Using expression arrays for copy number detection: an example from E. coli.

BACKGROUND: The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable. RESULTS: We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection. We applied our approach to identify deleted and amplified regions in E. coli mutants obtained after prolonged starvation. CONCLUSION: The availability of Affymetrix expression chips for a wide variety of organisms makes the proposed array CGH methodology useful more generally.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The Reinforcing Therapist Performance (RTP) experiment: Study protocol for a cluster randomized trial

<p>Abstract</p> <p>Background</p> <p>Rewarding provider performance has been recommended by the Institute of Medicine as an approach to improve the quality of treatment, yet little empirical research currently exists that has examined the effectiveness and cost-effectiveness of such approaches. The aim of this study is to test the effectiveness and cost-effectiveness of providing monetary incentives directly to therapists as a method to improve substance abuse treatment service delivery and subsequent client treatment outcomes.</p> <p>Design</p> <p>Using a cluster randomized design, substance abuse treatment therapists from across 29 sites were assigned by site to either an implementation as usual (IAU) or pay-for-performance (P4P) condition.</p> <p>Participants</p> <p>Substance abuse treatment therapists participating in a large dissemination and implementation initiative funded by the Center for Substance Abuse Treatment.</p> <p>Intervention</p> <p>Therapists in both conditions received comprehensive training and ongoing monitoring, coaching, and feedback. However, those in the P4P condition also were given the opportunity to earn monetary incentives for achieving two sets of measurable behaviors related to quality implementation of the treatment.</p> <p>Outcomes</p> <p>Effectiveness outcomes will focus on the impact of the monetary incentives to increase the proportion of adolescents who receive a targeted threshold level of treatment, months that therapists demonstrate monthly competency, and adolescents who are in recovery following treatment. Similarly, cost-effectiveness outcomes will focus on cost per adolescent receiving targeted threshold level of treatment, cost per month of demonstrated competence, and cost per adolescent in recovery.</p> <p>Trial Registration</p> <p>Trial Registration Number: NCT01016704</p

Using expression arrays for copy number detection: an example from E. coli

Abstract Background The sequencing of many genomes and tiling arrays consisting of millions of DNA segments spanning entire genomes have made high-resolution copy number analysis possible. Microarray-based comparative genomic hybridization (array CGH) has enabled the high-resolution detection of DNA copy number aberrations. While many of the methods and algorithms developed for the analysis microarrays have focused on expression analysis, the same technology can be used to detect genetic alterations, using for example standard commercial Affymetrix arrays. Due to the nature of the resultant data, standard techniques for processing GeneChip expression experiments are inapplicable. Results We have developed a robust and flexible methodology for high-resolution analysis of DNA copy number of whole genomes, using Affymetrix high-density expression oligonucleotide microarrays. Copy number is obtained from fluorescence signals after processing with novel normalization, spatial artifact correction, data transformation and deletion/duplication detection. We applied our approach to identify deleted and amplified regions in E. coli mutants obtained after prolonged starvation. Conclusion The availability of Affymetrix expression chips for a wide variety of organisms makes the proposed array CGH methodology useful more generally.</p

Using expression arrays for copy number detection: an example from E. coli-6

<p><b>Copyright information:</b></p><p>Taken from "Using expression arrays for copy number detection: an example from E. coli"</p><p>http://www.biomedcentral.com/1471-2105/8/203</p><p>BMC Bioinformatics 2007;8():203-203.</p><p>Published online 14 Jun 2007</p><p>PMCID:PMC1914360.</p><p></p> panel shows signal before transformation (raw data), lower panel shows signal after transformation (grey dots) and result of fit to the HMM (black solid line)

Using expression arrays for copy number detection: an example from E. coli-0

<p><b>Copyright information:</b></p><p>Taken from "Using expression arrays for copy number detection: an example from E. coli"</p><p>http://www.biomedcentral.com/1471-2105/8/203</p><p>BMC Bioinformatics 2007;8():203-203.</p><p>Published online 14 Jun 2007</p><p>PMCID:PMC1914360.</p><p></p

Response to reduced nicotine content cigarettes among smokers with chronic health conditions

Individuals with chronic health conditions persist in smoking despite the presence of smoking-related illness. The aim of this study was to examine whether chronic health conditions moderate response to reduced nicotine content cigarettes (0.4, 2.4, 5.2, 15.8 mg/g of tobacco). This is a secondary analysis of a controlled clinical laboratory study that examined the acute effects of cigarettes varying in nicotine content among individuals especially vulnerable to smoking and tobacco dependence. Participants in the present study were categorized as having 0, 1–2, or ≥3 smoking-related chronic health conditions (i.e., chronic condition severity, CCS). Repeated-measures analysis of variance was used to examine whether CCS moderated response to cigarettes across measures of addiction potential (i.e., concurrent choice testing between nicotine dose pairs, Cigarette Purchase Task (CPT) performance, positive subjective effects), tobacco withdrawal, cigarette craving, and smoking topography. No main effects of CCS or interactions of CCS and nicotine dose were observed for concurrent choice testing, positive subjective effects, tobacco withdrawal, or smoking topography. Main effects of CCS were noted on the CPT with greater CCS being associated with less persistent demand. There was an interaction of CCS and nicotine dose on Factor 1 of the Questionnaire on Smoking Urges with the effects of dose significant only among those with 1–2 chronic conditions. Overall, we see minimal evidence that chronic condition severity affects response to reduced nicotine content cigarettes. A policy that reduces the nicotine content of cigarettes to minimally addictive levels may benefit smokers already experiencing smoking-related chronic conditions. Keywords: Reduced nicotine content cigarettes, Addiction potential, Abuse liability, Chronic health conditions, Medical comorbidities, Chronic conditions, Vulnerable population

Is exposure to an effective contingency management intervention associated with more positive provider beliefs?

This study empirically examined opinions of treatment providers regarding contingency management (CM) programs while controlling for experience with a specific efficacious CM program. In addition to empirically describing provider opinions, we examined whether the opinions of providers at the sites that implemented the CM program were more positive than those of matched providers at sites that did not implement it. Participants from 7 CM treatment sites (n = 76) and 7 matched nonparticipating sites (n = 69) within the same nodes of the National Institute of Drug Abuse Clinical Trials Network completed the Provider Survey of Incentives (PSI), which assesses positive and negative beliefs about incentive programs. An intent-to-treat analysis found no differences in the PSI summary scores of providers in CM program versus matched sites, but correcting for experience with tangible incentives showed significant differences, with providers from CM sites reporting more positive opinions than those from matched sites. Some differences were found in opinions regarding costs of incentives, and these generally indicated that participants from CM sites were more likely to see the costs as worthwhile. The results from the study suggest that exposing community treatment providers to incentive programs may itself be an effective strategy in prompting the dissemination of CM interventions