240 Works

Diversity, Phylogeography, and Taxonomy of Hard-Corals in the Genus Porites from the Arabian Peninsula

Tullia Isotta Terraneo
The genus Porites is one of the most important scleractinian genera in terms of species diversity and panmictic tropical distribution. However, Porites is notorious for challenging taxonomic identification based on colony gross morphology, micromorphology, and single gene analyses, suggesting that the current classification poorly represents real evolutionary relationships. This research integrates skeletal morphology data and single locus genetic evidence with genome-wide analyses and alternative line of evidence to taxonomy (i.e. symbiotic association data), with the...

Tomographic Measurements of Turbulent Flow through a Contraction

Vivek Mugundhan
We investigate experimentally the turbulent flow through a two-dimensional contraction. Using a water tunnel with an active grid we generate turbulence at Taylor microscale Reynolds number Reλ ~ 250 which is advected through a 2.5:1 contraction. Volumetric and time-resolved Tomo-PIV and Shake-The-Box velocity measurements are used to characterize the evolution of coherent vortical structures at three streamwise locations upstream of, and within the contraction. We confirm the conceptual picture of coherent large-scale vortices being stretched...

Fast High-order Integral Equation Solvers for Acoustic and Electromagnetic Scattering Problems

Noha Alharthi
Acoustic and electromagnetic scattering from arbitrarily shaped structures can be numerically characterized by solving various surface integral equations (SIEs). One of the most effective techniques to solve SIEs is the Nyström method. Compared to other existing methods,the Nyström method is easier to implement especially when the geometrical discretization is non-conforming and higher-order representations of the geometry and unknowns are desired. However,singularities of the Green’s function are more difficult to”manage”since they are not ”smoothened” through the...

Genome assembly and annotation datasets of the plant growth promoting bacterium Cellulosimicrobium sp. JZ28 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

Abdul Aziz Eida, Salim Bougouffa, Intikhab Alam, Maged Saad & Heribert Hirt
The files associated with this dataset are the Genbank, GFF and protein coding-sequence (CDSs) files of a plant growth promoting bacterium isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).

Effcient Monte Carlo Simulations for the Estimation of Rare Events Probabilities in Wireless Communication Systems

Chaouki Ben Issaid
Simulation methods are used when closed-form solutions do not exist. An interesting simulation method that has been widely used in many scientific fields is the Monte Carlo method. Not only it is a simple technique that enables to estimate the quantity of interest, but it can also provide relevant information about the value to be estimated through its confidence interval. However, the use of classical Monte Carlo method is not a reasonable choice when dealing...

Encounter of T7 Replisome with Abasic DNA Lesion

Lubna F. Alhudhali
In order to monitor the T7 replisome fate upon encountering abasic lesion, I optimized a single molecule flow stretching assay where the replisome encounters either abasic site or undamaged site inserted at 3.5 kilobases from the replication fork. The obtained events were categorized into three groups; bypass, restart and permanent stop. The results showed 52% bypass, 39% pause and 9% stop upon encountering the abasic lesion. The pause duration in the restart events was found...

Mechanistic basis for calcium-sensing by the protein-tyrosine kinase 2-beta (PYK2)

Afaque Ahmad Imtiyaz Momin
The focal adhesion kinase (FAK) and the protein tyrosine kinase 2-beta (PYK2) are two closely related non-receptor tyrosine kinases that link cell adhesion, migration and proliferation, and thus also promote cancer cell invasiveness. FAK and PYK2 have the same domain structure (comprising the FERM, kinase and FAT domains) and possess several overlapping functions, however their cellular roles can be different or even opposing. In particular, PYK2 can be activated by calcium, and has important functions...

An Experimental and Numerical Study to Investigate the Impact of Capillarity on Fluid Flow in Heterogeneous Porous Media

Ahmad Alabdulghani
Although the global energy demand is shifting towards a well-balanced energy mix, fossil fuels will continue to have a significant role in this transition and will maintain a big share in the energy mix portfolio. The production of oil and gas has already reached the apex in the time that most of the conventional giant reservoirs are depleting, and discoveries for new reserves have shrunk down. In conventional reservoirs, it is estimated that about two-thirds...

Design and Real-time Implementation of Model-free Control for Solar Collector

Mohammad Alharbi
This work addresses the design and real-time implementation of adaptive control strategies on the parabolic solar collector to enhance the production efficiency under varying working conditions. For example, the unpredictable variations of the solar irradiance and thermal losses, these factors can be a major problem in the control design. The control objective is to force the outlet temperature of the collector fluid, to track a predefined reference temperature regardless of the environmental changes. In this...

Swarm Localization and Control via On-board Sensing and Computation

Fat-Hy Omar Rajab
Multi-agent robotic system have been proved to be more superior in undertaking functionalities, arduous or even impossible when performed by single agents. The increased efficiency in multi agent systems is achieved by the execution of the task in cooperative manner. But to achieve cooperation in multi agent systems, a good localization system is an important prerequisite. Currently, most of the multi-agent system rely on the use of the GPS to provide global positioning information which...

Genome assembly and annotation datasets of the plant growth promoting bacterium Paenibacillus sp. JZ16 isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia

Abdul Aziz Eida, Salim Bougouffa, Intikhab Alam, Maged Saad & Heribert Hirt
The files associated with this dataset are the GenBank, GFF and protein coding-sequence (CDSs-FASTA) files of a plant growth promoting bacteria isolated from the root endosphere of a pioneer desert plant in Jizan, Saudi Arabia. Genome annotation was carried out using the Automatic Annotation of Microbial Genomes (AAMG) which is an integrated module in the in-house INDIGO-Desert v1.1 pipeline (Alam et al., 2013).

Functional diversity of herbivorous fishes in coral reefs in central Red Sea

Lucía Pombo-Ayora
In this research, I explore the changes in the functional diversity of herbivorous fishes in zones of coral reefs with different benthic composition: a zone dominated by corals, a zone dominated by algae and a transition zone in between the previous two. I choose to use functional traits which explain the feeding mechanics of this group of fish, as well their feeding rates and their previously established functional groups to understand how different assemblages of...

Multi-scale and Complex Metallic Structure Networks for Novel Solar Energy Harvesting-Conversion Applications

Yi Tian
The global consumption of fossil fuels continues to increase due to the rapid growth of energy demand, as a consequence of expanding population and human activities. Fast climate change is another inescapable issue caused by humans that need to be addressed. The development of solar energy conversion technologies is widely considered as one of the most promising solutions to sustainably maintain a modern lifestyle of the society and create a carbon-neutral social development operation mode....

Genetics of Salinity Tolerance in Rice

Nadia Al Tamimi
For more than half of the world’s population, rice (Oryza sativa L.), the most saltsensitive cereal, is a dietary staple. Soil salinity is a major constraint to rice production worldwide. Thus, to feed 9 billion people by 2050, we need to increase rice production while facing the challenges of rapid global environmental changes. To meet some of these challenges, there is a vital requirement to significantly increase rice production in salinized land and improve photosynthetic...

Consequences of Coral-Algal Phase Shifts for Tropical Reef Ecosystem Functioning

Florian Roth
Tropical coral reefs provide important ecosystem goods and services that are supported by one or more ecosystem functions (e.g., recruitment, primary production, calcification, and nutrient recycling). Scleractinian corals drive most of these functions, but a combination of global and local anthropogenic stressors has caused persistent shifts from coral- to algae-dominated benthic reef communities globally. Such phase shifts likely have major consequences for ecosystem functions; yet, related knowledge is scarce in general, but particularly at the...

GenRot - Software to generate rotamers of molecules from Gaussian input files

Michael Thulin, Kristin Munkerup & Kuo-Wei Huang
The GenRot program takes a typical Gaussian .gjf file (connectivity written after XYZ) as input, and generates new XYZ data based on inputs from the user. After opening the file in the program, the user clicks on 4 atoms to define a dihedral angle and determines the degree of rotation they wish for that angle. This is repeated until all the dihedral angles that the user wants to rotate have been defined. The program will...

Computational Analysis of Transcriptional Regulation after Single and Multiple Drug Administration

Trisevgeni Rapakoulia
Transcriptomics is the large-scale study of RNA molecules produced by the genome, in single cells or population of cells using high-throughput methods. With the advances in transcriptomic analysis, the monitoring of genome-wide gene expression provides a powerful approach for determining the action of drugs. In this study, we analyzed the transcriptional responses of cells treated with drugs either alone or in combinations to explore their effects in two different applications: breast cancer therapy and cell...

Theoretical and Experimental Studies of Optical Properties of BAlN and BGaN Alloys

Feras S. AlQatari
Wurtzite III-nitride semiconductor materials have many technically important applications in optical and electronic devices. As GaN-based visible light-emitting diodes (LEDs) and lasers starts to mature, interest in developing UV devices starts to rise. The search for materials with larger bandgaps and high refractive index contrast in the UV range has inspired multiple studies of BN-based materials and their alloys with traditional III-nitrides. Additionally, alloying III-nitrides with boron can reduce their lattice parameters giving a new...

Development of Reusable heterogeneous Catalysts for Sustainable formic acid production and methanol utilization

Ding-Jier Yuan
The green production of formic acid and utilization of methanol over heterogeneous catalysis system were investigated in this study. The heterogeneous catalysts are widely used in the chemical industry. They offer high stability and reusability which can enhance the production ability and lower the production cost, it can be considered as the sustainable energy solution for the future. In this work, we demonstrated several different heterogeneous catalysts for sustainable formic acid production and methanol utilization,...

The role of L-lactate in NMDAR-CaMKIIα Interaction

Rayyan T. Alamoudi
NMDA receptors are the most studied receptors in the field of neuroscience and are known to play an important role in development and plasticity. These receptors exhibit different kinetics depending on their subunit composition. NR2A and NR2B are the predominating NMDAR subunits in the brain. These receptors localize to synapses where they interact with other proteins including CaMKIIα, an abundant kinase which plays an important role in synaptic plasticity. Although CaMKIIα is known to bind...

Coral Bleaching – Breakdown of a Nutrient Exchange Symbiosis

Nils Rädecker
For millions of years, the nutrient exchange symbiosis between corals and their endosymbiotic algae has formed the foundation of the ecological success of coral reefs. Yet, in recent decades anthropogenic climate change is increasingly destabilizing this symbiosis, and thus the reefs that rely on it. High-temperature anomalies have caused mass mortality of corals due to repeated coral bleaching, the expulsion or digestion of symbionts by the host during stress. Hence, in-depth knowledge of the cellular...

Efficient Localization of Human Actions and Moments in Videos

Victor Escorcia
We are stumbling across a video tsunami flooding our communication channels. The ubiquity of digital cameras and social networks has increased the amount of visual media content generated and shared by people, in particular videos. Cisco reports that 82% of the internet traffic would be in the form of videos by 2022. The computer vision community has embraced this challenge by offering the first building blocks to translate the visual data in segmented video clips...

Automatic Protein Function Annotation Through Text Mining

Sumyyah Toonsi
The knowledge of a protein’s function is essential to many studies in molecular biology, genetic experiments and protein-protein interactions. The Gene Ontology (GO) captures gene products' functions in classes and establishes relationship between them. Manually annotating proteins with GO functions from the bio-medical litera- ture is a tedious process which calls for automation. We develop a novel, dictionary- based method to annotate proteins with functions from text. We extract text-based features from words matched against...

Understanding the Molecular Basis of Thermopriming in Plants

Natalia Lorena Gorron Serano
Plants acclimate to the changing environmental conditions by adjusting their molecular responses at different molecular levels including genome, epigenome, transcriptome, metabolome, and proteome levels to ensure survival. Plants adapt to abiotic stresses by establishing a ‘stress memory’ of previous exposures to mild stresses. Stress memory helps plants to develop tolerance and survive recurring exposures to the stress conditions. This memory establishes a new cellular state that differs from the state of unexposed naïve plants. This...

Compliant Electronics for Unusual Environments

Amani Saleh Saad Almislem
Compliant electronics are an emerging class of electronics which offer physical flexibility in their structure. Such mechanical flexibility opens up opportunities for wide ranging applications. Nonetheless, compliant electronics which can be functional in unusual environments are yet to be explored. Unusual environment can constitute a harsh environment where temperature and/or pressure is much higher or lower than the usual room temperature and/or pressure. Unusual environment can be an aquatic environment, such as ocean/sea/river/pond, industrial processing...

Registration Year

  • 2019

Resource Types

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  • King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia