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Search Results: 1 - 10 of 248 matches for " Bassam AlKindy "
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Gene Similarity-based Approaches for Determining Core-Genes of Chloroplasts
Bassam AlKindy,Christophe Guyeux,Jean-Fran?ois Couchot,Michel Salomon,Jacques M. Bahi
Computer Science , 2014,
Abstract: In computational biology and bioinformatics, the manner to understand evolution processes within various related organisms paid a lot of attention these last decades. However, accurate methodologies are still needed to discover genes content evolution. In a previous work, two novel approaches based on sequence similarities and genes features have been proposed. More precisely, we proposed to use genes names, sequence similarities, or both, insured either from NCBI or from DOGMA annotation tools. Dogma has the advantage to be an up-to-date accurate automatic tool specifically designed for chloroplasts, whereas NCBI possesses high quality human curated genes (together with wrongly annotated ones). The key idea of the former proposal was to take the best from these two tools. However, the first proposal was limited by name variations and spelling errors on the NCBI side, leading to core trees of low quality. In this paper, these flaws are fixed by improving the comparison of NCBI and DOGMA results, and by relaxing constraints on gene names while adding a stage of post-validation on gene sequences. The two stages of similarity measures, on names and sequences, are thus proposed for sequence clustering. This improves results that can be obtained using either NCBI or DOGMA alone. Results obtained with this quality control test are further investigated and compared with previously released ones, on both computational and biological aspects, considering a set of 99 chloroplastic genomes.
Finding the Core-Genes of Chloroplasts
Bassam AlKindy,Jean-Fran?ois Couchot,Christophe Guyeux,Arnaud Mouly,Michel Salomon,Jacques M. Bahi
Computer Science , 2014,
Abstract: Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison between sets of close species. An interesting question to answer is: what is the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, \textit{i.e.}, genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance.
Hybrid Genetic Algorithm and Lasso Test Approach for Inferring Well Supported Phylogenetic Trees based on Subsets of Chloroplastic Core Genes
Bassam AlKindy,Christophe Guyeux,Jean-Fran?ois Couchot,Michel Salomon,Christian Parisod,Jacques M. Bahi
Computer Science , 2015,
Abstract: The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of "problematic" genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained if the number of problematic genes is low, the problem being to determine the largest subset of core genes that produces the best supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, we propose an hybrid approach that embeds both genetic algorithms and statistical tests. Given a set of organisms, the result is a pipeline of many stages for the production of well supported phylogenetic trees. The proposal has been applied to different cases of plant families, leading to encouraging results for these families.
Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species
Bassam AlKindy,Huda Al-Nayyef,Christophe Guyeux,Jean-Fran?ois Couchot,Michel Salomon,Jacques M. Bahi
Computer Science , 2015, DOI: 10.1007/978-3-319-16483-0_38
Abstract: The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.
The Impact of Organizational Culture on Employee’s Satisfaction at the Jordanian Company of Investments “Safeway”  [PDF]
Bassam Mohammad Abu Khadar
American Journal of Industrial and Business Management (AJIBM) , 2018, DOI: 10.4236/ajibm.2018.81002
Abstract: This paper mainly studies a Safeway store” as a field study. Generally, job satisfaction is the main engine for all operations implemented in any business organization. In addition, communication among all the employees encourages on achieving cooperation and the planned aims highly and efficiently. So, organizations are interested in achieving the satisfaction of the employees in a way gains in growth, benefits, maintaining a good competitive position and achieving excellence in its performance. The Jordanian companies for investment and supply must pay attention to the elements and factors of organizational culture in which they coordinate all activities and procedures to execute all needs and requirements of the employees. Therefore, the problem of the study is to identify role playing by the organizational culture and its impact on job satisfaction in the Jordanian companies of investment and supplies.
The Relationship Learning and Knowledge Based View of Strategy  [PDF]
Bassam Abu Khudair
Open Journal of Business and Management (OJBM) , 2018, DOI: 10.4236/ojbm.2018.62024
Abstract:
The rate of learning is determined by the method that one comes up with the information. The identical substance can be realized often times quicker if properly formulated. This work aims at fostering multidisciplinary dialogue and study about knowledge-intensive methods to learning administration as well as studying procedures in the person, business and countrywide amounts, focusing information portrayal problems, sociable and organizational components, architectural, and layout concerns associated with studying supervision systems. Moreover, business strategy can be defined as set of plans in order to achieve the required goals. While nowadays, there is no accurate definition of strategy. In this work, collection of strategy definitions, research methods, industrial economics view of strategy, resources based view of strategy and the competitive dynamics view of strategy are explained in details. Moreover, the related research including strategy definitions is previewed.
Modification and Development of a Blow Molding Machine  [PDF]
Bassam A. Al-Helou
Engineering (ENG) , 2012, DOI: 10.4236/eng.2012.44025
Abstract: This study is based on the modification and development of a two-liter plastic container blow molding machine into a five-liter one provided with a translucent view stripe. This study considers some objectives including reducing the total cost, increasing the amount of plastic recovery, and raising the desired plastic materials. Proper designs were prepared and directly applied on spot. Tangible results were obtained. Among others, the modification of some components of the machine, e.g. the extruder, has led to the possible reuse of the milled (recovery) and extra material from the manufacturing processes. That was also conducive to an effective reduction in the cost of production to 50% in some cases. Prior to its modification, this old machine was used to produce polyvinyl chloride (PVC) containers that have become prohibited these days for their damaging effect on man’s life. For now, and after modification, it has become possible to use High Density Polyethylene (HDPE) material, a fact that has improved labor conditions, too.
Current Challenges of Organ Donation Programs in Syria
Bassam Saeed
International Journal of Organ Transplantation Medicine , 2010,
Abstract: Background: Renal transplantation is the optimal treatment for the majority of patients with end-stage renal disease.Objective: To examine the donor characteristics of kidney transplants in Syria and the impact of national Syrian legislation on the evolution of kidney transplantation activities in the private and public sectors.Methods: Available data on all kidney transplants performed in Syria over the last 2 decades was retrospectively analyzed to assess the characteristics of kidney donors and recipients with a focus upon transplants since 2003.Results: The kidney transplant rate has increased from 7 kidney transplants per million populations in 2002 to more than 17 in 2007. In the meantime, a substantial decline in the rate of kidney transplantation performed on Syrian nationals abroad was observed from 65% of all kidney transplantations in 1998 to less than 2% in 2007. Despite the prohibition to buy a kidney in Syria, vendors had found ways to sell their kidneys through disreputable brokers. Potential related donors were not inclined to donate kidneys to their relatives as long as kidneys could be bought from a non-related donor. By 2008, the percent of related donors in private sector represented only 8% of all donors, as compared to 50% in public hospitals. Consequently, in January 2008, the government of Syria issued a pronouncement restricting kidney transplantation to the public sector with a new national regulatory oversight of transplantation practices. Since this 2008 Administrative Order was promulgated, the kidney transplant rate in public hospitals has substantially increased by 55% with the establishmentof new public transplant centers in the 3 largest cities in Syria.Conclusion: The recommendations of the Istanbul Declaration and the Revised Guiding Principles of the World Health Organization have yet to be implemented in Syria but the expansion of kidney transplants in the public sector is an important initial step for initiating a deceased organ donation program as an essential component of a comprehensive approach to the problem of the organ shortage.
MESOT Fellowship Program
Bassam Saeed
International Journal of Organ Transplantation Medicine , 2011,
Abstract: MESOT Fellowship Program (MFP) is an initiative aimed at promoting and advancing organ transplantation in under-served areas of the Middle East by helping them to establish local transplantation programs or to improve an existing program. The fel lowship program gives a great opportunity to the young physicians and surgeons from this region willing to acquire some particular skills related to various aspects of organ transplantation and provides them with specific and hands-on training opportunities in host institutions. MESOT Fellows return home to share new skills and knowledge in medical and surgical transplantation and improve local standards. The proposal to establish MFP originated from Professor Nasser Simforoosh in Tehran. Later on, it was voted and approved during the general assembly of MESOT 2006 congress held in Kuwait. In fact, most of the credit goes to Professor Mustafa Mousawi from Kuwait who worked very hard to have it done and well established. The MESOT Council formed the MFP Commit tee and approved its training centers: Baskent in Ankara, Turkey; SIUT in Karachi, Pakistan; Labbafi Nezhad in Tehran, Iran; Shiraz Organ Transplant Center in Shiraz, Iran; Hamed El-Issa Organ Transplant Center in Kuwait, Kuwait; King Faisal Specialist Hospital and Research Cen ter in Riyadh, Saudi Arabia; and NUC in Mansoura, Egypt. The program was announced and well advertised. Some of the most eminent transplant surgeons and physicians from the Middle East region are heading the training process in the above-mentioned centers of excellence such as Professor Mehmet Haberal from Turkey, Professor Adib Rizvi and professor Anwar Naqvi from Pakistan, Professor Mustafa Mousawi from Kuwait, Professor Ali Malek-Hosseini and Professor Nasser Simforoosh from Iran, Professor Adel Bakr from Egypt and Professor Khalid El-Meshari from Saudi Arabia. The selection mechanism relies on five factors on the top of which is the availability of transplant activity of a given organ in the applicant center, city, and country and a written commitment by the applicant indicating his or her intent to return home upon completion of training to establish transplant unit at home center; in addition to affiliation of the applicant’s center, capability and suitability of the applicant’s center, academic position and age of the applicant. The application for MFP is online through MESOT Web site available at www.mesot-tx.org. The 30th of June of each year is the deadline to apply for MFP. The program was launched in January 2008. Yet 20 applicants from 10 Middle East countries have been
Requirements for optimal learning environment for an online project risk management game
Bassam Hussein
Journal of Project, Program & Portfolio Management , 2012,
Abstract: Several authors have questioned the effectiveness of using lecture-based teaching to provide students with enough confidence to apply project risk management. Gaming was proposed as a solution. However, despite widespread use of games in teaching project management, it is still not clear what conditions provide optimal learning through games. Another shortcoming with the existing games is oversimplification. This paper addresses these shortcomings and proposes a game design that captures real-life challenges associated with applying the project risk management process; a design that prompts an appreciation for project complexity as well as providing students with the opportunity to experience the consequences of ignoring or following the risk management process. The paper also identifies and elaborates on the requirements for optimum learning, and distinguishes between two types of requirements: 1) learning requirements, and 2) qualitative requirements. Learning requirements identify the learning outcomes of the game. These requirements were identified through structured and semi-structured interviews with senior project managers from several management-consulting firms. The challenges and the corresponding tactics that are adopted in practice in order to manage project risks were thus identified and ranked. These results are also presented in light of supporting literature. The challenges and associated tactics were mapped into a set of eight requirements representing the learning outcomes of the game. These requirements were then mapped to the design using four instructional methods: a briefing lecture, a team-based assignment, an online computer simulation, and a debriefing lecture. All these methods were linked by a real-life project case and executed in a gaming context to improve engagement. Qualitative requirements represent important conditions that must be present for optimal learning. These were identified through structured interviews with continuing education students taking a master's degree in project management. This empirical study resulted in four qualitative requirements that must be considered in the game design: 1) ownership, 2) relevance, 3) feedback, and 4) adaptation. The paper also presents the evaluation results of the game design. The purpose of the evaluation was to examine the game's ability to capture the two sets of requirements identified above.
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