Search results for: DNA sequence analysis
28122 Morphological and Molecular Identification of Endophytic Colletotrichum Species from Medicinal Plants and Their Antimicrobial Potential
Authors: Gauravi Agarkar, Mahendra Rai
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Endophytic fungi from medicinal plants are important source of numerous pharmacologically important compounds. In the present investigation, the endophytic fungi were isolated from three medicinal plants; Andrographis paniculata, Rauwolfia serpentina and Tridax procumbens. Endophytic Colletotrichum sp. were identified on the basis of cultural and morphological characteristics as well as internal transcribed spacer (ITS) sequence analysis. Antibacterial and antifungal activity of the ethyl acetate and methanol extract of endophytic Colletotrichum sp. was evaluated against seven different human pathogenic bacteria and six Candida sp. The extracts were effective and showed significant activity against all the test pathogens. In case of yeast Candida, the combined effect of extracts and standard antibiotic was enhanced greatly showing synergistic activity. Further, the extracts were assayed for Minimum Inhibitory Concentration (MIC) and Minimum Bactericidal/Fungicidal Concentration (MBC/MFC) where, MIC values were in the range of 100-250 μg/ml. These results suggest that the endophytic Colletotrichum sp. isolated from the medicinal plants are capable of producing promising antimicrobial metabolites.Keywords: antimicrobial, colletotrichum, endophytic fungi, medicinal plants
Procedia PDF Downloads 56228121 Molecular-Genetics Studies of New Unknown APMV Isolated from Wild Bird in Ukraine
Authors: Borys Stegniy, Anton Gerilovych, Oleksii Solodiankin, Vitaliy Bolotin, Anton Stegniy, Denys Muzyka, Claudio Afonso
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New APMV was isolated from white fronted goose in Ukraine. This isolate was tested serologically using monoclonal antibodies in haemagglutination-inhibition tests against APMV1-9. As the results obtained isolate showed cross reactions with APMV7. Following investigations were provided for the full genome sequencing using random primers and cloning into pCRII-TOPO. Analysis of 100 transformed colonies of E.coli using traditional sequencing gave us possibilities to find only 3 regions, which could identify by BLAST. The first region with the length of 367 bp had 70 % nucleotide sequence identity to the APMV 12 isolate Wigeon/Italy/3920_1/2005 at genome position 2419-2784. Next region (344 bp) had 66 % identity to the same APMV 12 isolate at position 4760-5103. The last region (365 bp) showed 71 % identity to Newcastle disease virus strain M4 at position 12569-12928.Keywords: APMV, Newcastle disease virus, Ukraine, full genome sequencing
Procedia PDF Downloads 44228120 An Overview of Bioinformatics Methods to Detect Novel Riboswitches Highlighting the Importance of Structure Consideration
Authors: Danny Barash
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Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods
Procedia PDF Downloads 23428119 Empirical Study of Running Correlations in Exam Marks: Same Statistical Pattern as Chance
Authors: Weisi Guo
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It is well established that there may be running correlations in sequential exam marks due to students sitting in the order of course registration patterns. As such, a random and non-sequential sampling of exam marks is a standard recommended practice. Here, the paper examines a large number of exam data stretching several years across different modules to see the degree to which it is true. Using the real mark distribution as a generative process, it was found that random simulated data had no more sequential randomness than the real data. That is to say, the running correlations that one often observes are statistically identical to chance. Digging deeper, it was found that some high running correlations have students that indeed share a common course history and make similar mistakes. However, at the statistical scale of a module question, the combined effect is statistically similar to the random shuffling of papers. As such, there may not be the need to take random samples for marks, but it still remains good practice to mark papers in a random sequence to reduce the repetitive marking bias and errors.Keywords: data analysis, empirical study, exams, marking
Procedia PDF Downloads 18128118 Evaluation of Real-Time Background Subtraction Technique for Moving Object Detection Using Fast-Independent Component Analysis
Authors: Naoum Abderrahmane, Boumehed Meriem, Alshaqaqi Belal
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Background subtraction algorithm is a larger used technique for detecting moving objects in video surveillance to extract the foreground objects from a reference background image. There are many challenges to test a good background subtraction algorithm, like changes in illumination, dynamic background such as swinging leaves, rain, snow, and the changes in the background, for example, moving and stopping of vehicles. In this paper, we propose an efficient and accurate background subtraction method for moving object detection in video surveillance. The main idea is to use a developed fast-independent component analysis (ICA) algorithm to separate background, noise, and foreground masks from an image sequence in practical environments. The fast-ICA algorithm is adapted and adjusted with a matrix calculation and searching for an optimum non-quadratic function to be faster and more robust. Moreover, in order to estimate the de-mixing matrix and the denoising de-mixing matrix parameters, we propose to convert all images to YCrCb color space, where the luma component Y (brightness of the color) gives suitable results. The proposed technique has been verified on the publicly available datasets CD net 2012 and CD net 2014, and experimental results show that our algorithm can detect competently and accurately moving objects in challenging conditions compared to other methods in the literature in terms of quantitative and qualitative evaluations with real-time frame rate.Keywords: background subtraction, moving object detection, fast-ICA, de-mixing matrix
Procedia PDF Downloads 9628117 A Comparative Study on Sampling Techniques of Polynomial Regression Model Based Stochastic Free Vibration of Composite Plates
Authors: S. Dey, T. Mukhopadhyay, S. Adhikari
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This paper presents an exhaustive comparative investigation on sampling techniques of polynomial regression model based stochastic natural frequency of composite plates. Both individual and combined variations of input parameters are considered to map the computational time and accuracy of each modelling techniques. The finite element formulation of composites is capable to deal with both correlated and uncorrelated random input variables such as fibre parameters and material properties. The results obtained by Polynomial regression (PR) using different sampling techniques are compared. Depending on the suitability of sampling techniques such as 2k Factorial designs, Central composite design, A-Optimal design, I-Optimal, D-Optimal, Taguchi’s orthogonal array design, Box-Behnken design, Latin hypercube sampling, sobol sequence are illustrated. Statistical analysis of the first three natural frequencies is presented to compare the results and its performance.Keywords: composite plate, natural frequency, polynomial regression model, sampling technique, uncertainty quantification
Procedia PDF Downloads 51228116 DNA Barcoding of Tree Endemic Campanula Species From Artvi̇n, Türki̇ye
Authors: Hayal Akyildirim Beğen, Özgür Emi̇nağaoğlu
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DNA barcoding is the method of description of species based on gene diversity. In current studies, registration, genetic identification and protection of especially endemic plants pecies are carried out by DNA barcoding techniques. Molecular studies are based on the amplification and sequencing of the barcode gene region by the PCR method. Endemic Campanula choruhensis Kit Tan & Sorger, Campanula troegera Damboldt and Campanula betulifolia K.Koch is widespread in Artvin, Erzurum and around Çoruh valley passing through it. Intense road and dam constructions are carried out in and around the distribution area of this species. This situation harms the habitat of the species and puts its extinction. In this study, the plastid matK barcode gene regions (650 bp) of three Campanula species were created. To make the identification of this species quickly and accurately, gene sequence compared with sequences of other Campanula L. species. As a result of phylogenetic analysis, C. choruhensis is close relative to C. betulifolia. Morphologically, these species were determined to be more similar to each other with flower and leaf characters. C. troegera formed a separate branch.Keywords: campanula, DNA barcoding, endemic, türkiye, artvin
Procedia PDF Downloads 6828115 A Computational Framework for Decoding Hierarchical Interlocking Structures with SL Blocks
Authors: Yuxi Liu, Boris Belousov, Mehrzad Esmaeili Charkhab, Oliver Tessmann
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This paper presents a computational solution for designing reconfigurable interlocking structures that are fully assembled with SL Blocks. Formed by S-shaped and L-shaped tetracubes, SL Block is a specific type of interlocking puzzle. Analogous to molecular self-assembly, the aggregation of SL blocks will build a reversible hierarchical and discrete system where a single module can be numerously replicated to compose semi-interlocking components that further align, wrap, and braid around each other to form complex high-order aggregations. These aggregations can be disassembled and reassembled, responding dynamically to design inputs and changes with a unique capacity for reconfiguration. To use these aggregations as architectural structures, we developed computational tools that automate the configuration of SL blocks based on architectural design objectives. There are three critical phases in our work. First, we revisit the hierarchy of the SL block system and devise a top-down-type design strategy. From this, we propose two key questions: 1) How to translate 3D polyominoes into SL block assembly? 2) How to decompose the desired voxelized shapes into a set of 3D polyominoes with interlocking joints? These two questions can be considered the Hamiltonian path problem and the 3D polyomino tiling problem. Then, we derive our solution to each of them based on two methods. The first method is to construct the optimal closed path from an undirected graph built from the voxelized shape and translate the node sequence of the resulting path into the assembly sequence of SL blocks. The second approach describes interlocking relationships of 3D polyominoes as a joint connection graph. Lastly, we formulate the desired shapes and leverage our methods to achieve their reconfiguration within different levels. We show that our computational strategy will facilitate the efficient design of hierarchical interlocking structures with a self-replicating geometric module.Keywords: computational design, SL-blocks, 3D polyomino puzzle, combinatorial problem
Procedia PDF Downloads 12928114 Analysis of Capillarity Phenomenon Models in Primary and Secondary Education in Spain: A Case Study on the Design, Implementation, and Analysis of an Inquiry-Based Teaching Sequence
Authors: E. Cascarosa-Salillas, J. Pozuelo-Muñoz, C. Rodríguez-Casals, A. de Echave
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This study focuses on improving the understanding of the capillarity phenomenon among Primary and Secondary Education students. Despite being a common concept in daily life and covered in various subjects, students’ comprehension remains limited. This work explores inquiry-based teaching methods to build a conceptual foundation of capillarity by examining the forces involved. The study adopts an inquiry-based teaching approach supported by research emphasizing the importance of modeling in science education. Scientific modeling aids students in applying knowledge across varied contexts and developing systemic thinking, allowing them to construct scientific models applicable to everyday situations. This methodology fosters the development of scientific competencies such as observation, hypothesis formulation, and communication. The research was structured as a case study with activities designed for Spanish Primary and Secondary Education students aged 9 to 13. The process included curriculum analysis, the design of an activity sequence, and its implementation in classrooms. Implementation began with questions that students needed to resolve using available materials, encouraging observation, experimentation, and the re-contextualization of activities to everyday phenomena where capillarity is observed. Data collection tools included audio and video recordings of the sessions, which were transcribed and analyzed alongside the students' written work. Students' drawings on capillarity were also collected and categorized. Qualitative analyses of the activities showed that, through inquiry, students managed to construct various models of capillarity, reflecting an improved understanding of the phenomenon. Initial activities allowed students to express prior ideas and formulate hypotheses, which were then refined and expanded in subsequent sessions. The generalization and use of graphical representations of their ideas on capillarity, analyzed alongside their written work, enabled the categorization of capillarity models: Intuitive Model: A visual and straightforward representation without explanations of how or why it occurs. Simple symbolic elements, such as arrows to indicate water rising, are used without detailed or causal understanding. It reflects an initial, immediate perception of the phenomenon, interpreted as something that happens "on its own" without delving into the microscopic level. Explanatory Intuitive Model: Students begin to incorporate causal explanations, though still limited and without complete scientific accuracy. They represent the role of materials and use basic terms such as ‘absorption’ or ‘attraction’ to describe the rise of water. This model shows a more complex understanding where the phenomenon is not only observed but also partially explained in terms of interaction, though without microscopic detail. School Scientific Model: This model reflects a more advanced and detailed understanding. Students represent the phenomenon using specific scientific concepts like ‘surface tension,’ cohesion,’ and ‘adhesion,’ including structured explanations connecting microscopic and macroscopic levels. At this level, students model the phenomenon as a coherent system, demonstrating how various forces or properties interact in the capillarity process, with representations on a microscopic level. The study demonstrated that the capillarity phenomenon can be effectively approached in class through the experimental observation of everyday phenomena, explained through guided inquiry learning. The methodology facilitated students’ construction of capillarity models and served to analyze an interaction phenomenon of different forces occurring at the microscopic level.Keywords: capillarity, inquiry-based learning, scientific modeling, primary and secondary education, conceptual understanding, Drawing analysis.
Procedia PDF Downloads 1328113 Legal Judgment Prediction through Indictments via Data Visualization in Chinese
Authors: Kuo-Chun Chien, Chia-Hui Chang, Ren-Der Sun
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Legal Judgment Prediction (LJP) is a subtask for legal AI. Its main purpose is to use the facts of a case to predict the judgment result. In Taiwan's criminal procedure, when prosecutors complete the investigation of the case, they will decide whether to prosecute the suspect and which article of criminal law should be used based on the facts and evidence of the case. In this study, we collected 305,240 indictments from the public inquiry system of the procuratorate of the Ministry of Justice, which included 169 charges and 317 articles from 21 laws. We take the crime facts in the indictments as the main input to jointly learn the prediction model for law source, article, and charge simultaneously based on the pre-trained Bert model. For single article cases where the frequency of the charge and article are greater than 50, the prediction performance of law sources, articles, and charges reach 97.66, 92.22, and 60.52 macro-f1, respectively. To understand the big performance gap between articles and charges, we used a bipartite graph to visualize the relationship between the articles and charges, and found that the reason for the poor prediction performance was actually due to the wording precision. Some charges use the simplest words, while others may include the perpetrator or the result to make the charges more specific. For example, Article 284 of the Criminal Law may be indicted as “negligent injury”, "negligent death”, "business injury", "driving business injury", or "non-driving business injury". As another example, Article 10 of the Drug Hazard Control Regulations can be charged as “Drug Control Regulations” or “Drug Hazard Control Regulations”. In order to solve the above problems and more accurately predict the article and charge, we plan to include the article content or charge names in the input, and use the sentence-pair classification method for question-answer problems in the BERT model to improve the performance. We will also consider a sequence-to-sequence approach to charge prediction.Keywords: legal judgment prediction, deep learning, natural language processing, BERT, data visualization
Procedia PDF Downloads 12128112 DNA Polymorphism Studies of β-Lactoglobulin Gene in Native Saudi Goat Breeds
Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek
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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis
Procedia PDF Downloads 50128111 A Cross Cultural Study of Jewish and Arab Listeners: Perception of Harmonic Sequences
Authors: Roni Granot
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Musical intervals are the building blocks of melody and harmony. Intervals differ in terms of their size, direction, or quality as consonants or dissonants. In Western music, perceptual dissonance is mostly associated with the sensation of beats or periodicity, whereas cognitive dissonance is associated with rules of harmony and voice leading. These two perceptions can be studied separately in musical cultures which include melodic with little or no harmonic structures. In the Arab musical system, there is a number of different quarter- tone intervals creating various combinations of consonant and dissonant intervals. While traditional Arab music includes only melody, today’s Arab pop music includes harmonization of songs, often using typical Western harmonic sequences. Therefore, the Arab population in Israel presents an interesting case which enables us to examine the distinction between perceptual and cognitive dissonance. In the current study, we compared the responses of 34 Jewish Western listeners and 56 Arab listeners to two types of stimuli and their relationships: Harmonic sequences and isolated harmonic intervals (dyads). Harmonic sequences were presented in synthesized piano tones and represented five levels of Harmonic prototypicality (Tonic ending; Tonic ending with half flattened third; Deceptive cadence; Half cadence; and Dissonant unrelated ending) and were rated on 5-point scales of closure and surprise. Here we report only findings related to the harmonic sequences. One-way repeated measures ANOVA with one within subjects factor with five levels (Type of sequence) and one between- subjects factor (Musical background) indicates a main effect of Type of sequence for surprise ratings F (4, 85) = 51 p<.001, and for closure ratings F (4, 78) 9.54 p < .001, no main effect of Background on either surprise or closure ratings, and a marginally significant Type X Background interaction for surprise F (4, 352) = 6.05 p = .069 and closure ratings F (4, 324) 3.89 p < .01). Planned comparisons show that the interaction of Type of sequence X Background center around surprise and closure ratings of the regular versus the half- flattened third tonic and the deceptive versus the half cadence. The half- flattened third tonic is rated as less surprising and as demanding less continuation than the regular tonic by the Arab listeners as compared to the Western listeners. In addition, the half cadence is rated as more surprising but demanding less continuation than the deceptive cadence in the Arab listeners as compared to the Western listeners. Together, our results suggest that despite the vast exposure of Arab listeners to Western harmony, sensitivity to harmonic rules seems to be partial with preference to oriental sonorities such as half flattened third. In addition, the percept of directionality which demands sensitivity to the level on which closure is obtained and which is strongly entrenched in Western harmony, may not be fully integrated into the Arab listeners’ mental harmonic scheme. Results will be discussed in terms of broad differences between Western and Eastern aesthetic ideals.Keywords: harmony, cross cultural, Arab music, closure
Procedia PDF Downloads 27528110 Protein Remote Homology Detection by Using Profile-Based Matrix Transformation Approaches
Authors: Bin Liu
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As one of the most important tasks in protein sequence analysis, protein remote homology detection has been studied for decades. Currently, the profile-based methods show state-of-the-art performance. Position-Specific Frequency Matrix (PSFM) is widely used profile. However, there exists noise information in the profiles introduced by the amino acids with low frequencies. In this study, we propose a method to remove the noise information in the PSFM by removing the amino acids with low frequencies called Top frequency profile (TFP). Three new matrix transformation methods, including Autocross covariance (ACC) transformation, Tri-gram, and K-separated bigram (KSB), are performed on these profiles to convert them into fixed length feature vectors. Combined with Support Vector Machines (SVMs), the predictors are constructed. Evaluated on two benchmark datasets, and experimental results show that these proposed methods outperform other state-of-the-art predictors.Keywords: protein remote homology detection, protein fold recognition, top frequency profile, support vector machines
Procedia PDF Downloads 12528109 Molecular Identification of Camel Tick and Investigation of Its Natural Infection by Rickettsia and Borrelia in Saudi Arabia
Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi
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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene
Procedia PDF Downloads 27628108 Approximation Property Pass to Free Product
Authors: Kankeyanathan Kannan
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On approximation properties of group C* algebras is everywhere; it is powerful, important, backbone of countless breakthroughs. For a discrete group G, let A(G) denote its Fourier algebra, and let M₀A(G) denote the space of completely bounded Fourier multipliers on G. An approximate identity on G is a sequence (Φn) of finitely supported functions such that (Φn) uniformly converge to constant function 1 In this paper we prove that approximation property pass to free product.Keywords: approximation property, weakly amenable, strong invariant approximation property, invariant approximation property
Procedia PDF Downloads 67528107 Multiscale Process Modeling Analysis for the Prediction of Composite Strength Allowables
Authors: Marianna Maiaru, Gregory M. Odegard
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During the processing of high-performance thermoset polymer matrix composites, chemical reactions occur during elevated pressure and temperature cycles, causing the constituent monomers to crosslink and form a molecular network that gradually can sustain stress. As the crosslinking process progresses, the material naturally experiences a gradual shrinkage due to the increase in covalent bonds in the network. Once the cured composite completes the cure cycle and is brought to room temperature, the thermal expansion mismatch of the fibers and matrix cause additional residual stresses to form. These compounded residual stresses can compromise the reliability of the composite material and affect the composite strength. Composite process modeling is greatly complicated by the multiscale nature of the composite architecture. At the molecular level, the degree of cure controls the local shrinkage and thermal-mechanical properties of the thermoset. At the microscopic level, the local fiber architecture and packing affect the magnitudes and locations of residual stress concentrations. At the macroscopic level, the layup sequence controls the nature of crack initiation and propagation due to residual stresses. The goal of this research is use molecular dynamics (MD) and finite element analysis (FEA) to predict the residual stresses in composite laminates and the corresponding effect on composite failure. MD is used to predict the polymer shrinkage and thermomechanical properties as a function of degree of cure. This information is used as input into FEA to predict the residual stresses on the microscopic level resulting from the complete cure process. Virtual testing is subsequently conducted to predict strength allowables. Experimental characterization is used to validate the modeling.Keywords: molecular dynamics, finite element analysis, processing modeling, multiscale modeling
Procedia PDF Downloads 9128106 The Advantages of Using DNA-Barcoding for Determining the Fraud in Seafood
Authors: Elif Tugce Aksun Tumerkan
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Although seafood is an important part of human diet and categorized highly traded food industry internationally, it is remain overlooked generally in the global food security aspect. Food product authentication is the main interest in the aim of both avoids commercial fraud and to consider the risks that might be harmful to human health safety. In recent years, with increasing consumer demand for regarding food content and it's transparency, there are some instrumental analyses emerging for determining food fraud depend on some analytical methodologies such as proteomic and metabolomics. While, fish and seafood consumed as fresh previously, within advanced technology, processed or packaged seafood consumption have increased. After processing or packaging seafood, morphological identification is impossible when some of the external features have been removed. The main fish and seafood quality-related issues are the authentications of seafood contents such as mislabelling products which may be contaminated and replacement partly or completely, by lower quality or cheaper ones. For all mentioned reasons, truthful consistent and easily applicable analytical methods are needed for assurance the correct labelling and verifying of seafood products. DNA-barcoding methods become popular robust that used in taxonomic research for endangered or cryptic species in recent years; they are used for determining food traceability also. In this review, when comparing the other proteomic and metabolic analysis, DNA-based methods are allowing a chance to identification all type of food even as raw, spiced and processed products. This privilege caused by DNA is a comparatively stable molecule than protein and other molecules. Furthermore showing variations in sequence based on different species and founding in all organisms, make DNA-based analysis more preferable. This review was performed to clarify the main advantages of using DNA-barcoding for determining seafood fraud among other techniques.Keywords: DNA-barcoding, genetic analysis, food fraud, mislabelling, packaged seafood
Procedia PDF Downloads 16828105 Physical Education Teacher's Interpretation toward Teaching Games for Understanding Model
Authors: Soni Nopembri
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The objective of this research is to evaluate the implementation of teaching games for Understanding model by conducting action to physical education teacher who have got long teaching experience. The research applied Participatory Action Research. The subjects of this research were 19 physical education teachers who had got training of Teaching Games for Understanding. Data collection was conducted intensively through a questionnaire, in-depth interview, Focus Group Discussion (FGD), observation, and documentation. The collected data was analysis zed qualitatively and quantitatively. The result showed that physical education teachers had got an appropriate interpretation on TGfU model. Some indicators that were the focus of this research indicated this points; they are: (1) physical education teachers had good understanding toward TGfU model, (2) PE teachers’ competence in applying TGfU model on Physical Education at school were adequate, though some improvement were needed, (3) the influence factors in the implementation of TGfU model, in sequence, were teacher, facilities, environment, and students factors, (4) PE teachers’ perspective toward TGfU model were positively good, although some teachers were less optimistic toward the development of TGfU model in the future.Keywords: TGfU, physical education teacher, teaching games, FGD
Procedia PDF Downloads 54528104 Antioxidant Activity of Probiotic Lactic Acid Bacteria and Their Application in Fermented Milk Products
Authors: Vitheejongjaroen P., Jaisin Y., Pachekrepapol U., Taweechotipatr M.
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Lactic acid bacteria (LAB) are the most common type of microorganisms that had been used as probiotics also known for many beneficial health effects. The antioxidant activity of LAB is associated with numerous health-protective effects. This research aimed to investigate the antioxidant activity of lactic acid bacteria isolated from Thai sour pork sausage for their application in fermented milk products. Antioxidant activity determined by DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging assay showed that the isolate FN33-7, as 1 of 8 isolated exhibited scavenging activity in intact cell 5-7%, and supernatant 13-16%, intracellular cell free extract 42-48% respectively. This isolate was identified using 16S ribosomal DNA sequence analysis as Lactobacillus plantarum. The effect of milk fermented with L. plantarum FN33-7 on microbial count, pH and syneresis was assessed during refrigerated storage period of 28 days. The strain showed increased viability, pH level decreased, while syneresis increased. These results are similar to dairy products fermented with commercial starter cultures. Additionally, microstructure analysis of fermented milk by fluorescent microscopy showed that curd structure appeared to be dense and less porous in this fermented milk than commercial yogurt. The results of this study indicated that L. plantarum FN33-7 was a good probiotic candidate to be used in cultured milk products to reduce the risk of diseases caused by oxidative stress.Keywords: Lactobacillus plantarum, probiotics, free radical, antioxidant, oxidative stress, fermented milk products
Procedia PDF Downloads 13028103 Sustaining Language Learning: A Case Study of Multilingual Writers' ePortfolios
Authors: Amy Hodges, Deanna Rasmussen, Sherry Ward
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This paper examines the use of ePortfolios in a two-course sequence for ESL (English as a Second Language) students at an international branch campus in Doha, Qatar. ePortfolios support the transfer of language learning, but few have examined the sustainability of that transfer across an ESL program. Drawing upon surveys and interviews with students, we analyze three case studies that complicate previous research on metacognition, language learning, and ePortfolios. Our findings have implications for those involved in ESL programs and assessment of student writing.Keywords: TESOL, electronic portfolios, assessment, technology
Procedia PDF Downloads 26128102 A CORDIC Based Design Technique for Efficient Computation of DCT
Authors: Deboraj Muchahary, Amlan Deep Borah Abir J. Mondal, Alak Majumder
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A discrete cosine transform (DCT) is described and a technique to compute it using fast Fourier transform (FFT) is developed. In this work, DCT of a finite length sequence is obtained by incorporating CORDIC methodology in radix-2 FFT algorithm. The proposed methodology is simple to comprehend and maintains a regular structure, thereby reducing computational complexity. DCTs are used extensively in the area of digital processing for the purpose of pattern recognition. So the efficient computation of DCT maintaining a transparent design flow is highly solicited.Keywords: DCT, DFT, CORDIC, FFT
Procedia PDF Downloads 47828101 Drought Alters the Expression of a Candidate Zea Mays P-Coumarate 3-Hydroxylase Gene and Caffeic Acid Biosynthesis
Authors: Zintle Kolo, Ndiko Ludidi
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The enzymatic activity of p-coumarate 3-hydroxylase (C3H) synthesize caffeic acid from p-coumaric acid. We recently showed that exogenously applied caffeic acid confers salinity tolerance in soybean (Glycine max) by inducing antioxidant enzymatic activity to promote enhanced scavenging or reactive oxygen species, thus limiting salinity-induced oxidative stress. Recent evidence also establishes that pre-treatment of plants with exogenously supplied caffeic acid improves plant tolerance to osmotic stress by improving plant antioxidant capacity and enhancing biosynthesis of compatible solutes. We aimed to identify a C3H in maize (Zea mays) and evaluate the effect of drought on the spatial and temporal expression of the gene encoding the candidate maize C3H (ZmC3H). Primary sequence analysis shows that ZmC3H shares 71% identity with an Arabidopsis thaliana C3H that is implicated in the control of Arabidopsis cell expansion, growth, and responses to stress. In silico ZmC3H promoter analysis reveals the presence of cis-acting elements that interact with transcription factors implicated in plant responses to drought. Spatial expression analysis by semi-quantitative RT-PCR shows that ZmC3H is expressed in both leaves and roots under normal conditions. However, drought represses the expression of ZmC3H in leaves whereas it up-regulates its expression in roots. These changes in ZmC3H expression correlate with the changes in the content of caffeic acid in maize in response to drought. We illustrate the implications of these changes in the expression of the gene in relation to maize responses to drought and discuss the potential of regulating caffeic acid biosynthesis towards genetic improvement of maize tolerance to drought stress. These findings have implications for food security because of the potential of the implications of the study for drought tolerance in maize.Keywords: caffeic acid, drought-responsive expression, maize drought tolerance, p-coumarate 3-hydroxylase
Procedia PDF Downloads 47228100 Differential Expression Profile Analysis of DNA Repair Genes in Mycobacterium Leprae by qPCR
Authors: Mukul Sharma, Madhusmita Das, Sundeep Chaitanya Vedithi
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Leprosy is a chronic human disease caused by Mycobacterium leprae, that cannot be cultured in vitro. Though treatable with multidrug therapy (MDT), recently, bacteria reported resistance to multiple antibiotics. Targeting DNA replication and repair pathways can serve as the foundation of developing new anti-leprosy drugs. Due to the absence of an axenic culture medium for the propagation of M. leprae, studying cellular processes, especially those belonging to DNA repair pathways, is challenging. Genomic understanding of M. Leprae harbors several protein-coding genes with no previously assigned function known as 'hypothetical proteins'. Here, we report identification and expression of known and hypothetical DNA repair genes from a human skin biopsy and mouse footpads that are involved in base excision repair, direct reversal repair, and SOS response. Initially, a bioinformatics approach was employed based on sequence similarity, identification of known protein domains to screen the hypothetical proteins in the genome of M. leprae, that are potentially related to DNA repair mechanisms. Before testing on clinical samples, pure stocks of bacterial reference DNA of M. leprae (NHDP63 strain) was used to construct standard graphs to validate and identify lower detection limit in the qPCR experiments. Primers were designed to amplify the respective transcripts, and PCR products of the predicted size were obtained. Later, excisional skin biopsies of newly diagnosed untreated, treated, and drug resistance leprosy cases from SIHR & LC hospital, Vellore, India were taken for the extraction of RNA. To determine the presence of the predicted transcripts, cDNA was generated from M. leprae mRNA isolated from clinically confirmed leprosy skin biopsy specimen across all the study groups. Melting curve analysis was performed to determine the integrity of the amplification and to rule out primer‑dimer formation. The Ct values obtained from qPCR were fitted to standard curve to determine transcript copy number. Same procedure was applied for M. leprae extracted after processing a footpad of nude mice of drug sensitive and drug resistant strains. 16S rRNA was used as positive control. Of all the 16 genes involved in BER, DR, and SOS, differential expression pattern of the genes was observed in terms of Ct values when compared to human samples; this was because of the different host and its immune response. However, no drastic variation in gene expression levels was observed in human samples except the nth gene. The higher expression of nth gene could be because of the mutations that may be associated with sequence diversity and drug resistance which suggests an important role in the repair mechanism and remains to be explored. In both human and mouse samples, SOS system – lexA and RecA, and BER genes AlkB and Ogt were expressing efficiently to deal with possible DNA damage. Together, the results of the present study suggest that DNA repair genes are constitutively expressed and may provide a reference for molecular diagnosis, therapeutic target selection, determination of treatment and prognostic judgment in M. leprae pathogenesis.Keywords: DNA repair, human biopsy, hypothetical proteins, mouse footpads, Mycobacterium leprae, qPCR
Procedia PDF Downloads 10328099 Neuroimaging Markers for Screening Former NFL Players at Risk for Developing Alzheimer's Disease / Dementia Later in Life
Authors: Vijaykumar M. Baragi, Ramtilak Gattu, Gabriela Trifan, John L. Woodard, K. Meyers, Tim S. Halstead, Eric Hipple, Ewart Mark Haacke, Randall R. Benson
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NFL players, by virtue of their exposure to repetitive head injury, are at least twice as likely to develop Alzheimer's disease (AD) and dementia as the general population. Early recognition and intervention prior to onset of clinical symptoms could potentially avert/delay the long-term consequences of these diseases. Since AD is thought to have a long preclinical incubation period, the aim of the current research was to determine whether former NFL players, referred to a depression center, showed evidence of incipient dementia in their structural imaging prior to diagnosis of dementia. Thus, to identify neuroimaging markers of AD, against which former NFL players would be compared, we conducted a comprehensive volumetric analysis using a cohort of early stage AD patients (ADNI) to produce a set of brain regions demonstrating sensitivity to early AD pathology (i.e., the “AD fingerprint”). A cohort of 46 former NFL players’ brain MRIs were then interrogated using the AD fingerprint. Brain scans were done using a T1-weighted MPRAGE sequence. The Free Surfer image analysis suite (version 6.0) was used to obtain the volumetric and cortical thickness data. A total of 55 brain regions demonstrated significant atrophy or ex vacuo dilatation bilaterally in AD patients vs. healthy controls. Of the 46 former NFL players, 19 (41%) demonstrated a greater than expected number of atrophied/dilated AD regions when compared with age-matched controls, presumably reflecting AD pathology.Keywords: alzheimers, neuroimaging biomarkers, traumatic brain injury, free surfer, ADNI
Procedia PDF Downloads 15428098 A Long Short-Term Memory Based Deep Learning Model for Corporate Bond Price Predictions
Authors: Vikrant Gupta, Amrit Goswami
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The fixed income market forms the basis of the modern financial market. All other assets in financial markets derive their value from the bond market. Owing to its over-the-counter nature, corporate bonds have relatively less data publicly available and thus is researched upon far less compared to Equities. Bond price prediction is a complex financial time series forecasting problem and is considered very crucial in the domain of finance. The bond prices are highly volatile and full of noise which makes it very difficult for traditional statistical time-series models to capture the complexity in series patterns which leads to inefficient forecasts. To overcome the inefficiencies of statistical models, various machine learning techniques were initially used in the literature for more accurate forecasting of time-series. However, simple machine learning methods such as linear regression, support vectors, random forests fail to provide efficient results when tested on highly complex sequences such as stock prices and bond prices. hence to capture these intricate sequence patterns, various deep learning-based methodologies have been discussed in the literature. In this study, a recurrent neural network-based deep learning model using long short term networks for prediction of corporate bond prices has been discussed. Long Short Term networks (LSTM) have been widely used in the literature for various sequence learning tasks in various domains such as machine translation, speech recognition, etc. In recent years, various studies have discussed the effectiveness of LSTMs in forecasting complex time-series sequences and have shown promising results when compared to other methodologies. LSTMs are a special kind of recurrent neural networks which are capable of learning long term dependencies due to its memory function which traditional neural networks fail to capture. In this study, a simple LSTM, Stacked LSTM and a Masked LSTM based model has been discussed with respect to varying input sequences (three days, seven days and 14 days). In order to facilitate faster learning and to gradually decompose the complexity of bond price sequence, an Empirical Mode Decomposition (EMD) has been used, which has resulted in accuracy improvement of the standalone LSTM model. With a variety of Technical Indicators and EMD decomposed time series, Masked LSTM outperformed the other two counterparts in terms of prediction accuracy. To benchmark the proposed model, the results have been compared with traditional time series models (ARIMA), shallow neural networks and above discussed three different LSTM models. In summary, our results show that the use of LSTM models provide more accurate results and should be explored more within the asset management industry.Keywords: bond prices, long short-term memory, time series forecasting, empirical mode decomposition
Procedia PDF Downloads 13628097 Functional Role of Tyr12 in the Catalytic Activity of Zeta-Like Glutathione S-Transferase from Acidovorax sp. KKS102
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Glutathione S-transferases (GSTs) are family of enzymes that function in the detoxification of variety of electrophilic substrates. In the present work, we report a novel zeta-like GST (designated as KKSG9) from the biphenyl/polychlorobiphenyl degrading organism Acidovorax sp. KKS102. KKSG9 possessed low sequence similarity but similar biochemical properties to zeta class GSTs. The gene for KKSG9 was cloned, purified and biochemically characterized. Functional analysis showed that the enzyme exhibits wider substrate specificity compared to most zeta class GSTs by reacting with 1-chloro-2,4-dinitrobenzene (CDNB), p-nitrobenzyl chloride (NBC), ethacrynic acid (EA), hydrogen peroxide, and cumene hydroperoxide (CuOOH). The enzyme also displayed dehalogenation function against dichloroacetate (a common substrate for zeta class GSTs) in addition to permethrin, and dieldrin. The functional role of Tyr12 was also investigated by site-directed mutagenesis. The mutant (Y12C) displayed low catalytic activity and dehalogenation function against all the substrates when compared with the wild type. Kinetic analysis using NBC and GSH as substrates showed that the mutant (Y12C) displayed a higher affinity for NBC when compared with the wild type, however, no significant change in GSH affinity was observed. These findings suggest that the presence of tyrosine residue in the motif might represent an evolutionary trend toward improving the catalytic activity of the enzyme. The enzyme as well could be useful in the bioremediation of various types of organochlorine pollutants.Keywords: Acidovorax sp. KKS102, bioremediation, glutathione s-transferase, site-directed mutagenesis, zeta
Procedia PDF Downloads 15028096 Fixed Point of Lipschitz Quasi Nonexpansive Mappings
Authors: Maryam Moosavi, Hadi Khatibzadeh
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The main purpose of this paper is to study the proximal point algorithm for quasi-nonexpansive mappings in Hadamard spaces. △-convergence and strong convergence of cyclic resolvents for a finite family of quasi-nonexpansive mappings one to a fixed point of the mappings are establishedKeywords: Fixed point, Hadamard space, Proximal point algorithm, Quasi-nonexpansive sequence of mappings, Resolvent
Procedia PDF Downloads 9028095 Sensory and Microbial Properties of Fresh and Canned Calocybe indica
Authors: Apotiola Z. O., Anyakorah C. I., Kuforiji O. O.
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Sensory and microbial properties of fresh and canned Calocybe indica (milky mushroom) were evaluated. The mushroom was grown under a controlled environment with hardwood (Cola nitida) and rice bran substrate (4:1) canned in a brine solution of salt and citric acid. Analysis was carried out using standard methods. The overall acceptability ranged between 5.62 and 6.50, with sample S30 adjudged the best. In all, significant differences p<0.01 exist in the panelist judgment. Thus, the incorporation of salt and citric acid at 3.5g and 1.5g, respectively, improved sensory attributes such as texture, aroma, color, and overall acceptability. There was no coliform and fungi growth on the samples throughout the storage period. The bacterial count, on the other hand, was observed only in the fifth and sixth week of the storage period which varied between 0.2 to 0.9 x 103 cfu/g. The highest value was observed in sample S20 of the sixth week of storage, while the lowest value was recorded in sample S30 of the sixth week of storage. Based on 16S rRNA gene sequencing, bacterial species were taxonomically confirmed as Bacillus thuringiensis. The percentile compositions and Sequence ID of the bacterial species in the mushroom was 90%.Keywords: bacterial count, microbial property, sensory, sawdust, texture
Procedia PDF Downloads 6228094 Heterogeneity of Genes Encoding the Structural Proteins of Avian Infectious Bronchitis Virus
Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule
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Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity
Procedia PDF Downloads 43428093 Probiotic Properties of Lactic Acid Bacteria Isolated from Fermented Food
Authors: Wilailak Siripornadulsil, Siriyanapat Tasaku, Jutamas Buahorm, Surasak Siripornadulsil
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The objectives of this study were to isolate LAB from various sources, dietary supplement, Thai traditional fermented food, and freshwater fish and to characterize their potential as probiotic cultures. Out of 1,558 isolates, 730 were identified as LAB based on isolation on MRS agar supplemented with a bromocresol purple indicator and CaCO3 and gram-positive, catalase and oxidase negative characteristics. Eight isolates showed the potential probiotic properties including tolerance to acid, bile salt and heat, proteolytic, amylolytic and lipolytic activities and oxalate-degrading capability. They all showed the antimicrobial activity against some Gram-negative and Gram-positive pathogenic bacteria. Based on 16S rDNA sequence analysis, they were identified as Enterococcus faecalis BT2 and MG30, Leconostoc mesenteroides SW64 and Pediococcus pentosaceous BD33, CF32, NP6, PS34 and SW5. The health beneficial effects and food safety will be further investigated and developed as a probiotic or protective culture used in Nile tilapia belly flap meat fermentation.Keywords: probiotic, lactic acid bacteria, pathogen, protective culture
Procedia PDF Downloads 382