Storage Coalescing

Typically, when a program executes, it creates objects dynamically and requests storage for its objects from the underlying storage allocator. The patterns of such requests can potentially lead to internal fragmentation as well as external fragmentation. Internal fragmentation occurs when the storage allocator allocates a contiguous block of storage to a program, but the program uses only a fraction of that block to satisfy a request. The unused portion of that block is wasted since the allocator cannot use it to satisfy a subsequent allocation request. External fragmentation, on the other hand, concerns chunks of memory that reside between allocated blocks. External fragmentation becomes problematic when these chunks are not large enough to satisfy an allocation request individually. Consequently, these chunks exist as useless holes in the memory system. In this thesis, we present necessary and sufficient storage conditions for satisfying allocation and deallocation sequences for programs that run on systems that use a binary-buddy allocator. We show that these sequences can be serviced without the need for defragmentation. We also explore the effects of buddy-coalescing on defragmentation and on overall program performance when using a defragmentation algorithm that implements buddy system policies. Our approach involves experimenting with Sun’s Java Virtual Machine and a buddy system simulator that embodies our defragmentation algorithm. We examine our algorithm in the presence of two approximate collection strategies, namely Reference Counting and Contaminated Garbage Collection, and one complete collection strategy - Mark and Sweep Garbage Collection. We analyze the effectiveness of these approaches with regards to how well they manage storage when we alter the coalescing strategy of our simulator. Our analysis indicates that prompt coalescing minimizes defragmentation and delayed coalescing minimizes number of coalescing in the three collection approaches

Garbage collection in distributed systems

PhD ThesisThe provision of system-wide heap storage has a number of advantages. However, when the technique is applied to distributed systems automatically recovering inaccessible variables becomes a serious problem. This thesis presents a survey of such garbage collection techniques but finds that no existing algorithm is entirely suitable. A new, general purpose algorithm is developed and presented which allows individual systems to garbage collect largely independently. The effects of these garbage collections are combined, using recursively structured control mechanisms, to achieve garbage collection of the entire heap with the minimum of overheads. Experimental results show that new algorithm recovers most inaccessible variables more quickly than a straightforward garbage collection, giving an improved memory utilisation

Cloning, Fed-Batch Expression And Purification Of A Novel Anti-Candida Peptide And Development Of A Cleavage Resistant Variant Of Green Fluorescence Protein

This work illustrates that the intelligent design of a bioprocess for the production of peptides of various length is possible by having a prior knowledge of desired product, cell line, fermentation conditions, and choices for downstream recovery. Cloning, expression, and recovery of a novel 12-mer anti-Candida peptide served as an illustrative case for a proposed Escherichia coli platform. The antifungal peptide, expressed as a fusion to GFPUV during high call density fed-batch, was recovered from cell lysate, concentrated using ion exchange chromatography, and finally cleaved with cyanogen bromide. The platform was capable of producing active peptide capable of arresting the growth of yeast, used as an indicator strain. During processing, a new E. coli cell line (Lotus®) was used for expression to investigate the effect of certain mutations that reduced the downstream burden of host cell proteins (HCPs). A 37% improvement in initial capture efficiency of diethylaminoethyl (DEAE) resin was observed and attributed to less HCPs. To further streamline downstream purification, a mutant of GFPUV was designed that was resistant to cleavage using cyanogen bromide. Finally, an economic analysis demonstrated the positive economic implications of the suggested improvements

Strategies for New Product Development in an Emerging Market

Some organizational leaders in emerging markets lack strategies for successful development of new products. By 2025, emerging markets will account for 50% of global consumption and represent significant opportunities for organizational leaders to steer their organizations toward market dominance. The purpose of this multiple case study was to explore the strategies that organizational leaders used to successfully develop new products. The target population comprised leaders of 3 organizations in Nigeria who have successfully developed new products. The conceptual framework for this study was the disruptive innovation theory. Data were gathered from semistructured interviews with the organizational leaders and review of company documents. Data analysis involved the compilation of data, coding to organize the data, identification of themes that emerged, and linking those themes with the research. Triangulation and member checking were used to help ensure the trustworthiness of interpretations. Four themes emerged from data analyses relating to strategies used by organizational leaders to successfuly develop new products: leadership and business models, organizational structure and culture, target population and market needs, and affordability. The implications of this study for positive social change include the potential to improve the standard of living in Nigerian communities, which might enhance the participation of the rural people and local businesses in the global economy. Furthermore, the findings of the study may provide knowledge for organizations to become more profitable in emerging markets

Application of advanced on-board processing concepts to future satellite communications systems

An initial definition of on-board processing requirements for an advanced satellite communications system to service domestic markets in the 1990's is presented. An exemplar system architecture with both RF on-board switching and demodulation/remodulation baseband processing was used to identify important issues related to system implementation, cost, and technology development

Studying Large Multi-Protein Complexes Using Single Molecule Localization Microscopy

Biology would not be where it is today without fluorescence microscopy. It is arguably one of the most commonly used tools in the biologists toolbox and it has helped scientists study the localization of cellular proteins and other small things for decades, but it is not without its limitations. Due to the diffraction limit, conventional fluorescence microscopy is limited to micrometer-range structures. Science has long relied upon electron microscopy and X-ray crystallography to study phenomena that occur below this limit. However, many of lifes processes occur between these two spatial domains. Super-resolution microscopy, the next stage of evolution of fluorescence microscopy, has the potential to bridge this gap between micro and nano. It combines superior resolutions of down to a few nanometers with the ability to view objects in their natural environments. It is the ideal tool for studying the large, multi-protein complexes that carry out most of lifes functions, but are too complex and fragile to put on an electron microscope or into a synchrotron. A form of super-resolution microscopy called SMLM Microscopy shows especially high promise in this regard. With its ability to detect individual molecules, it combines the high resolution needed for structural studies with the quantitative readout required for obtaining data on the stoichiometry of multi-protein complexes. This thesis describes new tools which expand the toolbox of SMLM with the specific aim of studying multi-protein complexes. First, the development of a novel fluorescent tagging system that is a mix of genetic tagging and immuno-staining. The system, termed BC2, consists of a short, genetically encodable peptide that is targeted by a nanobody (BC2 nanobody). The system brings several advantages. The small tag is not disruptive to the protein it is attached to and the small nanobody can get into tight spaces, making it an excellent tag for dense multi-protein structures. Next, several new variants of some commonly used green-to-red fluorescent proteins. The novel variants, which can be converted with a combination of blue and infrared light are especially useful for live-cell imaging. The developed fluorescent proteins can also be combined with photo-activatable fluorescent proteins to enable imaging of several targets with the same color protein. Finally, an application of the latter technique to study the multi-protein kinetochore complex and gain first glimpses into its spatial organization and the stoichiometry of its subunits

Single Walled Carbon Nanotubes Assembly: Nanohybrids toward Photodetection and Junction Engineering.

PhD ThesesBy synergistically combining the individual properties of more than one nanoscale component, novel features of hybrid structure assemblies represent a key motivation for making future functional nanomaterials. In this thesis, the successful construction of a multiplexed photo-responsive chip from DNA-wrapped single walled carbon nanotubes (DNA-CNTs) and DNA-CNT templated inorganic-organic hybrid structures is first demonstrated. The effective assembly of the hybrids was characterized by atomic force microscopy (AFM) and the corresponding device performance as well as the key mechanisms behind were investigated. Then a facile approach for the fabrication of end-to-end SWCNT junctions exploiting oligonucleotides as molecular linkers is presented. The assembled junctions show clear stimuli-responsive features stemming from the designed sequences of oligonucleotides; this grants the SWCNTs the ability to self-assemble and disassemble under specific conditions in aqueous solutions. The junction formation was confirmed by Atomic Force Microscopy (AFM) and time-dependent fluorescence analysis. Moreover, an efficient strategy to sort DNA-wrapped SWCNTs (DNA-CNTs) by length via a gel electrophoresis technique was developed (confirmed by AFM). In addition to the application of oligonucleotides, the use of diazonium salts not only as a molecular linker but also the major reactive agent for CNT junction formation was also explored. In conclusion, by integrating DNA-CNTs with other active components, we have achieved the assembly for organic-inorganic nanohybrids of multiplexed photo-sensing capabilities and the assembly of reconfigurable SWCNT junctions with stimuli-responsive features. Moreover, the facile and efficient strategies developed in our work can contribute to the controlled assembly of CNT based functional nanohybrids

Head and Neck Cancer Invasion: Contributions of Actin Regulatory Proteins and the Microenvironment

Metastasis of primary tumor lesions is the leading cause of cancer-related death. In head and neck cancer, a local-regional disease, metastasis is achieved mainly through invasion into surrounding tissue and spreads to cervical lymph nodes. Movement from the initial tumor site requires dynamic reorganization of the actin cytoskeleton, which utilizes the coordinated action of many actin regulatory proteins. However, there is increasing evidence that the tumor microenvironment is also a driver of invasion. This work aims to determine the contributions of proteins which regulate the actin cytoskeleton during head and neck cancer invasion both in vitro and in vivo, and provide details on how the HNSCC tumor microenvironment influences progression. This was accomplished, by the following Studies. In Study one, the actin binding protein coronin 1B is found to be amplified and overexpressed in invasive HNSCC patient samples, and a novel function in the regulation of protrusive membrane structures called invadopodia is described. Study two defines an in vivo role for the actin regulatory protein cortactin, which has been previously associated with more aggressive cancers in vitro and in patients. This work finds that cortactin expression is dispensable for tongue tumor invasion in a transgenic model of oral cancer, implicating the tumor microenvironment as being the major contributor to driving oral cancer invasion. Study three describes a technique for monitoring and biopsying cervical lymph nodes of mice using high frequency ultrasound. By using this technique, alterations in cervical lymph node size and blood flow were discovered in mice given the carcinogen 4-NQO to induce oral carcinogenesis. Collectively, these studies shed light on the importance of choosing comprehensive model systems for studying roles of actin binding proteins in cancer invasion