Search results for: sequence variants

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: Dimitris Varsamis, Christos Talagkozis, Alkiviadis Tsimpiris, Paris Mastorocostas

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The aim of this work is the parallel implementation of k-means in MATLAB, in order to reduce the execution time. Specifically, a new function in MATLAB for serial k-means algorithm is developed, which meets all the requirements for the conversion to a function in MATLAB with parallel computations. Additionally, two different variants for the definition of initial values are presented. In the sequel, the parallel approach is presented. Finally, the performance tests for the computation times respect to the numbers of features and classes are illustrated.

Keywords: K-means algorithm, clustering, parallel computations, Matlab

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Authors: Priyanka Mazumdar, Ananya Mukhopadhyay

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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

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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: 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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Authors: Angela U. Makolo

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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

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

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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

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Authors: Rene Hellmuth, Jorg Frohnmayer

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The requirements of the factory planning and the building concerned have changed in the last years. Factory planning has the task of designing products, plants, processes, organization, areas, and the building of a factory. Regular restructuring gains more importance in order to maintain the competitiveness of a factory. Even today, the methods and process models used in factory planning are predominantly based on the classical planning principles of Schmigalla, Aggteleky and Kettner, which, however, are not specifically designed for reorganization. In addition, they are designed for a largely static environmental situation and a manageable planning complexity as well as for medium to long-term planning cycles with a low variability of the factory. Existing approaches already regard factory planning as a continuous process that makes it possible to react quickly to adaptation requirements. However, digital factory models are not yet used as a source of information for building data. Approaches which consider building information modeling (BIM) or digital factory models in general either do not refer to factory conversions or do not yet go beyond a concept. This deficit can be further substantiated. A method for factory conversion planning using a current digital building model is lacking. A corresponding approach must take into account both the existing approaches to factory planning and the use of digital factory models in practice. A literature review will be conducted first. In it, approaches to classic factory planning and approaches to conversion planning are examined. In addition, it will be investigated which approaches already contain digital factory models. In the second step, an approach is presented how digital factory models based on building information modeling can be used as a basis for augmented reality tablet applications. This application is suitable for construction sites and provides information on the costs and time required for conversion variants. Thus a fast decision making is supported. In summary, the paper provides an overview of existing factory planning approaches and critically examines the use of digital tools. Based on this preliminary work, an approach is presented, which suggests the sensible use of digital factory models for decision support in the case of conversion variants of the factory building. The augmented reality application is designed to summarize the most important information for decision-makers during a reconstruction process.

Keywords: augmented reality, digital factory model, factory planning, restructuring

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

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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

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

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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

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Authors: Sadaf Ilyas

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Recombinant cytokines have been employed successfully as potential therapeutic agent. Some cytokine therapies are already used as a part of clinical practice, ranging from early exploratory trials to well established therapies that have already received approval. Interleukin 15 is a pleiotropic cytokine having multiple roles in peripheral innate and adaptive immune cell function. It regulates the activation, proliferation and maturation of NK cells, T-cells, monocytes/macrophages and granulocytes, and the interactions between them thus acting as a bridge between innate and adaptive immune responses. Unraveling the biology of IL-15 has revealed some interesting surprises that may point toward some of the first therapeutic applications for this cytokine. In this study, the human interleukin 15 gene was isolated, amplified and ligated to a TA vector which was then transfected to a bacterial host, E. coli Top10F’. The sequence of cloned gene was confirmed and it showed 100% homology with the reported sequence. The confirmed gene was then subcloned in pET Expression system to study the IPTG induced expression of IL-15 gene. Positive expression was obtained for number of clones that showed 15 kd band of IL-15 in SDS-PAGE analysis, indicating the successful strain development that can be studied further to assess the potential therapeutic intervention of this cytokine in relevance to human diseases.

Keywords: Interleukin 15, pET expression system, immune therapy, protein purification

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Authors: Elena I. Oprita, Oana Craciunescu, Rodica Tatia, Teodora Ciucan, Reka Barabas, Orsolya Raduly, Anca Oancea

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Healing of osteochondral defects requires repair of the damaged articular cartilage, the underlying subchondral bone and the interface between these tissues (the functional calcified layer). For this purpose, developing a single monophasic scaffold that can regenerate two specific lineages (cartilage and bone) becomes a challenge. The aim of this work was to develop variants of biodegradable cross-linked composite hydrogel based on natural polypeptides (gelatin), polysaccharides components (chondroitin-4-sulphate and hyaluronic acid), in a ratio of 2:0.08:0.02 (w/w/w) and mixed with Si-hydroxyapatite (Si-Hap), in two ratios of 1:1 and 2:1 (w/w). Si-Hap was synthesized and characterized as a better alternative to conventional Hap. Subsequently, both composite hydrogel variants were cross-linked with (N, N-(3-dimethylaminopropyl)-N-ethyl carbodiimide (EDC) and enriched with a small bioactive molecule (icariin). The small molecule icariin (Ica) (C33H40O15) is the main active constituent (flavonoid) of Herba epimedium used in traditional Chinese medicine to cure bone- and cartilage-related disorders. Ica enhances osteogenic and chondrogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), facilitates matrix calcification and increases the specific extracellular matrix (ECM) components synthesis by chondrocytes. Afterward, the composite hydrogels were characterized for their physicochemical properties in terms of the enzymatic biodegradation in the presence of type I collagenase and trypsin, the swelling capacity and the degree of crosslinking (TNBS assay). The cumulative release of Ica and real-time concentration were quantified at predetermined periods of time, according to the standard curve of standard Ica, after hydrogels incubation in saline buffer at physiological parameters. The obtained cross-linked composite hydrogels enriched with small-molecule Ica were also characterized for morphology by scanning electron microscopy (SEM). Their cytocompatibility was evaluated according to EN ISO 10993-5:2009 standard for medical device testing. Thus, analyses regarding cell viability (Live/Dead assay), cell proliferation (Neutral Red assay) and cell adhesion to composite hydrogels (SEM) were performed using NCTC clone L929 cell line. The final results showed that both cross-linked composite hydrogel variants enriched with Ica presented optimal physicochemical, structural and biological properties to be used as a natural scaffold able to repair osteochondral defects. The data did not reveal any toxicity of composite hydrogels in NCTC stabilized cell lines within the tested range of concentrations. Moreover, cells were capable of spreading and proliferating on both composite hydrogel surfaces. In conclusion, the designed biodegradable cross-linked composites enriched with Si and Ica are recommended for further testing as natural temporary scaffolds, which can allow cell migration and synthesis of new extracellular matrix within osteochondral defects.

Keywords: composites, gelatin, osteochondral defect, small molecule

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Authors: Sidramappa Gaddnakeri, Lokanath Malligawad

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Any kind of research on production technology of individual crop / commodity /breed has not brought sustainability or stability in crop production. The sustainability of the system over years depends on the maintenance of the soil health. Organic production system includes use of organic manures, biofertilizers, green manuring for nutrient supply and biopesticides for plant protection helps to sustain the productivity even under adverse climatic condition. The study was initiated to evaluate the performance of different cropping systems under organic, inorganic and integrated production systems at The Institute of Organic Farming, University of Agricultural Sciences, Dharwad (Karnataka-India) under ICAR Network Project on Organic Farming. The trial was conducted for four years (2013-14 to 2016-17) on fixed site. Five cropping systems viz., sequence cropping of cowpea – safflower, greengram– rabi sorghum, maize-bengalgram, sole cropping of pigeonpea and intercropping of groundnut + cotton were evaluated under six nutrient management practices. The nutrient management practices are NM1 (100% Organic farming (Organic manures equivalent to 100% N (Cereals/cotton) or 100% P2O5 (Legumes), NM2 (75% Organic farming (Organic manures equivalent to 75% N (Cereals/cotton) or 100% P2O5 (Legumes) + Cow urine and Vermi-wash application), NM3 (Integrated farming (50% Organic + 50% Inorganic nutrients, NM4 (Integrated farming (75% Organic + 25% Inorganic nutrients, NM5 (100% Inorganic farming (Recommended dose of inorganic fertilizers)) and NM6 (Recommended dose of inorganic fertilizers + Recommended rate of farm yard manure (FYM). Among the cropping systems evaluated for different production systems indicated that the Groundnut + Hybrid cotton (2:1) intercropping system found more remunerative as compared to Sole pigeonpea cropping system, Greengram-Sorghum sequence cropping system, Maize-Chickpea sequence cropping system and Cowpea-Safflower sequence cropping system irrespective of the production systems. Production practices involving application of recommended rates of fertilizers + recommended rates of organic manures (Farmyard manure) produced higher net monetary returns and higher B:C ratio as compared to integrated production system involving application of 50 % organics + 50 % inorganic and application of 75 % organics + 25 % inorganic and organic production system only Both the two organic production systems viz., 100 % Organic production system (Organic manures equivalent to 100 % N (Cereals/cotton) or 100 % P2O5 (Legumes) and 75 % Organic production system (Organic manures equivalent to 75 % N (Cereals) or 100 % P2O5 (Legumes) + Cow urine and Vermi-wash application) are found to be on par. Further, integrated production system involving application of organic manures and inorganic fertilizers found more beneficial over organic production systems.

Keywords: cropping systems, production systems, cowpea, safflower, greengram, pigeonpea, groundnut, cotton

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Authors: Ghada Badr, Arwa Alturki

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The biological function of an RNA molecule depends on its structure. The objective of the alignment is finding the homology between two or more RNA secondary structures. Knowing the common functionalities between two RNA structures allows a better understanding and a discovery of other relationships between them. Besides, identifying non-coding RNAs -that is not translated into a protein- is a popular application in which RNA structural alignment is the first step A few methods for RNA structure-to-structure alignment have been developed. Most of these methods are partial structure-to-structure, sequence-to-structure, or structure-to-sequence alignment. Less attention is given in the literature to the use of efficient RNA structure representation and the structure-to-structure alignment methods are lacking. In this paper, we introduce an O(N2) Component-based Pairwise RNA Structure Alignment (CompPSA) algorithm, where structures are given as a component-based representation and where N is the maximum number of components in the two structures. The proposed algorithm compares the two RNA secondary structures based on their weighted component features rather than on their base-pair details. Extensive experiments are conducted illustrating the efficiency of the CompPSA algorithm when compared to other approaches and on different real and simulated datasets. The CompPSA algorithm shows an accurate similarity measure between components. The algorithm gives the flexibility for the user to align the two RNA structures based on their weighted features (position, full length, and/or stem length). Moreover, the algorithm proves scalability and efficiency in time and memory performance.

Keywords: alignment, RNA secondary structure, pairwise, component-based, data mining

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Authors: Yakup Ulusu, Numan Eczacıoğlu, İsa Gökçe, Helen Waller, Jeremy H. Lakey

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Besides having the appropriate amino acid sequence to perform the function of proteins, it is important to have correct conformation after this sequence to process. To consist of this conformation depends on the amino acid sequence at the primary structure, hydrophobic interaction, chaperones and enzymes in charge of folding etc. Misfolded proteins are not functional and tend to be aggregated. Cysteine originating disulfide cross-links make stable this conformation of functional proteins. When two of the cysteine amino acids come side by side, disulfide bond is established that forms a cystine bridge. Due to this feature cysteine plays an important role on the formation of three-dimensional structure of many proteins. There are two cysteine amino acids (C44, C69) in the Tol-A-III protein. Unlike protein disulfide bonds from within his own, any non-specific cystine bridge causes a change in the three dimensional structure of the protein. Proteins can be expressed in various host cells as directly or fusion (chimeric). As a result of overproduction of the recombinant proteins, aggregation of insoluble proteins in the host cell can occur by forming a crystal structure called inclusion body. In general fusion proteins are produced for provide affinity tags to make proteins more soluble and production of some toxic proteins via fusion protein expression system like pTolT. Proteins can be modified by using a site-directed mutagenesis. By this way, creation of non-specific disulfide crosslinks can be prevented at fusion protein expression system via the present cysteine replaced by another amino acid such as serine, glycine or etc. To do this, we need; a DNA molecule that contains the gene that encodes for the target protein, required primers for mutation to be designed according to site directed mutagenesis reaction. This study was aimed to be replaced cysteine encoding codon TGT with serine encoding codon AGT. For this sense and reverse primers designed (given below) and used site-directed mutagenesis reaction. Several new copy of the template plasmid DNA has been formed with above mentioned mutagenic primers via polymerase chain reaction (PCR). PCR product consists of both the master template DNA (wild type) and the new DNA sequences containing mutations. Dpn-l endonuclease restriction enzyme which is specific for methylated DNA and cuts them to the elimination of the master template DNA. E. coli cells obtained after transformation were incubated LB medium with antibiotic. After purification of plasmid DNA from E. coli, the presence of the mutation was determined by DNA sequence analysis. Developed this new plasmid is called PtolT-δ.

Keywords: site directed mutagenesis, Escherichia coli, pTolT, protein expression

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Authors: Sila Akhan, Muge Toygar, Murat Sayan, Simge Fidan

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Chronic viral hepatitis B, C, and D can cause hepatocellular carcinoma (HCC), cirrhosis and death. The proper treatment reduce the risk of development of HCC importantly, but not to zero point. Materials and Methods: We analysed retrospectively our chronic viral hepatitis B, C and D patients who attended to our Infectious Diseases policlinic between 2004-2018. From 589 biopsy-proven chronic hepatitis patients 3 have hepatocellular carcinoma on our follow up. First case is 74 years old patient. His HCV infection diagnosis was made 8 years ago. First treatment was pegylated interferon plus ribavirin only 28 weeks, because of HCV RNA breakthrough under treatment. In 2013 he was retreated with telaprevir, pegylated interferon plus ribavirin 24 weeks. But at the end of the therapy HCV RNA was found 1.290.000 IU/mL. He has abdominal ultrasonography (US) controls and alpha-fetoprotein (AFP) at 6 months intervals. All seemed normal until 2015 then he has an abdominal magnetic resonance imaging (MRI) and found HCC by chance. His treatment began in Oncology Clinic after verified with biopsy of HCC. And then sofosbuvir/ledipasvir was given to him for HCV 24 weeks. Sustained virologic response (SVR) was obtained. He is on cure for HCV infection and under control of Oncology for HCC. Second patient is 36 years old man. He knows his HBV infection since 2008. HBsAg and HBeAg positive; HDV RNA negative. Liver biopsy revealed grade:4, stage 3-4 according modified Knodell scoring system. In 2010 tenofovir treatment was began. His abdominal US and AFP were normal. His controls took place at 6 months intervals and HBV DNA negative, US, and AFP were normal until 2016 continuously. AFP found 37 above the normal range and then HCC was found in MRI. Third patient is 57 years old man. As hepatitis B infection was first diagnosed; he has cirrhosis and was began tenofovir as treatment. In short time he has HCC despite normal AFP values. Conclusion: In Mediterranian countries including Turkey naturally occurring pre-S/S variants are more than 75% of all chronic hepatitis B patients. This variants may contribute to the development of progressive liver damage and hepatocarcinogenesis. HCV-induced development of HCC is a gradual process and is affected by the duration of disease and viral genotype. All the chronic viral hepatitis patients should be followed up in 6 months intervals not only with US and AFP for HCC. Despite they have proper treatment there is always the risk development of HCC. Chronic hepatitis patients cannot be dropped from follow up even treated well.

Keywords: HCC, HCV, HBV, DAA

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Authors: Bouchemha Amel, Chachoui Takieddine, H. Maalem

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Automatic detection of targets in a modern communication system RADAR is based primarily on the concept of adaptive CFAR detector. To have an effective detection, we must minimize the influence of disturbances due to the clutter. The detection algorithm adapts the CFAR detection threshold which is proportional to the average power of the clutter, maintaining a constant probability of false alarm. In this article, we analyze the performance of two variants of adaptive algorithms CA-CFAR and OS-CFAR and we compare the thresholds of these detectors in the marine environment (no-Gaussian) with a Weibull distribution.

Keywords: CFAR, threshold, clutter, distribution, Weibull, detection

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Authors: Alcardo Alex Barakabitze, Tan Xiaoheng

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Orthogonal Frequency Division Multiplexing (OFDM) is a special case of Multi-Carrier Modulation (MCM) technique which transmits a stream of data over a number of lower data rate subcarriers. OFDM splits the total transmission bandwidth into a number of orthogonal and non-overlapping subcarriers and transmit the collection of bits called symbols in parallel using these subcarriers. This paper explores the Peak to Average Power Reduction (PAPR) using the Partial Transmit Sequence technique. We provide the distribution analysis and the basics of OFDM signals and then show how the PAPR increases as the number of subcarriers increases. We provide the performance analysis of CCDF and PAPR expressed in decibels through MATLAB simulations. The simulation results show that, in PTS technique, the performance of PAPR reduction in OFDM systems improves significantly as the number of sub-blocks increases. However, by keeping the same number of sub-blocks variation, oversampling factor and the number of OFDM blocks’ iteration for generating the CCDF, the OFDM systems with 128 subcarriers have an improved performance in PAPR reduction compared to OFDM systems with 256, 512 or >512 subcarriers.

Keywords: OFDM, peak to average power reduction (PAPR), bit error rate (BER), subcarriers, wireless communications

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Authors: Sorin Oancea

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More than half a century after Ivan Sutherland’s seminal essay, ‘The Ultimate Display’ (1965), 3D Virtual Reality is still an emergent and exploratory medium in terms of its narrative potential, production methodology, and market penetration. Traditionally positioned in front of the screen/canvas as a ‘window-on-the-world’, the storyboarder and animation director transcend the medium and its narrative reality entirely while designing a linear cinematic sequence. This paper proposes a gradual transition from the traditional linear sequence design process based on a transcendent position of the storyboarder and animation director to an increasingly immersed one characterized by a sense of unmediated presence and immanence. Employing a quaitative analysis of the current exploratory storyboarding processes for 3D VR, this research uses a practice-based methodology based on producing a short-form 3D VR narrative experience to derive its findings. The original contribution to knowledge is charting an empirically derived conceptual framework for VR storyboarding and animation directing, with the documented reflective and reflexive process as a map for directorial transitioning between converging mediums by articulating the new VR lexical categories and expounding links to allied performative arts, such as film and theatre.

Keywords: storyboarding, immersive, virtual reality, transitioning

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Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

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Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

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Authors: Katarina Rogulj, Ivana Racetin, Jelena Kilic

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In this study, the fuzzy logic approach (FLA) was developed for construction project management (CPM) under uncertainty and duality. The focus was on decision making in selecting the type of the glass facade for a residential-commercial building in the main design. The adoption of fuzzy sets was capable of reflecting construction managers’ reliability level over subjective judgments, and thus the robustness of the system can be achieved. An α-cuts method was utilized for discretizing the fuzzy sets in FLA. This method can communicate all uncertain information in the optimization process, taking into account the values of this information. Furthermore, FLA provides in-depth analyses of diverse policy scenarios that are related to various levels of economic aspects when it comes to the construction projects' valid decision making. The developed approach is applied to CPM to demonstrate its applicability. Analyzing the materials of glass facades, variants were defined. The development of the FLA for the CPM included relevant construction projec'ts stakeholders that were involved in the criteria definition to evaluate each variant. Using fuzzy Decision-Making Trial and Evaluation Laboratory Method (DEMATEL) comparison of the glass facade was conducted. This way, a rank, according to the priorities for inclusion into the main design, of variants is obtained. The concept was tested on a residential-commercial building in the city of Rijeka, Croatia. The newly developed methodology was then compared with the existing one. The aim of the research was to define an approach that will improve current judgments and decisions when it comes to the material selection of buildings facade as one of the most important architectural and engineering tasks in the main design. The advantage of the new methodology compared to the old one is that it includes the subjective side of the managers’ decisions, as an inevitable factor in each decision making. The proposed approach can help construction projects managers to identify the desired type of glass facade according to their preference and practical conditions, as well as facilitate in-depth analyses of tradeoffs between economic efficiency and architectural design.

Keywords: construction projects management, DEMATEL, fuzzy logic approach, glass façade selection

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Authors: Joseph Dodson, Robert Roth, Alexander Hodakowski, Leah Greenfield, Melissa Porterhouse, Natalie Maltby, Rachel Sadowsky

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Introduction: Throughout the COVID-19 pandemic, countless research publications were released regarding SARS-CoV-2 and its variants, suggested treatments, and vaccine safety and efficacy. Daily publication of research became overwhelming for health professionals and the general public to stay informed. To address this problem, a group of 70 students across the four colleges at Rush University created the “Rush University COVID-19 Journal Club.” To broaden the available audience, the journal club then expanded to social media. Methods: Easily accessible and understandable summaries of the research were written by students and sent to faculty sponsors for feedback. Following the revision, summaries were published weekly on the Rush University COVID-19 Journal Club website for clinicians and students to use for reference. An Instagram page was then created, and information was further condensed into succinct posts to address COVID-19 “FAQs.” Next, a survey was distributed to followers of the Instagram page with questions meant to assess the effectiveness of the platform and gain feedback. A 5-point Likert scale was used as the primary question format. Results: The Instagram page accrued 749 followers and posted 52 unique posts over a 2 year period. Preliminary results from the surveys demonstrate that over 80% of respondents strongly agree that the Instagram posts 1) are an effective platform for the public presentation of factual COVID-19-related information; 2) provide relevant and valuable information; 3) provide information that is clear, concise, and can be easily understood. Conclusion: These results suggest that the Rush COVID-19 Journal Club was able to successfully create a social media presence and convey information without sacrificing scholarly integrity. Other academic institutions may benefit from the application of this model to help students and clinicians with the interpretation and evaluation of research topics with large bodies of evidence.

Keywords: SARS-CoV-2, COVID-19, public health, social media, SARS-CoV-2 vaccine, SARS-CoV-2 variants

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Authors: Ouahab Kadri, Leila Hayet Mouss

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In this paper, we present three diagnostic modules for complex and dynamic systems. These modules are based on three ant colony algorithms, which are AntTreeStoch, Lumer & Faieta and Binary ant colony. We chose these algorithms for their simplicity and their wide application range. However, we cannot use these algorithms in their basement forms as they have several limitations. To use these algorithms in a diagnostic system, we have proposed three variants. We have tested these algorithms on datasets issued from two industrial systems, which are clinkering system and pasteurization system.

Keywords: ant colony algorithms, complex and dynamic systems, diagnosis, classification, optimization

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Authors: Jin-Hyeong Park, Hong-Seok Kim, Jin-Hyeok Yim, Young-Ji Kim, Dong-Hyeon Kim, Jung-Whan Chon, Kun-Ho Seo

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Salmonella contamination in chicken samples can cause major health problems in humans. However, not only the effects of antibiotic treatment during growth but also the impacts of poultry slaughter line on the prevalence of Salmonella in final chicken meat sold to consumers are unknown. In this study, we compared the isolation rates and antimicrobial resistance of Salmonella between antibiotic-free, conventional, conventional Korean native retail chicken meat samples and clonal divergence of Salmonella isolates by multilocus sequence typing. In addition, the distribution of extended-spectrum β-lactamase (ESBL) genes in ESBL-producing Salmonella isolates was analyzed. A total of 72 retail chicken meat samples (n = 24 antibiotic-free broiler [AFB] chickens, n = 24 conventional broiler [CB] chickens, and n = 24 conventional Korean native [CK] chickens) were collected from local retail markets in Seoul, South Korea. The isolation rates of Salmonella were 66.6% in AFB chickens, 45.8% in CB chickens, and 25% in CK chickens. By analyzing the minimum inhibitory concentrations of β -lactam antibiotics with the disc-diffusion test, we found that 81.2% of Salmonella isolates from AFB chickens, 63.6% of isolates from CB chickens, and 50% of isolates from CK chickens were ESBL producers; all ESBL-positive isolates had the CTX-M-15 genotype. Interestingly, all ESBL-producing Salmonella were revealed as ST16 by multilocus sequence typing. In addition, all CTX-M-15-positive isolates had the genetic platform of blaCTX-M gene (IS26-ISEcp1-blaCTX-M-15-IS903), to the best of our knowledge, this is the first report in Salmonella around the world. The Salmonella ST33 strain (S. Hadar) isolated in this study has never been reported in South Korea. In conclusion, our findings showed that antibiotic-free retail chicken meat products were also largely contaminated with ESBL-producing Salmonella and that their ESBL genes and genetic platforms were the same as those isolated from conventional retail chicken meat products.

Keywords: antibiotic-free poultry, conventional poultry, multilocus sequence typing, extended-spectrum β-lactamase, antimicrobial resistance

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Authors: Surajit Chakrabarty, Piyush Chauhan, Subhasis Panda, Sujoy Bhattacharya

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A large proportion of roads in India are not well maintained as per the laid down public safety guidelines leading to loss of direction control and fatal accidents. We propose a technique to detect speed breakers and potholes using mobile sensor data captured from multiple vehicles and provide a profile of the road. This would, in turn, help in monitoring roads and revolutionize digital maps. Incorporating randomness in the model formulation for detection of speed breakers and potholes is crucial due to substantial heterogeneity observed in data obtained using a mobile application from multiple vehicles driven by different drivers. This is accomplished with Hidden Markov Models, whose hidden state sequence is found for each time step given the observables sequence, and are then fed as input to LSTM network with peephole connections. A precision score of 0.96 and 0.63 is obtained for classifying bumps and potholes, respectively, a significant improvement from the machine learning based models. Further visualization of bumps/potholes is done by converting time series to images using Markov Transition Fields where a significant demarcation among bump/potholes is observed.

Keywords: deep learning, hidden Markov model, pothole, speed breaker

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Authors: J. Adeppa, S. Samanta, O. K. Raina

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Fasciolosis is a widespread economically important parasitic infection throughout the world caused by Fasciola hepatica and F. gigantica. In order to identify novel immunogen conferring significant protection against fasciolosis, currently, research has been focused on the defined antigens viz. glutathione S-transferase, fatty acid binding protein, cathepsin-L, fluke hemoglobin, paramyosin, myosin and F. hepatica- Kunitz Type Molecule. Among various antigens, GST which plays a crucial role in detoxification processes, i.e. phase II defense mechanism of this parasite, has a unique position as a novel vaccine candidate and a drug target in the control of this disease. For producing the antigens in large quantities and their purification to complete homogeneity, the recombinant DNA technology has become an important tool to achieve this milestone. RT- PCR was carried out using F. gigantica total RNA as template, and an amplicon of 657 bp GST gene was obtained. TA cloning vector was used for cloning of this gene, and the presence of insert was confirmed by blue-white selection for recombinant colonies. Sequence analysis of the present isolate showed 99.1% sequence homology with the published sequence of the F. gigantica GST gene of cattle origin (accession no. AF112657), with six nucleotide changes at 72, 74, 423, 513, 549 and 627th bp found in the present isolate, causing an overall change of 4 amino acids. The 657 bp GST gene was cloned at BamH1 and HindIII restriction sites of the prokaryotic expression vector pPROEXHTb in frame with six histidine residues and expressed in E. coli DH5α. Recombinant protein was purified from the bacterial lysate under non-denaturing conditions by the process of sonication after lysozyme treatment and subjecting the soluble fraction of the bacterial lysate to Ni-NTA affinity chromatography. Western blotting with rabbit hyper-immune serum showed immuno-reactivity with 25 kDa recombinant GST. Recombinant protein detected F. gigantica experimental as well as field infection in buffaloes by dot-ELISA. However, cross-reactivity studies on Fasciola gigantica GST antigen are needed to evaluate the utility of this protein in the serodiagnosis of fasciolosis.

Keywords: fasciola gigantic, fasciola hepatica, GST, RT- PCR

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Authors: C. E. Nugraheni, L. Abednego

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This paper is concerned with minimization of mean tardiness and flow time in a real single machine production scheduling problem. Two variants of genetic algorithm as meta-heuristic are combined with hyper-heuristic approach are proposed to solve this problem. These methods are used to solve instances generated with real world data from a company. Encouraging results are reported.

Keywords: hyper-heuristics, evolutionary algorithms, production scheduling, meta-heuristic

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Authors: Jessica Lopez Espejel, Mahaman Sanoussi Yahaya Alassan, Walid Dahhane, El Hassane Ettifouri

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Pretrained transformer-based models have shown high performance in natural language generation tasks. However, a new wave of interest has surged: automatic programming language code generation. This task consists of translating natural language instructions to a source code. Despite the fact that well-known pre-trained models on language generation have achieved good performance in learning programming languages, effort is still needed in automatic code generation. In this paper, we introduce JaCoText, a model based on Transformer neural network. It aims to generate java source code from natural language text. JaCoText leverages the advantages of both natural language and code generation models. More specifically, we study some findings from state of the art and use them to (1) initialize our model from powerful pre-trained models, (2) explore additional pretraining on our java dataset, (3) lead experiments combining the unimodal and bimodal data in training, and (4) scale the input and output length during the fine-tuning of the model. Conducted experiments on CONCODE dataset show that JaCoText achieves new state-of-the-art results.

Keywords: java code generation, natural language processing, sequence-to-sequence models, transformer neural networks

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