Random matrix analysis of localization properties of Gene co-expression network

We analyze gene co-expression network under the random matrix theory framework. The nearest neighbor spacing distribution of the adjacency matrix of this network follows Gaussian orthogonal statistics of random matrix theory (RMT). Spectral rigidity test follows random matrix prediction for a certain range, and deviates after wards. Eigenvector analysis of the network using inverse participation ratio (IPR) suggests that the statistics of bulk of the eigenvalues of network is consistent with those of the real symmetric random matrix, whereas few eigenvalues are localized. Based on these IPR calculations, we can divide eigenvalues in three sets; (A) The non-degenerate part that follows RMT. (B) The non-degenerate part, at both ends and at intermediate eigenvalues, which deviate from RMT and expected to contain information about {\it important nodes} in the network. (C) The degenerate part with $zero$ eigenvalue, which fluctuates around RMT predicted value. We identify nodes corresponding to the dominant modes of the corresponding eigenvectors and analyze their structural properties

Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism

We investigate the ability of algorithms developed for reverse engineering of transcriptional regulatory networks to reconstruct metabolic networks from high-throughput metabolite profiling data. For this, we generate synthetic metabolic profiles for benchmarking purposes based on a well-established model for red blood cell metabolism. A variety of data sets is generated, accounting for different properties of real metabolic networks, such as experimental noise, metabolite correlations, and temporal dynamics. These data sets are made available online. We apply ARACNE, a mainstream transcriptional networks reverse engineering algorithm, to these data sets and observe performance comparable to that obtained in the transcriptional domain, for which the algorithm was originally designed.Comment: 14 pages, 3 figures. Presented at the DIMACS Workshop on Dialogue on Reverse Engineering Assessment and Methods (DREAM), Sep 200

Successful network inference from time-series data using Mutual Information Rate

This work uses an information-based methodology to infer the connectivity of complex systems from observed time-series data. We first derive analytically an expression for the Mutual Information Rate (MIR), namely, the amount of information exchanged per unit of time, that can be used to estimate the MIR between two finite-length low-resolution noisy time-series, and then apply it after a proper normalization for the identification of the connectivity structure of small networks of interacting dynamical systems. In particular, we show that our methodology successfully infers the connectivity for heterogeneous networks, different time-series lengths or coupling strengths, and even in the presence of additive noise. Finally, we show that our methodology based on MIR successfully infers the connectivity of networks composed of nodes with different time-scale dynamics, where inference based on Mutual Information fails

Parental Feeding Practices in Mexican American Families: Initial Test of an Expanded Measure

Background: Although obesity rates are high among Latino children, relatively few studies of parental feeding practices have examined Latino families as a separate group. Culturally-based approaches to measurement development can begin to identify parental feeding practices in specific cultural groups. This study used qualitative and quantitative methods to develop and test the Parental Feeding Practices (PFP) Questionnaire for use with Mexican American parents. Items reflected both parent’s use of control over child eating and child-centered feeding practices. Methods: In the qualitative phase of the research, 35 Latino parents participated in focus groups. Items for the PFP were developed from focus group discussions, as well as adapted from existing parent feeding practice measures. Cognitive interviews were conducted with 37 adults to evaluate items. In the quantitative phase, mothers and fathers of 174 Mexican American children ages 8–10 completed the PFP and provided demographic information. Anthropometric measures were obtained on family members. Results: Confirmatory factor analyses identified four parental feeding practice dimensions: positive involvement in child eating, pressure to eat, use of food to control behavior, and restriction of amount of food. Factorial invariance modeling suggested equivalent factor meaning and item response scaling across mothers and fathers. Mothers and fathers differed somewhat in their use of feeding practices. All four feeding practices were related to child body mass index (BMI) percentiles, for one or both parents. Mothers reporting more positive involvement had children with lower BMI percentiles. Parents using more pressure to eat had children with lower BMI percentiles, while parents using more restriction had children with higher BMI percentiles. Fathers using food to control behavior had children with lower BMI percentiles. Conclusions: Results indicate good initial validity and reliability for the PFP. It can be used to increase understanding of parental feeding practices, children’s eating, and obesity among Mexican Americans, a population at high risk of obesity

Lower cerebrospinal fluid/plasma fibroblast growth factor 21 (FGF21) ratios and placental FGF21 production in gestational diabetes

Objectives: Circulating Fibroblast Growth Factor 21 (FGF21) levels are increased in insulin resistant states such as obesity, type 2 diabetes mellitus and gestational diabetes mellitus (GDM). In addition, GDM is associated with serious maternal and fetal complications. We sought to study human cerebrospinal fluid (CSF) and corresponding circulating FGF21 levels in women with gestational diabetes mellitus (GDM) and in age and BMI matched control subjects. We also assessed FGF21 secretion from GDM and control human placental explants. Design: CSF and corresponding plasma FGF21 levels of 24 women were measured by ELISA [12 GDM (age: 26–47 years, BMI: 24.3–36.3 kg/m2) and 12 controls (age: 22–40 years, BMI: 30.1–37.0 kg/m2)]. FGF21 levels in conditioned media were secretion from GDM and control human placental explants were also measured by ELISA. Results: Glucose, HOMA-IR and circulating NEFA levels were significantly higher in women with GDM compared to control subjects. Plasma FGF21 levels were significantly higher in women with GDM compared to control subjects [234.3 (150.2–352.7) vs. 115.5 (60.5–188.7) pg/ml; P<0.05]. However, there was no significant difference in CSF FGF21 levels in women with GDM compared to control subjects. Interestingly, CSF/Plasma FGF21 ratio was significantly lower in women with GDM compared to control subjects [0.4 (0.3–0.6) vs. 0.8 (0.5–1.6); P<0.05]. FGF21 secretion into conditioned media was significantly lower in human placental explants from women with GDM compared to control subjects (P<0.05). Conclusions: The central actions of FGF21 in GDM subjects maybe pivotal in the pathogenesis of insulin resistance in GDM subjects. The significance of FGF21 produced by the placenta remains uncharted and maybe crucial in our understanding of the patho-physiology of GDM and its associated maternal and fetal complications. Future research should seek to elucidate these points

Annotation and query of tissue microarray data using the NCI Thesaurus

<p>Abstract</p> <p>Background</p> <p>The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, specifying the pathological diagnoses for each sample. These text annotations are not structured according to any ontology, making future integration of this resource with other biological and clinical data difficult.</p> <p>Results</p> <p>We developed methods to map these annotations to the NCI thesaurus. Using the NCI-T we can effectively represent annotations for about 86% of the samples. We demonstrate how this mapping enables ontology driven integration and querying of tissue microarray data. We have deployed the mapping and ontology driven querying tools at the TMAD site for general use.</p> <p>Conclusion</p> <p>We have demonstrated that we can effectively map the diagnosis-related terms describing a sample in TMAD to the NCI-T. The NCI thesaurus terms have a wide coverage and provide terms for about 86% of the samples. In our opinion the NCI thesaurus can facilitate integration of this resource with other biological data.</p

Parental feeding practices and child weight status in Mexican American families: a longitudinal analysis

Parental feeding practices are thought to influence children\u27s weight status, through children\u27s eating behavior and nutritional intake. However, because most studies have been cross-sectional, the direction of influence is unclear. Moreover, although obesity rates are high among Latino children, few studies of parental feeding practices have focused on this population. This 2-year longitudinal study examined mutual influences over time between parental feeding practices and children\u27s weight status, in Mexican American families with children 18 years old at baseline. Mothers (n = 322) and fathers (n = 182) reported on their feeding practices at baseline, 1-year follow-up, and 2-year follow-up. Weight status, defined by waist-height ratio (WHtR) and body mass index (BMI), was ascertained at all assessments. Cross-lagged panel models were used to examine the mutual influences of parental feeding practices and child weight status over time, controlling for covariates. Both mothers\u27 and fathers\u27 restriction of food predicted higher subsequent child weight status at Year 1, and for fathers this effect was also found at Year 2. Mothers\u27 and fathers\u27 pressure to eat predicted lower weight status among boys, but not girls, at Year 1. Child weight status also predicted some parental feeding practices: boys\u27 heavier weight predicted mothers\u27 less pressure to eat at Year 1, less use of food to control behavior at Year 2, and greater restriction at Year 2; and girls\u27 heavier weight at Year 1 predicted fathers\u27 less pressure to eat and less positive involvement in child eating at Year 2. This study provides longitudinal evidence that some parental feeding practices influence Mexican American children\u27s weight status, and that children\u27s weight status also influences some parental feeding practices. Feeding practices of both mothers and fathers were related to children\u27s weight status, underscoring the importance of including fathers in research on parental feeding practices and child obesity