Search results for: sequence

Authors: Gurjit Kaur, Shashank Johri, Arpit Mehrotra

Abstract:

In this paper we have analyzed and compared the performance of various coding schemes. The basic ID prime sequence codes are unique in only dimension i.e. time slots whereas 2D coding techniques are not unique by their time slots but with their wavelengths also. In this research we have evaluated and compared the performance of 1D and 2D coding techniques constructed using prime sequence coding pattern for OCDMA system on a single platform. Results shows that 1D Extended Prime Code (EPC) can support more number of active users compared to other codes but at the expense of larger code length which further increases the complexity of the code. Modified Prime Code (MPC) supports lesser number of active users at λc=2 but it has a lesser code length as compared to 1D prime code. Analysis shows that 2D prime code supports lesser number of active users than 1D codes but they are having large code family and are the most secure codes compared to other codes. The performance of all these codes is analyzed on basis of number of active users supported at a Bit Error Rate (BER) of 10-9.

Keywords: CDMA, OCDMA, BER, OOC, PC, EPC, MPC, 2-D PC/PC, λc, λa

Procedia PDF Downloads 479

Authors: Abdesselem Dakhli, Wajdi Bellil, Chokri Ben Amar

Abstract:

DNA Barcode, a short mitochondrial DNA fragment, made up of three subunits; a phosphate group, sugar and nucleic bases (A, T, C, and G). They provide good sources of information needed to classify living species. Such intuition has been confirmed by many experimental results. Species classification with DNA Barcode sequences has been studied by several researchers. The classification problem assigns unknown species to known ones by analyzing their Barcode. This task has to be supported with reliable methods and algorithms. To analyze species regions or entire genomes, it becomes necessary to use similarity sequence methods. A large set of sequences can be simultaneously compared using Multiple Sequence Alignment which is known to be NP-complete. To make this type of analysis feasible, heuristics, like progressive alignment, have been developed. Another tool for similarity search against a database of sequences is BLAST, which outputs shorter regions of high similarity between a query sequence and matched sequences in the database. However, all these methods are still computationally very expensive and require significant computational infrastructure. Our goal is to build predictive models that are highly accurate and interpretable. This method permits to avoid the complex problem of form and structure in different classes of organisms. On empirical data and their classification performances are compared with other methods. Our system consists of three phases. The first is called transformation, which is composed of three steps; Electron-Ion Interaction Pseudopotential (EIIP) for the codification of DNA Barcodes, Fourier Transform and Power Spectrum Signal Processing. The second is called approximation, which is empowered by the use of Multi Llibrary Wavelet Neural Networks (MLWNN).The third is called the classification of DNA Barcodes, which is realized by applying the algorithm of hierarchical classification.

Keywords: DNA barcode, electron-ion interaction pseudopotential, Multi Library Wavelet Neural Networks (MLWNN)

Procedia PDF Downloads 287

Authors: Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Y. Rafii

Abstract:

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas) system can facilitate targeted genome editing in organisms. Dual or single guide RNA (gRNA) can program the Cas9 nuclease to cut target DNA in particular areas; thus, introducing concise mutations either via error-prone non-homologous end-joining repairing or via incorporating foreign DNAs by homologous recombination between donor DNA and target area. In spite of high demand of such promising technology, developing a well-organized procedure in order for reliable mining of potential target sites for gRNAs in large genomic data is still challenging. Hence, we aimed to perform high-throughput detection of target sites by specific PAMs for not only common Streptococcus pyogenes (SpCas9) but also for Neisseria meningitides (NmCas9) CRISPR-Cas systems. Previous research confirmed the successful application of such RNA-guided Cas9 orthologs for effective gene targeting and subsequently genome manipulation. However, Cas9 orthologs need their particular PAM sequence for DNA cleavage activity. Activity levels are based on the sequence of the protospacer and specific combinations of favorable PAM bases. Therefore, based on the specific length and sequence of PAM followed by a constant length of the target site for the two orthogonals of Cas9 protein, we created a reliable procedure to explore possible gRNA sequences. To mine CRISPR target sites, four different searching modes of sgRNA binding to target DNA strand were applied. These searching modes are as follows i) coding strand searching, ii) anti-coding strand searching, iii) both strand searching, and iv) paired-gRNA searching. Finally, a complete list of all potential gRNAs along with their locations, strands, and PAMs sequence orientation can be provided for both SpCas9 as well as another potential Cas9 ortholog (NmCas9). The artificial design of potential gRNAs in a genome of interest can accelerate functional genomic studies. Consequently, the application of such novel genome editing tool (CRISPR/Cas technology) will enhance by presenting increased versatility and efficiency.

Keywords: CRISPR/Cas9 genome editing, gRNA mining, SpCas9, NmCas9

Procedia PDF Downloads 227

Authors: M. Michael Gromiha, A. Mary Thangakani, Sandeep Kumar, D. Velmurugan

Abstract:

The main cause of several neurodegenerative diseases such as Alzhemier, Parkinson, and spongiform encephalopathies is formation of amyloid fibrils and plaques in proteins. We have analyzed different sets of proteins and peptides to understand the influence of sequence-based features on protein aggregation process. The comparison of 373 pairs of homologous mesophilic and thermophilic proteins showed that aggregation-prone regions (APRs) are present in both. But, the thermophilic protein monomers show greater ability to ‘stow away’ the APRs in their hydrophobic cores and protect them from solvent exposure. The comparison of amyloid forming and amorphous b-aggregating hexapeptides suggested distinct preferences for specific residues at the six positions as well as all possible combinations of nine residue pairs. The compositions of residues at different positions and residue pairs have been converted into energy potentials and utilized for distinguishing between amyloid forming and amorphous b-aggregating peptides. Our method could correctly identify the amyloid forming peptides at an accuracy of 95-100% in different datasets of peptides.

Keywords: aggregation, amyloids, thermophilic proteins, amino acid residues, machine learning techniques

Procedia PDF Downloads 583

Authors: Ovidiu Domşa, Nicolae Bold

Abstract:

Using Information and Communication Technologies (ICT) notions in education and three basic processes of education (teaching, learning and assessment) can bring benefits to the pupils and the professional development of teachers. In this matter, we refer to these notions as concepts taken from the informatics area and apply them to the domain of education. These notions refer to genetic algorithms and arborescent structures, used in the specific process of assessment or evaluation. This paper uses these kinds of notions to generate subtrees from a main tree of tests related between them by their degree of difficulty. These subtrees must contain the highest number of connections between the nodes and the lowest number of missing edges (which are subtrees of the main tree) and, in the particular case of the non-existence of a subtree with no missing edges, the subtrees which have the lowest (minimal) number of missing edges between the nodes, where a node is a test and an edge is a direct connection between two tests which differs by one degree of difficulty. The subtrees are represented as sequences. The tests are the same (a number coding a test represents that test in every sequence) and they are reused for each sequence of tests.

Keywords: chromosome, genetic algorithm, subtree, test

Procedia PDF Downloads 296

Authors: Harveen Kaur Tatla, Parisa Niknejad, Rajender Gupta, Bipro Ranjan Dhar, Mohd. Adana Khan

Abstract:

Sewage sludge management presents a pressing challenge in the realm of wastewater treatment, calling for sustainable and efficient solutions. This study explores the integration of Hydrothermal Liquefaction (HTL) and Anaerobic Digestion (AD) as a promising approach to address the complexities associated with sewage sludge treatment. The integration of these two processes offers a complementary and synergistic framework, allowing for the mitigation of inherent limitations, thereby enhancing overall efficiency, product quality, and the comprehensive utilization of sewage sludge. In this research, we investigate the optimal sequencing of HTL and AD within the treatment framework, aiming to discern which sequence, whether HTL followed by AD or AD followed by HTL, yields superior results. We explore a range of HTL working temperatures, including 250°C, 300°C, and 350°C, coupled with residence times of 30 and 60 minutes. To evaluate the effectiveness of each sequence, a battery of tests is conducted on the resultant products, encompassing Total Ammonia Nitrogen (TAN), Chemical Oxygen Demand (COD), and Volatile Fatty Acids (VFA). Additionally, elemental analysis is employed to determine which sequence maximizes energy recovery. Our findings illuminate the intricate dynamics of HTL and AD integration for sewage sludge management, shedding light on the temperature-residence time interplay and its impact on treatment efficiency. This study not only contributes to the optimization of sewage sludge treatment but also underscores the potential of integrated processes in sustainable waste management strategies. The insights gleaned from this research hold promise for advancing the field of wastewater treatment and resource recovery, addressing critical environmental and energy challenges.

Keywords: Anaerobic Digestion (AD), aqueous phase, energy recovery, Hydrothermal Liquefaction (HTL), sewage sludge management, sustainability.

Procedia PDF Downloads 46

Authors: Harsh Panchal, Saurabh Amrutkar

Abstract:

Quality management is an essential part of any project that has directly related to the performance of a project. Quality management is depended on multiple factors at different stages in a project, right from time management to construction logistics. A project is a mixture of various components that include iternary management, health and safety, crew productivity, and many more. From the survey conducted, we came to the conclusion that advancement in technology and indigenous approach to any project will result in maximum quality standards and better project performance. In this paper, we discuss various components of the factors above that lead to compromise the quality of a project and how it can be controlled in order to achieve maximum quality assurance using quality planning and total quality management. The paper also focuses on limitations and problems faced in each factor responsible for quality management and to tackle them using techniques and processes based on activities and identifying the sequence, approaching critical path, and duration. The project management concept that deals with the sequence of scope cost time give us an overview regarding the ongoing quality management, in a nutshell, giving us hints to regulate the current procedure for maximum achievable quality. It also deals with the problems faced by engineers that make the mundane work process slow, reducing the quality outcome drastically.

Keywords: management, performance, project, quality

Procedia PDF Downloads 126

Authors: Sabeen Alam, Mehboob Alam

Abstract:

The research work entitled “Effect of Bacillus pumilus strains on heavy metal accumulation in lettuce grown on contaminated soil” focused on functional role of Bacillus pumilus strains inoculated with lettuce seed in mitigating heavy metal in chromite mining soil. In this experiment, factor A was three Bacillus pumilus strains (sequence C-2PMW-8, C-1 SSK-8 and C-1 PWK-7) while soil used for this experiment was collected from Prang Ghar mining site and lettuce seeds were grown in three levels of chromite mining soil (2.27, 4.65 and 7.14 %). For mining soil minimum days to germinate noted in lettuce grown on garden soil inoculated with sequence. Maximum germination percentage noted was for C-1 SSK-8 grown on garden soil, maximum lettuce height for sequence C-2 PWM-8, fresh leaf weight for C-1 PWK-7 inoculated lettuce, dry weight of lettuce leaf for lettuce inoculated with C-1 SSK-8 and C-1 PWK-7 strains, number of leaves per plant for lettuce inoculated with C-1 SSK-8, leaf area for C-2 PMW-8 inoculated lettuce, survival percentage for C-1 SSK-8 treated lettuce and chlorophyll content for C-2 PMW-8. Results related to heavy metals accumulation showed that minimum chromium was in lettuce and in soil for all three sequences, cadmium (Cd) in lettuce and in soil for all three sequences, manganese (Mn) in lettuce and in soil for three sequences, lead (Pb) in lettuce and in soil for three sequences. It can be concluded that chromite mining soil significantly reduced the growth and survival of lettuce, but when lettuce was inoculated with Bacillus.pumilus strains, it enhances growth and survival. Similarly, minimum heavy metal accumulation in plant and soil, regardless of type of Bacillus pumilus used, all three sequences has same mitigating effect on heavy metal in both soil and lettuce. All the three Bacillus pumilus strains ensured reduction in heavy metals content (Mn, Cd, Cr) in lettuce, below the maximum permissible limits of WHO 2011.

Keywords: bacillus pumilus, heavy metals, permissible limits, lettuce, chromite mining soil, mitigating effect

Procedia PDF Downloads 18

Authors: Isabelle Snyder

Abstract:

Microgrid protection presents challenges to conventional protection techniques due to the low induced fault current. Protection relays present in microgrid applications require a combination of settings groups to adjust based on the architecture of the microgrid in islanded and grid-connected mode. In a radial system where the microgrid is at the other end of the feeder, directional elements can be used to identify the direction of the fault current and switch settings groups accordingly (grid connected or microgrid connected). However, with multiple microgrid connections, this concept becomes more challenging, and the direction of the current alone is not sufficient to identify the source of the fault current contribution. ORNL has previously developed adaptive relaying schemes through other DOE-funded research projects that will be evaluated and used as a baseline for this research. The four protection techniques in this study are the following: (1) Adaptive Current only Protection System (ACPS), Intentional (2) Unbalanced Control for Protection Control (IUCPC), (3) Adaptive Protection System with Communication Controller (APSCC) (4) Adaptive Model-Driven Protective Relay (AMDPR). The first two methods focus on identifying the islanded mode without communication by monitoring the current sequence component generated by the system (ACPS) or induced with inverter control during islanded mode (IUCPC) to identify the islanding condition without communication at the relay to adjust the settings. These two methods are used as a backup to the APSCC, which relies on a communication network to communicate the islanded configuration to the system components. The fourth method relies on a short circuit model inside the relay that is used in conjunction with communication to adjust the system configuration and computes the fault current and adjusts the settings accordingly.

Keywords: adaptive relaying, microgrid protection, sequence components, islanding detection, communication controlled protection, integrated short circuit model

Procedia PDF Downloads 57

Authors: Harsh Vikram Singh, Ankur Rai, Anand Mohan

Abstract:

In this paper, we propose secure and robust data hiding algorithm based on DCT by Arnold transform and chaotic sequence. The watermark image is scrambled by Arnold cat map to increases its security and then the chaotic map is used for watermark signal spread in middle band of DCT coefficients of the cover image The chaotic map can be used as pseudo-random generator for digital data hiding, to increase security and robustness .Performance evaluation for robustness and imperceptibility of proposed algorithm has been made using bit error rate (BER), normalized correlation (NC), and peak signal to noise ratio (PSNR) value for different watermark and cover images such as Lena, Girl, Tank images and gain factor .We use a binary logo image and text image as watermark. The experimental results demonstrate that the proposed algorithm achieves higher security and robustness against JPEG compression as well as other attacks such as addition of noise, low pass filtering and cropping attacks compared to other existing algorithm using DCT coefficients. Moreover, to recover watermarks in proposed algorithm, there is no need to original cover image.

Keywords: data hiding, watermarking, DCT, chaotic sequence, arnold transforms

Procedia PDF Downloads 485

Authors: Dwi Arisandi Wijaya, Ernawati Arifin Giri-Rachman, Neni Nurainy

Abstract:

Typhoid fever disease can be prevented by using a polysaccharide-based vaccine Vi which is a virulence factor of S.typhi. To produce high yield Vi polysaccharide from bacteria, it is important to know the biosynthesis of Vi polysaccharide and the regulators involved. In the In vivo condition, S. typhi faces different osmolarity, and the bacterial two-component system OmpR-EnvZ, regulate by up and down Capsular Vi polysaccharide biosynthesis. A high yielded Vi Polysaccharide strain, S. typhi strain C6524 used to study the effect of media osmolarity on Vi polysaccharide biosynthesis and the osmoregulation pattern of S. typhi strain C6524. The methods were performed by grown S. typhi strain C6524 grown on medium with 50 mM, 100 mM, and 150 mM osmolarity with the batch system. Vi polysaccharide concentration was measured by ELISA method. For further investigation of the osmoregulation pattern of strain C6524, the osmoregulator gene, OmpR, has been isolated and sequenced using the specific primer of the OmpR gene. Nucleotide sequence analysis is done with BLAST and Lallign. Amino Acid sequence analysis is done with Prosite and Multiple Sequence Alignment. The results of cultivation showed the average content of polysaccharide Vi for 50 mM, 100 mM, and 150 mM osmolarities 11.49 μg/mL, 12.06 μg/mL, and 14.53 μg/mL respectively. Analysis using Anova stated that the osmolarity treatment of 150 mM significantly affects Vi content. Analysis of nucleotide sequences shows 100% identity between S. typhi strain C6524 and Ty2. Analysis of amino acid sequences shows that the OmpR response regulator protein of the C6524 strain also has a α4-β5-α5 motif which is important for the regulatory activation system when phosphorylation occurs by domain kinase. This indicates that the regulator osmolarity response of S. typhi strain C6524 has no difference with the response regulator owned by S. typhi strain Ty2. A high Vi response rate in the 150 mM osmolarity treatment requires further research for RcsB-RcsC, another two-component system involved in Vi Biosynthesis.

Keywords: osmoregulator, OmpR, Salmonella, Vi polysaccharide

Procedia PDF Downloads 163

Authors: Moneesh Thakur, Hridayesh Prasad, Nikitasha Bora, Parimal Roy Choudhary, A. K. Samanta, Sanjeev Kumar

Abstract:

Canine demodicosis is a common parasitic condition which involves dog skin. Demodicosis in dogs is due the prominent growth of Demodex. Out of various canine Demodex spp., Demodex canis is the most often involved species. Canine demodicosis can occur as either a localized or generalized form of demodicosis severely affect the dogs and in non-treated dogs may cause death. This study was planned with the aim to screen and characterize the 18S rRNA gene of isolated Demodex canis. A total of 1200 dogs were screened during this study period. The skin scrapings of all the suspected dogs were examined under a microscope at 100X magnification for the presence of Demodex canis. The skin scrapings positive for Demodex canis were examined using PCR for confirmation. A total of 35 dogs were confirmed a positive result for D. canis based on 18S rRNA gene amplification by PCR. Further, the 18S rRNA gene of isolated Demodex canis was cloned and sequenced for genome analysis. On the sequence analysis, it was found that isolated sequence (GenBank Accession No. MK177513) had close similarity (99.7%) to that of D. canis genotype of China (Accession No. MG372254).

Keywords: PCR, phylogenetic analysis, cloning and sequening, Demodex canis

Procedia PDF Downloads 55

Authors: Girma Yohannis Bade, Olga Kolesnikova, Grigori Sidorov

Abstract:

Named entity recognition (NER) is a building block for information extraction. Though the information extraction process has been automated using a variety of techniques to find and extract a piece of relevant information from unstructured documents, the discovery of targeted knowledge still poses a number of research difficulties because of the variability and lack of structure in Web data. NER, a subtask of information extraction (IE), came to exist to smooth such difficulty. It deals with finding the proper names (named entities), such as the name of the person, country, location, organization, dates, and event in a document, and categorizing them as predetermined labels, which is an initial step in IE tasks. This survey paper presents the roles and importance of NER to IE from the perspective of different algorithms and application area domains. Thus, this paper well summarizes how researchers implemented NER in particular application areas like finance, medicine, defense, business, food science, archeology, and so on. It also outlines the three types of sequence labeling algorithms for NER such as feature-based, neural network-based, and rule-based. Finally, the state-of-the-art and evaluation metrics of NER were presented.

Keywords: the role of NER, named entity recognition, information extraction, sequence labeling algorithms, named entity application area

Procedia PDF Downloads 48

Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

Abstract:

The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

Procedia PDF Downloads 229

Authors: Avent Grange, Frederic Bertrand, Jean-Baptiste Droin, Amandine Marrel, Jean-Henry Ferrasse, Olivier Boutin

Abstract:

CEA and its industrial partners are designing a gas Power Conversion System (PCS) based on a Brayton cycle for the ASTRID Sodium-cooled Fast Reactor. Investigations of control and regulation requirements to operate this PCS during operating, incidental and accidental transients are necessary to adapt core heat removal. To this aim, we developed a methodology to optimize the thermal-hydraulic behavior of the reactor during normal operations, incidents and accidents. This methodology consists of a multi-objective optimization for a specific sequence, whose aim is to increase component lifetime by reducing simultaneously several thermal stresses and to bring the reactor into a stable state. Furthermore, the multi-objective optimization complies with safety and operating constraints. Operating, incidental and accidental sequences use specific regulations to control the thermal-hydraulic reactor behavior, each of them is defined by a setpoint, a controller and an actuator. In the multi-objective problem, the parameters used to solve the optimization are the setpoints and the settings of the controllers associated with the regulations included in the sequence. In this way, the methodology allows designers to define an optimized and specific control strategy of the plant for the studied sequence and hence to adapt PCS piloting at its best. The multi-objective optimization is performed by evolutionary algorithms coupled to surrogate models built on variables computed by the thermal-hydraulic system code, CATHARE2. The methodology is applied to a loss of off-site power sequence. Three variables are controlled: the sodium outlet temperature of the sodium-gas heat exchanger, turbomachine rotational speed and water flow through the heat sink. These regulations are chosen in order to minimize thermal stresses on the gas-gas heat exchanger, on the sodium-gas heat exchanger and on the vessel. The main results of this work are optimal setpoints for the three regulations. Moreover, Proportional-Integral-Derivative (PID) control setting is considered and efficient actuators used in controls are chosen through sensitivity analysis results. Finally, the optimized regulation system and the reactor control procedure, provided by the optimization process, are verified through a direct CATHARE2 calculation.

Keywords: gas power conversion system, loss of off-site power, multi-objective optimization, regulation, sodium fast reactor, surrogate model

Procedia PDF Downloads 280

Authors: Rizka Ardhiyana, Liesbetini Haditjaroko, Sri Mulijani, Reki Ashadi Wicaksono, Raafqi Ranasasmita

Abstract:

Designing a sensitive, specific and easy to use method to detect pork contamination in the food industry remains a major challenge. In the current study, we developed a sensitive thiol-bond AuNP-Probe biosensor that will change color when detecting pork DNA in the Cytochrome B region. The interaction between the biosensors and DNA sample is measured by spectrophotometer at 540 nm. The biosensor is made by reducing gold with trisodium citrate to produce gold nanoparticle with 39.05 nm diameter. The AuNP-Probe biosensor (gold nanoprobe) achieved 16.04 ng DNA/µl limit of detection and 53.48 ng DNA/µl limit of quantification. The linearity (R2) between color absorbance changes and DNA concentration is 0.9916. The biosensor has a good specificty as it does not cross-react with DNA of chicken and beef. To verify specificity towards the target sequence, PCR was tested to the target sequence and reacted to the PCR product with the biosensor. The PCR DNA isolate resulted in a 2.7 fold higher absorbance compared to pork-DNA isolate alone (without PCR). The sensitivity and specificity of the method show the promising application of the thiol-bond AuNP biosensor in pork-detection.

Keywords: biosensor, DNA probe, gold nanoparticle (AuNP), pork meat, qPCR

Procedia PDF Downloads 330

Authors: Shin-Pin Tseng

Abstract:

Nowadays, numerous spectral amplitude coding (SAC) fiber-optic code-division-multiple-access (FO-CDMA) techniques were appealing due to their capable of providing moderate security and relieving the effects of multiuser interference (MUI). Nonetheless, the performance of the previous network is degraded due to fixed in-phase cross-correlation (IPCC) value. Based on the above problems, a new SAC FO-CDMA network using partial M-sequence (PMS) code is presented in this study. Because the proposed PMS code is originated from M-sequence code, the system using the PMS code could effectively suppress the effects of MUI. In addition, two-code keying (TCK) scheme can applied in the proposed SAC FO-CDMA network and enhance the whole network performance. According to the consideration of system flexibility, simple optical encoders/decoders (codecs) using fiber Bragg gratings (FBGs) were also developed. First, we constructed a diagram of the SAC FO-CDMA network, including (N/2-1) optical transmitters, (N/2-1) optical receivers, and one N×N star coupler for broadcasting transmitted optical signals to arrive at the input port of each optical receiver. Note that the parameter N for the PMS code was the code length. In addition, the proposed SAC network was using superluminescent diodes (SLDs) as light sources, which then can save a lot of system cost compared with the other FO-CDMA methods. For the design of each optical transmitter, it is composed of an SLD, one optical switch, and two optical encoders according to assigned PMS codewords. On the other hand, each optical receivers includes a 1 × 2 splitter, two optical decoders, and one balanced photodiode for mitigating the effect of MUI. In order to simplify the next analysis, the some assumptions were used. First, the unipolarized SLD has flat power spectral density (PSD). Second, the received optical power at the input port of each optical receiver is the same. Third, all photodiodes in the proposed network have the same electrical properties. Fourth, transmitting '1' and '0' has an equal probability. Subsequently, by taking the factors of phase‐induced intensity noise (PIIN) and thermal noise, the corresponding performance was displayed and compared with the performance of the previous SAC FO-CDMA networks. From the numerical result, it shows that the proposed network improved about 25% performance than that using other codes at BER=10-9. This is because the effect of PIIN was effectively mitigated and the received power was enhanced by two times. As a result, the SAC FO-CDMA network using PMS codes has an opportunity to apply in applications of the next-generation optical network.

Keywords: spectral amplitude coding, SAC, fiber-optic code-division multiple-access, FO-CDMA, partial M-sequence, PMS code, fiber Bragg grating, FBG

Procedia PDF Downloads 350

Authors: Kuei-Ling Sun, Emily Chia-Yu Su

Abstract:

Allergy is a hypersensitive overreaction of the immune system to environmental stimuli, and a major health problem. These overreactions include rashes, sneezing, fever, food allergies, anaphylaxis, asthmatic, shock, or other abnormal conditions. Allergies can be caused by food, insect stings, pollen, animal wool, and other allergens. Their development of allergies is due to both genetic and environmental factors. Allergies involve immunoglobulin E antibodies, a part of the body’s immune system. Immunoglobulin E antibodies will bind to an allergen and then transfer to a receptor on mast cells or basophils triggering the release of inflammatory chemicals such as histamine. Based on the increasingly serious problem of environmental change, changes in lifestyle, air pollution problem, and other factors, in this study, we both collect allergens and non-allergens from several databases and use several machine learning methods for classification, including logistic regression (LR), stepwise regression, decision tree (DT) and neural networks (NN) to do the model comparison and determine the permutations of allergen amino acid’s sequence.

Keywords: allergy, classification, decision tree, logistic regression, machine learning

Procedia PDF Downloads 277

Authors: Xiaoqin Wang, Li Yin

Abstract:

Background and purpose: In many practices, one estimates causal effects arising from a complex stochastic process, where a sequence of treatments are assigned to influence a certain outcome of interest, and there exist time-dependent covariates between treatments. When covariates are plentiful and/or continuous, statistical modeling is needed to reduce the huge dimensionality of the problem and allow for the estimation of causal effects. Recently, Wang and Yin (Annals of statistics, 2020) derived a new general formula, which expresses these causal effects in terms of the point effects of treatments in single-point causal inference. As a result, it is possible to conduct the modeling via point effects. The purpose of the work is to study the modeling of these causal effects via point effects. Challenges and solutions: The time-dependent covariates often have influences from earlier treatments as well as on subsequent treatments. Consequently, the standard parameters – i.e., the mean of the outcome given all treatments and covariates-- are essentially all different (null paradox). Furthermore, the dimension of the parameters is huge (curse of dimensionality). Therefore, it can be difficult to conduct the modeling in terms of standard parameters. Instead of standard parameters, we have use point effects of treatments to develop likelihood-based parametric approach to the modeling of these causal effects and are able to model the causal effects of a sequence of treatments by modeling a small number of point effects of individual treatment Achievements: We are able to conduct the modeling of the causal effects from a sequence of treatments in the familiar framework of single-point causal inference. The simulation shows that our method achieves not only an unbiased estimate for the causal effect but also the nominal level of type I error and a low level of type II error for the hypothesis testing. We have applied this method to a longitudinal study of COVID-19 mortality among Scandinavian countries and found that the Swedish approach performed far worse than the other countries' approach for COVID-19 mortality and the poor performance was largely due to its early measure during the initial period of the pandemic.

Keywords: causal effect, point effect, statistical modelling, sequential causal inference

Procedia PDF Downloads 174

Authors: Woo Young Jung, Sung Min Park, Ho Young Son, Viriyavudh Sim

Abstract:

This study presents a way to reduce earthquake damage and emergency rehabilitation of critical structures such as schools, high-tech factories, and hospitals due to strong ground motions associated with climate changes. Regarding recent trend, a strong earthquake causes serious damage to critical structures and then the critical structure might be influenced by sequence aftershocks (or tsunami) due to fault plane adjustments. Therefore, in order to improve seismic performance of critical structures, retrofitted or strengthening study of the structures under aftershocks sequence after emergency rehabilitation of the structures subjected to strong earthquakes is widely carried out. Consequently, this study used composite material for emergency rehabilitation of the structure rather than concrete and steel materials because of high strength and stiffness, lightweight, rapid manufacturing, and dynamic performance. Also, this study was to develop or improve the seismic performance or seismic retrofit of critical structures subjected to strong ground motions and earthquake aftershocks, by utilizing GFRP-Corrugated Infill Panels (GCIP).

Keywords: aftershock, composite material, GFRP, infill panel

Procedia PDF Downloads 308

Authors: Rajkumar Ghosh

Abstract:

The study focuses on the tectonics of out-of-sequence thrusting (OOST) in the NW region of the Himalaya, particularly in Himachal Pradesh. The research aims to identify the features and nature of OOST in the field and the associated rock types and lithological boundaries in the field of NW Himalaya, Himachal Pradesh, India. The research employs fieldwork and micro-structure observations, correlations, and analyses to identify and analyze the OOST features and associated rock types. The study reveals the presence of three OOSTs, namely Jhakri Thrust (JT), Sarahan Thrust (ST), and Chaura Thrust (CT), which consist of several branches, some of which are still active. The thrust system exhibits varying internal geometry, including box folds, boudins, scar folds, crenulation cleavages, kink folds, and tension gashes. The CT, which is concealed beneath Jutogh Thrust sheet, represents a steepened downward thrust, while the JT has a western dip and is south-westward verging. The research provides crucial information on the tectonics of OOST in the NW region of the Himalaya, particularly in Himachal Pradesh, which is crucial in understanding the regional geological evolution and associated hazards. The data were collected through fieldwork and micro-structure observations, correlations, and analyses of rock samples. The data were analyzed using tectonic and geochronological techniques to identify the nature and characteristics of OOST. The research addressed the question of identifying Higher Himalayan OOST in the field of NW Himalaya, Himachal Pradesh, India, and the associated rock types and lithological boundaries. The study concludes that there is minimal documentation and a lack of suitable exposure of rocks to generalize the features of OOST in the field in NW Higher Himalaya, Himachal Pradesh. The study recommends more extensive mapping and fieldwork to improve understanding of OOST in the region.

Keywords: out-of-sequence thrust (OOST), main central thrust (MCT), jhakri thrust (JT), sarahan thrust (ST), chaura thrust (CT), higher himalaya (HH)

Procedia PDF Downloads 60

Authors: Ling Qi, Matloob Khushi, Josiah Poon

Abstract:

This paper introduces a pre-trained Masked Candlestick Model (MCM) for trading time-series data. The pre-trained model is based on three core designs. First, we convert trading price data at each data point as a set of normalized elements and produce embeddings of each element. Second, we generate a masked sequence of such embedded elements as inputs for self-supervised learning. Third, we use the encoder mechanism from the transformer to train the inputs. The masked model learns the contextual relations among the sequence of embedded elements, which can aid downstream classification tasks. To evaluate the performance of the pre-trained model, we fine-tune MCM for three different downstream classification tasks to predict future price trends. The fine-tuned models achieved better accuracy rates for all three tasks than the baseline models. To better analyze the effectiveness of MCM, we test the same architecture for three currency pairs, namely EUR/GBP, AUD/USD, and EUR/JPY. The experimentation results demonstrate MCM’s effectiveness on all three currency pairs and indicate the MCM’s capability for signal extraction from trading data.

Keywords: masked language model, transformer, time series prediction, trading prediction, embedding, transfer learning, self-supervised learning

Procedia PDF Downloads 88

Authors: Priyanka Mazumdar, Ananya Mukhopadhyay

Abstract:

A lot of progress has been achieved in the research of turbidites during the last decades. However, their relationship to delta systems still deserves further attention. This paper addresses example of fine grained turbidite from a pro-deltaic deposit of a Proterozoic mixed energy delta system exposed along Chaossa-Baliana river section of the Chaossa Formation of the Simla Basin. Lithostratigraphic analysis of the Chaossa Formation reveals three major facies associations (prodelta deposit-FA1, delta slope deposit-FA2 and delta front deposit-FA3) based on lithofacies types, petrography and sedimentary structures. Detailed process-based facies and paleoenvironmental analysis of the study area have led to identification of more than150 m thick coarsening-upwards deltaic successions composed of fine grained turbidites overlain by delta slope deposits. Erosional features are locally common at the base of turbidite beds and still more widespread at the top. The complete sequence has eight sub-divisions that are here termed T1 to T8. The basal subdivision (T1) comprises a massive graded unit with a sharp, scoured base, internal parallel-lamination and cross-lamination. The overlying sequence shows textural and compositional grading through alternating silt and mud laminae (T2). T2 is overlying by T3 which is characterized by climbing ripple and cross lamination. Parallel laminae are the predominant facies attributes of T4 which caps the T3 unit. T5 has a loaded scour base and is mainly characterized laminated silt. The topmost three divisions, graded mud (T6), ungraded mud (T7) and laminated mud (T8). The proposed sequence is analogous to the Bouma (1962) structural scheme for sandy turbidites. Repetition of partial sequences represents deposition from different stages of evolution of a large, muddy, turbidity flow. Detailed facies analysis of the study area reveals that the sediments of the turbidites developed during normal regression at the stage of stable or marginally rising sea level. Thin-bedded turbidites were deposited predominantly by turbidity currents in the relatively shallower part of the Simla basin. The fine-grained turbidites are developed by resedimentation of delta-front sands and slumping of upper pro-delta muds.

Keywords: turbidites, prodelta, proterozoic, Simla Basin, Bouma sequence

Procedia PDF Downloads 241

Authors: Xueying Zhao, Ke Ma, Hui Li, Yu Cao, Fan Yang, Qingwen Xu, Wenbin Liu

Abstract:

Massively parallel sequencing (MPS) technologies allow high-throughput sequencing analyses with a relatively affordable price and have gradually been applied to forensic casework. MPS technology identifies short tandem repeat (STR) loci based on sequence so that repeat motif variation within STRs can be detected, which may help one to infer the origin of the mutation in some cases. Here, we report on one case with one three-step mismatch (D18S51) in family trios based on both capillary electrophoresis (CE) and MPS typing. The alleles of the alleged father (AF) are [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₁₅. The mother’s alleles are [AGAA]₁₉ and [AGAA]₉AGGA[AGAA]₃. The questioned child’s (QC) alleles are [AGAA]₁₉ and [AGAA]₁₂. Given that the sequence variants in repeat regions of AF and mother are not observed in QC’s alleles, the QC’s allele [AGAA]₁₂ was likely inherited from the AF’s allele [AGAA]₁₅ by loss of three repeat [AGAA]. Besides, two new alleles of D18S51 in this study, [AGAA]₁₇AGAG[AGAA]₃ and [AGAA]₉AGGA[AGAA]₃, have not been reported before. All the results in this study were verified using Sanger-type sequencing. In summary, the MPS typing method can offer valuable information for forensic genetics research and play a promising role in paternity testing.

Keywords: family trios analysis, forensic casework, ion torrent personal genome machine (PGM), massively parallel sequencing (MPS)

Procedia PDF Downloads 275

Authors: Hsin-Yang Wang, K. M. A. Salam, Ying-Jia Lin, Daniel Tan, Tzu-Hsuan Chou, Hung-Yu Kao

Abstract:

Detecting user intent from natural language expression has a wide variety of use cases in different natural language processing applications. Recently few-shot training has a spike of usage on commercial domains. Due to the lack of significant sample features, the downstream task performance has been limited or leads to an unstable result across different domains. As a state-of-the-art method, the pre-trained BERT model gathering the sentence-level information from a large text corpus shows improvement on several NLP benchmarks. In this research, we are proposing a method to change multi-class classification tasks into binary classification tasks, then use the confidence score to rank the results. As a language model, BERT performs well on sequence data. In our experiment, we change the objective from predicting labels into finding the relations between words in sequence data. Our proposed method achieved 71.0% accuracy in the internal intent detection dataset and 63.9% accuracy in the HuffPost dataset. Acknowledgment: This work was supported by NCKU-B109-K003, which is the collaboration between National Cheng Kung University, Taiwan, and SoftBank Corp., Tokyo.

Keywords: OSML, BERT, text classification, one shot

Procedia PDF Downloads 78

Authors: Y. Yulnafatmawita, H. Hermansah

Abstract:

Topography is a factor affecting soil characteristics. Chemical characteristics of a soil is a factor determining the productivity of the land. A research was conducted in Bukit Sarasah Padang, an area receiving > 5000 mm rainfall annually. The purpose of this research was to determine the chemical characteristics of soils at sequence topography in hill-slope of Bukit Sarasah. Soils were sampled at 3 different altitudes in the research area from 315 m – 515 m asl with 100 m interval. At each location, soil samples were taken from two depths (0-20 cm and 30-50 cm) for soil chemical characteristics (pH, CEC, organic-C, N-total, C/N, Ca-, Mg-, K-, Na-, Al-, and H-exchangeable). Based on the data resulted, it was found that there was a tendency of decreasing soil organic matter (SOC) content by increasing location from 315 to 515 m asl as well as from the top 0-20 cm to 30-50 cm soil depth. The same tendency was also found for the CEC, pH, N-total, and C/N ratio of the soil. On the other hand, exchangeable-Al and -H tended to increase by increasing elevation in Bukit Sarasah. There was no significant difference found for the concentration of exchangeable cations among the elevations and between the depths. The soil chemical characteristics on the top 20 cm were generally better than those on 30-50 cm soil depth, however, different elevation did not gave significant difference of the concentration.

Keywords: soil chemical characteristics, soil depths, topo-sequence, wet tropical area

Procedia PDF Downloads 448

Authors: Angela U. Makolo

Abstract:

Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

Procedia PDF Downloads 26

Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

Abstract:

The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: zika, biomolecular interactions, electrostatic interactions, molecular mechanisms

Procedia PDF Downloads 94

Authors: Thanthrige Thiunuwan Priyathilaka, Don Anushka Sandaruwan Elvitigala, Bong-Soo Lim, Hyung-Bok Jeong, Jehee Lee

Abstract:

Toll like receptors (TLRs) are a phylogeneticaly conserved family of pattern recognition receptors, which participates in the host immune responses against various pathogens and pathogen derived mitogen. TLR21, a non-mammalian type, is almost restricted to the fish species even though those can be identified rarely in avians and amphibians. Herein, this study was carried out to identify and characterize TLR21 from rock bream (Oplegnathus fasciatus) designated as RbTLR21, at transcriptional and genomic level. In this study, the full length cDNA and genomic sequence of RbTLR21 was identified using previously constructed cDNA sequence database and BAC library, respectively. Identified RbTLR21 sequence was characterized using several bioinformatics tools. The quantitative real time PCR (qPCR) experiment was conducted to determine tissue specific expressional distribution of RbTLR21. Further, transcriptional modulation of RbTLR21 upon the stimulation with Streptococcus iniae (S. iniae), rock bream iridovirus (RBIV) and Edwardsiella tarda (E. tarda) was analyzed in spleen tissues. The complete coding sequence of RbTLR21 was 2919 bp in length which can encode a protein consisting of 973 amino acid residues with molecular mass of 112 kDa and theoretical isoelectric point of 8.6. The anticipated protein sequence resembled a typical TLR domain architecture including C-terminal ectodomain with 16 leucine rich repeats, a transmembrane domain, cytoplasmic TIR domain and signal peptide with 23 amino acid residues. Moreover, protein folding pattern prediction of RbTLR21 exhibited well-structured and folded ectodomain, transmembrane domain and cytoplasmc TIR domain. According to the pair wise sequence analysis data, RbTLR21 showed closest homology with orange-spotted grouper (Epinephelus coioides) TLR21with 76.9% amino acid identity. Furthermore, our phylogenetic analysis revealed that RbTLR21 shows a close evolutionary relationship with its ortholog from Danio rerio. Genomic structure of RbTLR21 consisted of single exon similar to its ortholog of zebra fish. Sevaral putative transcription factor binding sites were also identified in 5ʹ flanking region of RbTLR21. The RBTLR 21 was ubiquitously expressed in all the tissues we tested. Relatively, high expression levels were found in spleen, liver and blood tissues. Upon induction with rock bream iridovirus, RbTLR21 expression was upregulated at the early phase of post induction period even though RbTLR21 expression level was fluctuated at the latter phase of post induction period. Post Edwardsiella tarda injection, RbTLR transcripts were upregulated throughout the experiment. Similarly, Streptococcus iniae induction exhibited significant upregulations of RbTLR21 mRNA expression in the spleen tissues. Collectively, our findings suggest that RbTLR21 is indeed a homolog of TLR21 family members and RbTLR21 may be involved in host immune responses against bacterial and DNA viral infections.

Keywords: rock bream, toll like receptor 21 (TLR21), pattern recognition receptor, genomic characterization

Procedia PDF Downloads 519

Authors: Putul Haldar, Yogendra Singh, D. K. Paul

Abstract:

Un-Reinforced Masonry (URM) infilled RC framed buildings are the most common construction practice for modern multi-storey buildings in India like many other parts of the world. Although the behavior and failure pattern of the global structure changes significantly due to infill-frame interaction, the general design practice is to treat them as non-structural elements and their stiffness, strength and interaction with frame is often ignored, as it is difficult to simulate. Indian Standard, like many other major national codes, does not provide any explicit guideline for modeling of infills. This paper takes a stock of controlling design provisions in some of the major national seismic design codes (BIS 2002; CEN 2004; NZS-4230 2004; ASCE-41 2007) to ensure the desired seismic performance of infilled frame. Most of the national codes on seismic design of buildings still lack in adequate guidelines on modeling and design of URM infilled frames results in variable assumption in analysis and design. This paper, using nonlinear pushover analysis, also presents the effect of one of such assumptions of conventional ‘simultaneous’ analysis procedure of infilled frame on the seismic performance of URM infilled RC frame buildings.

Keywords: URM infills, RC frame, seismic design codes, construction sequence of infilled frame

Procedia PDF Downloads 362