Data management and analysis for high-throughput DNA sequencingprojects

The rapid advances in molecular biology have begun to shift many of the bottlenecks in genome research from the laboratory to the data analysis facility. The pace at which this has occurred creates a situation in which software development always has to catch up with the flow of data. Since such large-scale processes were not anticipated, the analysis infrastructure has not been fully established. Furthermore, most systems that have been built were designed by the biologists who collected the data. More recently, computer scientists, mathematicians, and engineers have taken an interest in this problem. This has had a positive effect, since it has created a tight synergy between the informatics and the biology. Several principles affected the design of the system developed at TIGR. Each of the sample preparation, sequencing, and analysis steps had to be managed, scheduled, and tracked. This information had to be made readily available to those who needed it for carrying out their tasks. Different skill levels of the users had to be taken into account. The degree of human intervention at each step had to be evaluated and built into the design. A mixed processing environment of Macintosh and Unix platforms had to be integrated. Most importantly, the system had to save time, reduce error, and ensure uniformity of the analysis and quality of the results. In the authors' experience, the tools they have built work well because of their early decisions as to which systems to use for development. The authors settled on a robust relational database management system (Sybase) and a portable development environment (C, C++)     

Prolonged hypoxaemia after nebulised salbutamol

Pulse oximetry is increasingly used to assess hypoxaemia in respiratory illnesses. Six children presenting with acute asthma and prolonged falls in oxygen saturation values after treatment with salbutamol are described who were subsequently shown to have pneumonic consolidation on chest radiography.     

Analysis of thin walled structures using the boundary element method

In this article the direct boundary element formulations of stretching and bending plate problems are combined together to solve thin walled structures and other similar frames. The final system is obtained by assuming each individual plane structural element as a subregion. After the necessary transforms of these equations they can be combined together taking into account the displacement compatibility and equilibrium conditions.     

EU-Weißbuch Erneuerbare Energien und die Ergebnisse von Kyoto

The Kyoto Protocol to the United Nationsl Framework Convention on Climate Change gives a target for the reduction of greenhouse gases in the EU and most associated states of 8% from 1990 levels to 2010. The European Commissions Whitebook on Renewable Energy is setting a target of doubling the share of Renewable Energy from 6% now to 12% in 2010 for the European Union. There is no contradiction between these targets.     

Accelerated aging of extruded dielectric power cables. I. Controland monitoring methodology

An improved accelerated cable life test is described. Through the use of programmable logic controllers (PLCs), very precise and consistent control of the accelerated aging process has been achieved. A computer has been utilized to make continuous real-time acquisition and storage of key operating parameters possible. This precise control and monitoring methodology has permitted the study of the synergistic effects of voltage and temperature on the accelerated aging of full-sized cables in the laboratory     

Multipoint communication: a survey of protocols, functions, andmechanisms

Group communication supports information transfer between a set of participants. It is becoming more and more relevant in distributed environments. For distributed or replicated data, it provides efficient communication without overloading the network. For some types of multimedia applications, it is the only way to control data transmission to group members. This paper surveys protocol functions and mechanisms for data transmission within a group, from multicast routing problems up to end-to-end multipoint transmission control. We provide a bibliography which is organized by topic     

NMR IMAGING, CALORIMETRIC, and MATHEMATICAL MODELING STUDIES of FOOD FREEZING

Nuclear magnetic resonance imaging (MRI), calorimetry, and temperature measurements were used to monitor cylindrical potato sections frozen at -11C and -42C. MRI showed the advance of the nonsymmetric freezing zone and loss of signal intensity as liquid water turned to ice. Differential calorimetry was used to follow heat removal during transient freezing. Measured times to 95% enthalpy change were 24 min (-42C) and 49 min (-11C), as compared to modeled values of 29 min (-42C) and 100 min (-11C). Times to 95% change in the NMR signal, integrated over the area of the image, were 21 min (-42C) and 56 min (-11C). Changes in NMR signal intensity could be correlated with the amount of unfrozen water remaining after a steady-state had been reached. At -42C, NMR indicated 25% unfrozen water remaining as compared to 26% by calorimetry, and 22% by modeling. At -11C, NMR measured 67% unfrozen water remaining as compared to 48% by calorimetry, and 25% by equilibrium modeling.     

Image coding by multistep, adaptive flux interpolation

The authors describe and discuss the new technique, multistep adaptive flux interpolation (MAFI), and its application to image data for coding. When applied to an image, MAFI produces an output which is also in an image form, but which has a more uniform feature density and a greatly reduced size. MAFI warps the input image by removing those rows and columns which contain a majority of redundant pixels. The side information required for reconstruction is minimal, and the image can be further compressed using conventional coders, making the compression ratio even higher. Because of its warped nature, the MAFI output's statistics are also more consistent with the properties assumed by block-based discrete cosine transform (DCT) methods     

Dynamic programming implementation on array processor architectures

Dynamic Programming (DP) applies to many signal and image processing applications including boundary following, the Viterbi algorithm, dynamic time warping, etc. This paper presents an array processor implementation of generic dynamic programming. Our architecture is a SIMD array attached to a host computer. The processing element of the architecture is based on an ASIC design opting for maximum speed-up. By adopting a torus interconnection network, a dual buffer structure, and a multilevel pipeline, the performance of the DP chip is expected to reach the order of several GOPS. The paper discusses both the dedicated hardware design and the data flow control of the DP chip and the total array.This work was supported in part by the NATO, Scientific and Environmental Affairs Division, Collaborative Research Grant SA.5-2-05(CRG.960201)424/96/JARC-501.