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

DeVega versus ring annuloplasty in severe functional tricuspid insufficiency and their impact on the right ventricle

Background: Functional tricuspid valve regurgitation secondary to left-sided valve disease is common. DeVega repair is simple, but residual regurgitation with subsequent impairment of the right ventricular function is a concern. This study aims to compare tricuspid valve repair using DeVega vs. ring annuloplasty and their impact on the right ventricle in the early postoperative period and after six months. Methods: This is a prospective cohort study of 51 patients with rheumatic heart disease who underwent tricuspid valve repair for secondary severe tricuspid regurgitation. Patients were divided into two groups: group A; DeVega repair (n=34) and group B; ring annuloplasty repair (n=17). Patients were assessed clinically and by echocardiography before discharge and after six months for the degree of tricuspid regurgitation, right ventricular diameter and tricuspid annular plane systolic excursion (TAPSE). Results: Preoperative echocardiographic assessment showed no difference in left ventricular end-systolic diameter, end-diastolic diameter, ejection fraction and right ventricular diameter, however; group A had significantly better preoperative right ventricular function measured by TAPSE (1.96 ± 0.27 vs1.75 ± 0.31 cm; p=0.02). Group B had significantly longer cardiopulmonary bypass time (127.65 ± 13.56 vs. 111.74 ± 18.74 minutes; p= 0.003) and ischemic time (99.06 ± 11.80 vs. 87.15 ± 16.01 minutes; p= 0.009). Pre-discharge, there was no statistically significant difference in the degree of tricuspid regurgitation, but the right ventricular diameter was significantly lower in group B (2.66 ± 0.41 and 2.40 ± 0.48 cm; p=0.049). After six months of follow up, the degree of tricuspid regurgitation (p= 0.029) and the right ventricular diameter were significantly lower in the ring annuloplasty group (2.56 ± 0.39 and 2.29 ± 0.44 cm; p=0.029). Although there was a statistically significant difference in preoperative TAPSE, this difference disappeared after six months. Conclusion: Both DeVega and ring annuloplasty techniques were effective in the early postoperative period, ring annuloplasty was associated with lesser residual regurgitation and better right ventricular remodeling in severe functional tricuspid regurgitation than DeVega procedure after 6-months of follow up

FastRNABindR: Fast and Accurate Prediction of Protein-RNA Interface Residues

A wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses are mediated by RNA-protein interactions. However, experimental determination of the structures of protein-RNA complexes is expensive and technically challenging. Hence, a number of computational tools have been developed for predicting protein-RNA interfaces. Some of the state-of-the-art protein-RNA interface predictors rely on position-specific scoring matrix (PSSM)-based encoding of the protein sequences. The computational efforts needed for generating PSSMs severely limits the practical utility of protein-RNA interface prediction servers. In this work, we experiment with two approaches, random sampling and sequence similarity reduction, for extracting a representative reference database of protein sequences from more than 50 million protein sequences in UniRef100. Our results suggest that random sampled databases produce better PSSM profiles (in terms of the number of hits used to generate the profile and the distance of the generated profile to the corresponding profile generated using the entire UniRef100 data as well as the accuracy of the machine learning classifier trained using these profiles). Based on our results, we developed FastRNABindR, an improved version of RNABindR for predicting protein-RNA interface residues using PSSM profiles generated using 1% of the UniRef100 sequences sampled uniformly at random. To the best of our knowledge, FastRNABindR is the only protein-RNA interface residue prediction online server that requires generation of PSSM profiles for query sequences and accepts hundreds of protein sequences per submission. Our approach for determining the optimal BLAST database for a protein-RNA interface residue classification task has the potential of substantially speeding up, and hence increasing the practical utility of, other amino acid sequence based predictors of protein-protein and protein-DNA interfaces.Edward Frymoyer Endowed Professorship in Information Sciences and Technology. The Center for Big Data Analytics and Discovery Informatics which is co-sponsored by the Institute for Cyberscience, the Huck Institutes of the Life Sciences, the Social Science Research Institute, and the College of Information Sciences and Technology at the Pennsylvania State University. NPRP grant No. 4-1454-1-233 from the Qatar National Research Fund (a member of Qatar Foundation)

Calcified Bronchogenic Cyst

Herein, we reported the case of a 32-year-old male patient presented with intermittent attacks of mild right chest pain and dyspnea for 2 years. On contrast-enhanced computed tomography (CT) of the chest, a non-enhancing subcarinal cystic lesion about 6×6.5 cm was detected in the posterior mediastinum, consistent with the features of bronchogenic cyst. The lesion showed small calcific focus changing its position posteriorly when patient changes his position from supine to prone. The flecks of calcium within the fluid in a cystic lesion constitute the origin of the future cyst wall calcifications and may reflect the long-standing nature of the lesion. Surgical excision is preferred to avoid the expected complications, including fistula formation, ulceration, and infection

BUILDING EXTRACTION FROM VERY HIGH-RESOLUTION SATELLITE IMAGES FOR MAP UPDATING IN EGYPT

Robust building detection from satellite images has been a subject of interest for several decades. Very High Resolution (VHR) satellite images support the efficient extraction of manmade objects. The main aim of this paper is to present an approach for building extraction from VHR satellite images for map updating in Egypt. To achieve this aim, a comparison of pixel and object-based classification techniques has been applied. Then, different refinement processes based on shadow, context, shape, and Digital Surface Model (DSM) data are carried out. Two study areas from the VHR satellite images for Assuit and Sohag cities are used. A comparison of the classification techniques shows that the Maximum Likelihood Classifier (MLC) for pixel-based technique and Support Vector Machine (SVM) for object-based technique give the highest overall accuracy results. Refinement based on shadow, context, shape, and DSM information improves the overall accuracy with an average of 18%. Thus, the building extraction results can contribute significantly to update maps in Egypt

Traumatic Dural Venous Sinuses Injury

The traumatic dural venous sinus injury is one of the most dangerous complications of TBI, either due to fatal intracranial compressing venous bleeding, or disturbing the intracranial pressure which could be caused by injury to the SSS On the other hand, post traumatic dural sinus thrombosis is considered a rare complication which may lead to hemorrhagic infarction with its serious consequences including epilepsy, neurological deficits, or death. Therefore, knowledge of the appropriate treatment of this kind of head injury is essential

UTJECAJ DULJINE IGS BAZE NA TOČNOST POZICIONIRANJA GNSS-A

Since the establishment of the International GNSS Service (IGS) stations, they have been used as control stations for assigning the Precise point positioning (PPP) positions using one Global Navigation Satellite System (GNSS) receiver, which has increased from day-to-day. There are some factors affecting the accuracy of PPP positioning. This research aims to investigate the relation between the IGS distance and observed field points as well as to attempt to describe that relation mathematically/statically. For the realization of that aim, two field points are fixed inside the Assiut University campus and observed successively for a session of 24 hour observation. The position of each field point is assigned with the help of each one of the available IGS station products. It must be known that these products are found after observations in three files (IGU, IGR, and final IGS), whereas IGU is used directly as real-time data (ultra-rapid), IGR (rapid) is used through (17-41 hours) after observation, and (final IGS) used after 12 – 18 days. Coordinates and point errors of each field points are computed and represented. It has been found that the errors have a positive relation with the available IGS stations distances. The relation between these distances and point positioning errors have been represented and described according to a model. The accuracy of the presented model is (R ≅ .98, x2 ≅ 2.5 × 10-3).Od uspostave postaja Međunarodnoga GNSS servisa (IGS) iz dana u dan povećava se korištenje kontrolnih stanica za dodjelu položaja precizne točke (PPP) pomoću jednoga prijamnika Globalnoga satelitskog navigacijskog sustava (GNSS). Postoje neki čimbenici koji utječu na točnost PPP pozicioniranja. Cilj je ovoga istraživanja istražiti odnos između IGS udaljenosti i promatranih točaka polja te opisati taj odnos matematički i statički. Za realizaciju toga cilja dvije terenske točke fiksirane su unutar kampusa Sveučilišta Assiut i promatrane sukcesivno tijekom sesije promatranja od 24 sata. Položaj svake točke polja dodjeljuje se uz pomoć svakoga od dostupnih proizvoda IGS stanica. Bitno je napomenuti da se ti produkti nalaze u tri datoteke (IGU, IGR i konačni IGS) nakon promatranja, dok se IGU koristi izravno kao podatci u stvarnome vremenu (ultra-rapid), IGR (rapid) kroz 17 – 41 sat nakon promatranja, a konačni IGS nakon 12 – 18 dana. Koordinate i pogreške točaka svake točke polja izračunane su i prikazane. Utvrđeno je da su pogreške u pozitivnom odnosu s dostupnim udaljenostima IGS postaja. Odnos između tih udaljenosti i pogrešaka pozicioniranja točke prikazan je i opisan prema modelu. Točnost je prikazanoga modela R ≅ .98, x2 ≅ 2.5 × 10-3

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

AUTOMATIC INDICES BASED CLASSIFICATION METHOD FOR MAP UPDATING USING VHR SATELLITE IMAGES

Urban land cover classification using Very High Resolution (VHR) satellite images is a very important source of information for map updating. Egyptian environment has more challenges in feature extraction. The main problem lies in the spectral similarity between different land cover classes. Also, great diversity in sizes, shapes, and materials of each class. The main aim of this work is to represent a new automatic indices-based classification method for map updating using VHR satellite images. The method uses a set of spectral indices with their thresholds in consecutive order, chosen based on WorldView-2 (WV-2) bands, to classify land cover in the Egyptian environment. For this study, WV-2 satellite images with eight spectral bands were used. The proposed method is compared with five traditional classification methods; Minimum distance, Spectral angle mapper, Mahalanobis distance, Spectral correlation mapper, and Maximum likelihood method, which included in ERDAS 2015 software, for validation purpose and checking its stability. The results show that the extracted features with the proposed method can contribute significantly to update Egyptian medium scale maps. The average overall accuracy achieved with the proposed approach (75.31%) is higher than those obtained using Minimum distance (54.0%), Spectral angle mapper (69.50%), and Mahalanobis distance (73.63%). Also, it is near to those obtained by the Spectral correlation mapper (76.50%), and Maximum likelihood method (78.25%)