Search results for: low discrepancy sequences

Authors: Hanna Poikonen, Petri Toiviainen, Mari Tervaniemi

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Event-related potentials (ERPs) evoked by simple tones in the brain have been extensively studied. However, in reality the music surrounding us is spectrally and temporally complex and dynamic. Thus, the research using natural sounds is crucial in understanding the operation of the brain in its natural environment. Music is an excellent example of natural stimulation, which, in various forms, has always been an essential part of different cultures. In addition to sensory responses, music elicits vast cognitive and emotional processes in the brain. When compared to laymen, professional musicians have stronger ERP responses in processing individual musical features in simple tone sequences, such as changes in pitch, timbre and harmony. Here we show that the ERP responses evoked by rapid changes in individual musical features are more intense in musicians than in laymen, also while listening to long excerpts of the composition Carmen. Interestingly, for professional dancers, the amplitudes of the cognitive P300 response are weaker than for musicians but still stronger than for laymen. Also, the cognitive P300 latencies of musicians are significantly shorter whereas the latencies of laymen are significantly longer. In contrast, sensory N100 do not differ in amplitude or latency between musicians and laymen. These results, acquired from a novel ERP methodology for natural music, suggest that we can take the leap of studying the brain with long pieces of natural music also with the ERP method of electroencephalography (EEG), as has already been made with functional magnetic resonance (fMRI), as these two brain imaging devices complement each other.

Keywords: electroencephalography, expertise, musical features, real-life music

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Authors: Suwattana Visetnan, Premruethai Supungul, Sureerat Tang, Ikuo Hirono, Anchalee Tassanakajon, Vichien Rimphanitchayakit

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In animals, infection by Gram-negative bacteria and certain viruses activates the Imd signaling pathway wherein the a NF-κB transcription factor, Relish, is a key regulatory protein for the synthesis of antimicrobial proteins. Infection by yellow head virus (YHV) activates the Imd pathway. To investigate the expression of genes involved in YHV infection and under the influence of PmRelish regulation, RNA interference and suppression subtractive hybridization (SSH) are employed. The genes in forward library expressed in shrimp after YHV infection and under the activity of PmRelish were obtained by subtracting the cDNAs from YHV-infected and PmRelish-knockdown shrimp with cDNAs from YHV-infected shrimp. Opposite subtraction gave a reverse library whereby an alternative set of genes under YHV infection and no PmRelish expression was obtained. Sequencing of 252 and 99 cDNA clones from the respective forward and reverse libraries were done and annotated through blast search against the GenBank sequences. Genes involved in defense and homeostasis were abundant in both libraries, 31% and 23% in the forward and reverse libraries, respectively. They were predominantly antimicrobial proteins, proteinases and proteinase inhibitors. The expression of antimicrobial protein genes, ALFPm3, crustinPm1, penaeidin3 and penaeidin5 were tested under PmRelish silencing and Gram-negative bacterium V. harveyi infection. Together with the results previously reported, the expression of penaeidin5 and also penaeidin3 but not ALFPm3 and crustinPm1 were under the regulation of PmRelish in the Imd pathway.

Keywords: relish, yellow head virus, penaeus monodon, antimicrobial proteins

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Authors: Samuel B. Dulay, Sandra Julich, Herbert Tomaso, Ciara K. O'Sullivan

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An early, rapid and definite detection for the presence of biowarfare agents, pathogens, viruses and toxins is required in different situations which include civil rescue and security units, homeland security, military operations, public transportation securities such as airports, metro and railway stations due to its harmful effect on the human population. In this work, an electrochemical genosensor array that allows simultaneous detection of different biowarfare agents within an integrated microsystem that provides an easy handling of the technology which combines a microfluidics setup with a multiplexing genosensor array has been developed and optimised for the following targets: Bacillus anthracis, Brucella abortis and melitensis, Bacteriophage lambda, Francisella tularensis, Burkholderia mallei and pseudomallei, Coxiella burnetii, Yersinia pestis, and Bacillus thuringiensis. The electrode array was modified via co-immobilisation of a 1:100 (mol/mol) mixture of a thiolated probe and an oligoethyleneglycol-terminated monopodal thiol. PCR products from these relevant biowarfare agents were detected reproducibly through a sandwich assay format with the target hybridised between a surface immobilised probe into the electrode and a horseradish peroxidase-labelled secondary reporter probe, which provided an enzyme based electrochemical signal. The potential of the designed microsystem for multiplexed genosensor detection and cross-reactivity studies over potential interfering DNA sequences has demonstrated high selectivity using the developed platform producing high-throughput.

Keywords: biowarfare agents, genosensors, multipled detection, microsystem

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Authors: Joanna Wozniak-Holecka, Sylwia Jaruga-Sekowska

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There are 45 statutory spa and treatment areas in Poland, and the demand for spa and treatment services increases year by year. Within each type of spa treatment facilities, nutritional education services are provided. During spa treatment, the patient learns the principles of rational nutrition and applied diet therapy. It should help him develop proper eating habits, which will also follow at home. However, the nutrition education system of spa resort patients should be considered as very imperfect and requiring a definite systemic correction. It has, at the same time, a wide human and infrastructure base, which guarantees to obtain positive reinforcement in the scope of undertaken activities and management. Unfortunately, this advantage is not fully used. The aim of the project was to assess the quality of implemented nutritional education and to assess the diet of patients in spa treatment entities from a nationwide perspective. The material for the study was data obtained as part of an in-depth interview conducted among nutrition department managers (25 interviews) and a survey addressed to patients (600 questionnaires) of a selected group of spa resorts from across the country about the implementation of nutritional education in institutions. Also, decade menus for the basic diet, easily digestible diet and diet with limitation of easily digestible carbohydrates (a total of 1,120 menus) were obtained for the study. Almost 2/3 of respondents (73.2%) were overweight or obese, but only 32.8% decided on an easily digestible or low-energy diet during the treatment. Most of the surveyed patients rated the nutrition in spa resorts as satisfactory. Classes on nutrition education were carried out mainly by a dietitian (65% of meetings), the other educators were doctors and nurses. The meetings (95%) were of a group nature and lasted only 30 minutes on average. The subjects of the classes concerned the principles of proper nutrition and composition of meals, a nutrition pyramid and a diet adapted to a given disease. The assessed menus did not meet the nutrition standards and, therefore, did not provide patients with the correct quality of nutrition. The norm of protein, fat, vitamin A, B12, phosphorus, iron and sodium was exceeded, while vitamin D, folic acid, magnesium and zinc were not enough than recommended. The study allowed to conclude that there is a large discrepancy between the recommendations presented during the nutrition education classes and the quality of diet implemented in the examined institutions. The project may contribute to the development of effective educational tools in nutrition, especially about a specific group of chronically ill patients.

Keywords: diet, management, nutritional education, spa resort

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Authors: Cathal Merz, Gareth O’Donnell

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Coil reinforced thin-walled (CRTW) tubes are used in medicine to treat problems affecting blood vessels within the body through minimally invasive procedures. The CRTW tube considered in this research makes up part of such a device and is inserted into the patient via their femoral or brachial arteries and manually navigated to the site in need of treatment. This procedure replaces the requirement to perform open surgery but is limited by reduction of blood vessel lumen diameter and increase in tortuosity of blood vessels deep in the brain. In order to maximize the capability of these procedures, CRTW tube devices are being manufactured with decreasing wall thicknesses in order to deliver treatment deeper into the body and to allow passage of other devices through its inner diameter. This introduces significant stresses to the device materials which have resulted in an observed increase in the breaking of the proximal segment of the device into two separate pieces after it has failed by buckling. As there is currently no international standard for measuring the mechanical properties of these CRTW tube devices, it is difficult to accurately analyze this problem. The aim of the current work is to address this discrepancy in the biomedical device industry by developing a measurement system that can be used to quantify the effect of process and design changes on CRTW tube performance, aiding in the development of better performing, next generation devices. Using materials testing frames, micro-computed tomography (micro-CT) imaging, experiment planning, analysis of variance (ANOVA), T-tests and regression analysis, test methods have been developed for assessing the impact of process and design changes on the device. The major findings of this study have been an insight into the suitability of buckle and three-point bend tests for the measurement of the effect of varying processing factors on the device’s performance, and guidelines for interpreting the output data from the test methods. The findings of this study are of significant interest with respect to verifying and validating key process and design changes associated with the device structure and material condition. Test method integrity evaluation is explored throughout.

Keywords: neurovascular catheter, coil reinforced tube, buckling, three-point bend, tensile

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Authors: Sarah Devi Silvian, Hanna Shobrina Iqomatul Haq, Fara Cholidatun Nabila, Agustin Krisna Wardani

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Bacteria ability to survive in antibiotic is controlled by the presence of gene that encodes the antibiotic resistance protein. The instability of the antibiotic resistance gene can be observed by exposing the bacteria under the lethal dose of antibiotic. Low concentration of antibiotic can induce mutation, which may take a role in bacterial adaptation through the antibiotic concentration. Lactobacillus casei FNCC 0090 is one of the probiotic bacteria that has an ability to survive in tetracycline by expressing the tetM gene. The aims of this study are to observe the possibilities of mutation happened in L.casei FNCC 0090 by exposing in sub-lethal dose of tetracycline and also observing the instability of the tetM gene by comparing the sequence between the wild type and mutant. L.casei FNCC 0090 has a lethal dose in 60 µg/ml, low concentration is applied to induce the mutation, the range from 10 µg/ml, 15 µg/ml, 30 µg/ml, 45 µg/ml, and 50 µg/ml. L.casei FNCC 0090 is exposed to the low concentration from lowest to the highest concentration to induce the adaptation. Plasmid is isolated from the highest concentration culture which is 50 µg/ml by using modified alkali lysis method with the addition of lysozyme. The tetM gene is isolated by using PCR (Polymerase Chain Reaction) method, then PCR amplicon is purified and sequenced. Sequencing is done on both samples, wild type and mutant. Both sequences are compared and the mutations can be traced in the presence of nucleotides changes. The changing of the nucleotides means that the tetM gene is instable.

Keywords: L. casei FNCC 0090, probiotic, tetM, tetracycline

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Authors: Lal Hussain, Wajid Aziz, Imtiaz Ahmed Awan, Sharjeel Saeed

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Multiscale entropy analysis (MSE) is a useful technique recently developed to quantify the dynamics of physiological signals at different time scales. This study is aimed at investigating the electroencephalogram (EEG) signals to analyze the background activity of alcoholic and control subjects by inspecting various coarse-grained sequences formed at different time scales. EEG recordings of alcoholic and control subjects were taken from the publically available machine learning repository of University of California (UCI) acquired using 64 electrodes. The MSE analysis was performed on the EEG data acquired from all the electrodes of alcoholic and control subjects. Mann-Whitney rank test was used to find significant differences between the groups and result were considered statistically significant for p-values<0.05. The area under receiver operator curve was computed to find the degree separation between the groups. The mean ranks of MSE values at all the times scales for all electrodes were higher control subject as compared to alcoholic subjects. Higher mean ranks represent higher complexity and vice versa. The finding indicated that EEG signals acquired through electrodes C3, C4, F3, F7, F8, O1, O2, P3, T7 showed significant differences between alcoholic and control subjects at time scales 1 to 5. Moreover, all electrodes exhibit significance level at different time scales. Likewise, the highest accuracy and separation was obtained at the central region (C3 and C4), front polar regions (P3, O1, F3, F7, F8 and T8) while other electrodes such asFp1, Fp2, P4 and F4 shows no significant results.

Keywords: electroencephalogram (EEG), multiscale sample entropy (MSE), Mann-Whitney test (MMT), Receiver Operator Curve (ROC), complexity analysis

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Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

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Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

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Authors: Jayashree S. Bhat, Megha Mohan

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Play is any activity spontaneously chosen, inherently motivated, and personally directed. There is a wide range of literature and research supporting the concept of play in promoting healthy development in young children. Modern children are experiencing nurture that has more structure and adult involvement than previous generations and free, unstructured, and child directed play is under peril. Play behaviors serve as a reflection of a child’s cultural and ethnic background and can be an index of a child’s development. The influence and impact of culture in children’s play is diverse. The culturally variable dimensions of play includes the choice of objects, the involvement of specific play partners, the amount of child initiations of social pretend play with caregivers along with its the components, and sequences and specific themes involved during play. India is a country well known for its cultural diversity. In this study, a cross sectional study design with convenient sampling was adopted. The mother child free play interaction was video clipped at their residence among typically developing children between 12 to 24 months in an urban city from South India. It was ascertained that all the children were first born and mothers were unemployed belonging to middle socioeconomic status. The video clippings were coded and analysed using SPSS software version 17. The results revealed interesting behaviors demonstrated by the mother as well as the child during the play interaction. The results high light the need for focusing on the play behaviors of children during their developmental assessment, especially so for children with challenges.

Keywords: culture, free play, interaction, typically developing

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Authors: Lindy Valdez, Daryl Parker

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Introduction: There has been much research on academic achievement in elementary schools. Most of the research has been on school leadership. While research has focused on the role of leadership on school improvement, little research has examined what variables the top elementary schools have in common. To undertake school improvement, it is important to understand what factors the best schools share. The purpose of this study was to examine data of the “Best Elementary Schools in California,” based on academic achievement as rated by three prominent websites and determine if these schools had any common factors which were different than the statewide averages. The variables examined included access to subject matter specialists (physical education, art, and music), librarians, after school programs, class size, socioeconomic status, and diversity. The participants consisted of the top public elementary schools in California based on the websites i)https://www.niche.com/k12/search/best-schools/, ii)https://www.finder.com/best-schools-california,and iii)https://www.schooldigger.com/go/CA/schoolrank.aspx. The data for subject matter specialists (physical education, art, and music), librarians, after school programs, class size, socioeconomic status, and diversity were collected from these top schools and compared to California statewide averages. Results indicate that top public elementary schools in California have a high number of subject matter specialists that teach physical education, art, and music. These positions are on the decline in the average public elementary school in California, but the top schools have abundant access to these specialists. The physical education specialist has the highest statistically significant difference between the nationwide average and the top schools—librarians, and after school programs are also most commonly high in top public elementary schools in California. The high presence of these programs may be aiding academic achievement in less visible ways. Class size is small, socio-economic status is high, and diversity is low among top public elementary schools in California when compared to the statewide average public elementary schools in California. The single largest area of discrepancy was between physical education specialists in a top school and their state and nationwide averages. The socioeconomic status of schools and parents may be an underlining factor affecting several other variables. This affluence could explain how these schools were able to have access to subject matter specialists, after-school activities, and, therefore, more opportunities for physical activity and greater learning opportunities affecting academic achievement.

Keywords: academic achievement, elementary education, factors, schools

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Authors: Nazanin Amanat, Alison Tayler, Steve Whyard

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While chemical insecticides effectively control many insect pests, they also harm many non-target species. Double-stranded RNA (dsRNA) pesticides, in contrast, can be designed to target unique gene sequences and thus act in a species-specific manner. DsRNA insecticides do not, however, work equally well for all insects, and for some species that are considered refractory to dsRNA, a primary factor affecting efficacy is the relative ease by which dsRNA can enter a target cell’s cytoplasm. In this study, we are examining how different structured dsRNAs (linear, hairpin, and paperclip) can enter mosquito and lepidopteran cells, as they represent dsRNA-sensitive and refractory species, respectively. To determine how the dsRNAs enter the cells, we are using chemical inhibitors and RNA interference (RNAi)-mediated knockdown of key proteins associated with different endocytosis processes. Understanding how different dsRNAs enter cells will ultimately help in the design of molecules that overcome refractoriness to RNAi or develop resistance to dsRNA-based insecticides. To date, we have conducted chemical inhibitor experiments on both cell lines and have evidence that linear dsRNAs enter the cells using clathrin-mediated endocytosis, while the paperclip dsRNAs (pcRNAs) can enter both species’ cells in a clathrin-independent manner to induce RNAi. An alternative uptake mechanism for the pcRNAs has been tentatively identified, and the outcomes of our RNAi-mediated knockdown experiments, which should provide corroborative evidence of our initial findings, will be discussed.

Keywords: dsRNA, RNAi, uptake, insecticides, dipteran, lepidopteran

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Authors: Pratibha Srivastava, Ayyamperumal Jeyaprakash, Gary Steck, Jason Stanley, Leroy Whilby

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Exotic, invasive tephritid fruit flies (Diptera: Tephritidae) are a major threat to fruit and vegetable industries in the United States. The establishment of pest fruit fly in the agricultural industries and produce severe ecological and economic impacts on agricultural diversification and trade. Detection and identification of these agricultural pests in a timely manner will facilitate the possibility of eradication from newly invaded areas. Identification of larval stages to species level is difficult, but is required to determine pest loads and their pathways into the United States. The aim of this study is the New World genus, Anastrepha which includes pests of major economic importance. Mitochondrial cytochrome c oxidase I (COI) gene sequences were amplified from Anastrepha fraterculus specimens collected from South America (Ecuador and Peru). Phylogenetic analysis was performed to characterize the Anastrepha fraterculus complex at a molecular level. During phylogenetics analysis numerous nuclear mitochondrial pseudogenes (numts) were discovered in different specimens. The numts are nonfunctional copies of the mtDNA present in the nucleus and are easily coamplified with the mitochondrial COI gene copy by using conserved universal primers. This is problematic for DNA Barcoding, which attempts to characterize all living organisms by using the COI gene. This study is significant for national quarantine use, as morphological diagnostics to separate larvae of the various members remain poorly developed.

Keywords: tephritid, Anastrepha fraterculus, COI, numts

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Authors: Foluke E. Sola-Ojo, Ibraheem A. Abubakar, Semiu F. Bello, Isiaka H. Fatima, Sule Bisola, Adesina M. Olusegun, Adeniyi C. Adeola

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The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required.

Keywords: Nigeria pigeon, COI, genetic diversity, genetic variation, conservation

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Authors: Zhang Lei, Zhao Qingrong, Wang Chen, Zhang Sufang, Zhang Hanguo

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Larch is the main afforestation and timber tree species in Northeast China, and drought is one of the main factors limiting the growth of Larch and other organisms in Northeast China. In order to further explore the mechanism of Larch drought resistance, PEG was used to simulate drought stress. The full-length sequencing of Larch embryogenic callus under PEG simulated drought stress was carried out by combining Illumina-Hiseq and SMRT-seq. A total of 20.3Gb clean reads and 786492 CCS reads were obtained from the second and third generation sequencing. The de-redundant transcript sequences were predicted by lncRNA, 2083 lncRNAs were obtained, and the target genes were predicted, and a total of 2712 target genes were obtained. The de-redundant transcripts were further screened, and 1654 differentially expressed genes (DEGs )were obtained. Among them, different DEGs respond to drought stress in different ways, such as oxidation-reduction process, starch and sucrose metabolism, plant hormone pathway, carbon metabolism, lignin catabolic/biosynthetic process and so on. This study provides basic full-length sequencing data for the study of Larch drought resistance, and excavates a large number of DEGs in response to drought stress, which helps us to further understand the function of Larch drought resistance genes and provides a reference for in-depth analysis of the molecular mechanism of Larch drought resistance.

Keywords: larch, drought stress, full-length transcriptome sequencing, differentially expressed genes

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Aymen Arfaoui, Abdelkader Soumaya, Ali Kadri, Noureddine Ben Ayed

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The Tunisian dorsal backland is located on the Eastern Atlas side of the Maghrebides (North Africa). The analysis of collected field data in the Rouas and Ruissate mountains area allowed us to develop new interpretations for its structural framework. Our kinematic analysis of fault-slip data reveals the presence of an extensional tectonic regime with NE-SW Shmin, characterizing the Mesozoic times. In addition, geophysical data shows that the synsedimentary normal faulting is accompanied by thickness variations of sedimentary sequences and Triassic salt movements. Then, after the Eurasia-Africa plate’s convergence during the Eocene, compressive tectonic deformations affected and reactivated the inherited NW-SE and N-S trending normal faults as dextral strike-slip and reverse faults, respectively. This tectonic inversion, with compression to the transpressional tectonic regime and NW-SE SHmax, continued during the successive shortening phases of the upper Miocene and Quaternary. The geometry of the Rouas and Ruissate belt is expressed as a fault propagation fold, affecting Jurassic and Cretaceous deposits. The Triassic evaporates constitute the decollement levels, facilitating the detachment and deformation of the sedimentary cover. The backland of this thrust belt is defined by NNE-SSW trending imbrication features that are controlled by a basement N-S fault.

Keywords: Tunisian dorsal backland, fault slip data; synsedimentary faults, tectonic inversion, decollement level, fault propagation fold

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Authors: Y. Kumru, K. Enhos, H. Köymen

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In this paper, we report the experimental results on using complementary Golay coded signals at 7.5 MHz to detect breast microcalcifications of 50 µm size. Simulations using complementary Golay coded signals show perfect consistence with the experimental results, confirming the improved signal to noise ratio for complementary Golay coded signals. For improving the success on detecting the microcalcifications, orthogonal complementary Golay sequences having cross-correlation for minimum interference are used as coded signals and compared to tone burst pulse of equal energy in terms of resolution under weak signal conditions. The measurements are conducted using an experimental ultrasound research scanner, Digital Phased Array System (DiPhAS) having 256 channels, a phased array transducer with 7.5 MHz center frequency and the results obtained through experiments are validated by Field-II simulation software. In addition, to investigate the superiority of coded signals in terms of resolution, multipurpose tissue equivalent phantom containing series of monofilament nylon targets, 240 µm in diameter, and cyst-like objects with attenuation of 0.5 dB/[MHz x cm] is used in the experiments. We obtained ultrasound images of monofilament nylon targets for the evaluation of resolution. Simulation and experimental results show that it is possible to differentiate closely positioned small targets with increased success by using coded excitation in very weak signal conditions.

Keywords: coded excitation, complementary golay codes, DiPhAS, medical ultrasound

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Authors: Nataliya L. Ogurechnikova

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The paper aims to clarify the function of articles in the English speech and specify their place and role in the English language, taking into account the use of articles for delimitation of speech. A focus of the paper is the use of the definite and the indefinite articles with different types of noun phrases which comprise either one noun with or without attributes, such as the King, the Queen, the Lion, the Unicorn, a dimple, a smile, a new language, an unknown dialect, or several nouns with or without attributes, such as the King and Queen of Hearts, the Lion and Unicorn, a dimple or smile, a completely isolated language or dialect. It is stated that the function of delimitation is related to perception: the number of speech units in a text correlates with the way the speaker perceives and segments the denotation. The two following combinations of words the house and garden and the house and the garden contain different numbers of speech units, one and two respectively, and reveal two different perception modes which correspond to the use of the definite article in the examples given. Thus, the function of delimitation is twofold, it is related to perception and cognition, on the one hand, and, on the other hand, to grammar, if the subject of grammar is the structure of speech. Analysis of speech units in the paper is not limited by noun phrases and is amplified by discussion of peripheral phenomena which are nevertheless important because they enable to qualify articles as a syntactic phenomenon whereas they are not infrequently described in terms of noun morphology. With this regard attention is given to the history of linguistic studies, specifically to the description of English articles by Niels Haislund, a disciple of Otto Jespersen. A discrepancy is noted between the initial plan of Jespersen who intended to describe articles as a syntactic phenomenon in ‘A Modern English Grammar on Historical Principles’ and the interpretation of articles in terms of noun morphology, finally given by Haislund. Another issue of the paper is correlation between description and denotation, being a traditional aspect of linguistic studies focused on articles. An overview of relevant studies, given in the paper, goes back to the works of G. Frege, which gave rise to a series of scientific works where the meaning of articles was described within the scope of logical semantics. Correlation between denotation and description is treated in the paper as the meaning of article, i.e. a component in its semantic structure, which differs from the function of delimitation and is similar to the meaning of other quantifiers. The paper further explains why the relation between description and denotation, i.e. the meaning of English article, is irrelevant for noun morphology and has nothing to do with nominal categories of the English language.

Keywords: delimitation of speech, denotation, description, perception, speech units, syntax

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Authors: Eun-Taek Sin, Hyun-Ju Jang, Chang Geun Song, Yong-Sik Han

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Due to the climate change, the coastal urban area repeatedly suffers from the loss of property and life by flooding. There are three main causes of inland submergence. First, when heavy rain with high intensity occurs, the water quantity in inland cannot be drained into rivers by increase in impervious surface of the land development and defect of the pump, storm sewer. Second, river inundation occurs then water surface level surpasses the top of levee. Finally, Coastal inundation occurs due to rising sea water. However, previous studies ignored the complex mechanism of flooding, and showed discrepancy and inadequacy due to linear summation of each analysis result. In this study, inland flooding and river inundation were analyzed together by HDM-2D model. Petrov-Galerkin stabilizing method and flux-blocking algorithm were applied to simulate the inland flooding. In addition, sink/source terms with exponentially growth rate attribute were added to the shallow water equations to include the inland flooding analysis module. The applications of developed model gave satisfactory results, and provided accurate prediction in comprehensive flooding analysis. The applications of developed model gave satisfactory results, and provided accurate prediction in comprehensive flooding analysis. To consider the coastal surge, another module was developed by adding seawater to the existing Inland Flooding-River Inundation binding module for comprehensive flooding analysis. Based on the combined modules, the Coastal Inundation – Inland & River Flow Interface was simulated by inputting the flow rate and depth data in artificial flume. Accordingly, it was able to analyze the flood patterns of coastal cities over time. This study is expected to help identify the complex causes of flooding in coastal areas where complex flooding occurs, and assist in analyzing damage to coastal cities. Acknowledgements—This research was supported by a grant ‘Development of the Evaluation Technology for Complex Causes of Inundation Vulnerability and the Response Plans in Coastal Urban Areas for Adaptation to Climate Change’ [MPSS-NH-2015-77] from the Natural Hazard Mitigation Research Group, Ministry of Public Safety and Security of Korea.

Keywords: flooding analysis, river inundation, inland flooding, 2D hydrodynamic model

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Authors: Muhammad Fiaz Qamar, Ahmad Faraz, Muhammad Arfan Zaman, Kazim Ali, Waleed Akram

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Babesiosis is reflected as the most important disease of cattle that are transmitted by arthropods. In Pakistan, its prevalence is up to 29% in the cattle and buffalo population in different regions. Cattle show a long lasting and durable immunity by giving an infection of B.bovis, B. bigemina, or Babesiadivergens. this is used in cattle to immunize them in a few countries as anti-babesiosis vaccine. Development of frozen vaccine allows for complete testing after production of each batch, However, once thawed, its reduced its shelf life, frozen vaccines are more difficult to transport as well as expensive to produce as compared to chilled vaccine. The contamination of blood derived vaccine has the potential risk that makes pre-production and post-production quality control necessary. For the trail master seed production of whole blood frozen bivalent Babesia(Babesiabovis and Babesiabigemina), 100 blood samples of Babesial positive suspected cattle was taken and processed for separation microscopic detection and rectification by PCR. Vaccine passages were done to reduce the parasitaemiasis in live calves. After 8 passages, parasitemia of Babesia reduced from 80% to 15%. Infected donor calf’s blood was taken by jugular cannulation by using preservative free lithium heparin as an anticoagulant (5 International Units IU heparin/ml blood). In lab, parasite containing blood was mixed in equal volumes with 3 M glycerol in PBS supplemented with 5 mM glucose (final concentration of glycerol 1.5 M) at 37°C. The mixture was then equilibrized at 37°C for 30 minutes and were dispensed in required containers (e.g., 5 ml cryovials).

Keywords: distribution, babesia, primer sequences, PCV

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Authors: Mun Yee Chan, Sin Ming Goh, Lisa Gaik Ai Ong

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Approximately 10,000 different types of dyes and pigments are being used in various industrial applications yearly, which include the textile and printing industries. However, these dyes are difficult to degrade naturally once they enter the aquatic system. Their high persistency in natural environment poses a potential health hazard to all form of life. Hence, there is a need for alternative dye removal strategy in the environment via bioremediation. In this study, fungi laccase is investigated via commercial agar dyes plates and submerged fermentation to explore the application of fungi laccase in textile dye wastewater treatment. Two locally isolated basidiomycetes were screened for laccase activity using media added with commercial dyes such as 2, 2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS), guaiacol and Remazol Brillant Blue R (RBBR). Isolate TBB3 (1.70±0.06) and EL2 (1.78±0.08) gave the highest results for ABTS plates with the appearance of greenish halo on around the isolates. Submerged fermentation performed on Isolate TBB3 with the productivity 3.9067 U/ml/day, whereas the laccase activity for Isolate EL2 was much lower (0.2097 U/ml/day). As isolate TBB3 showed higher laccase production, it was subjected to molecular characterization by DNA isolation, PCR amplification and sequencing of ITS region of nuclear ribosomal DNA. After being compared with other sequences in National Center for Biotechnology Information (NCBI database), isolate TBB3 is probably from species Trametes hirsutei. Further research work can be performed on this isolate by upscale the production of laccase in order to meet the demands of the requirement for higher enzyme titer for the bioremediation of textile dyes.

Keywords: bioremediation, dyes, fermentation, laccase

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Authors: Sofia Hartati

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This research is aimed at describing training in early childhood education program empirically, describing teachers ability to plan lessons empirically, and acquiring empirical data as well as analyzing the influence of guided and independent training toward teachers competence in planning early childhood learning program. The method used is an experiment. It collected data with a population of 76 early childhood educators in Tunjung Teja Sub District area through random sampling technique and grouped into two namely 38 people in an experiment class and 38 people in a controlled class. The technique used for data collections is a test. The result of the research shows that there is a significant influence between training for guided educators toward Teachers Ability toward Planning Early Childhood Learning Program. Guided training has been proven to improve the ability to comprehend planning a learning program. The ability to comprehend planning a learning program owned by teachers of early childhood program comprises of 1) determining the characteristics and competence of students prior to learning; 2) formulating the objective of the learning; 3) selecting materials and its sequences; 4) selecting teaching methods; 5) determining the means or learning media; 6) selecting evaluation strategy as a part of teachers pedagogic competence. The result of this research describes a difference in the competence level of teachers who have joined guided training which is relatively higher than the teachers who joined the independent training. Guided training is one of an effective way to improve the knowledge and competence of early childhood educators.

Keywords: competence, planning, teachers, training

Procedia PDF Downloads 241

Authors: Hedi Dghim, Ahmed El-Naggar, Istvan Erlich

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Power electronic converters are being introduced in low voltage (LV) grids at an increasingly rapid rate due to the growing adoption of power electronic-based home appliances in residential grid. Photovoltaic (PV) systems are considered one of the potential installed renewable energy sources in distribution power systems. This trend has led to high distortion in the supply voltage which consequently produces harmonic currents in the network and causes an inherent voltage unbalance. In order to investigate the effect of harmonic distortions, a case study of a typical LV grid configuration with high penetration of 3-phase and 1-phase rooftop mounted PV from southern Germany was first considered. Electromagnetic transient (EMT) simulations were then carried out under the MATLAB/Simulink environment which contain detailed models for power electronic-based loads, ohmic-based loads as well as 1- and 3-phase PV. Note that, the switching patterns of the power electronic circuits were considered in this study. Measurements were eventually performed to analyze the distortion levels when PV operating under different solar irradiance. The characteristics of the load-side harmonic impedances were analyzed, and their harmonic contributions were evaluated for different distortion levels. The effect of the high penetration of PV on the harmonic distortion of both positive and negative sequences was also investigated. The simulation results are presented based on case studies. The current distortion levels are in agreement with relevant standards, otherwise the Total Harmonic Distortion (THD) increases under low PV power generation due to its inverse relation with the fundamental current.

Keywords: harmonic distortion analysis, power quality, PV systems, residential distribution system

Procedia PDF Downloads 241

Authors: Muhammad Shahzad Iqbal, Zobia Sarwar, Salah-ud-Din

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Tomato spotted wilt virus (TSWV) belongs to the genus Tospoviruses (family Bunyaviridae). It is one of the most devastating pathogens of tomato (Solanum Lycopersicum) and heavily damages the crop yield each year around the globe. In this study, we retrieved 329 mature miRNA sequences from two microRNA databases (miRBase and miRSoldb) and checked the putative target sites in the downloaded-genome sequence of TSWV. A consensus of three miRNA target prediction tools (RNA22, miRanda and psRNATarget) was used to screen the false-positive microRNAs targeting sites in the TSWV genome. These tools calculated different target sites by calculating minimum free energy (mfe), site-complementarity, minimum folding energy and other microRNA-mRNA binding factors. R language was used to plot the predicted target-site data. All the genes having possible target sites for different miRNAs were screened by building a consensus table. Out of these 329 mature miRNAs predicted by three algorithms, only eight miRNAs met all the criteria/threshold specifications. MC-Fold and MC-Sym were used to predict three-dimensional structures of miRNAs and further analyzed in USCF chimera to visualize the structural and conformational changes before and after microRNA-mRNA interactions. The results of the current study show that the predicted eight miRNAs could further be evaluated by in vitro experiments to develop TSWV-resistant transgenic tomato plants in the future.

Keywords: tomato spotted wild virus (TSWV), Solanum lycopersicum, plant virus, miRNAs, microRNA target prediction, mRNA

Procedia PDF Downloads 124

Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

Procedia PDF Downloads 566

Authors: Z. Okay, M. Kalkan Erdoğan, M. Şahin, M. Saçak

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Polyacrylonitrile (PAN) is one of the most common and cheap fiber-forming polymers because of its high strength and high abrasion resistance properties. The result of alkaline hydrolysis of PAN fiber could be formed the products with conjugated sequences of –C=N–, acrylamide, sodium acrylate, and amidine. In this study, PAN fiber was hydrolyzed in a solution of sodium hydroxide, and this hydrolyzed PAN (HPAN) fiber was used to prepare conductive composite fiber by silver particles. The electrically conductive PAN fiber has the usage potential to produce variety of materials such as antistatic materials, life jackets and static charge reducing products. We monitored the change in the weight loss values of the PAN fiber with hydrolysis time. It was observed that a 60 % of weight loss was obtained in the fiber weight after 7h hydrolysis under the investigated conditions, but the fiber lost its fibrous structure. The hydrolysis time of 5h was found to be suitable in terms of preserving its fibrous structure. The change in the conductivity values of the composite with the preparation conditions such as hydrolysis time, silver ion concentration was studied. PAN fibers with different degrees of hydrolysis were treated with aqueous solutions containing different concentrations of silver ions by continuous stirring at 20 oC for 30 min, and the composite having the maximum conductivity of 2 S/cm could be prepared. The antibacterial property of the conductive HPAN fibers participated silver was also investigated. While the hydrolysis of the PAN fiber was characterized with FTIR and SEM techniques, the silver reduction process of the HPAN fiber was investigated with SEM and TGA-DTA techniques. The SEM micrographs showed that the surface of HPAN fiber was rougher and much more corroded than that of the PAN fiber. Composite, Conducting polymer, Fiber, Polyacrylonitrile.

Keywords: composite, conducting polymer, fiber, polyacrylonitrile

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Authors: Keyur Raval, Steffen Krohn, Bruno Moerschbacher

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Chitin, the biopolymer of the N-acetylglucosamine, is the most abundant biopolymer on the planet after cellulose. Industrially, chitin is isolated and purified from the shell residues of shrimps. A deacetylated derivative of chitin i.e. chitosan has more market value and applications owing to it solubility and overall cationic charge compared to the parent polymer. This deacetylation on an industrial scale is performed chemically using alkalis like sodium hydroxide. This reaction not only is hazardous to the environment owing to negative impact on the marine ecosystem. A greener option to this process is the enzymatic process. In nature, the naïve chitin is converted to chitosan by chitin deacetylase (CDA). This enzymatic conversion on the industrial scale is however hampered by the crystallinity of chitin. Thus, this enzymatic action requires the substrate i.e. chitin to be soluble which is technically difficult and an energy consuming process. We in this project wanted to address this shortcoming of CDA. In lieu of this, we have modeled a fusion protein with CDA and an auxiliary protein. The main interest being to increase the accessibility of the enzyme towards crystalline chitin. A similar fusion work with chitinases had improved the catalytic ability towards insoluble chitin. In the first step, suitable partners were searched through the protein data bank (PDB) wherein the domain architecture were sought. The next step was to create the models of the fused product using various in silico techniques. The models were created by MODELLER and evaluated for properties such as the energy or the impairment of the binding sites. A fusion PCR has been designed based on the linker sequences generated by MODELLER and would be tested for its activity towards insoluble chitin.

Keywords: chitin deacetylase, modeling, chitin binding domain, chitinases

Procedia PDF Downloads 221

Authors: H. Aldewachi, M. Hines, M. McCulloch, N. Woodroofe, P. Gardiner

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DPP-IV is an enzyme whose expression is affected in a variety of diseases, therefore, has been identified as possible diagnostic or prognostic marker for various tumours, immunological, inflammatory, neuroendocrine, and viral diseases. Recently, DPP-IV enzyme has been identified as a novel target for type II diabetes treatment where the enzyme is involved. There is, therefore, a need to develop sensitive and specific methods that can be easily deployed for the screening of the enzyme either as a tool for drug screening or disease marker in biological samples. A variety of assays have been introduced for the determination of DPP-IV enzyme activity using chromogenic and fluorogenic substrates, nevertheless these assays either lack the required sensitivity especially in inhibited enzyme samples or displays low water solubility implying difficulty for use in vivo samples in addition to labour and time-consuming sample preparation. In this study, novel strategies based on exploiting the high extinction coefficient of gold nanoparticles (GNPs) are investigated in order to develop fast, specific and reliable enzymatic assay by investigating synthetic peptide sequences containing a DPP IV cleavage site and coupling them to GNPs. The DPP IV could be detected by colorimetric response of peptide capped GNPs (P-GNPS) that could be monitored by a UV-visible spectrophotometer or even naked eyes, and the detection limit could reach 0.01 unit/ml. The P-GNPs, when subjected to DPP IV, showed excellent selectivity compared to other proteins (thrombin and human serum albumin) , which led to prominent colour change. This provided a simple and effective colorimetric sensor for on-site and real-time detection of DPP IV.

Keywords: gold nanoparticles, synthetic peptides, colorimetric detection, DPP-IV enzyme

Procedia PDF Downloads 281

Authors: Houda Khaled, Frederic Boulvain, Fredj Chaabani

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This paper focuses on the sedimentological and mineralogical studies of Aptian series outcrops in the Serdj and Bellouta Mountain situated in north-central Tunisia. In the Serdj Mountain, the Aptian series is about 590 meters thick and it is defined by tow formations corresponding respectively to the Sidi Hamada formation (Barremian-Gragasian) and the Serdj formation (Middle Gragasian-Late Clansaysian). This later is consisting of five limestones sequences separated by marly levels limestones associated to some siltstones bed. The Bellouta section is especially composed of carbonate rocks and it is attributed to the Middle Gragasian - Late Clansaysian. These sections are studied in detail regarding lithology, micropaleontology, microfacies, magnetic susceptibility and mineralogical composition in order to provide new insights into the paleoenvironmental evolution and paleoclimatological implications during Aptian. The following facies associations representing different ramp palaeoenvironments have been identified: mudstone-wackestone outer ramp facies; skeletal grainstone-packstone mid-ramp facies, packstone-grainstone inner-ramp facies which include a variety of organisms such as ooliths, rudists ostracods associated to athor bioclats. The coastal facies is especially defined by a mudstone -wackestone texture coastal rich with miliolidea and orbitolines. The magnetic susceptibility (Xin) of all samples was compared with the lithological and microfacies variation. The MS curves show that the high values are correlated with the distal facies and the low values are registred in the coastal environment. The X-ray diffractometer analysis show the presence of kaolinite and illite.

Keywords: Aptian, Serdj formation, mineralogy, petrography

Procedia PDF Downloads 168

Authors: Danzhao Cheng, Eugene Ch'ng

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Virtual Reality technologies can reconstruct cultural heritage objects and sites to a level of realism. Concentrating mostly on documenting authentic data and accurate representations of tangible contents, current virtual heritage is limited to accumulating visually presented objects. Such constructions, however, are fragmentary and may not convey the inherent significance of heritage in a meaningful way. In order to contextualise fragmentary historical contents where history can be told, a strategy is to create a guided narrative via role-playing. Such an approach can strengthen the logical connections of cultural elements and facilitate creative synthesis within the virtual world. This project successfully reconstructed the Ningbo Sanjiangkou VR site in Yuan Dynasty combining VR technology and role-play game approach. The results with 80 pairs of participants suggest that VR role-playing can be beneficial in a number of ways. Firstly, it creates thematic interactivity which encourages users to explore the virtual heritage in a more entertaining way with task-oriented goals. Secondly, the experience becomes highly engaging since users can interpret a historical context through the perspective of specific roles that exist in past societies. Thirdly, personalisation allows open-ended sequences of the expedition, reinforcing user’s acquisition of procedural knowledge relative to the cultural domain. To sum up, role-playing in VR poses great potential for experiential learning as it allows users to interpret a historical context in a more entertaining way.

Keywords: experiential learning, maritime silk road, role-playing, virtual heritage, virtual reality

Procedia PDF Downloads 135