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++)     

Study of Desorption and Adsorption During Grain Aeration

One requirement in designing and operating and operating system is to minimize the moisture change in stored grain. Moisture transfer during the aeration process is generally believed to be caused by the partial pressure difference between water in grain and water in air (P₃-P₄). A mathematical model was developed for rough rice, which predicts the partial pressure difference under various grain and ambient conditions. Observations of moisture change over 10 aeration tests confirmed the good correlation between sorption phenomena and partial pressure differences. Studies indicated that air relative humidity, air temperature, grain temperature and grain moisture are significant factors influencing the partial pressure differences and, thus, affecting     

Structured genetic algorithm for robust H∞ controlsystems design

A structured genetic algorithm (SGA) approach is developed for robust controller design based on the concept of an H^∞ loop-shaping technique and the method of inequalities. Such an SGA is capable of simultaneously searching the orders and coefficients of the precompensator and postcompensator for the weighted plant. It is, therefore, not necessary to predefine the order of compensators as in usual practice. A multiple objective ranking approach is also incorporated so that the design criteria of extreme plants can be easily achieved. The effectiveness of such a technique is illustrated by a high-purity distillation column design example     

A comparison of leaf-spring with aircushion trailer suspensions in the transport environment

Packaging engineers need to be able to accurately determine the forces present in the shipping environment in order to protect packaged goods. The purpose of this study was to determine the vertical vibration levels measured in three separate truck-trailer suspension systems; conventional leaf-spring, conventional air-ride and damaged air-ride. The main conclusion reached in this study is that the air-ride suspension when maintained gives lower power density (PD) levels on all road surfaces studied. A damaged air-ride suspension and leaf-spring suspension are very similar in response frequencies, although the damaged air-ride produces higher vibration levels at lower frequencies.     

The use of probability theory in fracture mechanics—A case study

A probabilistic approach to fracture mechanics in the form of a typical case study is described wherein the integrity of a high-pressure water pipeline is assessed. An analysis methodology is discussed incorporating the probability density functions of defect sizes, the statistics of defect occurrences and the statistical distribution of material properties. This method enables the analyst to supply a very simple assessment of safety, based on the probability of failure (a single number) which may be compared to accepted industrial standards (e.g. 10⁻⁶ for nuclear applications). It is argued that this method often offers the only way to scientifically and economically assess the integrity of fracture prone structures.     

Depth of intergranular oxygen diffusion during environment-dependent fatigue crack growth in alloy 718

The elevated-temperture fatigue crack growth behavior in alloy 718, when subjected to a loading frequency lower than the transitional frequency of this alloy, is viewed as fully environment dependent. In this process, the crack growth increment per loading cycle is assumed to be equal to the intergranular oxygen diffusion depth at the crack tip during the cycle effective oxidation time. In order to identify the trend of this diffusion depth an experimental program was carried out on compact tension specimens made of alloy 718 at 650 °C in which fatigue crack growth measurements were made for cyclic load conditions with and without hold time periods at minimum load level. This work resulted in establishing a relationship correlating the intergranular oxygen diffusion depth and the value of the stress intensity factor range ΔK. This relationship, when integrated over the cycle effective oxidation time, results in a closed-form solution describing the environment-dependent fatigue crack growth rate. A comparison is made between the results of this solution when applied to different loading frequencies and the corresponding experimental results. This comparison shows good agreement between the two sets of results. Furthermore, by combining the parabolic rate law of diffusion and the equation for the intergranular oxygen diffusion depth, an explicit expression for the oxygen diffusivity of grain boundaries is derived. It is found that this diffusivity is both a ΔK- and a frequency-dependent parameter.     

Analysis of a resonant-cavity enhanced GaAs/AlGaAs MSMphotodetector

The authors have developed a 2-D device simulator for heterostructure metal-semiconductor-metal (MSM) photodetectors. They have incorporated a model of multilayer optics into the simulator and used it to analyze the temporal response of a resonant-cavity enhanced heterostructure with a confining buffer layer and a distributed Bragg reflector (DBR). The authors show that through fine tuning the layer thicknesses, optical resonance enhancement of the light absorption can be obtained     

Calculation of the integral parameters of rotor-type granulators

Translated from Khimicheskoe i Neftyanoe Mashinostroenie, No. 4, p. 19, April, 1992.     

Multidimensional augmented current equation including velocityovershoot

The augmented drift-diffusion current equation, which includes velocity overshoot effects through the space derivatives of the electric field, cannot be directly extended beyond one dimension. A new formalism is developed which considers the carrier heating and the distribution relaxation effects to obtain a multidimensional augmented drift diffusion current equation. The equivalent mobility containing the velocity overshoot correction is derived from the perturbation analysis on the carrier temperature using the energy balance equation. The issues related to the numerical implementation of this generalized model and the validity of the assumptions are also discussed