Assessing the effects of data selection and representation on the development of reliable E. coli sigma 70 promoter region predictors

As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the key regulatory elements, which recruit the transcriptional machinery through binding to a variety of regulatory proteins (known as sigma factors). The identification of the promoter regions is very challenging because these regions do not adhere to specific sequence patterns or motifs and are difficult to determine experimentally. Machine learning represents a promising and cost-effective approach for computational identification of prokaryotic promoter regions. However, the quality of the predictors depends on several factors including: i) training data; ii) data representation; iii) classification algorithms; iv) evaluation procedures. In this work, we create several variants of E. coli promoter data sets and utilize them to experimentally examine the effect of these factors on the predictive performance of E. coli σ70 promoter models. Our results suggest that under some combinations of the first three criteria, a prediction model might perform very well on cross-validation experiments while its performance on independent test data is drastically very poor. This emphasizes the importance of evaluating promoter region predictors using independent test data, which corrects for the over-optimistic performance that might be estimated using the cross-validation procedure. Our analysis of the tested models shows that good prediction models often perform well despite how the non-promoter data was obtained. On the other hand, poor prediction models seems to be more sensitive to the choice of non-promoter sequences. Interestingly, the best performing sequence-based classifiers outperform the best performing structure-based classifiers on both cross-validation and independent test performance evaluation experiments. Finally, we propose a meta-predictor method combining two top performing sequence-based and structure-based classifiers and compare its performance with some of the state-of-the-art E. coli σ70 promoter prediction methods.NPRP grant No. 4-1454-1-233 from the Qatar National Research Fund (a member of Qatar Foundation).Scopu

Reconciliations and continued polarities in the works and theories of Halim and Bakri

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Architecture, 1994.Includes bibliographical references (p. 141-150).The Egyptian society today is facing many socio-economical, political and cultural challenges that are directly influencing the living standards and circumstances of its members despite their position in the society's hierarchy. The most important of these challenges is the struggle between the Inherited and the Imported that takes the modernization processes that were repeatedly implemented by the different rulers and elite class of the society as its active field. These modernization processes almost always mean Westernization . They have resulted in the separation of the society into two distinct segments; a Westernized rich and powerful high-middle class and up, and a more or less traditional poor and powerless low-middle class and down. As a direct result of these challenges the society is experiencing problems of inequality, class conflict, search for identity, among many others. These problems have a great impact on the living standards of the majority of the society. Additionally, they greatly influence the power relations both between the different segments of the society and between the society as a whole and the Western societies. This thesis discusses some of the attitudes and positions towards this issue of the Inherited versus the Imported and the problems that resulted from it. It attempts to achieve this from within the architectural profession by taking the attitudes, theories and works of two contemporary Egyptian architects -- Abdel Halim Ibrahim Abdel Halim and Carnal Bakri -- as examples of the moderate position that tries to rid itself from any emotional or unrealistic biases towards either end. Through the study of the origins and the nature of these two architects' attitudes, theories and works I have showed how they have raised the level of sophistication and complexity of the discussion of these challenges. In other words, certain levels of reconciliations have been achieved. Nevertheless, despite these reconciliations that narrow the gap between a number of polarities within the Egyptian society and despite the agreement on the nature of the main issues at stack, issues of the role of the Egyptian architect in the development process, the nature of the architectural profession -- being an art form or a social reform tool, how to deal with the latest available technologies that appear in the West, the universality of the current dominant civilization versus the regional identity of each society, and why and how do we relate to history, among many others, are still being debated. Thus, clear biases are evident in the two architects' underlying attitudes towards the two poles of this dilemma.by Yasser M. Nabil.M.S

Assessment of the Cognitive function in the epileptic patients and effect of anti epileptic drugs

This study is a prospective study that aimed to evaluate cognitive function in newly diagnosed epileptic patients before and 3 months after taking an antiepileptic drug by doing Wechsler IQ for patients before and 3 months after treatment and for their parents . the study included 40 patients. Divided into 4 groups  (each containing 10 patients ) and subjected to one of the following AEDs  for  3  months : 1. group A : receiving Carbamazepine (Tegretol)  in a dose of 10-20 mg/kg/day,2. group B receiving Na valproate (Depakine) in a dose of 20-40 mg/kg/day,3. group C : receiving Lamotrigine (Lamictal)  in a dose of 3-5 mg/kg/day,4. group D : receiving Topiramate in a dose of 3-6 mg/kg/day.Taking into consideration other factors that may be of Significance in affecting cognitive functions as seizure frequency ,age at onset of seizures and EEG abnormality. The results of the study were as following:1-There are statistically significant differences between IQs before and after treatment in the 4 groups. 2-there is +ve correlation between IQs before and after ttt in all groups.3- there is -ve correlation between IQs after ttt and frequency of seizures in group (B).4- There is +ve correlation between IQs of parents and patients? IQs before ttt in all groups.5-there is +ve correlation between IQs after ttt and parents' IQs  in all group,From these results we can conclude that  heredity is the main factor responsible for most of the decline in cognitive functions seen in epileptic patients after  treatment with AEDs and other factors as   seizure frequency, age at onset of seizures and EEG  abnormalities may also  play  a role,  By comparing the four groups we found that the impairment in cognitive function is mainly related to the impairment in cognitive function already present in those patients before the start of treatment. which were correlated and inherited in all groups. Keywords: Epilepsy,Cognition,Antiepileptic drug

Elastic properties of tellurite glasses

Elastic properties of binary and ternary tellurite glass systems of the composition (in mol%) (100-x) TeO2 - x Nb2O5, and (100-x) TeO2 - 0.5x (Nb2O5 + Li2O) were calculated from the measured densities as well as from longitudinal and shear ultrasonic velocities at room temperature. Ultrasonic velocity measurements were taken at 4 MHz ultrasonic frequency using the pulse echo technique. Elastic moduli, and Debye temperature calculated from experimental data and calculated theoretically using the bond compression model were used to obtain quantitative details about the structure of these glasses. The effect of adding either Nb2O5 alone or Nb2O5 and Li2 on the elastic moduli was investigated in terms of the number of network bonds of the glass systems. The average atomic ring size of the network was also calculated and it was found that it depends on the concentration of the modifiers. The obtained results show that these glasses become more stable and compact when modified with Nb2O5 or with Nb2O5 and Li2O, which increases the elastic moduli in the two systems

Investigating the Energy Dissipation Capability of Solid Piles Breakwater

In terms of the importance of coastal zones, this research started with the motivation of proposing an innovative coastal protection measure (solid piles, evenly distributed and staggered, breakwaters) and investigating their capability of energy dissipation, experimentally. Physical models of solid piles breakwater were designed and constructed. Experimental flume was arranged to test these models and measuring devices were arranged. Contributing parameters (i.e. wave height, period, steepness, piles arrangements and diameters) were varied, Based on the discussions and within the experimented range of parameters, it was clear that solid piles possess an enormous capability of dissipating the wave energy by a percentage that ranged between 20 to 75% which is considered to be significant amount from the coastal engineering point of view

Impact of Poultry Manure-Derived Biochar and Bio-Fertilizer Application to Boost Production of Black Cumin Plants (Nigella sativa L.) Grown on Sandy Loam Soil

Biochar derived from poultry manure increases nutrient availability and promotes plant growth. This study investigated the effect of biochar with mycorrhizal and/or plant growthpromoting rhizobacteria on soil fertility, chemical properties, oil, and seed yield of Black Cumin (Nigella sativa L.) plants. A split-plot design with three replicates was employed, with biochar derived from poultry litter (BC) applied at rates of 0, 5, and 10 t ha−1, with beneficial microbes such as arbuscular mycorrhizal fungi (AMF) and plant growth-promoting rhizobacteria (PGPR) affecting the growth of Black Cumin plants, and some soil properties, such as pH, electrical conductivity (EC), soil organic matter (SOM) and fertility index (FI), showing significant differences (p ≤ 0.05) among biochar and/or bio-fertilizer treatments. All biochar treatments with or without bio-fertilizers significantly increased pH, EC, OM and FI in comparison to the control treatment. The results demonstrated that applying biochar at the highest rate (10 t ha−1) increased fresh and dry capsule weights by 94.51% and 63.34%, respectively, compared to the control treatment (C). These values were significantly increased by 53.05 and 18.37%, compared to untreated plants when combined with AMF and PGPR. Furthermore, when biochar was applied in conjunction with both AMF and PGPR, fresh and dry capsule weights saw significant increases of 208.84% and 91.18%, respectively, compared to the untreated control treatment. The interaction between biochar, AMF, and PGPR significantly improved plant growth, yield, soil properties, and the fixed and volatile oil content of Black Cumin. These findings suggest that the combined application of biochar, AMF, and PGPR enhances nutrient availability and uptake, leading to improved growth and higher yields in Black Cumin plants, resulting in increased yield productio

The Role of Strategic Leadership in Activating Time Management Strategies to Enhance Administrative Creativity Skills

This study aimed to identify the role of strategic leadership in activating time management strategies to enhance administrative creativity skills at Al-Azhar University. The sample of the study was random stratified sample from (245) administrative employees using questionnaire as a main tool for primary data collection. Total respondent were (112) questioners. Descriptive and quantitative approach used in this study. The general results of the study showed high levels of strategic leadership at Al-Azhar University, average level of application of time management strategies and administrative creativity. This means there is acceptance approval that there is a statistically significant relationship between strategic leadership and time management strategies in Palestinian universities in Gaza Strip with a correlation level (0.724). Also, there is a statistically significant relationship between time management strategies and administrative creativity in Palestinian universities in Gaza Strip under study with a correlation level (0.848). According to static analysis, there is a statistically significant relationship between the dimensions of strategic leadership and administrative creativity in Palestinian universities in Gaza Strip under study, with a level of correlation (0.767%). This leases to high investment process for all available factors and elements in order to maximize and increase production and eliminate waste, wasted and unexploited employees' time and capabilities, which leads to achieving more effectiveness, positivity, productivity and increased organized effort. The study recommended necessity of having the elements of strategic academic leadership and activating time management strategies towards enhancing administrative creativity among workers in Palestinian universities in Gaza Strip. Also study recommended to encourage, support, and reward personal initiatives and creative ideas. Also study recommended available of wise and conscious strategic leadership to rationalize the behavior of individuals, mobilize their energies, mobilize their capabilities, coordinate their efforts, organize their affairs and direct them in the right direction towards achieving the desired goals and objectives

Bacterial flora-typing with targeted, chip-based Pyrosequencing

<p>Abstract</p> <p>Background</p> <p>The metagenomic analysis of microbial communities holds the potential to improve our understanding of the role of microbes in clinical conditions. Recent, dramatic improvements in DNA sequencing throughput and cost will enable such analyses on individuals. However, such advances in throughput generally come at the cost of shorter read-lengths, limiting the discriminatory power of each read. In particular, classifying the microbial content of samples by sequencing the < 1,600 bp 16S rRNA gene will be affected by such limitations.</p> <p>Results</p> <p>We describe a method for identifying the phylogenetic content of bacterial samples using high-throughput Pyrosequencing targeted at the 16S rRNA gene. Our analysis is adapted to the shorter read-lengths of such technology and uses a database of 16S rDNA to determine the most specific phylogenetic classification for reads, resulting in a weighted phylogenetic tree characterizing the content of the sample. We present results for six samples obtained from the human vagina during pregnancy that corroborates previous studies using conventional techniques.</p> <p>Next, we analyze the power of our method to classify reads at each level of the phylogeny using simulation experiments. We assess the impacts of read-length and database completeness on our method, and predict how we do as technology improves and more bacteria are sequenced. Finally, we study the utility of targeting specific 16S variable regions and show that such an approach considerably improves results for certain types of microbial samples. Using simulation, our method can be used to determine the most informative variable region.</p> <p>Conclusion</p> <p>This study provides positive validation of the effectiveness of targeting 16S metagenomes using short-read sequencing technology. Our methodology allows us to infer the most specific assignment of the sequence reads within the phylogeny, and to identify the most discriminative variable region to target. The analysis of high-throughput Pyrosequencing on human flora samples will accelerate the study of the relationship between the microbial world and ourselves.</p

The relation between Parkinson’s disease and non-steroidal anti-inflammatories; a systematic review and meta-analysis

Background: Parkinson’s disease (PD) is a neurological condition that typically shows up with aging. It is characterized by generalized slowness of movement, resting tremor or stiffness, and bradykinesia. PD patients’ brains mostly exhibit an increase in inflammatory mediators and microglial response. Nevertheless, a variety of non-steroidal anti-inflammatory medications (NSAIDS) offered neuroprotection in animal models and preclinical trials.Aim: The current systematic review and meta-analysis were designed to try to resolve the debate over the association of NSAID use with the development of PD because the results of several studies were somehow contradictory.Methods: An intense search was performed on Scopus, PubMed, and Web of Science databases for articles relating the incidence of PD to the use of NSAIDs. Statistical analysis of the included studies was carried out using Review Manager version 5.4.1 by random effect model. The outcome was identified as the development of PD in patients who were on NSAIDs, ibuprofen only, aspirin only, and non-aspirin NSAIDs. This was analyzed using pooled analysis of odds ratio (OR) at a significance level of ≤0.05 and a confidence level of 95%. A statistically significant decreased risk of PD was observed in patients taking NSAIDs, Ibuprofen, and non-aspirin NSAIDs.Results: The ORs of PD occurrence in patients who took NSAIDs, Ibuprofen, and non-aspirin NSAIDs were 0.88 [95% CI (0.8–0.97), p = 0.01], 0.73 [95% CI (0.53–1), p = 0.05] and 0.85 [95% CI (0.75–0.97), p = 0.01]. Meanwhile, the risk of PD in patients who took aspirin was not statistically significant.Conclusion: In conclusion, Ibuprofen, non-aspirin NSAIDs, and other types of NSAIDs could be associated with a reduction in PD risk. However, there was no association between aspirin intake and the development of PD

Assessment of seminal plasma laminin in fertile and infertile men

Abstract Aim: To assess laminin levels in the seminal plasma of infertile and fertile men, and to analyze the correlation of laminin levels with sperm count, age, sperm motility and semen volume. Methods: One hundred and twenty-five recruited men were equally divided into five groups according to their sperm concentration and clinical examination: fertile normozoospermia, oligoasthenozoospermia, non-obstructive azoospermia (NOA), obstructive azoospermia (OA) and congenital bilateral absent vas deferens (CBAVD). The patients&apos; medical history was investigated and patients underwent clinical examination, conventional semen analysis and estimation of seminal plasma laminin by radioimmunoassay. Results: Seminal plasma laminin levels of successive groups were: 2.82 ± 0.62, 2.49 ± 0.44, 1.77 ± 0.56, 1.72 ± 0.76, 1.35 ± 0.63 U/mL, respectively. The fertile normozoospermic group showed the highest concentration compared to all infertile groups with significant differences compared to azoospermic groups (P &lt; 0.05). Testicular contribution was estimated to be approximately one-third of the seminal laminin. Seminal plasma laminin demonstrated significant correlation with sperm concentration (r = 0.460, P &lt; 0.001) and nonsignificant correlation with age (r = 0.021, P = 0.940), sperm motility percentage (r = 0.142, P = 0.615) and semen volume (r = 0.035, P = 0.087). Conclusion: Seminal plasma laminin is derived mostly from prostatic and testicular portions and minimally from the seminal vesicle and vas deferens. Estimating seminal laminin alone is not conclusive in diagnosing different cases of male infertility. (Asian J Androl 2007 Jan; 9: 63-67