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.

A Survey of Digital Map Processing Techniques

Abstract: Maps depict natural and human-induced changes on earth at a fine resolution for large areas and over long periods of time. In addition, maps—especially historical maps—are often the only information source about the earth as surveyed using geodetic techniques. In order to preserve these unique documents, increasing numbers of digital map archives have been established, driven by advances in software and hardware technologies. Since the early 1980s, researchers from a variety of disciplines, including computer science and geography, have been working on computational methods for the extraction and recognition of geographic features from archived images of maps (digital map processing). The typical result from map processing is geographic information that can be used in spatial and spatiotemporal analyses in a Geographic Information System environment, which benefits numerous research fields in the spatial, social, environmental, and health sciences. However, map processing literature is spread across a broad range of disciplines in which maps are included as a special type of image. This article presents an overview of existing map processing techniques, with the goal of bringing together the past and current research efforts in this interdisciplinary field, to characterize the advances that have been made, and to identify future research directions and opportunities.

Short pyrosequencing reads suffice for accurate microbial community analysis

Abstract: Pyrosequencing technology allows us to characterize microbial communities using 16S ribosomal RNA (rRNA) sequences orders of magnitude faster and more cheaply than has previously been possible. However, results from different studies using pyrosequencing and traditional sequencing are often difficult to compare, because amplicons covering different regions of the rRNA might yield different conclusions. We used sequences from over 200 globally dispersed environments to test whether studies that used similar primers clustered together mistakenly, without regard to environment. We then tested whether primer choice affects sequence-based community analyses using UniFrac, our recently-developed method for comparing microbial communities. We performed three tests of primer effects. We tested whether different simulated amplicons generated the same UniFrac clustering results as near-full-length sequences for three recent large-scale studies of microbial communities in the mouse and human gut, and the Guerrero Negro microbial mat. We then repeated this analysis for short sequences (100-, 150-, 200- and 250-base reads) resembling those produced by pyrosequencing. The results show that sequencing effort is best focused on gathering more short sequences rather than fewer longer ones, provided that the primers are chosen wisely, and that community comparison methods such as UniFrac are surprisingly robust to variation in the region sequenced.

GPS measurements of present-day convergence across the Nepal Himalaya

Abstract: The high elevations of the Himalaya and Tibet result from the continuing collision between India and Asia, which started more than 60 million years ago1–4. From geological and seismic studies of the slip rate of faults in Asia5, it is believed that approximately one-third of the present-day convergence rate between India and Asia (58 ± 4mmyr−1) is responsible for the shortening, uplift and moderate seismicity of the Himalaya. Great earthquakes also occur infrequently in this region, releasing in minutes the elastic strain accumulated near the boundary zone over several centuries, and accounting for most of the advance of the Himalaya over the plains of India. The recurrence time for these great earthquakes is determined by the rate of slip of India beneath Tibet, which has hitherto been estimated indirectly from global plate motions6, from the slip rates of faults in Asia7,8, from seismic productivity9, and from the advance of sediments on the northern Ganges plain10. Here we report geodetic measurements, using the Global Positioning System (GPS), of the rate of contraction across the Himalaya, which we find to be 17.52 ± 2 mm yr −1. From the form of the deformation field, we estimate the rate of slip of India beneath Tibet to be 20.5 ± 2 mmyr–1. Strain sufficient to drive one or more great Himalayan earthquakes, with slip similar to that accompanying the magnitude 8.1 Bihar/Nepal 1934 earthquake, may currently be available in western Nepal.

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

Abstract: We present the Biological Observation Matrix (BIOM, pronounced “biome”) format: a JSON-based file format for representing arbitrary observation by sample contingency tables with associated sample and observation metadata. As the number of categories of comparative omics data types (collectively, the “ome-ome”) grows rapidly, a general format to represent and archive this data will facilitate the interoperability of existing bioinformatics tools and future meta-analyses. The BIOM file format is supported by an independent open-source software project (the biom-format project), which initially contains Python objects that support the use and manipulation of BIOM data in Python programs, and is intended to be an open development effort where developers can submit implementations of these objects in other programming languages. The BIOM file format and the biom-format project are steps toward reducing the “bioinformatics bottleneck” that is currently being experienced in diverse areas of biological sciences, and will help us move toward the next phase of comparative omics where basic science is translated into clinical and environmental applications. The BIOM file format is currently recognized as an Earth Microbiome Project Standard, and as a Candidate Standard by the Genomic Standards Consortium.

Dynamics of collapsing and exploding Bose–Einstein condensates

Abstract: When atoms in a gas are cooled to extremely low temperatures, they will-under the appropriate conditions-condense into a single quantum-mechanical state known as a Bose-Einstein condensate. In such systems, quantum-mechanical behaviour is evident on a macroscopic scale. Here we explore the dynamics of how a Bose-Einstein condensate collapses and subsequently explodes when the balance of forces governing its size and shape is suddenly altered. A condensate's equilibrium size and shape is strongly affected by the interatomic interactions. Our ability to induce a collapse by switching the interactions from repulsive to attractive by tuning an externally applied magnetic field yields detailed information on the violent collapse process. We observe anisotropic atom bursts that explode from the condensate, atoms leaving the condensate in undetected forms, spikes appearing in the condensate wavefunction and oscillating remnant condensates that survive the collapse. All these processes have curious dependences on time, on the strength of the interaction and on the number of condensate atoms. Although the system would seem to be simple and well characterized, our measurements reveal many phenomena that challenge theoretical models.