Search results for: genomic analyses

Authors: Mojtaba Heydarizad

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Andarokh basin is one of the main karstic regions in Khorasan Razavi province NE Iran. This basin is part of Kopeh-Dagh mega zone extending from Caspian Sea in the east to northern Afghanistan in the west. This basin is covered by Mozdooran Formation, Ngr evaporative formation and quaternary alluvium deposits in descending order of age. Mozdooran carbonate formation is notably karstified. The main surface karstic features in Mozdooran formation are Groove karren, Cleft karren, Rain pit, Rill karren, Tritt karren, Kamintza, Domes, and Table karren. In addition to surface features, deep karstic feature Andarokh Cave also exists in the region. Studying Ca, Mg, Mn, Sr, Fe concentration and Sr/Mn ratio in Mozdooran formation samples with distance to main faults and joints system using PCA analyses demonstrates intense meteoric digenesis role in controlling carbonate rock geochemistry. The karst evaluation in Andarokh basin varies from early stages 'deep seated karst' in Mesozoic to mature karstic system 'Exhumed karst' in quaternary period. Andarokh cave (the main cave in Andarokh basin) is rudimentary branch work consists of three passages of A, B and C and two entrances Andarokh and Sky.

Keywords: Andarokh basin, Andarokh cave, geochemical analyses, karst evaluation

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Authors: Afsheen Masood, Sumaira Rashid, Nadia Ijaz, Shama Mazahir

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The current study examined the relationship between moral disengagement, psychological contract, organizational citizenship behavior and counterproductive work behavior. It is hypothesized that there is likely to be a significant relationship between moral disengagement, psychological contract, organizational citizenship behavior and counterproductive work behavior. It is hypothesized that moral disengagement is likely to significantly predict counterproductive work behavior. It is hypothesized that psychological contract is likely to moderate the relationship between moral disengagement, and counterproductive work behavior. Cross-sectional survey research design was used for the study. The sample consisted of 500 middle managers, age ranging between 30-45 years working in private and public sector. The measures used were Moral Disengagement Scale, Psychological Contract Scale, and Counterproductive Work Behavior. Series of Correlation analyses, Regression analysis, moderation analysis and t-test was run in order to execute descriptive and inferential analyses. The findings revealed that there was a significant positive relationship between moral disengagement and counterproductive work behaviors. Psychological contract significantly mediated the relationship between moral disengagement and counterproductive work behaviors. There were significant gender differences reported in psychological contract and counterproductive work behaviors. The insightful findings carry significant implication for organizational psychologists and organizational stakeholders.

Keywords: psychological contract, moral disengagement, counterproductive work behaviors, mediation analysis

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Authors: Helen J. Spray, Karina J. Linnell

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Local-global bias in adulthood is strongly dependent on environmental factors and a global bias is not the universal characteristic of adult perception it was once thought to be: whilst Western adults typically demonstrate a global bias, Namibian adults living in traditional villages possess a strong local bias. Furthermore, environmental effects on local-global bias have been shown to be highly gender-specific; whereas urbanisation promoted a global bias in urbanised Namibian women but not men, education promoted a global bias in urbanised Namibian men but not women. Adult populations, however, provide only a snapshot of the gene-environment interactions which shape perceptual bias. Yet, to date, there has been little work on the development of local-global bias across environmental settings. In the current study, local-global bias was assessed using a similarity-matching task with Navon figures in children aged between 4 and 15 years from across three populations: traditional Namibians, urban Namibians, and urban British. For the two Namibian groups, measures of urbanisation and education were obtained. Data were subjected to both between-group and within-group analyses. Between-group analyses compared developmental trajectories across population and gender. These analyses revealed a global bias from even as early as 4 in the British sample, and showed that the developmental onset of a global bias is not fixed. Urbanised Namibian children ultimately developed a global bias that was indistinguishable from British children; however, a global bias did not emerge until much later in development. For all populations, the greatest developmental effects were observed directly following the onset of formal education. No overall gender effects were observed; however, there was a significant gender by age interaction which was difficult to reconcile with existing biological-level accounts of gender differences in the development of local-global bias. Within-group analyses compared the effects of urbanisation and education on local-global bias for traditional and urban Namibian boys and girls separately. For both traditional and urban boys, education mediated all effects of age and urbanisation; however, this was not the case for girls. Traditional Namibian girls retained a local bias regardless of age, education, or urbanisation, and in urbanised girls, the development of a global bias was not attributable to any one factor specifically. These results are broadly consistent with aforementioned findings that education promoted a global bias in urbanised Namibian men but not women. The development of local-global bias does not follow a fixed trajectory but is subject to environmental control. Understanding how variability in the development of local-global bias might arise, particularly in the context of gender, may have far-reaching implications. For example, a number of educationally important cognitive functions (e.g., spatial ability) are known to show consistent gender differences in childhood and local-global bias may mediate some of these effects. With education becoming an increasingly prevalent force across much of the developing world it will be important to understand the processes that underpin its effects and their implications.

Keywords: cross-cultural, development, education, gender, local-global bias, perception, urbanisation, urbanization

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: S. A. Agbalajobi, W. A. Bello

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The study carried out analysis on slope stability in an excavated gneiss rock using geological strength index (GSI) in Ilorin, Kwara State, Nigeria. A kinematic analysis of planar discontinuity sets in a gneiss deposit was carried out to ascertain the degree of slope stability. Discontinuity orientations in the rock mass were mapped using compass clinometers. The average result of physical and mechanical properties such as specific gravity, unit weight, uniaxial compressive strength, point load index, and Schmidt rebound value are 2.64 g/m3, 25.95 kN/m3, 156 MPa, 6.5 MPa, and 53.12 respectively. Also, a statistical model equation relating the rock strength was developed. The analyses states that the rock face is susceptible to wedge failures having all the geometrical conditions associated with the occurrence of such failures were noticeable. It can be concluded that analyses of discontinuity orientation in relation to cut face direction in rock excavation is essential for mine planning to forestall mine accidents. Assessment of excavated slope methods was evident that one excavation method (blasting and/or use of hydraulic hammer) is applicable for the given rock strength, the ease of excavation decreases as the rock mass quality increases, thus blasting most suitable for such operation.

Keywords: slope stability, wedge failure, geological strength index (GSI), discontinuities and excavated slope

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Authors: Hamed Homaei, Seyed Reza Hejazi, Iraj Mahdavi

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Return policy (RP) is a strategy for supply chain coordination, whereby the retailer returns the unsold products to the manufacturer or the manufacturer offers a credit on unsold products to the retailer at the end of selling season. Early order commitment (EOC) is another efficient mechanism for channel coordination wherein the retailer commits to purchasing from the manufacturer a fixed order quantity a few periods in advance of the regular delivery lead time. This paper studies the coordination issue of a two-level supply chain with one retailer and one manufacturer through combining two mentioned contracts. The main purpose of this paper is to present an analytical model to show that how the contract which is created by combining RP and EOC can improve supply chain performance. Numerical analyses show that the supply chain coordination through mentioned contract in compare with EOC mechanism, can improve supply chain performance under certain ranges of model parameters. Furthermore, some numerical analyses are done to determine the best buyback price in order to achieve maximum cost saving in the supply chain. Finally, a revenue sharing scheme is presented in order to achieve a win-win condition in the supply chain.

Keywords: supply chain coordination, early order commitment, return policy, revenue sharing

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Authors: R. Khrifou, M. Galai, R. Touir, M. Ebn Touhami, Y. Ramli

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A 2-(5-methyl-2-Nitro-1H-imidazol-1-yl)ethyl benzoate (IMDZ-B) was synthesized and characterized using elemental analyses, NMR, and Fourier transform infrared (FTIR) techniques. Its effect on brass corrosion in 1.0 M H₃PO₄ solution was investigated by using electrochemical measurements coupled with X-ray diffraction analysis (XRD), Scanning electron microscopy (SEM) and Energy-dispersive X-ray spectroscopy (EDX). The polarization measurements showed that the IMDZ-B acts as a mixed-type inhibitor. Indeed, it is found that the IMDZ-B compound is a very good inhibitor, and its inhibition efficiency increases with concentration to reach a maximum of 99.5 % at 10-³ M. In addition, the obtained electrochemical parameters from impedance indicated that the IMDZ-B molecules act by adsorption on metallic surfaces. This adsorption was found to obey Langmuir’s adsorption isotherm. However, the temperature effect on the performance of IMDZ-B was also studied. It is found that the IMDZ-B takes its performance at high temperatures. In addition, the obtained kinetic and thermodynamic parameters showed that the IMDZ-B molecules act via two adsorption modes, physisorption and chemisorptions, and its process is endothermic and spontaneous. Finally, the XRD and SEM/EDX analyses confirmed the electrochemical obtained results.

Keywords: low concentration, anti-corrosion brass, IMDZ-B product, phosphoric acid solution, electrochemical, SEM\EDAX analysis

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Authors: Saloni Diwakar, Hansika Kapoor

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The study undertook comparative analyses between 130 male and female managers in a power/electric company, relating to prevalent perceptions about gendered leadership, leadership efficacy, perceived organizational support, and diversity and inclusiveness. Results showed no significant difference in POS, leadership aspirations, expression, and self- and other leadership efficacy between male and female managers. However, within-groups analyses revealed that female managers reported a disparity between self and other leadership efficacy (value), to a far greater extent than male managers (value). Additionally, females reported a dip in POS during middle management, as compared to junior management, whereas men reported a steady increase in POS from junior, middle on to senior management. Descriptively, both men and women reported preferring gender neutral leadership traits, as compared to male or female centered traits, and both genders least preferred male centered leadership traits. Compared to women, male managers were found to significantly undervalue diversity and inclusion initiatives. Subjective feedback was elicited to corroborate quantitative output. Also, female participants provided subjective feedback regarding efficacy of existing D&I practices in the organization. Findings and implications are discussed relevant to existing gender inclusion agendas.

Keywords: gendered leadership, diversity, inclusivity, perceived organizational support

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Authors: Keisuke Fujioka, Yuta Itoh, Masaru Minagawa, Shunji Kusayanagi

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In this study, building information models of the underground temporary structures and adjacent embedded pipes were constructed to show the importance of the information on underground pipes adjacent to the structures to enhance the productivity of execution of construction. Next, the bar chart used in actual construction process were employed to make the Gantt chart, and the critical pass analysis was carried out to show that accurate information on the arrangement of underground existing pipes can be used for the enhancement of the productivity of the construction of underground structures. In the analyzed project, significant construction delay was not caused by unforeseeable existence of underground pipes by the management ability of the construction manager. However, in many cases of construction executions in the developing countries, the existence of unforeseeable embedded pipes often causes substantial delay of construction. Design change based on uncertainty on the position information of embedded pipe can be also important risk for contractors in domestic construction. So CPM analyses were performed by a project-management-software to the situation that influence of the tasks causing construction delay was assumed more significant. Through the analyses, the efficiency of information management on underground pipes and BIM analysis in the design stage for workability improvement was indirectly confirmed.

Keywords: building-information modelling, construction information modelling, design improvement, infrastructure

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Oday Al-Mamoori, J. Enrique Martinez-Rueda

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'C' shape yielding devices (C-devices) are effective tools for introducing supplemental sources of energy dissipation by hysteresis. Studies have shown that C-devices made of mild steel can be successfully applied as integral parts of seismic retrofitting schemes. However, explicit modelling of these devices can become cumbersome, expensive and time consuming. The device under study in this article has been previously used in non-invasive dissipative bracing for seismic retrofitting. The device is cut from a mild steel plate and has an overall shape that resembles that of a rectangular portal frame with circular interior corner transitions to avoid stress concentration and to control the extension of the dissipative region of the device. A number of inelastic finite element (FE) analyses using either inelastic 2D plane stress elements or inelastic fibre frame elements are reported and used to calibrate a 1D equivalent inelastic spring model that effectively reproduces the cyclic response of the device. The more elaborate FE model accounts for the frictional forces developed between the steel plate and the bolts used to connect the C-device to structural members. FE results also allow the visualization of the inelastic regions of the device where energy dissipation is expected to occur. FE analysis results are in a good agreement with experimental observations.

Keywords: C-device, equivalent nonlinear spring, FE analyses, reversed cyclic tests

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Authors: Fahimeh Palizban, Farshad Noravesh, Amir Hossein Saeidian, Mahya Mehrmohamadi

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In the recent decade, the emergence of liquid biopsy has significantly improved cancer monitoring and detection. Dying cells, including those originating from tumors, shed their DNA into the blood and contribute to a pool of circulating fragments called cell-free DNA. Accordingly, identifying the tissue origin of these DNA fragments from the plasma can result in more accurate and fast disease diagnosis and precise treatment protocols. Open chromatin regions are important epigenetic features of DNA that reflect cell types of origin. Profiling these features by DNase-seq, ATAC-seq, and histone ChIP-seq provides insights into tissue-specific and disease-specific regulatory mechanisms. There have been several studies in the area of cancer liquid biopsy that integrate distinct genomic and epigenomic features for early cancer detection along with tissue of origin detection. However, multimodal analysis requires several types of experiments to cover the genomic and epigenomic aspects of a single sample, which will lead to a huge amount of cost and time. To overcome these limitations, the idea of predicting OCRs from WGS is of particular importance. In this regard, we proposed a computational approach to target the prediction of open chromatin regions as an important epigenetic feature from cell-free DNA whole genome sequence data. To fulfill this objective, local sequencing depth will be fed to our proposed algorithm and the prediction of the most probable open chromatin regions from whole genome sequencing data can be carried out. Our method integrates the signal processing method with sequencing depth data and includes count normalization, Discrete Fourie Transform conversion, graph construction, graph cut optimization by linear programming, and clustering. To validate the proposed method, we compared the output of the clustering (open chromatin region+, open chromatin region-) with previously validated open chromatin regions related to human blood samples of the ATAC-DB database. The percentage of overlap between predicted open chromatin regions and the experimentally validated regions obtained by ATAC-seq in ATAC-DB is greater than 67%, which indicates meaningful prediction. As it is evident, OCRs are mostly located in the transcription start sites (TSS) of the genes. In this regard, we compared the concordance between the predicted OCRs and the human genes TSS regions obtained from refTSS and it showed proper accordance around 52.04% and ~78% with all and the housekeeping genes, respectively. Accurately detecting open chromatin regions from plasma cell-free DNA-seq data is a very challenging computational problem due to the existence of several confounding factors, such as technical and biological variations. Although this approach is in its infancy, there has already been an attempt to apply it, which leads to a tool named OCRDetector with some restrictions like the need for highly depth cfDNA WGS data, prior information about OCRs distribution, and considering multiple features. However, we implemented a graph signal clustering based on a single depth feature in an unsupervised learning manner that resulted in faster performance and decent accuracy. Overall, we tried to investigate the epigenomic pattern of a cell-free DNA sample from a new computational perspective that can be used along with other tools to investigate genetic and epigenetic aspects of a single whole genome sequencing data for efficient liquid biopsy-related analysis.

Keywords: open chromatin regions, cancer, cell-free DNA, epigenomics, graph signal processing, correlation clustering

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Authors: Apolinar Picado, Steve Alfaro, Rafael Gamero

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Energy and exergy analyses of thin-layer drying of pineapple slices (Ananas comosus L.) were conducted in a laboratory tunnel dryer. Drying experiments were carried out at three temperatures (100, 115 and 130 °C) and an air velocity of 1.45 m/s. The effects of drying variables on energy utilisation, energy utilisation ratio, exergy loss and exergy efficiency were studied. The enthalpy difference of the gas increased as the inlet gas temperature increase. It is observed that at the 75 minutes of the drying process the outlet gas enthalpy achieves a maximum value that is very close to the inlet value and remains constant until the end of the drying process. This behaviour is due to the reduction of the total enthalpy within the system, or in other words, the reduction of the effective heat transfer from the hot gas flow to the vegetable being dried. Further, the outlet entropy exhibits a significant increase that is not only due to the temperature variation, but also to the increase of water vapour phase contained in the hot gas flow. The maximum value of the exergy efficiency curve corresponds to the maximum value observed within the drying rate curves. This maximum value represents the stage when the available energy is efficiently used in the removal of the moisture within the solid. As the drying rate decreases, the available energy is started to be less employed. The exergetic efficiency was directly dependent on the evaporation flux and since the convective drying is less efficient that other types of dryer, it is likely that the exergetic efficiency has relatively low values.

Keywords: efficiency, energy, exergy, thin-layer drying

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Authors: Mosses E. Lufuke, Lorna M. Kamau

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This paper attempted to assess whether the size of the regional economic bloc has an impact to the flow of trade to a particular country. Two different sized blocs (COMESA and EAC) and one country (Tanzania) have been used as the point of references. Using the results from of the analyses, the paper also was anticipated to establish whether it was rational for Tanzania to withdraw its membership from COMESA (the larger bloc) to join EAC (the small one). Gravity model has been used to estimate the relationship between the variables, from which the bilateral trade flows between Tanzania and the eighteen member countries of the two blocs (COMESA and EAC) was employed for the time between 2000 and 2013. In the model, the dummy variable for regional bloc (bloc) at which the Tanzania trade partner countries belong are also added to the model to understand which trade bloc exhibit higher trade flow with Tanzania. From the findings, it was noted that over the period of study (2000-2013) Tanzania acknowledged more than 257% of trade volume in EAC than in COMESA. Conclusive, it was noted that the flow of trade is explained by many other variables apart from the size of regional bloc; and that the size by itself offer insufficient evidence in causality relationship. The paper therefore remain neutral on such staggered switching decision since more analyses are required to establish the country’s trade flow, especially when if it had been in multiple membership of COMESA and EAC.

Keywords: economic bloc, flow of trade, size of bloc, switching

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Authors: Giang Tran Thi Huong, Hieu Dong Van, Tung Dao Duy, Saadanov Iskender, Isakeev Mairambek, Tsutomu Omatsu, Yukie Katayama, Tetsuya Mizutani, Yuki Ozeki, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Newcastle disease virus (NDV) is a contagious viral disease of the poultry industry and other birds throughout the world. At present, very little is known about molecular epidemiological data regarding the causes of ND outbreak in commercial poultry farms in Kyrgyzstan. In the current study, the NDV isolated from the one out of three samples from the unvaccinated flock was confirmed as NDV. Phylogenetic analysis indicated that this NDV strain is clustered in the Class II subgenotype VIId, and closely related to the Chinese NDV isolate. Phylogenetic analyses revealed that the isolated NDV strain has an origin different from the 4 NDV strains previously identified in Kyrgyzstan. According to the mean death time (MDT: 61.1 h) and a multibasic amino acid (aa) sequence at the F0 proteolytic cleavage site (¹¹²R-R-Q-K-R-F¹¹⁷), the NDV isolate was determined as mesogenic strain. Several mutations in the neutralizing epitopes (notably, ³⁴⁷E→K) and the global head were observed in the hemagglutinin-neuraminidase (HN) protein of the current isolate. The present study represents the molecular characterization of the coding gene region of NDV in Kyrgyzstan. Additionally, further study will be investigated on the antigenic characterization using monoclonal antibody.

Keywords: Kyrgyzstan, Newcastle disease, genotype, genome characterization

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Authors: Ayesha Hasan

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This study offers unique perspectives and analyses of peace and conflict journalism through interpretative repertoire, media frames, and critical discourse analyses. Two major English publications in Pakistan, representing both long and short-form journalism, are investigated to uncover how the Afghan refugee repatriation from Pakistan in 2016-17 has been framed in Pakistani English media. Peace journalism focuses on concepts such as peace initiatives and peace building, finding common ground, and preventing further conflict. This study applies Jake Lynch’s Coding Criteria to guide the critical discourse analysis and Lee and Maslog’s Peace Journalism Quotient to examine the extent of peace journalism in each text. This study finds that peace journalism is missing in Pakistani English press, but represented, to an extent, in long-form print and online coverage. Two new alternative frames are also proposed. This study gives an in-depth understanding of if and how journalists in Pakistan are covering conflicts and framing stories that can be identified as peace journalism. This study represents significant contributions to the remarkably limited scholarship on peace and conflict journalism in Pakistan and extends Shabbir Hussain’s work on critical pragmatic perspectives on peace journalism in Pakistan.

Keywords: Afghan refugee repatriation, Critical discourse analysis, Media framing , Peace and conflict journalism

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Authors: Merve Ermis, Murat Yılmaz, Nihal Eratlı, Mehmet H. Omurtag

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The static and dynamic analyses of hyperboloidal helix having the closed and the open square box sections are investigated via the mixed finite element formulation based on Timoshenko beam theory. Frenet triad is considered as local coordinate systems for helix geometry. Helix domain is discretized with a two-noded curved element and linear shape functions are used. Each node of the curved element has 12 degrees of freedom, namely, three translations, three rotations, two shear forces, one axial force, two bending moments and one torque. Finite element matrices are derived by using exact nodal values of curvatures and arc length and it is interpolated linearly throughout the element axial length. The torsional moments of inertia for close and open square box sections are obtained by finite element solution of St. Venant torsion formulation. With the proposed method, the torsional rigidity of simply and multiply connected cross-sections can be also calculated in same manner. The influence of the close and the open square box cross-sections on the static and dynamic analyses of hyperboloidal helix is investigated. The benchmark problems are represented for the literature.

Keywords: hyperboloidal helix, squared cross section, thin walled cross section, torsional rigidity

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Authors: Narin Salehiyan

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The later sequencing of the complete genomes of Mycoplasma genitalium and M. pneumoniae has pulled in significant consideration to the atomic science of mycoplasmas, the littlest self-replicating living beings. It shows up that we are presently much closer to the objective of defining, in atomic terms, the complete apparatus of a self-replicating cell. Comparative genomics based on comparison of the genomic cosmetics of mycoplasmal genomes with those of other microbes, has opened better approaches of looking at the developmental history of the mycoplasmas. There's presently strong hereditary bolster for the speculation that mycoplasmas have advanced as a department of gram-positive microbes by a handle of reductive advancement. Amid this prepare, the mycoplasmas misplaced significant parcels of their ancestors’ chromosomes but held the qualities basic for life. In this way, the mycoplasmal genomes carry a tall rate of preserved qualities, incredibly encouraging quality comment. The critical genome compaction that happened in mycoplasmas was made conceivable by receiving a parasitic mode of life. The supply of supplements from their has clearly empowered mycoplasmas to lose, amid advancement, the qualities for numerous assimilative forms. Amid their advancement and adjustment to a parasitic mode of life, the mycoplasmas have created different hereditary frameworks giving a profoundly plastic set of variable surface proteins to avoid the have safe framework.

Keywords: mycoplasma, plasma, pathogen, genome

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Authors: Chong Zhang, Mu-Xuan Tao

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In several earthquakes, numerous reinforced concrete (RC) frames subjected to seismic excitation demonstrated a collapse pattern characterized by column hinges, though designed according to the Strong-Column-Weak-Beam (S-C-W-B) criteria. The effect of biaxial seismic excitation on the disparity between design and actual performance is carefully investigated in this article. First, a modified load contour method is proposed to derive a closed-form equation of biaxial bending moment strength, which is verified by numerical and experimental tests. Afterwards, a group of time history analyses of a simple frame modeled by fiber beam-column elements subjected to biaxial seismic excitation are conducted to verify that the current S-C-W-B criteria are not adequate to prevent the occurrence of column hinges. A biaxial over-strength factor is developed based on the proposed equation, and the reinforcement of columns is appropriately amplified with this factor to prevent the occurrence of column hinges under biaxial excitation, which is proved to be effective by another group of time history analyses.

Keywords: biaxial bending moment capacity, biaxial seismic excitation, fiber beam model, load contour method, strong-column-weak-beam

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Authors: Mulata Haile Nega, Derebew Fikadu Berhe, Vera Ribeiro Marques

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There is no epidemiologic data on this gene polymorphism in several countries. Therefore, this study aimed to assess the genotype and allele frequencies of the gene variant in three countries. This study involved healthy individuals from Colombia, Mozambique, and Portugal. Genomic DNA was isolated from blood samples using the Qiamp DNA Extraction Kit (Qiagen). The isolated DNA was genotyped using Polymerase Chain Reaction (PCR) - Restriction Fragment Length Polymorphism. Microstat and GraphPad quick cal software were used for the Chi-square test and evaluation of Hardy-Weinberg equilibrium, respectively. A total of 181 individuals’ blood sample was analyzed. Overall, TT (74.0%) genotype was the highest, and CC (7.8%) was the lowest. Country wise genotypic frequencies were Colombia 47(70.2%) TT, 12(17.9%) TC and 8(11.9%) CC; Mozambique 47(88.7%) TT, 5(9.4%) TC, and 1(1.9%) CC; and Portugal 40(65.6%) TT, 16(26.2%) TC, and 5(8.2%) CC. The reference (T) allele was highest among Mozambicans (93.4%) compared to Colombians (79.1%) and Portuguese (78.7%). Mozambicans showed statistically significant genotypic and allelic frequency differences compared to Colombians (p<0.01) and Portuguese (p <0.01). Overall and country-wise, the CC genotype was less frequent and relatively high for Colombians and Portuguese populations. This finding may imply statins risk-benefit variability associated with CC genotype among these populations that needs further understanding.

Keywords: c.521T>C, polymorphism, SLCO1B1, SNP, statins

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Authors: M. A. Hernández-Ceballos, M. Marín-Ferrer, G. Cinelli, L. De Felice, T. Tollefsen, E. Nweke, P. V. Tognoli, S. Vanzo, M. De Cort

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This study analyses the latitudinal impact of the spatial and temporal distribution on the cosmogenic isotope 7Be in surface air along Europe. The long-term database of the 6 sampling sites (Ivalo, Helsinki, Berlin, Freiburg, Sevilla and La Laguna), that regularly provide data to the Radioactivity Environmental Monitoring (REM) network managed by the Joint Research Centre (JRC) in Ispra, were used. The selection of the stations was performed attending to different factors, such as 1) heterogeneity in terms of latitude and altitude, and 2) long database coverage. The combination of these two parameters ensures a high degree of representativeness of the results. In the later, the temporal coverage varies between stations, being used in the present study sampling stations with a database more or less continuously from 1984 to 2011. The mean values of 7Be activity concentration presented a spatial distribution value ranging from 2.0 ± 0.9 mBq/m3 (Ivalo, north) to 4.8 ± 1.5 mBq/m3 (La Laguna, south). An increasing gradient with latitude was observed from the north to the south, 0.06 mBq/m3. However, there was no correlation with altitude, since all stations are sited within the atmospheric boundary layer. The analyses of the data indicated a dynamic range of 7Be activity for solar cycle and phase (maximum or minimum), having been observed different impact on stations according to their location. The results indicated a significant seasonal behavior, with the maximum concentrations occurring in the summer and minimum in the winter, although with differences in the values reached and in the month registered. Due to the large heterogeneity in the temporal pattern with which the individual radionuclide analyses were performed in each station, the 7Be monthly index was calculated to normalize the measurements and perform the direct comparison of monthly evolution among stations. Different intensity and evolution of the mean monthly index were observed. The knowledge of the spatial and temporal distribution of this natural radionuclide in the atmosphere is a key parameter for modeling studies of atmospheric processes, which are important phenomena to be taken into account in the case of a nuclear accident.

Keywords: Berilium-7, latitudinal impact in Europe, seasonal and monthly variability, solar cycle

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Authors: Enoch F. Sam, Kris Brijs, Stijn Daniels, Tom Brijs, Geert Wets

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Notwithstanding the growing body of literature that recognises the importance of personal safety to public transport (PT) users, it remains unclear what PT users consider regarding their safety. In this study, we explore the criteria PT users in Ghana use to assess bus safety. This knowledge will afford a better understanding of PT users’ risk perceptions and assessments which may contribute to theoretical models of PT risk perceptions. We utilised phenomenological research methodology, with data drawn from 61 purposively sampled participants. Data collection (through focus group discussions and in-depth interviews) and analyses were done concurrently to the point of saturation. Our inductive data coding and analyses through the constant comparison and content analytic techniques resulted in 4 code categories (conceptual dimensions), 27 codes (safety items/criteria), and 100 quotations (data segments). Of the number of safety criteria participants use to assess bus safety, vehicle condition, driver’s marital status, and transport operator’s safety records were the most considered. With each criterion, participants rightly demonstrated its respective relevance to bus safety. These findings imply that investment in and maintenance of safer vehicles, and responsible and safety-conscious drivers, and prioritization of passengers’ safety are key-targets for public bus/minibus operators in Ghana.

Keywords: safety evaluations, public bus/minibus, passengers, phenomenology, Ghana

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Authors: Zuzana Fišerová, Marie Paseková

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Debt relief (also labelled personal bankruptcy) is a bankruptcy settlement method which was implemented into Czech legislation by the Insolvency Act (Act No. 182/2006 Coll. on Insolvency and its Resolution) on 1 January 2008. The need to implement the institute of personal bankruptcy arose from the excessive over-indebtedness of many inhabitants of the Czech Republic after the crisis that arose around 2008 and 2009. The contribution analyses the development in the manner in which households approach personal bankruptcy and assesses and surveys the differences between indebtedness among men and women. The first section analyses the development in numbers of filed personal bankruptcy petitions and the successfulness thereof; it likewise analyses the impact of other economic influences (regional differences, unemployment etc.). The differences between debtors in dependency to gender are also surveyed. A survey of insolvency proceedings for 664 persons whose insolvency proceedings were commenced in 2008 was conducted, whilst the data were acquired from the publicly accessible insolvency register. The hypothesis on the equality of the average debt level of men and women was tested when comparing indebtedness in dependency to debtor gender. At a significance level of 0.05, the test confirmed that the mean value of debt level for women is lower than the mean value of debt level for men. Through analysis of further results, it was found that the average level of debt among women was CZK 537 thousand, while the average level of creditor satisfaction reached 46.2%. Men in the monitored sample had an average level of reported receivables of CZK 652 thousand, satisfaction of their creditors reached 58.8%. The main changes in the institute of personal bankruptcy are then evaluated in the closing discussion, and the impacts of these changes for households are assessed. The development of legislation in the Czech Republic and practice are shifting towards broader usage of personal bankruptcy, especially insofar as it can now also be used by entrepreneurs. Furthermore, the amendment of the Insolvency Act has enabled married couples to apply for joint debt relief, which has improved the position of the marriage partner with lower income and who would not get permission for debt relief on his/her own (mostly women are at issue). In current practice, the condition of adequate income is also solved by the fact that another person (usually a family member) undertakes to donate a certain monthly sum throughout the duration of the debt relief. Personal bankruptcy can thus be completed also by individuals to whom it would previously have been denied by the court.

Keywords: debtor, households, insolvency act, over-indebtedness, personal bankruptcy

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Authors: Ryan A. Black, Stacey A. McCaffrey

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Over the past few decades, great strides have been made towards improving the science in the measurement of psychological constructs. Item Response Theory (IRT) has been the foundation upon which statistical models have been derived to increase both precision and accuracy in psychological measurement. These models are now being used widely to develop and refine tests intended to measure an individual's level of academic achievement, aptitude, and intelligence. Recently, the field of clinical psychology has adopted IRT models to measure psychopathological phenomena such as depression, anxiety, and addiction. Because advances in IRT measurement models are being made so rapidly across various fields, it has become quite challenging for psychologists and other behavioral scientists to keep abreast of the most recent developments, much less learn how to employ and decide which models are the most appropriate to use in their line of work. In the same vein, IRT measurement models vary greatly in complexity in several interrelated ways including but not limited to the number of item-specific parameters estimated in a given model, the function which links the expected response and the predictor, response option formats, as well as dimensionality. As a result, inferior methods (a.k.a. Classical Test Theory methods) continue to be employed in efforts to measure psychological constructs, despite evidence showing that IRT methods yield more precise and accurate measurement. To increase the use of IRT methods, this study endeavors to provide a comprehensive overview of binary IRT models; that is, measurement models employed on test data consisting of binary response options (e.g., correct/incorrect, true/false, agree/disagree). Specifically, this study will cover the most basic binary IRT model, known as the 1-parameter logistic (1-PL) model dating back to over 50 years ago, up until the most recent complex, 4-parameter logistic (4-PL) model. Binary IRT models will be defined mathematically and the interpretation of each parameter will be provided. Next, all four binary IRT models will be employed on two sets of data: 1. Simulated data of N=500,000 subjects who responded to four dichotomous items and 2. A pilot analysis of real-world data collected from a sample of approximately 770 subjects who responded to four self-report dichotomous items pertaining to emotional consequences to alcohol use. Real-world data were based on responses collected on items administered to subjects as part of a scale-development study (NIDA Grant No. R44 DA023322). IRT analyses conducted on both the simulated data and analyses of real-world pilot will provide a clear demonstration of how to construct, evaluate, and compare binary IRT measurement models. All analyses will be performed using the new IRT procedure in SAS 9.4. SAS code to generate simulated data and analyses will be available upon request to allow for replication of results.

Keywords: instrument development, item response theory, latent trait theory, psychometrics

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Authors: Yee Hui Lim, Elena Gusareva, Irvan Luhung, Yulia Frank, Stephan Christoph Schuster

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Environmental pollution from microplastics (MPs) is an emerging concern worldwide. While the presence of microplastics has been well established in the marine and terrestrial environments, the prevalence of microplastics in the atmosphere is still poorly understood. Wet depositions such as rain or snow scavenge impurities from the atmosphere as it falls to the ground. These wet depositions serve as a useful tool in the removal of airborne particles that are suspended in the air. Therefore, the aim of this study is to investigate the presence of atmospheric microplastics and fibres through the analysis of air, rainwater and snow samples. Air samples were collected with filter-based air samplers from outdoor locations in Singapore. The sampling campaigns were conducted during and after each rain event. Rainwater samples from Singapore and Siberia were collected as well. Snow samples were also collected from Siberia as part of the ongoing study. Genomic DNA was then extracted from the samples and sequenced with shotgun metagenomics approach. qPCR analysis was conducted to quantify the total bacteria and fungi in the air, rainwater and snow samples. The results compared the bioaerosol profiles of all the samples. To observe the presence of microplastics, scanning electron microscope (SEM) was used. From the preliminary results, microplastics were detected. It can be concluded that there is a significant amount of atmospheric microplastics present, and its occurrence should be investigated in greater detail.

Keywords: atmospheric microplastics, metagenomics, scanning electron microscope, wet deposition

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Marzieh Jafarzadeh, Fatemeh Rezaee

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Introduction: The effect of ionizing radiation on human health can be effective for genomic integrity and cell viability. It also increases the risk of cancer and malignancy. Therefore, X-ray behavior and absorption dose calculation are considered. One of the applicable tools for calculating and evaluating the absorption dose in human tissues is Monte Carlo simulation. Monte Carlo offers a straightforward way to simulate and integrate, and because it is simple and straightforward, Monte Carlo is easy to use. The Monte Carlo BEAMnrc code is one of the most common diagnostic X-ray simulation codes used in this study. Method: In one of the understudy hospitals, a certain number of CT scan images of patients who had previously been imaged were extracted from the hospital database. BEAMnrc software was used for simulation. The simulation of the head of the device with the energy of 0.09 MeV with 500 million particles was performed, and the output data obtained from the simulation was applied for phantom construction using CT CREATE software. The percentage of depth dose (PDD) was calculated using STATE DOSE was then compared with international standard values. Results and Discussion: The ratio of surface dose to depth dose (D/Ds) in the measured energy was estimated to be about 4% to 8% for bone and 3% to 7% for bone marrow. Conclusion: MC simulation is an efficient and accurate method for simulating bone marrow and calculating the absorbed dose.

Keywords: Monte Carlo, absorption dose, BEAMnrc, bone marrow

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Authors: C. C. Igwe

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Several parts of Neem tree (Azadirachta indica) are used in traditional medicine in many West African countries for the treatment of various human diseases. The leaf, stem - bark and seed were air dried for 8, 5 and 7 days, respectively. The shells were carfully separated from the seeds, each powdered sample obtained with mechanical miller and 250 mm sieve. The neem samples were individually subjected to extraction with acetone, n-hexane for 48hr and 72 hr, respectively. Physico-chemical and antibacterial evaluation were carried out using standard methods. Results of physico - chemical analyses of the extracted oil from the seed shows that it has a brownish colour, with a smell similar to garlic while the moisture content, refractive index are 0.76% and 1.47 respectively. Other vital chemical results obtained from the neem oil such as saponification value (234.62), acid value (10.84 %), free fatty acid (5.84 %) and peroxide value (10.52%) indicated the oil extracted satisfied standard oils parameters for quality soap and cosmetics production. The antibacterial screening by disc diffusion revealed the oil demonstrated high activity against Staphylococcus aureus. Both the physio-chemical and antibacterial of samples have been certified by National Agency for Food and Drugs Administration and Control. The preliminary results of this study may validate the medicinal value of the plant. Further studies are in progress to clarify the in vivo potentials of neem extracts in the management of human communicable diseases and this is a subject of investigation in our group.

Keywords: anti-bacterial, neem extract, physico-chemical analyses, staphylococcus aureus

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Authors: Lamis Naddaf, Yuval Tabach

Abstract:

We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

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Authors: Bitan Kumar Sarkar, Akashdeep Agarwal, Rajib Dey, Gopes Chandra Das

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The rapid depletion of high-grade iron ore (Fe₂O₃) has gained attention on the use of other sources of iron ore. Titaniferous magnetite ore (TMO) is a special type of magnetite ore having high titania content (23.23% TiO₂ present in this case). Due to high TiO₂ content and high density, TMO cannot be treated by the conventional smelting reduction. In this present work, the TMO has been collected from high-grade metamorphic terrain of the Precambrian Chotanagpur gneissic complex situated in the eastern part of India (Shaltora area, Bankura district, West Bengal) and the hematite ore has been collected from Visakhapatnam Steel Plant (VSP), Visakhapatnam. At VSP, iron ore is received from Bailadila mines, Chattisgarh of M/s. National Mineral Development Corporation. The preliminary characterization of TMO and hematite ore (HMO) has been investigated by WDXRF, XRD and FESEM analyses. Similarly, good quality of coal (mainly coking coal) is also getting depleted fast. The basic purpose of this work is to find how lean grade coal can be utilised along with TMO for smelting to produce pig iron. Lean grade coal has been characterised by using TG/DTA, proximate and ultimate analyses. The boiler grade coal has been found to contain 28.08% of fixed carbon and 28.31% of volatile matter. TMO fines (below 75 μm) and HMO fines (below 75 μm) have been separately agglomerated with lean grade coal fines (below 75 μm) in the form of briquettes using binders like bentonite and molasses. These green briquettes are dried first in oven at 423 K for 30 min and then reduced isothermally in tube furnace over the temperature range of 1323 K, 1373 K and 1423 K for 30 min & 60 min. After reduction, the reduced briquettes are characterized by XRD and FESEM analyses. The best reduced TMO and HMO samples are taken and blended in three different weight percentage ratios of 1:4, 1:8 and 1:12 of TMO:HMO. The chemical analysis of three blended samples is carried out and degree of metallisation of iron is found to contain 89.38%, 92.12% and 93.12%, respectively. These three blended samples are briquetted using binder like bentonite and lime. Thereafter these blended briquettes are separately smelted in raising hearth furnace at 1773 K for 30 min. The pig iron formed is characterized using XRD, microscopic analysis. It can be concluded that 90% yield of pig iron can be achieved when the blend ratio of TMO:HMO is 1:4.5. This means for 90% yield, the maximum TMO that could be used in the blend is about 18%.

Keywords: briquetting reduction, lean grade coal, smelting reduction, TMO

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