Search results for: genome sequence
1044 JaCoText: A Pretrained Model for Java Code-Text Generation
Authors: Jessica Lopez Espejel, Mahaman Sanoussi Yahaya Alassan, Walid Dahhane, El Hassane Ettifouri
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Pretrained transformer-based models have shown high performance in natural language generation tasks. However, a new wave of interest has surged: automatic programming language code generation. This task consists of translating natural language instructions to a source code. Despite the fact that well-known pre-trained models on language generation have achieved good performance in learning programming languages, effort is still needed in automatic code generation. In this paper, we introduce JaCoText, a model based on Transformer neural network. It aims to generate java source code from natural language text. JaCoText leverages the advantages of both natural language and code generation models. More specifically, we study some findings from state of the art and use them to (1) initialize our model from powerful pre-trained models, (2) explore additional pretraining on our java dataset, (3) lead experiments combining the unimodal and bimodal data in training, and (4) scale the input and output length during the fine-tuning of the model. Conducted experiments on CONCODE dataset show that JaCoText achieves new state-of-the-art results.Keywords: java code generation, natural language processing, sequence-to-sequence models, transformer neural networks
Procedia PDF Downloads 2691043 Utilization of Developed Single Sequence Repeats Markers for Dalmatian Pyrethrum (Tanacetum cinerariifolium) in Preliminary Genetic Diversity Study on Natural Populations
Authors: F. Varga, Z. Liber, J. Jakše, A. Turudić, Z. Šatović, I. Radosavljević, N. Jeran, M. Grdiša
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Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.; Asteraceae), a source of the commercially dominant plant insecticide pyrethrin, is a species endemic to the eastern Adriatic. Genetic diversity of T. cinerariifolium was previously studied using amplified fragment length polymorphism (AFLP) markers. However, microsatellite markers (single sequence repeats - SSRs) are more informative because they are codominant, highly polymorphic, locus-specific, and more reproducible, and thus are most often used to assess the genetic diversity of plant species. Dalmatian pyrethrum is an outcrossing diploid (2n = 18) whose large genome size and high repeatability have prevented the success of the traditional approach to SSR markers development. The advent of next-generation sequencing combined with the specifically developed method recently enabled the development of, to the author's best knowledge, the first set of SSRs for genomic characterization of Dalmatian pyrethrum, which is essential from the perspective of plant genetic resources conservation. To evaluate the effectiveness of the developed SSR markers in genetic differentiation of Dalmatian pyrethrum populations, a preliminary genetic diversity study was conducted on 30 individuals from three geographically distinct natural populations in Croatia (northern Adriatic island of Mali Lošinj, southern Adriatic island of Čiovo, and Mount Biokovo) based on 12 SSR loci. Analysis of molecular variance (AMOVA) by randomization test with 10,000 permutations was performed in Arlequin 3.5. The average number of alleles per locus, observed and expected heterozygosity, probability of deviations from Hardy-Weinberg equilibrium, and inbreeding coefficient was calculated using GENEPOP 4.4. Genetic distance based on the proportion of common alleles (DPSA) was calculated using MICROSAT. Cluster analysis using the neighbor-joining method with 1,000 bootstraps was performed with PHYLIP to generate a dendrogram. The results of the AMOVA analysis showed that the total SSR diversity was 23% within and 77% between the three populations. A slight deviation from Hardy-Weinberg equilibrium was observed in the Mali Lošinj population. Allele richness ranged from 2.92 to 3.92, with the highest number of private alleles observed in the Mali Lošinj population (17). The average observed DPSA between 30 individuals was 0.557. The highest DPSA (0.875) was observed between several pairs of Dalmatian pyrethrum individuals from the Mali Lošinj and Mt. Biokovo populations, and the lowest between two individuals from the Čiovo population. Neighbor-joining trees, based on DPSA, grouped individuals into clusters according to their population affiliation. The separation of Mt. Biokovo clade was supported (bootstrap value 58%), which is consistent with the previous study on AFLP markers, where isolated populations from Mt. Biokovo differed from the rest of the populations. The developed SSR markers are an effective tool for assessing the genetic diversity and structure of natural Dalmatian pyrethrum populations. These preliminary results are encouraging for a future comprehensive study with a larger sample size across the species' range. Combined with the biochemical data, these highly informative markers could help identify potential genotypes of interest for future development of breeding lines and cultivars that are both resistant to environmental stress and high in pyrethrins. Acknowledgment: This work has been 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) and by project KK.01.1.1.01.0005, Biodiversity and Molecular Plant Breeding, at the Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia.Keywords: Asteraceae, genetic diversity, genomic SSRs, NGS, pyrethrum, Tanacetum cinerariifolium
Procedia PDF Downloads 1101042 Antibacterial Activity of Salvadora persica Extracts against Oral Cavity Bacteria
Authors: Sulaiman A. Alrumman, Abd El-Latif Hesham
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Despite medical progress worldwide, dental caries are still widespread. Miswak is derived from the plant arak (Salvadora persica). It is used by Muslim people as a natural product for the cleansing of teeth, to ensure oral and dental hygiene. This study was designed to evaluate the antimicrobial effects of ethanol, methanol, and ethanol/methanol extracts of miswak against three bacterial pathogens of the oral cavity. The pathogens were isolated from the oral cavity of volunteers/patients and were identified on the basis of 16S rRNA gene amplification data. Sequence comparisons were made with 16S rRNA gene sequences available in the GenBank database. The results of sequence alignment and phylogenetic analysis identified the three pathogens as being Staphylococcus aureus strain KKU-020, Enterococcus faecalis strain KKU-021 and Klebsiella pneumoniae strain KKU-022. All miswak extracts showed powerful antimicrobial activity against the three pathogens. The maximum zone of inhibition (40.67±0.88 mm) was observed against E. faecalis with ethanolic extracts whilst methanolic extracts showed the minimum zone of inhibition (10.33±0.88 mm) against K. pneumonia KKU-022. Based on the significant effects of the miswak extracts against the oral cavity pathogens in our study, we recommend that miswak is to be used as a dental hygiene method to prevent tooth caries.Keywords: antibacterial, miswak, Salvadora persica, oral cavity pathogens
Procedia PDF Downloads 2891041 Transcriptomic Analysis of Acanthamoeba castellanii Virulence Alteration by Epigenetic DNA Methylation
Authors: Yi-Hao Wong, Li-Li Chan, Chee-Onn Leong, Stephen Ambu, Joon-Wah Mak, Priyasashi Sahu
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Background: Acanthamoeba is a genus of amoebae which lives as a free-living in nature or as a human pathogen that causes severe brain and eye infections. Virulence potential of Acanthamoeba is not constant and can change with growth conditions. DNA methylation, an epigenetic process which adds methyl groups to DNA, is used by eukaryotic cells, including several human parasites to control their gene expression. We used qPCR, siRNA gene silencing, and RNA sequencing (RNA-Seq) to study DNA-methyltransferase gene family (DNMT) in order to indicate the possibility of its involvement in programming Acanthamoeba virulence potential. Methods: A virulence-attenuated Acanthamoeba isolate (designation: ATCC; original isolate: ATCC 50492) was subjected to mouse passages to restore its pathogenicity; a virulence-reactivated isolate (designation: AC/5) was generated. Several established factors associated with Acanthamoeba virulence phenotype were examined to confirm the succession of reactivation process. Differential gene expression of DNMT between ATCC and AC/5 isolates was performed by qPCR. Silencing on DNMT gene expression in AC/5 isolate was achieved by siRNA duplex. Total RNAs extracted from ATCC, AC/5, and siRNA-treated (designation: si-146) were subjected to RNA-Seq for comparative transcriptomic analysis in order to identify the genome-wide effect of DNMT in regulating Acanthamoeba gene expression. qPCR was performed to validate the RNA-Seq results. Results: Physiological and cytophatic assays demonstrated an increased in virulence potential of AC/5 isolate after mouse passages. DNMT gene expression was significantly higher in AC/5 compared to ATCC isolate (p ≤ 0.01) by qPCR. si-146 duplex reduced DNMT gene expression in AC/5 isolate by 30%. Comparative transcriptome analysis identified the differentially expressed genes, with 3768 genes in AC/5 vs ATCC isolate; 2102 genes in si-146 vs AC/5 isolate and 3422 genes in si-146 vs ATCC isolate, respectively (fold-change of ≥ 2 or ≤ 0.5, p-value adjusted (padj) < 0.05). Of these, 840 and 1262 genes were upregulated and downregulated, respectively, in si-146 vs AC/5 isolate. Eukaryotic orthologous group (KOG) assignments revealed a higher percentage of downregulated gene expression in si-146 compared to AC/5 isolate, were related to posttranslational modification, signal transduction and energy production. Gene Ontology (GO) terms for those downregulated genes shown were associated with transport activity, oxidation-reduction process, and metabolic process. Among these downregulated genes were putative genes encoded for heat shock proteins, transporters, ubiquitin-related proteins, proteins for vesicular trafficking (small GTPases), and oxidoreductases. Functional analysis of similar predicted proteins had been described in other parasitic protozoa for their survival and pathogenicity. Decreased expression of these genes in si146-treated isolate may account in part for Acanthamoeba reduced pathogenicity. qPCR on 6 selected genes upregulated in AC/5 compared to ATCC isolate corroborated the RNA sequencing findings, indicating a good concordance between these two analyses. Conclusion: To the best of our knowledge, this study represents the first genome-wide analysis of DNA methylation and its effects on gene expression in Acanthamoeba spp. The present data indicate that DNA methylation has substantial effect on global gene expression, allowing further dissection of the genome-wide effects of DNA-methyltransferase gene in regulating Acanthamoeba pathogenicity.Keywords: Acanthamoeba, DNA methylation, RNA sequencing, virulence
Procedia PDF Downloads 1891040 A Kernel-Based Method for MicroRNA Precursor Identification
Authors: Bin Liu
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MicroRNAs (miRNAs) are small non-coding RNA molecules, functioning in transcriptional and post-transcriptional regulation of gene expression. The discrimination of the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops) is necessary for the understanding of miRNAs’ role in the control of cell life and death. Since both their small size and sequence specificity, it cannot be based on sequence information alone but requires structure information about the miRNA precursor to get satisfactory performance. Kmers are convenient and widely used features for modeling the properties of miRNAs and other biological sequences. However, Kmers suffer from the inherent limitation that if the parameter K is increased to incorporate long range effects, some certain Kmer will appear rarely or even not appear, as a consequence, most Kmers absent and a few present once. Thus, the statistical learning approaches using Kmers as features become susceptible to noisy data once K becomes large. In this study, we proposed a Gapped k-mer approach to overcome the disadvantages of Kmers, and applied this method to the field of miRNA prediction. Combined with the structure status composition, a classifier called imiRNA-GSSC was proposed. We show that compared to the original imiRNA-kmer and alternative approaches. Trained on human miRNA precursors, this predictor can achieve an accuracy of 82.34 for predicting 4022 pre-miRNA precursors from eleven species.Keywords: gapped k-mer, imiRNA-GSSC, microRNA precursor, support vector machine
Procedia PDF Downloads 1551039 Prevalence and Mechanisms of Antibiotic Resistance in Escherichia coli Isolated from Mastitic Dairy Cattle in Canada
Authors: Satwik Majumder, Dongyun Jung, Jennifer Ronholm, Saji George
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Bovine mastitis is the most common infectious disease in dairy cattle, with major economic implications for the dairy industry worldwide. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from dairy farms is vital not only for animal husbandry but also for public health. In this study, the prevalence of AMR in 113 Escherichia coli isolates from cases of bovine clinical mastitis in Canada was investigated. Kirby-Bauer disk diffusion test with 18 antibiotics and microdilution method with three heavy metals (copper, zinc, and silver) was performed to determine the antibiotic and heavy-metal susceptibility. Resistant strains were assessed for efflux and ß-lactamase activities besides assessing biofilm formation and hemolysis. Whole-genome sequences for each of the isolates were examined to detect the presence of genes corresponding to the observed AMR and virulence factors. Phenotypic analysis revealed that 32 isolates were resistant to one or more antibiotics, and 107 showed resistance against at least one heavy metal. Quinolones and silver were the most efficient against the tested isolates. Among the AMR isolates, AcrAB-TolC efflux activity and ß-lactamase enzyme activities were detected in 13 and 14 isolates, respectively. All isolates produced biofilm but with different capacities, and 33 isolates showed α-hemolysin activity. A positive correlation (Pearson r = +0.89) between efflux pump activity and quantity of biofilm was observed. Genes associated with aggregation, adhesion, cyclic di-GMP, quorum sensing were detected in the AMR isolates, corroborating phenotype observations. This investigation showed the prevalence of AMR in E. coli isolates from bovine clinical mastitis. The results also suggest the inadequacy of antimicrobials with a single mode of action to curtail AMR bacteria with multiple mechanisms of resistance and virulence factors. Therefore, it calls for combinatorial therapy for the effective management of AMR infections in dairy farms and combats its potential transmission to the food supply chain through milk and dairy products.Keywords: antimicrobial resistance, E. coli, bovine mastitis, antibiotics, heavy-metals, efflux pump, ß-lactamase enzyme, biofilm, whole-genome sequencing
Procedia PDF Downloads 2081038 Transcription Skills and Written Composition in Chinese
Authors: Pui-sze Yeung, Connie Suk-han Ho, David Wai-ock Chan, Kevin Kien-hoa Chung
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Background: Recent findings have shown that transcription skills play a unique and significant role in Chinese word reading and spelling (i.e. word dictation), and written composition development. The interrelationships among component skills of transcription, word reading, word spelling, and written composition in Chinese have rarely been examined in the literature. Is the contribution of component skills of transcription to Chinese written composition mediated by word level skills (i.e., word reading and spelling)? Methods: The participants in the study were 249 Chinese children in Grade 1, Grade 3, and Grade 5 in Hong Kong. They were administered measures of general reasoning ability, orthographic knowledge, stroke sequence knowledge, word spelling, handwriting fluency, word reading, and Chinese narrative writing. Orthographic knowledge- orthographic knowledge was assessed by a task modeled after the lexical decision subtest of the Hong Kong Test of Specific Learning Difficulties in Reading and Writing (HKT-SpLD). Stroke sequence knowledge: The participants’ performance in producing legitimate stroke sequences was measured by a stroke sequence knowledge task. Handwriting fluency- Handwriting fluency was assessed by a task modeled after the Chinese Handwriting Speed Test. Word spelling: The stimuli of the word spelling task consist of fourteen two-character Chinese words. Word reading: The stimuli of the word reading task consist of 120 two-character Chinese words. Written composition: A narrative writing task was used to assess the participants’ text writing skills. Results: Analysis of covariance results showed that there were significant between-grade differences in the performance of word reading, word spelling, handwriting fluency, and written composition. Preliminary hierarchical multiple regression analysis results showed that orthographic knowledge, word spelling, and handwriting fluency were unique predictors of Chinese written composition even after controlling for age, IQ, and word reading. The interaction effects between grade and each of these three skills (orthographic knowledge, word spelling, and handwriting fluency) were not significant. Path analysis results showed that orthographic knowledge contributed to written composition both directly and indirectly through word spelling, while handwriting fluency contributed to written composition directly and indirectly through both word reading and spelling. Stroke sequence knowledge only contributed to written composition indirectly through word spelling. Conclusions: Preliminary hierarchical regression results were consistent with previous findings about the significant role of transcription skills in Chinese word reading, spelling and written composition development. The fact that orthographic knowledge contributed both directly and indirectly to written composition through word reading and spelling may reflect the impact of the script-sound-meaning convergence of Chinese characters on the composing process. The significant contribution of word spelling and handwriting fluency to Chinese written composition across elementary grades highlighted the difficulty in attaining automaticity of transcription skills in Chinese, which limits the working memory resources available for other composing processes.Keywords: orthographic knowledge, transcription skills, word reading, writing
Procedia PDF Downloads 4181037 Genetic Divergence and Morphogenic Analysis of Sugarcane Red Rot Pathogen Colletotrichum falcatum under South Gujarat Condition
Authors: Prittesh Patel, Ramar Krishnamurthy
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In the present study, nine strains of C. falcatum obtained from different places and cultivars were characterized for sporulation, growth rate, and 18S rRNA gene sequence. All isolates had characteristic fast-growing sparse and fleecy aerial mycelia on potato dextrose agar with sickle shape conidia (length x width: varied from 20.0 X 3.89 to 25.52 X 5.34 μm) and blackish to orange acervuli with setae (length x width: varied from 112.37X 2.78 to 167.66 X 6.73 μm). They could be divided into two groups on the base of morphology; P1, dense mycelia with concentric growth and P2, sparse mycelia with uneven growth. Genomic DNA isolation followed by PCR amplification with ITS1 and ITS4 primer produced ~550bp amplicons for all isolates. Phylogeny generated by 18S rRNA gene sequence confirmed the variation in isolates and mainly grouped into two clusters; cluster 1 contained CoC671 isolates (cfNAV and cfPAR) and Co86002 isolate (cfTIM). Other isolates cfMAD, cfKAM, and cfMAR were grouped into cluster 2. Remaining isolates did not fall into any cluster. Isolate cfGAN, collected from Co86032 was found highly diverse of all the nine isolates. In a nutshell, we found considerable genetic divergence and morphological variation within C. falcatum accessions collected from different areas of south Gujarat, India and these can be used for the breeding program.Keywords: Colletotrichum falcatum, ITS, morphology, red rot, sugarcane
Procedia PDF Downloads 1211036 Cloning, Expression and Protein Purification of AV1 Gene of Okra Leaf Curl Virus Egyptian Isolate and Genetic Diversity between Whitefly and Different Plant Hosts
Authors: Dalia. G. Aseel
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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins
Procedia PDF Downloads 1411035 Genetic Diversity in Capsicum Germplasm Based on Inter Simple Sequence Repeat Markers
Authors: Siwapech Silapaprayoon, Januluk Khanobdee, Sompid Samipak
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Chili peppers are the fruits of Capsicum pepper plants well known for their fiery burning sensation on the tongue after consumption. They are members of the Solanaceae or common nightshade family along with potato, tomato and eggplant. Thai cuisine has gained popularity for its distinct flavors due to usages of various spices and its heat from the addition of chili pepper. Though being used in little quantity for each dish, chili pepper holds a special place in Thai cuisine. There are many varieties of chili peppers in Thailand, and thirty accessions were collected at Rajamangala University of Technology Lanna, Lampang, Thailand. To effectively manage any germplasm it is essential to know the diversity and relationships among members. Thirty-six Inter Simple Sequence Repeat (ISSRs) DNA markers were used to analyze the germplasm. Total of 335 polymorphic bands was obtained giving the average of 9.3 alleles per marker. Unweighted pair-group mean arithmetic method (UPGMA) clustering of data using NTSYS-pc software indicated that the accessions showed varied levels of genetic similarity ranging from 0.57-1.00 similarity coefficient index indicating significant levels of variation. At SM coefficient of 0.81, the germplasm was separated into four groups. Phenotypic variation was discussed in context of phylogenetic tree clustering.Keywords: diversity, germplasm, Chili pepper, ISSR
Procedia PDF Downloads 1421034 Response Delay Model: Bridging the Gap in Urban Fire Disaster Response System
Authors: Sulaiman Yunus
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The need for modeling response to urban fire disaster cannot be over emphasized, as recurrent fire outbreaks have gutted most cities of the world. This necessitated the need for a prompt and efficient response system in order to mitigate the impact of the disaster. Promptness, as a function of time, is seen to be the fundamental determinant for efficiency of a response system and magnitude of a fire disaster. Delay, as a result of several factors, is one of the major determinants of promptgness of a response system and also the magnitude of a fire disaster. Response Delay Model (RDM) intends to bridge the gap in urban fire disaster response system through incorporating and synchronizing the delay moments in measuring the overall efficiency of a response system and determining the magnitude of a fire disaster. The model identified two delay moments (pre-notification and Intra-reflex sequence delay) that can be elastic and collectively plays a significant role in influencing the efficiency of a response system. Due to variation in the elasticity of the delay moments, the model provides for measuring the length of delays in order to arrive at a standard average delay moment for different parts of the world, putting into consideration geographic location, level of preparedness and awareness, technological advancement, socio-economic and environmental factors. It is recommended that participatory researches should be embarked on locally and globally to determine standard average delay moments within each phase of the system so as to enable determining the efficiency of response systems and predicting fire disaster magnitudes.Keywords: delay moment, fire disaster, reflex sequence, response, response delay moment
Procedia PDF Downloads 2011033 Effect of Laminating Sequence of MWCNTs and Fe₂O₃ Filled Nanocomposites on Emi Shielding Effectiveness
Authors: Javeria Ahmad, Ayesha Maryam, Zahid Rizwan, Nadeem Nasir, Yasir Nawab, Hafiz Shehbaz Ahmad
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Mitigation of electromagnetic interference (EMI) through thin, lightweight, and cost-effective materials is critical for electronic appliances as well as human health. The present research work discusses the design of composites that are suitable to minimize EMI through various stacking sequences. The carbon fibers reinforced composite structures impregnated with dielectric (MWCNTs) and magnetic nanofillers (Fe₂O₃) were developed to investigate their microwave absorption properties. The composite structure comprising a single type of nanofillers, each of MWCNTs & Fe₂O₃, was developed, and then their layers were stacked over each other with various stacking sequences to investigate the best stacking sequence, which presents good microwave absorption characteristics. A vector network analyzer (VNA) was used to analyze the microwave absorption properties of these developed composite structures. The composite structures impregnated with the layers of a dielectric nanofiller and sandwiched between the layers of a magnetic nanofiller show the highest EMI shielding value of 59 dB and a dielectric conductivity of 35 S/cm in the frequency range of 0.1 to 13.6 GHz. The results also demonstrate that the microwave absorption properties of the developed composite structures were dominant over reflection properties. The absence of an external peak in X-ray diffraction (XRD), marked the purity of the added nanofillers.Keywords: nanocomposites, microwave absorption, EMI shielding, skin depth, reflection loss
Procedia PDF Downloads 461032 Recursion, Merge and Event Sequence: A Bio-Mathematical Perspective
Authors: Noury Bakrim
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Formalization is indeed a foundational Mathematical Linguistics as demonstrated by the pioneering works. While dialoguing with this frame, we nonetheless propone, in our approach of language as a real object, a mathematical linguistics/biosemiotics defined as a dialectical synthesis between induction and computational deduction. Therefore, relying on the parametric interaction of cycles, rules, and features giving way to a sub-hypothetic biological point of view, we first hypothesize a factorial equation as an explanatory principle within Category Mathematics of the Ergobrain: our computation proposal of Universal Grammar rules per cycle or a scalar determination (multiplying right/left columns of the determinant matrix and right/left columns of the logarithmic matrix) of the transformable matrix for rule addition/deletion and cycles within representational mapping/cycle heredity basing on the factorial example, being the logarithmic exponent or power of rule deletion/addition. It enables us to propone an extension of minimalist merge/label notions to a Language Merge (as a computing principle) within cycle recursion relying on combinatorial mapping of rules hierarchies on external Entax of the Event Sequence. Therefore, to define combinatorial maps as language merge of features and combinatorial hierarchical restrictions (governing, commanding, and other rules), we secondly hypothesize from our results feature/hierarchy exponentiation on graph representation deriving from Gromov's Symbolic Dynamics where combinatorial vertices from Fe are set to combinatorial vertices of Hie and edges from Fe to Hie such as for all combinatorial group, there are restriction maps representing different derivational levels that are subgraphs: the intersection on I defines pullbacks and deletion rules (under restriction maps) then under disjunction edges H such that for the combinatorial map P belonging to Hie exponentiation by intersection there are pullbacks and projections that are equal to restriction maps RM₁ and RM₂. The model will draw on experimental biomathematics as well as structural frames with focus on Amazigh and English (cases from phonology/micro-semantics, Syntax) shift from Structure to event (especially Amazigh formant principle resolving its morphological heterogeneity).Keywords: rule/cycle addition/deletion, bio-mathematical methodology, general merge calculation, feature exponentiation, combinatorial maps, event sequence
Procedia PDF Downloads 1211031 The Structural Analysis of Out-of-Sequence Thrust: Insights from Chaura Thrust of Higher Himalaya in Himachal Pradesh, India
Authors: Rajkumar Ghosh
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This paper focuses on the structural analysis of Chaura Thrust in Himachal Pradesh, India. It investigates mylonitised zones under microscopic observation, characterizes the box fold and its signature in the regional geology of Himachal Himalaya, and documents the Higher Himalayan Out-of-Sequence Thrust (OOST) in the region. The study aims to provide field evidence and documentation for Chaura Thrust (CT), which was previously considered a blind thrust. The research methodology involves geological field observation, microscopic studies, and strain analysis of oriented samples collected along the Jhakri-Chaura transect. The study presents findings such as the activation ages of MCT and STDS, the identification of mylonitised zones and various types of crenulated schistosity, and the manifestation of box folds and OOST. The presence of meso- and micro-scale box folds around Chaura suggests structural upliftment, while kink folds and shear sense indicators were identified. The research highlights the importance of microscopic studies and contributes to the understanding of the structural analysis of CT and its implications in the regional geology of the Himachal Himalaya. Mylonitised zones with S-C fabric were observed under the microscope, along with dynamic and bulging recrystallization and sub-grain formation. Various types of crenulated schistosity were documented, including a rare case of crenulation cleavage and sigmoid Muscovite occurring together. The conclusions emphasize the non-blind nature of Chaura Thrust, the characterization of box folds, the activation timing of different thrusts, and the significance of microscopic observations. Jhakri/Chaura/Sarahan thrusts are the zone of tectonic imbrication that transport Higher Himalayan gneissic rock on Rampur Quartzite. The evidence of frequent earthquakes and landslides in the Jhakri region confirm the study of morphometric conclusion that there is considerable neo-tectonic activity along an active fault in the Sutlej river basin. The study also documents the presence of OOST in Himachal Pradesh and its potential impact on strain accumulation.Keywords: Main Central Thrust, Jhakri Thrust, Chaura Thrust, Higher Himalaya, Out-of-Sequence Thrust, Sarahan Thrust
Procedia PDF Downloads 801030 Stability Characteristics of Angle Ply Bi-Stable Laminates by Considering the Effect of Resin Layers
Authors: Masih Moore, Saeed Ziaei-Rad
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In this study, the stability characteristics of a bi-stable composite plate with different asymmetric composition are considered. The interest in bi-stable structures comes from their ability that these structures can have two different stable equilibrium configurations to define a discrete set of stable shapes. The structures can easily change the first stable shape to the second one by a simple snap action. The main purpose of the current research is to consider the effect of including resin layers on the stability characteristics of bi-stable laminates. To this end and In order to determine the magnitude of the loads that are responsible for snap through and snap back phenomena between two stable shapes of the laminate, a non-linear finite element method (FEM) is utilized. An experimental investigation was also carried out to study the critical loads that caused snapping between two different stable shapes. Several specimens were manufactured from T300/5208 graphite-epoxy with [0/90]T, [-30/60]T, [-20/70]T asymmetric stacking sequence. In order to create an accurate finite element model, different thickness of resin layers created during the manufacturing process of the laminate was measured and taken into account. The geometry of each lamina and the resin layers was characterized by optical microscopy from different locations of the laminates thickness. The exact thickness of each lamina and the resin layer in all specimens with [0/90]T,[-30/60]T, [-20/70]T stacking sequence were determined by using image processing technique.Keywords: bi-stable laminates, finite element method, graphite-epoxy plate, snap behavior
Procedia PDF Downloads 2391029 Understanding the Impact of Out-of-Sequence Thrust Dynamics on Earthquake Mitigation: Implications for Hazard Assessment and Disaster Planning
Authors: Rajkumar Ghosh
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Earthquakes pose significant risks to human life and infrastructure, highlighting the importance of effective earthquake mitigation strategies. Traditional earthquake modelling and mitigation efforts have largely focused on the primary fault segments and their slip behaviour. However, earthquakes can exhibit complex rupture dynamics, including out-of-sequence thrust (OOST) events, which occur on secondary or subsidiary faults. This abstract examines the impact of OOST dynamics on earthquake mitigation strategies and their implications for hazard assessment and disaster planning. OOST events challenge conventional seismic hazard assessments by introducing additional fault segments and potential rupture scenarios that were previously unrecognized or underestimated. Consequently, these events may increase the overall seismic hazard in affected regions. The study reviews recent case studies and research findings that illustrate the occurrence and characteristics of OOST events. It explores the factors contributing to OOST dynamics, such as stress interactions between fault segments, fault geometry, and mechanical properties of fault materials. Moreover, it investigates the potential triggers and precursory signals associated with OOST events to enhance early warning systems and emergency response preparedness. The abstract also highlights the significance of incorporating OOST dynamics into seismic hazard assessment methodologies. It discusses the challenges associated with accurately modelling OOST events, including the need for improved understanding of fault interactions, stress transfer mechanisms, and rupture propagation patterns. Additionally, the abstract explores the potential for advanced geophysical techniques, such as high-resolution imaging and seismic monitoring networks, to detect and characterize OOST events. Furthermore, the abstract emphasizes the practical implications of OOST dynamics for earthquake mitigation strategies and urban planning. It addresses the need for revising building codes, land-use regulations, and infrastructure designs to account for the increased seismic hazard associated with OOST events. It also underscores the importance of public awareness campaigns to educate communities about the potential risks and safety measures specific to OOST-induced earthquakes. This sheds light on the impact of out-of-sequence thrust dynamics in earthquake mitigation. By recognizing and understanding OOST events, researchers, engineers, and policymakers can improve hazard assessment methodologies, enhance early warning systems, and implement effective mitigation measures. By integrating knowledge of OOST dynamics into urban planning and infrastructure development, societies can strive for greater resilience in the face of earthquakes, ultimately minimizing the potential for loss of life and infrastructure damage.Keywords: earthquake mitigation, out-of-sequence thrust, seismic, satellite imagery
Procedia PDF Downloads 821028 Design of DNA Origami Structures Using LAMP Products as a Combined System for the Detection of Extended Spectrum B-Lactamases
Authors: Kalaumari Mayoral-Peña, Ana I. Montejano-Montelongo, Josué Reyes-Muñoz, Gonzalo A. Ortiz-Mancilla, Mayrin Rodríguez-Cruz, Víctor Hernández-Villalobos, Jesús A. Guzmán-López, Santiago García-Jacobo, Iván Licona-Vázquez, Grisel Fierros-Romero, Rosario Flores-Vallejo
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The group B-lactamic antibiotics include some of the most frequently used small drug molecules against bacterial infections. Nevertheless, an alarming decrease in their efficacy has been reported due to the emergence of antibiotic-resistant bacteria. Infections caused by bacteria expressing extended Spectrum B-lactamases (ESBLs) are difficult to treat and account for higher morbidity and mortality rates, delayed recovery, and high economic burden. According to the Global Report on Antimicrobial Resistance Surveillance, it is estimated that mortality due to resistant bacteria will ascend to 10 million cases per year worldwide. These facts highlight the importance of developing low-cost and readily accessible detection methods of drug-resistant ESBLs bacteria to prevent their spread and promote accurate and fast diagnosis. Bacterial detection is commonly done using molecular diagnostic techniques, where PCR stands out for its high performance. However, this technique requires specialized equipment not available everywhere, is time-consuming, and has a high cost. Loop-Mediated Isothermal Amplification (LAMP) is an alternative technique that works at a constant temperature, significantly decreasing the equipment cost. It yields double-stranded DNA of several lengths with repetitions of the target DNA sequence as a product. Although positive and negative results from LAMP can be discriminated by colorimetry, fluorescence, and turbidity, there is still a large room for improvement in the point-of-care implementation. DNA origami is a technique that allows the formation of 3D nanometric structures by folding a large single-stranded DNA (scaffold) into a determined shape with the help of short DNA sequences (staples), which hybridize with the scaffold. This research aimed to generate DNA origami structures using LAMP products as scaffolds to improve the sensitivity to detect ESBLs in point-of-care diagnosis. For this study, the coding sequence of the CTM-X-15 ESBL of E. coli was used to generate the LAMP products. The set of LAMP primers were designed using PrimerExplorerV5. As a result, a target sequence of 200 nucleotides from CTM-X-15 ESBL was obtained. Afterward, eight different DNA origami structures were designed using the target sequence in the SDCadnano and analyzed with CanDo to evaluate the stability of the 3D structures. The designs were constructed minimizing the total number of staples to reduce costs and complexity for point-of-care applications. After analyzing the DNA origami designs, two structures were selected. The first one was a zig-zag flat structure, while the second one was a wall-like shape. Given the sequence repetitions in the scaffold sequence, both were able to be assembled with only 6 different staples each one, ranging between 18 to 80 nucleotides. Simulations of both structures were performed using scaffolds of different sizes yielding stable structures in all the cases. The generation of the LAMP products were tested by colorimetry and electrophoresis. The formation of the DNA structures was analyzed using electrophoresis and colorimetry. The modeling of novel detection methods through bioinformatics tools allows reliable control and prediction of results. To our knowledge, this is the first study that uses LAMP products and DNA-origami in combination to delect ESBL-producing bacterial strains, which represent a promising methodology for diagnosis in the point-of-care.Keywords: beta-lactamases, antibiotic resistance, DNA origami, isothermal amplification, LAMP technique, molecular diagnosis
Procedia PDF Downloads 2111027 Studies on Phylogeny of Helicoverpa armigera Populations from North Western Himalaya Region with Help of Cytochromeoxidase I Sequence
Authors: R. M. Srivastava, Subbanna A.R.N.S, Md Abbas Ahmad, S. P.More, Shivashankar, B. Kalyanbabu
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The similar morphology associated with high genetic variability poses problems in phylogenetic studies of Helicoverpa armigera (Hubner). To identify genetic variation of North Western Himalayan population’s, partial (Mid to terminal region) cytochrome c oxidase subunit I (COX-1) gene was amplified and sequenced for three populations collected from Pantnagar, Almora, and Chinyalisaur. The alignment of sequences with other two populations, Nagpur representing central India population and Anhui, China representing complete COX-1 sequence revealed unanimity in middle region with eleven single nucleotide polymorphisms (SNPs) in Nagpur populations. However, the consensus is missing when approaching towards terminal region, which is associated with 15 each SNPs and pair base substitutions in Chinyalisaur populations. In minimum evolution tree, all the five populations were majorly separated into two clades, one comprising of only Nagpur population and the other with rest. Amongst, North Western populations, Chinyalisaur one is promising by farming a separate clade. The pairwise genetic distance ranges from 0.025 to 0.192 with the maximum between H. armigera populations of Nagpur and Chinyalisaur. This genetic isolation of populations can be attributed to a key role of topological barriers of weather and mountain ranges and temporal barriers due to cropping patterns.Keywords: cytochrome c oxidase subunit I, northwestern Himalayan population, Helicoverpa armigera (Noctuidae: Lepidoptera), phylogenetic relationship, genetic variation
Procedia PDF Downloads 3041026 Automated Feature Detection and Matching Algorithms for Breast IR Sequence Images
Authors: Chia-Yen Lee, Hao-Jen Wang, Jhih-Hao Lai
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In recent years, infrared (IR) imaging has been considered as a potential tool to assess the efficacy of chemotherapy and early detection of breast cancer. Regions of tumor growth with high metabolic rate and angiogenesis phenomenon lead to the high temperatures. Observation of differences between the heat maps in long term is useful to help assess the growth of breast cancer cells and detect breast cancer earlier, wherein the multi-time infrared image alignment technology is a necessary step. Representative feature points detection and matching are essential steps toward the good performance of image registration and quantitative analysis. However, there is no clear boundary on the infrared images and the subject's posture are different for each shot. It cannot adhesive markers on a body surface for a very long period, and it is hard to find anatomic fiducial markers on a body surface. In other words, it’s difficult to detect and match features in an IR sequence images. In this study, automated feature detection and matching algorithms with two type of automatic feature points (i.e., vascular branch points and modified Harris corner) are developed respectively. The preliminary results show that the proposed method could identify the representative feature points on the IR breast images successfully of 98% accuracy and the matching results of 93% accuracy.Keywords: Harris corner, infrared image, feature detection, registration, matching
Procedia PDF Downloads 2961025 CRISPR/Cas9 Based Gene Stacking in Plants for Virus Resistance Using Site-Specific Recombinases
Authors: Sabin Aslam, Sultan Habibullah Khan, James G. Thomson, Abhaya M. Dandekar
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Losses due to viral diseases are posing a serious threat to crop production. A quick breakdown of resistance to viruses like Cotton Leaf Curl Virus (CLCuV) demands the application of a proficient technology to engineer durable resistance. Gene stacking has recently emerged as a potential approach for integrating multiple genes in crop plants. In the present study, recombinase technology has been used for site-specific gene stacking. A target vector (pG-Rec) was designed for engineering a predetermined specific site in the plant genome whereby genes can be stacked repeatedly. Using Agrobacterium-mediated transformation, the pG-Rec was transformed into Coker-312 along with Nicotiana tabacum L. cv. Xanthi and Nicotiana benthamiana. The transgene analysis of target lines was conducted through junction PCR. The transgene positive target lines were used for further transformations to site-specifically stack two genes of interest using Bxb1 and PhiC31 recombinases. In the first instance, Cas9 driven by multiplex gRNAs (for Rep gene of CLCuV) was site-specifically integrated into the target lines and determined by the junction PCR and real-time PCR. The resulting plants were subsequently used to stack the second gene of interest (AVP3 gene from Arabidopsis for enhancing cotton plant growth). The addition of the genes is simultaneously achieved with the removal of marker genes for recycling with the next round of gene stacking. Consequently, transgenic marker-free plants were produced with two genes stacked at the specific site. These transgenic plants can be potential germplasm to introduce resistance against various strains of cotton leaf curl virus (CLCuV) and abiotic stresses. The results of the research demonstrate gene stacking in crop plants, a technology that can be used to introduce multiple genes sequentially at predefined genomic sites. The current climate change scenario highlights the use of such technologies so that gigantic environmental issues can be tackled by several traits in a single step. After evaluating virus resistance in the resulting plants, the lines can be a primer to initiate stacking of further genes in Cotton for other traits as well as molecular breeding with elite cotton lines.Keywords: cotton, CRISPR/Cas9, gene stacking, genome editing, recombinases
Procedia PDF Downloads 1461024 Evaluation of the Physico-Chemical and Microbial Properties of the Compost Leachate (CL) to Assess Its Role in the Bioremediation of Polyaromatic Hydrocarbons (PAHs)
Authors: Omaima A. Sharaf, Tarek A. Moussa, Said M. Badr El-Din, H. Moawad
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Background: Polycyclic aromatic hydrocarbons (PAHs) pose great environmental and human health concerns for their widespread occurrence, persistence, and carcinogenic properties. PAHs releases due to anthropogenic activities to the wider environment have led to higher concentrations of these contaminants than would be expected from natural processes alone. This may result in a wide range of environmental problems that can accumulate in agricultural ecosystems, which threatened to become a negative impact on sustainable agricultural development. Thus, this study aimed to evaluate the physico-chemical, and microbial properties of the compost leachate (CL) to assess its role as nutrient and microbial source (biostimulation/bioaugmentation) for developing a cost-effective bioremediation technology for PAHs contaminated sites. Material and Methods: PAHs-degrading bacteria were isolated from CL that was collected from a composting site located in central Scotland, UK. Isolation was carried out by enrichment using phenanthrene (PHR), pyrene (PYR) and benzo(a)pyrene (BaP) as the sole source of carbon and energy. The isolates were characterized using a variety of phenotypic and molecular properties. Six different isolates were identified based on the difference in morphological and biochemical tests. The efficiency of these isolates in PAHs utilization was assessed. Further analysis was performed to define taxonomical status and phylogenic relation between the most potent PAHs-utilizing bacterial strains and other standard strains, using molecular approach by partial 16S rDNA gene sequence analysis. Results indicated that the 16S rDNA sequence analysis confirmed the results of biochemical identification, as both of biochemical and molecular identification of the isolates assigned them to Bacillus licheniformis, Pseudomonas aeruginosa, Alcaligenes faecalis, Serratia marcescens, Enterobacter cloacae and Providenicia which were identified as the prominent PAHs-utilizers isolated from CL. Conclusion: This study indicates that the CL samples contain a diverse population of PAHs-degrading bacteria and the use of CL may have a potential for bioremediation of PAHs contaminated sites.Keywords: polycyclic aromatic hydrocarbons, physico-chemical analyses, compost leachate, microbial and biochemical analyses, phylogenic relations, 16S rDNA sequence analysis
Procedia PDF Downloads 2601023 A Comprehensive Analysis of the Phylogenetic Signal in Ramp Sequences in 211 Vertebrates
Authors: Lauren M. McKinnon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge
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Background: Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Methods: Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences were analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene. Results: Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance. Discussion: Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.Keywords: codon usage bias, phylogenetics, phylogenomics, ramp sequence
Procedia PDF Downloads 1521022 Modeling Competition Between Subpopulations with Variable DNA Content in Resource-Limited Microenvironments
Authors: Parag Katira, Frederika Rentzeperis, Zuzanna Nowicka, Giada Fiandaca, Thomas Veith, Jack Farinhas, Noemi Andor
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Resource limitations shape the outcome of competitions between genetically heterogeneous pre-malignant cells. One example of such heterogeneity is in the ploidy (DNA content) of pre-malignant cells. A whole-genome duplication (WGD) transforms a diploid cell into a tetraploid one and has been detected in 28-56% of human cancers. If a tetraploid subclone expands, it consistently does so early in tumor evolution, when cell density is still low, and competition for nutrients is comparatively weak – an observation confirmed for several tumor types. WGD+ cells need more resources to synthesize increasing amounts of DNA, RNA, and proteins. To quantify resource limitations and how they relate to ploidy, we performed a PAN cancer analysis of WGD, PET/CT, and MRI scans. Segmentation of >20 different organs from >900 PET/CT scans were performed with MOOSE. We observed a strong correlation between organ-wide population-average estimates of Oxygen and the average ploidy of cancers growing in the respective organ (Pearson R = 0.66; P= 0.001). In-vitro experiments using near-diploid and near-tetraploid lineages derived from a breast cancer cell line supported the hypothesis that DNA content influences Glucose- and Oxygen-dependent proliferation-, death- and migration rates. To model how subpopulations with variable DNA content compete in the resource-limited environment of the human brain, we developed a stochastic state-space model of the brain (S3MB). The model discretizes the brain into voxels, whereby the state of each voxel is defined by 8+ variables that are updated over time: stiffness, Oxygen, phosphate, glucose, vasculature, dead cells, migrating cells and proliferating cells of various DNA content, and treat conditions such as radiotherapy and chemotherapy. Well-established Fokker-Planck partial differential equations govern the distribution of resources and cells across voxels. We applied S3MB on sequencing and imaging data obtained from a primary GBM patient. We performed whole genome sequencing (WGS) of four surgical specimens collected during the 1ˢᵗ and 2ⁿᵈ surgeries of the GBM and used HATCHET to quantify its clonal composition and how it changes between the two surgeries. HATCHET identified two aneuploid subpopulations of ploidy 1.98 and 2.29, respectively. The low-ploidy clone was dominant at the time of the first surgery and became even more dominant upon recurrence. MRI images were available before and after each surgery and registered to MNI space. The S3MB domain was initiated from 4mm³ voxels of the MNI space. T1 post and T2 flair scan acquired after the 1ˢᵗ surgery informed tumor cell densities per voxel. Magnetic Resonance Elastography scans and PET/CT scans informed stiffness and Glucose access per voxel. We performed a parameter search to recapitulate the GBM’s tumor cell density and ploidy composition before the 2ⁿᵈ surgery. Results suggest that the high-ploidy subpopulation had a higher Glucose-dependent proliferation rate (0.70 vs. 0.49), but a lower Glucose-dependent death rate (0.47 vs. 1.42). These differences resulted in spatial differences in the distribution of the two subpopulations. Our results contribute to a better understanding of how genomics and microenvironments interact to shape cell fate decisions and could help pave the way to therapeutic strategies that mimic prognostically favorable environments.Keywords: tumor evolution, intra-tumor heterogeneity, whole-genome doubling, mathematical modeling
Procedia PDF Downloads 651021 Antibody Reactivity of Synthetic Peptides Belonging to Proteins Encoded by Genes Located in Mycobacterium tuberculosis-Specific Genomic Regions of Differences
Authors: Abu Salim Mustafa
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The comparisons of mycobacterial genomes have identified several Mycobacterium tuberculosis-specific genomic regions that are absent in other mycobacteria and are known as regions of differences. Due to M. tuberculosis-specificity, the peptides encoded by these regions could be useful in the specific diagnosis of tuberculosis. To explore this possibility, overlapping synthetic peptides corresponding to 39 proteins predicted to be encoded by genes present in regions of differences were tested for antibody-reactivity with sera from tuberculosis patients and healthy subjects. The results identified four immunodominant peptides corresponding to four different proteins, with three of the peptides showing significantly stronger antibody reactivity and rate of positivity with sera from tuberculosis patients than healthy subjects. The fourth peptide was recognized equally well by the sera of tuberculosis patients as well as healthy subjects. Predication of antibody epitopes by bioinformatics analyses using ABCpred server predicted multiple linear epitopes in each peptide. Furthermore, peptide sequence analysis for sequence identity using BLAST suggested M. tuberculosis-specificity for the three peptides that had preferential reactivity with sera from tuberculosis patients, but the peptide with equal reactivity with sera of TB patients and healthy subjects showed significant identity with sequences present in nob-tuberculous mycobacteria. The three identified M. tuberculosis-specific immunodominant peptides may be useful in the serological diagnosis of tuberculosis.Keywords: genomic regions of differences, Mycobacterium tuberculossis, peptides, serodiagnosis
Procedia PDF Downloads 1771020 Integration of Microarray Data into a Genome-Scale Metabolic Model to Study Flux Distribution after Gene Knockout
Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati
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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.Keywords: metabolic network, gene knockout, flux balance analysis, microarray data, integration
Procedia PDF Downloads 5741019 Speech Detection Model Based on Deep Neural Networks Classifier for Speech Emotions Recognition
Authors: A. Shoiynbek, K. Kozhakhmet, P. Menezes, D. Kuanyshbay, D. Bayazitov
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Speech emotion recognition has received increasing research interest all through current years. There was used emotional speech that was collected under controlled conditions in most research work. Actors imitating and artificially producing emotions in front of a microphone noted those records. There are four issues related to that approach, namely, (1) emotions are not natural, and it means that machines are learning to recognize fake emotions. (2) Emotions are very limited by quantity and poor in their variety of speaking. (3) There is language dependency on SER. (4) Consequently, each time when researchers want to start work with SER, they need to find a good emotional database on their language. In this paper, we propose the approach to create an automatic tool for speech emotion extraction based on facial emotion recognition and describe the sequence of actions of the proposed approach. One of the first objectives of the sequence of actions is a speech detection issue. The paper gives a detailed description of the speech detection model based on a fully connected deep neural network for Kazakh and Russian languages. Despite the high results in speech detection for Kazakh and Russian, the described process is suitable for any language. To illustrate the working capacity of the developed model, we have performed an analysis of speech detection and extraction from real tasks.Keywords: deep neural networks, speech detection, speech emotion recognition, Mel-frequency cepstrum coefficients, collecting speech emotion corpus, collecting speech emotion dataset, Kazakh speech dataset
Procedia PDF Downloads 921018 Orbital Tuning of Marl-Limestone Alternations (Upper Tithonian to Upper Berriasian) in North-South Axis (Tunisia): Geochronology and Sequence Implications
Authors: Hamdi Omar Omar, Hela Fakhfakh, Chokri Yaich
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This work reflects the integration of different techniques, such as field sampling and observations, magnetic susceptibility measurement, cyclostratigaraphy and sequence stratigraphy. The combination of these results allows us to reconstruct the environmental evolution of the Sidi Khalif Formation in the North-South Axis (NOSA), aged of Upper Tithonian, Berriasian and Lower Valanginian. Six sedimentary facies were identified and are primarily influenced by open marine sedimentation receiving increasing terrigenous influx. Spectral analysis, based on MS variation (for the outcropped section) and wireline logging gamma ray (GR) variation (for the sub-area section) show a pervasive dominance of 405-kyr eccentricity cycles with the expression of 100-kyr eccentricity, obliquity and precession. This study provides (for the first time) a precise duration of 2.4 myr for the outcropped Sidi Khalif Formation with a sedimentation rate of 5.4 cm/kyr and the sub-area section to 3.24 myr with a sedimentation rate of 7.64 cm/kyr. We outlined 27 5th-order depositional sequences, 8 Milankovitch depositional sequences and 2 major 3rd-order cycles for the outcropping section, controlled by the long eccentricity (405 kyr) cycles and the precession index cycles. This study has demonstrated the potential of MS and GR to be used as proxies to develop an astronomically calibrated time-scale for the Mesozoic era.Keywords: Berriasian, magnetic susceptibility, orbital tuning, Sidi Khalif Formation
Procedia PDF Downloads 2591017 Sequential Pattern Mining from Data of Medical Record with Sequential Pattern Discovery Using Equivalent Classes (SPADE) Algorithm (A Case Study : Bolo Primary Health Care, Bima)
Authors: Rezky Rifaini, Raden Bagus Fajriya Hakim
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This research was conducted at the Bolo primary health Care in Bima Regency. The purpose of the research is to find out the association pattern that is formed of medical record database from Bolo Primary health care’s patient. The data used is secondary data from medical records database PHC. Sequential pattern mining technique is the method that used to analysis. Transaction data generated from Patient_ID, Check_Date and diagnosis. Sequential Pattern Discovery Algorithms Using Equivalent Classes (SPADE) is one of the algorithm in sequential pattern mining, this algorithm find frequent sequences of data transaction, using vertical database and sequence join process. Results of the SPADE algorithm is frequent sequences that then used to form a rule. It technique is used to find the association pattern between items combination. Based on association rules sequential analysis with SPADE algorithm for minimum support 0,03 and minimum confidence 0,75 is gotten 3 association sequential pattern based on the sequence of patient_ID, check_Date and diagnosis data in the Bolo PHC.Keywords: diagnosis, primary health care, medical record, data mining, sequential pattern mining, SPADE algorithm
Procedia PDF Downloads 3951016 Biocultural Biographies and Molecular Memories: A Study of Neuroepigenetics and How Trauma Gets under the Skull
Authors: Elsher Lawson-Boyd
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In the wake of the Human Genome Project, the life sciences have undergone some fascinating changes. In particular, conventional beliefs relating to gene expression are being challenged by advances in postgenomic sciences, especially by the field of epigenetics. Epigenetics is the modification of gene expression without changes in the DNA sequence. In other words, epigenetics dictates that gene expression, the process by which the instructions in DNA are converted into products like proteins, is not solely controlled by DNA itself. Unlike gene-centric theories of heredity that characterized much of the 20th Century (where the genes were considered as having almost god-like power to create life), gene expression in epigenetics insists on environmental ‘signals’ or ‘exposures’, a point that radically deviates from gene-centric thinking. Science and Technology Studies (STS) scholars have shown that epigenetic research is having vast implications for the ways in which chronic, non-communicable diseases are conceptualized, treated, and governed. However, to the author’s knowledge, there have not yet been any in-depth sociological engagements with neuroepigenetics that examine how the field is affecting mental health and trauma discourse. In this paper, the author discusses preliminary findings from a doctoral ethnographic study on neuroepigenetics, trauma, and embodiment. Specifically, this study investigates the kinds of causal relations neuroepigenetic researchers are making between experiences of trauma and the development of mental illnesses like complex post-traumatic stress disorder (PTSD), both throughout a human’s lifetime and across generations. Using qualitative interviews and nonparticipant observation, the author focuses on two public-facing research centers based in Melbourne: Florey Institute of Neuroscience and Mental Health (FNMH), and Murdoch Children’s Research Institute (MCRI). Preliminary findings indicate that a great deal of ambiguity characterizes this infant field, particularly when animal-model experiments are employed and the results are translated into human frameworks. Nevertheless, researchers at the FNMH and MCRI strongly suggest that adverse and traumatic life events have a significant effect on gene expression, especially when experienced during early development. Furthermore, they predict that neuroepigenetic research will have substantial implications for the ways in which mental illnesses like complex PTSD are diagnosed and treated. These preliminary findings shed light on why medical and health sociologists have good reason to be chiming in, engaging with and de-black-boxing ideations emerging from postgenomic sciences, as they may indeed have significant effects for vulnerable populations not only in Australia but other developing countries in the Global South.Keywords: genetics, mental illness, neuroepigenetics, trauma
Procedia PDF Downloads 1221015 Valorization of Waste Reverse Osmosis Desalination Brine and Crystallization Sequence Approach for Kainite Recovery
Authors: Ayoub Bouazza, Ali Faddouli, Said Amal, Rachid Benhida, Khaoula Khaless
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Brine waste generated from reverse osmosis (RO) desalination plants contains various valuable compounds, mainly salts, trace elements, and organic matter. These wastes are up to two times saltier than standard seawater. Therefore, there is a strong economic interest in recovering these salts. The current practice in desalination plants is to reject the brine back to the sea, which affects the marine ecosystem and the environment. Our study aims to bring forth a reliable management solution for the valorisation of waste brines. Natural evaporation, isothermal evaporation at 25°C and 50°C, and evaporation using continuous heating were used to crystallize valuable salts from a reverse osmosis desalination plant brine located on the Moroccan Atlantic coast. The crystallization sequence of the brine was studied in comparison with standard seawater. The X-Ray Diffraction (XRD) of the precipitated solid phases showed similar results, where halite was the main solid phase precipitated from both the brine and seawater. However, Jänecke diagram prediction, along with FREZCHEM simulations, showed that Kainite should crystallize before Epsomite and Carnallite. As the absence of kainite formation in many experiments in the literature has been related to the metastability of kainite and the critical relative humidity conditions, and the precipitation of K–Mg salts is very sensitive to climatic conditions. An evaporation process is proposed as a solution to achieve the predicted crystallization path and to affirm the recovery of Kainite.Keywords: salts crystallization, reverse osmosis, solar evaporation, frezchem, ZLD
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