Search results for: target gene database

Authors: Abdoulie K. Ceesay

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Within the sequence of the whole genome, it is known that 99.9% of the human genome is similar, whilst our difference lies in just 0.1%. Among these minor dissimilarities, the most common type of genetic variations that occurs in a population is SNP, which arises due to nucleotide substitution in a protein sequence that leads to protein destabilization, alteration in dynamics, and other physio-chemical properties’ distortions. While causing variations, they are equally responsible for our difference in the way we respond to a treatment or a disease, including various cancer types. There are two types of SNPs; synonymous single nucleotide polymorphism (sSNP) and non-synonymous single nucleotide polymorphism (nsSNP). sSNP occur in the gene coding region without causing a change in the encoded amino acid, while nsSNP is deleterious due to its replacement of a nucleotide residue in the gene sequence that results in a change in the encoded amino acid. Predicting the effects of cancer related nsSNPs on protein stability, function, and dynamics is important due to the significance of phenotype-genotype association of cancer. In this thesis, Data of 5 oncogenes (ONGs) (AKT1, ALK, ERBB2, KRAS, BRAF) and 5 tumor suppressor genes (TSGs) (ESR1, CASP8, TET2, PALB2, PTEN) were retrieved from ClinVar. Five common in silico tools; Polyphen, Provean, Mutation Assessor, Suspect, and FATHMM, were used to predict and categorize nsSNPs as deleterious, benign, or neutral. To understand the impact of each variation on the phenotype, Maestro, PremPS, Cupsat, and mCSM-NA in silico structural prediction tools were used. This study comprises of in-depth analysis of 10 cancer gene variants downloaded from Clinvar. Various analysis of the genes was conducted to derive a meaningful conclusion from the data. Research done indicated that pathogenic variants are more common among ONGs. Our research also shows that pathogenic and destabilizing variants are more common among ONGs than TSGs. Moreover, our data indicated that ALK(409) and BRAF(86) has higher benign count among ONGs; whilst among TSGs, PALB2(1308) and PTEN(318) genes have higher benign counts. Looking at the individual cancer genes predisposition or frequencies of causing cancer according to our research data, KRAS(76%), BRAF(55%), and ERBB2(36%) among ONGs; and PTEN(29%) and ESR1(17%) among TSGs have higher tendencies of causing cancer. Obtained results can shed light to the future research in order to pave new frontiers in cancer therapies.

Keywords: tumor suppressor genes (TSGs), oncogenes (ONGs), non synonymous single nucleotide polymorphism (nsSNP), single nucleotide polymorphism (SNP)

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Authors: M. Vassou, A. Karasimos

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A primary concern in the field of Second Language Acquisition (SLA) research is to determine the innate mechanisms of second language learning and acquisition through the systematic study of a learner's interlanguage. Errors emerge while a learner attempts to communicate using the target-language and can be seen either as the observable linguistic product of the latent cognitive and language process of mental representations or as an indispensable learning mechanism. Therefore, the study of the learner’s erroneous forms may depict the various strategies and mechanisms that take place during the language acquisition process resulting in deviations from the target-language norms and difficulties in communication. Mapping the erroneous utterances of a late adult learner in the process of acquiring Greek as a second language constitutes one of the main aims of this study. For our research purposes, we created an error-tagged learner corpus composed of the participant’s written texts produced throughout a period of a 4- year instructed language acquisition. Error analysis and interlanguage theory constitute the methodological and theoretical framework, respectively. The research questions pertain to the learner's most frequent errors per linguistic category and per year as well as his choices concerning the Greek Article System. According to the quantitative analysis of the data, the most frequent errors are observed in the categories of the stress system and syntax, whereas a significant fluctuation and/or gradual reduction throughout the 4 years of instructed acquisition indicate the emergence of developmental stages. The findings with regard to the article usage bespeak fossilization of erroneous structures in certain contexts. In general, our results point towards the existence and further development of an established learner’s (inter-) language system governed not only by mother- tongue and target-language influences but also by the learner’s assumptions and set of rules as the result of a complex cognitive process. It is expected that this study will contribute not only to the knowledge in the field of Greek as a second language and SLA generally, but it will also provide an insight into the cognitive mechanisms and strategies developed by multilingual learners of late adulthood.

Keywords: Greek as a second language, error analysis, interlanguage, late adult learner

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Authors: Jie Zhang, Chaomin Zhang

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Mergers and Acquisitions (M&A) are important market tools to support economic transformation and upgrading to achieve high-quality development. Based on the employee value distribution in the context of M&A and reorganization of Chinese enterprises, this paper takes China's A-share listed companies from 2007 to 2022 as research samples to explore the impact of employee labor income share fluctuation on the success rate of M&A. The research finds that, first, when employees of the target party expect the share of labor income to decline after the merger, it will significantly inhibit the success rate of the merger. Second, when there is a vertical gap (that is, the target party has a larger scale and a higher level of corporate governance) or a horizontal gap (that is, the merger parties are in different industries and strategies) .Third, for enterprises that have completed the M&A process, the decline of labor income share will lead to higher post-M&A goodwill impairment. The research conclusions of this paper enrich the literature on the economic consequences of labor income share and the influencing factors of M&A, and provide useful reference for enterprises to better coordinate the value distribution of employees in M&A.

Keywords: labor income share, the success rate of M&A, value distribution, goodwill impairment

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Authors: Andres Pinilla Palacios, Ricardo Tamayo

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Emotional contagion is characterized as an automatic tendency to synchronize behaviors that facilitate emotional convergence among humans. It might thus play a pivotal role to understand the dynamics of key social interactions. However, a few research has investigated its potential mechanisms. We suggest two complementary but independent processes that may underlie emotional contagion. The efficient contagion hypothesis, based on fast and implicit bottom-up processes, modulated by familiarity and spread of activation in the emotional associative networks of memory. Secondly, the emotional contrast hypothesis, based on slow and explicit top-down processes guided by deliberated appraisal and hypothesis-testing. In order to assess these two hypotheses, an experiment with 39 participants was conducted. In the first phase, participants were induced (between-groups) to an emotional state (positive, neutral or negative) using a standardized video taken from the FilmStim database. In the second phase, participants classified and rated (within-subject) the emotional state of 15 faces (5 for each emotional state) taken from the POFA database. In the third phase, all participants were returned to a baseline emotional state using the same neutral video used in the first phase. In a fourth phase, participants classified and rated a new set of 15 faces. The accuracy in the identification and rating of emotions was partially explained by the efficient contagion hypothesis, but the speed with which these judgments were made was partially explained by the emotional contrast hypothesis. However, results are ambiguous, so a follow-up experiment is proposed in which emotional expressions and activation of the sympathetic system will be measured using EMG and EDA respectively.

Keywords: electromyography, emotional contagion, emotional valence, identification of emotions, imitation

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Authors: Yeon Ho Je

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A novel recombinant baculovirus, NeuroBactrus, was constructed to develop an improved baculovirus insecticide with additional beneficial properties, such as a higher insecticidal activity and improved recovery, compared to wild-type baculovirus. For the construction of NeuroBactrus, the Bacillus thuringiensis crystal protein gene (here termed cry1-5) was introduced into the Autographa californica nucleopolyhedrovirus (AcMNPV) genome by fusion of the polyhedrin–cry1-5–polyhedrin genes under the control of the polyhedrin promoter. In the opposite direction, an insect-specific neurotoxin gene, AaIT, from Androctonus australis was introduced under the control of an early promoter from Cotesia plutellae bracovirus by fusion of a partial fragment of orf603. The polyhedrin–Cry1-5–polyhedrin fusion protein expressed by the NeuroBactrus was not only occluded into the polyhedra, but it was also activated by treatment with trypsin, resulting in an_65-kDa active toxin. In addition, quantitative PCR revealed that the neurotoxin was expressed from the early phase of infection. NeuroBactrus showed a high level of insecticidal activity against Plutella xylostella larvae and a significant reduction in the median lethal time against Spodoptera exigua larvae compared to those of wild-type AcMNPV. Rerecombinant mutants derived from NeuroBactrus in which AaIT and/or cry1-5 were deleted were generated by serial passages in vitro. Expression of the foreign proteins (B. thuringiensis toxin and AaIT) was continuously reduced during the serial passage of the NeuroBactrus. Moreover, polyhedra collected from S. exigua larvae infected with the serially passaged NeuroBactrus showed insecticidal activity similar to that of wild-type AcMNPV. These results suggested that NeuroBactrus could be recovered to wild-type AcMNPV through serial passaging.

Keywords: baculovirus, insecticide, neurotoxin, neurobactrus

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Authors: Branimir Jurun, Elza Jurun

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Focus of this paper is description and functioning manner of the instrument for wave pressure metering. Moreover, an essential component of this paper is the proposal of a metering unit for the direct wave pressure measurement determined by the shape and surface of the instrument including the number of sensors and angle between them. Namely, far applied instruments by means of height, length, direction, wave time period and other components determine wave pressure on a particular area. This instrument, allows the direct measurement i.e. measurement without additional calculation, of the wave pressure expressed in a standardized unit of measure. That way the instrument has a standardized form, surface, number of sensors and the angle between them. In addition, it is made with the status that follows the wave and always is on the water surface. Database quality which is listed by the instrument is made possible by using the Arduino chip. This chip is programmed for receiving by two data from each of the sensors each second. From these data by a pre-defined manner a unique representative value is estimated. By this procedure all relevant wave pressure measurement results are directly and immediately registered. Final goal of establishing such a rich database is a comprehensive statistical analysis that ranges from multi-criteria analysis across different modeling and parameters testing to hypothesis accepting relating to the widest variety of man-made activities such as filling of beaches, security cages for aquaculture, bridges construction.

Keywords: instrument, metering, water, waves

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Authors: Leila Baghaarabani, Parvin Razzaghi, Mennatolla Magdy Mostafa, Ahmad Albaqsami, Al Warith Al Rushaidi, Masoud Al Rawahi

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Predicting the interaction between drugs and their molecular targets is pivotal for advancing drug development processes. Due to the time and cost limitations, computational approaches have emerged as an effective approach to drug-target interaction (DTI) prediction. Most of the introduced computational based approaches utilize the drug molecule and protein sequence as input. This study does not only utilize these inputs, it also introduces a protein representation developed using a masked protein language model. In this representation, for every individual amino acid residue within the protein sequence, there exists a corresponding probability distribution that indicates the likelihood of each amino acid being present at that particular position. Then, the similarity between each pair of amino acids is computed to create a similarity matrix. To encode the knowledge of the similarity matrix, Bi-Level Routing Attention (BiFormer) is utilized, which combines aspects of transformer-based models with protein sequence analysis and represents a significant advancement in the field of drug-protein interaction prediction. BiFormer has the ability to pinpoint the most effective regions of the protein sequence that are responsible for facilitating interactions between the protein and drugs, thereby enhancing the understanding of these critical interactions. Thus, it appears promising in its ability to capture the local structural relationship of the proteins by enhancing the understanding of how it contributes to drugprotein interactions, thereby facilitating more accurate predictions. To evaluate the proposed method, it was tested on two widely recognized datasets: Davis and KIBA. A comprehensive series of experiments was conducted to illustrate its effectiveness in comparison to cutting edge techniques.

Keywords: BiFormer, transformer, protein language processing, self-attention mechanism, binding affinity, drug target interaction, similarity matrix, protein masked representation, protein language model

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Authors: Patricia M. B. Saint-Vincent, Anna Furches, Stephanie Galanie, Erica Teixeira Prates, Piet Jones, Nancy Engle, David Kainer, Wellington Muchero, Daniel Jacobson, Timothy J. Tschaplinski

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Uridine diphosphate-glycosyltransferases (UGTs) are enzymes that catalyze sugar transfer to a variety of plant metabolites. UGT substrates, which include plant secondary metabolites involved in lignification, demonstrate new activities and incorporation when glycosylated. Knowledge of UGT function, substrate specificity, and enzyme products is important for plant engineering efforts, especially related to increasing plant biomass through lignification. UGTs in Populus trichocarpa, a biofuel feedstock, and model woody plant, were selected from a pool of gene candidates using rapid prioritization strategies. A functional genomics workflow, consisting of a metabolite genome-wide association study (mGWAS), expression of synthetic codon-optimized genes, and high-throughput biochemical assays with mass spectrometry-based analysis, was developed for determining the substrates and products of previously-uncharacterized enzymes. A total of 40 UGTs from P. trichocarpa were profiled, and the biochemical assay results were compared to predicted mGWAS connections. Assay results confirmed seven of 11 leaf mGWAS associations and demonstrated varying levels of substrate specificity among candidate UGTs. P. trichocarpa UGT substrate processing confirms the role of these newly-characterized enzymes in lignan, flavonoid, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress responses.

Keywords: Populus, metabolite-gene associations, GWAS, bio feedstocks, glycosyltransferase

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Authors: A. Anandha Selvan, B. Malarvizhi

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In recent year the problem of space debris have become very serious. The mass of the artificial objects in orbit increased quite steadily at the rate of about 145 metric tons annually, leading to a total tally of approximately 7000 metric tons. Now most of space debris object orbiting in LEO region about 97%. The catastrophic collision can be mostly occurred in LEO region, where this collision generate the new debris. Thus, we propose a concept for cleaning the space debris in the region of thermosphere by passing the Extreme Ultraviolet (EUV) radiation to in front of space debris object from the re-orbiter. So in our concept the Extreme Ultraviolet (EUV) radiation will create the thermosphere expansion by reacting with atmospheric gas particles. So the drag is produced in front of the space debris object by thermosphere expansion. This drag force is high enough to slow down the space debris object’s relative velocity. Therefore the space debris object gradually reducing the altitude and finally enter into the earth’s atmosphere. After the first target is removed, the re-orbiter can be goes into next target. This method remove the space debris object without catching debris object. Thus it can be applied to a wide range of debris object without regard to their shapes or rotation. This paper discusses the operation of re-orbiter for removing the space debris in thermosphere region.

Keywords: active space debris removal, space debris, LEO, extreme ultraviolet, re-orbiter, thermosphere

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Authors: Heba Esaily, Rawhia Eledl, Daila Aboelela, Rasha Noreldin

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Objective: Assess serum level of Transforming growth factor beta 2 (TGF-β2) and Matrilin-3 (MATN3) SNP6 polymorphism in osteoarthritic patients Background: Osteoarthritis (OA) is a musculoskeletal disease characterized by pain and joint stiffness. TGF-β 2 is involved in chondrogenesis and osteogenesis, It has found that MATN3 gene and protein expression was correlated with the extent of tissue damage in OA. Findings suggest that regulation of MATN3 expression is essential for maintenance of the cartilage extracellular matrix microenvironment Subjects and Methods: 72 cases of primary OA (56 with knee OA and 16 with generalized OA were compared with that of 18 healthy controls. Radiographs were scored with the Kellgren-Lawrence scale. Serum TGF-β2 was measured by using (ELISA), levels of marker were correlated to radiographic grading of disease and MATN3 SNP6 polymorphism was determined by (PCR-RFLP). Results: MATN3 SNP6 polymorphism and serum level of TGF-β2 were higher in OA compared with controls. Genotype, NN and N allele frequency were higher in patients with OA compared with controls. NN genotype and N allele frequency were higher in knee osteoarthritis than generalized OA. Significant positive correlation between level of TGFβ2 and radiographic grading in group with knee OA, but no correlation between serum level of TGFβ2 and radiographic grading in generalized OA. Conclusion: MATN3 SNP6 polymorphism and TGF-β2 implicated in the pathogenesis of osteoarthritis. Association of N/N genotype with primary osteoarthritis emphasizes on the need for prospective study include larger sample size to confirm the results of the present study.

Keywords: Matrilin-3, transforming growth factor beta 2, primary osteoarthritis, knee osteoarthritis

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Authors: F. Haddadj, S. Hamdi, A. Milla, S. Zenia, A. Smai, H. Saadi, F. Marniche, B. Doumandji-Mitiche

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The use of a biopesticide based on a microorganism scale requires particular care including safety against the useful auxiliary fauna and mammals among other human beings. Due to its persistence in soil and its apparent human and animal safety, Beauveria bassiana is a cryptogram used for controlling pests organizations, particularly in the locust where its effectiveness has been proven. This fungus is also called for greater respect for biotic communities and the environment. Indeed, biopesticides have several environmental benefits: biodegradability, their activity and selectivity decrease unintended non-target species effects, decreased resistance to some of them. It is in this sense that we contribute by presenting our work on the safety of B. bassiana against mammals. For this we conducted a toxicological study of this fungus strain on Wistar rats Rattus norvegicus, first its effect on weight gain. In a second time were performed histological target organ is the liver. After 20 days of treatment, the results of the toxicological studies have shown that B. bassiana caused no change in the physiological state of rats or weight gain, behavior and diet. On cuts in liver histology revealed no disturbance on the organ.

Keywords: B. bassiana, entomopathogenic fungus, histology, Rattus norvegicus

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Authors: Ranjeet Kumar, Pravin Suryakantrao Deshmukh, Sonal Sharma, Basudev Banerjee

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With the tremendous increase in exposure to radiofrequency microwaves emitted by mobile phones, globally public awareness has grown with regard to the potential health hazards of microwaves on the nervous system in the brain. India alone has more than one billion mobile users out of 4.3 billion globally. Our studies have suggested that radio frequency able to affect neuronal alterations in the brain, and hence, affecting cognitive behaviour. However, adverse effect of low-intensity microwave exposure with endoplasmic reticulum stress and autophagy has not been evaluated yet. In this study, we explore whether low-intensity microwave induces endoplasmic reticulum stress and autophagy with varying frequency and time duration in Wistar rat. Ninety-six male Wistar rat were divided into 12 groups of 8 rats each. We studied at 900 MHz, 1800 MHz, and 2450 MHz frequency with reference to sham-exposed group. At the end of the exposure, the rats were sacrificed to collect brain tissue and expression of CHOP, ATF-4, XBP-1, Bcl-2, Bax, LC3 and Atg-4 gene was analysed by real-time PCR. Significant fold change (p < 0.05) of gene expression was found in all groups of 1800 MHz and 2450 MHz exposure group in comparison to sham exposure group. In conclusion, the microwave exposure able to induce ER stress and modulate autophagy. ER (endoplasmic reticulum) stress and autophagy vary with increasing frequency as well as the duration of exposure. Our results suggested that microwave exposure is harmful to neuronal health as it induces ER stress and hampers autophagy in neuron cells and thereby increasing the neuron degeneration which impairs cognitive behaviour of experimental animals.

Keywords: autophagy, ER stress, microwave, nervous system, rat

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Authors: Noriko Hanakawa, Masaki Obana

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A simulation tool has been proposed for big-scale projection mapping events. The tool has four main functions based on Mapbox and Unity utilities. The first function is building a 3D model of real cities by MapBox. The second function is a movie projection to some buildings in real cities by Unity. The third function is a movie sending function from a PC to a virtual projector. The fourth function is mapping movies with fitting buildings. The simulation tool was adapted to a real projection mapping event that was held in 2019. The event has been finished. The event had a serious problem in the movie projection to the target building. The extra tents were set in front of the target building. The tents became the obstacles to the movie projection. The simulation tool can be reappeared the problems of the event. Therefore, if the simulation tool was developed before the 2019 projection mapping event, the problem of the tents’ obstacles could be avoided with the simulation tool. In addition, we confirmed that the simulation tool is useful to make a plan of future projection mapping events in order to avoid obstacles of various extra equipment such as utility poles, planting trees, monument towers.

Keywords: projection mapping, projector position, real 3D map, avoiding obstacles

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Authors: Jiang Xu, Daoping Wang, Yinghong Pan

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The jointing-booting stage is a critical period of both vegetative growth and reproductive growth in rice. Therefore, the proteomic analysis of the mutant Osbri1, whose corresponding gene OsBRI1 encodes the putative BRs receptor OsBRI1, at jointing-booting stage is very important for understanding the effects of BRs on vegetative and reproductive growth. In this study, the proteomes of leaves from an allelic mutant of the DWARF 61 (D61, OsBRI1) gene, Fn189 (dwarf54, d54) and its wild-type variety T65 (Taichung 65) at jointing-booting stage were analysed by using a Q Exactive plus orbitrap mass spectrometer, and more than 3,100 proteins were identified in each sample. Ontology analysis showed that these proteins distribute in various space of the cells, such as the chloroplast, mitochondrion, and nucleus, they functioned as structural components and/or catalytic enzymes and involved in many physiological processes. Moreover, quantitative analysis displayed that 266 proteins were differentially expressed in two samples, among them, 77 proteins decreased and 189 increased more than two times in Fn189 compared with T65, the proteins whose content decreased in Fn189 including b5-like Heme/Steroid binding domain containing protein, putative retrotransposon protein, putative glutaminyl-tRNA synthetase, and higher content proteins such as mTERF, putative Oligopeptidase homologue, zinc knuckle protein, and so on. A former study founded that the transcription level of a mTERF was up-regulated in the leaves of maize seedling after EBR treatment. In our experiments, it was interesting that one mTERF protein increased, but another mTERF decreased in leaves of Fn189 at jointing-booting stage, which suggested that BRs may have differential regulation mechanisms on the expression of various mTERF proteins. The relationship between other differential proteins with BRs is still unclear, and the effects of BRs on rice protein contents and its regulation mechanisms still need further research.

Keywords: bri1 mutant, jointing-booting stage, proteomic analysis, rice

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Authors: Yin Zhang, Kai Qiao, Xiyang Zhi, Jinnan Gong, Jianming Hu

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In order to effectively detect aerial targets over long distances, an optimal matching design method of space-based optical payload is proposed. Firstly, main factors affecting optical detectability of small targets under complex environment are analyzed based on the full link of a detection system, including band center, band width and spatial resolution. Then a performance characterization model representing the relationship between image signal-to-noise ratio (SCR) and the above influencing factors is established to describe a detection system. Finally, an optimal matching design example is demonstrated for a typical aerial target by simulating and analyzing its SCR under different scene clutter coupling with multi-scale characteristics, and the optimized detection band and spatial resolution are presented. The method can provide theoretical basis and scientific guidance for space-based detection system design, payload specification demonstration and information processing algorithm optimization.

Keywords: space-based detection, aerial targets, optical system design, detectability characterization

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Authors: Sarah Almuhayya, Andrew Mcbain, Gavin Humphreys

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Background. The microbiome of the upper respiratory tract (URT) has received less research attention than other body sites. This study aims to investigate the microbial ecology of the human URT with a focus on the antagonism between the corynebacteria and staphylococci. Methods. Mucosal swabs were collected from the anterior nares and nasal turbinates of 20 healthy adult subjects. Genomic DNA amplification targeting the (V4) of the 16Sr RNA gene was conducted and analyzed using QIIME. Nasal swab isolates were cultured and identified using near full-length sequencing of the 16S rRNA gene. Isolates identified as corynebacteria or staphylococci were typed using (rep-PCR). Antagonism was determined using an agar-based inhibition assay. Results. Four major bacterial phyla (Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria) were identified from all volunteers. The typing of cultured staphylococci and corynebacteria suggested that intra-individual strain diversity was limited. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between staphylococci and corynebacteria. Despite the apparent antagonism between these genera, it was limited when investigated on agar. Of 1000 pairwise interactions, observable zones of inhibition were only reported between a single strain of C.pseudodiphtheriticum and S.aureus. Imaging under EM revealed this effect to be bactericidal with clear lytic effects on staphylococcal cell morphology. Conclusion. Nasal microbiota is complex, but culturable staphylococci and corynebacteria were limited in terms of clone type. Analysis of generated nasal microbiota profiles suggested an inverse correlation in terms of relative abundance between these genera suggesting an antagonism or competition between these taxonomic groups.

Keywords: nasal, microbiota, S.aureus, microbioal interaction

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Authors: V. S. S. Kumar, V. Ramya

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In the modern electronic warfare, the signal scenario is changing at a rapid pace with the introduction of Low Probability of Intercept (LPI) radars. In the modern battlefield, radar system faces serious threats from passive intercept receivers such as Electronic Attack (EA) and Anti-Radiation Missiles (ARMs). To perform necessary target detection and tracking and simultaneously hide themselves from enemy attack, radar systems should be LPI. These LPI radars use a variety of complex signal modulation schemes together with pulse compression with the aid of advancement in signal processing capabilities of the radar such that the radar performs target detection and tracking while simultaneously hiding enemy from attack such as EA etc., thus posing a major challenge to the ES/ELINT receivers. Today an increasing number of LPI radars are being introduced into the modern platforms and weapon systems so these LPI radars created a requirement for the armed forces to develop new techniques, strategies and equipment to counter them. This paper presents various modulation techniques used in generation of LPI signals and development of Time Frequency Algorithms to analyse those signals.

Keywords: anti-radiation missiles, cross terms, electronic attack, electronic intelligence, electronic warfare, intercept receiver, low probability of intercept

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Authors: Tripatjot S. Panag, J. S. Dhillon

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The lifetime of a wireless sensor network can be effectively increased by using scheduling operations. Once the sensors are randomly deployed, the task at hand is to find the largest number of disjoint sets of sensors such that every sensor set provides complete coverage of the target area. At any instant, only one of these disjoint sets is switched on, while all other are switched off. This paper proposes a heuristic search method to find the maximum number of disjoint sets that completely cover the region. A population of randomly initialized members is made to explore the solution space. A set of heuristics has been applied to guide the members to a possible solution in their neighborhood. The heuristics escalate the convergence of the algorithm. The best solution explored by the population is recorded and is continuously updated. The proposed algorithm has been tested for applications which require sensing of multiple target points, referred to as point coverage applications. Results show that the proposed algorithm outclasses the existing algorithms. It always finds the optimum solution, and that too by making fewer number of fitness function evaluations than the existing approaches.

Keywords: coverage, disjoint sets, heuristic, lifetime, scheduling, Wireless sensor networks, WSN

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Authors: Wenjiang Deng, Tian Mou, Yudi Pawitan, Trung Nghia Vu

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Estimation of isoform-level gene expression from RNA-seq data depends on simplifying assumptions, such as uniform reads distribution, that are easily violated in real data. Such violations typically lead to biased estimates. Most existing methods provide a bias correction step(s), which is based on biological considerations, such as GC content–and applied in single samples separately. The main problem is that not all biases are known. For example, new technologies such as single-cell RNA-seq (scRNA-seq) may introduce new sources of bias not seen in bulk-cell data. This study introduces a method called XAEM based on a more flexible and robust statistical model. Existing methods are essentially based on a linear model Xβ, where the design matrix X is known and derived based on the simplifying assumptions. In contrast, XAEM considers Xβ as a bilinear model with both X and β unknown. Joint estimation of X and β is made possible by simultaneous analysis of multi-sample RNA-seq data. Compared to existing methods, XAEM automatically performs empirical correction of potentially unknown biases. XAEM implements an alternating expectation-maximization (AEM) algorithm, alternating between estimation of X and β. For speed XAEM utilizes quasi-mapping for read alignment, thus leading to a fast algorithm. Overall XAEM performs favorably compared to other recent advanced methods. For simulated datasets, XAEM obtains higher accuracy for multiple-isoform genes, particularly for paralogs. In a differential-expression analysis of a real scRNA-seq dataset, XAEM achieves substantially greater rediscovery rates in an independent validation set.

Keywords: alternating EM algorithm, bias correction, bilinear model, gene expression, RNA-seq

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Authors: Feng Zhang, Li Chen, Desong Kong, Xiaoping Zhang, Xiaojing Zhu, Yin Lu, Shizhong Zheng

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Sinusoidal pathological angiogenesis is a novel therapeutic target for liver fibrosis. We demonstrated that curcumin ameliorated fibrotic injury and sinusoidal angiogenesis in rat liver with fibrosis caused by carbon tetrachloride. Curcumin reduced the expression of angiogenic markers in fibrotic liver. Experiments in vitro showed that the viability and vascularization of rat liver sinusoidal endothelial cells (LSECs) were not impaired by curcumin. Further investigations showed that curcumin inhibited VEGF expression in hepatic stellate cells (HSCs) by disrupting PDGF-βR/ERK and mTOR pathways. HSC motility and vascularization were also suppressed by curcumin via blocking PDGF-βR/FAK/RhoA cascade. Gain- or loss-of-function analyses revealed that activation of PPARγ was required for curcumin to inhibit angiogenic properties of HSCs. We concluded that curcumin attenuated sinusoidal angiogenesis in liver fibrosis possibly by targeting HSCs via a PPARγ activation-dependent mechanism. PPARγ could be a target molecule for reducing pathological angiogenesis during liver fibrosis.

Keywords: angiogenesis, hepatic stellate cell, curcumin, peroxisome proliferator-activated receptor-γ

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Authors: Batool Ismaeel, Umair Farooq, Saad Mushtaq

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Construction projects in the oil industry can be very complex, having unknown outcomes and uncertainties that cannot be easily predicted. Each project has its unique risks generated by a number of factors which, if not controlled, will impact the successful completion of the project mainly in terms of schedule, cost, quality, and safety. This paper highlights the historic risks associated with projects in the south and east region of Kuwait Oil Company (KOC) collated from the company’s lessons learned database. Starting from Contract Award through to handover of the project to the Asset owner, the gaps in project execution in terms of managing risk will be brought to discussion and where a well-defined systematic approach in project risk management reflecting many claims, change of scope, exceeding budget, delays in engineering phase as well as in the procurement and fabrication of long lead items should be adopted. This study focuses on a proposed feasible approach in risk management for engineering, procurement and construction (EPC) level projects including the various stakeholders involved in executing the works from International to local contractors and vendors in KOC. The proposed approach covers the areas categorized into organizational, design, procurement, construction, pre-commissioning, commissioning and project management in which the risks are identified and require management and mitigation. With the effective deployment and implementation of the proposed risk management system and the consideration of it as a vital key in achieving the project’s target, the outcomes will be more predictable in the future, and the risk triggers will be managed and controlled. The correct resources can be allocated on a timely basis for the company for avoiding any unpredictable outcomes during the execution of the project. It is recommended in this paper to apply this risk management approach as an integral part of project management and investigate further in the future, the effectiveness of this proposed system for newly awarded projects and compare the same with those projects of similar budget/complexity that have not applied this approach to risk management.

Keywords: construction, project completion, risk management, uncertainties

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Authors: Josef Novák, Alena Kohoutková

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The performance of concrete structures in fire depends on several factors which include, among others, the change in material properties due to the fire. Today, fiber reinforced concrete (FRC) belongs to materials which have been widely used for various structures and elements. While the knowledge and experience with FRC behavior under ambient temperature is well-known, the effect of elevated temperature on its behavior has to be deeply investigated. This paper deals with an experimental investigation and stress‑strain relations for hybrid fiber reinforced concrete (HFRC) which contains siliceous aggregates, polypropylene and steel fibers. The main objective of the experimental investigation is to enhance a database of mechanical properties of concrete composites with addition of fibers subject to elevated temperature as well as to validate existing stress-strain relations for HFRC. Within the investigation, a unique heat transport test, compressive test and splitting tensile test were performed on 150 mm cubes heated up to 200, 400, and 600 °C with the aim to determine a time period for uniform heat distribution in test specimens and the mechanical properties of the investigated concrete composite, respectively. Both findings obtained from the presented experimental test as well as experimental data collected from scientific papers so far served for validating the computational accuracy of investigated stress-strain relations for HFRC which have been developed during last few years. Owing to the presence of steel and polypropylene fibers, HFRC becomes a unique material whose structural performance differs from conventional plain concrete when exposed to elevated temperature. Polypropylene fibers in HFRC lower the risk of concrete spalling as the fibers burn out shortly with increasing temperature due to low ignition point and as a consequence pore pressure decreases. On the contrary, the increase in the concrete porosity might affect the mechanical properties of the material. To validate this thought requires enhancing the existing result database which is very limited and does not contain enough data. As a result of the poor database, only few stress-strain relations have been developed so far to describe the structural performance of HFRC at elevated temperature. Moreover, many of them are inconsistent and need to be refined. Most of them also do not take into account the effect of both a fiber type and fiber content. Such approach might be vague especially when high amount of polypropylene fibers are used. Therefore, the existing relations should be validated in detail based on other experimental results.

Keywords: elevated temperature, fiber reinforced concrete, mechanical properties, stress strain relation

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Authors: Axel Mancebo, Ana M. Bada, Angel Casacó, Bárbara González, Avelina León, María E. Arteaga, Consuelo González, Belinda Sánchez, Adriana Carr, Nuris Ledón, Arianna Iglesias

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Despite the many preventive and therapeutic modalities aimed at curing cancer, it remains as a serious world health problem. Promising recent developments suggest that cancer immunotherapy may be the next great hope for cancer treatment. EGFRs are receptor tyrosine kinases and it is considered an important therapeutic target related with tumor progression, and several types of molecular therapies, including monoclonal antibodies, small molecules, and vaccines, have been developed to target the HER family of receptors. On the other hand, gangliosides are membrane glycosphingolipids that contain two variants of sialic acid, the N-acetylated (NeuAc) and the N-glycolylated (NeuGc) variant. The high expression of this antigen-specific molecule has been associated with malignant tumor progression and immunosuppressive mechanisms, so ganglioside could be considered as the target for cancer immunotherapy. We have been working for several years in the safety evaluation of cancer vaccines targeting these two systems, the EGF receptor and ganglioside. We presented in this work results of repeated dose toxicity studies performed in Sprague Dawley rats and Cynomolgus monkeys, including clinical observations, body weight and rectal temperature measuring, clinical pathology analysis, gross necropsy and histological examination in rodent studies, and immunological evaluation. Immunizations were capable of inducing mainly inflammatory effects at the injection site, with findings largely attributable to the adjuvants used and probably enhanced by the immunological properties of the antigens. In general, these vaccines were shown to be well tolerated, and these studies in relevant species allow treating cancer patients with tumors during long periods with relative weight safety margin.

Keywords: cancer vaccines, safety, toxicology, rats, non human primates

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Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Samy S. Eleawa, Mahmoud A. Alkhateeb, Fahaid H. Alhashem, Ismaeel bin-Jaliah, Hussein F. Sakr, Hesham M. Elrefaey, Abbas O. Elkarib, Mohammad A. Haidara, Abdullah S. Shatoor, Mohammad A. Khalil

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This effect of Resveratrol (RES) against CdCl2- induced toxicity in the rat testes was investigated. Seven experimental groups of adult male rats were formulated as follows: A) Controls + NS, B) Control+ vehicle (saline solution of hydroxypropyl cyclodextrin), C) RES treated, D) CdCl2 +NS, E) CdCl2+ vehicle, F) RES followed by CdCl2 and M) CdCl2 followed by RES. At the end of the protocol, serum levels of FSH, LH, and testosterone were measured in all groups. Testicular levels of TBARS and Super Oxide Dismutase (SOD) activity were also measured. Epidydidimal semen analysis was performed and testicular expression of Bcl-2, p53 and Bax were assessed by RT-PCR. Also, histopathological changes of testes were examined microscopically and described. Pre and Post administration of RES in cadmium chloride-intoxicated rats improved semen parameters including count, motility, daily sperm production and morphology, increased serum concentrations of gonadotropins and testosterone, decreased testicular lipid peroxidation and increased SOD activity. Not only RES attenuated cadmium chloride induced testicular histopathology but was also able to protect against the onset of cadmium chloride testicular toxicity. Cadmium chloride downregulated the anti-apoptotic gene Bcl2 and upregulated the expression of both pro-apoptotic genes p53 and Bax. Resveratrol protected from and partially reversed cadmium chloride testicular via upregulation of Bcl2 and down regulation of p53 and Bax gene expression. Antioxidant activity of RES protects against cadmium chloride testicular toxicity and partially reverses its effect via upregulation of BCl2 and downregulation of p53 and Bax expression. These findings have far reaching implications on subfertility and impotency frequently seen in hypertensive as well as metabolic syndrome patients.

Keywords: resveratrol, cadmium, infertility, sperm, testis, metabolic syndrome

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Authors: Mohammad Aladwan, Adelia Skripova

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Bioremediation aspects of crude oil-polluted fields can be achieved by isolation and identification of bacterial species from oil-contaminated soil in order to choose the most active isolates and increase the strength of others. In this study, oil-degrading bacteria were isolated and identified from oil-contaminated soil samples in northeastern Jordan. The bacterial growth count (CFU/g) was between 1.06×10⁵ and 0.75×10⁹. Eighty-two bacterial isolates were characterized by their morphology and biochemical tests. The identified bacterial genera included: Klebsiella, Staphylococcus, Citrobacter, Lactobacillus, Alcaligenes, Pseudomonas, Hafnia, Micrococcus, Rhodococcus, Serratia, Enterobacter, Bacillus, Salmonella, Mycobacterium, Corynebacterium, and Acetobacter. Molecular identification of a universal primer 16S rDNA gene was used to identify four bacterial isolates: Microbacterium esteraromaticum strain L20, Pseudomonas stutzeri strain 13636M, Klebsilla pneumoniae, and uncultured Klebsilla sp., known as new strains. Our results indicate that their specific oil-degrading bacteria isolates might have a high strength of oil degradation from oil-contaminated sites. Staphylococcus intermedius (75%), Corynebacterium xerosis (75%), and Pseudomonas fluorescens (50%) showed a high growth rate on different types of hydrocarbons, such as crude oil, toluene, naphthalene, and hexane. In addition, monooxygenase and catechol 2,3-dioxygenase were detected in 17 bacterial isolates, indicating their superior hydrocarbon degradation potential. Total petroleum hydrocarbons were analyzed using gas chromatography for soil samples. Soil samples M5, M7, and M8 showed the highest levels (43,645, 47,805, and 45,991 ppm, respectively), and M4 had the lowest level (7,514 ppm). All soil samples were analyzed for heavy metal contamination (Cu, Cd, Mn, Zn, and Pb). Site M7 contains the highest levels of Cu, Mn, and Pb, while Site M8 contains the highest levels of Mn and Zn. In the future, these isolates of bacteria can be used for the cleanup of oil-contaminated soil.

Keywords: bioremediation, 16S rDNA gene, oil-degrading bacteria, hydrocarbons

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Authors: Javed Mohammed

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Right now, bio-medical infrastructure lags well behind the curve. Our healthcare system is dispersed and disjointed; medical records are a bit of a mess; and we do not yet have the capacity to store and process the crazy amounts of data coming our way from widespread whole-genome sequencing. And then there are privacy issues. Despite these infrastructure challenges, some researchers are plunging into bio medical Big Data now, in hopes of extracting new and actionable knowledge. They are doing delving into molecular-level data to discover bio markers that help classify patients based on their response to existing treatments; and pushing their results out to physicians in novel and creative ways. Computer scientists and bio medical researchers are able to transform data into models and simulations that will enable scientists for the first time to gain a profound under-standing of the deepest biological functions. Solving biological problems may require High-Performance Computing HPC due either to the massive parallel computation required to solve a particular problem or to algorithmic complexity that may range from difficult to intractable. Many problems involve seemingly well-behaved polynomial time algorithms (such as all-to-all comparisons) but have massive computational requirements due to the large data sets that must be analyzed. High-throughput techniques for DNA sequencing and analysis of gene expression have led to exponential growth in the amount of publicly available genomic data. With the increased availability of genomic data traditional database approaches are no longer sufficient for rapidly performing life science queries involving the fusion of data types. Computing systems are now so powerful it is possible for researchers to consider modeling the folding of a protein or even the simulation of an entire human body. This research paper emphasizes the computational biology's growing need for high-performance computing and Big Data. It illustrates this article’s indispensability in meeting the scientific and engineering challenges of the twenty-first century, and how Protein Folding (the structure and function of proteins) and Phylogeny Reconstruction (evolutionary history of a group of genes) can use HPC that provides sufficient capability for evaluating or solving more limited but meaningful instances. This article also indicates solutions to optimization problems, and benefits Big Data and Computational Biology. The article illustrates the Current State-of-the-Art and Future-Generation Biology of HPC Computing with Big Data.

Keywords: high performance, big data, parallel computation, molecular data, computational biology

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Authors: A. Kourou, M. Panoutsopoulou

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Nowadays, disaster risk reduction requires innovative ways of working collaboratively, monitoring tools, management methods, risk communication, and knowledge, as key factors for decision-making actors. Experience has shown that the assessment of seismic risk and its effective management is still an important challenge. In Greece, Ionian Islands region is characterized as the most seismic area of the country and one of the most active worldwide. It is well known that in case of a disastrous earthquake the local authorities need to assess the situation in the affected area and coordinate the disaster response. In particular, the main outcomes of 'Telemachus' project are the development of an innovative operational system that hosts the needed data of seismic risk management in the Ionian Islands and the implementation of educational actions for the involved target groups. This project is funded in the Priority Axis 'Environmental Protection and Sustainable Development' of Operational Plan 'Ionian Islands 2014-2020'. EPPO is one of the partners of the project and it is responsible, among others, for the development of proper training material. This paper presents the training material of 'Telemachus' and its usage as a helpful, managerial tool in case of earthquake emergency. This material is addressed to different target groups, such as civil protection staff, people that involved with the tourism industry, educators of disabled people, etc. Very positive aspect of the project is the involvement of end-users that should evaluate the training products; test standards; clarify the personnel’s roles and responsibilities; improve interagency coordination; identify gaps in resources; improve individual performance; and identify opportunities for improvement. It is worth mentioning that even though the abovementioned material developed is useful for the training of specific target groups on emergency management issues within Ionian Islands Region, it could be used throughout Greece and other countries too.

Keywords: education of civil protection staff, Ionian Islands Region of Greece, seismic risk, training material

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Authors: Elahe Kamari

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Research on translation process has been conducted for more than 20 years, investigating various issues and using different research methodologies. Most recently, researchers have started to use eye tracking to study translation processes. They believed that the observable, measurable data that can be gained from eye tracking are indicators of unobservable cognitive processes happening in the translators’ mind during translation tasks. The aim of this study was to investigate directionality in translation processes through using eye tracking. The following hypotheses were tested: 1) processing the target text requires more cognitive effort than processing the source text, in both directions of translation; 2) L2 translation tasks on the whole require more cognitive effort than L1 tasks; 3) cognitive resources allocated to the processing of the source text is higher in L1 translation than in L2 translation; 4) cognitive resources allocated to the processing of the target text is higher in L2 translation than in L1 translation; and 5) in both directions non-professional translators invest more cognitive effort in translation tasks than do professional translators. The performance of a group of 30 male professional translators was compared with that of a group of 30 male non-professional translators. All the participants translated two comparable texts one into their L1 (Persian) and the other into their L2 (English). The eye tracker measured gaze time, average fixation duration, total task length and pupil dilation. These variables are assumed to measure the cognitive effort allocated to the translation task. The data derived from eye tracking only confirmed the first hypothesis. This hypothesis was confirmed by all the relevant indicators: gaze time, average fixation duration and pupil dilation. The second hypothesis that L2 translation tasks requires allocation of more cognitive resources than L1 translation tasks has not been confirmed by all four indicators. The third hypothesis that source text processing requires more cognitive resources in L1 translation than in L2 translation and the fourth hypothesis that target text processing requires more cognitive effort in L2 translation than L1 translation were not confirmed. It seems that source text processing in L2 translation can be just as demanding as in L1 translation. The final hypothesis that non-professional translators allocate more cognitive resources for the same translation tasks than do the professionals was partially confirmed. One of the indicators, average fixation duration, indicated higher cognitive effort-related values for professionals.

Keywords: translation processes, eye tracking, cognitive resources, directionality

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Authors: Julio C. Ferreira, Maria T. A. Steiner

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The aim of this work is to present a solution procedure referred to here as the Multi-objective Optimization for Green Vehicle Routing Problem (MOOGVRP) to provide solutions for a case study. The proposed methodology consists of three stages to resolve Scenario A. Stage 1 consists of the “treatment” of data; Stage 2 consists of applying mathematical models of the p-Median Capacitated Problem (with the objectives of minimization of distances and homogenization of demands between groups) and the Asymmetric Traveling Salesman Problem (with the objectives of minimizing distances and minimizing time). The weighted method was used as the multi-objective procedure. In Stage 3, an analysis of the results is conducted, taking into consideration the environmental aspects related to the case study, more specifically with regard to fuel consumption and air pollutant emission. This methodology was applied to a (partial) database that addresses newspaper distribution in the municipality of Curitiba, Paraná State, Brazil. The preliminary findings for Scenario A showed that it was possible to improve the distribution of the load, reduce the mileage and the greenhouse gas by 17.32% and the journey time by 22.58% in comparison with the current scenario. The intention for future works is to use other multi-objective techniques and an expanded version of the database and explore the triple bottom line of sustainability.

Keywords: Asymmetric Traveling Salesman Problem, Green Vehicle Routing Problem, Multi-objective Optimization, p-Median Capacitated Problem

Procedia PDF Downloads 111