Search results for: somatic sequence mutations

Authors: Izabela Poprawa, Alina Chachulska-Zymelka, Lukasz Chajec, Grazyna Wilczek, Piotr Wilczek, Sebastian Student, Magdalena Rost-Roszkowska

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Heavy metals polluting the environment, especially soil, have a harmful effect on organisms, because they can damage the organ structure, disturb their function and cause developmental disorders. They can affect not only the somatic tissues but also the germinal tissues. In the natural environment, plants and animals are exposed to short- and long-term exposure to these stressors, which have a major influence on the functioning of these organisms. Numerous animals have been treated as the bioindicators of the environment. Therefore, studies on any alterations caused by, e.g., heavy metals are in the center of interests of not only environmental but also medical and biological science. Myriapods are invertebrates which are bioindicators of the environment. One of the species which lives in the upper layers of soil, particularly under stones and rocks is Lithobius forficatus (Chilopoda), commonly known as the brown centipede or stone centipede. It is a European species of the family Lithobiidae. This centipede living in the soil is exposed to, e.g., heavy metals such as cadmium, lead, arsenic. The main goal of our project was to analyze the impact of long-term exposure to cadmium on the structure of ovary with the emphasis on the course of oogenesis. As the material for analysis of cadmium exposure to ovaries, we chose the centipede species, L. forficatus. Animals were divided into two experimental groups: C – the control group, the animals cultured in laboratory conditions in a horticultural soil; Cd2 – the animals cultured in a horticultural soil supplemented with 80 mg/kg (dry weight) of CdCl2 for 45 days – long-term exposure. Animals were fed with Acheta and Chironomus larvae maintained in tap water. The analyzes were carried out using transmission electron microscopy (TEM), flow cytometry and laser scanning (confocal) microscopy. Here we present the results of long-term exposure to cadmium concentration in soil on the organ responsible for female germ cell formation. Analysis with the use of the transmission electron microscope showed changes in the ultrastructure of both somatic and germ cells in the ovary. Moreover, quantitative analysis revealed the decrease in the percentage of cells viability, the increase in the percentage of cells with depolarized mitochondria and increasing the number of early apoptotic cells. All these changes were statistically significant compared to the control. Additionally, an increase in the ADP/ATP index was recorded. However, changes were not statistically significant to the control. Acknowledgment: The study has been financed by the National Science Centre, Poland, grant no 2017/25/B/NZ4/00420.

Keywords: cadmium, centipede, ovary, ultrastructure

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

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

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

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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: Abishek Rajkumar

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Antibiotic resistance can occur naturally given the selective pressure placed on antibiotics. Within a large population of bacteria, there is a significant chance that some of those bacteria can develop resistance via mutations or genetic recombination. However, a growing public health concern has arisen over the fact that antibiotic resistance has increased significantly over the past few decades. This is because humans have been over-consuming and producing antibiotics, which has ultimately accelerated the antibiotic resistance seen in these bacteria. The product of all of this is an ongoing race between scientists and the bacteria as bacteria continue to develop resistance, which creates even more demand for an antibiotic that can still terminate the newly resistant strain of bacteria. This paper will focus on a myriad of aspects of antibiotic resistance in bacteria starting with how it occurs on a molecular level and then focusing on the antibiotic concentrations and how they affect the resistance and fitness seen in bacteria.

Keywords: antibiotic, molecular, mutation, resistance

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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: 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: 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: Wael M. Rabeh, Cesar Carrasco-Lopez, Juliana C. Ferreira, Pance Naumov

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Bioluminescence, the emission of light from a biological process, is found in various living organisms including bacteria, fireflies, beetles, fungus and different marine organisms. Luciferase is an enzyme that catalyzes a two steps oxidation of luciferin in the presence of Mg2+ and ATP to produce oxyluciferin and releases energy in the form of light. The luciferase assay is used in biological research and clinical applications for in vivo imaging, cell proliferation, and protein folding and secretion analysis. The luciferase enzyme consists of two domains, a large N-terminal domain (1-436 residues) that is connected to a small C-terminal domain (440-544) by a flexible loop that functions as a hinge for opening and closing the active site. The two domains are separated by a large cleft housing the active site that closes after binding the substrates, luciferin and ATP. Even though all insect luciferases catalyze the same chemical reaction and share 50% to 90% sequence homology and high structural similarity, they emit light of different colors from green at 560nm to red at 640 nm. Currently, the majority of the structural and biochemical studies have been conducted on green-emitting firefly luciferases. To address the color emission mechanism, we expressed and purified two luciferase enzymes with blue-shifted green and red emission from indigenous Brazilian species Amydetes fanestratus and Phrixothrix, respectively. The two enzymes naturally emit light of different colors and they are an excellent system to study the color-emission mechanism of luciferases, as the current proposed mechanisms are based on mutagenesis studies. Using a vapor-diffusion method and a high-throughput approach, we crystallized and solved the crystal structure of both enzymes, at 1.7 Å and 3.1 Å resolution respectively, using X-ray crystallography. The free enzyme adopted two open conformations in the crystallographic unit cell that are different from the previously characterized firefly luciferase. The blue-shifted green luciferase crystalized as a monomer similar to other luciferases reported in literature, while the red luciferases crystalized as an octamer and was also purified as an octomer in solution. The octomer conformation is the first of its kind for any insect’s luciferase, which might be relate to the red color emission. Structurally designed mutations confirmed the importance of the transition between the open and close conformations in the fine-tuning of the color and the characterization of other interesting mutants is underway.

Keywords: bioluminescence, enzymology, structural biology, x-ray crystallography

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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: Yew Mun Yip, Dawei Zhang

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Proteins are the biological machinery that executes specific vital functions in every cell of the human body by folding into their 3D structures. When a protein misfolds from its native structure, the machinery will malfunction and lead to misfolding diseases. Although in vitro experiments are able to conclude that the mutations of the amino acid sequence lead to incorrectly folded protein structures, these experiments are unable to decipher the folding process. Therefore, molecular dynamic (MD) simulations are employed to simulate the folding process so that our improved understanding of the folding process will enable us to contemplate better treatments for misfolding diseases. MD simulations make use of force fields to simulate the folding process of peptides. Secondary structures are formed via the hydrogen bonds formed between the backbone atoms (C, O, N, H). It is important that the hydrogen bond energy computed during the MD simulation is accurate in order to direct the folding process to the native structure. Since the atoms involved in a hydrogen bond possess very dissimilar electronegativities, the more electronegative atom will attract greater electron density from the less electronegative atom towards itself. This is known as the polarization effect. Since the polarization effect changes the electron density of the two atoms in close proximity, the atomic charges of the two atoms should also vary based on the strength of the polarization effect. However, the fixed atomic charge scheme in force fields does not account for the polarization effect. In this study, we introduce the polarized structure-specific backbone charge (PSBC) model. The PSBC model accounts for the polarization effect in MD simulation by updating the atomic charges of the backbone hydrogen bond atoms according to equations derived between the amount of charge transferred to the atom and the length of the hydrogen bond, which are calculated from quantum-mechanical calculations. Compared to other polarizable models, the PSBC model does not require quantum-mechanical calculations of the peptide simulated at every time-step of the simulation and maintains the dynamic update of atomic charges, thereby reducing the computational cost and time while accounting for the polarization effect dynamically at the same time. The PSBC model is applied to two different β-peptides, namely the Beta3s/GS peptide, a de novo designed three-stranded β-sheet whose structure is folded in vitro and studied by NMR, and the trpzip peptides, a double-stranded β-sheet where a correlation is found between the type of amino acids that constitute the β-turn and the β-propensity.

Keywords: hydrogen bond, polarization effect, protein folding, PSBC

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Authors: Siham Soulaimi

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Europe has become a difficult destination due to strict migration policies and border controls, making Morocco an immigration country. Morocco is currently at the center of the international migration debate because it not only hosts regular migrants but also must deal with the problem of irregular migrants entering its territory. Sub-Saharan irregular migration is full of challenges that might cause a delay for the migrants, announcing a death sentence for many others. The journey's hurdles are likely to cause a crisis in expectations, resulting in serious consequences on the migrants' mental health. Our research study emphasizes that sub-Saharan migrants begin irregular journeys with high hopes, only to be disappointed by how unexpectedly cruel it turns out to be. We also pointed to specific physical and, more crucially, mental health problems that they end up with after survival, resulting in somatic disorders.

Keywords: irregular migration, Sub-Saharan migrants, challenges, experiences crisis, mental health, somatoform disorder

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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: Tareg Belali, Mosleh Abomughaid, Muhanad Alhujaily

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HNF4a is one of the steroid hormone receptor family of transcription factors with roles in the development of the liver and the regulation of several critical metabolic pathways, such as glycolysis, drug metabolism, and apolipoproteins and blood coagulation. The transcriptional potency of HNF4a is well known due to its involvement in diabetes and other metabolic diseases. However, recently HNF4a has been discovered to be closely associated with several haematological disorders, mainly because of genetic mutations, drugs, and hepatic disorders. We review HNF4a structure and function and its role in haematological disorders. We discuss possible good therapies that are based on targeting HNF4a.

Keywords: hepatocyte nuclear factor 4 alpha, HNF4a nuclear receptor, steroid hormone receptor family of transcription factors, hematological disorders

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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: Hassan Habibi, Hossein Soltani, Amir Moghadam, Najmeh Bakhshi

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The purpose of this study was to compare competitive state anxiety among elite and non-elite futsal players and its relationship with situational factors. 130 non-elite and 70 elite male futsal players participated in the study. Competitive State Anxiety Inventory-2 and situational factors Inventory were applied. Data was analyzed using one-way ANOVA and product moment correlation. Results showed there was significant difference between competitive state anxiety subscales (cognitive anxiety somatic anxiety & self-confidence) and situational factors among elite and non-elite futsal players (P<0.05) but there was no significant correlations between situational factors subscales among elite and non-elite futsal players (P<0.05).

Keywords: competitive state anxiety, situational factors, elite players, non-elite players

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Authors: Fern Baedyananda, Arkom Chaiwongkot, Somchai Niruthisard, Nakarin Kitkumthorn, Parvapan Bhattarakosol

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High-risk human papillomavirus (HPV) infections cause transformation of the host cells by down-regulating and inhibiting host regulatory proteins such as p53 and pRb by overexpressing the viral oncoproteins E6 and E7. However, the E1 protein which is the only enzyme encoded by HPV has also been shown to cause DNA instability leading to the integration of the virus into the host genome and triggering carcinogenic events. A 63bp duplication in the E1 helicase region has been detected in European patients. However, the clinical prognosis of these patients is still controversial. This study was performed to determine the presence of the HPV-16 E1 63bp duplication in patient cervical samples in Thai women and determine the sequence of the variant in the Thai population. Detection of the HPV-16 E1 duplication in the helicase region was performed in 90 patient cell samples across normal, cervical intraepithelial neoplasia I-III, and squamous cervical carcinoma stages by PCR. The PCR products were purified and sequenced to determine the presence of duplication variants.The variant form was found in 10% of all CIN 1 patients. In this study, the presence of the 63 bp duplication variant in the Thai population was found to be present and was further characterized. Interestingly, all samples that exhibited the variant form of HPV-16 E1 were classified as CIN I. Presence of the variant, constricted to mild dysplasia signifies the importance of HPV-16 E1 in carcinogenesis.

Keywords: carcinogenesis, cervical cancer, human papillomavirus, HPV-16 E1

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Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: Diaa Ahmed Mohamed Ahmedien

Abstract:

Nowadays, it cannot be denied that the most important interactive arts trends have appeared as a result of significant scientific mutations in the modern sciences, and holographic art is not an exception, where it is considered as a one of the most important major contemporary interactive arts trends in visual arts. Holographic technique had been evoked through the modern physics application in late 1940s, for the improvement of the quality of electron microscope images by Denis Gabor, until it had arrived to Margaret Benyon’s art exhibitions, and then it passed through a lot of procedures to enhance its quality and artistic applications technically and visually more over 70 years in visual arts. As a modest extension to these great efforts, this research aimed to invoke extraordinary attempt to enroll sample of normal people in Egyptian community in holographic recording program to record their appreciated objects or antiques, therefore examine their abilities to interact with modern techniques in visual communication arts. So this research tried to answer to main three questions: 'can we use the analog holographic techniques to unleash new theoretical and practical knowledge in interactive arts for public in Egyptian community?', 'to what extent holographic art can be familiar with public and make them able to produce interactive artistic samples?', 'are there possibilities to build holographic interactive program for normal people which lead them to enhance their understanding to visual communication in public and, be aware of interactive arts trends?' This research was depending in its first part on experimental methods, where it conducted in Laser lab at Cairo University, using Nd: Yag Laser 532 nm, and holographic optical layout, with selected samples of Egyptian people that they have been asked to record their appreciated object, after they had already learned recording methods, and in its second part on a lot of discussion panel had conducted to discuss the result and how participants felt towards their holographic artistic products through survey, questionnaires, take notes and critiquing holographic artworks. Our practical experiments and final discussions have already lead us to say that this experimental research was able to make most of participants pass through paradigm shift in their visual and conceptual experiences towards more interaction with contemporary visual arts trends, as an attempt to emphasize to the role of mature relationship between the art, science and technology, to spread interactive arts out in our community through the latest scientific and artistic mutations around the world and the role of this relationship in our societies particularly with those who have never been enrolled in practical arts programs before.

Keywords: Egyptian community, holographic art, laser art, visual art

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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: Urszula Malaga-Toboła, Marek Gugała, Rafał Kornas, Robert Rusinek, Marek Gancarz

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The work focused on presenting the elements that determine the quality of fresh milk in the context of the quality of its transport. The quality of the raw material depends on the quality of transport. Milk transport involves many activities in which, apart from the temperature and sterility of the means of transport, it is important not to expose the raw material to shocks. Recently, there have been changes in the milk supply chain, thus affecting the logistics processes between its links. Based on the conducted research and analyses, it was found that the condition of the road surface on which milk is transported affects its quality. For the T1 milk transport route- gravel roads of very poor and poor quality, the lowest number of bacteria and the highest number of somatic cells, fat content, and temperature of the transported milk were obtained. A well-organized integrated transport system is a real need for most companies today. The analysis showed significant differences in the quality of milk delivered to the dairy.

Keywords: fresh milk, transport, milk quality, dairy

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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: 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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Authors: Sulaiman A. Alrumman, Abd El-Latif Hesham

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Despite medical progress worldwide, dental caries are still widespread. Miswak is derived from the plant arak (Salvadora persica). It is used by Muslim people as a natural product for the cleansing of teeth, to ensure oral and dental hygiene. This study was designed to evaluate the antimicrobial effects of ethanol, methanol, and ethanol/methanol extracts of miswak against three bacterial pathogens of the oral cavity. The pathogens were isolated from the oral cavity of volunteers/patients and were identified on the basis of 16S rRNA gene amplification data. Sequence comparisons were made with 16S rRNA gene sequences available in the GenBank database. The results of sequence alignment and phylogenetic analysis identified the three pathogens as being Staphylococcus aureus strain KKU-020, Enterococcus faecalis strain KKU-021 and Klebsiella pneumoniae strain KKU-022. All miswak extracts showed powerful antimicrobial activity against the three pathogens. The maximum zone of inhibition (40.67±0.88 mm) was observed against E. faecalis with ethanolic extracts whilst methanolic extracts showed the minimum zone of inhibition (10.33±0.88 mm) against K. pneumonia KKU-022. Based on the significant effects of the miswak extracts against the oral cavity pathogens in our study, we recommend that miswak is to be used as a dental hygiene method to prevent tooth caries.

Keywords: antibacterial, miswak, Salvadora persica, oral cavity pathogens

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Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

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Authors: Bin Liu

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MicroRNAs (miRNAs) are small non-coding RNA molecules, functioning in transcriptional and post-transcriptional regulation of gene expression. The discrimination of the real pre-miRNAs from the false ones (such as hairpin sequences with similar stem-loops) is necessary for the understanding of miRNAs’ role in the control of cell life and death. Since both their small size and sequence specificity, it cannot be based on sequence information alone but requires structure information about the miRNA precursor to get satisfactory performance. Kmers are convenient and widely used features for modeling the properties of miRNAs and other biological sequences. However, Kmers suffer from the inherent limitation that if the parameter K is increased to incorporate long range effects, some certain Kmer will appear rarely or even not appear, as a consequence, most Kmers absent and a few present once. Thus, the statistical learning approaches using Kmers as features become susceptible to noisy data once K becomes large. In this study, we proposed a Gapped k-mer approach to overcome the disadvantages of Kmers, and applied this method to the field of miRNA prediction. Combined with the structure status composition, a classifier called imiRNA-GSSC was proposed. We show that compared to the original imiRNA-kmer and alternative approaches. Trained on human miRNA precursors, this predictor can achieve an accuracy of 82.34 for predicting 4022 pre-miRNA precursors from eleven species.

Keywords: gapped k-mer, imiRNA-GSSC, microRNA precursor, support vector machine

Procedia PDF Downloads 133