Showing papers by "San Diego State University published in 2010"

QIIME allows analysis of high-throughput community sequencing data.

Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.

The Analysis of Spatial Association by Use of Distance Statistics

Abstract: Introduced in this paper is a family of statistics, G, that can be used as a measure of spatial association in a number of circumstances. The basic statistic is derived, its properties are identified, and its advantages explained. Several of the G statistics make it possible to evaluate the spatial association of a variable within a specified distance of a single point. A comparison is made between a general G statistic and Moran’s I for similar hypothetical and empirical conditions. The empirical work includes studies of sudden infant death syndrome by county in North Carolina and dwelling unit prices in metropolitan San Diego by zip-code districts. Results indicate that G statistics should be used in conjunction with I in order to identify characteristics of patterns not revealed by the I statistic alone and, specifically, the G i and G i ∗ statistics enable us to detect local “pockets” of dependence that may not show up when using global statistics.

Kepler Planet-Detection Mission: Introduction and First Results

Abstract: The Kepler mission was designed to determine the frequency of Earth-sized planets in and near the habitable zone of Sun-like stars. The habitable zone is the region where planetary temperatures are suitable for water to exist on a planet’s surface. During the first 6 weeks of observations, Kepler monitored 156,000 stars, and five new exoplanets with sizes between 0.37 and 1.6 Jupiter radii and orbital periods from 3.2 to 4.9 days were discovered. The density of the Neptune-sized Kepler-4b is similar to that of Neptune and GJ 436b, even though the irradiation level is 800,000 times higher. Kepler-7b is one of the lowest-density planets (~0.17 gram per cubic centimeter) yet detected. Kepler-5b, -6b, and -8b confirm the existence of planets with densities lower than those predicted for gas giant planets.

The Impact of Conservation on the Status of the World’s Vertebrates

Abstract: Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

Geographical Detectors-Based Health Risk Assessment and its Application in the Neural Tube Defects Study of the Heshun Region, China

Abstract: Physical environment, man-made pollution, nutrition and their mutual interactions can be major causes of human diseases. These disease determinants have distinct spatial distributions across geographical units, so that their adequate study involves the investigation of the associated geographical strata. We propose four geographical detectors based on spatial variation analysis of the geographical strata to assess the environmental risks of health: the risk detector indicates where the risk areas are; the factor detector identifies factors that are responsible for the risk; the ecological detector discloses relative importance between the factors; and the interaction detector reveals whether the risk factors interact or lead to disease independently. In a real-world study, the primary physical environment (watershed, lithozone and soil) was found to strongly control the neural tube defects (NTD) occurrences in the Heshun region (China). Basic nutrition (food) was found to be more important than man-made pollution (chemical fertilizer) in the control of the spatial NTD pattern. Ancient materials released from geological faults and subsequently spread along slopes dramatically increase the NTD risk. These findings constitute valuable input to disease intervention strategies in the region of interest.

Viruses in the faecal microbiota of monozygotic twins and their mothers

Abstract: Viral diversity and life cycles are poorly understood in the human gut and other body habitats. Phages and their encoded functions may provide informative signatures of a human microbiota and of microbial community responses to various disturbances, and may indicate whether community health or dysfunction is manifest after apparent recovery from a disease or therapeutic intervention. Here we report sequencing of the viromes (metagenomes) of virus-like particles isolated from faecal samples collected from healthy adult female monozygotic twins and their mothers at three time points over a one-year period. We compared these data sets with data sets of sequenced bacterial 16S ribosomal RNA genes and total-faecal-community DNA. Co-twins and their mothers share a significantly greater degree of similarity in their faecal bacterial communities than do unrelated individuals. In contrast, viromes are unique to individuals regardless of their degree of genetic relatedness. Despite remarkable interpersonal variations in viromes and their encoded functions, intrapersonal diversity is very low, with >95% of virotypes retained over the period surveyed, and with viromes dominated by a few temperate phages that exhibit remarkable genetic stability. These results indicate that a predatory viral-microbial dynamic, manifest in a number of other characterized environmental ecosystems, is notably absent in the very distal intestine.

The development of a walkability index: application to the Neighborhood Quality of Life Study

Abstract: Emerging evidence supports a link between neighbourhood built environment and physical activity. Systematic methodologies for characterising neighbourhood built environment are needed that take advantage of available population information such as census-level demographics. Based on transportation and urban planning literatures, an integrated index for operationalising walkability using parcel-level information is proposed. Validity of the walkability index is examined through travel surveys among areas examined in the Neighborhood Quality of Life Study (NQLS), a study investigating built environment correlates of adults' physical activity.

Professional Noticing of Children's Mathematical Thinking.

Abstract: The construct professional noticing of children’s mathematical thinking is introduced as a way to begin to unpack the in-the-moment decision making that is foundational to the complex view of teaching endorsed in national reform documents. We define this expertise as a set of interrelated skills including (a) attending to children’s strategies, (b) interpreting children’s understandings, and (c) deciding how to respond on the basis of children’s understandings. This construct was assessed in a cross-sectional study of 131 prospective and practicing teachers, differing in the amount of experience they had with children’s mathematical thinking. The findings help to characterize what this expertise entails; provide snapshots of those with varied levels of expertise; and document that, given time, this expertise can be learned.

The Ectocarpus genome and the independent evolution of multicellularity in brown algae

Abstract: Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further

A Review of the Empirical Evidence on Generational Differences in Work Attitudes

Abstract: Purpose This article reviews the evidence for generational differences in work values from time-lag studies (which can separate generation from age/career stage) and cross-sectional studies (which cannot). Understanding generational shifts is especially important given the coming retirement of Baby Boomer workers and their replacement by those born after 1982 (GenMe/GenY/Millennials).

Fore-arc basalts and subduction initiation in the Izu-Bonin-Mariana system

Abstract: Recent diving with the JAMSTEC Shinkai 6500 manned submersible in the Mariana fore arc southeast of Guam has discovered that MORB-like tholeiitic basalts crop out over large areas These ''fore-arc basalts'' (FAB) underlie boninites and overlie diabasic and gabbroic rocks Potential origins include eruption at a spreading center before subduction began or eruption during near-trench spreading after subduction began FAB trace element patterns are similar to those of MORB and most Izu-Bonin-Mariana (IBM) back-arc lavas However, Ti/V and Yb/V ratios are lower in FAB reflecting a stronger prior depletion of their mantle source compared to the source of basalts from mid-ocean ridges and back-arc basins Some FAB also have higher concentrations of fluid-soluble elements than do spreading center lavas Thus, the most likely origin of FAB is that they were the first lavas to erupt when the Pacific Plate began sinking beneath the Philippine Plate at about 51 Ma The magmas were generated by mantle decompression during near-trench spreading with little or no mass transfer from the subducting plate Boninites were generated later when the residual, highly depleted mantle melted at shallow levels after fluxing by a water-rich fluid derived from the sinking Pacific Plate This magmatic stratigraphy of FAB overlain by transitional lavas and boninites is similar to that found in many ophiolites, suggesting that ophiolitic assemblages might commonly originate from near-trench volcanism caused by subduction initiation Indeed, the widely dispersed Jurassic and Cretaceous Tethyan ophiolites could represent two such significant subduction initiation events

Global research priorities for sea turtles: informing management and conservation in the 21st century

Abstract: Over the past 3 decades, the status of sea turtles and the need for their protection to aid population recovery have increasingly captured the interest of government agencies, non-governmental organisations (NGOs) and the general public worldwide. This interest has been matched by increased research attention, focusing on a wide variety of topics relating to sea turtle biology and ecology, together with the interrelations of sea turtles with the physical and natural environments. Although sea turtles have been better studied than most other marine fauna, management actions and their evaluation are often hindered by the lack of data on turtle biology, human–turtle interactions, turtle population status and threats. In an effort to inform effective sea turtle conservation a list of priority research questions was assembled based on the opinions of 35 sea turtle researchers from 13 nations working in fields related to turtle biology and/or conservation. The combined experience of the contributing researchers spanned the globe as well as many relevant disciplines involved in conservation research. An initial list of more than 200 questions gathered from respondents was condensed into 20 metaquestions and classified under 5 categories: reproductive biology, biogeography, population ecology, threats and conservation strategies.

Does plantation forestry restore biodiversity or create green deserts? A synthesis of the effects of land-use transitions on plant species richness.

Abstract: Plantations are established for a variety of reasons including wood production, soil and water conservation, and more recently, carbon sequestration. The effect of this growing land-use change on biodiversity, however, is poorly understood and considerable debate exists as to whether plantations are ‘green deserts’ or valuable habitat for indigenous flora and fauna. This paper synthesizes peer-reviewed articles that provide quantitative data on plant species richness in plantations and paired land uses, most often representative of pre-plantation land cover. The results of this synthesis suggest that the value of plantations for biodiversity varies considerably depending on whether the original land cover is grassland, shrubland, primary forest, secondary forest, or degraded or exotic pasture, and whether native or exotic tree species are planted. The results of this study suggest that plantations are most likely to contribute to biodiversity when established on degraded lands rather than replacing natural ecosystems, such as forests, grasslands, and shrublands, and when indigenous tree species are used rather than exotic species. These findings can help guide afforestation and reforestation programs, including those aimed at increasing terrestrial carbon sequestration.

Objective light-intensity physical activity associations with rated health in older adults.

Abstract: The extent to which light-intensity physical activity contributes to health in older adults is not well known. The authors examined associations between physical activity across the intensity spectrum (sedentary to vigorous) and health and well-being variables in older adults. Two 7-day assessments of accelerometry from 2005 to 2007 were collected 6 months apart in the observational Senior Neighborhood Quality of Life Study of adults aged >65 years in Baltimore, Maryland, and Seattle, Washington. Self-reported health and psychosocial variables (e.g., lower-extremity function, body weight, rated stress) were also collected. Physical activity based on existing accelerometer thresholds for moderate/vigorous, high-light, low-light, and sedentary categories were examined as correlates of physical health and psychosocial well-being in mixed-effects regression models. Participants (N = 862) were 75.4 (standard deviation, 6.8) years of age, 56% female, 71% white, and 58% overweight/obese. After adjustment for study covariates and time spent in moderate/vigorous physical activity and sedentary behavior, low-light and high-light physical activity were positively related to physical health (all P < 0.0001) and well-being (all P < 0.001). Additionally, replacing 30 minutes/day of sedentary time with equal amounts of low-light or high-light physical activity was associated with better physical health (all P < 0.0001). Objectively measured light-intensity physical activity is associated with physical health and well-being variables in older adults.

Kepler-9: a system of multiple planets transiting a Sun-like star, confirmed by timing variations.

Abstract: The Kepler spacecraft is monitoring more than 150,000 stars for evidence of planets transiting those stars. We report the detection of two Saturn-size planets that transit the same Sun-like star, based on 7 months of Kepler observations. Their 19.2- and 38.9-day periods are presently increasing and decreasing at respective average rates of 4 and 39 minutes per orbit; in addition, the transit times of the inner body display an alternating variation of smaller amplitude. These signatures are characteristic of gravitational interaction of two planets near a 2:1 orbital resonance. Six radial-velocity observations show that these two planets are the most massive objects orbiting close to the star and substantially improve the estimates of their masses. After removing the signal of the two confirmed giant planets, we identified an additional transiting super-Earth–size planet candidate with a period of 1.6 days.

Comorbidity of Anxiety and Depression in Youth: Implications for Treatment and Prevention.

Abstract: The high level of concurrent and sequential comorbidity between anxiety and depression in children and adolescents may result from (a) substantial overlap in both the symptoms and items used to assess these putatively different disorders, (b) common etiological factors (e.g., familial risk, negative affectivity, information processing biases, neural substrates) implicated in the development of each condition, and (c) negative sequelae of anxiety conferring increased risk for the development of depression. Basic research on their various common and unique etiological mechanisms has guided the development of efficacious treatments for anxiety and depressive disorders in youth. Potential processes through which the successful treatment of childhood anxiety might prevent subsequent depression are described.

Viral and microbial community dynamics in four aquatic environments.

Abstract: The species composition and metabolic potential of microbial and viral communities are predictable and stable for most ecosystems. This apparent stability contradicts theoretical models as well as the viral-microbial dynamics observed in simple ecosystems, both of which show Kill-the-Winner behavior causing cycling of the dominant taxa. Microbial and viral metagenomes were obtained from four human-controlled aquatic environments at various time points separated by one day to >1 year. These environments were maintained within narrow geochemical bounds and had characteristic species composition and metabolic potentials at all time points. However, underlying this stability were rapid changes at the fine-grained level of viral genotypes and microbial strains. These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-the-Winner manner at the level of viral genotypes and microbial strains.

Are psychosocial factors mediators of socioeconomic status and health connections? A progress report and blueprint for the future.

Abstract: The association between socioeconomic status (SES) and physical health is robust. Yet, the psychosocial mediators of SES-health association have been studied in relatively few investigations. In this chapter, we summarize and critique the recent literature regarding negative emotions and cognitions, psychological stress, and resources as potential pathways connecting SES and physical health. We discuss the psychosocial origins of the SES-health links and outline how psychosocial factors may lead to persistently low SES. We conclude that psychosocial resources may play a critical mediating role, and the origins of the SES-health connection are apparent in childhood. We offer a blueprint for future research, which we hope contributes to a better understanding of how SES gets under the skin across the life span.

A faint type of supernova from a white dwarf with a helium-rich companion

Abstract: Supernovae are thought to arise from two different physical processes. The cores of massive, short-lived stars undergo gravitational core collapse and typically eject a few solar masses during their explosion. These are thought to appear as type Ib/c and type II supernovae, and are associated with young stellar populations. In contrast, the thermonuclear detonation of a carbon-oxygen white dwarf, whose mass approaches the Chandrasekhar limit, is thought to produce type Ia supernovae. Such supernovae are observed in both young and old stellar environments. Here we report a faint type Ib supernova, SN 2005E, in the halo of the nearby isolated galaxy, NGC 1032. The ‘old’ environment near the supernova location, and the very low derived ejected mass (~0.3 solar masses), argue strongly against a core-collapse origin. Spectroscopic observations and analysis reveal high ejecta velocities, dominated by helium-burning products, probably excluding this as a subluminous, or a regular type Ia supernova. We conclude that it arises from a low-mass, old progenitor, likely to have been a helium-accreting white dwarf in a binary. The ejecta contain more calcium than observed in other types of supernovae and probably large amounts of radioactive ^(44)Ti.

Evaluation of comprehensive treatment models for individuals with autism spectrum disorders.

Abstract: Multiple dimensions of comprehensive treatment models (CTMs) for learners with autism were evaluated in this study. The purpose of the study was to provide evaluative information upon which service providers, family members, and researchers could make decisions about model adoption, selection for a family member, or future research. Thirty CTMs were identified, with the majority based on an applied behavior analysis framework, although a substantial minority followed a developmental or relationship-based model. As a group, CTMs were strongest in the operationalization of their models, although relatively weaker in measurement of implementation, and with notable exceptions, weak in evidence of efficacy.

The First Systematic Study of Type Ibc Supernova Multi-band Light Curves

Abstract: We present detailed optical photometry for 25 Type Ibc supernovae within d\approx150 Mpc obtained with the robotic Palomar 60-inch telescope in 2004-2007. This study represents the first uniform, systematic, and statistical sample of multi-band SNe Ibc light curves available to date. We correct the light curves for host galaxy extinction using a new technique based on the photometric color evolution, namely, we show that the (V-R) color of extinction-corrected SNe Ibc at t\approx10 days after V-band maximum is tightly distributed, (V-R)=0.26+-0.06 mag. Using this technique, we find that SNe Ibc typically suffer from significant host galaxy extinction, E(B-V)\approx0.4 mag. A comparison of the extinction-corrected light curves for SNe Ib and Ic reveals that they are statistically indistinguishable, both in luminosity and decline rate. We report peak absolute magnitudes of M_R=-17.9+-0.9 mag and M_R=-18.3+-0.6 mag for SNe Ib and Ic, respectively. Focusing on the broad-lined SNe Ic, we find that they are more luminous than the normal SNe Ibc sample, M_R=-19.0+-1.1 mag, with a probability of only 1.6% that they are drawn from the same population of explosions. By comparing the peak absolute magnitudes of SNe Ic-BL with those inferred for local engine-driven explosions (GRB-SN 1998bw, XRF-SN 2006aj, and SN2009bb) we find a 25% probability that they are drawn from the SNe Ic-BL population. Finally, we fit analytic models to the light-curves to derive typical Ni-56 masses of M_Ni \approx0.2 and 0.5 M_sun for SNe Ibc and SNe Ic-BL, respectively. With reasonable assumptions for the photospheric velocities, we extract kinetic energy and ejecta mass values of M_ej \approx 2 M_sun and E_K\approx1e+51 erg for SNe Ibc, while for SNe Ic-BL we find higher values, M_ej\approx5 M_sun and E_K\approx1e+52 erg. We discuss the implications for the progenitors of SNe Ibc and their relation to engine-driven explosions [ABRIDGED].

Reliability and validity of the Sedentary Behavior Questionnaire (SBQ) for adults.

Abstract: Background: Sedentary behavior is related to obesity, but measures of sedentary behaviors are lacking for adults. The purpose of this study was to examine the reliability and validity of the Sedentary Behavior Questionnaire (SBQ) among overweight adults. Methods: Participants were 49 adults for the 2 week test-retest reliability study (67% female, 53% white, mean age = 20) and 401 overweight women (mean age = 41, 61% white) and 441 overweight men (mean age = 44, 81% white) for the validity study. The SBQ consisted of reports of time spent in 9 sedentary behaviors. Outcomes for validity included accelerometer measured inactivity, sitting time (International Physical Activity Questionnaire), and BMI. Intraclass correlation coefficients (ICCs) assessed reliability and partial correlations assessed validity. Results: ICCs were acceptable for all items and the total scale (range = .51–.93). For men, there were significant relationships of SBQ items with IPAQ sitting time and BMI. For women, there were relationships between the SBQ and accelerometer inactivity minutes, IPAQ sitting time, and BMI. Conclusions: The SBQ has acceptable measurement properties for use among overweight adults. Specific measures of sedentary behavior should be included in studies and population surveillance.