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2011

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Articles 151 - 180 of 10326

Full-Text Articles in Physical Sciences and Mathematics

The Effect Of Small Molecules In Modulating The Chaperone Activity Of Alpha B-Crystallin Against Ordered And Disordered Protein Aggregation, Heath Ecroyd, John Carver Dec 2011

The Effect Of Small Molecules In Modulating The Chaperone Activity Of Alpha B-Crystallin Against Ordered And Disordered Protein Aggregation, Heath Ecroyd, John Carver

Heath Ecroyd

Protein aggregation can proceed via disordered or ordered mechanisms, with the latter being associated with amyloid fibril formation, which has been linked to a number of debilitating conditions including Alzheimer's, Parkinson's and Creutzfeldt-Jakob diseases. Small heat-shock proteins (sHsps), such as alpha B-crystallin, act as chaperones to prevent protein aggregation and are thought to play a key role in the prevention of protein-misfolding diseases. In this study, we have explored the potential for small molecules such as arginine and guanidine to affect the chaperone activity of alpha B-crystallin against disordered (amorphous) and ordered (amyloid fibril) forms of protein aggregation. The effect …

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The Interaction Of Unfolding Α-Lactalbumin And Malate Dehydrogenase With The Molecular Chaperone Αb-Crystallin: A Light And X-Ray Scattering Investigation, J W. Regini, Heath Ecroyd, Sarah Meehan, Kristen Bremmell, Matthew J. Clarke, Donna Lammie, Tim Wess, John A. Carver Dec 2011

The Interaction Of Unfolding Α-Lactalbumin And Malate Dehydrogenase With The Molecular Chaperone Αb-Crystallin: A Light And X-Ray Scattering Investigation, J W. Regini, Heath Ecroyd, Sarah Meehan, Kristen Bremmell, Matthew J. Clarke, Donna Lammie, Tim Wess, John A. Carver

Heath Ecroyd

Purpose: The molecular chaperone αB-crystallin is found in high concentrations in the lens and is present in all major body tissues. Its structure and the mechanism by which it protects its target protein from aggregating and precipitating are not known. Methods: Dynamic light scattering and X-ray solution scattering techniques were used to investigate structural features of the αB-crystallin oligomer when complexed with target proteins under mild stress conditions, i.e., reduction of α- lactalbumin at 37 °C and malate dehydrogenase when heated at 42 °C. In this investigation, the size, shape and particle distribution of the complexes were determined in real-time …

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Analysis Of The Mechanism By Which Calcium Negatively Regulates The Tyrosine Phosphorylation Cascade Associated With Sperm Capacitation, Mark Baker, Louise Hethrington, Heath Ecroyd, Shaun Roman, Robert Aitken Dec 2011

Analysis Of The Mechanism By Which Calcium Negatively Regulates The Tyrosine Phosphorylation Cascade Associated With Sperm Capacitation, Mark Baker, Louise Hethrington, Heath Ecroyd, Shaun Roman, Robert Aitken

Heath Ecroyd

The capacitation of mammalian spermatozoa involves the activation of a cAMP-mediated signal transduction pathway that drives tyrosine phosphorylation via mechanisms that are unique to this cell type. Controversy surrounds the impact of extracellular calcium on this process, with positive and negative effects being recorded in independent publications. We clearly demonstrate that the presence of calcium in the external medium decreases tyrosine phosphorylation in both human and mouse spermatozoa. Under these conditions, a rise in intracellular pH was recorded, however, this event was not responsible for the observed changes in phosphotyrosine expression. Rather, the impact of calcium on tyrosine phosphorylation in …

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(-)-Epigallocatechin-3-Gallate (Egcg) Maintains K-Casein In Its Pre-Fibrillar State Without Redirecting Its Aggregation Pathway, Sean A. Hudson, Heath Ecroyd, Francis C. Dehle, Ian F. Musgrave, John Carver Dec 2011

(-)-Epigallocatechin-3-Gallate (Egcg) Maintains K-Casein In Its Pre-Fibrillar State Without Redirecting Its Aggregation Pathway, Sean A. Hudson, Heath Ecroyd, Francis C. Dehle, Ian F. Musgrave, John Carver

Heath Ecroyd

The polyphenol (-)-epigallocatechin-3-gallate (EGCG) has recently attracted much research interest in the field of protein-misfolding diseases because of its potent anti-amyloid activity against amyloid-beta, alpha-synuclein and huntingtin, the amyloid-fibril-forming proteins involved in Alzheimer's, Parkinson's and Huntington's diseases, respectively. EGCG redirects the aggregation of these polypeptides to a disordered off-folding pathway that results in the formation of non-toxic amorphous aggregates. whether this anti-fibril activity is specific to these disease-related target proteins or ismore generic remains to be established. In addition, the mechanism by which EGCG exerts its effects, as with all anti-amyloidogenic polyphenols, remains unclear. To address these aspects, we have …

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The Two Faced Nature Of Milk Casein Proteins: Amyloid Fibril Formation And Chaperone-Like Activity, David Thorn, Heath Ecroyd, John Carver Dec 2011

The Two Faced Nature Of Milk Casein Proteins: Amyloid Fibril Formation And Chaperone-Like Activity, David Thorn, Heath Ecroyd, John Carver

Heath Ecroyd

Molecular chaperones are a diverse group of proteins that stabilise partially folded target proteins to prevent their misfolding, aggregation and potential precipitation under conditions of cellular stress, e.g. elevated temperature. Protein aggregation, particularly the formation of highly ordered protein aggregates termed amyloid fibrils, is of considerable research interest because of its intimate association with a wide range of debilitating diseases, including Alzheimer's, Parkinson's and Huntington's diseases and type II diabetes. In this review, we discuss the ability of the milk casein proteins to act in a chaperone-like manner. This property is of biological importance since at least two of the …

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New Proteins Identified In Epididymal Fluid From The Platypus (Ornithorhynchus Anatinus), Jean-Louis Dacheux, Francoise Dacheux, Valerie Labas, Heath Ecroyd, Brett Nixon, Russell C. Jones Dec 2011

New Proteins Identified In Epididymal Fluid From The Platypus (Ornithorhynchus Anatinus), Jean-Louis Dacheux, Francoise Dacheux, Valerie Labas, Heath Ecroyd, Brett Nixon, Russell C. Jones

Heath Ecroyd

The platypus epididymal proteome is being studied because epididymal proteins are essential for male fertility in mammals and it is considered that knowledge of the epididymal proteome in an early mammal would be informative in assessing the convergence and divergence of proteins that are important in the function of the mammalian epididymis. Few of the epididymal proteins that have been identified in eutherian mammals were found in platypus caudal epididymal fluid, and the major epididymal proteins in the platypus (PXN-FBPL, SPARC and E-OR20) have never been identified in the epididymis of any other mammal.

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Mimicking Phosphorylation Of Alphab-Crystallin Affects Its Chaperone Activity, Heath W. Ecroyd, Sarah Meehan, J Horwitz, Andrew Aquilina, J L Benesch, C V Robinson, Cait Macphee, John Carver Dec 2011

Mimicking Phosphorylation Of Alphab-Crystallin Affects Its Chaperone Activity, Heath W. Ecroyd, Sarah Meehan, J Horwitz, Andrew Aquilina, J L Benesch, C V Robinson, Cait Macphee, John Carver

Heath Ecroyd

No abstract provided.

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The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver Dec 2011

The Thioflavin T Fluorescence Assay For Amyloid Fibril Detection Can Be Biased By The Presence Of Exogenous Compounds, Sean A. Hudson, Heath Ecroyd, Tak W. Kee, John A. Carver

Heath Ecroyd

Thioflavin T (ThT) dye fluorescence is used regularly to quantify the formation and inhibition of amyloid fibrils in the presence of anti-amyloidogenic compounds such as polyphenols. However, in this study, it was shown, using three polyphenolics (curcumin, quercetin and resveratrol), that ThT fluorescence should be used with caution in the presence of such exogenous compounds. The strong absorptive and fluorescent properties of quercetin and curcumin were found to significantly bias the ThT fluorescence readings in both in situ real-time ThT assays and single time-point dilution ThT-type assays. The presence of curcumin at concentrations as low as 0.01 and 1 uM …

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Unraveling The Mysteries Of Protein Folding And Misfolding, Heath Ecroyd, John A. Carver Dec 2011

Unraveling The Mysteries Of Protein Folding And Misfolding, Heath Ecroyd, John A. Carver

Heath Ecroyd

This mini-review focuses on the processes and consequences of protein folding and misfolding. The latter process often leads to protein aggregation and precipitation with the aggregates adopting either highly ordered (amyloid fibril) or disordered (amorphous) forms. In particular, the amyloid fibril is discussed because this form has gained considerable notoriety due to its close links to a variety of debilitating diseases including Alzheimer's, Parkinson's, Huntington's, and Creutzfeldt-Jakob diseases, and type-II diabetes. In each of these diseases a different protein forms fibrils, yet the fibrils formed have a very similar structure. The mechanism by which fibrils form, fibril structure, and the …

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Crystallin Proteins And Amyloid Fibrils, Heath Ecroyd, John A. Carver Dec 2011

Crystallin Proteins And Amyloid Fibrils, Heath Ecroyd, John A. Carver

Heath Ecroyd

Improper protein folding (misfolding) can lead to the formation of disordered (amorphous) or ordered (amyloid fibril) aggregates. The major lens protein, alpha-crystallin, is a member of the small heat-shock protein (sHsp) family of intracellular molecular chaperone proteins that prevent protein aggregation. Whilst the chaperone activity of sHsps against amorphously aggregating proteins has been well studied, its action against fibril-forming proteins has received less attention despite the presence of sHsps in deposits found in fibril-associated diseases (e.g. Alzheimer's and Parkinson's). In this review, the literature on the interaction of alpha B-crystallin and other sHsps with fibril-forming proteins is summarized. In particular, …

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Amyloid Fibril Formation By Bovine Milk Alpha(S2)-Casein Occurs Under Physiological Conditions Yet Is Prevented By Its Natural Counterpart, Alpha(S1)-Casein, David Thorn, Heath Ecroyd, M Sunde, Stephen Poon, John Carver Dec 2011

Amyloid Fibril Formation By Bovine Milk Alpha(S2)-Casein Occurs Under Physiological Conditions Yet Is Prevented By Its Natural Counterpart, Alpha(S1)-Casein, David Thorn, Heath Ecroyd, M Sunde, Stephen Poon, John Carver

Heath Ecroyd

The calcified proteinaceous deposits, or corpora amylacea, of bovine mammary tissue often comprise a network of amyloid fibrils, the origins of which have not been fully elucidated. Here, we demonstrate by transmission electron microscopy, dye binding assays, and X-ray fiber diffraction that bovine milk alpha(s2)-casein, a protein synthesized and secreted by mammary epithelial cells, readily forms fibrils in vitro. As a component of whole alpha(s)-casein, alpha(s2)-casein was separated from alpha(s1)-casein under nonreducing conditions via cation-exchange chromatography. Upon incubation at neutral pH and 37 degrees C, the spherical particles typical of alpha(s2)-casein rapidly converted to twisted, ribbon-like fibrils similar to 12 …

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Alphab-Crystallin Inhibits The Cell Toxicity Associated With Amyloid Fibril Formation By Kappa-Casein And The Amyloid-Beta Peptide, Francis C. Dehle, Heath Ecroyd, Ian F. Musgrave, John A. Carver Dec 2011

Alphab-Crystallin Inhibits The Cell Toxicity Associated With Amyloid Fibril Formation By Kappa-Casein And The Amyloid-Beta Peptide, Francis C. Dehle, Heath Ecroyd, Ian F. Musgrave, John A. Carver

Heath Ecroyd

Amyloid fibril formation is associated with diseases such as Alzheimer’s, Parkinson’s, and prion diseases. Inhibition of amyloid fibril formation by molecular chaperone proteins, such as the small heat-shock protein αB-crystallin, may play a protective role in preventing the toxicity associated with this form of protein misfolding. Reduced and carboxymethylated κ-casein (RCMκ-CN), a protein derived from milk, readily and reproducibly forms fibrils at physiological temperature and pH. We investigated the toxicity of fibril formation by RCMκ-CN using neuronal model PC12 cells and determined whether the inhibition of fibril formation altered its cell toxicity. To resolve ambiguities in the literature, we also …

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The Epididymal Soluble Prion Protein Forms A High-Molecular-Mass Complex In Association With Hydrophobic Proteins, Heath W. Ecroyd, Maya Belghazi, Jean-Louis Dacheux, Jean-Luc Gatti Dec 2011

The Epididymal Soluble Prion Protein Forms A High-Molecular-Mass Complex In Association With Hydrophobic Proteins, Heath W. Ecroyd, Maya Belghazi, Jean-Louis Dacheux, Jean-Luc Gatti

Heath Ecroyd

We have shown previously that a 'soluble' form of PrP (prion protein), not associated with membranous vesicles, exists in the male reproductive fluid [Ecroyd, Sarradin, Dacheux and Gatti (2004) Biol. Reprod. 71, 993-1001]. Attempts to purify this 'soluble' PrP indicated that it behaves like a high-molecular-mass complex of more than 350 kDa and always co-purified with the same set of proteins. The main associated proteins were sequenced by MS and were found to match to clusterin (apolipoprotein J), BPI (bacterial permeability-increasing protein), carboxylesterase-like urinary excreted protein (cauxin), beta-mannosidase and beta-galactosidase. Immunoblotting and enzymatic assay confirmed the presence of clusterin and …

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Compartmentalization Of Prion Isoforms Within The Reproductive Tract Of The Ram, Heath W. Ecroyd, Pierre Sarradin, Jean-Louis Dacheux, Jean-Luc Gatti Dec 2011

Compartmentalization Of Prion Isoforms Within The Reproductive Tract Of The Ram, Heath W. Ecroyd, Pierre Sarradin, Jean-Louis Dacheux, Jean-Luc Gatti

Heath Ecroyd

Cellular prion protein (Prp(C)) is a glycoprotein usually associated with membranes via its glycosylphosphatidylinositol (GPI) anchor. The trans-conformational form of this protein (Prp(SC)) is the suggested agent responsible for transmissible neurodegenerative spongiform encephalopathies. This protein has been shown on sperm and in the reproductive fluids of males. Antibodies directed against the C-terminal sequence near the GPI-anchor site, an N-terminal sequence, and against the whole protein showed that the Prp isoforms were compartmentalized within the reproductive tract of the ram. Immunoblotting with the three antibodies showed that the complete protein and both N- and C-terminally truncated and glycosylated isoforms are present …

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Post-Testicular Sperm Environment And Fertility, Jean-Luc Gatti, Sandrine Castella, Francoise Dacheux, Heath Ecroyd, S Metayer, Veronique Thimon, Jean-Louis Dacheux Dec 2011

Post-Testicular Sperm Environment And Fertility, Jean-Luc Gatti, Sandrine Castella, Francoise Dacheux, Heath Ecroyd, S Metayer, Veronique Thimon, Jean-Louis Dacheux

Heath Ecroyd

When mammalian spermatozoa exit the testis, they show a highly specialized morphology; however, they are not yet able to carry out their task: to fertilize an oocyte. This property, that includes the acquisition of motility and the ability to recognize and to fuse with the oocyte investments, is gained only after a transit through the epididymis during which the spermatozoa from the testis travel to the vas deferens. The exact molecular mechanisms that turn these cells into fertile gametes still remain mysterious, but surface-modifying events occurring in response to the external media are key steps in this process. Our laboratory …

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Protective Interactions Of Dairy Peptides With Fibril Structures And Relevance To Alzheimer's Disease, Louise Bennett, Williams Roderick, Heath Ecroyd, Yanqin Liu, Sunanda Sudharmarajan, John Carver Dec 2011

Protective Interactions Of Dairy Peptides With Fibril Structures And Relevance To Alzheimer's Disease, Louise Bennett, Williams Roderick, Heath Ecroyd, Yanqin Liu, Sunanda Sudharmarajan, John Carver

Heath Ecroyd

Selected dairy caseins have been shown to have capacity for chaperone-like regulation of folding pathways of other caseins, specifically in preventing development of fibrillar aggregates of beta sheet structure. An assay based on fibril formation by reduced and carboxymethylated-kappa casein (RCM-kCn) was thus used to screen for anti-fibril activity among a selection of dairy protein hydrolysates, in order to discover peptides with possible anti-fibril, chaperone activity. From the selection of eight dairy hydrolysates based on different dairy protein fractions, two of the hydrolysates of whey protein exhibited superior anti-fibril bioactivity against RCM-kCn and amyloid beta (Aβ), the peptide associated with …

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Small Heat-Shock Proteins Interact With A Flanking Domain To Suppress Polyglutamine Aggregation, Amy L. Roberston, Stephen J. Headey, Helen M. Saunders, Heath Ecroyd, Martin J. Scanlon, John A. Carver, Stephen P. Bottomley Dec 2011

Small Heat-Shock Proteins Interact With A Flanking Domain To Suppress Polyglutamine Aggregation, Amy L. Roberston, Stephen J. Headey, Helen M. Saunders, Heath Ecroyd, Martin J. Scanlon, John A. Carver, Stephen P. Bottomley

Heath Ecroyd

Small heat-shock proteins (sHsps) are molecular chaperones that play an important protective role against cellular protein misfolding by interacting with partially unfolded proteins on their off-folding pathway, preventing their aggregation. Polyglutamine (polyQ) repeat expansion leads to the formation of fibrillar protein aggregates and neuronal cell death in nine diseases, including Huntington disease and the spinocerebellar ataxias (SCAs). There is evidence that sHsps have a role in suppression of polyQ-induced neurodegeneration; for example, the sHsp alphaB-crystallin (αB-c) has been identified as a suppressor of SCA3 toxicity in a Drosophila model. However, the molecular mechanism for this suppression is unknown. In this …

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Testicular Descent, Sperm Maturation And Capacitation. Lessons From Our Most Distant Relatives, The Monotremes, Russell Jones, Heath Ecroyd, Jean-Louis Dacheux, Brett Nixon Dec 2011

Testicular Descent, Sperm Maturation And Capacitation. Lessons From Our Most Distant Relatives, The Monotremes, Russell Jones, Heath Ecroyd, Jean-Louis Dacheux, Brett Nixon

Heath Ecroyd

The present review examines whether monotremes may help to resolve three questions relating to sperm production in mammals: why the testes descend into a scrotum in most mammals, why spermatozoa are infertile when they leave the testes and require a period of maturation in the specific milieu provided by the epididymides, and why ejaculated spermatozoa cannot immediately fertilise an ovum until they undergo capacitation within the female reproductive tract. Comparisons of monotremes with other mammals indicate that there is a need for considerable work on monotremes. It is hypothesised that testicular descent should be related to epididymal differentiation. Spermatozoa and …

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The Development Of Signal Transduction Pathways During Epididymal Maturation Is Calcium Dependent, Heath W. Ecroyd, Kelly Asquith, Russell C. Jones, Robert J. Aitken Dec 2011

The Development Of Signal Transduction Pathways During Epididymal Maturation Is Calcium Dependent, Heath W. Ecroyd, Kelly Asquith, Russell C. Jones, Robert J. Aitken

Heath Ecroyd

Capacitation has been correlated with the activation of a cAMP-PKA-dependent signaling pathway leading to protein tyrosine phosphorylation. The ability to exhibit this response to cAMP matures during epididymal maturation in concert with the ability of the sperrnatozoa to capacitate. In this study, we have addressed the mechanisms by which spermatozoa gain the potential to activate this signaling pathway during epididymal maturation. In a modified Tyrode's medium containing 1.7 mM calcium, caput spermatozoa had significantly higher [Ca2+](i) than caudal cells and could not tyrosine phosphorylate in response to cAMP. However, in calcium-depleted medium both caput and caudal cells could exhibit a …

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The Interaction Of Alphab-Crystallin With Mature Alpha-Synuclein Amyloid Fibrils Inhibits Their Elongation, Christopher A. Waudby, Tuomas P. J Knowles, Glyn L. Devlin, Jeremy N. Skepper, Heath Ecroyd, John A. Carver, Mark E. Welland, John Christodoulou, Christopher M. Dobson, Sarah Meehan Dec 2011

The Interaction Of Alphab-Crystallin With Mature Alpha-Synuclein Amyloid Fibrils Inhibits Their Elongation, Christopher A. Waudby, Tuomas P. J Knowles, Glyn L. Devlin, Jeremy N. Skepper, Heath Ecroyd, John A. Carver, Mark E. Welland, John Christodoulou, Christopher M. Dobson, Sarah Meehan

Heath Ecroyd

alphaB-Crystallin is a small heat-shock protein (sHsp) that is colocalized with alpha-synuclein (alphaSyn) in Lewy bodies—the pathological hallmarks of Parkinson's disease—and is an inhibitor of alphaSyn amyloid fibril formation in an ATP-independent manner in vitro. We have investigated the mechanism underlying the inhibitory action of sHsps, and here we establish, by means of a variety of biophysical techniques including immunogold labeling and nuclear magnetic resonance spectroscopy, that alphaB-crystallin interacts with alphaSyn, binding along the length of mature amyloid fibrils. By measurement of seeded fibril elongation kinetics, both in solution and on a surface using a quartz crystal microbalance, this binding …

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Automatic Classification Of Ground-Penetrating-Radar Signals For Railway-Ballast Assessment, Wenbin Shao, Abdesselam Bouzerdoum, Son Lam Phung, Lijun Su, Buddhima Indraratna, Cholachat Rujikiatkamjorn Dec 2011

Automatic Classification Of Ground-Penetrating-Radar Signals For Railway-Ballast Assessment, Wenbin Shao, Abdesselam Bouzerdoum, Son Lam Phung, Lijun Su, Buddhima Indraratna, Cholachat Rujikiatkamjorn

Buddhima Indraratna

The ground-penetrating radar (GPR) has been widely used in many applications. However, the processing and interpretation of the acquired signals remain challenging tasks since an experienced user is required to manage the entire operation. In this paper, we present an automatic classification system to assess railway-ballast conditions. It is based on the extraction of magnitude spectra at salient frequencies and their classification using support vector machines. The system is evaluated on real-world railway GPR data. The experimental results show that the proposed method efficiently represents the GPR signal using a small number of coefficients and achieves a high classification rate …

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Framework To Secure Cloud-Based Medical Image Storage And Management System Communications, Timothy James Rostrom Dec 2011

Framework To Secure Cloud-Based Medical Image Storage And Management System Communications, Timothy James Rostrom

Theses and Dissertations

Picture Archiving and Communication Systems (PACS) have been traditionally constrained to the premises of the healthcare provider. This has limited the availability of these systems in many parts of the world and mandated major costs in infrastructure for those who employ them. Public cloud services could be a solution that eases the cost of ownership and provides greater flexibility for PACS implementations. This could make it possible to bring medical imaging services to places where it was previously unavailable and reduce the costs associated with these services for those who utilize them. Moving these systems to public cloud infrastructure requires …

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Second-Order Weak Lensing From Modified Gravity, R. Ali Vanderveld, Robert R. Caldwell, Jason Rhodes Dec 2011

Second-Order Weak Lensing From Modified Gravity, R. Ali Vanderveld, Robert R. Caldwell, Jason Rhodes

Dartmouth Scholarship

We explore the sensitivity of weak gravitational lensing to second-order corrections to the spacetime metric within a cosmological adaptation of the parametrized post-Newtonian framework. Whereas one might expect nonlinearities of the gravitational field to introduce non-Gaussianity into the statistics of the lensing convergence field, we show that such corrections are actually always small within a broad class of scalar-tensor theories of gravity. We show this by first computing the weak lensing convergence within our parametrized framework to second order in the gravitational potential, and then computing the relevant post-Newtonian parameters for scalar-tensor gravity theories. In doing so we show that …

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Kb-Anonymity: A Model For Anonymized Behavior-Preserving Test And Debugging Data, Aditya Budi, David Lo, Lingxiao Jiang, Lucia Lucia Dec 2011

Kb-Anonymity: A Model For Anonymized Behavior-Preserving Test And Debugging Data, Aditya Budi, David Lo, Lingxiao Jiang, Lucia Lucia

David LO

It is often very expensive and practically infeasible to generate test cases that can exercise all possible program states in a program. This is especially true for a medium or large industrial system. In practice, industrial clients of the system often have a set of input data collected either before the system is built or after the deployment of a previous version of the system. Such data are highly valuable as they represent the operations that matter in a client's daily business and may be used to extensively test the system. However, such data often carries sensitive information and cannot …

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Nort: Runtime Anomaly-Based Monitoring Of Malicious Behavior For Windows, Narcisa Andrea Milea, Siau-Cheng Khoo, David Lo, Cristi Pop Dec 2011

Nort: Runtime Anomaly-Based Monitoring Of Malicious Behavior For Windows, Narcisa Andrea Milea, Siau-Cheng Khoo, David Lo, Cristi Pop

David LO

Protecting running programs from exploits has been the focus of many host-based intrusion detection systems. To this end various formal methods have been developed that either require manual construction of attack signatures or modelling of normal program behavior to detect exploits. In terms of the ability to discover new attacks before the infection spreads, the former approach has been found to be lacking in flexibility. Consequently, in this paper, we present an anomaly monitoring system, NORT, that verifies on-the-fly whether running programs comply to their expected normal behavior. The model of normal behavior is based on a rich set of …

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Code Search Via Topic-Enriched Dependence Graph Matching, Shaowei Wang, David Lo, Lingxiao Jiang Dec 2011

Code Search Via Topic-Enriched Dependence Graph Matching, Shaowei Wang, David Lo, Lingxiao Jiang

David LO

Source code contains textual, structural, and semantic information, which can all be leveraged for effective search. Some studies have proposed semantic code search where users can specify query topics in a natural language. Other studies can search through system dependence graphs. In this paper, we propose a semantic dependence search engine that integrates both kinds of techniques and can retrieve code snippets based on expressive user queries describing both topics and dependencies. Users can specify their search targets in a free form format describing desired topics (i.e., high-level semantic or functionality of the target code); a specialized graph query language …

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Search-Based Fault Localization, Shaowei Wang, David Lo, Lingxiao Jiang, - Lucia, Hoong Chuin Lau Dec 2011

Search-Based Fault Localization, Shaowei Wang, David Lo, Lingxiao Jiang, - Lucia, Hoong Chuin Lau

David LO

Many spectrum-based fault localization measures have been proposed in the literature. However, no single fault localization measure completely outperforms others: a measure which is more accurate in localizing some bugs in some programs is less accurate in localizing other bugs in other programs. This paper proposes to compose existing spectrum-based fault localization measures into an improved measure. We model the composition of various measures as an optimization problem and present a search-based approach to explore the space of many possible compositions and output a heuristically near optimal composite measure. We employ two search-based strategies including genetic algorithm and simulated annealing …

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Towards More Accurate Retrieval Of Duplicate Bug Reports, Chengnian Sun, David Lo, Siau-Cheng Khoo, Jing Jiang Dec 2011

Towards More Accurate Retrieval Of Duplicate Bug Reports, Chengnian Sun, David Lo, Siau-Cheng Khoo, Jing Jiang

David LO

In a bug tracking system, different testers or users may submit multiple reports on the same bugs, referred to as duplicates, which may cost extra maintenance efforts in triaging and fixing bugs. In order to identify such duplicates accurately, in this paper we propose a retrieval function (REP) to measure the similarity between two bug reports. It fully utilizes the information available in a bug report including not only the similarity of textual content in summary and description fields, but also similarity of non-textual fields such as product, component, version, etc. For more accurate measurement of textual similarity, we extend …

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Bug Signature Minimization And Fusion, David Lo, Hong Cheng, Xiaoyin Wang Dec 2011

Bug Signature Minimization And Fusion, David Lo, Hong Cheng, Xiaoyin Wang

David LO

Debugging is a time-consuming activity. To help in debugging, many approaches have been proposed to pinpoint the location of errors given labeled failures and correct executions. While such approaches have been shown to be accurate, at times the location alone is not sufficient in helping programmers understand why the bug happens and how to fix it. Furthermore, a single location might not be powerful enough to discriminate failures from correct executions. To address the above challenges, there have been recent studies on extracting bug signatures which are composed of multiple locations appearing together in a particular order signifying an occurrence …

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Finding Relevant Answers In Software Forums, Swapna Gottopati, David Lo, Jing Jiang Dec 2011

Finding Relevant Answers In Software Forums, Swapna Gottopati, David Lo, Jing Jiang

David LO

Online software forums provide a huge amount of valuable content. Developers and users often ask questions and receive answers from such forums. The availability of a vast amount of thread discussions in forums provides ample opportunities for knowledge acquisition and summarization. For a given search query, current search engines use traditional information retrieval approach to extract webpages containing relevant keywords. However, in software forums, often there are many threads containing similar keywords where each thread could contain a lot of posts as many as 1,000 or more. Manually finding relevant answers from these long threads is a painstaking task to …

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