University of Colorado Boulder

About: University of Colorado Boulder is a education organization based out in Boulder, Colorado, United States. It is known for research contribution in the topics: Population & Galaxy. The organization has 48794 authors who have published 115151 publications receiving 5387328 citations. The organization is also known as: CU Boulder & UCB.

Detection of the baryon acoustic peak in the large-scale correlation function of SDSS luminous red galaxies

Abstract: We present the large-scale correlation function measured from a spectroscopic sample of 46,748 luminous red galaxies from the Sloan Digital Sky Survey. The survey region covers 0.72h −3 Gpc 3 over 3816 square degrees and 0.16 < z < 0.47, making it the best sample yet for the study of large-scale structure. We find a well-detected peak in the correlation function at 100h −1 Mpc separation that is an excellent match to the predicted shape and location of the imprint of the recombination-epoch acoustic oscillations on the low-redshift clustering of matter. This detection demonstrates the linear growth of structure by gravitational instability between z ≈ 1000 and the present and confirms a firm prediction of the standard cosmological theory. The acoustic peak provides a standard ruler by which we can measure the ratio of the distances to z = 0.35 and z = 1089 to 4% fractional accuracy and the absolute distance to z = 0.35 to 5% accuracy. From the overall shape of the correlation function, we measure the matter density mh 2 to 8% and find agreement with the value from cosmic microwave background (CMB) anisotropies. Independent of the constraints provided by the CMB acoustic scale, we find m = 0.273 ±0.025+0.123(1+ w0)+0.137K. Including the CMB acoustic scale, we find that the spatial curvature is K = −0.010 ± 0.009 if the dark energy is a cosmological constant. More generally, our results provide a measurement of cosmological distance, and hence an argument for dark energy, based on a geometric method with the same simple physics as the microwave background anisotropies. The standard cosmological model convincingly passes these new and robust tests of its fundamental properties. Subject headings: cosmology: observations — large-scale structure of the universe — distance scale — cosmological parameters — cosmic microwave background — galaxies: elliptical and lenticular, cD

An introduction to latent semantic analysis

Abstract: Latent Semantic Analysis (LSA) is a theory and method for extracting and representing the contextual‐usage meaning of words by statistical computations applied to a large corpus of text (Landauer & Dumais, 1997). The underlying idea is that the aggregate of all the word contexts in which a given word does and does not appear provides a set of mutual constraints that largely determines the similarity of meaning of words and sets of words to each other. The adequacy of LSA's reflection of human knowledge has been established in a variety of ways. For example, its scores overlap those of humans on standard vocabulary and subject matter tests; it mimics human word sorting and category judgments; it simulates word‐word and passage‐word lexical priming data; and, as reported in 3 following articles in this issue, it accurately estimates passage coherence, learnability of passages by individual students, and the quality and quantity of knowledge contained in an essay.

Guidelines for the use and interpretation of assays for monitoring autophagy

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

Abstract: Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a 'taxonomy to tree' approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408,315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

Solitons, Nonlinear Evolution Equations and Inverse Scattering

Abstract: Solitons have been of considerable interest to mathematicians since their discovery by Kruskal and Zabusky. This book brings together several aspects of soliton theory currently only available in research papers. Emphasis is given to the multi-dimensional problems arising and includes inverse scattering in multi-dimensions, integrable nonlinear evolution equations in multi-dimensions and the ∂ method. Thus, this book will be a valuable addition to the growing literature in the area and essential reading for all researchers in the field of soliton theory.