San Diego State University

About: San Diego State University is a education organization based out in San Diego, California, United States. It is known for research contribution in the topics: Population & Poison control. The organization has 12418 authors who have published 27950 publications receiving 1192375 citations. The organization is also known as: SDSU & San Diego State College.

Quantitative and Qualitative β Diversity Measures Lead to Different Insights into Factors That Structure Microbial Communities

Abstract: The assessment of microbial diversity and distribution is a major concern in environmental microbiology. There are two general approaches for measuring community diversity: quantitative measures, which use the abundance of each taxon, and qualitative measures, which use only the presence/absence of data. Quantitative measures are ideally suited to revealing community differences that are due to changes in relative taxon abundance (e.g., when a particular set of taxa flourish because a limiting nutrient source becomes abundant). Qualitative measures are most informative when communities differ primarily by what can live in them (e.g., at high temperatures), in part because abundance information can obscure significant patterns of variation in which taxa are present. We illustrate these principles using two 16S rRNA-based surveys of microbial populations and two phylogenetic measures of community β diversity: unweighted UniFrac, a qualitative measure, and weighted UniFrac, a new quantitative measure, which we have added to the UniFrac website (http://bmf.colorado.edu/unifrac). These studies considered the relative influences of mineral chemistry, temperature, and geography on microbial community composition in acidic thermal springs in Yellowstone National Park and the influences of obesity and kinship on microbial community composition in the mouse gut. We show that applying qualitative and quantitative measures to the same data set can lead to dramatically different conclusions about the main factors that structure microbial diversity and can provide insight into the nature of community differences. We also demonstrate that both weighted and unweighted UniFrac measurements are robust to the methods used to build the underlying phylogeny.

The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes

Abstract: The release of the 1000th complete microbial genome will occur in the next two to three years. In anticipation of this milestone, the Fellowship for Interpretation of Genomes (FIG) launched the Project to Annotate 1000 Genomes. The project is built around the principle that the key to improved accuracy in high-throughput annotation technology is to have experts annotate single subsystems over the complete collection of genomes, rather than having an annotation expert attempt to annotate all of the genes in a single genome. Using the subsystems approach, all of the genes implementing the subsystem are analyzed by an expert in that subsystem. An annotation environment was created where populated subsystems are curated and projected to new genomes. A portable notion of a populated subsystem was defined, and tools developed for exchanging and curating these objects. Tools were also developed to resolve conflicts between populated subsystems. The SEED is the first annotation environment that supports this model of annotation. Here, we describe the subsystem approach, and offer the first release of our growing library of populated subsystems. The initial release of data includes 180 177 distinct proteins with 2133 distinct functional roles. This data comes from 173 subsystems and 383 different organisms.

Low-Speed Aerodynamics

Abstract: Low-speed aerodynamics is important in the design and operation of aircraft flying at low Mach number, and ground and marine vehicles. This 2001 book offers a modern treatment of the subject, both the theory of inviscid, incompressible, and irrotational aerodynamics and the computational techniques now available to solve complex problems. A unique feature of the text is that the computational approach (from a single vortex element to a three-dimensional panel formulation) is interwoven throughout. Thus, the reader can learn about classical methods of the past, while also learning how to use numerical methods to solve real-world aerodynamic problems. This second edition has a new chapter on the laminar boundary layer (emphasis on the viscous-inviscid coupling), the latest versions of computational techniques, and additional coverage of interaction problems. It includes a systematic treatment of two-dimensional panel methods and a detailed presentation of computational techniques for three-dimensional and unsteady flows. With extensive illustrations and examples, this book will be useful for senior and beginning graduate-level courses, as well as a helpful reference tool for practising engineers.

Neighborhood-Based Differences in Physical Activity: An Environment Scale Evaluation

Abstract: Objectives This study evaluated a neighborhood environment survey and compared the physical activity and weight status of the residents in 2 neighborhoods. Methods On 2 occasions, 107 adults from neighborhoods with differing "walkability" were selected to complete a survey on their neighborhood environment. Physical activity was assessed by self-report and by accelerometer; height and weight were assessed by self-report. Results Neighborhood environment characteristics had moderate to high test-retest reliabilities. Residents of high-walkability neighborhoods reported higher residential density, land use mix, street connectivity, aesthetics, and safety. They had more than 70 more minutes of physical activity and had lower obesity prevalence (adjusted for individual demographics) than did residents of low-walkability neighborhoods. Conclusions The reliability and validity of self-reported neighborhood environment subscales were supported. Neighborhood environment was associated with physical activity and overweight prevalence.

The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants

Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.