title: A Predictive Model for the Parallel Processing of Digital Libraries

authors: Thompson, John Matthew

subjects: Digital Library

abstract: The computing world is facing the problem of a seemingly exponential increase in the amount of raw digital data, and the speed at which it is being collected, is eclipsing our ability to manage it manually. Combine this with the increasing expectations of a growing number of experienced computer users—including real-time access and a demand for expensive-to-process file types such as multimedia—and it is not hard to understand why managing data of this scale and providing timely access to useful information requires specialized algorithms, techniques, and software.

Digital libraries are being used to help address these challenges. Drawing upon knowledge learned through traditional library science, digital libraries excel in providing structured user access to a wide variety of documents. They increasingly include tools for managing, moderating, and marking up these documents. Furthermore, they often feature phases where documents are independently processed and so can benefit from the application of parallel processing techniques—the focus of this thesis. Whether a digital library collection can benefit from parallel processing depends on considerations such as document type, processing cost per document, number of documents, and file-system input/output.

To aid in deciding when to apply parallel processing techniques to digital libraries, this thesis explores the creation a model for predicting key outcomes of leveraging such techniques. It does so by implementing parallel processing in three distinct open-source digital library tools, undertaking experiments designed to measure key processing features (such as processing time versus number of compute nodes), and applying machine learning techniques to these features in order to derive a predictive model.

The model created predicts parallel processing performance at 96% accuracy (adjusted r-squared) for a number of exemplar collection types. The result is a generally applicable tool for estimating the benefits of applying parallel processing to a wide range of digital collections.

text: A Predictive Model for the Parallel Processing of Digital Libraries The computing world is facing the problem of a seemingly exponential increase in the amount of raw digital data, and the speed at which it is being collected, is eclipsing our ability to manage it manually. Combine this with the increasing expectations of a growing number of experienced computer users—including real-time access and a demand for expensive-to-process file types such as multimedia—and it is not hard to understand why managing data of this scale and providing timely access to useful information requires specialized algorithms, techniques, and software.

Digital libraries are being used to help address these challenges. Drawing upon knowledge learned through traditional library science, digital libraries excel in providing structured user access to a wide variety of documents. They increasingly include tools for managing, moderating, and marking up these documents. Furthermore, they often feature phases where documents are independently processed and so can benefit from the application of parallel processing techniques—the focus of this thesis. Whether a digital library collection can benefit from parallel processing depends on considerations such as document type, processing cost per document, number of documents, and file-system input/output.

To aid in deciding when to apply parallel processing techniques to digital libraries, this thesis explores the creation a model for predicting key outcomes of leveraging such techniques. It does so by implementing parallel processing in three distinct open-source digital library tools, undertaking experiments designed to measure key processing features (such as processing time versus number of compute nodes), and applying machine learning techniques to these features in order to derive a predictive model.

The model created predicts parallel processing performance at 96% accuracy (adjusted r-squared) for a number of exemplar collection types. The result is a generally applicable tool for estimating the benefits of applying parallel processing to a wide range of digital collections.

year: 2015

title: Review: The denaturation and degradation of stable enzymes at high temperatures

authors: Daniel, Roy M.

subjects: enzyme

abstract: Now that enzymes are available that are stable above 100 °C it is possible to investigate conformational stability at this temperature, and also the effect of high-temperature degradative reactions in functioning enzymes and the inter-relationship between degradation and denaturation. The conformational stability of proteins depends upon stabilizing forces arising from a large number of weak interactions, which are opposed by an almost equally large destabilizing force due mostly to conformational entropy. The difference between these, the net free energy of stabilization, is relatively small, equivalent to a few interactions. The enhanced stability of very stable proteins can be achieved by an additional stabilizing force which is again equivalent to only a few stabilizing interactions. There is currently no strong evidence that any particular interaction (e.g. hydrogen bonds, hydrophobic interactions) plays a more important role in proteins that are stable at 100 °C than in those stable at 50 °C, or that the structures of very stable proteins are systematically different from those of less stable proteins. The major degradative mechanisms are deamidation of asparagine and glutamine, and succinamide formation at aspartate and glutamate leading to peptide bond hydrolysis. In addition to being temperature-dependent, these reactions are strongly dependent upon the conformational freedom of the susceptible amino acid residues. Evidence is accumulating which suggests that even at 100 °C deamidation and succinamide formation proceed slowly or not at all in conformationally intact (native) enzymes. Whether this is the case at higher temperatures is not yet clear, so it is not known whether denaturation or degradation will set the upper limit of stability for enzymes.

text: Review: The denaturation and degradation of stable enzymes at high temperatures Now that enzymes are available that are stable above 100 °C it is possible to investigate conformational stability at this temperature, and also the effect of high-temperature degradative reactions in functioning enzymes and the inter-relationship between degradation and denaturation. The conformational stability of proteins depends upon stabilizing forces arising from a large number of weak interactions, which are opposed by an almost equally large destabilizing force due mostly to conformational entropy. The difference between these, the net free energy of stabilization, is relatively small, equivalent to a few interactions. The enhanced stability of very stable proteins can be achieved by an additional stabilizing force which is again equivalent to only a few stabilizing interactions. There is currently no strong evidence that any particular interaction (e.g. hydrogen bonds, hydrophobic interactions) plays a more important role in proteins that are stable at 100 °C than in those stable at 50 °C, or that the structures of very stable proteins are systematically different from those of less stable proteins. The major degradative mechanisms are deamidation of asparagine and glutamine, and succinamide formation at aspartate and glutamate leading to peptide bond hydrolysis. In addition to being temperature-dependent, these reactions are strongly dependent upon the conformational freedom of the susceptible amino acid residues. Evidence is accumulating which suggests that even at 100 °C deamidation and succinamide formation proceed slowly or not at all in conformationally intact (native) enzymes. Whether this is the case at higher temperatures is not yet clear, so it is not known whether denaturation or degradation will set the upper limit of stability for enzymes.

year: 1996

title: Te Arawa– Kaitaki of Te Arawa Lakes

authors: Curtis, Sir Toby

abstract: The Te Arawa Lakes Trust has embarked on a project to develop a Te Arawa Cultural Values Framework, in regard to the 14 lakes located in our tribal region. There are a host of positives that we believe can accrue as an outcome of this exercise. Already the calibre of people acknowledged for their cultural expertise have added a lot by their attendance. Their presence and contribution injected a level of enthusiasm and confidence in the compilation of the final draft. It is hoped that distribution among the wider community will elicit constructive feedback.

text: Te Arawa– Kaitaki of Te Arawa Lakes The Te Arawa Lakes Trust has embarked on a project to develop a Te Arawa Cultural Values Framework, in regard to the 14 lakes located in our tribal region. There are a host of positives that we believe can accrue as an outcome of this exercise. Already the calibre of people acknowledged for their cultural expertise have added a lot by their attendance. Their presence and contribution injected a level of enthusiasm and confidence in the compilation of the final draft. It is hoped that distribution among the wider community will elicit constructive feedback.

year: 2015