Comparative evaluation of gene-set analysis methods

Background  

Multiple data-analytic methods have been proposed for evaluating gene-expression levels in specific biological pathways, assessing differential expression associated with a binary phenotype. Following Goeman and Bühlmann's recent review, we compared statistical performance of three methods, namely Global Test, ANCOVA Global Test, and SAM-GS, that test "self-contained null hypotheses" Via. subject sampling. The three methods were compared based on a simulation experiment and analyses of three real-world microarray datasets.     

Comparative evaluation of the embryotoxic effect of various antibiotics

A broad spectrum of antibacterial antibiotics used in treatment of purulent inflammatory diseases in pregnant women was studied experimentally. The antibiotics included oxacillin, fusidin, kanamycin, gentamicin, cefuroxime, cephalothin and tetracycline. The embryotoxic action of the antibiotics was investigated on embryos of rats cultivated in vitro. The mediated antenatal action of tetracycline and gentamicin was studied during various gestation terms before implantation (days 1 to 7), during organogenesis (days 8 to 14) and during fetal growth++ (days 14 to 20). Prior to the delivery the data on the intrauterine death, development of the fetoplacental unit and the presence of external and internal anomalies were considered. The placenta, liver and kidneys of the fetus were examined morphologically. It was shown that tetracycline and gentamicin had embryotoxic properties as evidenced by a higher intrauterine death rate and congenital anomalies in individual fetuses.     

Comparative evaluation of various control schemes for fed-batch fermentation

The crucial problem associated with control of fed-batch fermentation process is its time-varying characteristics. A successful controller should be able to deal with this feature in addition to the inherent nonlinear characteristics of the process. In this work, various schemes for controlling the glucose feed rate of fed-batch baker's yeast fermentation were evaluated. The controllers evaluated are fixed-gain proportional-integral (PI), scheduled-gain PI, adaptive neural network and hybrid neural network PI. The difference between the specific carbon dioxide evolution rate and oxygen uptake rate (Q_c-Q_o) was used as the controller variable. The evaluation was carried out by observing the performance of the controllers in dealing with setpoint tracking and disturbance rejection. The results confirm the unsatisfactory performance of the conventional controller where significant oscillation and offsets exist. Among the controllers considered, the hybrid neural network PI controller shows good performance.     

Comparative study of various methods for determining Vibrio cholerae toxigenicity

Testing of 138 Vibrio cholerae strains for gene determinants responsible for the production of cholera enterotoxin by the polymerase chain reaction (PCR) and gene probing using molecular CT-probe showed good correlation of the results of different methods and correlation of these data with studies of V. cholerae strain virulence in vivo and in hemolytic activity test. The advantages of PCR in rapid assessment of the toxigenicity and epidemic significance of V. cholerae strains are demonstrated.     

Comparative analysis of various root active promoters by evaluation of GUS expression in transgenic Arabidopsis

To prepare various root active promoters for expressing transgenes and prevent gene silencing caused by the repeated use of the same promoter, the expression characteristics of various root active promoters were comparatively evaluated using GUS as a reporter gene. The high-affinity potassium transporter (HKT1;1), the Shaker family potassium ion channel (SKOR), the Shaker family inward rectifying potassium channel (AKT1), the major facilitator superfamily protein (MFS1), and the senescence associated gene 14 (SAG14) promoter from Arabidopsis (Arabidopsis thaliana) were used, and for comparison, four additional constitutive or green tissue specific promoters in the expression vectors were also employed. As the Gateway cloning technology provided by Invitrogen can offer high efficiency and cloning reliability, and easy manipulation of fusion constructs in vitro, our expression vectors are based on binary (destination) vectors compatible with this cloning technique. These destination vectors are also advantageous for stable expression of the transgene, as the heat shock protein terminator is utilized. The AtHKT1;1, SKOR, AKT1, MFS1 and SAG14 promoters were all active in roots but showed slightly different tissue specificities: AtHKT1;1, SKOR, and MFS1 were dominantly active in vascular bundle tissue, while AtHKT1;1 and MFS1— but not SKOR, AKT1, and SAG14—were active in root tips. SKOR showed the strongest root-specificity, and SAG14 showed the highest activity among the five root active promoters. The activity of MFS was developmentally regulated. These destination vectors are now available to express multiple transgenes in transgenic plants, especially in roots.     

Comparative evaluation of different preservation methods for cyanobacterial strains

Maintaining pure cultures using preservation methods is of high importance for biotechnological purposes. However, preservation does not necessarily guarantee the genetic stability of these cultures. Therefore, preservation methods are currently needed to assure viability as well as genetic, physiological, and morphological integrity across storage periods. In this study, preservation of five isolates from the microalgae and cyanobacteria collection of the Plant Biology Department, Federal University of Viçosa, Minas Gerais, Brazil was investigated via monthly analyses of cell viability, biomass recovery, and contaminant concentrations over a period of 120 days. Lyophilization was adequate for both heterocystous cyanobacteria and other strains that were able to differentiate hormogones or to synthesize thick layers of exopolysaccharides. Lyophilization was also able to maintain cultures with low levels of contaminants. Dimethyl sulfoxide was relatively efficient, though some of the strains were susceptible to its cytotoxic effects. Our results demonstrated that cryopreservation with glycerol was the most efficient method. The ability to routinely preserve cyanobacterial strains reduces costs associated with maintaining large culture collections and reduces the risks of losing particular strains or species through contamination and genetic drift. The results obtained in this study are therefore discussed in the context of the efficiency of the methods and the current need to develop suitable methods for maintenance of cyanobacterial collections.     

Comparative evaluation of methods for detecting HBsAg in sera

The results of the analysis of 1209 serum samples, made with a view to detecting those containing HBsAg, are presented. This analysis was made by the radioimmunoassay (RIA) on a polyethylene film, by the standard RIA technique with the use of a diagnostic kit obtained from Abbott Laboratories (USA) and by the passive hemagglutination (PHA) test. The RIA film technique was found to have the sensitivity of about 2 ng/ml HBsAg, which is similar to the sensitivity of the kit from Abbott Laboratories and exceeds the sensitivity of the PHA test approximately 50-fold. The percentage of detected HBsAg-positive sera, yielded by analysis with the use of the RIA film technique and the standard RIA technique, is the same. The RIA technique make it possible to detect more positive sera than the PHA test by about 2.5%.     

Comparative evaluation of various analgesics in reducing pain in irreversible pulpitis

It is of interest to evaluate a single dose of three different analgesics compared to placebo in patients with symptomatic irreversible pulpitis. 120 patients were enrolled with severe pain in this prospective clinical trial. Patients were randomly divided into four groups after shaping and cleaning of root canals. This includes placebo, piroxicam 20mg, acetaminophen 325mg with aceclofenac sodium 100mg and acetaminophen 650mg. Participants were given a questionnaire to note the pain scores at various time intervals (6 hrs, 12 hrs, and 24 hrs) along with the respective tablets in a concealed manner. Data thus collected was analyzed for statistical significance. The severity of pain decreased in all the three interventional groups compared to the control group (p <0.01) at 6 hours. Zerodol-P and dolonex showed better pain reduction in comparison to the placebo and dolo 650 group (p <0.05) at 12 and 24 hours. Data shows that both zerodol-P and dolonex groups had similar effects at all time intervals. Thus, a single dose of analgesic such as Zerodol-P and Dolonex following shaping and cleaning of root canals relieved pain at all time intervals of the treatment. However, Dolo 650 performed better during the initial 6hrs after completion of the shaping and cleaning of root canals compared to the placebo.