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++)     

Specimen size effect during tensile testing of an unreinforced polymer

Various specimen sizes of an unreinforced polymer, Hercules 3501 -6 thermosetting epoxy, were subjected to a tensile test. The general specimen geometry was a rectangular dog-bone shape with constant gauge length, but with each specimen size having a different crosssectional area. These cross-sectional areas were obtained by varying the thickness of the epoxy during casting, and the gauge section width during grinding. The resulting failure surfaces of the specimens were observed and photographed using scanning electron microscopy. The results indicate that failure stress, dimensions of the critical flaw which caused failure, and a quantity which is proportional to the fracture toughness, are all correlated with specimen size.     

Effects of α‐form or β‐form nuclei on polymorphic crystalline morphology of poly(butylene adipate)

The effects of α‐form and β‐form nuclei on polymorphic morphology of poly(butylene adipate) (PBA) upon recrystallization from the molten state up to various T_max values were examined by differential scanning calorimetry (DSC), wide‐angle X‐ray diffraction (WAXD) and polarized light microscopy (PLM). In this study, PBA with complex melting and polymorphism behaviour was used as a model for examining different types and extents of residual nuclei. As the PBA initially containing the sole α‐crystal was brought to a molten state of various T_max, the extents of trace α‐form crystal nuclei varied and were dependent on T_max. Furthermore, it did not matter whether, initially, the PBA contained α‐ or β‐form crystals (or both) because only a single type of α‐nuclei could be left upon treatment to the molten liquid state at T_max. Therefore, only the α‐crystal in PBA had ‘memory capacity’ in the molten liquid state while the β‐crystal did not. This was so because the latter had been completely transformed into the solid state prior to being heated into a liquid. PBA crystallized before α‐nuclei could be packed into α‐crystal, regardless of the crystallization temperature (T_c). For recrystallization from molten PBA without any nuclei, the crystalline polymorphism was correspondingly influenced by T_c. Copyright © 2005 Society of Chemical Industry     

Heparin effect on hydrolysis of fibrin clots in a bull and a man with varying fibrinolytic systems

Heparin was studied for its effect on the hydrolysis time of clots from desAA fibrin (FB), desAABB fibrin (F0) and fibrinogen (Fg) of a bull and a man by gly-or lys-plasminogen which is activated by the tissue activator. It is shown that heparin in the concentration to 4.6 M does not affect that hydrolysis time of clots from human and bovine Fg and human Fg by gly-plasminogen which is activated by the tissue activator. Heparin increases the hydrolysis time of clots from bovine Fg and F0 by gly-and lys-plasminogen, the tissue activator being present. It firstly increases (in concentrations below 0.5 (microM), and then decreases (in concentrations above 0.5 (microM) the hydrolysis time of clots from human FB, F0 and Fg and bovine FB and F0 by plasmin. In concentration 4.6 microM heparin increases the hydrolysis time of clots from human fibrinogen by fibrinolytic systems. Effect of heparin on fibrinolytic process from the viewpoint of affine interactions between the components of fibrin clots is discussed.     

Is homophobia associated with homosexual arousal?

The authors investigated the role of homosexual arousal in exclusively heterosexual men who admitted negative affect toward homosexual individuals. Participants consisted of a group of homophobic men (n?=?35 ) and a group of nonhomophobic men (n?=?29); they were assigned to groups on the basis of their scores on the Index of Homophobia (W. W. Hudson & W. A. Ricketts, 1980). The men were exposed to sexually explicit erotic stimuli consisting of heterosexual, male homosexual, and lesbian videotapes, and changes in penile circumference were monitored. They also completed an Aggression Questionnaire (A. H. Buss & M. Perry, 1992). Both groups exhibited increases in penile circumference to the heterosexual and female homosexual videos. Only the homophobic men showed an increase in penile erection to male homosexual stimuli. The groups did not differ in aggression. Homophobia is apparently associated with homosexual arousal that the homophobic individual is either unaware of or denies. (PsycINFO Database Record (c) 2010 APA, all rights reserved)