http://hdl.handle.net/2144/1002 2013-06-19T12:13:50Z http://hdl.handle.net/2144/3149 An Obesity Dietary Quality Index Predicts Abdominal Obesity in Women: Potential Opportunity for New Prevention and Treatment Paradigms Wolongevicz, Dolores M.; Zhu, Lei; Pencina, Michael J.; Kimokoti, Ruth W.; Newby, P. K.; D'Agostino, Ralph B.; Millen, Barbara E. Background. Links between dietary quality and abdominal obesity are poorly understood. Objective. To examine the association between an obesity-specific dietary quality index and abdominal obesity risk in women. Methods. Over 12 years, we followed 288 Framingham Offspring/Spouse Study women, aged 30–69 years, without metabolic syndrome risk factors, cardiovascular disease, cancer, or diabetes at baseline. An 11-nutrient obesity-specific dietary quality index was derived using mean ranks of nutrient intakes from 3-day dietary records. Abdominal obesity (waist circumference >88cm) was assessed during follow-up. Results. Using multiple logistic regression, women with poorer dietary quality were more likely to develop abdominal obesity compared to those with higher dietary quality (OR 1.87; 95% CI, 1.01, 3.47; P for trend = .048) independent of age, physical activity, smoking, and menopausal status. Conclusions. An obesity-specific dietary quality index predicted abdominal obesity in women, suggesting targets for dietary quality assessment, intervention, and treatment to address abdominal adiposity. 2010-01-05T00:00:00Z http://hdl.handle.net/2144/3150 Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex Kramer, Mark A.; Roopun, Anita K.; Carracedo, Lucy M.; Traub, Roger D.; Whittington, Miles A.; Kopell, Nancy J. Rhythmic voltage oscillations resulting from the summed activity of neuronal populations occur in many nervous systems. Contemporary observations suggest that coexistent oscillations interact and, in time, may switch in dominance. We recently reported an example of these interactions recorded from in vitro preparations of rat somatosensory cortex. We found that following an initial interval of coexistent gamma (∼25 ms period) and beta2 (∼40 ms period) rhythms in the superficial and deep cortical layers, respectively, a transition to a synchronous beta1 (∼65 ms period) rhythm in all cortical layers occurred. We proposed that the switch to beta1 activity resulted from the novel mechanism of period concatenation of the faster rhythms: gamma period (25 ms)+beta2 period (40 ms) = beta1 period (65 ms). In this article, we investigate in greater detail the fundamental mechanisms of the beta1 rhythm. To do so we describe additional in vitro experiments that constrain a biologically realistic, yet simplified, computational model of the activity. We use the model to suggest that the dynamic building blocks (or motifs) of the gamma and beta2 rhythms combine to produce a beta1 oscillation that exhibits cross-frequency interactions. Through the combined approach of in vitro experiments and mathematical modeling we isolate the specific components that promote or destroy each rhythm. We propose that mechanisms vital to establishing the beta1 oscillation include strengthened connections between a population of deep layer intrinsically bursting cells and a transition from antidromic to orthodromic spike generation in these cells. We conclude that neural activity in the superficial and deep cortical layers may temporally combine to generate a slower oscillation. Author SummarySince the late 19th century, rhythmic electrical activity has been observed in the mammalian brain. Although subject to intense scrutiny, only a handful of these rhythms are understood in terms of the biophysical elements that produce the oscillations. Even less understood are the mechanisms that underlie interactions between rhythms; how do rhythms of different frequencies coexist and affect one another in the dynamic environment of the brain? In this article, we consider a recent proposal for a novel mechanism of cortical rhythm generation: period concatenation, in which the periods of faster rhythms sum to produce a slower oscillation. To model this phenomenon, we implement simple—yet biophysical—computational models of the individual neurons that produce the brain's voltage activity. We utilize established models for the faster rhythms, and unite these in a particular way to generate a slower oscillation. Through the combined approach of experimental recordings (from thin sections of rat cortex) and mathematical modeling, we identify the cell types, synaptic connections, and ionic currents involved in rhythm generation through period concatenation. In this way the brain may generate new activity through the combination of preexisting elements. 2008-09-05T00:00:00Z http://hdl.handle.net/2144/3151 Machine Learning for Regulatory Analysis and Transcription Factor Target Prediction in Yeast Holloway, Dustin T.; Kon, Mark; DeLisi, Charles High throughput technologies, including array-based chromatin immunoprecipitation, have rapidly increased our knowledge of transcriptional maps-the identity and location of regulatory binding sites within genomes. Still, the full identification of sites, even in lower eukaryotes, remains largely incomplete. In this paper we develop a supervised learning approach to site identification using support vector machines (SVMs) to combine 26 different data types. A comparison with the standard approach to site identification using position specific scoring matrices (PSSMs) for a set of 104 Saccharomyces cerevisiae regulators indicates that our SVM-based target classification is more sensitive (73 vs. 20%) when specificity and positive predictive value are the same. We have applied our SVM classifier for each transcriptional regulator to all promoters in the yeast genome to obtain thousands of new targets, which are currently being analyzed and refined to limit the risk of classifier over-fitting. For the purpose of illustration we discuss several results, including biochemical pathway predictions for Gcn4 and Rap1. For both transcription factors SVM predictions match well with the known biology of control mechanisms, and possible new roles for these factors are suggested, such as a function for Rap1 in regulating fermentative growth. We also examine the promoter melting temperature curves for the targets of YJR060W, and show that targets of this TF have potentially unique physical properties which distinguish them from other genes. The SVM output automatically provides the means to rank dataset features to identify important biological elements. We use this property to rank classifying k-mers, thereby reconstructing known binding sites for several TFs, and to rank expression experiments, determining the conditions under which Fhl1, the factor responsible for expression of ribosomal protein genes, is active. We can see that targets of Fhl1 are differentially expressed in the chosen conditions as compared to the expression of average and negative set genes. SVM-based classifiers provide a robust framework for analysis of regulatory networks. Processing of classifier outputs can provide high quality predictions and biological insight into functions of particular transcription factors. Future work on this method will focus on increasing the accuracy and quality of predictions using feature reduction and clustering strategies. Since predictions have been made on only 104 TFs in yeast, new classifiers will be built for the remaining 100 factors which have available binding data. ELECTRONIC SUPPLEMENTARY MATERIAL. Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s11693-006-9003-3 and is accessible for authorized users. 2006-10-31T00:00:00Z http://hdl.handle.net/2144/3145 The impact of complex informative missingness on the validity of the transmission/disequilibrium test (TDT) Guo, Chao-Yu The transmission/disequilibrium test was introduced to test for linkage and association between a marker and a putative disease locus using case-parent triads. Several extensions have been proposed to accommodate incomplete triads. Some strategies assumed that parental genotypes were missing completely at random and some methods allowed informative missingness for parental genotypes. However, the above tests assumed that offspring genotypes were missing completely at random and concluded that the transmission/disequilibrium test remained a valid test by excluding incomplete triads from the analysis. In this article, the conditional distribution of ascertained triads allowing informative missingness for offspring genotypes, as well as their parental genotypes, was derived and several tests under such scenarios were evaluated. In simulations, independent triads from the Genetic Analysis Workshop 15 simulated data (Problem 3) was ascertained. When offspring genotypes were missing informatively, simulation results revealed inflated type I error and/or reduced power for the transmission/disequilibrium test excluding incomplete triads. 2007-12-18T00:00:00Z