Search results for: expression surface form

Authors: Al-Mutary M., Alhimaidi A., Al-Ghadi M. Iwamoto D., Javed Ahmad. Abdulaziz A. Al-Khedhairy

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The aim of the present study was to evaluate the effect of ovine follicular fluid supplementation during IVM of sheep oocytes on the resumption of meiosis, glutathione (GSH) content and expression of Bax, Bcl-2, and HSPB1 genes. Sheep ovaries were collected from Riyadh slaughterhouse, KSA. Oocytes were aspirated from 3-6 mm follicles. Ovine oocytes were cultured in maturation medium with 0% (control), 10%, 20%, 40% of ovine follicular fluid for 24 h. Results indicated that the rate of oocyte maturation was significantly (P≤0.05) decreased in 40% OFF (36.87%) versus the control (61.3%), 10% OFF (63.95%) and 20% OFF (64.08%). Supplementation of 10% OFF to IVM medium induced an intra-oocyte GSH concentration significantly higher than that found in ovine oocytes cultured with 20% OFF and 40% OFF and similar to the GSH content in oocytes cultured without FF. Real time polymerase chain reaction analysis for gene expression revealed no differences in Bax, Bcl-2, HSPB1 genes between control and 10% OFF group, whereas they were strongly expressed in 20% OFF and 40% OFF (P < 0.05) when compared to the control and 10% OFF. In conclusion the addition of 10% OFF to the IVM culture of sheep oocytes is recommended to support cytoplasmic maturation and increase oocytes competence.

Keywords: IVM, oocyte maturation, gene expression, follicular fluid

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Authors: K. Sathishkumar, V. Thiagarasu

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Due to recent advances in DNA microarray technology, it is now feasible to obtain gene expression profiles of tissue samples at relatively low costs. Many scientists around the world use the advantage of this gene profiling to characterize complex biological circumstances and diseases. Microarray techniques that are used in genome-wide gene expression and genome mutation analysis help scientists and physicians in understanding of the pathophysiological mechanisms, in diagnoses and prognoses, and choosing treatment plans. DNA microarray technology has now made it possible to simultaneously monitor the expression levels of thousands of genes during important biological processes and across collections of related samples. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. A first step toward addressing this challenge is the use of clustering techniques, which is essential in the data mining process to reveal natural structures and identify interesting patterns in the underlying data. This work presents an analysis of several clustering algorithms proposed to deals with the gene expression data effectively. The existing clustering algorithms like Support Vector Machine (SVM), K-means algorithm and evolutionary algorithm etc. are analyzed thoroughly to identify the advantages and limitations. The performance evaluation of the existing algorithms is carried out to determine the best approach. In order to improve the classification performance of the best approach in terms of Accuracy, Convergence Behavior and processing time, a hybrid clustering based optimization approach has been proposed.

Keywords: microarray technology, gene expression data, clustering, gene Selection

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Authors: Lina Wu, Ye Li

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An equivalent relation between a harmonic form and a closed co-closed form is established on a complete non-compact manifold. This equivalence has been generalized for a differential k-form ω from Lq spaces to non-Lq spaces when q=2 in the context of p-balanced growth where p=2. Especially for a simple differential k-form on a complete non-compact manifold, the equivalent relation has been verified with the extended scope of q for from finite q-energy in Lq spaces to infinite q-energy in non-Lq spaces when with 2-balanced growth. Generalized Hadamard Theorem, Cauchy-Schwarz Inequality, and Calculus skills including Integration by Parts as well as Convergent Series have been applied as estimation techniques to evaluate growth rates for a differential form. In particular, energy growth rates as indicated by an appropriate power range in a selected test function lead to a balance between a harmonic differential form and a closed co-closed differential form. Research ideas and computational methods in this paper could provide an innovative way in the study of broadening Lq spaces to non-Lq spaces with a wide variety of infinite energy growth for a differential form.

Keywords: closed forms, co-closed forms, harmonic forms, L^q spaces, p-balanced growth, simple differential k-forms

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Authors: Seyed Davar Siadat, Samira Tarashi, Abolfazl Fateh, Arfa Moshiri

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Background: The global health issue of tuberculosis (TB) still affects patients in every country. TB control may not be as effective as it should be, especially when resistant strains are involved. In this regard, mycobacterial MTases play a major role in tuberculosis, but the mechanisms underlying their function have yet to be fully deciphered. Methods: Five resistant isolates of M.tb were accumulated. As a reference strain, M.tb H37Rv (ATCC 27249) was used. For this analysis, seven putative mycobacterial MTase genes (Rv0645c, Rv1694, Rv2966c, Rv3919c, Rv2756c, Rv1988, and Rv3263), as well as Rv1392 as SAM synthase, were selected. Comparing mutations and expression levels of MTases in different strains was accomplished by PCR-sequencing and qRT-PCR. The relative expression levels of these genes were calculated using the 2 -ΔΔCt method. Results: The Rv3919c gene (T to G in codon 341) and Rv1392 gene (G to A in codon 97) were the only mutations found in the INHR strain. In all sensitive and resistant isolates, Rv0645c, Rv3263, Rv2756c, and Rv2966c were overexpressed. However, the expression of Rv1988 and Rv3919c decreased in the sensitive strains, whereas the expression of Rv1694 increased. There was also a decreased expression of Rv1392 in the INHR isolate. Conclusion: The presence of mycobacterial MTases as well as resistance to antibiotics were found to be correlated in M.tb strains. Undoubtedly, there are some MTases that are associated with the virulence process. It is necessary to conduct additional studies to fully explore the impact of mycobacterial MTases within specific strains of M.tb to develop novel diagnostic and treatment strategies.

Keywords: mycobacterium tuberculosis, drug resistance, methyltransferases, s-adenosylmethionine

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Authors: Dorota Miroslaw-Swiatek, Mateusz Grygoruk, Sylwia Szporak

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We applied a two-dimensional surface water flow model with irregular wet boundaries. In this model, flow equations are in the form of a 2-D, non-linear diffusion equations which allows to account spatial variations in flow resistance and topography. Calculation domain to simulate the flow pattern in the floodplain is congruent with a Digital Elevation Model (DEM) grid. The rate and direction of sheet flow in wetlands is affected by vegetation type and density, therefore the developed model take into account spatial distribution vegetation resistance to the water flow. The model was tested in a part of the Biebrza Valley, of an outstanding heterogeneity in the elevation and flow resistance distributions due to various ecohydrological conditions and management measures. In our approach we used the highest-possible quality of the DEM in order to obtain hydraulic slopes and vegetation distribution parameters for the modelling. The DEM was created from the cloud of points measured in the LiDAR technology. The LiDAR reflects both the land surface as well as all objects on top of it such as vegetation. Depending on the density of vegetation cover the ability of laser penetration is variable. Therefore to obtain accurate land surface model the “vegetation effect” was corrected using data collected in the field (mostly the vegetation height) and satellite imagery such as Ikonos (to distinguish different vegetation types of the floodplain and represent them spatially). Model simulation was performed for the spring thaw flood in 2009.

Keywords: floodplain flow, Biebrza valley, model simulation, 2D surface flow model

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Authors: F. Nameni, H. Poursadra

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The present study investigated resistance and progressive training alters the expression of chaperone proteins. These proteins function to maintain homeostasis, facilitate repair from injury, and provide protection. Nineteen training female in 2 groups taking part in the intervention volunteered to give blood samples. Levels of chaperone proteins were measured in response to resistance and progressive training. Hsp 70 levels were increased immediately after 2 h progressive training but decreased after resistance training. The data showed that human skeletal muscle responds to the stress of a single period of progressive training by up-regulating and resistance training by down-regulating expression of HSP70. Physical exercise can elevate core temperature and muscle temperatures and the expression pattern of HSP70 due to training status may be attributed to adaptive mechanisms.

Keywords: resistance training, heat shock proteins, leukocytes, Hsp 70

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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: Akhmadjon Sultanov, Eun-Ho Lee, Hye-Jin Park, Young-Je Cho

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This study tested the anti-inflammatory effect of wild indigo (Baptisia tinctoria) root in Raw 264.7 cells. We prepared two extracts of B. tinctoria; one in water and the other in 50% ethanol. Then we evaluated the toxicities of the B. tinctoria root extracts at 10 to 100 mg mL-1 concentrations in raw 264.7 cells and observed 80% cell viability. The anti-inflammatory effect of B. tinctoria root extract in lipopolysaccharide (LPS)-stimulated Raw 264.7 cells were observed with concentrations at 10, 30, and 50 μg mL-1. The results showed that 77.27-66.82% of nitric oxide (NO) production was inhibited by 50 μg mL-1 B. tinctoria root extract. The protein expression of Inducible NO synthase (iNOS) expression dramatically decreased by 93.14% and 52.65% in raw 264.7 cells treated with water and ethanol extracts of B. tinctoria root, respectively. Moreover, cyclooxygenase-2 (COX-2) protein expression decreased by 42.85% and 69.70% in raw 264.7 cells treated with water and ethanol extracts of B. tinctoria root, respectively. Furthermore, the mRNA expression of pro-inflammatory markers, such as tumor necrosis factor-alpha, interleukin-1β, interleukin-6, monocyte chemoattractant protein-1, and prostaglandin E synthase 2, was significantly suppressed in a concentration-dependent manner. Additionally, the B. tinctoria root extracts effectively inhibited enzymes involved in physiological activities. The B. tinctoria root extracts showed excellent anti-inflammatory effects and can be used as a functional material for biological activities.

Keywords: cytokine, macrophage, pro-inflammatory, protein expression, real-time PCR

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Authors: Moses E. Emetere, M. L. Akinyemi

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Agricultural activities in the South–West Nigeria are mitigated by the global increase in temperature. The unpredictive surface temperature of the area had increased health challenges amongst other social influence. The satellite data of surface temperatures were compared with the ground station Davis weather station. The differential heating of the lower atmosphere were represented mathematically. A numerical predictive model was propounded to forecast future surface temperature.

Keywords: numerical predictive model, surface temperature, satellite date, ground data

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Authors: Urszula Stachewicz

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Surface properties of materials are the key parameter in many applications, especially in the biomedical field, to control cell-material interactions. In our work, we want to achieve the controllability of surface properties of polymer fibers via a single-step electrospinning process by alternating voltage polarities. Voltage polarity defines the charge accumulated on the surface of the liquid jet and the surface of the fibers. Positive polarity attracts negatively charged groups to fibers’ surface, whereas negative polarity moves the negatively charged functional groups away from the surface. This way, we can control the surface chemistry, wettability, and additionally surface potential of electrospun fibers. Within our research, we characterized surface chemistry using X-ray photoelectron microscopy (XPS) and surface potential with Kelvin probe force microscopy (KPFM) on electrospun fibers of commonly used polymers such as PCL, PVDF, and PMMA, often used as biomaterials. We proved the significant effect of fibers' surface potential on cell integration with the scaffolds and further cells development for the regeneration processes based on the osteoblast and fibroblast culture studies. Acknowledgments: The study was conducted within ‘Nanofiber-based sponges for atopic skin treatment’ project, which is carried out within the First TEAM programme of the Foundation for Polish Science co-financed by the European Union under the European Regional Development Fund, project no POIR.04.04.00-00- 4571/18-00.

Keywords: cell attachment, fibers, fibroblasts, osteoblast, proliferation, surface potential

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Authors: Yuanrui Xu, Zailin Yang, Yunqiu Song, Guanxixi Jiang

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It is an important subject of seismology on the influence of local topography on ground motion during earthquake. In mountainous areas with complex terrain, the construction of the tunnel is often the most effective transportation scheme. In these projects, the local terrain can be simplified into hills with different shapes, and the underground tunnel structure can be regarded as a subsurface cavity. The presence of the subsurface cavity affects the strength of the rock mass and changes the deformation and failure characteristics. Moreover, the scattering of the elastic waves by underground structures usually interacts with local terrains, which leads to a significant influence on the surface displacement of the terrains. Therefore, it is of great practical significance to study the surface displacement of local terrains with underground tunnels in earthquake engineering and seismology. In this work, the region is divided into three regions by the method of region matching. By using the fractional Bessel function and Hankel function, the complex function method, and the wave function expansion method, the wavefield expression of SH waves is introduced. With the help of a constitutive relation between the displacement and the stress components, the hoop stress and radial stress is obtained subsequently. Then, utilizing the continuous condition at different region boundaries, the undetermined coefficients in wave fields are solved by the Fourier series expansion and truncation of the finite term. Finally, the validity of the method is verified, and the surface displacement amplitude is calculated. The surface displacement amplitude curve is discussed in the numerical results. The results show that different parameters, such as radius and buried depth of the tunnel, wave number, and incident angle of the SH wave, have a significant influence on the amplitude of surface displacement. For the underground tunnel, the increase of buried depth will make the response of surface displacement amplitude increases at first and then decreases. However, the increase of radius leads the response of surface displacement amplitude to appear an opposite phenomenon. The increase of SH wave number can enlarge the amplitude of surface displacement, and the change of incident angle can obviously affect the amplitude fluctuation.

Keywords: method of region matching, scattering of SH wave, subsurface cavity, trapezoidal hill

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Authors: Shu-Jun Li, Cheng-Cao Sun, De-Jia Li

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Recently, long noncoding RNAs (lncRNAs) have been emerged as crucial regulators of human diseases and prognostic markers in numerous of cancers, including colorectal carcinoma (CRC). Here, we identified an oncogenetic lncRNA HULC, which may promote colorectal tumorigenesis. HULC has been found to be up-regulated and acts as oncogene in gastric cancer and hepatocellular carcinoma, but its expression pattern, biological function and underlying mechanism in CRC is still undetermined. Here, we reported that HULC expression is also over-expressed in CRC, and its increased level is associated with poor prognosis and shorter survival. Knockdown of HULC impaired CRC cells proliferation, migration and invasion, facilitated cell apoptosis in vitro, and inhibited tumorigenicity of CRC cells in vivo. Mechanistically, RNA immunoprecipitation (RIP) and RNA pull-down experiment demonstrated that HULC could simultaneously interact with EZH2 to repress underlying targets NKD2 transcription. In addition, rescue experiments determined that HULC oncogenic function is partly dependent on repressing NKD2. Taken together, our findings expound how HULC over-expression endows an oncogenic function in CRC.

Keywords: long noncoding RNA, HULC, NKD2, colorectal carcinoma, proliferation, apoptosis

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Authors: Punit Kumar, Niraj Kumar

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The influence of transverse surface roughness on EHL characteristics has been investigated numerically using an extensive set of full EHL line contact simulations for shear-thinning lubricants under pure sliding condition. The shear-thinning behavior of lubricant is modeled using Carreau viscosity equation along with Doolittle-Tait equation for lubricant compressibility. The surface roughness is assumed to be sinusoidal and it is present on the stationary surface. It is found that surface roughness causes sharp pressure peaks along with reduction in central and minimum film thickness. With increasing amplitude of surface roughness, the minimum film thickness decreases much more rapidly as compared to the central film thickness.

Keywords: EHL, Carreau, shear-thinning, surface roughness, amplitude, wavelength

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Authors: Yiping Meng, Yiming Sun

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The traditional construction industry is unable to meet the requirements for novel fabrication and construction. Automated construction and digital design have emerged as industry development trends that compensate for this shortcoming under the backdrop of Industrial Revolution 4.0. Benefitting from more flexible working space and more various end-effector tools compared to CNC methods, robot fabrication and construction techniques have been used in irregular architectural design. However, there is a lack of a systematic and comprehensive design and optimisation workflow considering geometric form, material, and fabrication methods. This paper aims to propose a design optimisation workflow for improving the rationality of a free-form timber structure fabricated by the robotic arm. Firstly, the free-form surface is described by NURBS, while its structure is calculated using the finite element analysis method. Then, by considering the characteristics and limiting factors of robotic timber fabrication, strain energy and robustness are set as optimisation objectives to optimise structural morphology by gradient descent method. As a result, an optimised structure with axial force as the main force and uniform stress distribution is generated after the structure morphology optimisation process. With the decreased strain energy and the improved robustness, the generated structure's bearing capacity and mechanical properties have been enhanced. The results prove the feasibility and effectiveness of the proposed optimisation workflow for free-form timber structure morphology design.

Keywords: robotic fabrication, free-form timber structure, Multi-objective optimisation, Structural morphology, rational design

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Authors: Hala Demerdash, Ola M. Zanaty, Emad Eldin Arida

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Background: This study investigated the micoRNA expression changes induced by Sevoflurane and Propofol and their effects on liver functions. Patients and methods: The study was designed as randomized controlled study, carried out on 200 adult patients, scheduled for major surgeries under general anesthesia (GA). Patients were randomly divided into four groups; groups SC and PC included chronic hepatitis C (CHC) patients where SC group are patients receiving Sevoflurane, and PC group are patients receiving Propofol anesthesia. While S and P groups included non- hepatitis patients; S group are patients receiving Sevoflurane and P group are patients receiving Propofol. Anesthesia in Group S and SC patients was maintained by sevoflurane, while anesthesia in Group P and PC patients was maintained by propofol infusion. Blood samples were analyzed for PT, PTT and liver enzymes. Serum samples were analyzed for microRNA before and after surgery. Results: Results show miRNA-122 and miRNA-21 were absent in serum of S and P groups in pre-operative samples. However, they were expressed in SC and PC groups. In post-operative samples; miRNA-122 revealed an increased expression in all groups; with more exaggerated response in SC group. On the other hand miRNA-21 revealed increased expression in both SC and PC groups; a slight expression in S group with absent expression in P group. There was a post-operative negative correlation between miR-122 and ALT (r=-0.46) in SC group and (r=-0.411) in PC group and positive correlation between ALT and miR-21 (r=0.335) in SC group and (r=0.379) in PC group. The amount of blood loss was positively correlated with miR-122 (r=0.366) in SC group and (r=0.384) in PC group. Conclusion: Propofol anesthesia is safer than Sevoflurane anesthesia in patients with CHC. Sevoflurane and Propofol anesthesia affect miRNA expression in both CHC and non-hepatitis patients.

Keywords: anesthesia, chronic hepatitis C, micoRNA, propofol, sevoflurane

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Authors: P. R. Prabhu, S. M. Kulkarni, S. S. Sharma, K. Jagannath, Achutha Kini U.

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In the present study, response surface methodology has been used to optimize turn-assisted deep cold rolling process of AISI 4140 steel. A regression model is developed to predict surface hardness and surface roughness using response surface methodology and central composite design. In the development of predictive model, deep cold rolling force, ball diameter, initial roughness of the workpiece, and number of tool passes are considered as model variables. The rolling force and the ball diameter are the significant factors on the surface hardness and ball diameter and numbers of tool passes are found to be significant for surface roughness. The predicted surface hardness and surface roughness values and the subsequent verification experiments under the optimal operating conditions confirmed the validity of the predicted model. The absolute average error between the experimental and predicted values at the optimal combination of parameter settings for surface hardness and surface roughness is calculated as 0.16% and 1.58% respectively. Using the optimal processing parameters, the hardness is improved from 225 to 306 HV, which resulted in an increase in the near surface hardness by about 36% and the surface roughness is improved from 4.84µm to 0.252 µm, which resulted in decrease in the surface roughness by about 95%. The depth of compression is found to be more than 300µm from the microstructure analysis and this is in correlation with the results obtained from the microhardness measurements. Taylor Hobson Talysurf tester, micro Vickers hardness tester, optical microscopy and X-ray diffractometer are used to characterize the modified surface layer.

Keywords: hardness, response surface methodology, microstructure, central composite design, deep cold rolling, surface roughness

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Authors: K. Nikovics, D. Riccobono, M. Oger, H. Morin, L. Barbier, T. Poyot, X. Holy, A. Bendahmane, M. Drouet, A. L. Favier

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Muscle regeneration after injury (as irradiation) is of great importance. However, the molecular and cellular mechanisms are still unclear. Cytokines are believed to play fundamental role in the different stages of muscle regeneration. They are secreted by many cell populations, but the predominant producers are macrophages and helper T cells. On the other hand, it has been shown that adipose tissue derived stromal/stem cell (ASC) injection could improve muscle regeneration. Stem cells probably induce the coordinated modulations of gene expression in different macrophage cells. Therefore, we investigated the patterns and timing of changes in gene expression of different cytokines occurring upon stem cells loading. Muscle regeneration was studied in an irradiated muscle of minipig animal model in presence or absence of ASC treatment (irradiated and treated with ASCs, IRR+ASC; irradiated not-treated with ASCs, IRR; and non-irradiated no-IRR). We characterized macrophage populations by immunolabeling in the different conditions. In our study, we found mostly M2 and a few M1 macrophages in the IRR+ASC samples. However, only few M2b macrophages were noticed in the IRR muscles. In addition, we found intensive fibrosis in the IRR samples. With in situ hybridization and immunolabeling, we analyzed the cytokine expression of the different macrophages and we showed that M2d macrophage are the most abundant in the IRR+ASC samples. By in situ hybridization, strong expression of the transforming growth factor β (TGF-β) was observed in the IRR+ASC but very week in the IRR samples. But when we analyzed TGF-β level with immunolabeling the expression was very different: many M2 macrophages showed week expression in IRR+ASC and few cells expressing stronger level in IRR muscles. Therefore, we investigated the MMP expressions in the different muscles. Our data showed that the M2 macrophages of the IRR+ASC muscle expressed MMP2 proteins. Our working hypothesis is that MMP2 expression of the M2 macrophages can decrease fibrosis in the IRR+ASC muscle by capturing TGF-β.

Keywords: adipose tissue derived stromal/stem cell, cytokine, macrophage, muscle regeneration

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Authors: Sadia Arshad, Yifa Tang, Dumitru Baleanu

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A fractional order mathematical model is proposed that incorporate CD8+ cells, natural killer cells, cytokines and tumor cells. The tumor cells growth in the absence of an immune response is modeled by logistic law as it was the simplest form for which predictions also agreed with the experimental data. Natural Killer Cells are our first line of defense. NK cells directly kill tumor cells through several mechanisms, including the release of cytoplasmic granules containing perforin and granzyme, expression of tumor necrosis factor (TNF) family members. The effect of the NK cells on the tumor cell population is expressed with the product term. Rational form is used to describe interaction between CD8+ cells and tumor cells. A number of cytokines are produced by NKs, including tumor necrosis factor TNF, IFN, and interleukin (IL-10). Source term for cytokines is modeled by Michaelis-Menten form to indicate the saturated effects of the immune response. Stability of the equilibrium points is discussed for biologically significant values of bifurcation parameters. We studied the treatment of fractional order system by investigating analytical conditions of tumor eradication. Numerical simulations are presented to illustrate the analytical results.

Keywords: cancer model, fractional calculus, numerical simulations, stability analysis

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Authors: K. R. Thabethe, G. A. Adefolaju, M. J. Hosie

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Cervical cancer is the third most commonly diagnosed cancer globally and it is one of three AIDS defining malignancies. Highly active antiretroviral therapy (HAART) is a combination of three or more antiretroviral drugs and has been shown to play a significant role in reducing the incidence of some AIDS defining malignancies, although its effect on cervical cancer is still unclear. The aim of this study was to investigate the relationship between cervical cancer and HAART. This was achieved by studying the expression of two signalling molecules expressed in cervical cancer; MUC1 and P65. Following the 24 hour treatment of a cervical cancer cell line, HCS-2, with drugs which are commonly used as part of HAART at their clinical plasma concentrations, real-time qPCR and immunofluorescence were used in order to study gene and protein expression. A one way ANOVA followed by a Tukey Kramer Post Hoc test was conducted using JMP 11 software on both sets of data. The drug classified as a protease inhibitor (PI) (i.e. LPV/r) reduced MUC1 and P65 gene and protein expression more than the other drug tested. PIs are known to play a significant role in cell death, therefore the cells were thought to be more susceptible to cell death following treatment with PIs. In conclusion, the drugs used, especially the PI showed some anticancer effects by facilitating cell death through decreased gene and protein expression of MUC1 and P65 and present promising agents for cancer treatment.

Keywords: cervical cancer, haart, MUC1, P65

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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: Justyna Humięcka-Jakubowska

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1. Background in music analysis. Traditionally, when we think about a composer’s sketches, the chances are that we are thinking in terms of the working out of detail, rather than the evolution of an overall concept. Since music is a “time art’, it follows that questions of a form cannot be entirely detached from considerations of time. One could say that composers tend to regard time either as a place gradually and partially intuitively filled, or they can look for a specific strategy to occupy it. In my opinion, one thing that sheds light on Stockhausen's compositional thinking is his frequent use of 'form schemas', that is often a single-page representation of the entire structure of a piece. 2. Background in music technology. Sonic Visualiser is a program used to study a musical recording. It is an open source application for viewing, analysing, and annotating music audio files. It contains a number of visualisation tools, which are designed with useful default parameters for musical analysis. Additionally, the Vamp plugin format of SV supports to provide analysis such as for example structural segmentation. 3. Aims. The aim of my paper is to show how SV may be used to obtain a better understanding of the specific musical work, and how the compositional strategy does impact on musical structures and musical surfaces. I want to show that ‘traditional” music analytic methods don’t allow to indicate interrelationships between musical surface (which is perceived) and underlying musical/acoustical structure. 4. Main Contribution. Stockhausen had dealt with the most diverse musical problems by the most varied methods. A characteristic which he had never ceased to be placed at the center of his thought and works, it was the quest for a new balance founded upon an acute connection between speculation and intuition. In the case with Mikrophonie I (1964) for tam-tam and 6 players Stockhausen makes a distinction between the "connection scheme", which indicates the ground rules underlying all versions, and the form scheme, which is associated with a particular version. The preface to the published score includes both the connection scheme, and a single instance of a "form scheme", which is what one can hear on the CD recording. In the current study, the insight into the compositional strategy chosen by Stockhausen was been compared with auditory image, that is, with the perceived musical surface. Stockhausen's musical work is analyzed both in terms of melodic/voice and timbre evolution. 5. Implications The current study shows how musical structures have determined of musical surface. My general assumption is this, that while listening to music we can extract basic kinds of musical information from musical surfaces. It is shown that an interactive strategies of musical structure analysis can offer a very fruitful way of looking directly into certain structural features of music.

Keywords: automated analysis, composer's strategy, mikrophonie I, musical surface, stockhausen

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Authors: Jahanshah Ashkani, Kevin J. Naidoo

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Glycosylation is the major posttranslational modification (PTM) process in cellular development. In tumour development, it is marked by structural alteration of carbohydrates (glycans) that is the result of aberrant glycosylation. Altered glycan structures affect cell surface ligand-receptor interactions that interfere with the regulation of cell adhesion, migration, and proliferation. The resulting changes in glycan biosynthesis pathways originate from altered expression of glycosyltransferases and glycosidases. While the alteration in glycosylation patterns is a recognized “hallmark of cancer”, the influential overview of the biology of cancer proposes eight hallmarks with no explicit suggestion to connectivity with glycosylation. Recently, we have discovered a connection between the glycosyltransferase gene expression and cancer type and subtype. Here we present an association between aberrant glycosylation and the biological hallmarks of breast cancer by exploring the common regulatory mechanisms at the genomic scale. The result of this study bridges the glycobiological and biological pathways that are accepted hallmarks of cancer by connecting their common regulatory pathways. This is an impetus for further investigation as target therapies of breast cancer are very likely to be uncovered from this.

Keywords: aberrant glycosylation, biological hallmarks, breast cancer, regulatory mechanism

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Authors: A. T. Siacara, A. T. Beck, M. M. Futai

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This paper shows how accurately and efficiently reliability analyses of geotechnical installations can be performed by directly coupling geotechnical software with a reliability solver. An earth slope is used as the study object. The limit equilibrium method of Morgenstern-Price is used to calculate factors of safety and find the critical slip surface. The deterministic software package Seep/W and Slope/W is coupled with the StRAnD reliability software. Reliability indexes of critical probabilistic surfaces are evaluated by the first-order reliability methods (FORM). By means of sensitivity analysis, the effective cohesion (c') is found to be the most relevant uncertain geotechnical parameter for slope equilibrium. The slope was tested using different geometries, taking into account unsaturated soil properties. Finally, a critical slip surface, identified in terms of minimum factor of safety, is shown here not to be the critical surface in terms of reliability index.

Keywords: slope, unsaturated, reliability, safety, seepage

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Authors: Peter Thissen

Abstract:

In this work, we report about the influence of the chemical potential of water on the carbonation reaction of wollastonite (CaSiO3) as model surface of cement and concrete. Total energy calculations based on density functional theory (DFT) combined with kinetic barrier predictions based on nudge elastic band (NEB) method show that the exposure of the water-free wollastonite surface to CO2 results in a barrier-less carbonation. CO2 reacts with the surface oxygen and forms carbonate (CO32-) complexes together with a major reconstruction of the surface. The reaction comes to a standstill after one carbonate monolayer has been formed. In case one water monolayer is covering the wollastonite surface, the carbonation is no more barrier-less, yet ending in a localized monolayer. Covered with multilayers of water, the thermodynamic ground state of the wollastonite completely changes due to a metal-proton exchange reaction (MPER, also called early stage hydration) and Ca2+ ions are partially removed from solid phase into the H2O/wollastonite interface. Mobile Ca2+ react again with CO2 and form carbonate complexes, ending in a delocalized layer. By means of high resolution time-of-flight secondary-ion mass-spectroscopy images (ToF-SIMS), we confirm that hydration can lead to a partially delocalization of Ca2+ ions on wollastonite surfaces. Finally, we evaluate the impact of our model surface results by means of Low Energy Ion Scattering (LEIS) spectroscopy combined with careful discussion about the competing reactions of carbonation vs. hydration.

Keywords: Calcium-silicate, carbonation, hydration, metal-proton exchange reaction

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Authors: S. Kherchaoui, A. Houacine

Abstract:

This paper presents a facial expression recognition system. It performs identification and classification of the seven basic expressions; happy, surprise, fear, disgust, sadness, anger, and neutral states. It consists of three main parts. The first one is the detection of a face and the corresponding facial features to extract the most expressive portion of the face, followed by a normalization of the region of interest. Then calculus of curvelet coefficients is performed with dimensionality reduction through principal component analysis. The resulting coefficients are combined with two ratios; mouth ratio and face edge ratio to constitute the whole feature vector. The third step is the classification of the emotional state using the SVM method in the feature space.

Keywords: facial expression identification, curvelet coefficient, support vector machine (SVM), recognition system

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Authors: Mohammad Sadeghian, Mohsen Sadeghian

Abstract:

In this paper, planning catamaran and mono-hull vessels resistance and trim in calm waters were considered. Hydrodynamic analysis of fast mono-hull planning vessel was also investigated. For hull form geometry optimization, numerical methods of different parameters were used for this type of vessels. Hull material was selected as carbon fiber composite. Exact architectural aspects were specified and stability calculations were performed, as well. Hydrodynamic calculations to extract the resistance force using semi-analytical methods and numerical modeling were carried out. Free surface numerical analysis of vessel in designed draft using finite volume method and double phase were evaluated and verified by experimental tests.

Keywords: fast vessel, hydrostatic and hydrodynamic optimization, free surface flow, computational fluid dynamics

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Authors: Aspen W. Glaspell, Victoria J. Rouse, Brian K. Friedrich, Kyosung Choo

Abstract:

Heat transfer of two-phase impinging jet on a flat plate surface are experimentally investigated. The effects of the nozzle-to-surface distance and volumetric quality on the Nusselt number are considered. The results show that the normalized stagnation Nusselt number drastically increase with decreasing the nozzle-to-surface distance due to the jet deflection effect. Based on the experimental results, new correlations for the stagnation Nusselt number are developed as a function of the nozzle-to-surface distance.

Keywords: jet impingement, water jet, air assisted, circular jet

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Authors: Han-Qin Zheng, Yi-Fan Chiang-Hsieh, Chia-Hung Chien, Wen-Chi Chang

Abstract:

As the most important non-vascular plants, algae have many research applications, including high species diversity, biofuel sources, adsorption of heavy metals and, following processing, health supplements. With the increasing availability of next-generation sequencing (NGS) data for algae genomes and transcriptomes, an integrated resource for retrieving gene expression data and metabolic pathway is essential for functional analysis and systems biology in algae. However, gene expression profiles and biological pathways are displayed separately in current resources, and making it impossible to search current databases directly to identify the cellular response mechanisms. Therefore, this work develops a novel AlgaePath database to retrieve gene expression profiles efficiently under various conditions in numerous metabolic pathways. AlgaePath, a web-based database, integrates gene information, biological pathways, and next-generation sequencing (NGS) datasets in Chlamydomonasreinhardtii and Neodesmus sp. UTEX 2219-4. Users can identify gene expression profiles and pathway information by using five query pages (i.e. Gene Search, Pathway Search, Differentially Expressed Genes (DEGs) Search, Gene Group Analysis, and Co-Expression Analysis). The gene expression data of 45 and 4 samples can be obtained directly on pathway maps in C. reinhardtii and Neodesmus sp. UTEX 2219-4, respectively. Genes that are differentially expressed between two conditions can be identified in Folds Search. Furthermore, the Gene Group Analysis of AlgaePath includes pathway enrichment analysis, and can easily compare the gene expression profiles of functionally related genes in a map. Finally, Co-Expression Analysis provides co-expressed transcripts of a target gene. The analysis results provide a valuable reference for designing further experiments and elucidating critical mechanisms from high-throughput data. More than an effective interface to clarify the transcript response mechanisms in different metabolic pathways under various conditions, AlgaePath is also a data mining system to identify critical mechanisms based on high-throughput sequencing.

Keywords: next-generation sequencing (NGS), algae, transcriptome, metabolic pathway, co-expression

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Authors: Kathy Stein, Mariola Lysson, Anja Schmidt, Beatrix Schumak, Sabine Specht, Hicham Bouabe, Jürgen Heesemann, Axel Roers, Joerg C. Kalff, Sven Wehner

Abstract:

Objective: Postoperative ileus (POI) is a common complication of abdominal surgery. Monocyte infiltration is a hallmark of POI. The polarization of macrophages/monocytes in this process is not well understood. We aimed to investigate if and how M2 macrophage/monocyte differentiation is involved in POI pathogenesis. Design: POI was induced by intestinal manipulation (IM). C57Bl/6, CCR2-/-, IL-10 reporter (ITIB), IL-10-/- and LysMcre/IL-10fl/fl mice underwent IM. At various points in time leukocyte influx, gene and protein expression of cytokines, chemokines and M2 differentiation markers and intestinal motility were analyzed. Results: IM induced the postoperative expression of the M2 markers Arginase-1 and YM-1, predominantly in F4/80+Ly6C+ monocytes. Gene expression analyses indicated an IL-10-dependent, IL-4-independent M2 polarization of these monocytes. IL-10 dependency of M2 differentiation was confirmed in IL-10 deficient mice. Leukocytes, in the order of infiltrating monocytes, neutrophils, and resident macrophages were the main IL-10 producers during POI. IL-10 producing monocytes as well as M2 marker expression were almost absent in CCR2-deficient mice. However, postoperative IL-10 expression was not altered in CCR2-/- mice. The loss of M2 polarized monocytes neither protected CCR2-/- mice from nor affected resolution of POI. In contrast, IL-10 deficiency reduced postoperative neutrophil numbers and ameliorated POI. IL-10Ra expression was strongly induced in neutrophils but not in monocytes. Conclusion: We conclude that IL-10 counteracts POI resolution by activating IL-10Ra-expressing neutrophils in the late phase of disease while IL-10-dependent M2 differentiation is not pivotal to POI manifestation and resolution.

Keywords: interleukin-10, macrophages, neutrophils, postoperative ileus

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Authors: Badawia Ibrahim, Iman Hussein, Samar El Sheikh, Fatma Abou Elkasem, Hazem Abo Ismael

Abstract:

Background: Response of breast carcinoma to neoadjuvant chemotherapy (NAC) varies regarding many factors including hormonal receptor status. Breast cancer is a heterogenous disease with different outcomes, hence a need arises for new markers predicting the outcome of NAC especially for the triple negative group when estrogen, progesterone receptors and Her2/neu are negative. FOXP3 is a promising target with unclear role. Aim: To examine the value of FOXP3 expression in locally advanced triple negative breast cancer tumoral cells as well as tumor infiltrating lymphocytes (TILs) and to elucidate its relation to the extent of NAC response. Material and Methods: Forty five cases of immunohistochemically confirmed to be triple negative breast carcinoma were evaluated for NAC (Doxorubicin, Cyclophosphamide AC x 4 cycles + Paclitaxel x 12 weeks, patients with ejection fraction less than 60% received Taxotere or Cyclophosphamide, Methotrexate, Fluorouracil CMF) response in both tumour and lymph nodes status according to Miller & Payne's and Sataloff's systems. FOXP3 expression in tumor as well as TILs evaluated in the pretherapy biopsies was correlated with NAC response in breast tumor and lymph nodes as well as other clinicopathological factors. Results: Breast tumour cells showed FOXP3 positive cytoplasmic expression in (42%) of cases. High FOXP3 expression percentage was detected in (47%) of cases. High infiltration by FOXP3+TILs was detected in (49%) of cases. Positive FOXP3 expression was associated with negative lymph node metastasis. High FOXP3 expression percentage and high infiltration by FOXP3+TILs were significantly associated with complete therapy response in axillary lymph nodes. High FOXP3 expression in tumour cells was associated with high infiltration by FOXP3+TILs. Conclusion: This result may provide evidence that FOXP3 marker is a good prognostic and predictive marker for triple negative breast cancer (TNBC) indicated for neoadjuvant chemotherapy and can be used for stratifications of TNBC cases indicated for NAC. As well, this study confirmed the fact that the tumour cells and the surrounding microenvironment interact with each other and the tumour microenvironment can influence the treatment outcomes of TNBC.

Keywords: breast cancer, FOXP3 expression, prediction of neoadjuvant chemotherapy effect, triple negative

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