Enhanced microarray performance using low complexity representations of the transcriptome

Low abundance mRNAs are more difficult to examine using microarrays than high abundance mRNAs due to the effect of concentration on hybridization kinetics and signal-to-noise ratios. This report describes the use of low complexity representations (LCRs) of mRNA as the targets for cDNA microarrays. Individual sequences in LCRs are more highly represented than in the mRNA populations from which they are derived, leading to favorable hybridization kinetics. LCR targets permit the measurement of abundance changes that are difficult to measure using oligo(dT) priming for target synthesis. An oligo(dT)-primed target and three LCRs detect twice as many differentially regulated genes as could be detected by the oligo(dT)-primed target alone, in an experiment in which serum-starved fibroblasts responded to the reintroduction of serum. Thus, this target preparation strategy considerably increases the sensitivity of cDNA microarrays

Examining the influence of drop-outs in a follow-up of maintained opiate users.

INTRODUCTION: In most longitudinal studies of problem opiate users, drop-outs are frequent, but not taken into account. However, missing data can induce important bias in parameters estimates. OBJECTIVE: The aim of this study was to examine the influence of drop-outs in the statistical analysis of a follow-up of opiate users in maintenance treatment. METHODS: Participants were 519 patients who had sought maintenance treatment between 1994 and 2001. Drug use was studied using the drug composite score of the Addiction Severity Index. A classical data analysis (linear mixed effects model for repeated measurements) was compared with a selection model, which consists, in this case, of a joint modelling of the score and of the drop-out probability in order to reduce bias induced by drop-outs. RESULTS: At 18 months, 38% of the patients were available for evaluation. Drop-outs were associated with low drug use and were informative. Each model showed that the score decreased over time and that it was associated with psychiatric problems. Unlike the classical method, the joint model showed no significant association between the score and age or treatment setting. CONCLUSIONS: These results show the importance of accounting for informative drop-outs in data analysis before drawing conclusions from such studies

complexity representations

microarray performance using lo

Anthropometric data and parent’s level at 2 years of age.

<p>SD: Standard deviation</p><p>Anthropometric data and parent’s level at 2 years of age.</p

Comparison in Outcomes at Two-Years of Age of Very Preterm Infants Born in 2000, 2005 and 2010

<div><p>Objective</p><p>To investigate alteration in 2-year neurological/behavioral outcomes of very preterm infants born in a French level three neonatal intensive care unit.</p><p>Methods</p><p>We conducted a prospective, comparative study of very preterm infants born before 33 weeks’ gestation at 5-year intervals in 2000, 2005 and 2010 at Rouen University Hospital. Neonatal mortality/morbidities, ante- and neonatal treatments, and at age 2 years motor, cognitive and behavioral data were collected by standardized questionnaires.</p><p>Results</p><p>We included 536 very preterm infants. Follow-up rates at two years old were 78% in 2000, 93% in 2005 and 92% in 2010 respectively. No difference in gestational age, birthweight, neonatal mortality/morbidities was observed except a decrease in low grade subependymal/intraventricular hemorrhages. Care modifications concerned use of antenatal magnesium sulfate, breast-feeding and post-natal corticosteroid therapy. Significant improvement in motor outcome and dramatic decrease in cerebral palsy rates (12% in 2000, 6% in 2005, 1% in 2010, <i>p</i><0.001) were observed, as were improvements in feeding behavior. Although a non significant difference to better psychosocial behavior was reported, there was no difference in cognitive outcome.</p><p>Conclusions</p><p>Improvement in neuromotor outcome and behavior was reported. This could be due to multiple modifications in care: including administration of magnesium sulfate to women at risk of preterm birth, increase in breast-feeding, decrease in low grade subependymal/intraventricular hemorrhages, and decrease in post-natal corticosteroid therapy, all of which require further investigation in other studies. Extended follow-up until school age is mandatory for better detection of cognitive, learning and behavioral disorders.</p></div

Comprehensive analysis of a large genomic sequence at the putative B-cell chronic lymphocytic leukaemia (B-CLL) tumour suppresser gene locus

In many haematological diseases, and more particularly in B-cell chronic lymphocytic leukaemia (B-CLL), the existence of a tumour suppressor gene located within the frequently deleted region 13q14.3, has been put forward. A wide candidate region spanning from marker D13S273 to D13S25 has been proposed and an extensive physical map has been constructed by several teams. In this study, we sequenced a minimal core deleted region that we have previously defined and annotated it with flanking available public sequences. Our analysis shows that this region is gene-poor. Furthermore, our work allowed us to identify new alternative transcripts, spanning core regions, of the previously defined candidate genes DLEU1 and DLEU2. Since their putative involvement in B-CLL was controversial, our present study provide support for reconsidering the DLEU1 and DLEU2 genes as B-CLL candidate genes, with a new definition of their organisation and context. © 2001 Elsevier Science B.V. All rights reserved

Perinatal characteristics of 2000, 2005 and 2010 cohorts.

<p># Persistence difference between 2005 and 2010,</p><p>† Persistence difference between 2000 and 2010,</p><p>■ Persistence difference between 2000 and 2005SD: Standard deviation, PDA: patent ductus arteriosus</p><p>Perinatal characteristics of 2000, 2005 and 2010 cohorts.</p

Flow chart of the study.

<p>Flow chart of the study.</p

Outcomes at 2 years of age in the survivors of 2000, 2005 and 2010 cohorts.

<p>† Persistance difference between 2000 and 2010,</p><p>■ Persistance difference between 2000 and 2005</p><p>Outcomes at 2 years of age in the survivors of 2000, 2005 and 2010 cohorts.</p