Application of high-throughput computing in bioinformatics

We describe the challenges faced when developing a Linux/PC-based cluster to apply bioinformatics algorithms to the rapidly increasing raw genomics data available. The calculations, which take around two months to complete, result in a powerful resource that can be used for data mining--most obviously for the human genome. Our current infrastructure consists of a 1314 node cluster with 1734 processors supporting both production and research. This paper highlights the problems in achieving high data throughput with such systems and shows that raw computer power is only one component of a complex problem.     

Detection of hydrogen peroxide at mesoporous platinum microelectrodes

Mesoporous (H(I)-ePt) platinum microelectrodes electrodeposited from the hexagonal (H(I)) lyotropic liquid crystalline phase are shown to be excellent amperometric sensors for the detection of hydrogen peroxide over a wide range of concentrations. Good reproducibility, high precision, and accuracy of measurements are demonstrated. Mesoporous microelectrodes retain the high rates of mass transport typical of conventional microelectrodes, and their high real surface area greatly enhances their catalytic activity. This unique combination of properties overcomes the limitations of previous amperometric hydrogen peroxide sensors and yields outstanding qualitative and quantitative results.     

We Need A New Vocabulary

KNOWLEDGE IS LOST in equal proportion to the size of the enterprise. This should come as no surprise, because the greater the institution, the greater the amount of information there is to be managed. However, the reasons for knowledge mismanagement vary greatly, depending upon the size and breadth of the institution. To propose useful solutions to this very human problem, some definitions are required.     

Relative Effectiveness of Project Delivery and Contract Strategies

Project delivery systems define the roles and responsibilities of the parties involved in a project. They also establish an execution framework in terms of sequencing of design, procurement, and construction. The decision made in the selection of a project delivery system for a project impacts all phases of execution of the project and greatly impacts the efficiency of project execution. Such decisions should be facilitated by thorough analysis. Structured, quantitative decision analysis processes have been shown to have several benefits over the simplistic, holistic, and informal processes that typically characterize subjective evaluations. However, a dearth of quantitative values of project delivery systems established and validated through research has invariably left project managers with no alternative than to make project delivery selection decisions on the basis of subjective evaluations. Development of the needed quantitative values for application in a decision analysis process would greatly enhance the quality of the decision-making process and provide a defensible rationale for selection of project delivery systems for capital projects. This paper presents research findings that provide the needed quantitative values in this area. Based on the quantitative values defined here, interested parties can develop and implement quantitative evaluation of project delivery alternatives to identify the optimal solution for a given project. Multicriteria decision analysis was found to be the suitable approach for a quantitative, analytical evaluation of project delivery systems. Consequently, the quantitative values presented in this paper were developed in accordance with the requirements of the multicriteria decision analysis technique known as simple multiattribute rating technique with swing weights (SMARTS). Utilizing the quantitative values presented here and applying the analysis technique of SMARTS, a decision support tool has been developed and validated for the Construction Industry Institute. The decision support tool is presently being utilized by member companies of the Construction Industry Institute that were privy to its development. With the presentation of the quantitative values in this paper, other parties interested in developing similar tools would benefit from the research results presented here.     

WIRE3: Driving Around the Information Super-Highway

Interactive voice browsers offer an alternative paradigm that affords ubiquitous mobile access to the WWW using a wide range of consumer devices. This technology can facilitate a safe, “hands-free” browsing environment that is of importance both to car drivers and various mobile and technical professionals. This paper describes the challenges of architecting an interactive voice browser that combines digital audio with the features of a speech synthesizer to make structural elements of the document explicit to the listener. The aesthetics of the audio rendition can simultaneously help reduce the monotony factor and enhance comprehension. The evolution of the voice browser gave rise to a new conceptual model of the HTML document structure and its mapping to a 3D audio space. A number of novel features are discussed for improving both the user’s comprehension of the HTML document structure and their orientation within it. These factors, in turn, can improve the effectiveness of the browsing experience.     

Effect of plasma TNF-alpha on filgrastim-stimulated hematopoiesis in mice and humans

Marshall syndrome is a rare, autosomal dominant skeletal dysplasia that is phenotypically similar to the more common disorder Stickler syndrome. For a large kindred with Marshall syndrome, we demonstrate a splice-donor-site mutation in the COL11A1 gene that cosegregates with the phenotype. The G+1-->A transition causes in-frame skipping of a 54-bp exon and deletes amino acids 726-743 from the major triple-helical domain of the alpha1(XI) collagen polypeptide. The data support the hypothesis that the alpha1(XI) collagen polypeptide has an important role in skeletal morphogenesis that extends beyond its contribution to structural integrity of the cartilage extracellular matrix. Our results also demonstrate allelism of Marshall syndrome with the subset of Stickler syndrome families associated with COL11A1 mutations.     

Routine intraoperative laparoscopic cholangiography

BACKGROUND: Whether intraoperative laparoscopic cholangiography should be routine is debatable. METHODS: We reviewed the cholangiography experience in 669 consecutive laparoscopic cholecystectomies. RESULTS: Mean age of the patients was 39 years, 78% were female, and 29% had acute cholecystitis. Cholecystectomy was completed laparoscopically in 606 (91%). Laparoscopic cholangiography was completed in 562 (93%) and 348 (62%) were routine (no preoperative indication). The mean operating time in 1996 was 61 minutes. Out of the 348 routine cholangiograms, 17 demonstrated evidence of unsuspected choledocholithiasis. Five patients had choledocholithiasis documented by laparoscopic common bile duct exploration and/or endoscopic retrograde cholangiopancreatography. Two patients had normal postoperative cholangiopancreatography. One of 10 patients managed expectantly was readmitted postoperatively with obstructive jaundice. In 4 patients, routine cholangiography revealed unexpected anatomy, and in 2, this prevented misidentification and transection of the common bile duct. CONCLUSION: Laparoscopic cholangiography is safe, quick, detects unsuspected choledocholithiasis, and can prevent common bile duct transection. It should be routine.     

Epithelial carcinogenesis in the mouse: correlating the genetics and the biology

Tumour formation relies on a complex combination of genetic and environmental factors. In particular, the contributions from inherited predisposition genes as well as carcinogens, for example from cigarettes or in the diet, are amongst the major contributors to tumorigenesis. Since the study of such processes in particularly difficult in human cancers, the availability of a well-defined model system is of obvious benefit. The mouse skin model of multistage carcinogenesis offers an excellent tool for the study of the target cells, the target genes and the biological events associated with neoplasia. In this system, tumorigenesis occurs in a series of defined stages, each of which is characterized by specific and reproducible alterations in genes such as H-ras, cyclin D1, p53 and p16INK4A. Additional changes occur in the production of, or response to, factors such as transforming growth factor beta (TGF beta). These genetic and biological alterations are mirrored in human tumours of epithelial origin. Hence, research into the general principles of tumour initiation, promotion and progression in the context of the mouse skin model is likely to prove valuable in the continual search for new methods for the diagnosis, prevention, and therapeutic treatment of human cancers.     

Contingent time off to increase verbal behavior: A case report.

Describes the case of a withdrawn adolescent male outpatient at a mental health clinic who was instructed to record his own verbal behavior. Consequences were implemented to increase the frequency of verbal responses. S "earned" his way out of the clinic by increasing his verbal behavior to an established criterion performance. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

On the identification of repeatedly presented brief visual stimuli.

Discusses 2 hypotheses concerning the explanation of increasing perceptual performance with temporal repetition of tachistoscopically-presented visual stimuli. R. N. Haber's conception in terms of increasing phenomenal clarity is criticized, primarily for the confounding influence of the "stimulus error." An alternative explanation in terms of the perceptual independence of successive inputs is presented. The assumption of independence is built into a model that combines aspects of C. W. Eriksen's "clearest form" approach with Bayesian decision theory. 4 items of support for independence are presented. Eriksen found (a) no effect of interstimulus interval on accuracy; and (b) no difference in accuracy whether a form was preceded by the same or a different form, or by a flash. Previous studies by the present authors found (a) lack of influence of the locus on an inconsistent stimulus in a sequence, and (b) quite accurate Bayesian predictions of multiple observation performance in 3 experiments using equal prior probabilities of the stimulus states. (39 ref.) (PsycINFO Database Record (c) 2010 APA, all rights reserved)