Search results for: gene transfer

Authors: Aakash Kumar R. G., Anees K. Ahamed, Raj M. Mohan

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Effective engine cooling can improve the engine’s life and efficacy. The design of the fin of the cylinder head and block determines the cooling mechanism of air cooled engine. The heat conduction takes place through the engine parts and convection of heat from the surface of the fins takes place with air as the heat transferring medium. The air surrounding the cooling fins helps in removal of heat built up by the air cooled engine. If the heat removal rate is inadequate, it will result in lower engine efficiency and high thermal stresses in the engine. The main drawback of the air cooled engine is the low heat transfer rate of the cooling fins .This work is based on scrutiny of previous researches that involves enhancing of heat transfer rate of cooling fins. The current research is about augmentation of heat transfer rate of longitudinal rectangular fin profiles by varying the length of the fin and diameter of holes on the fins. Thermal and flow analysis is done for two different models of fins. One is simple fin without holes and the other is perforated (consist of holes). It can be inferred from the research that the fins with holes have a higher fin efficiency than the fins without holes. The geometry of the fin is done in CREO. The heat transfer analysis is done using ANSYS software.

Keywords: fins, heat transfer, perforated fins, thermal analysis, thermal flux

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Authors: Peter Parkinson

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The research investigates the effects of temperature, humidity, wind speed, and fabric composition on the drying times of blood and assesses the degree of blood transfer that can occur during the drying process. An assortment of fabrics, of different composition and thicknesses, were collected and stained using two blood volumes and exposed to varying environmental conditions. The conclusion reached was that temperature, humidity, wind speed, and fabric thickness do have an effect on drying times. An increase in temperature and wind speed results in a decrease in drying times while an increase in fabric thickness and humidity extended the drying times of blood under similar conditions. Transfer experimentation utilized three donor fabrics, 100% white cotton, 100% acrylic, and 100% cotton denim, which were bloodstained using two blood volumes. The fabrics were subjected to both full and low/light force contact from the donor fabrics onto the recipient fabric, under different environmental conditions. Transfer times onto the 100% white cotton (recipient fabric) from all donor fabrics were shorter than the drying times observed. The intensities of the bloodstains decreased from high to low with time during the drying process. The degree of transfer at high, medium, and low intensities varied significantly between different materials and is dependent on the environmental conditions, fabric compositions, blood volumes, the type of contact (full or light force), and the drying times observed for the respective donor fabrics. These factors should be considered collectively and conservatively when assessing the time frame of secondary transfer in casework.

Keywords: blood, drying time, blood stain transfer, different environmental conditions, fabrics

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Ahmad Ali Shahid, Mukhtar Ahmed

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The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

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Authors: Zixi You

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With the demand of multilingual speakers increasing in the job market, multi-language learning programs have become more and more popular among undergraduate students. A study on multi-language learning strategies is therefore highly demanded on both practical and theoretical levels. Based on previous classification of learning strategies in SLA, and an investigation of BA Modern Language program students (with post-A level L2 and ab initio L3 learning experience from year one), this study explores and compares different types of learning strategies used by multi-language speakers and learners, transferable learning strategies between L2 and L3, and factors affecting the transfer. The results indicate that all the 23 types of learning strategies of L2 are employed when learning L3 from ab initio level, yet with different tendencies. Learning strategy transfer from L2 to L3 (i.e., the learners attribute the applying of these L3 learning strategies to be a direct result of their L2 learning experience) are observed in all 23 types of learning strategies. Comparatively, six types of “cognitive strategies” have higher transfer tendency than others. With regard to the failure of the transfer of some particular L2 strategies and the development of independent L3 strategies of individual learners, factors such as language proficiency, language typology and learning environment have played important roles among others. The presentation of this study will provide audiences with detailed data, insightful analysis and discussion on both theoretical and practical aspects of multi-language learning that will benefit both students and educators.

Keywords: learning strategy, multi-language acquisition, second language acquisition, strategy transfer

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Authors: Neda Menbari, Ramin Mehdiabadi

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Background: breast cancer remains a critical global health issue, constituting a leading cause of cancer-related mortality in women. MicroRNAs (miRs) are natural RNA molecules that play an important role in cellular processes and regulate post-transcriptional gene expression. MiR-216b-5p is a miR that acts as a tumor suppressor. The expression levels of FoxM1 and miR-216b-5p in malignant and control cells have been evaluated by quantitative polymerase chain reaction (qPCR) technique and flow cytometry. Results: the results of this study revealed a significant downregulation of miR-216b-5p in cancerous cells compared to the control MCF-10A cells (P=0.0004). Interestingly, the expression of miR-216b-5p exhibited an inverse relationship with key clinical indicators such as tumor size, grade, and lymph node invasion. Conclusion: The study's findings showed the prognostic value of miR-216b-5p levels in breast cancer, and its reduced expression correlates with unfavorable tumor characteristics. This research recommends performing more studies on the role of FoxM1 and miR-216b-5p in breast cancer pathology which potentially paving the way for targeted therapeutic interventions.

Keywords: breast cancer, gene expression, FOXM1, microRNA

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Authors: Amel Boulemtafes-Boukadoum, Ahmed Benzaoui

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Solar air heaters (SAH) are widely used in heating and drying applications using solar energy. Their efficiency needs to be improved to be competitive towards solar water heater. In this work, our goal is to study heat transfer enhancement in SAHs by the use of artificial roughness on the absorber. For this purpose, computational fluid dynamics (CFD) simulations were carried out to analyze the flow and heat transfer in the air duct of a solar air heater provided with transverse ribs. The air flows in forced convection and the absorber is heated with uniform flux. The effect of major parameters (Reynolds number, solar radiation, air inlet temperature, geometry of roughness) is examined and discussed. To highlight the effect of artificial roughness, we plotted the distribution of the important parameters: Nusselt number, friction factor, global thermohydraulic performance parameter etc. The results obtained are concordant to those found in the literature and shows clearly the heat transfer enhancement due to artifical roughness.

Keywords: solar air heater, artificial roughness, heat transfer enhancement, CFD

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

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

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

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: Debjit Ray

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Horizontal gene transfer (HGT) and recombination leads to the emergence of bacterial antibiotic resistance and pathogenic traits. HGT events can be identified by comparing a large number of fully sequenced genomes across a species or genus, define the phylogenetic range of HGT, and find potential sources of new resistance genes. In-depth comparative phylogenomics can also identify subtle genome or plasmid structural changes or mutations associated with phenotypic changes. Comparative phylogenomics requires that accurately sequenced, complete and properly annotated genomes of the organism. Assembling closed genomes requires additional mate-pair reads or “long read” sequencing data to accompany short-read paired-end data. To bring down the cost and time required of producing assembled genomes and annotating genome features that inform drug resistance and pathogenicity, we are analyzing the performance for genome assembly of data from the Illumina NextSeq, which has faster throughput than the Illumina HiSeq (~1-2 days versus ~1 week), and shorter reads (150bp paired-end versus 300bp paired end) but higher capacity (150-400M reads per run versus ~5-15M) compared to the Illumina MiSeq. Bioinformatics improvements are also needed to make rapid, routine production of complete genomes a reality. Modern assemblers such as SPAdes 3.6.0 running on a standard Linux blade are capable in a few hours of converting mixes of reads from different library preps into high-quality assemblies with only a few gaps. Remaining breaks in scaffolds are generally due to repeats (e.g., rRNA genes) are addressed by our software for gap closure techniques, that avoid custom PCR or targeted sequencing. Our goal is to improve the understanding of emergence of pathogenesis using sequencing, comparative genomics, and machine learning analysis of ~1000 pathogen genomes. Machine learning algorithms will be used to digest the diverse features (change in virulence genes, recombination, horizontal gene transfer, patient diagnostics). Temporal data and evolutionary models can thus determine whether the origin of a particular isolate is likely to have been from the environment (could it have evolved from previous isolates). It can be useful for comparing differences in virulence along or across the tree. More intriguing, it can test whether there is a direction to virulence strength. This would open new avenues in the prediction of uncharacterized clinical bugs and multidrug resistance evolution and pathogen emergence.

Keywords: genomics, pathogens, genome assembly, superbugs

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Ceyda Okudu, Secil Eroglu, Khandakar A. S. M. Saadat, Sibel O. Balci

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Ring Finger Protein 2 (RNF2) is a member of polycomb repressive complex 1 (PRC1), which is one of the epigenetic regulators in the genome. When RNF2 combines with other PRC1 members, it mediates the mono-ubiquitination of Histon2A (H2A). In breast cancer, RNF2 is commonly overexpressed, and also it promotes metastasis and invasion in other aggressive tumors like melanoma, prostate, and hepatocarcinoma. The role of RNF2 in the metastasis and invasion of breast cancer has not yet been elucidated. Our aim is to observe the role of RNF2 in metastasis and invasion in this study by miRNA mediated RNF2 gene silencing in breast cancer cell lines. We selected miRNAs, targeting to RNF2 by searching online databases. miR-17-5p, miR20a-5p, and miR-106b-5p were transfected to breast cancer cell lines (MCF-7, MDA-MB-231, SK-BR-3, and ZR-75-1), and also we used normal breast epithelial cell line (hTERT-HME1) to compare RNF2 gene expression level. After 48-72 hours post-transfection, mRNAs were isolated from the cells, and gene expressions were measured by RT-qPCR after from cDNA syntheses. We observed that RNF2 was highly expressed in SK-BR-3 and MDA-MB-231 cell lines opposite to MCF-7 and ZR-75-1 cell lines. RNF2 was downregulated 5, 5 and 7 fold by miR17-5p, miR20a-5p and miR106b-5p respectively in MCF-7. However, in SK-BR-3 and ZR-75-1 cell lines, miRNAs did not affect significantly RNF2 gene expression level. miR20a-5p decreased RNF2 3 fold and miR17-5p and miR106b-5p did not affect MDA-MB-231. After gene expression analysis, we performed metastasis and invasion assay in MCF-7 cells. For metastasis, we used both wound healing assay and Transwell Cell Migration Assay, and we used Transwell Cell Invasion Assay for invasion. The data of this assay showed that miR17-5p and miR20a-5p decreased both invasion and metastasis level, but miR106b-5p has no effect. We would like to conclude that RNF2 can be targeted by miR17-5p, miR20a-5p and miR106b-5p in MCF-7 cells and also RNF2, which is one of the upregulated genes in aggressive tumor, can be decreased by using these miRNAs. In future, we would like to confirm these results at the protein level and also whether these miRNAs are direct target of RNF2 or not.

Keywords: breast cancer, epigenetic, microRNAs, RNF2

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Authors: Ahmed Ramadhan Al-Obaidi, Jassim Alhamid

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In this investigation, the flow pattern, characteristics of thermal-hydraulic, and improvement of heat transfer performance are evaluated using a numerical technique in three dimensions corrugated pipe heat exchanger. The modification was made under different corrugated pipe geometrical parameters, including corrugated ring angle (CRA), distance between corrugated ring (DBCR), and corrugated diameter (CD), the range of Re number from 2000 to 12000. The numerical results are validated with available experimental data. The numerical outcomes reveal that there is an important change in flow field behaviour and a significant increase in friction factor and improvement in heat transfer performance owing to the use of the corrugated shape in the heat exchanger pipe as compared to the conventional smooth pipe. Using corrugated pipe with different configurations makes the flow more turbulence, flow separation, boundary layer distribution, flow mixing, and that leads to augmenting the performance of heat transfer. Moreover, the value of pressure drop, and the Nusselt number increases as the corrugated pipe geometrical parameters increase. Furthermore, the corrugation configuration shapes have an important influence on the thermal evaluation performance factor, and the maximum value was more than 1.3. Numerical simulation can be performed to predict the various geometrical configurations effects on fluid flow, thermal performance, and heat transfer enhancement.

Keywords: corrugated ring angle, corrugated diameter, Nusselt number, heat transfer

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Authors: Hamed Djalal

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The thermal analysis of the mechanical draft wet cooling tower is performed in this study by the heat and mass transfer modelization in the packing zone. After combining the heat and mass transfer laws, the mass and energy balances and by involving the Merkel assumptions; firstly, an ordinary differential equations system is derived and solved numerically by the Runge-Kutta method to determine the water and air temperatures, the humidity, and also other properties variation along the packing zone. Secondly, by making some linear assumptions for the air saturation curve, an analytical solution is formed, which is developed for the air washer calculation, but in this study, it is applied for the cooling tower to express also the previous parameters mathematically as a function of the packing height. Finally, a good agreement with experimental data is achieved by both solutions, but the numerical one seems to be the more accurate for modeling the heat and mass transfer process in the wet cooling tower.

Keywords: evaporative cooling, cooling tower, air washer, humidification, moist air, heat, and mass transfer

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Authors: Wanlapa Boonsod, Nisachon Yangprasong, Udomsak Kitthawee

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Thermal physics education is a complicated and challenging topic to discuss in any classroom. As a result, most students tend to be uninterested in learning this topic. In the current study, a convection experiment set was devised to show how heat can be transferred by a convection system to a thermoelectric plate until a LED flashes. This research aimed to 1) create a natural convection experimental set, 2) study learning achievement on the convection experimental set with the predict-observe-explain (POE) technique, and 3) study satisfaction for the convection experimental set with the predict-observe-explain (POE) technique. The samples were chosen by purposive sampling and comprised 28 students in grade 11 at Patumkongka School in Bangkok, Thailand. The primary research instrument was the plan for predict-observe-explain (POE) technique on heat transfer using a convection experimental set. Heat transfer experimental set by convection. The instruments used to collect data included a heat transfer achievement model by convection, a Satisfaction Questionnaire after the learning activity, and the predict-observe-explain (POE) technique for heat transfer using a convection experimental set. The research format comprised a one-group pretest-posttest design. The data was analyzed by GeoGebra program. The statistics used in the research were mean, standard deviation and t-test for dependent samples. The results of the research showed that achievement on heat transfer using convection experimental set was composed of thermo-electrics on the top side attached to the heat sink and another side attached to a stainless plate. Electrical current was displayed by the flashing of a 5v LED. The entire set of thermo-electrics was set up on the top of the box and heated by an alcohol burner. The achievement of learning was measured with the predict-observe-explain (POE) technique, with the natural convection experimental set statistically higher than before learning at a 0.01 level. Satisfaction with POE for physics learning of heat transfer by using convection experimental set was at a high level (4.83 from 5.00).

Keywords: convection, heat transfer, physics education, POE

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Authors: Lancelot Boulet, Pierre Benard, Ghislain Lartigue, Vincent Moureau, Nicolas Chauvet, Sheddia Didorally

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International aeronautic standards demand a fire certification for engines that demonstrate their resistance. This demonstration relies on tests performed with prototype engines in the late stages of the development. Hardest tests require to place a kerosene standardized flame in front of the engine casing during a given time with imposed temperature and heat flux. The purpose of this work is to provide a better characterization of a kerosene/air certification burner in order to minimize the risks of test failure. A first Large-Eddy Simulation (LES) study of the certification burner permitted to model and simulate this burner, including both adiabatic and Conjugate Heat Transfer (CHT) computations. Carried out on unstructured grids with 40 million tetrahedral cells, using the finite-volume YALES2 code, spray combustion, forced convection on walls and conduction in the solid parts of the burner were coupled to achieve a detailed description of heat transfer. It highlighted the fact that conduction inside the solid has a real impact on the flame topology and the combustion regime. However, in the absence of radiative heat transfer, unrealistic temperature of the equipment was obtained. The aim of the present study is to include the radiative heat transfer in order to reach the same temperature given by experimental measurements. First, various test-cases are conducted to validate the coupling between the different heat solvers. Then, adiabatic case, CHT case, as well as CHT including radiative transfer are studied and compared. The LES model is finally applied to investigate the heat transfer in a flame impaction configuration. The aim is to progress on fire test modeling so as to reach a good confidence level as far as success of the certification test is concerned.

Keywords: conjugate heat transfer, fire resistance test, large-eddy simulation, radiative transfer, turbulent combustion

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Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

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The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

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Authors: Xiaoping Su, Gabriel G. Malouf

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Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

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Authors: Ankan Roy, Niharika, Samir Kumar Patra

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Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

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Authors: Huirui Han, Chao Zhang

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The rod bundle is used in the fuel assembly of the supercritical water-cooled nuclear reactor. In the rod bundle, the coolant absorbs the heat contributed by the fission process. Because of the dramatic variations in the thermophysical properties of water at supercritical conditions, it is essential to investigate the heat transfer characteristics of supercritical water in the rod bundle to ensure the safety of the nuclear power plant. In this study, the effects of the flow direction, including horizontal, upward, and downward, on the fluid flow and heat transfer of the supercritical water in the rod bundle were studied numerically. The results show the possibility of gap vortices in the flow subchannels of the rod bundle. In addition, the distributions of the circumferential wall temperature show differences in different flow direction conditions. It was also found that the circumferential cladding surface temperature distribution in the upward flow condition is extremely non-uniform, and there is a large difference between the maximum wall temperatures for different fuel rods.

Keywords: heat transfer, rod bundle, supercritical water, wall temperature

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Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

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Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

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Authors: G. Ravindranath, S. Savitha

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This paper presents heat transfer analysis of single horizontal bare tube and heat transfer analysis of staggered arrangement of bare tube bundles bare tube bundles in gas-solid (air-solid) fluidized bed and predictions are done by using Artificial Neural Network (ANN) based on experimental data. Fluidized bed provide nearly isothermal environment with high heat transfer rate to submerged objects i.e. due to through mixing and large contact area between the gas and the particle, a fully fluidized bed has little temperature variation and gas leaves at a temperature which is close to that of the bed. Measurement of average heat transfer coefficient was made by local thermal simulation technique in a cold bubbling air-fluidized bed of size 0.305 m. x 0.305 m. Studies were conducted for single horizontal Bare Tube of length 305mm and 28.6mm outer diameter and for bare tube bundles of staggered arrangement using beds of large (average particle diameter greater than 1 mm) particle (raagi and mustard). Within the range of experimental conditions influence of bed particle diameter ( Dp), Fluidizing Velocity (U) were studied, which are significant parameters affecting heat transfer. Artificial Neural Networks (ANNs) have been receiving an increasing attention for simulating engineering systems due to some interesting characteristics such as learning capability, fault tolerance, and non-linearity. Here, feed-forward architecture and trained by back-propagation technique is adopted to predict heat transfer analysis found from experimental results. The ANN is designed to suit the present system which has 3 inputs and 2 out puts. The network predictions are found to be in very good agreement with the experimental observed values of bare heat transfer coefficient (hb) and nusselt number of bare tube (Nub).

Keywords: fluidized bed, large particles, particle diameter, ANN

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Authors: Gangacharyulu Dasaroju, Sumeet Sharma, Sanjay Singh

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Heat pipe is characterised as superconductor of heat because of its excellent heat removal ability. The operation of several engineering system results in generation of heat. This may cause several overheating problems and lead to failure of the systems. To overcome this problem and to achieve desired rate of heat dissipation, there is need to study the performance of heat pipe with annular fins under free convection at different inclinations. This study demonstrates the effect of different mass flow rate of hot fluid into evaporator section on the condenser side heat transfer coefficient with annular fins under natural convection at different inclinations. In this study annular fins are used for the experimental work having dimensions of length of fin, thickness of fin and spacing of fin as 10 mm, 1 mm and 6 mm, respectively. The main aim of present study is to discover at what inclination angles the maximum heat transfer coefficient shall be achieved. The heat transfer coefficient on the external surface of heat pipe condenser section is determined by experimental method and then predicted by empirical correlations. The results obtained from experimental and Churchill and Chu relation for laminar are in fair agreement with not more than 22% deviation. It is elucidated the maximum heat transfer coefficient of 31.2 W/(m²-K) at 25˚ tilt angle and minimal condenser heat transfer coefficient of 26.4 W/(m²-K) is seen at 45˚ tilt angle and 200 ml/min mass flow rate. Inclination angle also affects the thermal performance of heat pipe. Beyond 25^o inclination, heat transport rate starts to decrease.

Keywords: heat pipe, annular fins, natural convection, condenser heat transfer coefficient, tilt angle

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Authors: Shashank Patidar, Sumit Kumar, Atul Srivastava, Suneet Singh

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Present work is concerned with the numerical investigation of thermal response of biological tissues during laser-based photo-thermal therapy for destroying cancerous/abnormal cells with minimal damage to the surrounding normal cells. Light propagation through the biological sample is mathematically modelled by transient radiative transfer equation. In the present work, application of the Lattice Boltzmann Method is extended to analyze transport of short-pulse radiation in a participating medium.In order to determine the two-dimensional temperature distribution inside the tissue medium, the RTE has been coupled with Penne’s bio-heat transfer equation based on Fourier’s law by several researchers in last few years.

Keywords: lattice Boltzmann method, transient radiation transfer equation, dual phase lag model

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Authors: Ali Bayram, Remzi Yiğiter

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Objective: Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disease. At present, diagnosis of AD is rather late in the disease. Therefore, we attempted to find peripheral biomarkers for the early diagnosis of AD. Herein, we conducted a study to investigate the unc-51 like autophagy activating kinase-1 (ULK1) mRNA expression levels in human peripheral blood mononuclear cells from patients with Alzheimer's disease. Method: To determine whether ULK1 gene expression are altered in AD patients, we measured their gene expression in human peripheral blood cell in 50 patients with AD and 50 age and gender matched healthy controls by quantitative real-time PCR technique. Results: We found that both ULK1 gene expression in peripheral blood cell were significantly decreased in patients with AD as compared with controls (p <0.05). Lower levels of ULK1 gene expression were significantly associated with the increased risk for AD. Conclusions: Serine/threonine-protein kinase involved in autophagy in response to starvation. Acts upstream of phosphatidylinositol 3-kinase PIK3C3 to regulate the formation of autophagophores, the precursors of autophagosomes. Part of regulatory feedback loops in autophagy: acts both as a downstream effector and negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK and also acts as a regulator of AMPK by mediating phosphorylation of AMPK subunits PRKAA1, PRKAB2, and PRKAG1, leading to negatively regulate AMPK activity. May phosphorylate ATG13/KIAA0652 and RPTOR; however such data need additional evidences. Plays a role early in neuronal differentiation and is required for granule cell axon formation. Alzheimer is the most common neurodegenerative disease. Our results provide useful information that the ULK1 gene expression is decreased in the neurodegeneration and AD patients with, indicating their possible systemic involvement in AD.

Keywords: Alzheimer’s sisease, ULK1, mRNA expression, RT-PCR

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Authors: Yasser Mahmoudi, Nader Karimi

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The present work investigates numerically the effect of thermal radiation from the solid phase on the rate of heat transfer inside a porous medium. Forced convection heat transfer process within a pipe filled with a porous media is considered. The Darcy-Brinkman-Forchheimer model is utilized to represent the fluid transport within the porous medium. A local thermal non-equilibrium (LTNE), two-equation model is used to represent the energy transport for the solid and fluid phases. The radiative heat transfer equation is solved by discrete ordinate method (DOM) to compute the radiative heat flux in the porous medium. Two primary approaches (models A and B) are used to represent the boundary conditions for constant wall heat flux. The effects of radiative heat transfer on the Nusselt numbers of the two phases are examined by comparing the results obtained by the application of models A and B. The fluid Nusselt numbers calculated by the application of models A and B show that the Nusselt number obtained by model A for the radiative case is higher than those predicted for the non-radiative case. However, for model B the fluid Nusselt numbers obtained for the radiative and non-radiative cases are similar.

Keywords: porous media, local thermal non-equilibrium, forced convection heat transfer, thermal radiation, Discrete Ordinate Method (DOM)

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Authors: Muhammad Shahrukh Saeed, Syed Ahmad Nameer, Shafiq Ur Rehman, Aisha Jillani

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Heat exchangers play a critical role in industrial applications of thermal systems. Its physical size and performance are vital parameters; therefore enhancement of heat transfer through different techniques remained a major research area for both academia and industry. This research reports the main purpose of heat exchanger with better kit design which plays a vital role during the process of heat transfer. Plate type heat exchanger mainly requires a design in which the plates can be easily be installed and removed without having any problem with the plates. For the flow of the fluid within the heat exchanger, it requires a flow should be fully developed. As natural laws allows the driving energy of the system to flow until equilibrium is achieved. As with a plate type heat exchanger heat the heat penetrates the surface which separates the hot medium with the cold one very easily. As some of the precautions should be considered while taking the heat exchanger accountable like heat should transfer from hot medium to cold, there should always be difference in temperature present and heat loss from hot body should be equal to the heat gained by the cold body regardless of the losses present to the surroundings. Aluminum plates of same grade are used in all experiments to ensure similarity. Size of all plates was 254 mm X 100 mm and thickness was taken as 5 mm.

Keywords: heat transfer coefficient, aluminium, entry length, design

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Authors: Dipanshu Sur, Ratnabali Chakravorty

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Background: Polycystic ovary syndrome (PCOS) is the most common metabolic abnormality such as changes in lipid profile, diabetes, hypertension and metabolic syndrome occurring in young women of reproductive age. Low vitamin D levels were found to be associated with the development of obesity and insulin resistance in women with PCOS. Variants on vitamin D receptor (VDR) gene have also been related to metabolic comorbidities in general population. Aim: The aim of this case-control study was to investigate whether the VDR gene polymorphisms are associated with susceptibility to PCOS. Methods: Women with PCOS and a control group, all aged 16-40 years, were enrolled. Genotyping of VDR Fok-I (rs2228570), VDR Apa-I (rs7975232) as well as GC (rs2282679), DHCR7 (rs12785878) SNPs between groups were determined by using direct sequencing. Serum 25-hydroxyvitamin D [25(OH)] levels were measured by ELISA. Results: Mean serum 25(OH)D in the PCOS and control samples were 19.08±7 and 23.27±6.03 (p=0.048) which were significantly lower in PCOS patients compared with controls. CC genotype of the VDR Apa-I SNP was same frequent in PCOS (25.6%) and controls (25.6%) (OR: 0.9995; 95%CI: 0.528 to 1.8921; p= 0.9987). The CC genotype was also significantly associated with both lower E2 (p=0.031) and Androstenedione levels (p=0.062). We observed a significant association of GC polymorphism with 25(OH)D levels. PCOS women carrying the GG genotype (in GC genes) had significantly higher risk for vitamin D deficiency than women carrying the TT genotype. Conclusions: In conclusion, data from this study indicate that vitamin D levels are lower, and vitamin D deficiency more frequent, in PCOS than in controls. The present findings suggest that the Apa-I, Fok-I polymorphism of the VDR gene is associated with PCOS and seems to modulate ovarian steroid secretion. Further studies are needed to better clarify the biological mechanisms by which the polymorphism influences PCOS risk.

Keywords: vitamin D receptor, polymorphism, vitamin D, polycystic ovary syndrome

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Authors: Micheale Yifter Weldemichael, Hailay Mehari Gebremedhn, Teklehaimanot Hailesslasie

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The advancement of target-specific genome editing tools, including clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9 (Cas9), mega-nucleases, base editing (BE), prime editing (PE), transcription activator-like endonucleases (TALENs), and zinc-finger nucleases (ZFNs), have paved the way for a modern era of gene editing. CRISPR/Cas9, as a versatile, simple, cost-effective and robust system for genome editing, has dominated the genome manipulation field over the last few years. The application of CRISPR/Cas9 in sorghum improvement is particularly vital in the context of ecological, environmental and agricultural challenges, as well as global climate change. In this context, gene editing using CRISPR/Cas9 can improve nutritional value, yield, resistance to pests and disease and tolerance to different abiotic stress. Moreover, CRISPR/Cas9 can potentially perform complex editing to reshape already available elite varieties and new genetic variations. However, existing research is targeted at improving even further the effectiveness of the CRISPR/Cas9 genome editing techniques to fruitfully edit endogenous sorghum genes. These findings suggest that genome editing is a feasible and successful venture in sorghum. Newer improvements and developments of CRISPR/Cas9 techniques have further qualified researchers to modify extra genes in sorghum with improved efficiency. The fruitful application and development of CRISPR techniques for genome editing in sorghum will not only help in gene discovery, creating new, improved traits in sorghum regulating gene expression sorghum functional genomics, but also in making site-specific integration events.

Keywords: CRISPR/Cas9, genome editing, quality, sorghum, stress, yield

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Authors: Hamed Sanei, Mohammad Bagher Ayani

Abstract:

Optimizations of Plate Heat Exchangers (PHS) have received great attention in the past decade. In this study, heat transfer and pressure drop coefficients are compared for rectangular and circular PHS employing numerical simulations. Plates are designed to have equivalent areas. Simulations were implemented to investigate the efficiency of PHSs considering heat transfer, friction factor and pressure drop. Amount of heat transfer and pressure drop was obtained for different range of Reynolds numbers. These two parameters were compared with aim of F "weighting factor correlation". In this comparison, the minimum amount of F indicates higher efficiency. Results reveal that the F value for rectangular shape is less than circular plate, and hence using rectangular shape of PHS is more efficient than circular one. It was observed that, the amount of friction factor is correlated to the Reynolds numbers, such that friction factor decreased in both rectangular and circular plates with an increase in Reynolds number. Furthermore, such simulations revealed that the amount of heat transfer in rectangular plate is more than circular plate for different range of Reynolds numbers. The difference is more distinct for higher Reynolds number. However, amount of pressure drop in circular plate is less than rectangular plate for the same range of Reynolds numbers which is considered as a negative point for rectangular plate efficiency. It can be concluded that, while rectangular PHSs occupy more space than circular plate, the efficiency of rectangular plate is higher.

Keywords: Chevron corrugated plate heat exchanger, heat transfer, friction factor, Reynolds numbers

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