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     

High speed p-type SiGe modulation-doped field-effect transistors

We report on the fabrication and characterization of high-speed p-type modulation-doped field-effect transistors (MODFETs) with 0.7-μm and 1-μm gate-lengths having unity current-gain cut-off frequencies (f_T) of 9.5 GHz and 5.3 GHz, respectively. The devices were fabricated on a high hole mobility SiGe heterostructure grown by ultra-high-vacuum chemical vapor deposition (UHV-CVD). The dc maximum extrinsic transconductance (g_m) is 105 mS/mm (205 mS/mm) at room temperature (77 K) for the 0.7-μm gate length devices. The fabricated devices show good pinch-off characteristics and have a very low gate leakage current of a few μA/mm at room temperature and a few nA/mm at 77 K     

Criteria of cure and follow-up of central hyperthyroidism due to thyrotropin-secreting pituitary adenomas

The recorded number of patients with central hyperthyroidism due to TSH-secreting pituitary adenoma doubled in the last few years after the introduction of ultrasensitive TSH assays in the assessment of thyroid function; however, information about the results and the criteria for cure after pituitary surgery is scanty. Seventeen patients with a TSH-secreting adenoma, diagnosed on the basis of detectable TSH levels in the face of high free thyroid hormone concentrations and pituitary lesion at neuroimaging, underwent pituitary surgery. Hypersecretion of other pituitary hormones was diagnosed in 5 of 17 patients. Four patients were initially misdiagnosed and treated with thyroid surgery or radioiodine therapy. The majority (86%) of hyperthyroid patients normalized thyroid hormone concentrations and regained euthyroidism, although pituitary imaging, alpha-subunit, and alpha-subunit/TSH molar ratio normalized in only 47%, 54%, and 58% of patients, respectively. Moreover, TSH secretion was normally suppressed by T3 in 40% of the patients. Interestingly, the finding of undetectable TSH levels 7 days after surgery was highly predictive of successful outcome. During long term follow-up, there was one relapse of hyperthyroidism. Early diagnosis of TSH-secreting adenomas permits a high rate of remission of hyperthyroidism after surgery. However, normalization of thyroid function alone does not necessarily reflect complete removal of the tumor, and more comprehensive criteria of cure based on pituitary imaging, hormone measurement, and suppression of TSH during T3 administration should be used. Lastly, all patients need an accurate long term follow-up to monitor the possible recurrence of the adenoma.     

Composition and thermodynamics of the surface layer of binary melts based on iron,cobalt, and nickel

The composition, thickness, thermodynamic activities of components, Gibbs energy and excess energy of formation of the surface layer on binary melts of iron, cobalt and nickel-based alloys with different interatomic interactions were evaluated with the aid of data from the literature and the authors measurements of the concentration dependence of the surface tension and molar volume.     

Performance evaluation of air-conditioning units

A limited selection of samples of small and medium size air-conditioning equipment being marketed or manufactured in Kuwait was tested in an internationally reputed laboratory. The actual performance results obtained from laboratory tests were analyzed and compared with the commercially available information from the manufacturers for the same selected units. The analysis indicated the quality of air-conditioning equipment available to the Kuwaiti user.