selecting an appropriate attention-scoring function in improving the performance of seq2seq models for chatbots. Particularly, the model that integrates tanh activation proves to be a promising approach to improve the quality of chatbots in the customer support context.

Keywords: attention weight, chatbot, encoder-decoder, neural generative attention, score function, sequence-to-sequence

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Authors: Dorcas Ropo Abejide, Olamide Ahmed Falusi, Oladipupo Abdulazeez Yusuf Daudu, Bolaji Zuluqurineen Salihu, Muhammad Liman Muhammad

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This study evaluated the morpho-agronomic response of twenty-four (24) Nigerian Bambara groundnut landraces to water stress and genetic diversity of some selected accessions using SSR markers. The studies were carried out in the botanical garden of the Department of Plant Biology, Federal University of Technology, Minna, Niger State, Nigeria in a randomized complete block design using three replicates. Molecular analysis using SSR primers was carried out at the International Institute of Tropical Agriculture (IITA) Ibadan in order to characterize ten selected accessions comprising the seven most drought tolerant and three most susceptible accessions from the 24 accessions evaluated. Results revealed that water stress decreased morpho-agronomic traits such as plant height, leaf area, number of leaves per plant, seed yield, etc. A total of 22 alleles were detected by the SSR markers used with a mean number of 4 allelles. SSR markers MBamCO₃₃, Primer 65, and G358B2-D15 each detected 4 allelles, while Primer 3FR and 4FR detected 5 allelles each. The study revealed significantly high polymorphisms in 10 Loci. The mean value of polymorpic information content was 0.6997, implying the usefulness of the primers used in identifying genetic similarities and differences among the Bambara groundnut genotypes. The SSR analysis revealed a comparable pattern between genetic diversity and drought tolerance of the genotypes. The UPGMA dendrogram showed that at a genetic distance of 0.1, the accessions were grouped into three groups according to their level of tolerance to drought. The two most drought-tolerant accessions were grouped together, and the 5th and 6th most drought-tolerant accessions were also grouped together. This suggests that the genotypes grouped together may be genetically close, may possess similar genes, or have a common origin. The degree of genetic variants obtained from this profiling could be useful in Bambara groundnut breeding for drought tolerance. The identified drought tolerant Bambara groundnut landraces are important genetic resources for drought stress tolerance breeding programme of Bambara groundnut. The genotypes are also useful for germplasm conservation and global implications.

Keywords: Bambara groundnut, genetic diversity, germplasm, SSR markers, water stress

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Authors: Sandeep Vasaikar, Lary Obi

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Rapid and discriminative genotyping methods are useful for determining the clonality of the isolates in nosocomial or household outbreaks. Multilocus sequence typing (MLST) is a nucleotide sequence-based approach for characterising bacterial isolates. The genetic diversity and the clinical relevance of the drug-resistant Klebsiella isolates from Mthatha are largely unknown. For this reason, prospective, experimental study of the molecular epidemiology of Klebsiella isolates from patients being treated in Mthatha over a three-year period was analysed. Methodology: PCR amplification and sequencing of the drug-resistance-associated genes, and multilocus sequence typing (MLST) using 7 housekeeping genes mdh, pgi, infB, FusAR, phoE, gapA and rpoB were conducted. A total of 32 isolates were analysed. Results: The percentages of multidrug-resistant (MDR), extensively drug-resistance (XDR) and pandrug-resistant (PDR) isolates were; MDR 65.6 % (21) and XDR and PDR with 0 % each. In this study, K. pneumoniae was 19/32 (59.4 %). MLST results showed 22 sequence types (STs) were identified, which were further separated by Maximum Parsimony into 10 clonal complexes and 12 singletons. The most dominant group was Klebsiella pneumoniae with 23/32 (71.8 %) isolates, Klebsiella oxytoca as a second group with 2/32 (6.25 %) isolates, and a single (3.1 %) K. varricola as a third group while 6 isolates were of unknown sequences. Conclusions/significance: A phylogenetic analysis of the concatenated sequences of the 7 housekeeping genes showed that strains of K. pneumoniae form a distinct lineage within the genus Klebsiella, with K. oxytoca and K. varricola its nearest phylogenetic neighbours. With the analysis of 7 genes were determined 1 K. variicola, which was mistakenly identified as K. pneumoniae by phenotypic methods. Two misidentifications of K. oxytoca were found when phenotypic methods were used. No significant differences were observed between ESBL blaCTX-M, blaTEM and blaSHV groups in the distribution of Sequence types (STs) or Clonal complexes (CCs).

Keywords: phylogenetic analysis, phylogeny, klebsiella phylogenetic, klebsiella

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Authors: Yanyan Wang

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This paper on second language teaching and learning uses conversation analysis (CA) approach and focuses on how second language learners of Chinese do repair when making clarification requests. In order to demonstrate their behavior in interaction, a comparison was made to study the differences between native speakers of Chinese with non-native speakers of Chinese. The significance of the research is to make second language teachers and learners aware of repair and how to seek clarification. Utilizing the methodology of CA, the research involved two sets of naturally occurring recordings, one of native speaker students and the other of non-native speaker students. Both sets of recording were telephone talks between students and teachers. There were 50 native speaker students and 50 non-native speaker students. From multiple listening to the recordings, the parts with repairs for clarification were selected for analysis which included the moments in the talk when students had problems in understanding or hearing the speaker and had to seek clarification. For example, ‘Sorry, I do not understand ‘and ‘Can you repeat the question? ‘were the parts as repair to make clarification requests. In the data, there were 43 such cases from native speaker students and 88 cases from non-native speaker students. The non-native speaker students were more likely to use repair to seek clarification. Analysis on how the students make clarification requests during their conversation was carried out by investigating how the students initiated problems and how the teachers repaired the problems. In CA term, it is called other-initiated self-repair (OISR), which refers to student-initiated teacher-repair in this research. The findings show that, in initiating repair, native speaker students pay more attention to mutual understanding (inter-subjectivity) while non-native speaker students, due to their lack of language proficiency, pay more attention to their status of knowledge (epistemic) switch. There are three major differences: 1, native Chinese students more often initiate closed-class OISR (seeking specific information in the request) such as repeating a word or phrases from the previous turn while non-native students more frequently initiate open-class OISR (not specifying clarification) such as ‘sorry, I don’t understand ‘. 2, native speakers’ clarification requests are treated by the teacher as understanding of the content while non-native learners’ clarification requests are treated by teacher as language proficiency problem. 3, native speakers don’t see repair as knowledge issue and there is no third position in the repair sequences to close repair while non-native learners take repair sequence as a time to adjust their knowledge. There is clear closing third position token such as ‘oh ‘ to close repair sequence so that the topic can go back. In conclusion, this paper uses conversation analysis approach to compare differences between native Chinese speakers and non-native Chinese learners in their ways of conducting repair when making clarification requests. The findings are useful in future Chinese language teaching and learning, especially in teaching pragmatics such as requests.

Keywords: conversation analysis (CA), clarification request, second language (L2), teaching implication

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Authors: Amrit Ladhani

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The cyclic universe theory is a model of cosmic evolution according to which the universe undergoes endless cycles of expansion and cooling, each beginning with a “big bang” and ending in a “big crunch”. In this paper, we propose a unique property of Space-time. This particular and marvelous nature of space shows us that space can stretch, expand, and shrink. This property of space is caused by the size of the universe change over time: growing or shrinking. The observed accelerated expansion, which relates to the stretching of Shrunk space for the new theory, is derived. This theory is based on three underlying notions: First, the Big Bang is not the beginning of Space-time, but rather, at the very beginning fraction of a second, there was an infinite force of infinite Shrunk space in the cosmic singularity that force gave rise to the big bang and caused the rapidly growing of space, and all other forms of energy are transformed into new matter and radiation and a new period of expansion and cooling begins. Second, there was a previous phase leading up to it, with multiple cycles of contraction and expansion that repeat indefinitely. Third, the two principal long-range forces are the gravitational force and the repulsive force generated by shrink space. They are the two most fundamental quantities in the universe that govern cosmic evolution. They may provide the clockwork mechanism that operates our eternal cyclic universe. The universe will not continue to expand forever; no need, however, for dark energy and dark matter. This new model of Space-time and its unique properties enables us to describe a sequence of events from the Big Bang to the Big Crunch.

Keywords: dark matter, dark energy, cosmology, big bang and big crunch

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Authors: Dan Xie

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The use of discourse markers (DMs) can play a crucial role in representing discourse interaction and pragmatic competence. Learners’ use of DMs and differences between native speakers (NSs) and non-native speakers (NNSs) in the use of various DMs have been the focus of considerable research attention. However, some commonly used DMs, such as you know, have not received as much attention in comparative studies, especially in the Chinese context. This study analyses data in two corpora (COLSEC and Spoken BNC 2014 (14-25)) to investigate how Chinese learners differ from NNSs in their use of the DM you know and its functions in speech. The results show that there is a significant difference between the two corpora in terms of the frequency of use of you know. In terms of the functions of you know, the study shows that six functions can all be present in both corpora, although there are significant differences between the five functional dimensions, especially in introducing a claim linked to the prior discourse and highlighting particular points in the discourse. It is hoped to show empirically how Chinese learners and NSs use DMs differently.

Keywords: you know, discourse marker, native speaker, Chinese learner

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Authors: R. B. Mishra

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Hidden Markov Model (HMM) has been used in prediction and determination of states that generate different neural activations as well as mental working conditions. This paper addresses two applications of HMM; one to determine the optimal sequence of states for two neural states: Active (AC) and Inactive (IA) for the three emission (observations) which are for No Working (NW), Waiting (WT) and Working (W) conditions of human beings. Another is for the determination of optimal sequence of intentionality i.e. Believe (B), Desire (D), and Intention (I) as the states and three observational sequences: NW, WT and W. The computational results are encouraging and useful.

Keywords: hiden markov model, believe desire intention, neural activation, simulation

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Authors: Didem Can

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Scheduling problems are one of the most fundamental issues of production systems. Many different approaches and models have been developed according to the production processes of the parts and the main purpose of the problem. In this study, one of the bottleneck stations of a company serving in the aerospace industry is analyzed and considered as a single machine scheduling problem with sequence-dependent setup times. The objective of the problem is assigning a large number of similar parts to the same shift -to reduce chemical waste- while minimizing the number of tardy jobs. The goal programming method will be used to achieve two different objectives simultaneously. The assignment of parts to the shift will be expressed using the integer programming method. Finally, the constraint programming method will be used as it provides a way to find a result in a short time by avoiding worse resulting feasible solutions with the defined variables set. The model to be established will be tested and evaluated with real data in the application part.

Keywords: constraint programming, goal programming, integer programming, sequence-dependent setup, single machine scheduling

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Authors: Priyashri Kamlesh Sridhar, Suranga Nanayakkara

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Current frameworks in assessment follow lesson delivery and rely heavily on test performance or teacher’s observations. This, however, neglects the underlying cognitive load during the learning process. Identifying the pivotal points when the load occurs helps design effective pedagogies and tools that respond to learners’ cognitive state. There has been limited research on quantifying cognitive load in preschoolers, real-time. In this study, we recorded electrodermal activity and heart rate variability (HRV) from 10 kindergarteners performing executive function tasks and Johnson Woodcock test of cognitive abilities. Preliminary findings suggest that there are indeed sensitive task-dependent markers in skin conductance (number of SCRs and average amplitude of SCRs) and HRV (mean heart rate and low frequency component) captured during the learning process.

Keywords: early childhood, learning, methodologies, pedagogies

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Authors: Syeda Qamarunnisa, Ishrat Jamil, Abid Azhar, Zabta K. Shinwari, Syed Irtifaq Ali

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A phylogenetic analysis of family Solanaceae was conducted using sequence data from the chloroplast intergenic atpB-rbcL spacer. Sequence data was generated from 17 species representing 09 out of 14 genera of Solanaceae from Pakistan. Cladogram was constructed using maximum parsimony method and results indicate that Solanaceae is mainly divided into two subfamilies; Solanoideae and Cestroideae. Four major clades within Solanoideae represent tribes; Physaleae, Capsiceae, Datureae and Solaneae are supported by high bootstrap value and the relationships among them are not corroborating with the previous studies. The findings established that subfamily Cestroideae comprised of three genera; Cestrum, Lycium, and Nicotiana with high bootstrap support. Position of Nicotiana inferred with atpB-rbcL sequence is congruent with traditional classification, which placed the taxa in Cestroideae. In the current study Lycium unexpectedly nested with Nicotiana with 100% bootstrap support and identified as a member of tribe Nicotianeae. Expanded sampling of other genera from Pakistan could be valuable towards improving our understanding of intrafamilial relationships within Solanaceae.

Keywords: systematics, solanaceae, phylogenetics, intergenic spacer, tribes

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Authors: J. L. Liu, L. Wang, B. Zhu, J. Zhou, W. D. Gao

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Fabric textures are very common in our daily life. However, we never explore the representation of fabric textures from neuroscience view. Theoretical studies suggest that primary visual cortex (V1) uses a sparse code to efficiently represent natural images. However, how the simple cells in V1 encode the artificial textures is still a mystery. So, here we will take fabric texture as stimulus to study the response of independent component analysis that is established to model the receptive field of simple cells in V1. Experimental results based on 140 classical fabric images indicate that the receptive fields of simple cells have obvious selectivity in orientation, frequency, and phase when drifting gratings are used to determine their tuning properties. Additionally, the distribution of optimal orientation and frequency shows that the patch size selected from each original fabric image has a significant effect on the frequency selectivity.

Keywords: fabric texture, receptive filed, simple cell, spare coding

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Authors: Kazuya Sato, Toru Kasahara, Junji Kuroda

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In this paper, an autonomous hovering control method of multicopter using only Web camera is proposed. Recently, various control method of an autonomous flight for multicopter are proposed. But, in the previously proposed methods, a motion capture system (i.e., OptiTrack) and laser range finder are often used to measure the position and posture of multicopter. To achieve an autonomous flight control of multicopter with simple equipment, we propose an autonomous flight control method using AR marker and Web camera. AR marker can measure the position of multicopter with Cartesian coordinate in three dimensional, then its position connects with aileron, elevator, and accelerator throttle operation. A simple PID control method is applied to the each operation and adjust the controller gains. Experimental result are given to show the effectiveness of our proposed method. Moreover, another simple operation method for autonomous flight control multicopter is also proposed.

Keywords: autonomous hovering control, multicopter, Web camera, operation

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Madeleine Cox

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Objective: Discussion of diagnosis and management options for myometrial ectopic pregnancy Case: A 30 yo G1P0 presented to the emergency department with vaginal bleeding for the last 4 days. She had a positive home urine pregnancy test, confirmed with a serum HCG. When she presented for an ultrasound, there was no intrauterine pregnancy, no evidence of adnexal pregnancy, however, the anterior myometrium of the uterus was noted to be markedly abnormal. When she presented to the emergency department of a busy tertiary hospital in Queensland, she had a small amount of vaginal bleeding, was anxious but well, observations normal. Repeat blood testes demonstrated a serum HCG of 9246 IU/L, haemoglobin of 143g/L. The patient had an interesting history of a right oophorectomy and open myomectomy in another country. A repeat ultrasound again showed an abnormality within the myometrium of the uterus, which was initially reported as concerning for an AVM, or potentially invasive gestational trophoblastic disease. An MRI was organised 2 days later, which demonstrated a intramural/subserosal irregularity in the right lateral body measuring 35x38x42mm with peripheral enhancement and central cystic components, favouring a myometrial ectopic most likely at the site of previous myomectomy. Alternative diagnosis of AVM, GTD were considered less likely. After discussion with the patient, IV methotrexate was administered as an in patient 4 days after her initial presentation to emergency. After this, her HCG fell to 1236 IU/L on day 6 post treatment. Weekly reviews showed stable ultrasound appearances with a steadily dropping HCG level. A repeat MRI was performed 3 weeks after methotrexate administration which confirmed involution of the myometrial ectopic, however, showed ongoing progression of vascularity surrounding the site. Despite resolution of HCG, the patient persisted to have ongoing bleeding associated with this and went to have uterine artery embolisation. Follow up ultrasound showed resolution of abnormal vascularity and negative HCG levels. Conclusion: Myometrial ectopic pregnancies are a rare occurrence and require a multidisciplinary approach to achieve timely management for these patients. This patient was in a very well resourced setting with excellent access to Interventional Radiology and specialist Radiologists who could work together with the Obstetrics, Gynaecology, and Maternal Fetal Medicine team to provide multiple options of management which preserved her fertility. This case has a very good outcome, with the patient being referred back to our service 12 months later with an early intrauterine pregnancy.

Keywords: ectopic, pregnancy, miscarriage, gynaecology

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Authors: Parisi L., Hamili D., Azlan N.

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The aim of this study was to design and simulate a particular type of Asynchronous State Machine (ASM), namely a ‘traffic light controller’ (TLC), operated at a frequency of 0.5 Hz. The design task involved two main stages: firstly, designing a 4-bit binary counter using J-K flip flops as the timing signal and subsequently, attaining the digital logic by deploying ASM design process. The TLC was designed such that it showed a sequence of three different colours, i.e. red, yellow and green, corresponding to set thresholds by deploying the least number of AND, OR and NOT gates possible. The software Multisim was deployed to design such circuit and simulate it for circuit troubleshooting in order for it to display the output sequence of the three different colours on the traffic light in the correct order. A clock signal, an asynchronous 4-bit binary counter that was designed through the use of J-K flip flops along with an ASM were used to complete this sequence, which was programmed to be repeated indefinitely. Eventually, the circuit was debugged and optimized, thus displaying the correct waveforms of the three outputs through the logic analyzer. However, hazards occurred when the frequency was increased to 10 MHz. This was attributed to delays in the feedback being too high.

Keywords: asynchronous state machine, traffic light controller, circuit design, digital electronics

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Authors: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Ahemd Sameer, Braj Bhushan

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The objective of our study was to compare wayfinding strategies to remember route while navigation in an unfamiliar homogenous environment. Two videos developed using free ware Trimble Sketchup© each having nine identical turns (3 right, 3 left, 3 straight) with no distinguishing feature at any turn. Thirt-two male post-graduate students of IIT Kanpur participated in the study. The experiment was conducted in three phases. In the first phase participant generated a list of personally known items to be used as landmarks. In the second phase participant saw the first video and was required to remember the sequence of turns. In the second video participant was required to imagine a landmark from the list generated in the first phase at each turn and associate the turn with it. In both the task the participant was asked to recall the sequence of turns as it appeared in the video. In the third phase, which was 20 minutes after the second phase, participants again recalled the sequence of turns. Results showed that performance in the first condition i.e. without use of landmarks was better than imaginary landmark condition. The difference, however, became significant when the participant were tested again about 30 minutes later though performance was still better in no-landmark condition. The finding is surprising given the past research in memory and is explained in terms of cognitive factors such as mental workload.

Keywords: Wayfinding, Landmark, Homogenous Environment, Memory

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Authors: Amina Merghad, Cherif Abdennour

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Solvents are widely used in paint industry, where humans are highly exposed, especially from inhalation. A case report describes how paint affects reproductive markers and the health of workers. Sixty four subjects were chosen and divided into two groups; a control and an exposed group. A questionnaire was given to male workers from similar socio-economic status in order to know their ages, working conditions, clinical symptoms, working period, smoking history, shift, medical history and nutrition. Blood was withdrawn in the morning from volunteers. The measurement of blood testosterone and prolactin concentrations was then carried out. Results showed that the ages of the two groups were almost similar and were up to 47 and 43 years. The period of employment was 17 years and 14 years for the control and the exposed workers, respectively. Concerning clinical symptoms, the frequency of neuropsychological symptoms of the two groups are presented. It is clear that the symptom of memory loss, headaches are the highest among exposed workers followed by poor coordination, poor concentration and insomnia. On the other hand, the symptoms’ frequency in the control was less than that of the exposed group. Testosterone concentration has significantly decreased in group 2 (4.61±2,005 ng/ml) and group 3 (4.25±1.67 ng/ml) of exposed workers. On the other hand, prolactin concentration was higher in group 3 compared to other groups. To conclude, paint industry has disturbed reproductive markers and created high frequency of neuropsychological symptoms.

Keywords: blood, paint, prolactin, occupational exposure, organic solvent, reproductive toxicity, testosterone

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Authors: Amin Saeidi

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Using a representation-theoretic approach and considering G to be a finite primitive permutation group of degree n, our aim is to determine linear codes of length n that admit G as a permutation automorphism group. We can show that in some cases, every binary linear code admitting G as a permutation automorphism group is a submodule of a permutation module defined by a primitive action of G. As an illustration of the method, we consider the sporadic simple group M₁₁ and the unitary group U(3,3). We also construct some point- and block-primitive 1-designs from the supports of some codewords of the codes in the discussion.

Keywords: linear code, permutation representation, support design, simple group

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Authors: Jaomai Tungsiripat, Patompong Satapornpong

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Allopurinol have been used to treat diseases that relating with the reduction of uric acid and be a treatment preventing the severity of, including gout, chronic kidney disease, chronic heart failure, and diabetes mellitus (type 2). However, allopurinol metabolites can cause a severe cutaneous adverse reaction (SCARs) consist of Drug Rash with Eosinophilia and Systemic Symptoms (DRESS) and Stevens-Johnson Syndrome(SJS)/Toxic Epidermal Necrolysis (TEN). Previous studies, we found only HLA-B*58:01 allele has a strongly association with allopurinol-induced SCARs in many populations: Han Chinese [P value = 4.7 x 10−24], European [P value <10−6], and Thai [P value <0.001].However, there was no update the frequency of HLA-B alleles and pharmacogenetics markers distribution in healthy Thais and support for screening before the initiation of treatment. The aim of this study was to investigate the prevalence of HLA-B*58:01 allele associated with allopurinol-induced SCARs in healthy Thai population. A retrospective study of 260 individual healthy subjects who living in Thailand. HLA-B were genotyped using sequence-specific oligonucleotides (PCR-SSOs).In this study, we identified the prevalence of HLA-B alleles consist ofHLA-B*46:01 (12.69%), HLA-B*15:02 (8.85%), HLA-B*13:01 (6.35%), HLA-B*40:01 (6.35%), HLA-B*38:02 (5.00%), HLA-B*51:01 (5.00%), HLA-B*58:01 (4.81%), HLA-B*44:03 (4.62%), HLA-B*18:01 (3.85%) and HLA-B*15:25 (3.08%). Therefore, the distribution of HLA-B*58:01 will support the clinical implementation and screening usage of allopurinol in Thai population.

Keywords: allopurinol, HLA-B*58: 01, Thai population, SCARs

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Authors: Naso Isaiah Thanavisuth, Patompong Satapornpong

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Introduction: Covid-19 has been a global pandemic for some time now, causing severe symptoms to patients that received the virus. However, there has been no report on this gene in the Thai population. Objective: Our aim in this study is to explore and compare the frequency of HLA-C allele that is associated with severe COVID-19 symptoms in Thais and other populations. Method: 200 general Thai population were enrolled in this study. The genotyping of HLA -C alleles were determined by the polymerase chain reaction with sequence-specific oligonucleotide probes (PCR-SSOP) and Luminex®IS 100 system (Luminex Corporation, Austin, Texas, USA). Results: We found that the frequency of alleles HLA-C* 01:02 (16.00%), HLA-C* 08:01(10.50%), HLA-C* 03:04 (10.25%),HLA-C* 07:02 (10.00%), HLA-C* 03:02 (9.25%), HLA-C* 07:01 (6.75%), HLA-C* 04:01 (5.00%), HLA-C* 06:02 (4.00%), HLA-C* 04:03 (4.00%), and HLA-C* 07:04 (3.75%) were more common in the Thai population. HLA-C* 01:02 (16.00%) allele was the highest frequency in the North, Center, and North East groups in Thailand, but there was the South region that was not significantly different when compared with the other groups of the region. Additionally, HLA-C∗14:02 allele was similarly distributed in Thais (3.00%), African Americans (1.98%), Caucasians (2.08%), Hispanics (1.71%), North American Natives (1.34%) and Asians (5.01%) by p-value = 0.6506, 0.6506, 0.6506, 0.6135 and 0.7182, respectively. Conclusion: Genetic variation database is important to identify HLA can be a risk factor for severe COVID-19 in many populations. In this study, we will support the research of the HLA markers for screening severe COVID-19 in many populations.

Keywords: HLA-C * 14:02, COVID-19, allele frequency, Thailand

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Authors: Reza Hedayati, Meysam Jahanbakhshi

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Fracture Mechanics is used to predict debonding propagation in adhesive joint between aluminum and composite plates. Three types of loadings and two types of glass-epoxy composite sequences: [0/90]2s and [0/45/-45/90]s are considered for the composite plate and their results are compared. It was seen that generally the cases with stacking sequence of [0/45/-45/90]s have much shorter lives than cases with [0/90]2s. It was also seen that in cases with λ=0 the ends of the debonding front propagates forward more than its middle, while in cases with λ=0.5 or λ=1 it is vice versa. Moreover, regardless of value of λ, the difference between the debonding propagations of the ends and the middle of the debonding front is very close in cases λ=0.5 and λ=1. Another main conclusion was the non-dimensionalized debonding front profile is almost independent of sequence type or the applied load value.

Keywords: adhesive joint, debonding, fracture, LEFM, APDL

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Authors: Parshanth Maroju, Ramandeep Behl, Sandile S. Motsa

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In this study, we proposed a simple and interesting family of fourth-order multi-point methods without memory for obtaining simple roots. This family requires only three functional evaluations (viz. two of functions f(xn), f(yn) and third one of its first-order derivative f'(xn)) per iteration. Moreover, the accuracy and validity of new schemes is tested by a number of numerical examples are also proposed to illustrate their accuracy by comparing them with the new existing optimal fourth-order methods available in the literature. It is found that they are very useful in high precision computations. Further, the dynamic study of these methods also supports the theoretical aspect.

Keywords: basins of attraction, nonlinear equations, simple roots, Newton's method

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Authors: K. R. Parvathy, R. Rao Bhavani , M. L. McLain, Kamal Bijlani, R. Jayakrishnan

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Augmented Reality (AR) technology is considered to be an important emerging technology used in education today. One potentially key use of AR in education is to teach socio-scientific issues (SSI), topics that inure students towards social conscience and critical thinking. This work uses multiple markers and virtual buttons that interact with each other, creating a life-like visual spectacle. Learning about issues such as global warming by using AR technology, students will have an increased sense of experiencing immersion, immediacy, and presence, thereby enhancing their learning as well as likely improving their ability to make better informed decisions about considerations of such issues. Another advantage of AR is that it is a low cost technology, making it advantageous for educators to adapt to their classrooms. Also in this work we compare the effectiveness of AR versus ordinary video by polling a group of students to assess the content understandability, effectiveness and interaction of both the delivery methods.

Keywords: augmented reality, global warming, multiple markers, virtual buttons

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

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

Keywords: genome assembly, NGS, SSR, Tanacetum cinerariifolium

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Authors: Svetlana Strinyuk, Viacheslav Lanin

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Academic English has become lingua franca for international scientific community which stimulates universities to introduce English for Specific Purposes (EAP) courses into curriculum. Teaching L2 EAP students might be fulfilled with corpus technologies and digital stylistics. A special software developed to reach the manifold task of teaching, assessing and researching academic writing of L2 students on basis of digital stylistics and multidimensional analysis was created. A set of annotations (style markers) – grammar, lexical and syntactic features most significant of academic writing was built. Contrastive comparison of two corpora “model corpus”, subject domain limited papers published by competent writers in leading academic journals, and “students’ corpus”, subject domain limited papers written by last year students allows to receive data about the features of academic writing underused or overused by L2 EAP student. Both corpora are tagged with a special software created in GATE Developer. Style markers within the framework of research might be replaced depending on the relevance and validity of the result which is achieved from research corpora. Thus, selecting relevant (high frequency) style markers and excluding less relevant, i.e. less frequent annotations, high validity of the model is achieved. Software allows to compare the data received from processing model corpus to students’ corpus and get reports which can be used in teaching and assessment. The less deviation from the model corpus students demonstrates in their writing the higher is academic writing skill acquisition. The research showed that several style markers (hedging devices) were underused by L2 EAP students whereas lexical linking devices were used excessively. A special software implemented into teaching of EAP courses serves as a successful visual aid, makes assessment more valid; it is indicative of the degree of writing skill acquisition, and provides data for further research.

Keywords: corpus technologies in EAP teaching, multidimensional analysis, GATE Developer, corpus stylistics

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Authors: Amirhossen Zare Rahvard

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Freemium games based on the gacha mechanic have proven highly successful in recent years - games with simple graphics and simple gameplay systems but with a highly profitable market. Attempts at developing gacha games have even been made in Iran. Since gacha games are both profitable and easy to develop, they seem to be a suitable starting point for establishing a video game market in underdeveloped countries. This article aims to review the gacha games' approach to gaining revenue by studying the case of Arknights game in order to draw an outline of how simple games have led to great markets.

Keywords: gacha games, game’s economy, underdeveloped countries and games, arkngihts

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Authors: Shaoxi Wang, Pouya Rezai

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High aspect ratio is the necessary parts of complex microstructures. Some methods available to achieve high aspect ratio requires expensive materials or complex process; others is difficult to research simple high aspect ratio structures. The paper presents a simple and cheap two-step Polydimethylsioxane (PDMS) transferring process to get high aspect ratio single pillars, which only requires covering the PDMS mold with Brij@52 surface solution. The experimental results demonstrate the method efficiency and effective.

Keywords: high aspect ratio, microstructure, PDMS, Brij

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Authors: H. Imad, Y. Cheah, O. Aamera

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The aims of this research are to study the mitochondrial non-coding region by using the Sanger sequencing technique and establish the degree of variation characteristics of a fragment. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. A portion of a non-coding region encompassing positions 37 to 340 amplified in accordance with the Anderson reference sequence. PCR products purified by EZ-10 spin column then sequenced and detected by using the ABI 3730xL DNA Analyzer. New polymorphic positions 57, 63, and 101 are described may in future be suitable sources for identification purpose. The data obtained can be used to identify variable nucleotide positions characterized by frequent occurrence most promising for identification variants.

Keywords: encompassing nucleotide positions 37 to 340, HVII, Iraq, mitochondrial DNA, polymorphism, frequency

Procedia PDF Downloads 727

Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

Procedia PDF Downloads 142