Three public enemies: cut, copy, and paste

Many software developers know the feeling of desperately debugging a program only to discover after a sleepless night that the error stemmed from copy-pasted code segments that had become inconsistent in subsequent editing. The problems arising from copied code are not new, and many researchers have investigated how to automatically find copied code segments. Given the extensive use of copy-paste operations and their tendency to cause inconsistencies, there is clearly a pressing need to rethink current editor programs. One solution is to replace cut, copy, and paste with operations that correspond directly to the intended semantics behind their use. With these operations, the user can specify semantic relationships among copied objects, and the editor program can use that information to help in the long-term support of those relationships. It would thus avoid the inconsistencies that currently arise from the use of cut, copy, and paste.     

Automation for High-throughput Identification and Picking of GFP Expressing Colonies

Green fluorescent protein (GFP) has many applications as a marker in living cells, and has become widely used as a reporter gene in microbial, plant and animal cells. Screening microbial colonies for GFP expression enables various types of assays (e.g. for secretory mutations). However, this is laborious, non-quantitative and potentially hazardous to the operator (due to UV illumination) when performed manually. In order to address this the GloPix robot was developed. The imaging system discriminates between colonies based on the level of fluorescence activity and the picking function automatically transfers cells to microplate wells. Measuring fluorescent activity allows quantitation of fluorescent tag concentration/expression.     

Adenoma characteristics at first colonoscopy as predictors of adenoma recurrence and characteristics at follow-up. The Polyp Prevention Study Group

In Bacillus transformation, sexual isolation is known to be an exponential function of the sequence divergence between donor and recipient. Here, we have investigated the mechanism under which sequence divergence results in sexual isolation. We tested the effect of mismatch repair by comparing a wild-type strain and an isogenic mismatch-repair mutant for the relationship between sexual isolation and sequence divergence. Mismatch repair was shown to contribute to sexual isolation but was responsible for only a small fraction of the sexual isolation observed. Another possible mechanism of sexual isolation is that more divergent recipient and donor DNA strands have greater difficulty forming a heteroduplex because a region of perfect identity between donor and recipient is required for initiation of the heteroduplex. A mathematical model showed that this heteroduplex-resistance mechanism yields an exponential relationship between sexual isolation and sequence divergence. Moreover, this model yields an estimate of the size of the region of perfect identity that is comparable to independent estimates for Escherichia coli. For these reasons, and because all other mechanisms of sexual isolation may be ruled out, we conclude that resistance to heteroduplex formation is predominantly responsible for the exponential relationship between sexual isolation and sequence divergence in Bacillus transformation.     

Informed consent: how much information is enough?

BACKGROUND: Recent judicial decisions involving informed consent have led to some medical practitioners altering the way they obtain consent. The aim of this study was to determine the degree to which patients understood the risks associated with a surgical procedure after giving routine consent and whether providing additional detailed verbal and/or written information improved their understanding. It was further determined whether the provision of more extensive information altered patients' anxiety levels. METHODS: Patients undergoing femoral popliteal bypass or carotid surgery were randomized to obtain either routine consent only or routine consent with verbal or written or verbal and written consent. Patients undertook a pre-operative risk and complication questionnaire, a pre- and postoperative anxiety and depression evaluation and a follow-up questionnaire 6 weeks after discharge. RESULTS: Thirty-two patients were included in the trial. The comprehension questionnaire resulted in a correct percentage response of 48% for the routine information only, 59% with added verbal information, 59% with added written information and 55% with added written and verbal information. Twenty-five per cent of patients stated that they had a poor understanding of the risks and complications of the procedure. CONCLUSIONS: Additional written or verbal information did not improve a patient's understanding of risks and complications of the procedure. It also did not improve patients' perceived understanding of the operation or its complications. Patients' anxiety levels were unaltered by the increase in the information they were given. The information provided to patients should be simple, easy to understand and list any possible major complications to enable the patient to determine whether to undergo or decline a procedure.     

5-HT4 receptor antagonism does not affect motor and reward mechanisms in the rat

5-HT4 receptors are concentrated in areas of the brain which are rich in dopamine neuronal markers, which may suggest that they influence motor and reward processes. We tested this hypothesis by examining the effects of a 5-HT4 receptor antagonist, 8-amino-7-chloro-(N-butyl-4-piperidyl)methylbenzo-1,4-dioxan-5-car boxylate hydrochloride (SB-204070-A) on amphetamine- and nicotine-induced locomotor stimulation in intact rats. In rats with unilateral 6-hydroxydopamine-induced lesions of the ascending nigrostriatal dopaminergic projection, SB-204070-A was tested for its effects on amphetamine-induced rotation. SB-204070-A was also tested for its effects on rewarded behaviour maintained by intracranial self-stimulation. SB-204070-A did not alter behaviour under any of these conditions, suggesting a lack of involvement of the 5-HT4 receptor in motor and reward processes.     

Prevention of T cell anergy by signaling through the gamma c chain of the IL-2 receptor

When stimulated through their antigen receptor without requisite costimulation, T cells enter a state of antigen-specific unresponsiveness termed anergy. In this study, signaling through the common gamma chain of the interleukin-2 (IL-2), IL-4, and IL-7 receptors in the presence of antigen was found to be sufficient to prevent the induction of anergy. After culture with IL-2, IL-4, or IL-7, Jak3 kinase was tyrosine-phosphorylated, which correlated with the prevention of anergy. Therefore, a signal through the common gamma chain may regulate the decision of T cells to either clonally expand or enter a state of anergy.     

Octoxynol presence in bear-bile

The presence of octoxynol from dried bear-bile was examined. Octoxynol was coextracted when glycolipids by Folch-Suzuki partition method. Octoxynol formed mixed-micelles with glycosphingolipids. The glycolipids were purified by DEAE-Sephadex A-25 column chromatography. The fractions containing mixed micelles were obtained from linear gradient solvent of 0.05M-0.5M ammonium acetate in methanol. HPLC ( Bondapak-NH(2) - linked to a Bondapak-C(18) column) chromatogram showed five peaks. Two possible structures for the fourth peak fraction were proposed as (CH(3))(3)C-CH(2)-C(CH(3))(2)-C(6)H(4)-OR and (CH(3))(3)C-C(CH(3))(2)-CH(2)-C(6)H(4)-OR by NMR spectroscopy. The structure was further confirmed by electrospray tandem mass spectrometry (ESI MS/MS). The spectrum showed a protonated molecule at m/z 559 and three different series of ions with mass difference of 44 were detected in the MS/MS spectrum. Therefore, the structure of the fourth peak fraction from HPLC was confirmed as octoxynol, (CH(3))(3)C-CH(2)-C(CH(3))(2)-C(6)H(4)-(OCH(2)-CH(2))n-OH, based on mass spectrometry and NMR spectroscopy.