Showing papers by "Cairo University published in 2008"

The RAST Server: Rapid Annotations using Subsystems Technology

Abstract: The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12–24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

Fractional-Order Sinusoidal Oscillators: Design Procedure and Practical Examples

Abstract: Sinusoidal oscillators are known to be realized using dynamical systems of second-order or higher. Here we derive the Barhkausen condition for a linear noninteger-order (fractional-order) dynamical system to oscillate. We show that the oscillation condition and oscillation frequency of some famous integer-order sinusoidal oscillators can be obtained as special cases from general equations governing their fractional-order counterparts. Examples including fractional-order Wien oscillators, Colpitts oscillator, phase-shift oscillator and LC tank resonator are given supported by numerical and PSpice simulations.

Niosome-Encapsulated Gentamicin for Ophthalmic Controlled Delivery

Abstract: The objective of the present research was to investigate the feasibility of using non-ionic surfactant vesicles (niosomes) as carriers for the ophthalmic controlled delivery of a water soluble local antibiotic; gentamicin sulphate. Niosomal formulations were prepared using various surfactants (Tween 60, Tween 80 or Brij 35), in the presence of cholesterol and a negative charge inducer dicetyl phosphate (DCP) in different molar ratios and by employing a thin film hydration technique. The ability of these vesicles to entrap the studied drug was evaluated by determining the entrapment efficiency %EE after centrifugation and separation of the formed vesicles. Photomicroscopy and transmission electron microscopy as well as particle size analysis were used to study the formation, morphology and size of the drug loaded niosomes. Results showed a substantial change in the release rate and an alteration in the %EE of gentamicin sulphate from niosomal formulations upon varying type of surfactant, cholesterol content and presence or absence of DCP. In-vitro drug release results confirmed that niosomal formulations have exhibited a high retention of gentamicin sulphate inside the vesicles such that their in vitro release was slower compared to the drug solution. A preparation with 1:1:0.1 molar ratio of Tween 60, cholesterol and DCP gave the most advantageous entrapment (92.02% ± 1.43) and release results (Q8h = 66.29% ± 1.33) as compared to other compositions. Ocular irritancy test performed on albino rabbits, showed no sign of irritation for all tested niosomal formulations.

Shape and size dependence of the surface plasmon resonance of gold nanoparticles studied by Photoacoustic technique

Abstract: We report on the optical absorption properties of as prepared gold naoparticles of different shapes and sizes measured by photoacoustic (PA) method. The gold nanoparticles of two different shapes (dots, rods) have been prepared using the seed mediated growth method. The shape and the size of these different nanoparticles were determined by STM measurements. PA spectra show the splitting of the surface plasmon resonance (SPR) into two modes (transverse and longitudinal) in case of gold nanorods. The increase in the aspect ratio of the nanorods leads to clear redshifts of the longitudinal SPR. These shifts were used to determine the dielectric constant of the surrounding medium and its variation with the aspect ratios.

Production optimization and quality assessment of biodiesel from waste vegetable oil

Abstract: Biodiesel production is worthy of continued study and optimization of production procedures because of its environmentally beneficial attributes and its renewable nature. In Egypt, millions L. of oil used for frying foods are discarded each year into sewage systems. Thus, it adds to the cost of treating effluent or pollutes waterways. This study is intended to consider aspects related to the feasibility of the production of biodiesel from waste/recycled oils in an attempt to help reduce the cost of biodiesel and reduce waste and pollution coming from waste oils. The variables affecting the yield and characteristics of the biodiesel produced from used frying oil were studied, the achieved results were analyzed and a set of recommendations was proposed. From the obtained results, the best yield percentage was obtained using a methanol/oil molar ratio of 6:1, potassium hydroxide as catalyst (1%) and 65 °C temperature for one hour. The yield percentage obtained from waste vegetable oil was comparable to that obtained from neat vegetable oil which reached 96.15% under optimum conditions. From the results it was clear that the produced biodiesel fuel, whether from neat vegetable oil or waste vegetable oil, was within the recommended standards of biodiesel fuel.

First-order filters generalized to the fractional domain

Abstract: Traditional continuous-time filters are of integer order. However, using fractional calculus, filters may also be represented by the more general fractional-order differential equations in which case integer-order filters are only a tight subset of fractional-order filters. In this work, we show that low-pass, high-pass, band-pass, and all-pass filters can be realized with circuits incorporating a single fractance device. We derive expressions for the pole frequencies, the quality factor, the right-phase frequencies, and the half-power frequencies. Examples of fractional passive filters supported by numerical and PSpice simulations are given.

Rise and persistence of global M1T1 clone of Streptococcus pyogenes.

Abstract: The resurgence of severe invasive group A streptococcal infections in the 1980s is a typical example of the reemergence of an infectious disease. We found that this resurgence is a consequence of the diversification of particular strains of the bacteria. Among these strains is a highly virulent subclone of serotype M1T1 that has exhibited unusual epidemiologic features and virulence, unlike all other streptococcal strains. This clonal strain, commonly isolated from both noninvasive and invasive infection cases, is most frequently associated with severe invasive diseases. Because of its unusual prevalence, global spread, and increased virulence, we investigated the unique features that likely confer its unusual properties. In doing so, we found that the increased virulence of this clonal strain can be attributed to its diversification through phage mobilization and its ability to sense and adapt to different host environments; accordingly, the fittest members of this diverse bacterial community are selected to survive and invade host tissue.

Chitosan based nanocarriers for indomethacin ocular delivery

Abstract: Two different chitosan (CS) nanocarriers namely nanoparticles and nanoemulsion were developed to prolong Indomethacin (IM) precorneal residence time and to improve its ocular bioavailability the main limitations in its management of post-operative inflammation and intraocular irritation after cataract extraction. CS-nanoparticles were developed by modified ionic gelation of CS with tripolyphosphate while nanoemulsion was prepared by spontaneous emulsification technique. Transmission electron microscopy revealed regular well-identified spherical shape. The nanoparticles had a mean size of 280 nm, a zeta potential of + 17 mV and high loading efficiency of 84.8 % while the mean size of nanoemulsion was affected by the nature of the surfactant used and varies between 220-690 nm. In vitro release studies, performed under sink conditions, revealed small initial burst release during the first hour followed by slow gradual drug release of 76 and 86% from nanoparticles and nanoemulsion respectively during a 24 h period. In vivo studies and histopathological examination revealed that eyes of rabbits treated with nanoemulsion showed clearer healing of corneal chemical ulcer with moderate effective inhibition of polymorph nuclear leukocytic infiltration (PMNLs) compared with nanoparticles preparation. Moreover, following topical instillation of CS-nanoemulsion to rabbits, it was possible to achieve therapeutic concentration of IM in the cornea through out the duration of the study and fairly high IM level in inner ocular structure, aqueous humor. These levels were significantly higher than those obtained following instillation of IM solution. Therefore, CS nanocarriers developed in this study were able to contact intimately with the cornea providing slow gradual IM release with long-term drug level thereby increasing delivery to both external and internal ocular tissues.

Caveolin 1 and Caveolin 2 are associated with breast cancer basal-like and triple-negative immunophenotype

Abstract: Caveolin-1 (CAV1) and caveolin 2 (CAV2) are the principal structural proteins of caveolae, sphingolipid and cholesterol-rich invaginations of the plasma membrane involved in vesicular trafficking and signal transduction. Over the recent years there has been controversy about their role in breast cancer and their suitability as markers of basal-like phenotype. Caveolin-1 and CAV2 protein expression was assessed on a tissue microarray containing 880 unselected invasive breast cancer cases, by means of immunohistochemistry. Caveolin-1 and CAV2 expression was observed in 13.4 and 5.9% of all breast cancer, respectively. Their expression was strongly associated with high histological grade, lack of steroid hormone receptor positivity (ER and PR), and expression of basal markers (basal cytokeratins, P63, P-cadherin). Furthermore, there was a significant association between CAV1 and CAV2 expression and basal-like phenotype. On univariate analysis only CAV2 had a prognostic impact on breast cancer-specific survival; however, this was not independent from other traditional markers on multivariate analysis. Our results demonstrate that both CAV1 and CAV2 are associated with basal-like phenotype. Further studies are warranted to determine whether they play an oncogenic role in basal-like/triple-negative breast cancer development or are just surrogate markers for this subgroup.

TextOntoEx: Automatic ontology construction from natural English text

Abstract: Most of existing ontologies construction tools support construction of ontological relations (e.g., taxonomy, equivalence, etc.) but they do not support construction of domain relations, non-taxonomic conceptual relationships (e.g., causes, caused by, treat, treated by, has-member, contain, material-of, operated-by, controls, etc.). Domain relations are found mainly in text sources. TextOntoEx constructs ontology from natural domain text using semantic pattern-based approach. TextOntoEx is a chain between linguistic analysis and ontology engineering. TextOntoEx analyses natural domain text to extract candidate relations and then maps them into meaning representation to facilitate constructing ontology. The paper explains this approach in more details and discusses some experiments on deriving ontology from natural text.

The changing patterns of bladder cancer in Egypt over the past 26 years

Abstract: Objective To evaluate temporal changes in histopathological types of bladder cancer and to assess associated changes in demographic, epidemiologic, and lifestyle risk factors.

Milk fermented by Lactobacillus gasseri SBT2055 influences adipocyte size via inhibition of dietary fat absorption in Zucker rats

Abstract: We have demonstrated previously that a diet containing skimmed milk (SM) fermented by Lactobacillus gasseri SBT2055 (LGSP) reduces adipocyte size in Sprague-Dawley rats. Two experiments were conducted to extend these observations in order to elucidate the mechanism involved. In experiment 1, lean and obese Zucker rats were fed a diet containing SM or LGSP for 4 weeks. The LGSP diet, compared with the SM diet, resulted in lowering of the mesenteric adipose tissue weight (23 %; P < 0.05), adipocyte sizes (28 %; P < 0.001) and serum leptin concentration (36 %; P < 0.05) in lean rats. Obese Zucker rats did not display such dietary effects. Only the number of smaller adipocytes was increased (P < 0.05) by the LGSP diet in the subcutaneous adipose tissue of obese rats. The LGSP diet significantly reduced the serum and hepatic cholesterol in rats. In addition, the LGSP diet led to an increased excretion of faecal fatty acids and total neutral faecal sterols in both rat strains. In experiment 2, Sprague-Dawley rats with permanent cannulation of the thoracic duct were fed either the SM or LGSP diets and their lymph was collected. The LGSP diet lowered the maximum transport rate of TAG and phospholipids. These results indicate that fermented milk regulates adipose tissue growth through inhibition at the stage of dietary fat absorption in lean Zucker rats.

Use of M-CHAT for a multinational screening of young children with autism in the Arab countries.

Abstract: There has been a decline in the mortality rate among infants and children under five years of age in the last decade in many developing countries. This has led to a shift in focus to look beyond su...

Improved LIBS limit of detection of Be, Mg, Si, Mn, Fe and Cu in aluminum alloy samples using a portable Echelle spectrometer with ICCD camera

Abstract: Laser-induced breakdown spectroscopy (LIBS) is a laser-based technique that can provide non-intrusive, qualitative and quantitative measurement of metals in various environments. LIBS uses the plasma generated by a high-energy laser beam to prepare and excite the sample in one step. In the present work, LIBS has been applied to perform elemental analysis of six trace elements simultaneously in aluminum alloy targets. The plasma is generated by focusing a pulsed Nd:YAG laser on the target in air at atmospheric pressure. LIBS limit of detection (LOD) is affected by many experimental parameters such as interferences, self-absorption, spectral overlap and matrix effect. We aimed to improve the LIBS LOD by optimizing these experimental parameters as possible. In doing so, a portable Echelle spectrometer with intensified CCD camera was used to detect the LIBS plasma emission. This advanced Echelle spectrometer provides a constant spectral resolution (CSR) of 7500 corresponding to 4 pixels FWHM over a wavelength range 200–1000 nm displayable in a single spectrum. Then, the calibration curves for iron, beryllium, magnesium, silicon, manganese and copper as minor elements were achieved with linear regression coefficients between 98–99% on average in aluminum standard sample alloys. New LOD values were achieved in the ppm range with high precision (RSD 3–8%). From the application view point, improving LIBS LOD is very important in the on-line industrial process control to follow-up multi-elements for the correct alloying in metals.

An architecture for autism: concepts of design intervention for the autistic user

Abstract: One in every 150 children is estimated to fall within the autistic spectrum, regardless of socio-cultural and economic aspects, with a 4:1 prevalence of males over females (ADDM, 2007). Architecture, as a profession, is responsible for creating environments that accommodate the needs of all types of users. Special needs individuals should not be exempt from such accommodation. Despite this high incidence of autism, there are yet to be developed architectural design guidelines catering specifically to the scope of autistic needs. The primary goal of this research is to correct this exclusion by developing a preliminary framework of architectural design guidelines for autism. This will be done through a two phase study. The first phase will determine, through a questionnaire of first hand caregivers of autistic children, the impact of architectural design elements on autistic behaviour, to determine the most influential. The second phase, based on the findings of the first, will test the conclusive highest ranking architectural elements in an intervention study on autistic children in their school environment. Specific behavioural indicators, namely attention span, response time and behavioural temperament, will be tracked to determine each child’s progress pre and post intervention, for a control and study group. This study concludes in outlining the findings of both phases of the study, the first being the determination of the most influential architectural design elements on autistic behaviour, according to the sample surveyed. The second group of findings outlines design strategies for autism in three points. The first is the presentation of a "sensory design matrix" which matches architectural elements with autistic sensory issues and is used to generate suggested design guidelines. The second is the presentation of these hypothetical guidelines, two of which are tested in the presented study. These guidelines are presented as possible interventions for further testing. The third is a group of specific design guidelines resultant from the intervention study. It is hoped that these will provide a basis for the further development of autistic specific design standards, and take us one step further towards more conducive environments for autistic individuals.

Smart stability-indicating spectrophotometric methods for determination of binary mixtures without prior separation.

Abstract: Ratio subtraction and isosbestic point methods are 2 innovating spectrophotometric methods used to determine vincamine in the presence of its acid degradation product and a mixture of cinnarizine (CN) and nicergoline (NIC). Linear correlations were obtained in the concentration range from 8–40 g/mL for vincamine (I), 6–22 g/mL for CN (II), and 6–36 g/mL for NIC (III), with mean accuracies 99.72 ± 0.917% for I, 99.91 ± 0.703% for II, and 99.58 ± 0.847 and 99.83 ± 1.039% for III. The ratio subtraction method was utilized for the analysis of laboratory-prepared mixtures containing different ratios of vincamine and its degradation product, and it was valid in the presence of up to 80% degradation product. CN and NIC in synthetic mixtures were analyzed by the 2 proposed methods with the total content of the mixture determined at their respective isosbestic points of 270.2 and 235.8 nm, and the content of CN was determined by the ratio subtraction method. The proposed method was validated and found to be suitable as a stability-indicating assay method for vincamine in pharmaceutical formulations. The standard addition technique was applied to validate the results and to ensure the specificity of the proposed methods.

On the recursive sequence xn+1=A∏i=lkxn−2i−1B+C∏i=lk−1xn−2i

Abstract: The aim of this work is to investigate the global stability, periodic nature, oscillation and the boundedness of solutions of the difference equation x n + 1 = A ∏ i = l k x n − 2 i − 1 B + C ∏ i = l k − 1 x n − 2 i , n = 0 , 1 , … where A , B , C are nonnegative real numbers and l , k are nonnegative integers, l k . We discuss the existence of unbounded solutions under certain conditions when l = 0 .

Effects of milk fermented by Lactobacillus gasseri SBT2055 on adipocyte size in rats

Abstract: Despite adequate scientific evidence of the potential benefits of probiotics to human health or disease prevention, their contribution to the growth of adipose tissue remains to be established. Four-week-old male Sprague-Dawley rats were fed a diet containing skim milk (control diet) or skim milk fermented by Lactobacillus gasseri SBT2055 (LGSP diet) for 4 weeks. Their body weight gain, adipose tissue weight, adipocyte size distribution profile, blood and hepatic lipids, and serum leptin, glucose and adiponectin levels were determined. There was a significant reduction in average adipocyte size in mesenteric white adipose tissue (P = 0.004). Moreover, the rats fed the LGSP diet displayed greater numbers of small adipocytes from mesenteric and retroperitoneal adipose tissues than did those on the control diet. Whereas adiponectin concentrations did not differ between the groups, serum leptin concentrations were decreased to 32 % in the LGSP diet group compared with the control group. Concentrations of serum glucose and lipids, and liver lipids, except for the liver TAG level, were similar in the two groups. These results indicate a possible role for a fermented milk product in the regulation of adipose tissue growth.

Optimum reaction time, performance and exhaust emissions of biodiesel produced by microwave irradiation.

Abstract: While transesterification is well established, there remain considerable inefficiencies in existing transesterification processes. In this study an alternative energy stimulant, “microwave irradiation” was used for the production of the alternative energy source, biodiesel. The optimum parametric conditions obtained from the conventional technique were applied using microwave irradiation in order to compare both systems. The results showed that application of radio frequency microwave energy offers a fast, easy route to this valuable biofuel with advantages of enhancing the reaction rate and improving the separation process. The methodology allows for the use of high free fatty acid content feedstock, including used cooking oil; hence it helps to reduce the cost of production which constitutes a major hurdle towards widespread commercialization of biodiesel. The study also showed that the optimum reaction time for microwave-enhanced biodiesel production should be highly respected. Exceeding the optimum reaction time will lead to deterioration of both biodiesel yield and purity. This paper also reported the performance and exhaust emissions from a diesel engine when fuelled with a petroleum diesel fuel and two different biodiesel fuels; one obtained by the conventional technique and the other by microwave irradiation. It was concluded that microwave-enhanced biodiesel is not, at least, inferior to that produced by the conventional technique.

The effect of phosphorus deficiency on nutrient uptake, nitrogen fixation and photosynthetic rate in mashbean, mungbean and soybean

Abstract: Phosphorous (P) fertilization is the major mineral nutrient yield determinant among legume crops. However, legume crops vary widely in the ability to take up and use P during deficiency. The aim here was to compare P uptake and translocation, biological nitrogen fixing ability and photosynthetic rate among mashbean (Vigna aconitifolia cv. ‘Mash-88’), mungbean (Vigna radiata cv. ‘Moong-6601’) and soybean (Glycine max L. cv. ‘Tamahomare’) during deficiency in hydroponics. Two treatments, the withdrawal of P from the solution (P-deprivation) and continued P at 160 μM (P sufficient) were effected at the pod initiation stage. Plants were grown for 20 days. Short-term labeling with 32P showed the uptake and distribution of P into plant parts. Withdrawal of P from the solution reduced biomass, photosynthetic activity, and nitrogen fixing ability in mungbean, and mashbean more than in soybean. P deprivation decreased P accumulation more than N accumulation. The decrease was more severe in mungbean and mashbean than soybean. More P was translocated and distributed into leaves in soybean than in mungbean and mashbean. Leaf P amount was more correlated to leaf area than to photosynthetic rate per unit leaf area among all three legume species. The results indicate that selection for increased efficiency of P utilization and leaf area may be used to improve leguminous crops.