Torrey Pines Institute for Molecular Studies

About: Torrey Pines Institute for Molecular Studies is a nonprofit organization based out in San Diego, California, United States. It is known for research contribution in the topics: Antigen & T cell. The organization has 2323 authors who have published 2217 publications receiving 112618 citations.

Visualization of molecular fingerprints.

Abstract: A visualization plot of a data set of molecular data is a useful tool for gaining insight into a set of molecules. In chemoinformatics, most visualization plots are of molecular descriptors, and the statistical model most often used to produce a visualization is principal component analysis (PCA). This paper takes PCA, together with four other statistical models (NeuroScale, GTM, LTM, and LTM-LIN), and evaluates their ability to produce clustering in visualizations not of molecular descriptors but of molecular fingerprints. Two different tasks are addressed: understanding structural information (particularly combinatorial libraries) and relating structure to activity. The quality of the visualizations is compared both subjectively (by visual inspection) and objectively (with global distance comparisons and local k-nearest-neighbor predictors). On the data sets used to evaluate clustering by structure, LTM is found to perform significantly better than the other models. In particular, the clusters in LTM visualization space are consistent with the relationships between the core scaffolds that define the combinatorial sublibraries. On the data sets used to evaluate clustering by activity, LTM again gives the best performance but by a smaller margin. The results of this paper demonstrate the value of using both a nonlinear projection map and a Bernoulli noise model for modeling binary data.

Endothelial Protein C Receptor Function in Murine and Human Breast Cancer Development

Abstract: Several markers identify cancer stem cell-like populations, but little is known about the functional roles of stem cell surface receptors in tumor progression. Here, we show that the endothelial protein C receptor (EPCR), a stem cell marker in hematopoietic, neuronal and epithelial cells, is crucial for breast cancer growth in the orthotopic microenvironment of the mammary gland. Mice with a hypomorphic allele of EPCR show reduced tumor growth in the PyMT-model of spontaneous breast cancer development and deletion of EPCR in established PyMT tumor cells significantly attenuates transplanted tumor take and growth. We find expansion of EPCR+ cancer stem cell-like populations in aggressive, mammary fat pad-enhanced human triple negative breast cancer cells. In this model, EPCR-expressing cells have markedly increased mammosphere- and tumor-cell initiating activity compared to another stable progenitor-like subpopulation present at comparable frequency. We show that receptor blocking antibodies to EPCR specifically attenuate in vivo tumor growth initiated by either EPCR+ cells or the heterogenous mixture of EPCR+ and EPCR- cells. Furthermore, we have identified tumor associated macrophages as a major source for recognized ligands of EPCR, suggesting a novel mechanism by which cancer stem cell-like populations are regulated by innate immune cells in the tumor microenvironment.

Healing Touch With Guided Imagery for PTSD in Returning Active Duty Military: A Randomized Controlled Trial

Abstract: Post-traumatic stress disorder (PTSD) remains a significant problem in returning military and warrants swift and effective treatment. We conducted a randomized controlled trial to determine whether a complementary medicine intervention (Healing Touch with Guided Imagery [HT+GI]) reduced PTSD symptoms as compared to treatment as usual (TAU) returning combat-exposed active duty military with significant PTSD symptoms. Active duty military (n = 123) were randomized to 6 sessions (within 3 weeks) of HT+GI vs. TAU. The primary outcome was PTSD symptoms; secondary outcomes were depression, quality of life, and hostility. Repeated measures analysis of covariance with intent-to-treat analyses revealed statistically and clinically significant reduction in PTSD symptoms (p < 0.0005, Cohen's d = 0.85) as well as depression (p < 0.0005, Cohen's d = 0.70) for HT+GI vs. TAU. HT+GI also showed significant improvements in mental quality of life (p = 0.002, Cohen's d = 0.58) and cynicism (p = 0.001, Cohen's d = 0....

Discovery of RNA structural elements using evolutionary computation

Abstract: RNA molecules fold into characteristic secondary and tertiary structures that account for their diverse functional activities. Many of these RNA structures, or certain structural motifs within them, are thought to recur in multiple genes within a single organism or across the same gene in several organisms and provide a common regulatory mechanism. Search algorithms, such as RNAMotif, can be used to mine nucleotide sequence databases for these repeating motifs. RNAMotif allows users to capture essential features of known structures in detailed descriptors and can be used to identify, with high specificity, other similar motifs within the nucleotide database. However, when the descriptor constraints are relaxed to provide more flexibility, or when there is very little a priori information about hypothesized RNA structures, the number of motif ‘hits’ may become very large. Exhaustive methods to search for similar RNA structures over these large search spaces are likely to be computationally intractable. Here we describe a powerful new algorithm based on evolutionary computation to solve this problem. A series of experiments using ferritin IRE and SRP RNA stem‐loop motifs were used to verify the method. We demonstrate that even when searching extremely large search spaces, of the order of 10 23 potential solutions, we could find the correct solution in a fraction of the time it would have taken for exhaustive comparisons.