Using Evolutionary Conserved Modules in Gene Networks as a Strategy to Leverage High Throughput Gene Expression Queries

Background: Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seednetwork of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development. Methodology/Principal Findings: Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of correlated mouse genes is an effective tool for querying datasets and provides a context to generate hypotheses. Our query identified 46 genes correlated with our extracted seed-network members. Approximately 54% of these candidates had been previously linked to the developing brain and 33% had been previously linked to the developing retina. Five of six candidate genes investigated further were validated by experiments examining spatial and temporal protein expression in the developing retina. Conclusions/Significance: We present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse. Future implementation of this strategy will be useful to determine the extent of network conservation, not just gene conservation, between species and will facilitate the use of prior biological knowledge to develop rational systems-based hypotheses

Uptake of postplacental intrauterine device placement at cesarean deliveryAJOG Global Reports at a Glance

BACKGROUND: Several studies have investigated the effectiveness of intrauterine device placement at cesarean delivery as a contraceptive method. However, national-level use and outcomes of a postplacental intrauterine device at cesarean delivery are currently understudied in the United States. OBJECTIVE: This study aimed to examine the trends, characteristics, and outcomes of patients who received a postplacental intrauterine device at cesarean delivery. STUDY DESIGN: This retrospective cohort study used the National Inpatient Sample. The study cohort included patients who underwent cesarean delivery from October 2015 to December 2018. The exclusion criteria included hemorrhage, chorioamnionitis, uterine anomaly, hysterectomy, and permanent surgical sterilization. Eligible cases were grouped on the basis of the use of a postplacental intrauterine device at cesarean delivery. The primary outcome measures were temporal trends and characteristics associated with the use of a postplacental intrauterine device at cesarean delivery, assessed using the generalized estimating equation model in multivariable analysis. The secondary outcome measure was perioperative morbidity (leukocytosis, endometritis, myometritis, and sepsis). Propensity score matching was used to balance the baseline characteristics. RESULTS: Among 2,983,978 patients who met the inclusion criteria, 10,145 patients (0.3%) received a postplacental intrauterine device at cesarean delivery. The use of a postplacental intrauterine device increased from 0.1% in the fourth quarter of 2015 to 0.6% in the fourth quarter of 2018 (P<.001). In a multivariable analysis, the use of a postplacental intrauterine device increased by 14% every quarter-year (adjusted odds ratio, 1.14; 95% confidence interval, 1.13–1.15). In addition, (1) patient characteristics of young age, non-White race, obesity, tobacco use, lowest quartile median household income, and insured with Medicaid; (2) hospital characteristics of large bed capacity and urban teaching setting in Northeast region; and (3) pregnancy characteristics of early gestational age at cesarean delivery, hypertensive disease, previous cesarean delivery, multifetal pregnancy, grand multiparity, placenta previa, and nonelective cesarean delivery represented the independent characteristics associated with the use of a postplacental intrauterine device (all P<.05). A regression tree model identified 35 discrete patterns of the use of a postplacental intrauterine device based on 8 factors (time, race or ethnicity, primary expected payer, obesity, hospital bed capacity, hospital teaching status, hospital region, and previous cesarean delivery). There were 9 patterns, representing 8.8% of the study population, exhibiting a use rate of ≥1.0%, whereas there were 7 patterns, representing 16.0% of the study population, exhibiting no use of a postplacental intrauterine device (absolute rate difference from the highest group to the lowest group, 4.7%). In a propensity score–matched model, postplacental intrauterine device placement at cesarean delivery was not associated with increased risk of measured morbidity (any, 1.8% vs 1.7%; odds ratio, 1.06; 95% confidence interval, 0.66–1.69; P=.812), including postpartum endometritis (1.2% vs 1.0%; odds ratio, 1.19; 95% confidence interval, 0.67–2.14; P=.554). CONCLUSION: The use of a postplacental intrauterine device at cesarean delivery increased significantly in recent years in the United States