973 research outputs found
Design and provisioning of optical wireless data center networks: A traffic grooming approach
No full textTraditional wired data center networks (DCNs) suffer from cabling complexity, lack flexibility, and are limited by the speed of digital switches. In this paper, we alternatively develop a top-down traffic grooming (TG) approach for design and provisioning of optical wireless DCNs. While switches are modeled as hybrid opto-electronic cross-connects, links are modeled as wavelength division multiplexing (WDM) capable free-space optic (FSO) channels. Using the standard TG terminology, we formulate the optimal mixed integer linear problem considering the virtual topology, flow conversation, connection topology, non-bifurcation, and capacity constraints. Thereafter, we develop a fast sub-optimal solution where mice flows (MFs) are groomed and forwarded on predetermined rack-to-rack (R2R) lightpaths. On the other hand, elephant flows (EFs) are forwarded over dedicated server-to-server (S2S) express lightpaths whose routes and capacity are dynamically determined based on wavelength and capacity availability. Emulation results show that proposed models and algorithms provide a significant throughput improvement upon traditional DCNs for both MFs and EFs.</p
A Fish By Any Other Name Would Taste as Sweet: Applied Ethics of Transgenic Fish Commercialization
No full textModern aquaculture has grown into a vital industry over the past half-century, such that it now supplies half of all the fish we consume. Nevertheless, it has been found to cause significant economic, environmental, and health problems, while commercial fishing has led to the decline in wild fish stocks. In response to this dilemma and the growing demand, AquaBounty Technologies has created a genetically modified “AquAdvantage” Atlantic salmon using foreign genetic elements from the ocean pout and Chinook Pacific salmon, in hopes of improving their fish farming efficiency. These modifications allow the AquAdvantage salmon to grow twice as fast as their domesticated counterparts and four times as fast as their wild brethren.
The recent approval for commercialization of the AquAdvantage salmon as the first genetically modified animal by the Food and Drug Administration (FDA) in the U.S. market has sparked substantial controversy, with no small number of people urging for a moratorium or ban on genetically modified organisms (GMOs) altogether. The significance of this approval cannot be overstated, as it sets a regulatory precedent for other pending commercializations of genetically engineered animals and future axioms of molecular and synthetic biology.
In this article, I identify and evaluate some of the leading arguments for and against the adoption of GM salmon on store shelves, and this product’s position in terms of deep ecology, the precautionary principle, virtue ethics, and non-anthropocentrism. I rely on this pluralistic presentation to ensure that the key aspects are recognized, and that possible consequences are assessed from a plurality of positions to avoid a one-eyed perception of the topic and allow judgments to be made on a rational and informed basis, all ethical concerns considered
A Fish By Any Other Name Would Taste as Sweet: Applied Ethics of Transgenic Fish Commercialization
No full textModern aquaculture has grown into a vital industry over the past half-century, such that it now supplies half of all the fish we consume. Nevertheless, it has been found to cause significant economic, environmental, and health problems, while commercial fishing has led to the decline in wild fish stocks. In response to this dilemma and the growing demand, AquaBounty Technologies has created a genetically modified “AquAdvantage” Atlantic salmon using foreign genetic elements from the ocean pout and Chinook Pacific salmon, in hopes of improving their fish farming efficiency. These modifications allow the AquAdvantage salmon to grow twice as fast as their domesticated counterparts and four times as fast as their wild brethren.
The recent approval for commercialization of the AquAdvantage salmon as the first genetically modified animal by the Food and Drug Administration (FDA) in the U.S. market has sparked substantial controversy, with no small number of people urging for a moratorium or ban on genetically modified organisms (GMOs) altogether. The significance of this approval cannot be overstated, as it sets a regulatory precedent for other pending commercializations of genetically engineered animals and future axioms of molecular and synthetic biology.
In this article, I identify and evaluate some of the leading arguments for and against the adoption of GM salmon on store shelves, and this product’s position in terms of deep ecology, the precautionary principle, virtue ethics, and non-anthropocentrism. I rely on this pluralistic presentation to ensure that the key aspects are recognized, and that possible consequences are assessed from a plurality of positions to avoid a one-eyed perception of the topic and allow judgments to be made on a rational and informed basis, all ethical concerns considered
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Bogs, Bugs, Borgs, and Bacteriophages: Metagenomic and Biochemical Insights into the Enigmatic World of Extrachromosomal Genetic Elements
No full textAs a Ph.D. Candidate and National Science Foundation Predoctoral Fellow at the University of California, Berkeley, working in the labs of Dr. Jillian Banfield and Dr. Jennifer Doudna, I have dedicated my Ph.D. to the discovery and investigation of novel extrachromosomal elements and tools for biotechnological applications through a combination of genomics and biochemistry.The first chapter of this thesis uncovers 10 new clades of the largest bacteriophages ever found across many ecosystems worldwide, with genome sizes rivaling those of the smallest bacteria. We found that the phages are not only equipped with a wide variety of features typically associated with life and cellular organisms such as ribosomal proteins, tRNA synthetases and initiation and elongation factors, but also some of the viruses intriguingly utilize alternative genetic codes to translate their proteins. Notably, I discovered that the huge phage genomes encode CRISPR-Cas systems that may be used for inter-viral warfare. Some of these are miniature, previously undescribed CRISPR-Cas systems that are about half of the size of Cas9. This work was published in Nature.
The second chapter describes the analysis and testing of one of the novel phage CRISPR-Cas systems, CRISPR-CasΦ, that we have shown can indeed exclude mobile elements such as plasmids from infecting the same host cell despite their small size, and can be applicable for programmable genome editing in bacterial, plant, and mammalian cells as the most compact functional CRISPR-Cas systems to date, potentially circumventing cell delivery barriers exhibited with CRISPR-Cas9 gene editing. Intriguingly, the CRISPR-CasΦ system exhibited a previously undescribed consolidation of chemistries in a Cas nuclease as the RuvC active site mediated both double-stranded DNA cleavage and RNA processing in a metal-dependent manner. This work was published in Science.
The third chapter examines the discovery of enigmatic giant linear extrachromosomal elements, which we refer to as “Borgs”, inhabiting archaea. These elements that are about 1 Mbp long were recovered from multiple environments and may play a previously unrecognized role in controlling greenhouse gas emissions. Their genomes are represented in 2 uneven replichores, with inverted repeats >1.5kbp long on either end and dozens of tandem repeats throughout their genomes. They contain no obvious hallmarks of previously reported viruses or plasmids, and ~80% of their genes consist of novel and uncharacterized proteins. Our analysis of horizontal gene transfer suggests that many ribosomal, metabolic, and extracellular electron transfer genes and operons recently transferred from their hosts, including the nif operon for Nitrogen fixation and the MCR complex which was recently proposed to be involved in oxidation of methane. Evidence also suggests recent recombination events between different Borgs presumably within the same host cell. This work is currently in review at Nature.
The fourth chapter describes an open-science effort for robust viral discovery computational pipelines driven by the COVID-19 pandemic. Working with a truly collaborative global team of bioinformaticians, this work describes the discovery of over 100,000 species of viruses to which I have contributed novel huge phage genomes. This manuscript was published in Nature.
The final chapter examines the discovery of thousands of viruses encoding CRISPR-Cas systems, many of which target competing cryptic mobile elements that are predicted to infect the same bacterial hosts. From genome-resolved metagenomics and bioinformatics-enabled phylogenetic insights to biochemistry, structural biology, and eukaryotic genome editing, I describe hundreds of novel hypercompact and divergent CRISPR-Cas systems, with special consideration towards the novel Casλ family. Casλ possesses an aberrant RNA structure reminiscent of a naturally-occurring sgRNA and processes its own crRNA at the 3’ end, unlike any previously described single-RNA CRISPR-Cas system. The tertiary structure determined via cryo-EM reveals the machinery for PAM recognition, hybrid assembly, and DNA cleavage. RNA-targeting systems on viruses lack crucial residues or accessory proteins that would, in their bacterial counterparts, result in acute abortive infection, suggesting a potential strategy for phage systems to maintain host viability while preventing superinfection. In addition to their streamlined nature that is advantageous for cellular delivery, hypercompact phage systems can produce efficient genome editing in endogenous genes in mammalian and plant cells on par with, or in some cases, exceeding gold-standard Cas12a editing, demonstrating significant utility for biotechnological applications.Overall, this dissertation describes the use of a combination of bioinformatics and biochemistry to shed light on gigantic bacterial viruses, the proteins they encode on their genomes, and elements such as Borgs which we are only beginning to understand. Huge phages and Borgs represent little-known biology, the platforms for which are distinct from previously known systems, and significantly broaden our overall understanding of “non-living” selfish genetic entities. The metagenomic discovery and biochemical and structural characterization of hypercompact CRISPR-Cas systems in addition to analyses of their genome editing utility in eukaryotic cells pave the road for efficacious delivery of treatments to human cells in the near future
Determining the delay factors for reconstructed mega-project’s phases and the associated challenges / Basem Adnan Al Khatib
No full textIn recent decades, the construction industry has developed rapidly. Delays in construction projects are a common phenomenon throughout industry. It was and remains one of the most important challenges negatively affecting not only this industry but also the economy. Many studies were conducted to identify the delay factors in new construction projects in different regions, but very few have focused on finding an explanation for the delay causes in reconstruction projects. The study aims to conduct a comprehensive analysis of the delay factors in mega reconstruction projects which took place recently in the Middle East, namely Mataf Expansion Project in Mecca, Saudi Arabia. This project consists of two main parts, nonhistorical and historical and it clarifies the difficulties facing this type of reconstruction projects, which combine demolition and construction works at the same time while the project is under operation. In order to achieve the study goal, twenty-nine interviews were held with the experts working on the project to identify the delay factors and ninety-three questionnaires were distributed by hand to sort them. The results showed that these factors could be divided into three groups: the first one is related to the demolition phase and the second is related to construction phase, while the last is related to overall reconstruction duration. In addition, it has been observed that the materials challenges are considered the major delay factor in the historical building of this project. The questionnaire results were analyzed and delay factors were sorted in a descending order according to the relative importance index (RII). The three main factors affecting the overall reconstruction project duration were site conditions and constraints, electrical and mechanical rerouting works, and design constructability and modification. Finally, recommendations were provided to bridge or reduce the negative impacts of the delay factors in future reconstruction projects
Compressive Strength of Jordanian Cement Mortars
No full textMortars have been prepared from six cement Jordanian brands and tested for their compressive strengths at 2, 7 and 28 days. The strength has been related to some physical parameters. It has been concluded that the compressive strength and its development with age has some variations between the different cement brands. There is an inverse linear rela-tionship between compressive strength and water absorption, and a weaker positive relation with density. There is no clear relation between consistency and compressive strength. Inverse linear relations exist between less than 63 microns size fraction and strength. To account for the differences in compressive strength at different ages and using different cement brands, it is very important to identify the type and amount of cement mineral phases using concrete petrogra-phy and X-ray diffraction and fluorescence techniques
Deviance from the linguistic analogy in some linguistic structures in the Holy Quran
No full text هدفت هذه الدارسة إلى كشف حقيقة بعض التراكيب اللغويّة في القرآن الكريم وبعض قراءته، والتي تبدو في ظاهرها أنّها قد خالفت المقيس من كلام العرب. وبالنظرة المتأنيّة والمتفحّصة إلى تلك التراكيب، وردّها إلى أصولها المقيسة من كلام العرب يتبيّن لنا أنّ الحكم على هذه الظواهر يمكن أن يكون ناتجًا عن قصور في إدراك المنهجيّة اللغويّة التي يتبعها القرآن الكريم في التعبير عن معانيه ومقاصده.
ولتحقيق هدف الدراسة فقد تناول الباحثان عددا من هذه الظواهر اللغويّة في القرآن، من مثل: الخروج عن قواعد الإعراب، والخروج عن قواعد المطابقة أو عدمها بين اللفظ ومتعلقه من حيث العدد، ومن حيث الجنس، والتعبير بصيغة فِعْل عن صيغة أخرى، وغيرها، وقد خلصنا من خلال الربط بين هذه التراكيب والاستعمالات اللغويّة عند العرب والنظرة المتعمّقة للقواعد النحويّة إلى جملة من النتائج منها، أنّ ما بدا في بعض تراكيب القرآن خارجا عن سنن العربيّة هو من صلب الاستعمال اللغويّ عند العرب. وأنّ سببه قد يُعزى في بعض الأحيان إلى اعتماد النحاة في التقعيد اللغوي على كلام العرب وبالأخص الشعر بالدرجة الأولى بصورة تفوق الاعتماد على القرآن الكريم. This study aimes to uncover the truth about some of the linguistic structures in the Holy Quran, which may appear for the first glance deviating from the norms of the Arabic speech. When we take a deep and examining look and measuring them in accordance with the Arabic normative speech, we find that the rush to judgment was due mainly to the lack of understanding of the linguistic methodology which the Holy Quran used in expressing meanings and purposes.
To achieve the above purpose, researchers study some linguistic phenomena like: Deviance from the inflection system (Erab), matching between the verb and the subject, and replacing a structure with another. We have concluded through relating these structures to its usage by Arabs, and the deep look at the grammatical rule, that what have appeared to be deviant from Arabic rules and norms in the structures we have chosen was in part due to the fact that the Arab traditional grammarians have given priority in the process of setting the grammatical rules to the spoken language more than the Holy Quran itsel
Derivatives combining the fragment of pyrazinamide and 4-aminosalicylic acid as antimycobacterial compounds
No full textCharles University Faculty of Pharmacy in Hradec Králové Department of Pharmaceutical chemistry and Pharmaceutical analysis Author: Petr Šlechta Supervisor: doc. PharmDr. Jan Zitko, Ph.D. Consultant: MSc. Ghada Basem Bouz, Ph.D. Title of diploma thesis: Derivatives combining the fragment of pyrazinamide and 4-aminosalicylic acid as antimycobacterial compounds According to WHO, tuberculosis (TB) is the leading cause of death from a single infectious organism worldwide and the number of cases with drug resistant TB is still increasing, creating the need for new antituberculotics. Therefore, we report design, synthesis and antimicrobial evaluation of a series of hybrid compounds combining different pyrazinamide derivates and p- aminosalicylic acid as potential antituberculotic agents. The compounds were prepared by mixing different pyrazinecarboxylic acids, after activation by 1,1'-carbonyldiimidazole, with p- aminosalicylic acid in dimethylsulfoxide as a solvent. Obtained compounds were in vitro tested for their antimycobacterial activity against M. tuberculosis H37Rv, M. tuberculosis H37Ra and four other mycobacterial strains. Prepared compounds were also in vitro screened for antibacterial, antifungal, and cytotoxic (HepG2) activity. Most compounds showed antimycobacterial activity in range of..
Strategic Agility of School Principals in Palestine and its Relationship with Their Administrative Creativity and Teachers' Job Absorption
No full textهدفت الدراسة تعرف درجة الرشاقة الاستراتيجية لدى مديري المدارس في فلسطين، وعلاقتها بالإبداع الإداري لديهم، والاستغراق الوظيفي لدى المعلمين. وقد تكونت عينة الدراسة من (400) معلماً ومعلمة من معلمي المدارس في فلسطين والتي تم اختيارهم بالطريقة الطبقية العشوائية. ولتحقيق أهداف الدراسة تم تطوير أداة من أربعة أجزاء، بلغ عدد فقراتها (61) فقرة، والتي تم التحقق من صدقها وثباتها. وأظهرت نتائج الدراسة أن درجة ممارسة مديري المدارس في فلسطين للرشاقة الاستراتيجية كانت مرتفعة، كما أن الإبداع الإداري لدى مديري المدارس في فلسطين كان مرتفعاً، إضافة إلى أن الاستغراق الوظيفي لدى المعلمين جاء بدرجة مرتفعة أيضاً. وأظهرت النتائج عدم وجود فروق في درجة الرشاقة الاستراتيجية لدى مديري المدارس في فلسطين تعزى لمتغيرات (الجنس، والمؤهل العلمي، وسنوات الخبرة، ومستوى المدرسة)، ووجود علاقة إيجابية طردية مرتفعة ذات دلالة إحصائية بين درجة ممارسة الرشاقة الاستراتيجية لدى مديري المدارس في فلسطين، وممارسة الإبداع الإداري، حيث بلغ معامل الارتباط (90.) تقريبا، ووجود علاقة ارتباطية موجبة ذات دلالة إحصائية متوسطة بين درجة ممارسة الرشاقة الاستراتيجية لدى مديري المدارس في فلسطين ودرجة الاستغراق الوظيفي لدى المعلمين، حيث بلغ معامل الارتباط (56.) تقريبا. وفي ضوء هذه النتائج أوصى الباحث ضرورة تعزيز مقدرة مديري المدارس في فلسطين على ممارسة مهارات القيادة الإبداعية، وذلك من خلال عقد دورات تدريبية، وخاصة في مجال المقدرات الأساسية والتكنولوجية.The study aimed to determine the level of strategic agility among school principals in Palestine, its relationship with their administrative creativity, and the job absorption of teachers working with them. The study sample consisted of (400) teachers from schools in Palestine, selected randomly. A four-part tool was developed to achieve the study's objectives, composed of (61) items whose reliability and validity were confirmed. The results showed that the practice level of school principals in Palestine in strategic agility was high, as was their administrative creativity. Additionally, the job absorption of teachers was also high. The results indicated no differences in strategic agility among school principals in Palestine related to gender, educational qualification, experience, and school level. There was a significantly high positive correlation between the practice of strategic agility among school principals in Palestine and the practice of administrative creativity, with a correlation coefficient of (approximately 0.90). There was also a moderately significant positive correlation between the practice of strategic agility among school principals in Palestine and the job absorptions of teachers, with a correlation coefficient of (approximately 0.56). Based on these results, the researcher recommended enhancing the ability of school principals in Palestine to practice creative leadership skills through training programs concentrating on essential skills and technological competencies
The degree of crisis management at Al-Quds University, and how well the university is ready to deal with potential crises
No full textThis study aimed at identifying the degree of crisis management at Al-Quds University,
and how well the university is ready to deal with potential crises. Thus, identifying the
degree of strategic planning at the university and determine its relation to crisis
management. The study also sought to know the impact of demographic variables (gender,
educational qualification, years of experience and job title) on the views of the study
sample on the degree of crisis management and strategic planning at the university.
The researcher used the analytical descriptive approach to fit such studies to describe the
phenomenon, to indicate the relationship between the subject matters of the study and to
analyze its data. To achieve this, the researcher designed a questionnaire consisting of 49
categories and tested its credibility and stability. Then, it was distributed to the study
population which includes 152 senior and middle-class administrative staff.
The results of the study showed that the degree of crisis management at Al-Quds
University, as well as the degree of strategic planning, came with an average degree. It was
found that there was a direct statistical correlation at the level of significance (α ≤ 0.05)
between crisis management and strategic planning at Al-Quds University, where the
Pearson correlation coefficient for the total grade was (0.788). The results also showed that
the views of the respondents differ according to the demographic variables in the fields of
crisis management and strategic planning. One of the most prominent results was the
Israeli Occupation, which is considered one of the biggest obstacles facing the university in
achieving its goals. The university also lacks a clear crisis management plan. This is due to
the lack of an effective crisis management and strategic planning team, along with the poor
recourse to crisis management and strategic planning experts.
Based on the findings of the study, the researcher made several recommendations that
would raise the degree of crisis management and the degree of strategic planning at the
university. The most important of these is to take care of the early stages of crisis
management in an attempt to prevent crises and to avoid as much damage as possible. In
addition to the necessity of having clear systems and standards for crisis analysis, and
assessing the university's readiness to deal with crises. Furthermore, the researcher
emphasized on the importance of formulating the university’s vision, mission and
objectives based on the university’s available and potential capabilities. Also, she draw
attention to the importance of having crisis management and strategic planning teams with
appropriate competencies and experience
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