SPEDE: Simple Programming Environment for Distributed Execution

One of the main goals for people who use computer systems, particularly computational scientists, is speed. In the quest for ways to make applications run faster, engineers have developed parallel computers, which use more than one CPU to solve a task. However, many institutions already posses significant computational power in networks of workstations. Through software, it is possible to glue together clusters of machines to simulate a parallel environment. SPEDE is one such system, designed to place the potential of local machines at the fingertips of the programmer. Through a simple interface, users design computational objects that can be linked and run in parallel. The goal of the project is to have a small portable environment that allows various types of computer systems to interact. SPEDE requires no altering of the kernel and does not require system privileges to use. Using SPEDE, programmers can get significant speedup for computationally intensive problems. As an example, a Mandelbrot image generator was implemented, that attained a five-fold speedup with eight processors

SPEDE: A Simple Programming Environment for Distributed Execution (Users\u27 Manual)

Traditional single processor computers are quickly reaching their full computational potentials. The quest for faster and faster chips have brought technology to the point where the laws of physics are hampering future gains. Significant gains in speed must therefore come from using multiple processors instead of a single processor. This technology usually represents itself in the form of a parallel computer, such as the Connection Machine Model 5. Recently however, much interest has been focused on software that organizes single processor computers to behave like a parallel computer. This is desirable for sites which have large installations of workstations, since the cost of new parallel systems are prohibitive. SPEDE, a Simple Programming Environment for Distributed Execution, was designed for this purpose. It allows UNIX based machines of varying hardware types to be organized and utilized by a programmer of parallel applications. SPEDE is a user level system in that it requires no special privileges to run. Every user keeps a separate copy of the system so that security issues are covered by the normal UNIX operating environment. SPEDE is characterized as a large grained distributed environment. This means that applications which have a large processing to I/O ratio will be much more effective than those with a small ratio. SPEDE allows users to coordinate the use of many computers through a straightforward interface. Machines are organized by classes, which are terms that can be used to label and group them into more manageable units. For example, users might want to create a class based on the byte ordering of machines, or by their location. Users can then specify more completely which machines they want to use for a particular session. Sessions are essentially the interaction between objects in the SPEDE environment. A user creates an object to perform a certain task, such as constructing part of a fractal image. Objects can send and receive messages from other objects using a simple interface provided with SPEDE. Objects are machine independent, which means that the same object can be run simultaneously on different platforms. This is achieved by translating all messages into standard network byte ordering. However, if user data is being passed between objects, it is the user\u27s responsibility to make sure byte ordering is correct. The SPEDE system involves several major components. These components help control and manage object interactions. Figure 1 shows a running session running with three machines (each surrounded by an oval rectangle). There are also three objects running, two named MandComp and one named Mand. Each object is on a different machine, although it is possible to have multiple objects on a single machine. In the figure, the lines connecting the various entities represent socket connections. UNIX sockets are the transport mechanism used in SPEDE, although one could implement a lower level protocol for more efficient communication. Sockets can also be a problem because some machines have strict limits on the number of connections a user can have open at any given time

Prevalence, Characteristics, and Prognostic Significance of HFE Gene Mutations in Type 2 Diabetes: The Fremantle Diabetes Study

OBJECTIVE—To examine the relationship between iron status, hereditary hemochromatosis (HFE) gene mutations, and clinical features and outcomes of type 2 diabetes in a well-characterized representative sample of community-based patients

Prevalence of H63D, S65C and C282Y hereditary hemochromatosis gene mutations in Slovenian population by an improved high-throughput genotyping assay

<p>Abstract</p> <p>Background</p> <p>Hereditary hemochromatosis (HH) is a common genetic disease characterized by excessive iron overload that leads to multi-organ failure. Although the most prevalent genotype in HH is homozygosity for C282Y mutation of the <it>HFE </it>gene, two additional mutations, H63D and S65C, appear to be associated with a milder form of HH. The aim of this study was to develop a high-throughput assay for <it>HFE </it>mutations screening based on TaqMan technology and to determine the frequencies of <it>HFE </it>mutations in the Slovenian population.</p> <p>Methods</p> <p>Altogether, 1282 randomly selected blood donors from different Slovenian regions and 21 HH patients were analyzed for the presence of <it>HFE </it>mutations by an in-house developed real-time PCR assay based on TaqMan technology using shorter non-interfering fluorescent single nucleotide polymorphism (SNP)-specific MGB probes. The assay was validated by RFLP analysis and DNA sequencing.</p> <p>Results</p> <p>The genotyping assay of the H63D, S65C and C282Y mutations in the <it>HFE </it>gene, based on TaqMan technology proved to be fast, reliable, with a high-throughput capability and 100% concordant with genotypes obtained by RFLP and DNA sequencing. The observed frequency of C282Y homozygotes in the group of HH patients was only 48%, others were of the heterogeneous <it>HFE </it>genotype. Among 1282 blood donors tested, the observed H63D, S65C and C282Y allele frequency were 12.8% (95% confidence interval (CI) 11.5 – 14.2%), 1.8% (95% CI 1.4 – 2.5%) and 3.6% (95% CI 3.0 – 4.5%), respectively. Approximately 33% of the tested subjects had at least one of the three HH mutations, and 1% of them were C282Y homozygotes or compound heterozygotes C282Y/H63D or C282Y/S65C, presenting an increased risk for iron overload disease. A significant variation in H63D allele frequency was observed for one of the Slovenian regions.</p> <p>Conclusion</p> <p>The improved real-time PCR assay for H63D, S65C and C282Y mutations detection is accurate, fast, cost-efficient and ready for routine screening and diagnostic procedures. The genotype frequencies in the Slovenian population agree with those reported for the Central European populations although some deviations where observed in comparison with other populations of Slavic origin. Regional distribution of the mutations should be considered when planning population screening.</p

Allele frequencies of hemojuvelin gene (HJV) I222N and G320V missense mutations in white and African American subjects from the general Alabama population

BACKGROUND: Homozygosity or compound heterozygosity for coding region mutations of the hemojuvelin gene (HJV) in whites is a cause of early age-of-onset iron overload (juvenile hemochromatosis), and of hemochromatosis phenotypes in some young or middle-aged adults. HJV coding region mutations have also been identified recently in African American primary iron overload and control subjects. Primary iron overload unexplained by typical hemochromatosis-associated HFE genotypes is common in white and black adults in Alabama, and HJV I222N and G320V were detected in a white Alabama juvenile hemochromatosis index patient. Thus, we estimated the frequency of the HJV missense mutations I222N and G320V in adult whites and African Americans from Alabama general population convenience samples. METHODS: We evaluated the genomic DNA of 241 Alabama white and 124 African American adults who reported no history of hemochromatosis or iron overload to detect HJV missense mutations I222N and G320V using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Analysis for HJV I222N was performed in 240 whites and 124 African Americans. Analysis for HJV G320V was performed in 241 whites and 118 African Americans. RESULTS: One of 240 white control subjects was heterozygous for HJV I222N; she was also heterozygous for HFE C282Y, but had normal serum iron measures and bone marrow iron stores. HJV I222N was not detected in 124 African American subjects. HJV G320V was not detected in 241 white or 118 African American subjects. CONCLUSIONS: HJV I222N and G320V are probably uncommon causes or modifiers of primary iron overload in adult whites and African Americans in Alabama. Double heterozygosity for HJV I222N and HFE C282Y may not promote increased iron absorption

Redox regulation of hepatitis C in nonalcoholic and alcoholic liver

Hepatitis C virus (HCV) is an RNA virus of the Flaviviridae family that is estimated to have infected 170 million people worldwide. HCV can cause serious liver disease in humans, such as cirrhosis, steatosis, and hepatocellular carcinoma. HCV induces a state of oxidative/nitrosative stress in patients through multiple mechanisms, and this redox perturbation has been recognized as a key player in HCV-induced pathogenesis. Studies have shown that alcohol synergizes with HCV in the pathogenesis of liver disease, and part of these effects may be mediated by reactive species that are generated during hepatic metabolism of alcohol. Furthenriore, reactive species and alcohol may influence HCV replication and the outcome of interferon therapy. Alcohol consumption has also been associated with increased sequence heterogeneity of the HCV RNA sequences, suggesting multiple modes of interaction between alcohol and HCV. This review summarizes the current understanding of oxidative and nitrosative stress during HCV infection and possible combined effects of HCV, alcohol, and reactive species in the pathogenesis of liver disease. (c) 2007 Elsevier Inc. All rights reserved

SPEDE - A Simple Programming Environment for Distributed Execution

this paper, the term session is used to describe an interaction with SPEDE that lasts as long as any remote entity is running. When all processes associated with SPEDE have been terminated, the session is finished. Overvie

Some observations on the operation of the monastic scriptorium

Gochee William. Some observations on the operation of the monastic scriptorium. In: Scriptorium, Tome 31 n°2, 1977. pp. 242-246