Search results for: shotgun metagenomic sequence analysis

Authors: Lien Gysens, Bert Vanmechelen, Maarten Haspeslagh, Piet Maes, Ann Martens

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Bovine papillomavirus (BPV) types 1 and 2 play a central role in the etiology of the most common neoplasm in horses, the equine sarcoid. The unknown mechanism behind the unique variety in a clinical presentation on the one hand and the host-dependent clinical outcome of BPV-1 infection, on the other hand, indicate the involvement of additional factors. Earlier studies have reported the potential functional significance of intratypic sequence variants, along with the existence of sarcoid-sourced BPV variants. Therefore, intratypic sequence variation seems to be an important emerging viral factor. This study aimed to give a broad insight in sarcoid-sourced BPV variation and explore its potential association with disease presentation. In order to do this, a nanopore sequencing approach was successfully optimized for screening a wide spectrum of clinical samples. Specimens of each tumour were initially screened for BPV-1/-2 by quantitative real-time PCR. A custom-designed primer set was used on BPV-positive samples to amplify the complete viral genome in two multiplex PCR reactions, resulting in a set of overlapping amplicons. For phylogenetic analysis, separate alignments were made of all available complete genome sequences for BPV-1/-2. The resulting alignments were used to infer Bayesian phylogenetic trees. We found substantial genetic variation among sarcoid-derived BPV-1, although this variation could not be linked to disease severity. Several of the BPV-1 genomes had multiple major deletions. Remarkably, the majority of the cluster within the region coding for late viral genes. Together with the extensiveness (up to 603 nucleotides) of the described deletions, this suggests an altered function of L1/L2 in disease pathogenesis. By generating a significant amount of complete-length BPV genomes, we succeeded in introducing next-generation sequencing into veterinary research focusing on the equine sarcoid, thus facilitating the first report of both nanopore-based sequencing of complete sarcoid-sourced BPV-1/-2 and the simultaneous nanopore sequencing of multiple complete genomes originating from a single clinical sample.

Keywords: Bovine papillomavirus, equine sarcoid, horse, nanopore sequencing, phylogenetic analysis

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Authors: Ovidiu Domşa, Nicolae Bold

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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

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Authors: Salina Yahya Saddick

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Ovarian cancer remains the most lethal gynecological malignancy due to the lack of highly sensitive and specific screening tools for detection of early-stage disease. The OSE provides the progenitor cells for 90% of human ovarian cancers. Recent morphologic, immunohistochemical and molecular genetic studies have led to the development of a new paradigm for the pathogenesis and origin of epithelial ovarian cancer (EOC) based on a ualistic model of carcinogenesis that divides EOC into two broad categories designated Types I and II which are characterized by specific mutations, including KRAS, BRAF, ERBB2, CTNNB1, PTEN PIK3CA, ARID1A, and PPPR1A, which target specific cell signaling pathways. Type 1 tumors rarely harbor TP53. type I tumors are relatively genetically stable and typically display a variety of somatic sequence mutations that include KRAS, BRAF, PTEN, PIK3CA CTNNB1 (the gene encoding beta catenin), ARID1A and PPP2R1A but very rarely TP53 . The cancer stem cell (CSC) hypothesis postulates that the tumorigenic potential of CSCs is confined to a very small subset of tumor cells and is defined by their ability to self-renew and differentiate leading to the formation of a tumor mass. Potential protein biomarker miRNA, are promising biomarkers as they are remarkably stable to allow isolation and analysis from tissues and from blood in which they can be found as free circulating nucleic acids and in mononuclear cells. Recently, genomic anaylsis have identified biomarkers and potential therapeutic targets for ovarian cancer namely, FGF18 which plays an active role in controlling migration, invasion, and tumorigenicity of ovarian cancer cells through NF-κB activation, which increased the production of oncogenic cytokines and chemokines. This review summarizes update information on epithelial ovarian cancers and point out to the most recent ongoing research.

Keywords: epithelial ovarian cancers, somatic sequence mutations, cancer stem cell (CSC), potential protein, biomarker, genomic analysis, FGF18 biomarker

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

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

Keywords: poliovirus, eradication, environmental surveillance, laboratory diagnosis

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Authors: O. I. H. Dimitry, N. A. Mansour, A. L. G. Saad

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Natural sodium montmorillonite (NaMMT), Cloisite Na⁺ and two organophilic montmorillonites (OMMTs), Cloisites 20A and 15A were used. Polycaprolactone (PCL)/MMT composites containing 1, 3, 5, and 10 wt% of Cloisite Na⁺ and PCL/OMMT nanocomposites containing 5 and 10 wt% of Cloisites 20A and 15A were prepared via solution intercalation technique to study the influence of organic modifier loading on particle dispersion of PCL/ NaMMT composites. Thermal stabilities of the obtained composites were characterized by thermal analysis using the thermogravimetric analyzer (TGA) which showed that in the presence of nitrogen flow the incorporation of 5 and 10 wt% of filler brings some decrease in PCL thermal stability in the sequence: Cloisite Na+>Cloisite 15A > Cloisite 20A, while in the presence of air flow these fillers scarcely influenced the thermoxidative stability of PCL by slightly accelerating the process. The interaction between PCL and silicate layers was studied by Fourier transform infrared (FTIR) spectroscopy which confirmed moderate interactions between nanometric silicate layers and PCL segments. The electrical conductivity (σ) which describes the ionic mobility of the systems was studied as a function of temperature and showed that σ of PCL was enhanced on increasing the modifier loading at filler content of 5 wt%, especially at higher temperatures in the sequence: Cloisite Na⁺<Cloisite 20A<Cloisite 15A, and was then decreased to some extent with a further increase to 10 wt%. The activation energy E_σ obtained from the dependency of σ on temperature using Arrhenius equation was found to be lowest for the nanocomposite containing 5 wt% of Cloisite 15A. The dispersed behavior of clay in PCL matrix was evaluated by X-ray diffraction (XRD) and scanning electron microscopy (SEM) analyses which revealed partial intercalated structures in PCL/NaMMT composites and semi-intercalated/semi-exfoliated structures in PCL/OMMT nanocomposites containing 5 wt% of Cloisite 20A or Cloisite 15A.

Keywords: electrical conductivity, montmorillonite, nanocomposite, organoclay, polycaprolactone

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Authors: Harsh Panchal, Saurabh Amrutkar

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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

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Authors: Sabeen Alam, Mehboob Alam

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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

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Authors: Isabelle Snyder

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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

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Authors: Harsh Vikram Singh, Ankur Rai, Anand Mohan

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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

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Authors: A. Elain, M. Le Fellic, A. Le Pemp, N. Hachet

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Iodinated Compounds (IC) are widely detected contaminants in most aquatic environments including sewage treatment plant, surface water, ground water and even drinking water, up to the µg.L-1 range. As IC contribute in the adsorbable organic halides (AOX) level, their removal or dehalogenation is expected. We report here on the biodegradability of a mixture of IC from an industrial effluent using a microbial consortium adapted to grow on IC as well as the native microorganisms. Both aerobic and anaerobic treatments were studied during batch experiments in 500-mL flasks. The degree of mineralization and recovery of iodide were monitored by HPLC-UV, TOC analysis and potentiometric titration. Providing ethanol as an electron acceptor was found to stimulate anaerobic reductive deiodination of IC while sodium chloride even at high concentration (22 g.l-1) had no influence on the degradation rates nor on the microbial viability. Phylogenetic analysis of 16S RNA gene sequence (MicroSeq®) was applied to provide a better understanding of the degradative microbial community.

Keywords: iodinated compounds, biodegradability, deiodination, electron-accepting conditions, microbial consortium

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Authors: Girma Yohannis Bade, Olga Kolesnikova, Grigori Sidorov

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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

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Authors: Josephine Shamash, Stuart Smith

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We examine reasons for introducing definitions in teaching mathematics in a number of different cases. We try to determine if, where, and when to provide a definition, and which definition to choose. We characterize different types of definitions and the different purposes we may have for formulating them, and detail examples of each type. Giving a definition at a certain stage can sometimes be detrimental to the development of the concept image. In such a case, it is advisable to delay the precise definition to a later stage. We describe two models, the 'successive approximation model', and the 'model of the extending definition' that fit such situations. Detailed examples that fit the different models are given based on material taken from a number of textbooks, and analysis of the way the concept is introduced, and where and how its definition is given. Our conclusions, based on this analysis, is that some of the definitions given may cause discontinuities in the learning sequence and constitute obstacles and unnecessary cognitive conflicts in the formation of the concept definition. However, in other cases, the discontinuity in passing from definition to definition actually serves a didactic purpose, is unavoidable for the mathematical evolution of the concept image, and is essential for students to deepen their understanding.

Keywords: concept image, mathematical definitions, mathematics education, mathematics teaching

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

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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

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Authors: J. Bernasovská, R. Lohajová Behulová, E. Petrejčiková, I. Boroňová, I. Bernasovský

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Y chromosome microdeletions are the most common genetic cause of male infertility and screening for these microdeletions in azoospermic or severely oligospermic men is now standard practice. Analysis of the Y chromosome in men with azoospermia or severe oligozoospermia has resulted in the identification of three regions in the euchromatic part of the long arm of the human Y chromosome (Yq11) that are frequently deleted in men with otherwise unexplained spermatogenic failure. PCR analysis of microdeletions in the AZFa, AZFb and AZFc regions of the human Y chromosome is an important screening tool. The aim of this study was to analyse the type of microdeletions in men with fertility disorders in Slovakia. We evaluated 227 patients with azoospermia and with normal karyotype. All patient samples were analyzed cytogenetically. For PCR amplification of sequence-tagged sites (STS) of the AZFa, AZFb and AZFc regions of the Y chromosome was used Devyser AZF set. Fluorescently labeled primers for all markers in one multiplex PCR reaction were used and for automated visualization and identification of the STS markers we used genetic analyzer ABi 3500xl (Life Technologies). We reported 13 cases of deletions in the AZF region 5,73%. Particular types of deletions were recorded in each region AZFa,b,c .The presence of microdeletions in the AZFc region was the most frequent. The study confirmed that percentage of microdeletions in the AZF region is low in Slovak azoospermic patients, but important from a prognostic view.

Keywords: AZF, male infertility, microdeletions, Y chromosome

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

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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

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Authors: Xiaoqin Wang, Li Yin

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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

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Authors: Mohammad Vahed, Ana Sadeghitohidi, Majid Vahed, Hiroki Takahashi

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In the genomics field, the huge amounts of data have produced by the next-generation sequencers (NGS). Data volumes are very rapidly growing, as it is postulated that more than one billion bases will be produced per year in 2020. The growth rate of produced data is much faster than Moore's law in computer technology. This makes it more difficult to deal with genomics data, such as storing data, searching information, and finding the hidden information. It is required to develop the analysis platform for genomics big data. Cloud computing newly developed enables us to deal with big data more efficiently. Hadoop is one of the frameworks distributed computing and relies upon the core of a Big Data as a Service (BDaaS). Although many services have adopted this technology, e.g. amazon, there are a few applications in the biology field. Here, we propose a new algorithm to more efficiently deal with the genomics big data, e.g. sequencing data. Our algorithm consists of two parts: First is that BDaaS is applied for handling the data more efficiently. Second is that the hybrid method of MapReduce and Fuzzy logic is applied for data processing. This step can be parallelized in implementation. Our algorithm has great potential in computational analysis of genomics big data, e.g. de novo genome assembly and sequence similarity search. We will discuss our algorithm and its feasibility.

Keywords: big data, fuzzy logic, MapReduce, Hadoop, cloud computing

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

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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

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Authors: Rajkumar Ghosh

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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)

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Authors: Ling Qi, Matloob Khushi, Josiah Poon

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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

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Authors: Shivam Yadav, Neelam Atri

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Cyanobacteria are photoautotrophic prokaryotes able to grow in diverse ecological habitats, originated 2.5 - 3.5 billion years ago and brought oxygenic photosynthesis. Since then superoxide dismutases (SODs) acquired great significance due to their ability to catalyze detoxification of byproducts of oxygenic photosynthesis, i.e. superoxide radicals. Sequence information from several cyanobacterial genomes offers a unique opportunity to conduct a comprehensive comparative analysis of the superoxide dismutases family. In the present study, we extracted information regarding SODs from species of sequenced cyanobacteria and investigated their diversity, conservation, domain structure, and evolution. 144 putative SOD homologues were identified. SODs are present in all cyanobacterial species reflecting their significant role in survival. However, their distribution varies, fewer in unicellular marine strains whereas abundant in filamentous nitrogen-fixing cyanobacteria. Motifs and invariant amino acids typical in eukaryotic SODs were conserved well in these proteins. These SODs were classified into three major families according to their domain structures. Interestingly, they lack additional domains as found in proteins of other family. Phylogenetic relationships correspond well with phylogenies based on 16S rRNA and clustering occurs on the basis of structural characteristics such as domain organization. Similar conserved motifs and amino acids indicate that cyanobacterial SODs make use of a similar catalytic mechanism as eukaryotic SODs. Gene gain-and-loss is insignificant during SOD evolution as evidenced by absence of additional domain. This study has not only examined an overall background of sequence-structure-function interactions for the SOD gene family but also revealed variation among SOD distribution based on ecophysiological and morphological characters.

Keywords: comparative genomics, cyanobacteria, phylogeny, superoxide dismutases

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Authors: Pratyasha Patnaik, A. V. Asha

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Laminated composite plates are made up of plates consisting of layers bonded together and made up of materials chemically different from each other but combined macroscopically. These have an application in aircrafts, railway coaches, bridges etc. because they are easy to handle, have got improved properties and the cost of their fabrication is low. But their failure can lead to catastrophic disasters. And generally, the failure of these structures is due to the combined effect of excessive stresses on it and buckling. Hence, the buckling behavior of these kinds of plates should be analyzed properly. Holes are provided either at the center or elsewhere in the laminar plates for the purpose of pipes for electric cables or other purposes. Due to the presence of holes in the plates, the stress concentration is near to the holes and the stiffness of the plates is reduced. In this study, the effect of a cut-out, its shape, different boundary conditions, length/thickness ratio, stacking sequence, and ply orientation has been studied. The analysis was carried out with laminated composite plates with circular, square and triangular cut-outs. Results show the effect of different cut-out shapes, boundary conditions, the orientation of layers and length/thickness ratio of the buckling load

Keywords: buckling, composite plates, cut-out, stress

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Authors: Yasser M. Saad, Amr A. El Hanafy, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, security and capital in many countries, particularly in Saudi Arabia. Inter simple sequence repeat technique was used to detect the genetic variations among some camel breeds (Majaheim, Safra, Wadah, and Hamara). Actual number of alleles, effective number of alleles, gene diversity, Shannon’s information index and polymorphic bands were calculated for each evaluated camel breed. Neighbor-joining tree that re-constructed for evaluated these camel breeds showed that, Hamara breed is distantly related from the other evaluated camels. In addition, the polymorphic sites, haplotypes and nucleotide diversity were identified for some camelidae cox1 gene sequences (obtained from NCBI). The distance value between C. bactrianus and C. dromedarius (0.072) was relatively low. Analysis of genetic diversity is an important way for conserving Camelus dromedarius genetic resources.

Keywords: camel, genetics, ISSR, neighbor-joining

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Authors: Daniel Botero, Oscar Rubiano, Pedro P. Barragan, Jaime Baron, Leonardo Rodriguez Perdomo, Jaime Rodriguez

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In the last decade interval training (IT) has gained importance when is compare with strength training (ST). However, there are few studies analyzing the impact of these training over the autonomic nervous system (ANS). This work has aimed to compare the activity of the autonomic nervous system, when is expose to an IT or ST indoor cycling mode. After approval by the ethics committee, a cross-over clinical trial with 22 healthy participants (age 21 ± 3 years) was implemented. The selection of participants for the groups with sequence force-interval (F-I) and interval-force (I-F) was made randomly with assignation of 11 participants for each group. The temporal series of heart rate was obtained before and after each training using the POLAR TEAM® heart monitor. The evaluation of the ANS was performed with spectral analysis of the heart rate variability (HRV) using the fast Fourier transform (Kubios software). A training of 8 weeks in each sequence (4 weeks with each training) with an intermediate period of two weeks of washout was implemented for each group. The power parameter of the HRV in the low frequency band (LF = 0.04-0.15Hz related to the sympathetic nervous system), high frequency (HF = 0.15-0.4Hz, related to the parasympathetic) and LF/HF (with reference to a modulation of parasympathetic over the sympathetic), were calculated. Afterward, the difference between the parameters before and after was realized. Then, to evaluate statistical differences between each training was implemented the method of Wellek (Wellek and Blettner, 2012, Medicine, 109 (15), 276-81). To determine the difference of effect over parasympathetic when FT and IT are used, the T test is implemented obtaining a T value of 0.73 with p-value ≤ 0.1. For the sympathetic was obtained a T of 0.33 with p ≤ 0.1 and for LF/HF the T was 1.44 with a p ≥ 0.1. Then, the carry over effect was evaluated and was not present. Significant changes over autonomic activity with strength or interval training were not observed. However, a modulation of the parasympathetic over the sympathetic can be observed. Probably, these findings should be explained because the sample is little and/or the time of training was insufficient to generate changes.

Keywords: autonomic nervous, force training, indoor cycling, interval training

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

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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

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Authors: Maryam Beiranvand, Sajad Yaghoubi

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Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: Antibacterial activity, endophytic bacteria, multidrug-resistant bacteria, whole genom sequencing

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Authors: J. T. Manhire

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A tax authority wants to take actions it knows will foster the greatest degree of voluntary taxpayer compliance to reduce the “tax gap.” This paper suggests that even if a tax authority could attain a state of complete knowledge, there are constraints on whether and to what extent such actions would result in reducing the macro-level tax gap. These limits are not merely a consequence of finite agency resources. They are inherent in the system itself. To show that this is one possible interpretation of the tax gap data, the paper formulates known results in a different way by analyzing tax compliance as a population with a single covariate. This leads to a standard use of the logistic map to analyze the dynamics of non-compliance growth or decay over a sequence of periods. This formulation gives the same results as the tax gap studies performed over the past fifty years in the U.S. given the published margins of error. Limitations and recommendations for future work are discussed, along with some implications for tax policy.

Keywords: income tax, logistic map, tax compliance, tax law

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Authors: Satpal Yadav, Biswajit Basumatary, Arvind S. Sajwan, Ranjan Chakravarty

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The purpose of the study was to assess the effect of 2D kinematical selected variables on sprint start with sprinting performance of novice athletes. Six (3 National and 3 State level) athletes of sports authority of India, Guwahati has been selected for this study. The mean (M) and standard deviation (SD) of sprinters were age (17.44, 1.55), height (1.74m, .84m), weight (62.25 kg, 4.55), arm length (65.00 cm, 3.72) and leg length (96.35 cm, 2.71). Biokin-2D motion analysis system V4.5 can be used for acquiring two-dimensional kinematical data/variables on sprint start with Sprinting Performance. For the purpose of kinematic analysis a standard motion driven camera which frequency of the camera was 60 frame/ second i.e. handy camera of Sony Company were used. The sequence of photographic was taken under controlled condition. The distance of the camera from the athletes was 12 mts away and was fixed at 1.2-meter height. The result was found that National and State level athletes significant difference in there, trajectory knee, trajectory ankle, displacement knee, displacement ankle, linear velocity knee, linear velocity ankle, and linear acceleration ankle whereas insignificant difference was found between National and State level athletes in their linear acceleration knee joint on sprint start with sprinting performance. For all the Statistical test the level of significance was set at p<0.05.

Keywords: 2D kinematic analysis, sprinting performance, novice athletes, sprint start

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Authors: Awais Asif

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This article investigates fixed point theorems of Chatterjea type F-contraction in the setting of F-metric space. We relax the conditions of F-contraction and define modified F-contraction for two mappings. The study provides fixed point results for both single-valued and multivalued mappings. The results are further extended to common fixed point theorems for two mappings. Moreover, to discuss the applicability of our results, an application is provided, which shows the role of our results in finding the solution to functional equations in dynamic programming. Our results generalize and extend the existing results in the literature.

Keywords: Chatterjea type F-contraction, F-cauchy sequence, F-convergent, multi valued mappings

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Authors: Y. Yulnafatmawita, H. Hermansah

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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

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