Modeling gene expression regulatory networks with the sparse vector autoregressive model

Abstract Background To understand the molecular mechanisms underlying important biological processes, a detailed description of the gene products networks involved is required. In order to define and understand such molecular networks, some statistical methods are proposed in the literature to estimate gene regulatory networks from time-series microarray data. However, several problems still need to be overcome. Firstly, information flow need to be inferred, in addition to the correlation between genes. Secondly, we usually try to identify large networks from a large number of genes (parameters) originating from a smaller number of microarray experiments (samples). Due to this situation, which is rather frequent in Bioinformatics, it is difficult to perform statistical tests using methods that model large gene-gene networks. In addition, most of the models are based on dimension reduction using clustering techniques, therefore, the resulting network is not a gene-gene network but a module-module network. Here, we present the Sparse Vector Autoregressive model as a solution to these problems. Results We have applied the Sparse Vector Autoregressive model to estimate gene regulatory networks based on gene expression profiles obtained from time-series microarray experiments. Through extensive simulations, by applying the SVAR method to artificial regulatory networks, we show that SVAR can infer true positive edges even under conditions in which the number of samples is smaller than the number of genes. Moreover, it is possible to control for false positives, a significant advantage when compared to other methods described in the literature, which are based on ranks or score functions. By applying SVAR to actual HeLa cell cycle gene expression data, we were able to identify well known transcription factor targets. Conclusion The proposed SVAR method is able to model gene regulatory networks in frequent situations in which the number of samples is lower than the number of genes, making it possible to naturally infer partial Granger causalities without any a priori information. In addition, we present a statistical test to control the false discovery rate, which was not previously possible using other gene regulatory network models.

Objective reduction in adenoid tissue after mometasone furoate treatment

Objective: Chronic rhinitis and adenoid hypertrophy are the main causes of nasal obstruction in children and proper treatment of these factors seem essential for controlling nasal obstructive symptoms. This study aims to evaluate the effects of topical mometasone treatment on symptoms and size of adenoid tissue in children with complaints of nasal obstruction and to compare this approach to continuous nasal saline douching plus environmental control alone. Methods: Fifty-one children with nasal obstructive complaints were submitted to a semi-structured clinical questionnaire on nasal symptoms, prick test and nasoendoscopy. Nasoendoscopic images were digitalized, and both adenoid and nasopharyngeal areas were measured in pixels. The relation adenoid/nasopharyngeal area was calculated. Patients were subsequently re-evaluated in two different periods: following 40 days of treatment with nasal douching and environmental prophylaxis alone; and after an subsequent 40 day-period, when topical mometasone furoate (total dose: 100 mu g/day) was superposed. Results: Nasal symptoms and snoring significantly improved after nasal douching, and an additional gain was observed when mometasone furoate was included to treatment. Saline douching did not influence the adenoid area, whereas a significant reduction on adenoid tonsil was observed after 40 days of mometasone treatment (P < 0.0001). Conclusion: Nasal saline douching significantly improved nasal symptoms without interfering in adenoid dimension. In contrast, mometasone furoate significantly reduced adenoid tissue, and led to a supplementary improvement of nasal symptoms. (C) 2012 Elsevier Ireland Ltd. All rights reserved.

Effect of rapid maxillary expansion on the dimension of the nasal cavity and on facial morphology assessed by acoustic rhinometry and rhinomanometry

OBJECTIVE: To assess the effects of rapid maxillary expansion on facial morphology and on nasal cavity dimensions of mouth breathing children by acoustic rhinometry and computed rhinomanometry. METHODS: Cohort; 29 mouth breathing children with posterior crossbite were evaluated. Orthodontic and otorhinolaryngologic documentation were performed at three different times, i.e., before expansion, immediately after and 90 days following expansion. RESULTS: The expansion was accompanied by an increase of the maxillary and nasal bone transversal width. However, there were no significant differences in relation to mucosal area of the nose. Acoustic rhinometry showed no difference in the minimal cross-sectional area at the level of the valve and inferior turbinate between the periods analyzed, although rhinomanometry showed a statistically significant reduction in nasal resistance right after expansion, but were similar to pre-treatment values 90 days after expansion. CONCLUSION: The maxillary expansion increased the maxilla and nasal bony area, but was inefficient to increase the nasal mucosal area, and may lessen the nasal resistance, although there was no difference in nasal geometry. Significance: Nasal bony expansion is followed by a mucosal compensation.