Search results for: exponential expression profile

Authors: Christopher R. Triggle, Hong Ding, Khaled Machaca, Gnanapragasam Arunachalam

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The antidiabetic drug, metformin, has been in clinical use for over 50 years and remains the first choice drug for the treatment of type two diabetes. In addition to its effectiveness as an oral anti-hyperglycaemic drug metformin also possesses vasculoprotective effects that are assumed to be secondary to its ability to reduce insulin resistance and control glycated hemoglobin levels; however, recent data from our laboratory indicate that metformin also has direct vasoprotective effects that are mediated, at least in part, via the anti-ageing gene, SIRT1. Diabetes is a major risk factor for the development of cardiovascular disease (CVD) and it is also well established that tobacco use further enhances the risk of CVD; however, it is not known whether treatment with metformin can offset the negative effects of diabetes and tobacco use on cardiac function. The current study was therefore designed to investigate 1: the effects of hyperglycaemia (HG) either alone or in the presence of elevated fatty acids (palmitate) and nicotine on the protein expression levels of the deacetylase sirtuin 1 (the protein product of SIRT1), anti-apoptotic Bcl-2, pro-apoptotic BIM and the pro-apoptotic, tumour suppressor protein, acetylated p53 in cardiomyocytes. 2: the ability of metformin to prevent the detrimental effects of HG, palmitate and nicotine on cardiomyocyte survival. Cell culture protocols were designed using a rat cardiomyocyte cell line, H9c2, either under normal glycaemic (NG) conditions of 5.5mM glucose, or hyperglycaemic conditions (HG) of 25mM glucose with, or without, added palmitate (250μM) or nicotine (1.0mM) for 24h. Immuno-blotting was used to detect the expression of sirtuin 1, Bcl-2, BIM, acetylated (Ac)-p53, p53 with β-actin used as the reference protein. Exposure to HG, palmitate, or nicotine alone significantly reduced expression of sirtuin1, Bcl-2 and raised the expression levels of acetylated p53 and BIM; however, the combination of HG, palmitate and nicotine had a synergistic effect to significantly suppress the expression levels of sirtuin 1 and Bcl-2, but further enhanced the expression of Ac-p53, and BIM. The inclusion of 1000μM, but not 50μM, metformin in the H9c2 cell culture protocol prevented the effects of HG, palmitate and nicotine on the pro-apoptotic pathways. Collectively these data indicate that metformin, in addition to its anti-hyperglycaemic and vasculoprotective properties, also has direct cardioprotective actions that offset the negative effects of hyerglycaemia, elevated free fatty acids and nicotine on cardiac cell survival. These data are of particular significance for the treatment of patients with diabetes who are also smokers as the inclusion of metformin in their therapeutic treatment plan should help reduce cardiac-related morbidity and mortality.

Keywords: apoptosis, cardiac muscle, diabetes, metformin, nicotine

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Authors: Nan Deng, Zhenqiu Liu

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Thousands of patients with metastatic tumors were diagnosed with cancers of unknown primary sites each year. The inability to identify the primary cancer site may lead to inappropriate treatment and unexpected prognosis. Nowadays, a large amount of genomics and transcriptomics cancer data has been generated by next-generation sequencing (NGS) technologies, and The Cancer Genome Atlas (TCGA) database has accrued thousands of human cancer tumors and healthy controls, which provides an abundance of resource to differentiate cancer types. Meanwhile, deep convolutional neural networks (CNNs) have shown high accuracy on classification among a large number of image object categories. Here, we utilize 25 cancer primary tumors and 3 normal tissues from TCGA and convert their RNA-Seq gene expression profiling to color images; train, validate and test a CNN classifier directly from these images. The performance result shows that our CNN classifier can archive >80% test accuracy on most of the tumors and normal tissues. Since the gene expression pattern of distant metastases is similar to their primary tumors, the CNN classifier may provide a potential computational strategy on identifying the unknown primary origin of metastatic cancer in order to plan appropriate treatment for patients.

Keywords: bioinformatics, cancer, convolutional neural network, deep leaning, gene expression pattern

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Authors: Zhiguo Yang, Xiangan Yue, Minglu Shao, Yue Yang, Rongjie Yan

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It is difficult to realize deep profile control because of the small pore-throats and easy water channeling in low-permeability heterogeneous reservoir, and the traditional polymer microspheres have the contradiction between injection and plugging. In order to solve this contradiction, the controllable self-aggregating colloidal particles (CSA) containing amide groups on the surface of microspheres was prepared based on emulsion polymerization of styrene and acrylamide. The dispersed solution of CSA colloidal particles, whose particle size is much smaller than the diameter of pore-throats, was injected into the reservoir. When the microspheres migrated to the deep part of reservoir, , these CSA colloidal particles could automatically self-aggregate into large particle clusters under the action of the shielding agent and the control agent, so as to realize the plugging of the water channels. In this paper, the morphology, temperature resistance and self-aggregation properties of CSA microspheres were studied by transmission electron microscopy (TEM) and bottle test. The results showed that CSA microspheres exhibited heterogeneous core-shell structure, good dispersion, and outstanding thermal stability. The microspheres remain regular and uniform spheres at 100℃ after aging for 35 days. With the increase of the concentration of the cations, the self-aggregation time of CSA was gradually shortened, and the influence of bivalent cations was greater than that of monovalent cations. Core flooding experiments showed that CSA polymer microspheres have good injection properties, CSA particle clusters can effective plug the water channels and migrate to the deep part of the reservoir for profile control.

Keywords: heterogeneous reservoir, deep profile control, emulsion polymerization, colloidal particles, plugging characteristic

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Authors: S. R. A. Rahim, I. Musirin, M. M. Othman, M. H. Hussain

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Loss minimization is a long progressing issue mainly in distribution system. Nevertheless, its effect led to temperature rise due to significant voltage drop through the distribution line. Thus, compensation scheme should be proper scheduled in the attempt to alleviate the voltage drop phenomenon. Distributed generation has been profoundly known for voltage profile improvement provided that over-compensation or under-compensation phenomena are avoided. This paper addresses the issue of voltage improvement through different type DG installation. In ensuring optimal sizing and location of the DGs, predeveloped EMEFA technique was made to be used for this purpose. Incremental loading condition subjected to the system is the concern such that it is beneficial to the power system operator.

Keywords: distributed generation, EMEFA, power loss, voltage profile

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Authors: Y. M. Aiyesimi, G. T. Okedayo, O. W. Lawal

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An investigation is made for unsteady MHD thin film flow of a third grade fluid down an inclined plane with slip boundary condition. The non-linear partial differential equation governing the flow and heat transfer are evaluated numerically using computer software called Maple to obtain velocity and temperature profile. The effect of slip and other various physical parameter on both velocity and temperature profile obtained are studied through several graphs.

Keywords: non-Newtonian fluid, MHD flow, third-grade fluid, Maple, slip boundary condition, heat transfer

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Authors: Zelikha Labbani

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The In Vitro isolated micro spore culture is the most powerful androgenic pathway to produce doubled haploid plants in the short time. To deviate a micro spore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the micro spore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of micro spore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. As haploid single cells, micro spore became a strategy to achieve various objectives particularly in genetic engineering. In this study we would show the most recent advances in the producing haploid embryos via In Vitro isolated micro spore culture.

Keywords: haploid cells, In Vitro isolated microspore culture, success

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Authors: Siddharth Soni, Gourav Kumar Pandey, Sneha Kumari, Dev Mani Pandey, Koel Mukherjee

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The silkworm Bombyx mori is a commercially important insect, but a major roadblock in silk production are silkworm diseases. Flacherie is one of the diseases of the silkworm, that affects the midgut of the 4th and 5th instar larvae and eventually makes them lethargic, stop feeding and finally result in their death. The concerned disease is a result of bacterial and viral infection and in some instances a combination of both. The present study aims to identify and study the expression level of genes in the flacherie condition. For the said work, total RNA was isolated from the infected larvae at their most probable infectious instar and cDNA was synthesized using Reverse Transcriptase PCR (RT-PCR). This cDNA was then used to amplify disease relalted genes whose expression levels were checked using quantitaive PCR (qPCR) using the double delta Ct method. Cry toxin receptors like APN and BtR-175, ROS mediator Dual Oxidase are few proteins whose genes were overexpressed. Interestingly, pattern recognition receptors (PRRs) C-type lectins' genes were found to be downregulated. The results explain about the strong expression of genes that can distinguish the concerned protein in the midgut of diseased silkworm and thereby aiding knowledge in the field of inhibitor designing research.

Keywords: Bombyx mori, flacherie disease, inhibitor designing, up and down regulation

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Authors: Sai Radavaram

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A wideband low-profile circularly-polarized antenna, consisting of 2×2 sequentially-rotated, differentially-fed, slotted rectangular patch elements, is proposed. To realize the right-hand circular polarization, an anti-clockwise phase rotation of 0o, -90o, -180o and -270o is applied between the antenna elements. The proposed antenna, with a height of only 0.02lambda (where lambda is the wavelength of the antenna at the center frequency of the antenna), exhibits a 68% impedance bandwidth from 2 to 4.05 GHz with a 3dB axial ratio bandwidth in the order of 56% from 2.25 to 4.05 GHz. Moreover, a wide 3dB axial ratio beamwidth of 140o is obtained at the center frequency of 3 GHz, along with symmetrical radiation patterns over the operating frequency band.

Keywords: circular polarization, sequentially rotated, slotted patch antennas, wideband

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Authors: José Alberto García Fernández, Zhimin Du, Xinqiao Jin

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Nowadays, data center industry faces strong challenges for increasing the speed and data processing capacities while at the same time is trying to keep their devices a suitable working temperature without penalizing that capacity. Consequently, the cooling systems of this kind of facilities use a large amount of energy to dissipate the heat generated inside the servers, and developing new cooling techniques or perfecting those already existing would be a great advance in this type of industry. The installation of a temperature sensor matrix distributed in the structure of each server would provide the necessary information for collecting the required data for obtaining a temperature profile instantly inside them. However, the number of temperature probes required to obtain the temperature profiles with sufficient accuracy is very high and expensive. Therefore, other less intrusive techniques are employed where each point that characterizes the server temperature profile is obtained by solving differential equations through simulation methods, simplifying data collection techniques but increasing the time to obtain results. In order to reduce these calculation times, complicated and slow computational fluid dynamics simulations are replaced by simpler and faster finite element method simulations which solve the Burgers‘ equations by backward, forward and central discretization techniques after simplifying the energy and enthalpy conservation differential equations. The discretization methods employed for solving the first and second order derivatives of the obtained Burgers‘ equation after these simplifications are the key for obtaining results with greater or lesser accuracy regardless of the characteristic truncation error.

Keywords: Burgers' equations, CFD simulation, data center, discretization methods, FEM simulation, temperature profile

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Authors: Christine Demaecker

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Many researchers have underlined the importance of metaphors in specialised language. Their use of specific domains helps us understand the conceptualisations used to communicate new ideas or difficult topics. Within the wide area of specialised discourse, wine tasting is a very specific example because it is almost exclusively metaphoric. Wine tasting metaphors express various conceptualisations. They are not linguistic but rather conceptual, as defined by Lakoff & Johnson. They correspond to the linguistic expression of a mental projection from a well-known or more concrete source domain onto the target domain, which is the taste of wine. But unlike most specialised terminologies, the vocabulary is never clearly defined. When metaphorical terms are listed in dictionaries, their definitions remain vague, unclear, and circular. They cannot be replaced by literal linguistic expressions. This makes it impossible to transfer them into another language with the traditional linguistic translation methods. Qualitative research investigates whether wine tasting metaphors could rather be translated with the cognitive translation process, as well described by Nili Mandelblit (1995). The research is based on a corpus compiled from two high-profile wine guides; the Parker’s Wine Buyer’s Guide and its translation into French and the Guide Hachette des Vins and its translation into English. In this small corpus with a total of 68,826 words, 170 metaphoric expressions have been identified in the original English text and 180 in the original French text. They have been selected with the MIPVU Metaphor Identification Procedure developed at the Vrije Universiteit Amsterdam. The selection demonstrates that both languages use the same set of conceptualisations, which are often combined in wine tasting notes, creating conceptual integrations or blends. The comparison of expressions in the source and target texts also demonstrates the use of the cognitive translation approach. In accordance with the principle of relevance, the translation always uses target language conceptualisations, but compared to the original, the highlighting of the projection is often different. Also, when original metaphors are complex with a combination of conceptualisations, at least one element of the original metaphor underlies the target expression. This approach perfectly integrates into Lederer’s interpretative model of translation (2006). In this triangular model, the transfer of conceptualisation could be included at the level of ‘deverbalisation/reverbalisation’, the crucial stage of the model, where the extraction of meaning combines with the encyclopedic background to generate the target text.

Keywords: cognitive translation, conceptual integration, conceptual metaphor, interpretative model of translation, wine tasting metaphor

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Authors: Nisreen Al-Khawaldeh

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The study investigates the expressions voiced by Jordanian youth as rejoinders to the expressions of reprimands. It also explores the impact sociocultural variables exert on such types of rejoinders. To our best knowledge, this study is the first of its kind. Despite the significance and sensitivity of such type of communicative act, there is a scarcity of research on it, and it has not been investigated in the Jordanian context. Data collected from observation of naturally occurring data. Data have been qualitatively and quantitatively analyzed in light of the rapport management approach (RMA). The analysis revealed different types of rejoinders, among which was the expression of apology, admitting responsibility, and trying to manage and fix the situation were the most used strategies. Variation in the types of strategies was attributed to the influence of the sociocultural variables. Promising ideas were recommended for future research.

Keywords: gender, rejoinder to reprimand, Jordanian youth, rapport management approach

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Authors: Paul Shize Li, Frank Alber

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A fundamental task of clinical genomics is to unravel the functions of genes and their associations with disorders. Although experimental biology has made efforts to discover and elucidate the molecular mechanisms of individual genes in the past decades, still about 40% of human genes have unknown functions, not to mention the diseases they may be related to. For those biologists who are interested in a particular gene with unknown functions, a powerful computational method tailored for inferring the functions and disease relevance of uncharacterized genes is strongly needed. Studies have shown that genes strongly linked to each other in multiple biological networks are more likely to have similar functions. This indicates that the densely connected subgraphs in multiple biological networks are useful in the functional and phenotypic annotation of uncharacterized genes. Therefore, in this work, we have developed an integrative network approach to identify the frequent local clusters, which are defined as those densely connected subgraphs that frequently occur in multiple biological networks and consist of the query gene that has few or no disease or function annotations. This is a local clustering algorithm that models multiple biological networks sharing the same gene set as a three-dimensional matrix, the so-called tensor, and employs the tensor-based optimization method to efficiently find the frequent local clusters. Specifically, massive public gene expression data sets that comprehensively cover dynamic, physiological, and environmental conditions are used to generate hundreds of gene co-expression networks. By integrating these gene co-expression networks, for a given uncharacterized gene that is of biologist’s interest, the proposed method can be applied to identify the frequent local clusters that consist of this uncharacterized gene. Finally, those frequent local clusters are used for function and disease annotation of this uncharacterized gene. This local tensor clustering algorithm outperformed the competing tensor-based algorithm in both module discovery and running time. We also demonstrated the use of the proposed method on real data of hundreds of gene co-expression data and showed that it can comprehensively characterize the query gene. Therefore, this study provides a new tool for annotating the uncharacterized genes and has great potential to assist clinical genomic diagnostics.

Keywords: local tensor clustering, query gene, gene co-expression network, gene annotation

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Authors: Gadiri Sabiha

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Introduction : IgE-dependent cow's milk protein allergy (APLV) is one of the most common allergies in children and is one of the three most common allergies observed in children under 6 years of age. Its natural evolution is most often towards healing. The objective is to determine the sensitization profile of patients allergic to cow's milk (VL). Material and method :A retrospective study carried out on a pediatric population (age < 12 years) over a period of four years (2018-2021) in the context of a suspected food allergy to cow's milk proteins carried out on 121 children aged between 8 months -12 years The search for specific IgE was carried out by immunodot (EUROLINE Pediatric; EUROIMMUN) test which allows a semi-quantitative determination of specific IgE. Results 36 patients (29.7%) had a cow's milk protein allergy (ALPV) with a slight female predominance (58.33% girls vs 41.66% boys) The main clinical signs were: acute diarrhoea; vomiting; Intense abdominal pain, and cutaneous signs (pruritus/urticaria) with respective frequencies of 72%; 58%; 44% and 19%. The 3 major and specific VL allergens identified were beta-lactoglobulin 59% caseins 51% and alpha-lactalbumin 29.7%, The profile of sensitization to LV varies according to age, in infants before 1 year of anti-casein, IgE are predominant 83.3%, followed by beta-lactoglobulin 66.66% and alpha-lactolbumin 50% Conclusion CMPA is a frequent pathology which ranks among the three most common food allergies in children. This is the first to appear, most often starting in infants under 6 months old.

Keywords: specific Ige, food allergy, cow 's milk, child

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Authors: Katerina H. Takova, Ivan N. Minkov, Gergana G. Zahmanova

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Molecular farming is the production of recombinant proteins in plants with the aim to use the protein as a purified product, crude extract or directly in the planta. Plants gain more attention as expression systems compared to other ones due to the cost effective production of pharmaceutically important proteins, appropriate post-translational modifications, assembly of complex proteins, absence of human pathogens to name a few. In addition, transient expression in plant leaves enables production of recombinant proteins within few weeks. Hepatitis E virus (HEV) is a causative agent of acute hepatitis. HEV causes epidemics in developing countries and is primarily transmitted through the fecal-oral route. Presently, all efforts for development of Hepatitis E vaccine are focused on the Open Read Frame 2 (ORF2) capsid protein as it contains epitopes that can induce neutralizing antibodies. For our purpose, we used the CMPV-based vector-pEAQ-HT for transient expression of HEV ORF2 in Nicotiana benthamina. Different molecular analysis (Western blot and ELISA) showed that HEV ORF2 capsid protein was expressed in plant tissue in high-yield up to 1g/kg of fresh leaf tissue. Electron microscopy showed that the capsid protein spontaneously assembled in low abundance virus-like particles (VLPs), which are highly immunogenic structures and suitable for vaccine development. The expressed protein was recognized by both human and swine HEV positive sera and can be used as a diagnostic reagent for the detection of HEV infection. Production of HEV capsid protein in plants is a promising technology for further HEV vaccine investigations. Here, we reported for a rapid high-yield transient expression of a recombinant protein in plants suitable for vaccine production as well as a diagnostic reagent. Acknowledgments -The authors’ research on HEV is supported with grants from the Project PlantaSYST under the Widening Program, H2020 as well as under the UK Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic Programme Grant ‘Understanding and Exploiting Plant and Microbial Secondary Metabolism’ (BB/J004596/1). The authors want to thank Prof. George Lomonossoff (JIC, Norwich, UK) for his contribution.

Keywords: hepatitis E virus, plant molecular farming, transient expression, vaccines

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Authors: Yousef M. Al-Roomi, Kaneez Fatema Hussain

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This work evaluates the thermal degradation kinetic parameters of CaSO₄-complex isolated after the inhibition effect of maleic-anhydride based polymer (YMR-polymers). Pyrolysis experiments were carried out at four heating rates (5, 10, 15 and 20°C/min). Several analytical model-free methods were used to determine the kinetic parameters, including Friedman, Coats and Redfern, Kissinger, Flynn-Wall-Ozawa and Kissinger-Akahira–Sunose methods. The Criado model fitting method based on real mechanism followed in thermal degradation of the complex has been applied to explain the degradation mechanism of CaSO₄-complex. In addition, a simple dynamic model was proposed over two temperature ranges for successive decomposition of CaSO₄-complex which has a combination of organic and inorganic part (adsorbed polymer + CaSO₄.2H₂O scale). The model developed enabled the assessment of pre-exponential factor (A) and apparent activation-energy (Eₐ) for both stages independently using a mathematical developed expression based on an integral solution. The unique reaction mechanism approach applied in this study showed that (Eₐ₁-160.5 kJ/mole) for organic decomposition (adsorbed polymer stage-I) has been lower than Eₐ₂-388 kJ/mole for the CaSO₄ decomposition (inorganic stage-II). Further adsorbed YMR-antiscalant not only reduced the decomposition temperature of CaSO₄-complex compared to CaSO₄-blank (CaSO₄.2H₂O scales in the absence of YMR-polymer) but also distorted the crystal lattice of the organic complex of CaSO₄ precipitates, destroying their compact and regular crystal structures observed from XRD and SEM studies.

Keywords: CaSO₄-complex, maleic-anhydride polymers, thermal degradation kinetics and mechanism, XRD and SEM studies

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Authors: Andleeb Zahra, Itrat Rubab, Sumaira Malik, Amina Khan, Muhammad Jawad Khan, M. Qaiser Fatmi

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Oral squamous cell carcinoma (OSCC) is one of the most common cancers worldwide. Recent studies have highlighted the role of miRNA in disease pathology, indicating its potential use in an early diagnostic tool. miRNAs are small, double stranded, non-coding RNAs that regulate gene expression by deregulating mRNAs. miRNAs play important roles in modifying various cellular processes such as cell growth, differentiation, apoptosis, and immune response. Dis-regulated expression of miRNAs is known to affect the cell growth, and this may function as tumor suppressors or oncogenes in various cancers. Objectives: The main objectives of this study were to characterize the extracellular miRNAs involved in oral cancer (OC) to assist early detection of cancer as well as to propose a list of genes that can potentially be used as biomarkers of OC. We used gene expression data by microarrays already available in literature. Materials and Methods: In the first step, a total of 318 miRNAs involved in oral carcinoma were shortlisted followed by the prediction of their target genes. Simultaneously, the differentially expressed genes (DEGs) of oral carcinoma from all experiments were identified. The common genes between lists of DEGs of OC based on experimentally proven data and target genes of each miRNA were identified. These common genes are the targets of specific miRNA, which is involved in OC. Finally, a list of genes was generated which may be used as biomarker of OC. Results and Conclusion: In results, we included some of pathways in cancer to show the change in gene expression under the control of specific miRNA. Ingenuity pathway analysis (IPA) provided a list of major biomarkers like CDH2, CDK7 and functional enrichment analysis identified the role of miRNA in major pathways like cell adhesion molecules pathway affected by cancer. We observed that at least 25 genes are regulated by maximum number of miRNAs, and thereby, they can be used as biomarkers of OC. To better understand the role of miRNA with respect to their target genes further experiments are required, and our study provides a platform to better understand the miRNA-OC relationship at genomics level.

Keywords: biomarkers, gene expression, miRNA, oral carcinoma

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Authors: Amani Waheed, Adel Mishriky, Rasha Farouk, Essam Abdallah, Sarah Hussein

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Background: Occupational stress plays a crucial role in professional drivers' health. They are exposed to high workloads, low physical activity, high demand and low decisions as well as poor lifestyle factors including poor diet, sedentary work, and smoking. Dyslipidemia is a well-established modifiable cardiovascular risk factor. Occupational stress and other forms of chronic stress have been associated with raised levels of atherogenic lipids. Although stress management has some evidence in improving lipid profile, the association between occupational stress and dyslipidemia is not clear. Objectives: To assess the relational between occupational stress and lipid profile among professional drivers. Methodology: A cross-sectional study conducted at a large company in Ismailia City, Egypt, where, 131 professional drivers divided into 44 car drivers, 43 bus drivers, and 44 truck drivers were eligible after applying exclusion criteria. Occupational stress index (OSI), non-occupational risk factors of dyslipidemia were assessed using interview structured questionnaire. Blood pressure, body mass index (BMI) and lipid profile were measured. Results: The mean of total OSI score was 79.98 ± 6.14. The total OSI score is highest among truck drivers (82.16 ± 4.62), then bus drivers (80.26 ± 6.02) and lowest among car drivers (77.55 ± 6.79) with statistically significant. Eighty percent had Dyslipidemia. The duration of driving hours per day, exposure to passive smoking and increased BMI were the risk factors. No statistical significance between Total OSI score and dyslipidemia. Using, logistic regression analysis, occupational stress, duration of driving hours per day, and BMI were positive significant predictors for dyslipidemia. Conclusion: Professional drivers are exposed to occupational stress. A high proportion of drivers have dyslipidemia. Total OSI score doesn't have statistically significant relation with dyslipidemia.

Keywords: body mass index, dyslipidaemia, occupational stress, professional drivers

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Authors: Soumya S., Manju Nidagodu Jayakumar, Vellore Kannan Gopinath

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Dental pulp inflammation resulting from dental caries often leads to a pathologic condition known as irreversible pulpitis and the currently managed by root canal treatment. Extirpation of the entire pulp tissue is done during this procedure, and the canal space is filled with synthetic materials. Recent studies in the stem cell biology state that some portion of the irreversibly inflamed pulp tissue could be viable with progenitor cells, having the properties similar to that of Mesenchymal stem cells. Hence, we aim to isolate Dental Pulp Stem Cells (DPSCs) from patients diagnosed with severe irreversible pulpitis and characterize the cells for the MSC specific markers. The pulp tissue was collected from the dental clinic and subjected to collagenase/dispase digestion. The isolated cells were expanded in culture, and the phenotypic characterization was done using flow cytometry. MSC specific markers such as CD-90, CD-73, and CD-105 were analysed along with negative markers such as CD-14 and CD-45. The isolated cells expressed positive expression for CD markers with CD90 and CD105 ( > 95%) and CD73 (19%). The cells did not express the negative markers CD-14 and CD-45. The commercially available DPSCs from vital extracted teeth, preferably molar/wisdom teeth with large pulp cavity or incomplete root growth in young patients (aged 15-30 years) showed more than 90% expression for all the CD markers such as CD-90, 73 and 105, whereas negative for CD-14 and CD-45. The DPSCs isolated from inflamed pulp tissue showed a less expression for CD-73 compared to the commercially available DPSCs whereas, as the other two markers were found to show similar percentage of positive expression. This could be attributed to the fact that the pulp population is very heterogeneous and we used the pooled tissue from different patients. Hence the phenotypic characterization and comparison with the commercially available DPSCs proved that the inflamed pulp tissue is a good source of MSC like cells which can be utilized further for regenerative application.

Keywords: collagenase/dispase, dental pulp stem cells, flow cytometry, irreversible pulpitis

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Authors: Cheng-Cao Sun, Shu-Jun Li, Cuili Yang, Yongyong Xi, Liang Wang, Feng Zhang, De-Jia Li

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MicroRNAs (miRNAs) act as key regulators of multiple cancers. Hsa-miR-329 (miR-329) functions as a tumor suppressor in some malignancies. However, its role on lung cancer remains poorly understood. In this study, we investigated the role of miR-329 on the development of lung cancer. The results indicated that miR-329 was decreased in primary lung cancer tissues compared with matched adjacent normal lung tissues and very low levels were found in a non-small cell lung cancer (NSCLC) cell lines. Ectopic expression of miR-329 in lung cancer cell lines substantially repressed cell growth as evidenced by cell viability assay, colony formation assay and BrdU staining, through inhibiting cyclin D1, cyclin D2, and up-regulatiing p57(Kip2) and p21(WAF1/CIP1). In addition, miR-329 promoted NSCLC cell apoptosis, as indicated by up-regulation of key apoptosis gene cleaved caspase-3, and down-regulation of anti-apoptosis gene Bcl2. Moreover, miR-329 inhibited cellular migration and invasiveness through inhibiting matrix metalloproteinases (MMP)-7 and MMP-9. Further, oncogene MET was revealed to be a putative target of miR-329, which was inversely correlated with miR-329 expression. Furthermore, down-regulation of MET by siRNA performed similar effects to over-expression of miR-329. Collectively, our results demonstrated that miR-329 played a pivotal role in lung cancer through inhibiting cell proliferation, migration, invasion, and promoting apoptosis by targeting oncogenic MET.

Keywords: hsa-miRNA-329(miR-329), MET, non-small cell lung cancer (NSCLC), proliferation, apoptosis

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Authors: Shidvash Vakilipour, Masoud Mohammadi, Rouzbeh Riazi, Scott Ormiston, Kimia Amiri, Sahar Barati

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An essential component of a finite volume method (FVM) is the advection scheme that estimates values on the cell faces based on the calculated values on the nodes or cell centers. The most widely used advection schemes are upwind schemes. These schemes have been developed in FVM on different kinds of structured and unstructured grids. In this research, the physical influence scheme (PIS) is developed for a cell-centered FVM that uses an implicit coupled solver. Results are compared with the exponential differencing scheme (EDS) and the skew upwind differencing scheme (SUDS). Accuracy of these schemes is evaluated for a lid-driven cavity flow at Re = 1000, 3200, and 5000 and a backward-facing step flow at Re = 800. Simulations show considerable differences between the results of EDS scheme with benchmarks, especially for the lid-driven cavity flow at high Reynolds numbers. These differences occur due to false diffusion. Comparing SUDS and PIS schemes shows relatively close results for the backward-facing step flow and different results in lid-driven cavity flow. The poor results of SUDS in the lid-driven cavity flow can be related to its lack of sensitivity to the pressure difference between cell face and upwind points, which is critical for the prediction of such vortex dominant flows.

Keywords: cell-centered finite volume method, coupled solver, exponential differencing scheme (EDS), physical influence scheme (PIS), pressure weighted interpolation method (PWIM), skew upwind differencing scheme (SUDS)

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Authors: Shangqing Song, Bin Xu, Yajun Cheng, Zhong Wang

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miRNAs derived from exosomes exist in a body fluid such as urine were regarded as potential biomarkers for various human cancers diagnosis and prognosis, as mature miRNAs can be steadily preserved by exosomes. However, its potential value in clear cell renal cell carcinoma (ccRCC) diagnosis and prognosis remains unclear. In the present study, differentially expressed miRNAs from urinal exosomes were identified by next-generation sequencing (NGS) technology. The 16 differentially expressed miRNAs were identified between ccRCC patients and healthy donors. To explore the specific diagnosis biomarker of ccRCC, we validated these urinary exosomes from 70 early-stage renal cancer patients, 30 healthy people and other urinary system cancers, including 30 early-stage prostate cancer patients and 30 early-stage bladder cancer patients by qRT-PCR. The results showed that urinary exosome miR-30c-5p could be stably amplified and meanwhile the expression of miR-30c-5p has no significant difference between other urinary system cancers and healthy control, however, expression level of miR-30c-5p in urinary exosomal of ccRCC patients was lower than healthy people and receiver operation characterization (ROC) curve showed that the area under the curve (AUC) values was 0.8192 (95% confidence interval was 0.7388-0.8996, P= 0.0000). In addition, up-regulating miR-30c-5p expression could inhibit renal cell carcinoma cells growth. Lastly, HSP5A was found as a direct target gene of miR-30c-5p. HSP5A depletion reversed the promoting effect of ccRCC growth casued by miR-30c-5p inhibitor, respectively. In conclusion, this study demonstrated that urinary exosomal miR-30c-5p is readily accessible as diagnosis biomarker of early-stage ccRCC, and miR-30c-5p might modulate the expression of HSPA5, which correlated with the progression of ccRCC.

Keywords: clear cell renal cell carcinoma, exosome, HSP5A, miR-30c-5p

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Authors: Masoud Sakhinia, Sajjad Ahmad

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Introduction: Though knowledge of the compositional makeup and structure of the limbal niche has progressed exponentially during the past decade, much is yet to be understood. Identifying the precise profile and role of the stromal makeup which spans the ocular surface may inform researchers of the most optimum conditions needed to effectively expand LESCs in vitro, whilst preserving their differentiation status and phenotype. Limbal fibroblasts, as opposed to corneal fibroblasts are thought to form an important component of the microenvironment where LESCs reside. Methods: The corneal stroma was tissue engineered in vitro using both limbal and corneal fibroblasts embedded within a tissue engineered 3D collagen matrix. The effect of these two different fibroblasts on LESCs and hTCEpi corneal epithelial cell line were then subsequently determined using phase contrast microscopy, histolological analysis and PCR for specific stem cell markers. The study aimed to develop an in vitro model which could be used to determine whether limbal, as opposed to corneal fibroblasts, maintained the stem cell phenotype of LESCs and hTCEpi cell line. Results: Tissue culture analysis was inconclusive and required further quantitative analysis for remarks on cell proliferation within the varying stroma. Histological analysis of the tissue-engineered cornea showed a comparable structure to that of the human cornea, though with limited epithelial stratification. PCR results for epithelial cell markers of cells cultured on limbal fibroblasts showed reduced expression of CK3, a negative marker for LESC’s, whilst also exhibiting a relatively low expression level of P63, a marker for undifferentiated LESCs. Conclusion: We have shown the potential for the construction of a tissue engineered human cornea using a 3D collagen matrix and described some preliminary results in the analysis of the effects of varying stroma consisting of limbal and corneal fibroblasts, respectively, on the proliferation of stem cell phenotype of primary LESCs and hTCEpi corneal epithelial cells. Although no definitive marker exists to conclusively illustrate the presence of LESCs, the combination of positive and negative stem cell markers in our study were inconclusive. Though it is less traslational to the human corneal model, the use of conditioned medium from that of limbal and corneal fibroblasts may provide a more simple avenue. Moreover, combinations of extracellular matrices could be used as a surrogate in these culture models.

Keywords: cornea, Limbal Stem Cells, tissue engineering, PCR

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Authors: Valizadeh Gever Bita, Joel Caren, Louisa Huand, Yu-Cheng Zhu, Esmaeil Amiri

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Within a honey bee colony, queen is the sole reproducer of fertilized eggs, while queens are safeguarded by worker bees, trophallactic behavior and food sharing activities could expose them to agrochemicals. Here, we assessed the effects of three widely used pesticides—Acephate, Bifenthrin, and Chlorantraniliprole— on worker bees, to investigate indirect effects on the physiology and reproductive traits of queens as well as the eggs they produce. Using RT-qPCR we measured the expression of several detoxification and immune genes in adult worker bees, queens, and freshly laid eggs after pesticide exposure. These analyses aimed to elucidate the physiological changes in queens and potential transgenerational effects. While no significant changes in reproductive traits were observed following Chlorantraniliprole and Bifenthrin exposure, Acephate caused adverse effects on egg size, egg-laying activity, and queen weight. The expression of detoxification, immune and antioxidant-related genes in workers, queens and freshly laid eggs changed over time in response to these pesticides. The results of this investigation revealed that pesticides can cause negative impact on queen physiology and reproduction indirectly through their effects on exposed worker bees. These effects can potentially extend to the next generation of honey bees.

Keywords: apis mellifera, egg laying, detoxification enzymes, gene expression, honey bee queen

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Authors: Vanessa Funk, Steven Blum, Stephanie Cole, Jorge Maciel, Matthew Lux

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Paper-based synthetic gene circuits offer a new paradigm for programmable, fieldable biodetection. We demonstrate that by freeze-drying gene circuits with in vitro expression machinery, we can use complimentary RNA sequences to trigger colorimetric changes upon rehydration. We have successfully utilized both green fluorescent protein and luciferase-based reporters for easy visualization purposes in solution. Through several efforts, we are aiming to use this new platform technology to address a variety of needs in portable detection by demonstrating several more expression and reporter systems for detection functions on paper. In addition to RNA-based biodetection, we are exploring the use of various mechanisms that cells use to respond to environmental conditions to move towards all-hazards detection. Examples include explosives, heavy metals for water quality, and toxic chemicals.

Keywords: cell-free lysates, detection, gene circuits, in vitro

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Authors: Yong Wook Kim

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The diversity of students in regular classrooms is increasing due to expand inclusive education and increase multicultural students in South Korea. In this diverse classroom environment, the universal design for learning (UDL) has been proposed as a way to meet both the educational need and social expectation of student achievement. UDL offers a variety of practical teaching methods, one of which is a differentiating instruction. The differentiating instruction has been pointed out resource limitation, organizational resistance, and lacks easy-to-implement framework. However, through the framework provided by the UDL, differentiating instruction is able to be flexible in their implementation. In practice, the UDL and differentiating instruction are complementary, but there is still a lack of research that suggests specific implementation methods that apply both concepts at the same time. This study was conducted to investigate the effects of differentiating instruction strategies according to learner characteristics (readiness, interest, learning profile), components of differentiating instruction (content, process, performance, learning environment), especially UDL principles (representation, behavior and expression, participation) existed in differentiating instruction, and implementation of UDL-based differentiating instruction through the Planning for All Learner (PAL) and UDL Lesson Plan Cycle. It is meaningful that such a series of studies can enhance the possibility of more concrete and realistic UDL-based teaching and learning strategies in the classroom, especially in inclusive settings.

Keywords: universal design for learning, differentiating instruction, UDL lesson plan, PAL

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Authors: Berengere Vire, Nicolas Salvetat, Yoann Lannay, Guillaume Marcellin, Siem Van Der Laan, Franck Molina, Dinah Weissmann

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Predicting suicidal behaviors is one of the most complex challenges of daily psychiatric practices. Today, suicide risk prediction using biological tools is not validated and is only based on subjective clinical reports of the at-risk individual. Therefore, there is a great need to identify biomarkers that would allow early identification of individuals at risk of suicide. Alterations of adenosine-to-inosine (A-to-I) RNA editing of neurotransmitter receptors and other proteins have been shown to be involved in etiology of different psychiatric disorders and linked to suicidal behavior. RNA editing is a co- or post-transcriptional process leading to a site-specific alteration in RNA sequences. It plays an important role in the epi transcriptomic regulation of RNA metabolism. On postmortem human brain tissue (prefrontal cortex) of depressed suicide victims, Alcediag found specific alterations of RNA editing activity on the mRNA coding for the serotonin 2C receptor (5-HT2cR). Additionally, an increase in expression levels of ADARs, the RNA editing enzymes, and modifications of RNA editing profiles of prime targets, such as phosphodiesterase 8A (PDE8A) mRNA, have also been observed. Interestingly, the PDE8A gene is located on chromosome 15q25.3, a genomic region that has recurrently been associated with the early-onset major depressive disorder (MDD). In the current study, we examined whether modifications in RNA editing profile of prime targets allow identifying disease-relevant blood biomarkers and evaluating suicide risk in patients. To address this question, we performed a clinical study to identify an RNA editing signature in blood of depressed patients with and without the history of suicide attempts. Patient’s samples were drawn in PAXgene tubes and analyzed on Alcediag’s proprietary RNA editing platform using next generation sequencing technology. In addition, gene expression analysis by quantitative PCR was performed. We generated a multivariate algorithm comprising various selected biomarkers to detect patients with a high risk to attempt suicide. We evaluated the diagnostic performance using the relative proportion of PDE8A mRNA editing at different sites and/or isoforms as well as the expression of PDE8A and the ADARs. The significance of these biomarkers for suicidality was evaluated using the area under the receiver-operating characteristic curve (AUC). The generated algorithm comprising the biomarkers was found to have strong diagnostic performances with high specificity and sensitivity. In conclusion, we developed tools to measure disease-specific biomarkers in blood samples of patients for identifying individuals at the greatest risk for future suicide attempts. This technology not only fosters patient management but is also suitable to predict the risk of drug-induced psychiatric side effects such as iatrogenic increase of suicidal ideas/behaviors.

Keywords: blood biomarker, next-generation-sequencing, RNA editing, suicide

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Authors: Amir Sattari, Mac Panah, Naeim Rashidfarokhi

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To enhance the mixing of fluid in a rectangular enclosure with a circular inlet and outlet, an energy-efficient approach is further investigated through computational fluid dynamics (CFD). Particle image velocimetry (PIV) measurements help confirm that the pulsation of the inflow velocity improves the mixing performance inside the enclosure considerably without increasing energy consumption. In this study, multiple CFD simulations with different turbulent models were performed. The results obtained were compared with experimental PIV results. This study investigates small-scale representations of flow patterns in a ventilated rectangular room. The objective is to validate the concept of an energy-efficient ventilation strategy with improved thermal comfort and reduction of stagnant air inside the room. Experimental and simulated results confirm that through pulsation of the inflow velocity, strong secondary vortices are generated downstream of the entrance wall-jet. The pulsatile inflow profile promotes a periodic generation of vortices with stronger eddies despite a relatively low inlet velocity, which leads to a larger boundary layer with increased kinetic energy in the occupied zone. A real-scale study was not conducted; however, it can be concluded that a constant velocity inflow profile can be replaced with a lower pulsated flow rate profile while preserving the mixing efficiency. Among the turbulent CFD models demonstrated in this study, SST-kω is most advantageous, exhibiting a similar global airflow pattern as in the experiments. The detailed near-wall velocity profile is utilized to identify the wall-jet instabilities that consist of mixing and boundary layers. The SAS method was later applied to predict the turbulent parameters in the center of the domain. In both cases, the predictions are in good agreement with the measured results.

Keywords: CFD, PIV, pulsatile inflow, ventilation, wall-jet

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Authors: Xinxiu Li, Chuqian Zheng, Yanyan Qian, Hong Fan

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Objectives: In hepatocellular carcinoma (HCC), oncogenes are continuously and robustly transcribed due to aberrant expression of essential components of the trans-acting super-enhancers (SE) complex. Preclinical and clinical trials are now being conducted on small-molecule inhibitors that target core-transcriptional components, including as transcriptional bromodomain protein 4 (BRD4) and cyclin-dependent kinase 7 (CDK7), in a number of malignant tumors. This study aims to explore whether co-overexpression of BRD4 and CDK7 is a potential marker of worse prognosis and a combined therapeutic target in HCC. Methods: The expression pattern of BRD4 and CDK7 and their correlation with prognosis in HCC were analyzed by RNA sequencing data and survival data of HCC patients from TCGA and GEO datasets. The protein levels of BRD4 and CDK7 were determined by immunohistochemistry (IHC), and survival data of patients were analyzed using the Kaplan-Meier method. The mRNA expression levels of genes in HCC cell lines were evaluated by quantitative PCR (q-PCR). CCK-8 and colony formation assays were conducted to assess cell proliferation of HCC upon treatment with BRD4 inhibitor JQ1 or/and CDK7 inhibitor THZ1. Results: It was shown that BRD4 and CDK7 were often overexpressed in HCCs and were associated with poor prognosis of HCC by analyzing the TCGA and GEO datasets. BRD4 or CDK7 overexpression was related to a lower survival rate. It's interesting to note that co-overexpression of CDK7 and BRD4 was a worse prognostic factor in HCC. Treatment with JQ1 or THZ1 alone had an inhibitory effect on cell proliferation; however, when JQ1 and THZ1 were combined, there was a more notable suppression of cell growth. At the same time, the combined use of JQ1 and THZ1 synergistically suppresses the expression of HCC driver genes. Conclusion: Our research revealed that BRD4 and CDK7 coupled can be a useful biomarker in HCC prognosis and the combination of JQ1 and THZ1 can be a promising therapeutic therapy against HCC.

Keywords: BRD4, CDK7, cell proliferation, combined inhibition

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Authors: Tom Spears, Zotique Laframboise

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Soil inorganic carbon is the most common form of carbon in arid and semiarid regions, and has a very long turnover time. However, little is known about dissolved inorganic carbon storage and its turnover time in these soils. With 81 arid soil samples taken from 6 profiles in the Nepean Desert, Canada, we investigated the soil inorganic carbon (SIC) and the soil dissolved inorganic carbon (SDIC) in whole profiles of saline and alkaline soils by analyzing their contents and ages with radiocarbon dating. The results showed that there is considerable SDIC content in SIC, and the variations of SDIC and SIC contents in the saline soil profile were much larger than that in the alkaline profile. We investigated the possible implications for tectonic platelet activity but identified none.

Keywords: soil, carbon storage, acidity, soil inorganic carbon (SIC)

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Authors: Misarah Abdelaziz, L Djenidi, Mergen H. Ghayesh, Rey Chin

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Measurements of a turbulent boundary layer over 3D sinusoidal roughness are performed for friction Reynolds numbers ranging from 650 < Reτ < 2700. This surface was fabricated by a Multicam CNC Router machine of an acrylic sheet to have an amplitude of k/2 = 0.8 mm and an equal wavelength of 8k in both streamwise and spanwise directions, a 0.6 mm stepover and 12 mm ball nose cutter was used. Single hotwire anemometry measurements are done at one location x=1.5 m downstream at different freestream velocities under zero-pressure gradient conditions. As expected, the roughness causes a downward shift on the wall-unit normalised streamwise mean velocity profile when compared to the smooth wall profile. The shift is increasing with increasing Reτ, 1.8 < ∆U+ < 6.2. The coefficient of friction is almost constant at all cases Cf = 0.0042 ± 0.0002. The results show a gradual reduction in the inner peak of profiles with increasing Reτ until fully destruction at Reτ of 2700.

Keywords: hotwire, roughness, TBL, ZPG

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