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++)     

Aromatic nitrations by mixed acid. Slow liquid-liquid reaction regime

Aromatic nitrations by mixed acid have been selected as a specific case of a heterogeneous liquid-liquid reaction. An extensive experimental programme has been followed using adiabatic and heat-flow calorimetry and pilot reactor experiments, supported by chemical analysis. A series of nitration experiments has been carried out to study the influences of different initial and operating conditions such as temperature, stirring speed and sulphuric acid concentration. In parallel, a mathematical model to predict the overall conversion rate has been developed. In this paper the mathematical modelling and the implementation and experimental validation for benzene, toluene and chlorobenzene mononitration in the kinetic control regime (slow liquid-liquid reaction) are presented and discussed.     

Pathway engineering for the production of aromatic compounds in Escherichia coli

The standard enzymatic assay for quantification of D-sorbitol in plasma was adapted to the automatic analyzer Cobas Mira S. In the assay, NAD (reagent) in the presence of sorbitoldehydrogenase (SDH; start reagent) converts D-sorbitol to fructose with formation of NADH, which was detected automatically as the difference between the first and last readings at 340 nm. The sample blank values for each specimen were subtracted to exclude both endogenous D-sorbitol and sugars, which also react as substrates for SDH. The method is simple, rapid (40 samples/h), precise down to endogenous concentrations (coefficient of variation < 5%; limit of determination: 0.38 mg/L) and linear up to 100 mg/L. Samples with higher D-sorbitol concentrations were estimated after dilution. The method was used to measure disposition curves of sorbitol in volunteers after a single intravenous dose of 0.8 g sorbitol.     

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     

Disappearing subdural hematomas in children

Serum glucose and plasma C-peptide response to i.v. glucagon administration was evaluated in 24 healthy dogs, 12 dogs with untreated diabetes mellitus, 30 dogs with insulin-treated diabetes mellitus, and 8 dogs with naturally acquired hyperadrenocorticism. Serum insulin response also was evaluated in all dogs, except 20 insulin-treated diabetic dogs. Blood samples for serum glucose, serum insulin, and plasma C-peptide determinations were collected immediately before and 5, 10, 20, 30, and (for healthy dogs) 60 minutes after i.v. administration of 1 mg glucagon per dog. In healthy dogs, the patterns of glucagon-stimulated changes in plasma C-peptide and serum insulin concentrations were identical, with single peaks in plasma C-peptide and serum insulin concentrations observed approximately 15 minutes after i.v. glucagon administration. Mean plasma C-peptide and serum insulin concentrations in untreated diabetic dogs, and mean plasma C-peptide concentration in insulin-treated diabetic dogs did not increase significantly after i.v. glucagon administration. The validity of serum insulin concentration results was questionable in 10 insulin-treated diabetic dogs, possibly because of anti-insulin antibody interference with the insulin radioimmunoassay. Plasma C-peptide and serum insulin concentrations were significantly increased (P < .001) at all blood sampling times after glucagon administration in dogs with hyperadrenocorticism, compared with healthy dogs, and untreated and insulin-treated diabetic dogs. Five-minute C-peptide increment, C-peptide peak response, total C-peptide secretion, and, for untreated diabetic dogs, insulin peak response and total insulin secretion were significantly lower (P < .00l) in diabetic dogs, compared with healthy dogs, whereas these same parameters were significantly increased (P < .01) in dogs with hyperadrenocorticism, compared with healthy dogs, and untreated and insulin-treated diabetic dogs. Although not statistically significant, there was a trend for higher plasma C-peptide concentrations in untreated diabetic dogs compared with insulin-treated diabetic dogs during the glucagon stimulation test. Baseline C-peptide concentrations also were significantly higher (P < .05) in diabetic dogs treated with insulin for less than 6 months, compared with diabetic dogs treated for longer than 1 year. Finally, 7 of 42 diabetic dogs had baseline plasma C-peptide concentrations greater than 2 SD (ie, > 0.29 pmol/mL) above the normal mean plasma C-peptide concentration; values that were significantly higher, compared with the results in healthy dogs (P < .001) and with the other 35 diabetic dogs (P < .001). In summary, measurement of plasma C-peptide concentration during glucagon stimulation testing allowed differentiation among healthy dogs, dogs with impaired beta-cell function (ie, diabetes mellitus), and dogs with increased beta-cell responsiveness to glucagon (ie, insulin resistance). Plasma C-peptide concentrations during glucagon stimulation testing were variable in diabetic dogs and may represent dogs with type-1 and type-2 diabetes or, more likely, differences in severity of beta-cell loss in dogs with type-1 diabetes.     

The sub-rating channel assignment strategy for PCS hand-offs

A new personal communications services (PCS) hand-off scheme is proposed. This scheme provides for hand-off to radio ports on which there is no free channel by “sub-rating” an existing connection. With sub-rating, an occupied full-rate channel is temporarily divided into two half-rate channels: one to serve the existing call and the other to serve the hand-off request. The blocking probabilities (combined forced terminations of existing calls and blocking of new call attempts) of this new scheme compare favorably with the standard scheme (nonprioritizing) and the previously proposed prioritizing schemes. The costs for this scheme are presented and discussed, as well as the additional procedural complexity of implementing on-the-fly sub-rating and the impact of continuing the conversation on a lower rate channel (which may lower speech quality of increase battery drain). Analytical models and simulations investigating the traffic impacts are presented, as are the results that show that even in the highest offered load considered a 3-min conversation in the busy hour experiences less than half a second of sub-rated conversation on average and only about 3% of the calls experience more than 5.12 s of sub-rated conversation. This scheme can increase capacity by 8-35% for systems with 1% call incompletion probability     

Calculation of optimum spacing for a three coil axially symmetric metal detector

When designing an in-line metal detector, a three coil axially symmetric design is often employed. For maximum sensitivity to small particles, the spacing of the coils is an important factor. A formula is derived which predicts the signal produced by a metal sphere when moved along the axis of such a detector and from this a graph is produced to determine the optimum coil spacing.<>