A method for the microlensed flux variance of QSOs

A fast and practical method is described for calculating the microlensed flux variance of an arbitrary source by uncorrelated stars. The required inputs are the mean convergence and shear due to the smoothed potential of the lensing galaxy, the stellar mass function, and the absolute square of the Fourier transform of the surface brightness in the source plane. The mathematical approach follows previous authors but has been generalized, streamlined, and implemented in publicly available code. Examples of its application are given for Dexter and Agol's inhomogeneous-disk models as well as the usual gaussian sources. Since the quantity calculated is a second moment of the magnification, it is only logarithmically sensitive to the sizes of very compact sources. However, for the inferred sizes of actual QSOs, it has some discriminatory power and may lend itself to simple statistical tests. At the very least, it should be useful for testing the convergence of microlensing simulations.Comment: 10 pages, 6 figure

Incremental Program Transformation Using Abstract Parallel Machines

Parallel processing is a key area of high-performance computing, providing the processing power to meet the needs of computation-intensive problems. Much research effort has therefore been invested in this area and it is growing. However, there are still several challenges that hinder its widespread use. In particular, parallel programs can be difficult to write because of the increase in the number of details to keep track of and design decisions to be made. Portability is also an important issue because the efficiency of a program depends heavily on the target machine. Another challenge arises when the issue of correctness is considered as the increased complexity and nondeterminism of parallel systems makes reasoning about them hard and renders traditional methods of testing unreliable. This thesis presents a methodology for developing parallel programs that addresses these issues. In it, executable parallel programs are derived incrementally from high-level specifications. A specification is given initially in mathematical notation and changed into an abstract functional specification. This is then transformed through a series of stages, during which additional information is given about the program, the target architecture and the parallelism. Finally it is transformed into the target language to produce an executable parallel program. This thesis uses C-f-MPI as an example target language, but many languages are possible. This methodology addresses several of the challenges of parallel programming. In particular, its incremental framework allows decisions about the program and its parallelism to be made one at a time, instead of all at once, easing the burden on the programmer and simplifying the decisions. Reasoning about the program is also made possible through the use of a pure functional language, such as Haskell, for intermediate versions of the program, as the program can then be transformed using equational reasoning, a correctness-preserving technique. The methodology is based on previous work on Abstract Parallel Machines and program derivation, which this thesis develops. It presents the basic infrastructure needed in the methodology, and therefore investigates how parallel systems can be modelled and manipulated in Haskell, and how the resultant programs can be transformed. It augments the basic methodology with the ability to introduce and reason about some key parallel programming features, including data distributions and program optimisations. The work is supported and demonstrated through two case studies

Heme oxygenase-1 enhances renal mitochondrial transport carriers and cytochrome C oxidase activity in experimental diabetes

Up-regulation of heme oxygenase (HO-1) by either cobalt protoporphyrin (CoPP) or human gene transfer improves vascular and renal function by several mechanisms, including increases in antioxidant levels and decreases in reactive oxygen species (ROS) in vascular and renal tissue. The purpose of the present study was to determine the effect of HO-1 overexpression on mitochondrial transporters, cytochrome c oxidase, and anti-apoptotic proteins in diabetic rats (streptozotocin, (STZ)-induced type 1 diabetes). Renal mitochondrial carnitine, deoxynucleotide, and ADP/ATP carriers were significantly reduced in diabetic compared with nondiabetic rats (p<0.05). The citrate carrier was not significantly decreased in diabetic tissue. CoPP administration produced a robust increase in carnitine, citrate, deoxynucleotide, dicarboxylate, and ADP/ATP carriers and no significant change in oxoglutarate and aspartate/ glutamate carriers. The increase in mitochondrial carriers (MCs) was associated with a significant increase in cytochrome c oxidase activity. The administration of tin mesoporphyrin (SnMP), an inhibitor of HO-1 activity, prevented the restoration of MCs in diabetic rats. Human HO-1 cDNA transfer into diabetic rats increased both HO-1 protein and activity, and restored mitochondrial ADP/ ATP and deoxynucleotide carriers. The increase in HO-1 by CoPP administration was associated with a significant increase in the phosphorylation of AKT and levels of BcL-XL proteins. These observations in experimental diabetes suggest that the cytoprotective mechanism of HO-1 against oxidative stress involves an increase in the levels of MCs and anti-apoptotic proteins as well as in cytochrome c oxidase activity

Internal and contextual factors, knowledge processes and performance: From the Chinese provider's perspective

This is the post-print version of the final paper published in Expert Systems with Applications. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2011 Elsevier B.V.This paper explores the influences of two internal factors, i.e. supplier team’s IT-based skills and communication with client’s team, and two contextual factors, i.e. supplier team’s understanding of client’s culture and collaboration with client’s team, on knowledge processes and performance in global sourcing of IT services from the Chinese provider’s perspective. Knowledge processes are characterized by knowledge sharing, knowledge-based coordination and expertise management, and performance is measured by product success and personal satisfaction. Data have been collected in 13 companies in Xi’an Software Park, with 26 in-depth, semi-structured interviews held with top and middle managers, and 200 structured questionnaires distributed to knowledge workers who are involved in global sourcing projects. The results indicate that supplier team’s IT-based skills, communication with client’s team, cultural understanding of client’s culture and collaboration with client’s team are positively associated with knowledge process and performance. Also, knowledge sharing, knowledge-based coordination and expertise management are found to be crucial for those influential factors to function positively and contribute to the performance. The findings of this study suggest that the effects of key factors on knowledge processes and performance in global sourcing of IT services appear to transcend the social and cultural differences; however, contextual factors seem to have more significant influences on knowledge processes and performance in global sourcing of IT services.National Natural Science Foundation of Chin

Nanostructured luminescently labeled nucleic acids

Important and emerging trends at the interface of luminescence, nucleic acids and nanotechnology are: (i) the conventional luminescence labeling of nucleic acid nanostructures (e.g. DNA tetrahedron); (ii) the labeling of bulk nucleic acids (e.g. single‐stranded DNA, double‐stranded DNA) with nanostructured luminescent labels (e.g. copper nanoclusters); and (iii) the labeling of nucleic acid nanostructures (e.g. origami DNA) with nanostructured luminescent labels (e.g. silver nanoclusters). This review surveys recent advances in these three different approaches to the generation of nanostructured luminescently labeled nucleic acids, and includes both direct and indirect labeling methods

Dark Matter from Minimal Flavor Violation

We consider theories of flavored dark matter, in which the dark matter particle is part of a multiplet transforming nontrivially under the flavor group of the Standard Model in a manner consistent with the principle of Minimal Flavor Violation (MFV). MFV automatically leads to the stability of the lightest state for a large number of flavor multiplets. If neutral, this particle is an excellent dark matter candidate. Furthermore, MFV implies specific patterns of mass splittings among the flavors of dark matter and governs the structure of the couplings between dark matter and ordinary particles, leading to a rich and predictive cosmology and phenomenology. We present an illustrative phenomenological study of an effective theory of a flavor SU(3)_Q triplet, gauge singlet scalar.Comment: 10 pages, 2 figures; v2: references added, minor changes to collider analysis, conclusions unchange

Allergenicity assessment of genetically modified crops—what makes sense?

GM crops have great potential to improve food quality, increase harvest yields and decrease dependency on certain chemical pesticides. Before entering the market their safety needs to be scrutinized. This includes a detailed analysis of allergenic risks, as the safety of allergic consumers has high priority. However, not all tests currently being applied to assessing allergenicity have a sound scientific basis. Recent events with transgenic crops reveal the fallacy of applying such tests to GM crops

Genetics of callous-unemotional behavior in children

Callous-unemotional behavior (CU) is currently under consideration as a subtyping index for conduct disorder diagnosis. Twin studies routinely estimate the heritability of CU as greater than 50%. It is now possible to estimate genetic influence using DNA alone from samples of unrelated individuals, not relying on the assumptions of the twin method. Here we use this new DNA method (implemented in a software package called Genome-wide Complex Trait Analysis, GCTA) for the first time to estimate genetic influence on CU. We also report the first genome-wide association (GWA) study of CU as a quantitative trait. We compare these DNA results to those from twin analyses using the same measure and the same community sample of 2,930 children rated by their teachers at ages 7, 9 and 12. GCTA estimates of heritability were near zero, even though twin analysis of CU in this sample confirmed the high heritability of CU reported in the literature, and even though GCTA estimates of heritability were substantial for cognitive and anthropological traits in this sample. No significant associations were found in GWA analysis, which, like GCTA, only detects additive effects of common DNA variants. The phrase ‘missing heritability’ was coined to refer to the gap between variance associated with DNA variants identified in GWA studies versus twin study heritability. However, GCTA heritability, not twin study heritability, is the ceiling for GWA studies because both GCTA and GWA are limited to the overall additive effects of common DNA variants, whereas twin studies are not. This GCTA ceiling is very low for CU in our study, despite its high twin study heritability estimate. The gap between GCTA and twin study heritabilities will make it challenging to identify genes responsible for the heritability of CU

Structuring an event ontology for disease outbreak detection

<p>Abstract</p> <p>Background</p> <p>This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is designed to support timely detection of disease outbreaks and rapid judgment of their alerting status by 1) bridging a gap between layman's language used in disease outbreak reports and public health experts' deep knowledge, and 2) making multi-lingual information available.</p> <p>Construction and content</p> <p>This event ontology integrates a model of experts' knowledge for disease surveillance, and at the same time sets of linguistic expressions which denote disease-related events, and formal definitions of events. In this ontology, rather general event classes, which are suitable for application to language-oriented tasks such as recognition of event expressions, are placed on the upper-level, and more specific events of the experts' interest are in the lower level. Each class is related to other classes which represent participants of events, and linked with multi-lingual synonym sets and axioms.</p> <p>Conclusions</p> <p>We consider that the design of the event ontology and the methodology introduced in this paper are applicable to other domains which require integration of natural language information and machine support for experts to assess them. The first version of the ontology, with about 40 concepts, will be available in March 2008.</p

Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids

Objectives: The secretin-stimulated endoscopic pancreatic function test (ePFT) allows for the safe collection of gastroduodenal and pancreatic fluid from the duodenum. We test the hypothesis that these endoscopically collected fluids have different proteomes. As such, we aim to show that the ePFT method can be used to collect fluid enriched in pancreatic proteins to test for pancreatic function. Methods: Gastroduodenal and pancreatic fluid were collected sequentially from chronic pancreatitis patients undergoing an ePFT. Proteins from each fluid type were extracted using previously published optimized methods and subjected to GeLC-MS/MS analysis for protein identification and bioinformatics analysis. Results: Mass spectrometry analysis identified proteins that were exclusive in either gastroduodenal (46) or pancreatic fluid (234). Subsequent quantitative analysis revealed proteins that were differentially abundant with statistical significance. As expected, proteolytic enzymes and protease inhibitors were among the differentially detected proteins. The proteases pepsinogens and gastrin were enriched in gastroduodenal fluid, while common pancreatic enzymes (e.g., aminopeptidase N, chymotrypsin C, elastase-3A, trypsin, and carboxypeptidase A1, and elastase 2B) were found in greater abundance in pancreatic fluid. Similarly for protease inhibitors, members of the cystatin family were exclusive to gastroduodenal fluid, while serpins A11, B4, and D1 were exclusive to pancreatic fluid. Conclusions: We have shown that ePFT collection coupled with mass spectrometry can be used to identify differentially detected proteins in gastroduodenal and pancreatic fluids. The data obtained using GeLC-MS/MS techniques provide further evidence supporting the feasibility of using ePFT-collected fluid to study specific diseases of the upper gastrointestinal tract, such as chronic pancreatitis