Search results for: adaptive SNPs

Authors: Shankha Sanyal, Archi Banerjee, Sayan Biswas, Sourya Sengupta, Sayan Nag, Ranjan Sengupta, Dipak Ghosh

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The term ‘gestalt’ has been widely used in the field of psychology which defined the perception of human mind to group any object not in part but as a 'unified' whole. Music, in general, is polyphonic - i.e. a combination of a number of pure tones (frequencies) mixed together in a manner that sounds harmonious. The study of human brain response due to different frequency groups of the acoustic signal can give us an excellent insight regarding the neural and functional architecture of brain functions. Hence, the study of music cognition using neuro-biosensors is becoming a rapidly emerging field of research. In this work, we have tried to analyze the effect of different frequency bands of music on the various frequency rhythms of human brain obtained from EEG data. Four widely popular Rabindrasangeet clips were subjected to Wavelet Transform method for extracting five resonant frequency bands from the original music signal. These frequency bands were initially analyzed with Detrended/Adaptive Fractal analysis (DFA/AFA) methods. A listening test was conducted on a pool of 100 respondents to assess the frequency band in which the music becomes non-recognizable. Next, these resonant frequency bands were presented to 20 subjects as auditory stimulus and EEG signals recorded simultaneously in 19 different locations of the brain. The recorded EEG signals were noise cleaned and subjected again to DFA/AFA technique on the alpha, theta and gamma frequency range. Thus, we obtained the scaling exponents from the two methods in alpha, theta and gamma EEG rhythms corresponding to different frequency bands of music. From the analysis of music signal, it is seen that loss of recognition is proportional to the loss of long range correlation in the signal. From the EEG signal analysis, we obtain frequency specific arousal based response in different lobes of brain as well as in specific EEG bands corresponding to musical stimuli. In this way, we look to identify a specific frequency band beyond which the music becomes non-recognizable and below which in spite of the absence of other bands the music is perceivable to the audience. This revelation can be of immense importance when it comes to the field of cognitive music therapy and researchers of creativity.

Keywords: AFA, DFA, EEG, gestalt in music, Hurst exponent

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Authors: Yara Bajnaid, Malak Zaidan, Eman Dakkak

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This research explores the use of Artificial Intelligence in Duolingo, a popular mobile application for language learning. Duolingo's success hinges on its gamified approach and adaptive learning system, both heavily reliant on AI functionalities. The research also analyzes user feedback regarding Duolingo's AI functionalities. While a significant majority (70%) consider Duolingo a reliable tool for language learning, there's room for improvement. Overall, AI plays a vital role in personalizing the learning journey and delivering interactive exercises. However, continuous improvement based on user feedback can further enhance the effectiveness of Duolingo's AI functionalities.

Keywords: AI, Duolingo, language learning, application

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Authors: W. Shin, Y. Kim

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This study focuses on disconfirming that wide-area networks can be made mobile, highly-available, and wireless. This methodological test shows that IPv7 and context-free grammar are mismatched. In the cases of robots, a similar tendency is also revealed. Further, we also prove that public-private key pairs could be built embedded, adaptive, and wireless. Finally, we disconfirm that although hash tables can be made distributed, interposable, and autonomous, XML and DNS can interfere to realize this purpose. Our experiments soon proved that exokernelizing our replicated Knesis keyboards was more significant than interrupting them. Our experiments exhibited degraded average sampling rate.

Keywords: collaborative communication, DNS, local-area networks, XML

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Authors: T. C. C. Soo, S. Bhassu

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Unlike the common presence of both innate and adaptive immunity in vertebrates, crustaceans, in particular, shrimps, have been discovered to possess only innate immunity. This further emphasizes the importance of innate immunity within shrimps in pathogenic resistance. Under the study of pathogenic immune challenge, different shrimp species actually exhibit varying degrees of immune resistance towards the same pathogen. Furthermore, even within the same shrimp species, different batches of challenged shrimps can have different strengths of immune defence. Several important pathways are activated within shrimps during pathogenic infection. One of them is JAK-STAT pathway that is activated during bacterial, viral and fungal infections by which STAT(Signal Transducer and Activator of Transcription) gene is the core element of the pathway. Based on theory of Central Dogma, the genomic information is transmitted in the order of DNA, RNA and protein. This study is focused in uncovering the important evolutionary patterns present within the DNA (non-coding region) and RNA (coding region). The three shrimp species involved are Macrobrachium rosenbergii, Penaeus monodon and Litopenaeus vannamei which all possess commercial significance. The shrimp species were challenged with a famous penaeid shrimp virus called white spot syndrome virus (WSSV) which can cause serious lethality. Tissue samples were collected during time intervals of 0h, 3h, 6h, 12h, 24h, 36h and 48h. The DNA and RNA samples were then extracted using conventional kits from the hepatopancreas tissue samples. PCR technique together with designed STAT gene conserved primers were utilized for identification of the STAT coding sequences using RNA-converted cDNA samples and subsequent characterization using various bioinformatics approaches including Ramachandran plot, ProtParam and SWISS-MODEL. The varying levels of immune STAT gene activation for the three shrimp species during WSSV infection were confirmed using qRT-PCR technique. For one sample, three biological replicates with three technical replicates each were used for qRT-PCR. On the other hand, DNA samples were important for uncovering the structural variations within the genomic region of STAT gene which would greatly assist in understanding the STAT protein functional variations. The partially-overlapping primers technique was used for the genomic region sequencing. The evolutionary inferences and event predictions were then conducted through the Bayesian Inference method using all the acquired coding and non-coding sequences. This was supplemented by the construction of conventional phylogenetic trees using Maximum likelihood method. The results showed that adaptive evolution caused STAT gene sequence mutations between different shrimp species which led to evolutionary divergence event. Subsequently, the divergent sites were correlated to the differing expressions of STAT gene. Ultimately, this study assists in knowing the shrimp species innate immune variability and selection of disease resistant shrimps for breeding purpose. The deeper understanding of STAT gene evolution from the perspective of both purifying and adaptive approaches not only can provide better immunological insight among shrimp species, but also can be used as a good reference for immunological studies in humans or other model organisms.

Keywords: gene evolution, JAK-STAT pathway, immunology, STAT gene

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Authors: Ahlem Mougaida, Hedi Bel Hadj Salah

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Several methods are suggested to improve the numerical integration in Galerkin weak form for Meshless methods. In fact, integrating without taking into account the characteristics of the shape functions reproduced by Meshless methods (rational functions, with compact support etc.), causes a large integration error that influences the PDE’s approximate solution. Comparisons between different methods of numerical integration for rational functions are discussed and compared. The algorithms are implemented in Matlab. Finally, numerical results were presented to prove the efficiency of our algorithms in improving results.

Keywords: adaptive methods, meshless, numerical integration, rational quadrature

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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: Anida Causevic-Ramosevac, Sabina Semiz

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The aim of this study was to investigate the association of four single nucleotide polymorphisms (SNPs) - rs673548, rs693 in ApoB gene, rs1800775 in CETP gene and rs4846914 in GALNT2 gene with parameters of type 2 diabetes (T2D) and diabetic dyslipidemia in the population of Bosnia and Herzegovina (BH). Materials and methods: Our study involved 352 patients with T2D and 156 healthy subjects. Biochemical and anthropometric parameters were measured in all participants. DNA was extracted from the peripheral blood for the purpose of genetic testing. Polymorphisms in ApoB (rs673548, rs693), CETP (rs1800775) and GALNT2 (rs4846914) genes were analyzed by using Sequenom IPLEX platform. Results: Our results demonstrated significant associations for rs180075 polymorphism in CETP gene with levels of fasting insulin (p = 0.020; p = 0.027; p = 0.044), triglycerides (p = 0.046) and ALT (p = 0.031) activity in control group. In group of diabetic patients, results showed a significant association of rs673548 in ApoB gene with levels of fasting insulin (p = 0.008), HOMA-IR (p = 0.013), VLDL-C (p = 0.037) and CRP (p = 0.029) and rs693 in ApoB gene with BMI (p = 0.025), systolic blood pressure (p = 0.027), fasting insulin (p = 0.037) and HOMA-IR (p = 0.023) levels. Significant associations were also observed for rs1800775 in CETP gene with triglyceride (p = 0.023) levels and rs4846914 in GALNT2 gene with HbA1C (p = 0.013) and triglyceride (p = 0.043) levels. Conclusion: In conclusion, this is the first study that examined the impact of variations of candidate genes on a wide range of metabolic parameters in BH population. Our results suggest an association of variations of ApoB, CETP and GALNT2 genes with specific markers of T2D and dyslipidemia. Further studies would be needed in order to confirm these genetic effects in other ethnic groups as well.

Keywords: ApoB, CETP, dyslipidemia, GALNT2, type 2 diabetes

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Authors: Sekena H. Abd El-Aziem, Heba A. M. Abd El-Kader, Sally S. Alam, Othman E. Othman

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Growth hormone (GH) is an anabolic hormone synthesized and secreted by the somatotroph cells of the anterior lobe of the pituitary gland in a circadian and pulsatile manner, the pattern of which plays an important role in postnatal longitudinal growth and development, tissue growth, lactation, reproduction as well as protein, lipid and carbohydrate metabolism. The aim of this study was to detect the genetic polymorphism of GH gene in five camel breeds reared in Egypt; Sudany, Somali, Mowaled, Maghrabi and Falahy, using PCR-RFLP technique. Also this work aimed to identify the single nucleotide polymorphism between different genotypes detected in these camel breeds. The amplified fragment of camel GH at 613-bp was digested with the restriction enzyme MspI and the result revealed the presence of three different genotypes; CC, CT and TT in tested breeds and significant differences were recorded in the genotype frequencies between these camel breeds. The result showed that the Maghrabi breed that is classified as a dual purpose camels had higher frequency for allele C (0.75) than those in the other tested four breeds. The sequence analysis declared the presence of a SNP (C→T) at position 264 in the amplified fragment which is responsible for the destruction of the restriction site C^CGG and consequently the appearance of two different alleles C and T. The nucleotide sequences of camel GH alleles T and C were submitted to nucleotide sequences database NCBI/Bankit/GenBank and have accession numbers: KP143517 and KP143518, respectively. It is concluded that only one SNP C→T was detected in GH gene among the five tested camel breeds reared in Egypt and this nucleotide substitution can be used as a marker for the genetic biodiversity between camel breeds reared in Egypt. Also, due to the possible association between allele C and higher growth rate, we can used it in MAS for camels and enter the camels possess this allele in breeding program as a way for enhancement of growth trait in camel breeds reared in Egypt.

Keywords: camel breeds in Egypt, GH, PCR-RFLP, SNPs

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Authors: Silpita Paul, Susanta Sadhukhan, Biswanath Maity, Madhusudan Das

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Neural tube defects (NTDs) are one of the most common forms of birth defect and affect ~300,000 new born worldwide each year. The prevalence is higher in Northern India (11 per 1000 birth) compare to southern India (5 per 1000 birth). NTDs are one of the common birth defects related with low blood folate and Hcy concentration. Though the mechanism is still unknown, but it is now established that, NTDs in human are polygenic in nature and follow the heterogeneous trait. In spite of its heterogeneity, polymorphism in few genes affects significantly the trait of NTDs. Polymorphisms in the genes FOLH1 and MTHFR plays important role in NTDs. In this study, the polymorphisms of these genes were screened by bi-directional sequencing from 30 mothers with NTD babies as case. The result revealed that 26.67% patients had bi-allelic FOLH1 polymorphism. The polymorphism has been identified as p.Y60H and frequent to cause NTDs. The study of MTHFR gene showed 2 different SNPs rs1801131 (at exon 4) and rs1801131 (at exon 7). The study showed 6.67% patients of both mono- and bi-allelic MTHFR-rs1801131 polymorphism and 6.67% patients of bi-allelic MTHFR-rs1801131 polymorphism. These polymorphisms has been responsible for p.A222V and p.E429A change respectively and frequently involved in NTD formation. Those polymorphisms affect mainly the absorption of dietary folate from intestine and the formation of 5-methylenetetrahydrofolate (5 MTHF) from 5,10-methylenetetrahydrofolate (5,10- MTHF), which is the functional folate form in our system. Though the study is not complete yet, but these polymorphisms play crucial roles in the formation of NTDs in other world population. Based on the result till date, it can be concluded that they also play significant role in our population too as in control samples we have not found any changes.

Keywords: neural tube defects, polymorphism, FOLH1, MTHFR

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Authors: Airy Huang, Fuji Foo, Aries Prasetya Wibowo

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In recent years, the focus of Natural Language Processing (NLP) development has been gradually shifting from the semantics-based approach to deep learning one, which performs faster with fewer resources. Although it performs well in many applications, the deep learning approach, due to the lack of semantics understanding, has difficulties in noticing and expressing a novel business case with a pre-defined scope. In order to meet the requirements of specific robotic services, deep learning approach is very labor-intensive and time consuming. It is very difficult to improve the capabilities of conversational AI in a short time, and it is even more difficult to self-learn from experiences to deliver the same service in a better way. In this paper, we present an adaptive conversational AI algorithm that combines both semantic knowledge and deep learning to address this issue by learning new business cases through conversations. After self-learning from experience, the robot adapts to the business cases originally out of scope. The idea is to build new or extended robotic services in a systematic and fast-training manner with self-configured programs and constructed dialog flows. For every cycle in which a chat bot (conversational AI) delivers a given set of business cases, it is trapped to self-measure its performance and rethink every unknown dialog flows to improve the service by retraining with those new business cases. If the training process reaches a bottleneck and incurs some difficulties, human personnel will be informed of further instructions. He or she may retrain the chat bot with newly configured programs, or new dialog flows for new services. One approach employs semantics analysis to learn the dialogues for new business cases and then establish the necessary ontology for the new service. With the newly learned programs, it completes the understanding of the reaction behavior and finally uses dialog flows to connect all the understanding results and programs, achieving the goal of self-learning process. We have developed a chat bot service mounted on a kiosk, with a camera for facial recognition and a directional microphone array for voice capture. The chat bot serves as a concierge with polite conversation for visitors. As a proof of concept. We have demonstrated to complete 90% of reception services with limited self-learning capability.

Keywords: conversational AI, chatbot, dialog management, semantic analysis

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Authors: Ishita Singh

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Social-dimension of Climate Change is no longer peripheral to Science, Technology and Innovation (STI). Indeed, STI is being mobilized to address small farmers’ vulnerability and adaptation to Climate Change. The experiences from the cold desert of Leh (Ladakh) in North-West Himalaya illustrate the potential of STI to address the challenges of Climate Change and the needs of small farmers through the use of Artificial Glacier Techniques. Small farmers have a unique technique of water harvesting to augment irrigation, called “Artificial Glaciers” - an intricate network of water channels and dams along the upper slope of a valley that are located closer to villages and at lower altitudes than natural glaciers. It starts to melt much earlier and supplements additional irrigation to small farmers’ improving their livelihoods. Therefore, the issue of vulnerability, adaptive capacity and adaptation strategy needs to be analyzed in a local context and the communities as well as regions where people live. Leh (Ladakh) in North-West Himalaya provides a Case Study for exploring the ways in which adaptation to Climate Change is taking place at a community scale using Artificial Glacier Technology. With the above backdrop, an attempt has been made to analyze the rural poor households' vulnerability and adaptation practices to Climate Change using this technology, thereby drawing lessons on vulnerability-livelihood interactions in the cold desert of Leh (Ladakh) in North-West Himalaya, India. The study is based on primary data and information collected from 675 households confined to 27 villages of Leh (Ladakh) in North-West Himalaya, India. It reveals that 61.18% of the population is driving livelihoods from agriculture and allied activities. With increased irrigation potential due to the use of Artificial Glaciers, food security has been assured to 77.56% of households and health vulnerability has been reduced in 31% of households. Seasonal migration as a livelihood diversification mechanism has declined in nearly two-thirds of households, thereby improving livelihood strategies. Use of tactical adaptations by small farmers in response to persistent droughts, such as selling livestock, expanding agriculture lands, and use of relief cash and foods, have declined to 20.44%, 24.74% and 63% of households. However, these measures are unsustainable on a long-term basis. The role of policymakers and societal stakeholders becomes important in this context. To address livelihood challenges, the role of technology is critical in a multidisciplinary approach involving multilateral collaboration among different stakeholders. The presence of social entrepreneurs and new actors on the adaptation scene is necessary to bring forth adaptation measures. Better linkage between Science and Technology policies, together with other policies, should be encouraged. Better health care, access to safe drinking water, better sanitary conditions, and improved standards of education and infrastructure are effective measures to enhance a community’s adaptive capacity. However, social transfers for supporting climate adaptive capacity require significant amounts of additional investment. Developing institutional mechanisms for specific adaptation interventions can be one of the most effective ways of implementing a plan to enhance adaptation and build resilience.

Keywords: climate change, adaptation, livelihood, stakeholders

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Authors: Mohammad Umar Azizi, Tetsuya Ando

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This study investigates the transformation of the traditional landscape of Kabul Old City through an examination of five case study areas. Based on physical observation, three types of houses are found: traditional, mixed and modern. Firstly, characteristics of the houses are described according to construction materials and the number of stories. Secondly, internal and external factors are considered in order to implement a conservation plan. Finally, an adaptive conservation plan is suggested to protect the traditional landscape of Kabul Old City.

Keywords: conservation, district 1, Kabul Old City, landscape, transformation, traditional houses

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Authors: J. Vinay , Kusumbati Besra, Niharika Pattnaik, Shivaram Prasad Singh, Manjusha Dixit

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Gallbladder cancer (GBC) is rare but highly malignant cancer; its prevalence is more in certain geographical regions and ethnic groups, which include the Northern and Eastern states of India. Previous studies in India have reported genetic predisposition as one of the risk factors in GBC pathogenesis. Although the matrix metalloproteinase-14 (MMP14) is a well-known modulator of the tumor microenvironment and tumorigenesis and TCGA data also suggests its upregulation yet, its role in the genetic predisposition for GBC is completely unknown. We elucidated the role of MMP14 promoter variants as genetic risk factors and their implications in expression modulation. We screened MMP14 promoter variants association with GBC using Sanger’s sequencing in approximately 300 GBC and 300 control subjects and 26 GBC tissue samples of Indian ethnicity. The immunohistochemistry was used to check the MMP14 protein expression in GBC tissue samples. The role of promoter variants on expression levels was elucidated using a luciferase reporter assay. The variants rs1004030 (p-value = 0.0001) and rs1003349 (p-value = 0.0008) were significantly associated with gallbladder cancer. The luciferase assay in two different cell lines, HEK-293 (p = 0.0006) and TGBC1TKB (p = 0.0036) showed a significant increase in relative luciferase activity in the presence of risk alleles for both the single nucleotide polymorphisms (SNPs). Similarly, genotype-phenotype correlation in patients samples confirmed that the presence of risk alleles at rs1004030 and rs1003349 increased MMP14 expression. Overall, this study unravels the genetic association of MMP14 promoter variants with gallbladder cancer, which may contribute to pathogenesis by increasing its expression.

Keywords: gallbladder cancer, matrix metalloproteinase-14, single nucleotide polymorphism, case control study, genetic association study

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Authors: Yasaman Ashrafi, Stephen Kajewski, Annastiina Silvennoinen, Madhav Nepal

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Mega projects either in construction, urban development or energy sectors are one of the key drivers that build the foundation of wealth and modern civilizations in regions and nations. Such projects require economic justification and substantial capital investment, often derived from individual and corporate investors as well as governments. Cost overruns and time delays in these mega projects demands a new approach to more accurately predict project costs and establish realistic financial plans. The significance of this paper is that the cost efficiency of megaprojects will improve and decrease cost overruns. This research will assist Project Managers (PMs) to make timely and appropriate decisions about both cost and outcomes of ongoing projects. This research, therefore, examines the oil and gas industry where most mega projects apply the classic methods of Cost Performance Index (CPI) and Schedule Performance Index (SPI) and rely on project data to forecast cost and time. Because these projects are always overrun in cost and time even at the early phase of the project, the probabilistic methods of Monte Carlo Simulation (MCS) and Bayesian Adaptive Forecasting method were used to predict project cost at completion of projects. The current theoretical and mathematical models which forecast the total expected cost and project completion date, during the execution phase of an ongoing project will be evaluated. Earned Value Management (EVM) method is unable to predict cost at completion of a project accurately due to the lack of enough detailed project information especially in the early phase of the project. During the project execution phase, the Bayesian adaptive forecasting method incorporates predictions into the actual performance data from earned value management and revises pre-project cost estimates, making full use of the available information. The outcome of this research is to improve the accuracy of both cost prediction and final duration. This research will provide a warning method to identify when current project performance deviates from planned performance and crates an unacceptable gap between preliminary planning and actual performance. This warning method will support project managers to take corrective actions on time.

Keywords: cost forecasting, earned value management, project control, project management, risk analysis, simulation

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Authors: Radwa Mabrook

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Virtual Reality (VR) content creation is a complex and an expensive process, which requires multi-disciplinary teams of content creators. Grant schemes from technology companies help media organisations to explore the VR potential in journalism and factual storytelling. Media organisations try to do as much as they can in-house, but they may outsource due to time constraints and skill availability. Journalists, game developers, sound designers and creative artists work together and bring in new cultures of work. This study explores the collaborative experimental nature of VR content creation, through tracing every actor involved in the process and examining their perceptions of the VR work. The study builds on Actor Network Theory (ANT), which decomposes phenomena into their basic elements and traces the interrelations among them. Therefore, the researcher conducted 22 semi-structured interviews with VR content creators between November 2017 and April 2018. Purposive and snowball sampling techniques allowed the researcher to recruit fact-based VR content creators from production studios and media organisations, as well as freelancers. Interviews lasted up to three hours, and they were a mix of Skype calls and in-person interviews. Participants consented for their interviews to be recorded, and for their names to be revealed in the study. The researcher coded interviews’ transcripts in Nvivo software, looking for key themes that correspond with the research questions. The study revealed that VR content creators must be adaptive to change, open to learn and comfortable with mistakes. The VR content creation process is very iterative because VR has no established work flow or visual grammar. Multi-disciplinary VR team members often speak different languages making it hard to communicate. However, adaptive content creators perceive VR work as a fun experience and an opportunity to learn. The traditional sense of competition and the strive for information exclusivity are now replaced by a strong drive for knowledge sharing. VR content creators are open to share their methods of work and their experiences. They target to build a collaborative network that aims to harness VR technology for journalism and factual storytelling. Indeed, VR is instilling collaborative and experimental cultures in journalism.

Keywords: collaborative culture, content creation, experimental culture, virtual reality

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Authors: Sahar Javadi-Novashnagh, Mohammad Moradi-Shahrbabak, Mostafa Sadeghi, Katarzyna Ropka-Molik, Hossein Moradi-Shahrbabak, Maria Consuelo Mura

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The objective of this study was to investigate two single nucleotide polymorphisms located in exon 2 (g.939A > G) and intron 3 (g.4349A > G) of fatty acid binding protein 3 (FABP3) gene in two Iranian sheep breeds, Lori-Bakhtiari and Zel, using polymerase chain reaction -restriction fragment length polymorphism (PCR-RFLP) approach. The association of the polymorphisms with growth traits and blood parameters was also examined. Results revealed a g.939A > G SNP (single nucleotide polymorphism) in the exon 2 exhibiting three genotypes: AA, AG, and GG. Statistical analysis indicated that this polymorphism significantly influenced blood triglyceride (P < 0.05) and cholesterol (P < 0.08) levels as well as weaning weight (P < 0.05). Animals with AG genotype had the highest blood triglyceride level and weaning weight while the highest amount of blood cholesterol was observed in animals with GG genotype. On the other hand, no significant effect was observed on birth and fat-tail weight traits. The intron 3 (g.4349A > G) was monomorphic across the studied samples. Lori-Bakhtiari breed showed significantly higher blood triglyceride and cholesterol levels, as also birth and weaning weight compared to Zel breed (P < 0.01). Considering that the literature is bereft of any report on the association study between FABP3 SNPs and sheep growth traits and blood parameters, our findings suggest that the investigated polymorphism might be one of the main genetic factors affecting growth and physiological traits in sheep.

Keywords: FABP3 gene, fatness, weaning weight, blood triglyceride, cholesterol, Zel, Lori-Bakhtiari

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Authors: Amr A. El Hanafy, Muhammad I. Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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β-Lactoglobulin (β-LG) is the dominant non-casein whey protein found in bovine milk and of most ruminants. The amino acid sequence of β-LG along with its 3-dimensional structure illustrates linkage with the lipocalin superfamily. Preliminary studies in goats indicated that milk yield can be influenced by polymorphism in genes coding for whey proteins. The aim of this study is to identify and evaluate the incidence of functional polymorphisms in the exonic and intronic portions of β-LG gene in native Saudi goat breeds (Ardi, Habsi, and Harri). Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted using QIAamp DNA extraction Kit. A fragment of the β-LG gene from exon 7 to 3’ flanking region was amplified with pairs of specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Two already established SNPs in exon 7 (+4601 and +4603) and one fresh SNP in the 3’ UTR region were detected in the β-LG fragments with designated AA genotype. The polymorphisms in exon 7 did not produce any amino acid change. Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, functional polymorphism, nucleotide sequencing, phylogenetic analysis

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Authors: I. Boroňová, J. Bernasovská, J. Kmec, E. Petrejčíková

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Dilated cardiomyopathy (DCM) is a primary myocardial disease, it is characterized by progressive systolic dysfunction due to cardiac chamber dilatation and inefficient myocardial contractility with estimated prevalence of 37 in 100 000 people. It is the most frequent cause of heart failure and cardiac transplantation in young adults. About one-third of all patients have a suspected familial disease indicating a genetic basis of DCM. Many candidate gene studies in humans have tested the association of single nucleotide polymorphisms (SNPs) in various genes coding for proteins with a known cardiovascular function. In our study we present the results of ZBTB17 gene rs10927875 polymorphism genotyping in relation to dilated cardiomyopathy in Slovak population. The study included 78 individuals, 39 patients with DCM and 39 healthy control persons. The mean age of patients with DCM was 50.7±11.5 years; the mean age of individuals in control group was 51.3±9.8 years. Risk factors detected at baseline in each group included age, sex, body mass index, smoking status, diabetes and blood pressure. Genomic DNA was extracted from leukocytes by a standard methodology and screened for rs10927875 polymorphism in intron of ZBTB17 gene using Real-time PCR method (Step One Applied Biosystems). The distribution of investigated genotypes for rs10927875 polymorphism in the group of patients with DCM was as follows: CC (89.74%), CT (10.26%), TT (0%), and the distribution in the control group: CC (92.31%), CT (5.13%), and TT (2.56%). Using the chi-square (χ2) test we compared genotype and allele frequencies between patients and controls. There was no difference in genotype or allele frequencies in ZBTB17 gene rs10927875 polymorphism between patients and control group (χ2=3.028, p=0.220; χ2=0.264, p=0.608). Our results represent an initial study, it can be considered as preliminary and first of its kind in Slovak population. Further studies of ZBTB17 gene polymorphisms of more numerous files and additional functional investigations are needed to fully understand the role of genetic associations.

Keywords: dilated cardiomyopathy, SNP polymorphism, ZBTB17 gene, bioscience

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Authors: Mengying Wang, Dongjing Liu, Holger Schwender, Ping Wang, Hongping Zhu, Tao Wu, Terri H Beaty

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Background: Maternal smoking is a recognized risk factor for nonsyndromic cleft lip with or without cleft palate (NSCL/P). It has been reported that the effect of maternal smoking on oral clefts is mediated through genes that influence nicotine dependence. The polymorphisms of cholinergic receptor nicotinic alpha (CHRNA) and beta (CHRNB) subunits genes have previously shown strong associations with nicotine dependence. Here, we attempted to investigate whether the above genes are associated with clefting risk through testing for potential gene-gene (G×G) and gene-environment (G×E) interaction. Methods: We selected 120 markers in 14 genes associated with nicotine dependence to conduct transmission disequilibrium tests among 806 Chinese NSCL/P case-parent trios ascertained in an international consortium which conducted a genome-wide association study (GWAS) of oral clefts. We applied Cordell’s method using “TRIO” package in R to explore G×G as well as G×E interaction involving environmental tobacco smoke (ETS) based on conditional logistic regression model. Results: while no SNP showed significant association with NSCL/P after Bonferroni correction, we found signals for G×G interaction between 10 pairs of SNPs in CHRNA3, CHRNA5, and CHRNB4 (p<10-8), among which the most significant interaction was found between RS3743077 (CHRNA3) and RS11636753 (CHRNB4, p<8.2×10-12). Linkage disequilibrium (LD) analysis revealed only low level of LD between these markers. However, there were no significant results for G×ETS interaction. Conclusion: This study fails to detect association between nicotine dependence genes and NSCL/P, but illustrates the importance of taking into account potential G×G interaction for genetic association analysis in NSCL/P. This study also suggests nicotine dependence genes should be considered as important candidate genes for NSCL/P in future studies.

Keywords: Gene-Gene Interaction, Maternal Smoking, Nicotine Dependence, Non-Syndromic Cleft Lip with or without Cleft Palate

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Authors: R. Latif, W. Jenkal, A. Toumanari, A. Hatim

Abstract:

This paper presents an efficient method of electrocardiogram signal denoising based on a hybrid approach. Two techniques are brought together to create an efficient denoising process. The first is an Adaptive Dual Threshold Filter (ADTF) and the second is the Discrete Wavelet Transform (DWT). The presented approach is based on three steps of denoising, the DWT decomposition, the ADTF step and the highest peaks correction step. This paper presents some application of the approach on some electrocardiogram signals of the MIT-BIH database. The results of these applications are promising compared to other recently published techniques.

Keywords: hybrid technique, ADTF, DWT, thresholding, ECG signal

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Authors: Jung-In Baik, Seung-Jun Yu, Young-Min Ko, Hyoung-Kyu Song

Abstract:

This paper proposes an efficient relaying algorithm to obtain diversity for improving the reliability of a signal. The algorithm achieves time or space diversity gain by multiple versions of the same signal through two routes. Relays are separated between a source and destination. The routes between the source and destination are set adaptive in order to deal with different channels and noises. The routes consist of one or more relays and the source transmits its signal to the destination through the routes. The signals from the relays are combined and detected at the destination. The proposed algorithm provides a better performance than the conventional algorithms in bit error rate (BER).

Keywords: multi-hop, OFDM, relay, relaying selection

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Authors: Ahmed Elbeltagy, Francesca Bertolini, Damarius Fleming, Angelica Van Goor, Chris Ashwell, Carl Schmidt, Donald Kugonza, Susan Lamont, Max Rothschild

Abstract:

The major factor in shaping genomic variation of the African indigenous rural chicken is likely natural selection drives the development genetic footprints in the chicken genomes. To investigate such a hypothesis of a selection footprint, a total of 292 birds were randomly sampled from three indigenous ecotypes from East Africa (Uganda, Rwanda) and North Africa (Egypt) and two registered Egyptian breeds (Fayoumi and Dandarawi), and from the synthetic Kuroiler breed. Samples were genotyped using the Affymetrix 600K Axiom® Array. A total of 526,652 SNPs were utilized in the downstream analysis after quality control measures. The intra-population runs of homozygosity (ROH) that were consensuses in > 50% of individuals of an ecotype or > 75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East- African populations in addition to population-pairwise combinations for overlapping windows (500Kb with an overlap of 250Kb). A total of 28,563 ROH were determined and were classified into three length categories. ROH and Fst detected sweeps were identified on several autosomes. Several genes in these regions are likely to be related to adaptation to local environmental stresses that include high altitude, diseases resistance, poor nutrition, oxidative and heat stresses and were linked to gene ontology terms (GO) related to immune response, oxygen consumption and heme binding, carbohydrate metabolism, oxidation-reduction, and behavior. Results indicated a possible effect of natural selection forces on shaping genomic structure for adaptation to local environmental stresses.

Keywords: African Chicken, runs of homozygosity, FST, selection footprints

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Authors: Othman E. Othman, Hassan R. Darwish, Amira M. Nowier

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Lactoferrin (LF) is a multifunctional protein involved in economically production traits like milk protein composition and skeletal structure in small ruminants including sheep and goat. So, LF gene - with its genetic polymorphisms associated with production traits - is considered a candidate genetic marker used in marker-assisted selection in goats. This study aimed to identify the different alleles and genotypes of this gene in three Egyptian goat breeds using PCR-SSCP (polymerase chain reaction-single-strand conformation polymorphism) and DNA sequencing. Genomic DNA was extracted from 120 animals belonging to Barki, Zaraibi, and Damascus goat breeds. Using specific primers, PCR amplified 247-bp fragments from exon 2 of LF goat gene. The PCR products were subjected to Single-Strand Conformation Polymorphism (SSCP) technique. The results showed the presence of two genotypes GG and AG in the tested animals. The frequencies of both genotypes varied among the three tested breeds with the highest frequencies of GG genotype in all tested goat breeds. The sequence analysis of PCR products representing these two detected genotypes declared the presence of an SNP (single nucleotide polymorphisms) substitution (G/A) among G and A alleles of this gene. The association between different LF genotypes and milk composition as well as body measurement was estimated. The comparison showed that the animals possess AG genotypes are superior over those with GG genotypes for different parameters of milk protein compositions and skeletal structures. This finding declared that allele A of LF gene is considered the promising marker for the productive traits in goat. In conclusion, the Egyptian goat breeds will be needed to enhance their milk protein composition and growth trait parameters through the increasing of allele A frequency in their herds depending on the superior production traits of this allele in goats.

Keywords: lLactoferrin gene, PCR-SSCP, SNPs, Egyptian goat

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Authors: Muhammad Awais Shafique, Eiji Hato, Hideki Yaginuma

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Recently GPS data is used in a lot of studies to automatically reconstruct travel patterns for trip survey. The aim is to minimize the use of questionnaire surveys and travel diaries so as to reduce their negative effects. In this paper data acquired from GPS and accelerometer embedded in smart phones is utilized to predict the mode of transportation used by the phone carrier. For prediction, Support Vector Machine (SVM) and Adaptive boosting (AdaBoost) are employed. Moreover a unique method to improve the prediction results from these algorithms is also proposed. Results suggest that the prediction accuracy of AdaBoost after improvement is relatively better than the rest.

Keywords: accelerometer, AdaBoost, GPS, mode prediction, support vector machine

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Authors: Haowen Xu, Xiaobing Liu, Jin Dong, Jianming Lian

Abstract:

Emerging smart buildings often employ cyberinfrastructure, cyber-physical systems, and Internet of Things (IoT) technologies to increase the automation and responsiveness of building operations for better energy efficiency and lower carbon emission. These operations include the control of Heating, Ventilation, and Air Conditioning (HVAC) and lighting systems, which are often considered a major source of energy consumption in both commercial and residential buildings. Developing energy-saving control models for optimizing HVAC operations usually requires the collection of high-quality instrumental data from iterations of in-situ building experiments, which can be time-consuming and labor-intensive. This abstract describes a digital twin approach to automate building energy experiments for optimizing HVAC operations through the design and development of an adaptive web-based platform. The platform is created to enable (a) automated data acquisition from a variety of IoT-connected HVAC instruments, (b) real-time situational awareness through domain-based visualizations, (c) adaption of HVAC optimization algorithms based on experimental data, (d) sharing of experimental data and model predictive controls through web services, and (e) cyber-physical control of individual instruments in the HVAC system using outputs from different optimization algorithms. Through the digital twin approach, we aim to replicate a real-world building and its HVAC systems in an online computing environment to automate the development of building-specific model predictive controls and collaborative experiments in buildings located in different climate zones in the United States. We present two case studies to demonstrate our platform’s capability for real-time situational awareness and cyber-physical control of the HVAC in the flexible research platforms within the Oak Ridge National Laboratory (ORNL) main campus. Our platform is developed using adaptive and flexible architecture design, rendering the platform generalizable and extendable to support HVAC optimization experiments in different types of buildings across the nation.

Keywords: energy-saving buildings, digital twins, HVAC, cyber-physical system, BIM

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Authors: Nassim Dennouni, Yvan Peter, Luigi Lancieri, Zohra Slama

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The objective of this article is to make a bibliographic study on the recommendation of mobile learning activities that are used as part of the field trip scenarios. Indeed, the recommendation systems are widely used in the context of mobility because they can be used to provide learning activities. These systems should take into account the history of visits and teacher pedagogy to provide adaptive learning according to the instantaneous position of the learner. To achieve this objective, we review the existing literature on field trip scenarios to recommend mobile learning activities.

Keywords: mobile learning, field trip, mobile learning activities, collaborative filtering, recommendation system, point of interest, ACO algorithm

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Authors: Pallavi Mane, Nikita Mankar, Shraddha Mazire, Rasika Pashankar

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Content sharing sites are very useful in sharing information and images. However, with the increasing demand of content sharing sites privacy and security concern have also increased. There is need to develop a tool for controlling user access to their shared content. Therefore, we are developing an Adaptive Privacy Policy Prediction (A3P) system which is helpful for users to create privacy settings for their images. We propose the two-level framework which assigns the best available privacy policy for the users images according to users available histories on the site.

Keywords: online information services, prediction, security and protection, web based services

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Authors: Khanh D.Do, Loi V.Nguyen, Thanh N.Nguyen, Thang M.Nguyen, Vu T.Tran

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Along with the development of Secondary surveillance radar (SSR) in air traffic surveillance systems, the Multipath phenomena has always been a noticeable problem. This following article discusses the geometrical aspect and power aspect of the Multipath interference caused by reflection in SSR and proposes a method to deal with these unwanted multipath targets (ghosts) by false-target position predicting and adaptive target suppressing. A field-experiment example is mentioned at the end of the article to demonstrate the efficiency of this measure.

Keywords: multipath, secondary surveillance radar, digital signal processing, reflection

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Authors: Fulufhelo Amanda Doboro, Kgomotso Sebeko, Stephen Njiro, Moritz Van Vuuren

Abstract:

Ovine herpesvirus 2 (OvHV-2) genome obtained from the lymphopblastoid cell line of a BJ1035 cow was recently sequenced in the United States of America (USA). Information on the sequences of OvHV-2 genes obtained from South African strains from bovine or other African countries and molecular characterization of OvHV-2 is not documented. Present investigation provides information on the nucleotide and derived amino acid sequences and genetic diversity of Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes, of these genes from OvHV-2 strains circulating in South Africa. Gene-specific primers were designed and used for PCR of DNA extracted from 42 bovine blood samples that previously tested positive for OvHV-2. The expected PCR products of 495 bp, 253 bp, 890 bp and 1632 bp respectively for Ov 7, Ov 8 ex2, ORF 27 and ORF 73 genes were sequenced and multiple sequence analysis done on the selected regions of the sequenced PCR products. Two genotypes for ORF 27 and ORF 73 gene sequences, and three genotypes for Ov 7 and Ov 8 ex2 gene sequences were identified, and similar groupings for the derived amino acid sequences were obtained for each gene. Nucleotide and amino acid sequence variations that led to the identification of the different genotypes included SNPs, deletions and insertions. Sequence analysis of Ov 7 and ORF 27 genes revealed variations that distinguished between sequences from SA and reference OvHV-2 strains. The implication of geographic origin among SA sequences was difficult to evaluate because of random distribution of genotypes in the different provinces, for each gene. However, socio-economic factors such as migration of people with animals, or transportation of animals for agricultural or business use from one province to another are most likely to be responsible for this observation. The sequence variations observed in this study have no impact on the antibody binding activities of glycoproteins encoded by Ov 7, Ov 8 ex2 and ORF 27 genes, as determined by prediction of the presence of B cell epitopes using BepiPred 1.0. The findings of this study will be used for selection of gene candidates for the development of diagnostic assays and vaccine development as well.

Keywords: amino acid, genetic diversity, genes, nucleotide

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Authors: Djamel Boussaa

Abstract:

Cultural heritage and tourism have become during the last two decades dynamic areas of development in the world. The idea of heritage is crucial to the critical decision-making process as to how irreplaceable resources are to be utilized by people of the present or conserved for future generations in a fast changing world. In view of the importance of ‘heritage’ to the development of a tourist destination the emphasis on developing appropriate adaptive reuse strategies cannot be overemphasized. In October 1999, the 12th general assembly of the ICOMOS in Mexico stated, that in the context of sustainable development, two interrelated issues need urgent attention, cultural tourism and historic towns and cities. These two issues underscore the fact that historic resources are non-renewable, belonging to all of humanity. Without adequate adaptive reuse actions to ensure a sustainable future for these historic resources, may lead to their complete vanishing. The growth of tourism and its role in dispersing cultural heritage to everyone is developing rapidly. According to the World Tourism Organization, natural and cultural heritage resources are and will remain motivating factors for travel in the foreseeable future. According to the experts, people choose travel destinations where they can learn about traditional and distinct cultures in their historic context. The Qatar rich urban heritage is now being recognized as a valuable resource for future development. This paper discusses the role of cultural heritage and tourism in regenerating Souk Waqif, and consequently the city of Doha. Therefore, in order to use cultural heritage wisely, it will be necessary to position heritage as an essential element of sustainable development, giving particular attention to cultural heritage and tourism. The research methodology is based on an empirical survey of the situation, based on several visits, meetings and interviews with the local heritage players. The rehabilitation project initiated since 2004 will be examined and assessed. Therefore, there is potential to assess the situation and propose directions for a sustainable future to this historic landmark. Conservation for the sake of conservation appears to be an outdated concept. Many irreplaceable natural and cultural sites are being compromised because local authorities are not giving economic consideration to the value of rehabilitating such sites. The question to be raised here is 'How can cultural heritage be used wisely for tourism without compromising its social sustainability within the emerging global world?'

Keywords: cultural heritage, tourism, regeneration, economy, social sustainability

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