Bellerophon: a program to detect chimeric sequences in multiple sequence alignments

Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments.

The development of an early warning system to detect trends in illicit drug use in Australia: The illicit drug reporting-system

Appropriate ways to monitor the availability and use of illicit drugs were examined. Four methods were tested concurrently: (1) a quantitative survey of injecting drug users, (2) a qualitative key informant study of illicit drug users and professionals working in the drug field, (3) examination of existing sources of survey, health and law enforcement data and (4) an ethnographic study of a high risk group of illicit drug users. The first three methods were recommended for inclusion in an ongoing national monitoring system, enabling the collection of both quantitative and qualitative data on a range of illicit drugs in a relatively brief, quick and cost-effective manner. A degree of convergent validity was also noted among these methods, improving the degree of confidence in drug trends. The importance of injecting drug users as a sentinel population of illicit drug users was highlighted, along with optimal methods for qualitative research.

Using the 6dF galaxy redshift survey to detect gravitationally-lensed quasars

It is possible to detect gravitationally-lensed quasars spectroscopically if the spectra obtained during galaxy surveys are searched for the presence of quasar emission lines. The up-coming 6 degree Field (6dF) redshift survey on the United Kingdom Schmidt Telescope will involve obtaining similar to 10(5) spectra of near-infrared selected galaxies to a magnitude limit of K = 13. Applying previously developed techniques implies that at least one lens should be discovered in the 6dF survey, but that as many as ten could be found if quasars typically have B-J - K similar or equal to 8. In this model there could be up to fifty lensed quasars in the, sample, but most of them could only be detected by infrared spectroscopy.

The effects of normalisation on the ability of business end-users to detect data anomalies: An experimental evaluation

With the proliferation of relational database programs for PC's and other platforms, many business end-users are creating, maintaining, and querying their own databases. More importantly, business end-users use the output of these queries as the basis for operational, tactical, and strategic decisions. Inaccurate data reduce the expected quality of these decisions. Implementing various input validation controls, including higher levels of normalisation, can reduce the number of data anomalies entering the databases. Even in well-maintained databases, however, data anomalies will still accumulate. To improve the quality of data, databases can be queried periodically to locate and correct anomalies. This paper reports the results of two experiments that investigated the effects of different data structures on business end-users' abilities to detect data anomalies in a relational database. The results demonstrate that both unnormalised and higher levels of normalisation lower the effectiveness and efficiency of queries relative to the first normal form. First normal form databases appear to provide the most effective and efficient data structure for business end-users formulating queries to detect data anomalies.

Analysis of Piezoelectric sensor to detect flexural waves

The electromechanical transfer characteristics of adhesively bonded piezoelectric sensors are investigated. By the use of dynamic piezoelectricity theory, Mindlin plate theory for flexural wave propagation, and a multiple integral transform method, the frequency-response functions of piezoelectric sensors with and without backing materials are developed and the pressure-voltage transduction functions of the sensors calculated. The corresponding simulation results show that the sensitivity of the sensors is not only dependent on the sensors' inherent features, such as piezoelectric properties and geometry, but also on local characteristics of the tested structures and the admittance and impedance of the attached electrical circuit. It is also demonstrated that the simplified rigid mass sensor model can be used to analyze successfully the sensitivity of the sensor at low frequencies, but that the dynamic piezoelectric continuum model has to be used for higher frequencies, especially around the resonance frequency of the coupled sensor-structure vibration system.

Using postoperative cardiac troponin-I (cTi) levels to detect myocardial ischaemia in patients undergoing vascular surgery

Background, Cardiac complications occur commonly in vascular surgery patients. Diagnosis of cardiac complications is difficult because of the inaccuracies associated with traditional cardiac enzyme measurements. CTi, a highly sensitive and specific marker of myocardial injury, may be able to detect cardiac complications with greater ease and accuracy. Methods. The study prospectively examined 100 consecutive patients who underwent major vascular surgery between 6/7/98 and 31/12/98 at the Royal Brisbane Hospital. Daily measurements of cTi, creatine kinase (CK), creatine kinase MB (CKMB), CKMB index, renal function and haemoglobin were taken for three postoperative days. One postoperative electrocardiograph (ECC) was taken. An extensive cardiac history was taken. Intraoperative and postoperative events were recorded. Findings. There were 100 patients, 18 patients (18%) had a cTi elevation. On the basis of classical diagnostic criteria, 15 patients (15%) suffered one or more cardiac complication (either myocardial infarction, congestive cardiac failure, unstable angina or atrial fibrillation), One patient (1%) who had a cTi elevation died. CTI elevation occurred in five patients (5%) who were not diagnosed with cardiac complications based on traditional criteria. Despite not meeting specific diagnostic criteria for cardiac complications, all patients showed signs and symptoms that could be attributed to myocardial ischaemia, Every patient who developed congestive cardiac failure or atrial fibrillation had a cTi elevation. A Chi-square analysis revealed a significant association between cTi elevation and postoperative cardiac complications. Four variables contributed small but significant amounts of unique variance to the prediction of peak cTi on linear regression analysis. These were peak CKMB index, postoperative congestive cardiac failure, postoperative chest pain and postoperative cardiac complications. Conclusions. Routine cTi monitoring of postoperative vascular patients would be an effective and inexpensive way to detect patients with cardiac complications. The relationship between postoperative cTi elevation and significant coronary artery disease remains to be shown, (C) 2001 The international Society for Cardiovascular Surgery. Published by Elsevier Science Ltd. All rights reserved.

Field evaluation of a sentinel mosquito (Diptera : culicidae) trap system to detect Japanese encephalitis in remote Australia

Incursions of Japanese encephalitis (JE) virus into northern Queensland are currently monitored using sentinel pigs. However, the maintenance of these pigs is expensive, and because pigs are the major amplifying hosts of the virus, they may contribute to JE transmission. Therefore, we evaluated a mosquito-based detection system to potentially replace the sentinel pigs. Single, inactivated JE-infected Culex annulirostris Skuse and C. sitiens Wiedemann were placed into pools of uninfected mosquitoes that were housed in a Mosquito Magnet Pro (MM) trap set under wet season field conditions in Cairns, Queensland for 0, 7, or 14 d. JE viral RNA was detected (cycling threshold [CT] = 40) in 11/ 12, 10/14, and 2/5 pools containing 200, 1,000, and 5,000 mosquitoes, respectively, using a TaqMan real-time reverse transcription-polymerase chain reaction (RT-PCR). The ability to detect virus was not affected by the length of time pools were maintained under field conditions, although the CT score tended to increase with field exposure time. Furthermore, JE viral RNA was detected in three pools of 1,000 mosquitoes collected from Badu Island using a MM trap. These results indicated that a mosquito trap system employing self-powered traps, such as the MosquitoMagnet, and a real-time PCR system, could be used to monitor for JE in remote areas.

Application of mixture models to detect differentially expressed genes

An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local FDR (false discovery rate) is provided for each gene. An attractive feature of the mixture model approach is that it provides a framework for the estimation of the prior probability that a gene is not differentially expressed, and this probability can subsequently be used in forming a decision rule. The rule can also be formed to take the false negative rate into account. We apply this approach to a well-known publicly available data set on breast cancer, and discuss our findings with reference to other approaches.

Using mixture models to detect differentially expressed genes

An important and common problem in microarray experiments is the detection of genes that are differentially expressed in a given number of classes. As this problem concerns the selection of significant genes from a large pool of candidate genes, it needs to be carried out within the framework of multiple hypothesis testing. In this paper, we focus on the use of mixture models to handle the multiplicity issue. With this approach, a measure of the local false discovery rate is provided for each gene, and it can be implemented so that the implied global false discovery rate is bounded as with the Benjamini-Hochberg methodology based on tail areas. The latter procedure is too conservative, unless it is modified according to the prior probability that a gene is not differentially expressed. An attractive feature of the mixture model approach is that it provides a framework for the estimation of this probability and its subsequent use in forming a decision rule. The rule can also be formed to take the false negative rate into account.

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulae for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.

Do different surrogate methods detect lateral genetic transfer events of different relative ages?

Non-tree-based ('surrogate') methods have been used to identify instances of lateral genetic transfer in microbial genomes but agreement among predictions of different methods can be poor. It has been proposed that this disagreement arises because different surrogate methods are biased towards the detection of certain types of transfer events. This conjecture is supported by a rigorous phylogenetic analysis of 3776 proteins in Escherichia coli K12 MG1655 to map the ages of transfer events relative to one another.