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Abbassia, Egypt

El-Nahass M.M.,Ain Shams University | Kamal H.,Ain ShamsUniversity | Elshorbagy M.H.,Minia University | Abdel-Hady K.,Minia University
Organic Electronics: physics, materials, applications | Year: 2013

The dark conductivity (dc and ac) and dielectric properties of chromotrope 2R (CHR) in pellet as well as in thin film forms have been investigated as function of frequency (100 Hz to 5 MHz) within the temperature range (293-423 K). The ac conductivity of CHR pellet in sandwich structure employing two symmetrical gold ohmic contacts shows both temperature and frequency dependence with relatively stronger dependence in the higher temperature and lower frequency ranges respectively. It is found that σac(ω) obey Jonscher's universal power law, σac(ω) = Aωs with s < 1 and the results has been analyzed with reference to various theoretical models. The correlated barrier hopping model (CBH) with single polaron process is found to be the dominant conduction mechanism for charge carrier transport in CHR material within the investigated temperature range. The dc conductivity has been measured in the considered temperature range for as deposited and annealed films. The results are fitted to Arhenius equation and the activation energy has been deduced at different frequencies. The results showed also that heating the deposited CHR films may reveal films with more stable electrical properties. Moreover, both the dielectric constant ε1 and the dielectric loss ε2 are found to increase with temperature and decrease with frequency which reveal that the CHR samples exists in molecular dipole form. The behavior of ε2 as a function of both frequency and temperature is analyzed according to Giuntini et al. model. © 2013 Elsevier B.V.

Abbas M.M.,Sinai University | Abouelhoda M.,Cairo University | Abouelhoda M.,Nile University | Bahig H.M.,Ain ShamsUniversity
BMC Bioinformatics | Year: 2012

Background: Given a set of DNA sequences s1,..., st, the (l, d) motif problem is to find an l-length motif sequence M, not necessary existing in any of the input sequences, such that for each sequence si, 1 ≤ i ≤ t, there is at least one subsequence differing with at most d mismatches from M. Many exact algorithms have been developed to solve the motif finding problem in the last three decades. However, the problem is still challenging and its solution is limited to small values of l and d. Results: In this paper we present a new efficient method to improve the performance of the exact algorithms for the motif finding problem. Our method is composed of two main steps: First, we process q ≤ t sequences to find candidate motifs. Second, the candidate motifs are searched in the remaining sequences. For both steps, we use the best available algorithms. Our method is a hybrid one, because it integrates currently existing algorithms to achieve the best running time. In this paper, we show how the optimal value of q is determined to achieve the best running time. Our experimental results show that there is about 24% speed-up achieved by our method compared to the best existing algorithm. Furthermore, we also present a parallel version of our method running on shared memory architecture. Our experiments show that the performance of our algorithm scales linearly with the number of processors. Using the parallel version, we were able to solve the (21, 8) challenging instance using 8 processors in 20.42 hours instead of 6.68 days of the serial version. Conclusions: Our method speeds up the solution of the exact motif problem. Our method is generic, because it can accommodate any new faster algorithm based on traditional methods. We expect that our method will help to discover longer motifs. The software we developed is available for free for academic research at http://www. nubios.nileu.edu.eg/tools/hymotif. © 2012 Abbas et al.

El-Nahass M.M.,Ain Shams University | Kamal H.,Ain ShamsUniversity | Elshorbagy M.H.,Minia University | Abdel-Hady K.,Minia University
Optik | Year: 2013

Chromotrope 2R (CHR) films of different thicknesses have been prepared using spin coater. The material has been characterized using FT-IR, DTA and X-ray diffraction. The XRD of the material in powder and thin film forms showed polycrystalline structure with triclinic phase. Preferred orientation at the (1 1 4) plane is observed for the deposited films. Initial indexing of the XRD pattern was performed using "Crystalfire" computer program. Miller indices, h k l, values for each diffraction line in X-ray diffraction (XRD) spectrum were calculated and indexed for the first time. The DTA thermograms of CHR powder have been recorded in the temperature range 25-350 C with different heating rates. The spectra of the infra-red absorption allow characterization of vibration modes for the powder and thin film. The effect of film thickness on the optical properties has been studied in the UV-visible-NIR regions. The films show high transmittance exceeding 0.90 in the NIR region λ > 800 nm. The intensity of the absorption peaks for λ < 800 nm are enhanced as the film thickness increase. The absorption bands are attributed to the (π-π*) and (n-π*) molecular transitions. The optical properties have been analyzed according to the single-oscillator model and the dispersion energy parameters as well as the free charge carrier concentration have been determined. The optical energy gap as well as the oscillator strength and electric dipole strength have been calculated. © 2013 Elsevier GmbH. All rights reserved.

Naga S.M.,National Research Center of Egypt | El-Maghraby H.F.,National Research Center of Egypt | Sayed M.,National Research Center of Egypt | Saad E.A.,Ain ShamsUniversity
Journal of Ceramic Science and Technology | Year: 2015

Nanosize hydroxyapatite powder synthesized indirectly from eggshells is used to produce 3D porous scaffolds. They are fabricated via a polymeric sponge method. X-ray diffraction (XRD) and transmission electron microscopy (TEM) are used to characterize the phase composition and grain size of the scaffolds, respectively. The results showed that the prepared powder is composed of pure hydroxyapatite with a grain size ranging between 35 and 122 nm. The prepared scaffolds calcined at 1250°C for 2 h possess interconnected porosity (≈73%). The studied scaffolds showed suitable mechanical strength necessary for bone tissue engineering. Their crushing and bending strengths were 0.82 MPa and 1.72 MPa, respectively. Thin film XRD, SEM and EDS confirmed the presence of a rich bone-like apatite layer post-immersion in SBF on the scaffold's surface. © 2015 Göller Verlag.

Elsebaie H.,Ain ShamsUniversity | Elchamy H.A.,Ain ShamsUniversity | Kaddah E.A.,Ain ShamsUniversity | Abdelfattah R.G.,Ain ShamsUniversity
Life Science Journal | Year: 2012

Background: Osteopontin; a small integrin-binding ligand; has been proved to be an important factor in bone mineralization, remodeling and metabolism. Upregulation of osteopontin was noticed in knee osteoarthritis. It may be involved in the molecular pathogenesis of the disease, contributing to progressive degeneration of articular cartilage. Aim: To measure plasma and synovial fluid osteopontin in patients with primary knee osteoarthritis in order to assess its relation to disease severity. Patients and Methods: This study included thirty patients (aged 44-66 years) diagnosed as having primary knee osteoarthritis according to the checklist of American College of Rheumatology criteria. Ten age and sex matched apparently healthy controls were also enrolled in this study. Full history taking, thorough clinical examination, routine laboratory investigations,and plasma osteopontin (OPN) level measurement were done for all patients and controls. While Synovial fluid OPN levels were measured in cases with knee effusion. Disease severity was assessed using Kellgren/ Lawrence (K/L) radiological score. Results: Statistically significantly elevated levels of both plasma and synovial fluid OPN were found in patients compared to controls (P<0.001&P<0.05 respectively). Synovial fluid OPN levels were statistically significantly higher than paired plasma samples (P<0.001). A significant positive correlation was found between plasma OPN and synovial fluid OPN levels and both of them showed positive correlation with disease severity grades as assessed by K/L radiological score. In Conclusion: Both plasma and synovial fluid OPN levels were increased in primary knee O.A patients and both of them correlated with more severe OA. Measurements of plasma and/or synovial fluid levels of osteopontin could possibly serve as a biochemical parameter for determining disease severity and predicting the progression of osteoarthritic disease process.

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