Search results for: electron-hole pairs

Authors: Anna Słupik, Patryk Wąsowski, Anna Mosiołek, Dariusz Białoszewski

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Introduction: Kinesiology Taping is one of the most popular techniques used for treatment and supporting physiological processes in sports medicine and physiotherapy. Often it is used to sensorimotor skills of lower limbs by athletes. The aim of the study was to determine the effect of the application of muscle Kinesiology Taping to feel the position setting in motion the joint active. Material and methods: The study involved 50 healthy people between 18 and 30 years of age, 30 men and 20 women (mean age 23.24 years). The participants were divided into two groups. The study group was qualified for Kinesiology Taping application (muscle application, type Y, for quadriceps femoris muscle), while the remaining people used the application made of plaster (placebo group). Testing was performed prior to applying taping, with the applied application (after 30 minutes), then 24 hours after wearing, and after removing the tape. Each evaluated joint position sense - Error of Active Reproduction of Joint Position. Results: The survey revealed no significant differences in measurement between the study group and the placebo group (p> 0.05). No significant differences in time taking into account all four measurements in the group with the applied CT application, which was supported by pairs (p> 0.05). Also in the placebo group showed no significant differences over time (p> 0.05). There was no significant difference between the errors committed in the direction of flexion and extension. Conclusions: 1. Application muscle Kinesiology Taping had no significant effect on the knee joint proprioception. Its use in order to improve sensorimotor seems therefore unjustified. 2. There are no differences between applications Kinesiology Taping and placebo indicates that the clinical effect of stretch tape is minimal or absent. 3. The results are the basis for the continuation of prospective, randomized trials of numerous and study group.

Keywords: joint position sense, kinesiology taping, knee joint, proprioception

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Authors: Srikrishna Pramanik, Sree Chithra, Saurabh Rai, Sameeksha Agrawal, Debanggana Shil, Saptarshi Mukherjee

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The understanding of interactions between organic chromophores and biologically useful luminescent noble metal nanoclusters (NCs) leading to an energy transfer process that has applications in light-harvesting materials is still in its nascent stage. This work describes a photoluminescent supramolecular assembly, made in two stages, employing an energy transfer process between silver (Ag) NCs as the donor and a host-guest system as the acceptor that can find potential applications in diverse fields. Initially, we explored the host-guest chemistry between a cationic guest, Ethidium Bromide and the anionic host Cucurbit[8]uril using spectroscopic and calorimetric techniques to decipher their interaction mechanism in modulating photophysical properties of the chromophore. Next, we synthesized a series of blue-emitting AgNCs using different templates such as protein, peptides, and cyclodextrin. The as-prepared AgNCs were characterized by various spectroscopic techniques. We have established that these AgNCs can be employed as donors in the FRET process with the above acceptor for FRET-based emission color tuning. Our in-depth studies revealed that surface ligands play a key role in modulating FRET efficiency. Overall, by employing a non-covalent strategy, we have tried to develop FRET pairs using blue-emitting NCs and a host-guest complex, which could find potential applications in constructing advanced white light-emitting, anti-counterfeiting materials, and developing biosensors.

Keywords: absorption spectroscopy, cavities, energy transfer, fluorescence, fluorescence resonance energy transfer

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Authors: Thedy Yogasara, Fredy Agus

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In designing a product, it is currently crucial to focus not only on the product’s usability based on performance measures, but also on user experience (UX) that includes pragmatic and hedonic aspects of product use. These aspects play a significant role in fulfillment of user needs, both functionally and psychologically. Pragmatic quality refers to as product’s perceived ability to support the fulfillment of behavioral goals. It is closely linked to functionality and usability of the product. In contrast, hedonic quality is product’s perceived ability to support the fulfillment of psychological needs. Hedonic quality relates to the pleasure of ownership and use of the product, including stimulation for personal development and communication of user’s identity to others through the product. This study evaluates the pragmatic and hedonic aspects of gaming mice G600 and Razer Krait using AttrakDiff tool to create an improved design that is able to generate positive UX. AttrakDiff is a method that measures pragmatic and hedonic scores of a product with a scale between -3 to +3 through four attributes (i.e. Pragmatic Quality, Hedonic Quality-Identification, Hedonic Quality-Stimulation, and Attractiveness), represented by 28 pairs of opposite words. Based on data gathered from 15 participants, it is identified that gaming mouse G600 needs to be redesigned because of its low grades (pragmatic score: -0.838, hedonic score: 1, attractiveness score: 0.771). The redesign process focuses on the attributes with poor scores and takes into account improvement suggestions collected from interview with the participants. The redesigned mouse G600 is evaluated using the previous method. The result shows higher scores in pragmatic quality (1.929), hedonic quality (1.703), and attractiveness (1.667), indicating that the redesigned mouse is more capable of creating pleasurable experience of product use.

Keywords: AttrakDiff, hedonic aspect, pragmatic aspect, product design, user experience

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Authors: Annet Namusoke, Annet Namayanja, Peter Wasswa, Shakirah Nampijja

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Common bean cultivar G2333 which offers broad resistance for anthracnose has been widely used as a source of resistance in breeding for anthracnose resistance. The cultivar is pyramided with three genes namely CO-4, CO-5 and CO-7 and of these three genes, the CO-4 gene has been found to offer the broadest resistance. The main aim of this work was to identify and validate easily assayable PCR based co-dominant molecular markers for selection of the CO-4 gene in segregating populations derived from crosses of G2333 with RWR 1946 and RWR 2075, two commercial Andean cultivars highly susceptible to anthracnose. Marker sequences for the study were obtained by blasting the sequence of the COK-4 gene in the Phaseolus gene database. Primer sequence pairs that were not provided from the Phaseolus gene database were designed by the use of Primer3 software. PCR conditions were optimized and the PCR products were run on 6% HPAGE gel. Results of the polymorphism test indicated that out of 18 identified markers, only two markers namely BM588 and BM211 behaved co-dominantly. Phenotypic evaluation for reaction to anthracnose disease was done by inoculating 21days old seedlings of three parents, F1 and F2 populations with race 7 of Colletotrichum lindemuthianum in the humid chamber. DNA testing of the BM588 marker onto the F2 segregating population of the crosses RWR 1946 x G 2333 and RWR 2075 x G2333 further revealed that the marker BM588 co-segregated with disease resistance with co-dominance of two alleles of 200bp and 400bp, fitting the expected segregation ratio of 1:2:1. The BM588 marker was significantly associated with disease resistance and gave promising results for marker assisted selection of the CO-4 gene in the breeding lines. Activities to validate the BM211 marker are also underway.

Keywords: codominant, Colletotrichum lindemuthianum, MAS, Phaseolus vulgaris

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Authors: Nkereke M. Essien

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The intention of this paper is to examine stress in the Educated Nigerian Accent of English (ENAE) with the aim of analyzing stress and rhythmic patterns of Nigerian English. Our aim also is to isolate differences and similarities in the stress patterns studied and also know what forms the accent of these Educated Nigerian English (ENE) which marks them off from other groups or English’s of the world, to ascertain and characterize it and to provide documented evidence for its existence. Nigerian stress and rhythmic patterns are significantly different from the British English stress and rhythmic patterns consequently, the educated Nigerian English (ENE) features more stressed syllables than the native speakers’ varieties. The excessive stressed of syllables causes a contiguous “Ss” in the rhythmic flow of ENE, and this brings about a “jerky rhythm’ which distorts communication. To ascertain this claim, ten (10) Nigerian speakers who are educated in the English Language were selected by a stratified Random Sampling technique from two Federal Universities in Nigeria. This classification belongs to the education to the educated class or standard variety. Their performance was compared to that of a Briton (control). The Metrical system of analysis was used. The respondents were made to read some words and utterance which was recorded and analyzed perceptually, statistically and acoustically using the one-way Analysis of Variance (ANOVA). The Turky-Kramer Post Hoc test, the Wilcoxon Matched Pairs Signed Ranks test, and the Praat analysis software were used in the analysis. It was revealed from our findings that the Educated Nigerian English speakers feature more stressed syllables in their productions by spending more time in pronouncing stressed syllables and sometimes lesser time in pronouncing the unstressed syllables. Their overall tempo was faster. The ENE speakers used tone to mark prominence while the native speaker used stress to mark pronounce, typified by the control. We concluded that the stress pattern of the ENE speakers was significantly different from the native speaker’s variety represented by the control’s performance.

Keywords: accent, Nigerian English, rhythm, stress

Procedia PDF Downloads 198

Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: Ayse Ozbil, Gorsev Argin, Demet Yesiltepe

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Data for this cross-sectional study were drawn from questionnaires conducted in 10 elementary schools (1000 students, ages 12-14) located in Istanbul, Turkey. School environments (1600 meter buffers around the school) were evaluated through GIS-based land-use data (parcel level land use density) and street-level topography. Street networks within the same buffers were evaluated by using angular segment analysis (Integration and Choice) implemented in Depthmap as well as two segment-based connectivity measures, namely Metric and Directional Reach implemented in GIS. Segment Angular Integration measures how accessible each space from all the others within the radius using the least angle measure of distance. Segment Angular Choice which measures how many times a space is selected on journeys between all pairs of origins and destinations. Metric Reach captures the density of streets and street connections accessible from each individual road segment. Directional Reach measures the extent to which the entire street network is accessible with few direction changes. In addition, socio-economic characteristics (annual income, car ownership, education-level) of parents, obtained from parental questionnaires, were also included in the analysis. It is shown that surrounding street network configuration is strongly associated with both walk-mode shares and average walking distances to/from schools when controlling for parental socio-demographic attributes as well as land-use compositions and topographic features in school environments. More specifically, findings suggest that the scale at which urban form has an impact on pedestrian travel is considerably larger than a few blocks around the school.

Keywords: Istanbul, street network layout, urban form, walking to/from school

Procedia PDF Downloads 379

Authors: Sarinra Thongmee, Adithep Mingsuan, Chanyapak Polkhet, Supattra Wongsuk, Krittaphon Prakobsaeng

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The purposes of this research and development was to develop and evaluation of clinical nursing practice guideline (CNPG) for the prevention of infection during intubation in patient withsuspected or confirmedCOVID-19 patient. This study was developed by using the evidence based practice model of Soukup (2000) as a conceptual framework. The study consisted of 4 steps: 1) situational analysis of intubation service in patients with confirmed COVID-19, 2) development the CNPG, 3) apply the NPG to trial, and 4) evaluation of the NPG. Thesample consisted of 52 nurse anesthetists and 25 infected or suspected COVID-19 patients. The research instrument consisted of 1) CNPG, 2) the nurses anesthetist opinion questionnaire to the guideline, 3) the evaluation practice form, and 4) the nurse anesthetist knowledge test on nursing care of patients infected with COVID-19. Data were analyzed by using descriptive statistics, and Wilcoxon matched-pairs signed rank test. The results found that this developed NPG consists of 4 sections: 1) NPG for Preventing Airborne Infection Prevention2) preparation of anesthetic and intubation equipments 3) roles and duties of the intubation team 4) guidelines for intubation in suspected or confirmed COVID-19patients. The result found that 1) provider: using NPG in providers revealed that nurse anesthetist had higher mean of knowledge scores than before using NPG statistically significant at the 0.05 level (p<0.01) and able to follow the NPG 100% in all activities. The anesthetic team was not infected with COVID-19from intubation outside operating room.2) Client: the patient was safe, no complications from intubation. Summary CNPG to prevent infection in intubation of suspected or confirmedCOVID-19 patient was appropriate and applicable to practice.

Keywords: nursing practice guideline, prevention of infection, endotracheal intubation, COVID-19

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Authors: Meryem Imane Babaghayou, Abdelhafidi Asma

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This study deals with the ageing of Blown extruded films of low-density polyethylene (LDPE), used for greenhouse covering. The LDPE have been subjected to climatic ageing in a sub-Saharan facility at Laghouat (Algeria) with direct exposure to sun. The microstructural changes in the films were analyzed by IRFT for different states of ageing. The mechanical characterization was performed on a uniaxial tensile apparatus. The mechanical properties such as Young's modulus, strain at break, and stress at break have been followed for different states of exposure time (0 to 6 months). The Climatic ageing of LDPE films shows the effect of ageing on the microstructural Plan which leads to: i) To an oxidation of the molecular chains. ii) To the formation of cross-linkings and breaking chains, which both of them are responsible for the mechanical behavior’s modifications of the material. Cross-links are in favor of strengthening of the mechanical properties at break (the increase of σr and εr). In other side, the chains breaking leads to a decrease of these properties. The increase in the Young's modulus also seems to be related to those structural changes since the cross-links increase the average molecular weight. Branchings and tangles are favorable pairs for the ductile nature of the material. And in other side, the chains breaking reduces the average molecular weight and therefore promotes the stiffening (following to morphological changes) so the material becomes fragile. The post-mortem analysis of the samples shows that the mechanical stress has an effect on the molecular structure of the material. Although if quantitatively the concentrations of different chemical species exchanges, from a quantitative point of view only the unsaturations raises the polemics of a possible microstructural modification induced by mechanical stress applied during the tensile test. Also, we recommend a more rigorous analysis with other means of investigation.

Keywords: low-density polyethylene, ageing, mechanical properties, IRTF

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Authors: P. Moskal, T. Bednarski, P. Bialas, E. Czerwinski, A. Gajos, A. Gruntowski, D. Kaminska, L. Kaplon, G. Korcyl, P. Kowalski, T. Kozik, W. Krzemien, E. Kubicz, Sz. Niedzwiecki, M. Palka, L. Raczynski, Z. Rudy, P. Salabura, N. G. Sharma, M. Silarski, A. Slomski, J. Smyrski, A. Strzelecki, A. Wieczorek, W. Wislicki, M. Zielinski, N. Zon

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A new concept and results of the performance tests of the TOF-PET detection system developed at the Jagiellonian University will be presented. The novelty of the concept lies in employing long strips of polymer scintillators instead of crystals as detectors of annihilation quanta, and in using predominantly the timing of signals instead of their amplitudes for the reconstruction of Lines-of-Response. The diagnostic chamber consists of plastic scintillator strips readout by pairs of photo multipliers arranged axially around a cylindrical surface. To take advantage of the superior timing properties of plastic scintillators the signals are probed in the voltage domain with the accuracy of 20 ps by a newly developed electronics, and the data are collected by the novel trigger-less and reconfigurable data acquisition system. The hit-position and hit-time are reconstructed by the dedicated reconstruction methods based on the compressing sensing theory and the library of synchronized model signals. The solutions are subject to twelve patent applications. So far a time-of-flight resolution of ~120 ps (sigma) was achieved for a double-strip prototype with 30 cm field-of-view (FOV). It is by more than a factor of two better than TOF resolution achievable in current TOF-PET modalities and at the same time the FOV of 30 cm long prototype is significantly larger with respect to typical commercial PET devices. The Jagiellonian PET (J-PET) detector with plastic scintillators arranged axially possesses also another advantage. Its diagnostic chamber is free of any electronic devices and magnetic materials thus giving unique possibilities of combining J-PET with CT and J-PET with MRI for scanning the same part of a patient at the same time with both methods.

Keywords: PET-CT, PET-MRI, TOF-PET, scintillator

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Authors: Meimei Shi

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Objectives: The identification of endangered species, especially simultaneous detection of multiple species in complex samples, plays a critical role in alleged wildlife crime incidents and prevents illegal trade. This study was to develop a multi-locus DNA metabarcoding method for endangered animal species identification. Methods: Several pairs of universal primers were designed according to the mitochondria conserved gene regions. Experimental mixtures were artificially prepared by mixing well-defined species, including endangered species, e.g., forest musk, bear, tiger, pangolin, and sika deer. The artificial samples were prepared with 1-16 well-characterized species at 1% to 100% DNA concentrations. After multiplex-PCR amplification and parameter modification, the amplified products were analyzed by capillary electrophoresis and used for NGS library preparation. The DNA metabarcoding was carried out based on Illumina MiSeq amplicon sequencing. The data was processed with quality trimming, reads filtering, and OTU clustering; representative sequences were blasted using BLASTn. Results: According to the parameter modification and multiplex-PCR amplification results, five primer sets targeting COI, Cytb, 12S, and 16S, respectively, were selected as the NGS library amplification primer panel. High-throughput sequencing data analysis showed that the established multi-locus DNA metabarcoding method was sensitive and could accurately identify all species in artificial mixtures, including endangered animal species Moschus berezovskii, Ursus thibetanus, Panthera tigris, Manis pentadactyla, Cervus nippon at 1% (DNA concentration). In conclusion, the established species identification method provides technical support for customs and forensic scientists to prevent the illegal trade of endangered animals and their products.

Keywords: DNA metabarcoding, endangered animal species, mitochondria nucleic acid, multi-locus

Procedia PDF Downloads 87

Authors: Shayli Varasteh Moradi, Wayne A. Johnston, Dejan Gagoski, Kirill Alexandrov

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The demand for a rapid and more efficient technique to identify protein-protein interaction particularly in the areas of therapeutics and diagnostics development is growing. The method described here is a rapid in vitro protein-protein interaction analysis approach based on AlphaLISA technology combined with Leishmania tarentolae cell-free protein production (LTE) system. Cell-free protein synthesis allows the rapid production of recombinant proteins in a multiplexed format. Among available in vitro expression systems, LTE offers several advantages over other eukaryotic cell-free systems. It is based on a fast growing fermentable organism that is inexpensive in cultivation and lysate production. High integrity of proteins produced in this system and the ability to co-express multiple proteins makes it a desirable method for screening protein interactions. Following the translation of protein pairs in LTE system, the physical interaction between proteins of interests is analysed by AlphaLISA assay. The assay is performed using unpurified in vitro translation reaction and therefore can be readily multiplexed. This approach can be used in various research applications such as epitope mapping, antigen-antibody analysis and protein interaction network mapping. The intra-viral protein interaction network of Zika virus was studied using the developed technique. The viral proteins were co-expressed pair-wise in LTE and all possible interactions among viral proteins were tested using AlphaLISA. The assay resulted to the identification of 54 intra-viral protein-protein interactions from which 19 binary interactions were found to be novel. The presented technique provides a powerful tool for rapid analysis of protein-protein interaction with high sensitivity and throughput.

Keywords: AlphaLISA technology, cell-free protein expression, epitope mapping, Leishmania tarentolae, protein-protein interaction

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Authors: Prashanth Pillai, Purnaprajna Mangsuli

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Oil exploration and production companies invest considerable time and efforts to extract essential well attributes (like well status, surface, and target coordinates, wellbore depths, event timelines, etc.) from unstructured data sources like technical reports, which are often non-standardized, multimodal, and highly domain-specific by nature. It is also important to consider the context when extracting attribute values from reports that contain information on multiple wells/wellbores. Moreover, semantically similar information may often be depicted in different data syntax representations across multiple pages and document sources. We propose a hierarchical multi-source fact extraction workflow based on a deep learning framework to extract essential well attributes at scale. An information retrieval module based on the transformer architecture was used to rank relevant pages in a document source utilizing the page image embeddings and semantic text embeddings. A question answering framework utilizingLayoutLM transformer was used to extract attribute-value pairs incorporating the text semantics and layout information from top relevant pages in a document. To better handle context while dealing with multi-well reports, we incorporate a dynamic query generation module to resolve ambiguities. The extracted attribute information from various pages and documents are standardized to a common representation using a parser module to facilitate information comparison and aggregation. Finally, we use a probabilistic approach to fuse information extracted from multiple sources into a coherent well record. The applicability of the proposed approach and related performance was studied on several real-life well technical reports.

Keywords: natural language processing, deep learning, transformers, information retrieval

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Authors: H. F. Shi, C. L. Zhang

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Visible-light-responsive g-C3N4/NaNbO3 nanowires photocatalysts were fabricated by introducing polymeric g-C3N4 on NaNbO3 nanowires. The microscopic mechanisms of interface interaction, charge transfer and separation, as well as the influence on the photocatalytic activity of g-C3N4/NaNbO3 composite were systematic investigated. The HR-TEM revealed that an intimate interface between C3N4 and NaNbO3 nanowires formed in the g-C3N4/NaNbO3 heterojunctions. The photocatalytic performance of photocatalysts was evaluated for CO2 reduction under visible-light illumination. Significantly, the activity of g-C3N4/NaNbO3 composite photocatalyst for photoreduction of CO2 was higher than that of either single-phase g-C3N4 or NaNbO3. Such a remarkable enhancement of photocatalytic activity was mainly ascribed to the improved separation and transfer of photogenerated electron-hole pairs at the intimate interface of g-C3N4/NaNbO3 heterojunctions, which originated from the well-aligned overlapping band structures of C3N4 and NaNbO3. Pt loaded NaNbO3-xNx (Pt-NNON), a visible-light-sensitive photocatalyst, was synthesized by an in situ photodeposition method from H2PtCl6•6H2O onto NaNbO3-xNx (NNON) sample. Pt-NNON exhibited a much higher photocatalytic activity for gaseous 2-propanol (IPA) degradation under visible-light irradiation in contrast to NNON. The apparent quantum efficiency (AQE) of Pt-NNON sample for IPA photodegradation achieved up to 8.6% at the wavelength of 419 nm. The notably enhanced photocatalytic performance was attributed to the promoted charge separation and transfer capability in the Pt-NNON system. This work suggests that surface nanosteps possibly play an important role as an electron transfer at high way, which facilitates to the charge carrier collection onto Pt rich zones and thus suppresses recombination between photogenerated electrons and holes. This method can thus be considered as an excellent strategy to enhance photocatalytic activity of organic decomposition in addition to the commonly applied noble metal doping method.

Keywords: CO2 reduction, NaNbO3, nanowires, g-C3N4

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Authors: Amy Yee Kai Wan

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The arrival of a new baby to first-time parents is an exciting and joyous occasion, yet, the daunting task of raising the baby and the uncertainty of how it will affect the lives of the couple present a great challenge to them. This study examines the causes of conflicts and needs of the new parents through a qualitative research of five pairs of new parents in Hong Kong. Semi-structured in-depth qualitative interviews were conducted to explore the changes babies brought to their marriages, sources of support they received and found important and assistance they felt would help with their transition to parenthood. Thematic analysis was used to analyze the commonalities and differences between the five couples’ subjective experiences. Narrative analysis was used to compare the experiences of two parents who are the under-functioning parent of the couple, to study the different strategies they employed in response to the over-functioning parent and to analyze how the marital relationships were affected. Four main themes emerged from the study: 1) Change and adjustment in marital relationship, 2) parents’ level of involvement, 3) support in childcaring, and 4) challenges faced by the parents. Results from the study indicated that father involvement in childcaring is an important element in mother’s marital satisfaction Father’s marital satisfaction is dependent upon the mother – her satisfaction with father involvement, which affects the mother’s marital satisfaction. Marital convergence and co-parenting alliance acted as moderators for marital satisfaction. Implications from the study include: i) offering programmes that improve couple relationship and enhance parenting efficacy in tandem to improve overall marital satisfaction, and ii) offering prenatal counselling services or provide education to new parents from prenatal to postnatal period that can help couples reduce discrepancies between expectations and realities of their marital relationship and parenting responsibilities after their baby is born.

Keywords: co-parenting alliance, father involvement, marital convergence, maternal gatekeeping, new parents, transition to parenthood

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Authors: Sarinra Thongmee, Krittaporn Prakobsaeng, Adithep Mingsuan, Chanyapak Polkhet, Supattra Wongsuk

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The purposes of this research and developmentwasto develop and evaluation of the clinical nursingpractice guideline (CNPG) for the prevention infection during intubation in patient with suspected or confirmedCOVID-19 patient. This study was developed by using the evidencebased practice model of Soukup (2000) asa conceptual framework. The study consisted of 4 steps: 1) situational analysis of intubation service in patientswith confirmed COVID-19; 2) development of the CNPG; 3) apply the NPG to trial; and 4) evaluation of the CNPG. The sample consisted of 52 nurse anesthetists and 25 infected or suspected COVID-19 patients. The research instrument consisted of 1) the CNPG, which was developed by the researchers; 2) the nurses anesthetist opinion questionnaire to the guideline; 3) the evaluation practice form; and 4) the nurse anesthetist knowledge test on nursing care of patients infected with COVID-19. Data were analyzed by using descriptive statistics, and Wilcoxon matched-pairs signed rank test. The results revealed this developed CNPG consists of 4 sections: 1)the CNPG for airborne precautions2) the preparation of anesthetic and intubation equipments3) the roles and duties of the intubation team, 4) the guidelines for intubation in suspected or confirmed COVID-19 patients. The results of CNPG use found that 1)the provider: using NPG in providers revealed that nurse anesthetist had a higher mean of knowledge scores than before using CNPG statistically significant at the 0.05 level (p<0.01) and able to follow the NPG 100% inall activities. The anesthetic team was not infected with COVID-19 from intubation outside the operating room. 2)the client: the patient was safe, with no complications from intubation. Summary CNPG to prevent infection during reintubation of suspected or confirmedCOVID-19patient was appropriate and applicable to practice.

Keywords: clinical nursing practice guideline, prevention of infection, endotracheal intubation, COVID-19

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Authors: Tahani Amutairi, Paul May, Neil Allan

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Many properties of semiconductor materials (mechanical, electronic, magnetic, and optical) can be significantly modified by introducing a point defect. Diamond offers extraordinary properties as a semiconductor, and doping seems to be a viable method of solving the problem associated with the fabrication of diamond-based electronic devices in order to exploit those properties. The dopants are believed to play a significant role in reducing the energy barrier to conduction and controlling the mobility of the carriers and the resistivity of the film. Although it has been proven that the n-type diamond semiconductor can be obtained with phosphorus doping, the resulting ionisation energy and mobility are still inadequate for practical application. Theoretical studies have revealed that this is partly because the effects of the many phosphorus atoms incorporated in the diamond lattice are compensated by acceptor states. Using spin-polarised hybrid density functional theory and a supercell approach, we explored the effects of bonding one N atom to a P in adjacent substitutional sites in diamond. A range of hybrid functional, including HSE06, B3LYP, PBE0, PBEsol0, and PBE0-13, were used to calculate the formation, binding, and ionisation energies, in order to explore the solubility and stability of the point defect. The equilibrium geometry and the magnetic and electronic structures were analysed and presented in detail. The defect introduces a unique reconstruction in a diamond where one of the C atoms coordinated with the N atom involved in the elongated C-N bond and creates a new bond with the P atom. The simulated infrared spectra of phosphorus-nitrogen defects were investigated with different supercell sizes and found to contain two sharp peaks at the edges of the spectrum, one at a high frequency 1,379 cm⁻¹ and the second appearing at the end range, 234 cm⁻¹, as obtained with the largest supercell (216).

Keywords: DFT, HSE06, B3LYP, PBE0, PBEsol0, PBE0-13

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Authors: Amal Sellami, Ahlem Ammar

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Writing is acknowledged to be a cognitively demanding and complex task. Indeed, the writing process is composed of three iterative sub-processes, namely planning, translating (writing), and reviewing. Not only do second or foreign language learners need to write according to this process, but they also need to respect the norms and rules of language and writing in the text to-be-produced. Accordingly, researchers have suggested to approach writing as a collaborative task in order to al leviate its complexity. Consequently, collaboration has been implemented during the whole writing process or only during planning orreviewing. Researchers report that implementing collaboration during the whole process might be demanding in terms of time in comparison to individual writing tasks. Consequently, because of time constraints, teachers may avoid it. For this reason, it might be pedagogically more realistic to limit collaboration to one of the writing sub-processes(i.e., planning or reviewing). However, previous research implementing collaboration in planning or reviewing is limited and fails to explore the effects of the seconditionson the written text. Consequently, the present study examines the effects of collaboration in planning and collaboration in reviewing on the written text. To reach this objective, quantitative as well as qualitative methods are deployed to examine the written texts holistically and in terms of fluency, complexity, and accuracy. Participants of the study include 4 pairs in each group (n=8). They participated in two experimental conditions, which are: (1) collaborative planning followed by individual writing and individual reviewing and (2) individual planning followed by individual writing and collaborative reviewing. The comparative research findings indicate that while collaborative planning resulted in better overall text quality (precisely better content and organization ratings), better fluency, better complexity, and fewer lexical errors, collaborative reviewing produces better accuracy and less syntactical and mechanical errors. The discussion of the findings suggests the need to conduct more comparative research in order to further explore the effects of collaboration in planning or in reviewing. Pedagogical implications of the current study include advising teachers to choose between implementing collaboration in planning or in reviewing depending on their students’ need and what they need to improve.

Keywords: collaboration, writing, collaborative planning, collaborative reviewing

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Authors: Miriam Sosa-Díaz, Faustino Sánchez-Garduño

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In population dynamics the study of both, the abundance and the spatial distribution of the populations in a given habitat, is a fundamental issue a From ecological point of view, the determination of the factors influencing such changes involves important problems. In this paper a mathematical model to describe the temporal dynamic and the spatiotemporal dynamic of the interaction of three populations (pollinators, plants and herbivores) is presented. The study we present is carried out by stages: 1. The temporal dynamics and 2. The spatio-temporal dynamics. In turn, each of these stages is developed by considering three cases which correspond to the dynamics of each type of interaction. For instance, for stage 1, we consider three ODE nonlinear systems describing the pollinator-plant, plant-herbivore and plant-pollinator-herbivore, interactions, respectively. In each of these systems different types of dynamical behaviors are reported. Namely, transcritical and pitchfork bifurcations, existence of a limit cycle, existence of a heteroclinic orbit, etc. For the spatiotemporal dynamics of the two mathematical models a novel factor are introduced. This consists in considering that both, the pollinators and the herbivores, move towards those places of the habitat where the plant population density is high. In mathematical terms, this means that the diffusive part of the pollinators and herbivores equations depend on the plant population density. The analysis of this part is presented by considering pairs of populations, i. e., the pollinator-plant and plant-herbivore interactions and at the end the two mathematical model is presented, these models consist of two coupled nonlinear partial differential equations of reaction-diffusion type. These are defined on a rectangular domain with the homogeneous Neumann boundary conditions. We focused in the role played by the density dependent diffusion term into the coexistence of the populations. For both, the temporal and spatio-temporal dynamics, a several of numerical simulations are included.

Keywords: bifurcation, heteroclinic orbits, steady state, traveling wave

Procedia PDF Downloads 274

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

Abstract:

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: E. N. Masri, E. Takács

Abstract:

Amplitude Versus Offset (AVO) and simultaneous model-based impedance inversion techniques have not been utilized for geothermal exploration commonly; however, some recent publications called the attention that they can be very useful in the geothermal investigations. In this study, we present rock physical attributes obtained from 3D pre-stack seismic data and well logs collected in a study area of the NW part of Pannonian Basin where the geothermal reservoir is located in the fractured zones of Triassic basement and it was hit by three productive-injection well pairs. The holes were planned very successfully based on the conventional 3D migrated stack volume prior to this study. Subsequently, the available geophysical-geological datasets provided a great opportunity to test modern inversion procedures in the same area. In this presentation, we provide a summary of the theory and application of the most promising seismic inversion techniques from the viewpoint of geothermal exploration. We demonstrate P- and S-wave impedance, as well as the velocity (Vp and Vs), the density, and the Vp/Vs ratio attribute volumes calculated from the seismic and well-logging data sets. After a detailed discussion, we conclude that P-wave impedance and Vp/Vp ratio are the most helpful parameters for lithology discrimination in the study area. They detect the hot water saturated fracture zone very well thus they can be very useful in mapping the investigated reservoir. Integrated interpretation of all the obtained rock-physical parameters is essential. We are extending the above discussed pre-stack seismic tools by studying the possibilities of Elastic Impedance Inversion (EII) for geothermal exploration. That procedure provides two other useful rock-physical properties, the compressibility and the rigidity (Lamé parameters). Results of those newly created elastic parameters will also be demonstrated in the presentation. Geothermal extraction is of great interest nowadays; and we can adopt several methods have been successfully applied in the hydrocarbon exploration for decades to discover new reservoirs and reduce drilling risk and cost.

Keywords: fractured zone, seismic, well-logging, inversion

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Authors: Nadia Allouache

Abstract:

Solar radiation is by far the largest and the most world’s abundant, clean and permanent energy source. The amount of solar radiation intercepted by the Earth is much higher than annual global energy use. The energy available from the sun is greater than about 5200 times the global world’s need in 2006. In recent years, many promising technologies have been developed to harness the sun's energy. These technologies help in environmental protection, economizing energy, and sustainable development, which are the major issues of the world in the 21st century. One of these important technologies is the solar cooling systems that make use of either absorption or adsorption technologies. The solar adsorption cooling systems are good alternative since they operate with environmentally benign refrigerants that are natural, free from CFCs, and therefore they have a zero ozone depleting potential (ODP). A numerical analysis of thermal and solar performances of an adsorption solar refrigerating system using different adsorbent/adsorbate pairs such as activated carbon AC35 and activated carbon BPL/Ammoniac; is undertaken in this study. The modeling of the adsorption cooling machine requires the resolution of the equation describing the energy and mass transfer in the tubular adsorber that is the most important component of the machine. The Wilson and Dubinin- Astakhov models of the solid-adsorbat equilibrium are used to calculate the adsorbed quantity. The porous medium is contained in the annular space and the adsorber is heated by solar energy. Effect of key parameters on the adsorbed quantity and on the thermal and solar performances are analysed and discussed. The performances of the system that depends on the incident global irradiance during a whole day depends on the weather conditions: the condenser temperature and the evaporator temperature. The AC35/methanol pair is the best pair comparing to the BPL/Ammoniac in terms of system performances.

Keywords: activated carbon-methanol pair, activated carbon-ammoniac pair, adsorption, performance coefficients, numerical analysis, solar cooling system

Procedia PDF Downloads 40

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

Abstract:

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: Jiajia Peng, Jianqing Qiu, Jianjun Ren, Yu Zhao

Abstract:

Background: Insufficient sleep has been focused on as a public health epidemic. However, a comprehensive analysis of disease trajectory associated with unhealthy sleep habits is still unclear currently. Objective: This study sought to comprehensively clarify the disease's trajectory in relation to the overall poor sleep pattern and unhealthy sleep behaviors separately. Methods: 410,682 participants with available information on sleep behaviors were collected from the UK Biobank at the baseline visit (2006-2010). These participants were classified as having high- and low risk of each sleep behavior and were followed from 2006 to 2020 to identify the increased risks of diseases. We used Cox regression to estimate the associations of high-risk sleep behaviors with the elevated risks of diseases, and further established diseases trajectory using significant diseases. The low-risk unhealthy sleep behaviors were defined as the reference. Thereafter, we also examined the trajectory of diseases linked with the overall poor sleep pattern by combining all of these unhealthy sleep behaviors. To visualize the disease's trajectory, network analysis was used for presenting these trajectories. Results: During a median follow-up of 12.2 years, we noted 12 medical conditions in relation to unhealthy sleep behaviors and the overall poor sleep pattern among 410,682 participants with a median age of 58.0 years. The majority of participants had unhealthy sleep behaviors; in particular, 75.62% with frequent sleeplessness, and 72.12% had abnormal sleep durations. Besides, a total of 16,032 individuals with an overall poor sleep pattern were identified. In general, three major disease clusters were associated with overall poor sleep status and unhealthy sleep behaviors according to the disease trajectory and network analysis, mainly in the digestive, musculoskeletal and connective tissue, and cardiometabolic systems. Of note, two circularity disease pairs (I25→I20 and I48→I50) showed the highest risks following these unhealthy sleep habits. Additionally, significant differences in disease trajectories were observed in relation to sex and sleep medication among individuals with poor sleep status. Conclusions: We identified the major disease clusters and high-risk diseases following participants with overall poor sleep health and unhealthy sleep behaviors, respectively. It may suggest the need to investigate the potential interventions targeting these key pathways.

Keywords: sleep, poor sleep, unhealthy sleep behaviors, disease trajectory, UK Biobank

Procedia PDF Downloads 57

Authors: Morteza Khashehchi, Kamel Hooman

Abstract:

Thermal effects on the dynamics and stability of the flow past a circular cylinder operating in the mixed convection regime is studied experimentally for Reynolds number (ReD) between 1000 and 4000, and different cylinder wall temperatures (Tw) between 25 and 75°C by means of Particle Image Velocimetry (PIV). The experiments were conducted in a horizontal wind tunnel with the heated cylinder placed horizontally. With such assumptions, the direction of the thermally induced buoyancy force acting on the fluid surrounding the heated cylinder would be perpendicular to the flow direction. In each experiment, to acquire 3000 PIV image pairs, the temperature and Reynolds number of the approach flow were held constant. By adjusting different temperatures in different Reynolds numbers, the corresponding Richardson number (RiD = Gr/Re^2) was varied between 0:0 (unheated) and 10, resulting in a change in the heat transfer process from forced convection to mixed convection. With increasing temperature of the wall cylinder, significant modifications of the wake flow pattern and wake vortex shedding process were clearly revealed. For cylinder at low wall temperature, the size of the wake and the vortex shedding process are found to be quite similar to those of an unheated cylinder. With high wall temperature, however, the high temperature gradient in the wake shear layer creates a type of vorticity with opposite sign to that of the shear layer vorticity. This temperature gradient vorticity weakens the strength of the shear layer vorticity, causing delay in reaching the recreation point. In addition to the wake characteristics, the shedding frequency for the heated cylinder is determined for all aforementioned cases. It is found that, as the cylinder wall is heated, the organization of the vortex shedding is altered and the relative position of the first detached vortices with respect to the second one is changed. This movement of the first detached vortex toward the second one increases the frequency of the shedding process. It is also found that the wake closure length decreases with increasing the Richardson number.

Keywords: heated cylinder, PIV, wake, Reynolds number

Procedia PDF Downloads 368

Authors: N. Allouache, W. Elgahri, A. Gahfif, M. Belmedani

Abstract:

Solar radiation is by far the largest and the most world’s abundant, clean and permanent energy source. The amount of solar radiation intercepted by the Earth is much higher than annual global energy use. The energy available from the sun is greater than about 5200 times the global world’s need in 2006. In recent years, many promising technologies have been developed to harness the sun's energy. These technologies help in environmental protection, economizing energy, and sustainable development, which are the major issues of the world in the 21st century. One of these important technologies is the solar cooling systems that make use of either absorption or adsorption technologies. The solar adsorption cooling systems are a good alternative since they operate with environmentally benign refrigerants that are natural, free from CFCs, and therefore they have a zero ozone depleting potential (ODP). A numerical analysis of thermal and solar performances of an adsorption solar refrigerating system using different adsorbent/adsorbate pairs, such as activated carbon AC35 and activated carbon BPL/Ammoniac; is undertaken in this study. The modeling of the adsorption cooling machine requires the resolution of the equation describing the energy and mass transfer in the tubular adsorber, that is the most important component of the machine. The Wilson and Dubinin- Astakhov models of the solid-adsorbat equilibrium are used to calculate the adsorbed quantity. The porous medium is contained in the annular space, and the adsorber is heated by solar energy. Effect of key parameters on the adsorbed quantity and on the thermal and solar performances are analysed and discussed. The performances of the system that depends on the incident global irradiance during a whole day depends on the weather conditions: the condenser temperature and the evaporator temperature. The AC35/methanol pair is the best pair comparing to the BPL/Ammoniac in terms of system performances.

Keywords: activated carbon-methanol pair, activated carbon-ammoniac pair, adsorption, performance coefficients, numerical analysis, solar cooling system

Procedia PDF Downloads 53

Authors: E. Karacabey, Ş. G. Özçelik, M. S. Turan, C. Baltacıoğlu, E. Küçüköner

Abstract:

Main concern about deep-fat-fried food materials is their high final oil contents absorbed during frying process and/or after cooling period, since diet including high content of oil is accepted unhealthy by consumers. Different methods have been evaluated to decrease oil content of fried food stuffs. One promising method is partially drying of food material before frying. In the present study it was aimed to control and decrease the final oil content of zucchini slices by means of partial drying and to optimize process conditions. Conventional oven drying was used to decrease moisture content of zucchini slices at a certain extent. Process performance in terms of oil uptake was evaluated by comparing oil content of predried and then fried zucchini slices with those determined for directly fried ones. For predrying and frying processes, oven temperature and weight loss and frying oil temperature and time pairs were controlled variables, respectively. Zucchini slices were also directly fried for sensory evaluations revealing preferred properties of final product in terms of surface color, moisture content, texture and taste. These properties of directly fried zucchini slices taking the highest score at the end of sensory evaluation were determined and used as targets in optimization procedure. Response surface methodology was used for process optimization. The properties, determined after sensory evaluation, were selected as targets; meanwhile oil content was aimed to be minimized. Results indicated that final oil content of zucchini slices could be reduced from 58% to 46% by controlling conditions of predrying and frying processes. As a result, it was suggested that predrying could be one choose to reduce oil content of fried zucchini slices for health diet. This project (113R015) has been supported by TUBITAK.

Keywords: health process, optimization, response surface methodology, oil uptake, conventional oven

Procedia PDF Downloads 347

Authors: Rakesh C. Mathad, G. Y. Lokesh, Basavegowda

Abstract:

In agriculture using quality seeds of improved varieties is very important to ensure higher productivity thereby food security and sustainability. To ensure good productivity, seeds should have characters as described by the breeder. To know whether the characters as described by the breeder are expressing in a variety such as genuineness or genetic purity, field grow out test (GOT) is done. In pigeon pea which is long durational crop, conducting a GOT may take very long time and expensive also. Since in pigeon pea flower character is a most distinguishing character from the contaminants, conducting a field grow out test require 120-130 days or till flower emergence, which may increase cost of storage and seed production. This will also delay the distribution of seed inventory to the pigeon pea growing areas. In this view during 2014-15 with financial support of Govt. of Karnataka, India, a project to develop a molecular genetic test for newly developed variety of pigeon pea cv.TS3R was commissioned at Seed Unit, UAS, Raichur. A molecular test was developed with the help SSR markers to identify pure variety from possible off types in newly released pigeon pea variety TS3R. In the investigation, 44 primer pairs were screened to identify the specific marker associated with this variety. Pigeon pea cv. TS3R could be clearly identified by using the primer CCM 293 based on the banding pattern resolved on gel electrophoresis and PCR reactions. However some of the markers like AHSSR 46, CCM 82 and CCM 57 can be used to test other popular varieties in the region like Asha, GRG-811 and Maruti respectively. Further to develop this in to a lab test, the seed sample size was standardized to 200 seeds and a grow out matrix was developed. This matrix was used to sample 12 days old leaves to extract DNA. The lab test results were validated with actual field GOT test results and found variations within the acceptable limit of 1%. This molecular method can now be employed to test the genetic purity in pigeon pea cv TS3R which reduces the time and can be a cheaper alternative method for field GOT.

Keywords: genuineness, grow-out matrix, molecular genetic purity, SSR markers

Procedia PDF Downloads 251

Authors: Vacharee Svamivastu

Abstract:

This research investigates the application of geometrical relationship to the ancient religious assembly hall (Vihara) housing a reclining Buddha statue of Thailand's Kamphaeng Phet Historical Park. The study utilizes the archaeological and wooden roof structure remains of the Vihara as the prima facie evidence, supplemented with evidence from other active archaeological sites with architectural kinship as well as Buddhist ideology. At present, the wooden roofs of the Vihara fell prey to the elements and there remain only the base, columns and enclosing walls. Unlike typical Viharas whose floor plan are of rectangular shape, the floor plan of the Vihara housing the reclining Buddha is of square configuration of 25x25m. Further observation has revealed the utilization of large laterite boulders as the principal construction material of the assembly hall (Vihara) columns. The laterite columns are of square shape (1x1m) and various heights (H), ranging from 3.50m to 5.50m. The erection of the Vihara required a total of 36 laterite columns. The pattern of columns arrangement is of two rows of inner columns, two rows of outer columns and two rows of verandah columns. The space between pairs of the verandah columns was stacked with laterite blocks of varying sizes to form the Vihara walls with small openings for ventilation. Upon applying the geometrical relationship-grid system to the Vihara, the results reveal that the placement of the columns was deliberately and masterfully undertaken such that the center of the square-shaped Vihara is conspicuously spacious so as to accommodate the sacred reclining Buddha statue. The elegance of the Vihara demonstrates the ingenious application of geometrical relationship to transforming a space into a structure (i.e. Vihara) of architectural and religious significance.

Keywords: geometrical relationship, the religious assembly hall, Vihara, Kamphaeng Phet School of Master Builder

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Authors: Eirini Konstanta, Cedric Gouedard, Aggeliki Delimitsou, Stefania Patera, Samuel Murray

Abstract:

Introduction: Quality reference DNA standards (QRS) for molecular testing by next-generation sequencing (NGS) are essential for accurate quantitation of copy number variations (CNV) for germline and variant allelic frequencies (VAF) for somatic analyses. Objectives: Presently, several molecular analytics for oncology patients are reliant upon quantitative metrics. Test validation and standardisation are also reliant upon the availability of surrogate control materials allowing for understanding test LOD (limit of detection), sensitivity, specificity. We have developed a dual calibration platform allowing for QRS pairs to be included in analysed DNA samples, allowing for accurate quantitation of CNV and VAF metrics within and between patient samples. Methods: QRS™ blocks up to 500nt were designed for common NGS panel targets incorporating ≥ 2 identification tags (IDTDNA.com). These were analysed upon spiking into gDNA, somatic, and ctDNA using a proprietary CalSuite™ platform adaptable to common LIMS. Results: We demonstrate QRS™ calibration reproducibility spiked to 5–25% at ± 2.5% in gDNA and ctDNA. Furthermore, we demonstrate CNV and VAF within and between samples (gDNA and ctDNA) with the same reproducibility (± 2.5%) in a clinical sample of lung cancer and HBOC (EGFR and BRCA1, respectively). CNV analytics was performed with similar accuracy using a single pair of QRS calibrators when using multiple single targeted sequencing controls. Conclusion: Dual paired QRS™ calibrators allow for accurate and reproducible quantitative analyses of CNV, VAF, intrinsic sample allele measurement, inter and intra-sample measure not only simplifying NGS analytics but allowing for monitoring clinically relevant biomarker VAF across patient ctDNA samples with improved accuracy.

Keywords: calibrator, CNV, gene copy number, VAF

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