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++)     

The radiation crosslinking and scission of ethylene-propylene copolymers studied by solid-state nuclear magnetic resonance

Methyl groups from chain scission and H-crosslinks have been identified by solid-state nuclear magnetic resonance in amorphous ethylene-propylene copolymers containing 23 and 36 mole % propylene after γ-irradiation to 10 MGy at 30°C. G (scission) and G (crosslink) values determined from the n.m.r. spectra and by extraction are in agreement, which suggests that the crosslinks are not clustered. This may differ from the situation in polyethylene where there is a substantial crystalline content. G(S). G(X) and the ratio G(S)/G(X) increase with increasing propylene content of the copolymers.     

Phosphorus Inputs to Lake Simcoe from 1990 to 2003: Declines in Tributary Loads and Observations on Lake Water Quality

Total phosphorus (TP) inputs to Lake Simcoe have led to hypolimnetic dissolved oxygen (DO) depletion and loss of cold water fish habitat. Since 1990, efforts have been made to reduce the total TP input to the lake below a defined target of 75 t/year, which was predicted to lead to reductions in spring TP concentration and improvements in end-of-summer hypolimnetic DO concentrations. The total TP load to the lake during the most recent period of record (1998/99-2003/04) ranged from 53 to 76 t/yr and averaged 67 t/yr, compared to an average of 114 t/yr estimated between 1990/91 and 1997/98 (range 85-157 t/yr). Reductions in TP loads from the catchment via tributary discharge (∼26 t) accounted for the majority of the decrease in total load between the two time periods. Total P concentrations decreased significantly in four out of six long-term monitored tributaries; however, concentrations in all six tributaries remain above the level recommended to avoid nuisance plant growth (30 μg/L). Although TP loads to the lake are currently below the target 75 t/yr, excessive growths of filamentous algae and macrophytes continue to be a problem in the nearshore zone. End-of-summer minimum hypolimnetic DO concentrations (average 4.3 mg/L, 1998/99-2003/04) remain substantially below the level (7 mg/L) that is considered protective of lake trout. Efforts to reduce TP loads to the lake therefore need to continue.     

Implementing Information Systems: Some Practical Advice and a Richer Model

Recent research suggests that implementing information systems presents considerable difficulties and that many implementations are total or partial failures. This paper argues that what both practitioners and students require are richer and more acceptable models of information systems implementation. Accordingly, case study data concerning the introduction of manufacturing resource planning (MRP II) are used to illustrate five patterns of behaviour (rites) which capture important social actions; and four components of changing psychological orientation. It is argued that appreciation of the rites and psychological developments identified here will support effective change programmes. Guidelines based on our model are provided for practitioners.     

Effects of viscosity on the bitterness and astringency of grape seed tannin

To examine the separate effects of viscosity and sweetness on astringency, aqueous solutions of grape seed tannin (GST) were thickened with carboxymethyl cellulose (CMC) from 2 to 45 cP (experiment 1) or sweetened with 0 to 1.8 g/L aspartame (experiment 2). Trained subjects continuously rated astringency and bitterness in duplicate. Subjects were categorized by the salivary flow induced by citric acid and ability to taste n-propyl thiouracil (PROP). In experiment 1, maximum intensity and total duration of astringency were significantly decreased as viscosity rose, although time to maximum intensity of astringency was not affected. Maximum intensity and total duration of bitterness were not significantly affected by increasing viscosity; however, the onset of bitterness was significantly delayed. In experiment 2, increasing sweetness had no affect on any astringency parameter, although maximum intensity of bitterness was significantly decreased. Neither PROP nor salivary flow-status had any effect on perception of bitterness or astringency in either experiment.     

Egg Thiamine Status of Lake Ontario Salmonines 1995–2004 with Emphasis on Lake Trout

Alewives (Alosa pseudoharengus), the major prey fish for Lake Ontario, contain thiaminase. They are associated with development of a thiamine deficiency in salmonines which greatly increases the potential for developing an early mortality syndrome (EMS). To assess the possible effects of thiamine deficiency on salmonine reproduction we measured egg thiamine concentrations for five species of Lake Ontario salmonines. From this we estimated the proportion of families susceptible to EMS based on whether they were below the ED20, the egg thiamine concentration associated with 20% mortality due to EMS. The ED20s were 1.52, 2.63, and 2.99 nmol/g egg for Chinook salmon (Oncorhynchus tshawytscha), lake trout (Salvelinus namaycush), and coho salmon (Oncorhynchus kisutch), respectively. Based on the proportion of fish having egg thiamine concentrations falling below the ED20, the risk of developing EMS in Lake Ontario was highest for lake trout, followed by coho (O. kisutch), and Chinook salmon, with the least risk for rainbow trout (O. mykiss). For lake trout from western Lake Ontario, mean egg thiamine concentration showed significant annual variability during 1994 to 2003, when the proportion of lake trout at risk of developing EMS based on ED20 ranged between 77 and 100%. Variation in the annual mean egg thiamine concentration for western Lake Ontario lake trout was positively related (p < 0.001, r² = 0.94) with indices of annual adult alewife biomass. While suggesting the possible involvement of density-dependent changes in alewives, the changes are small relative to egg thiamine concentrations when alewife are not part of the diet and are of insufficient magnitude to allow for natural reproduction by lake trout.     

The Climate for Creativity and Change in Teams

This article reports the results of a study conducted to examine the ability of the Situational Outlook Questionnaire (SOQ^TM) to effectively discern climates that either encourage or discourage creativity and the ability to initiate change in a team setting. The purpose of the study is to examine the concurrent criterion–related validity of the SOQ. The article explores the characteristics in an organisational climate that promote teamwork and some of the tripwires one needs to be aware of in the formation and management of teams. Nine dimensions of the climate for creativity and change as measured by the Situational Outlook Questionnaire are put forward and defined in relation to teams. The methodology and results of the study are reported. The results show that when subjects (N7equals;154) complete the SOQ based on their recollection of a best– and worst–case team experience, the measure is able to consistently and significantly discriminate between the two types of experiences. Conclusions, implications, and areas for future research to further examine the validity of the SOQ are explored.