Showing papers by "San Diego State University published in 2005"

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.

Isolation by distance, web service

Abstract: The population genetic pattern known as "isolation by distance" results from spatially limited gene flow and is a commonly observed phenomenon in natural populations. However, few software programs exist for estimating the degree of isolation by distance among populations, and they tend not to be user-friendly. We have created Isolation by Distance Web Service (IBDWS) a user-friendly web interface for determining patterns of isolation by distance. Using this site, population geneticists can perform a variety of powerful statistical tests including Mantel tests, Reduced Major Axis (RMA) regression analysis, as well as calculate F ST between all pairs of populations and perform basic summary statistics (e.g., heterozygosity). All statistical results, including publication-quality scatter plots in Postscript format, are returned rapidly to the user and can be easily downloaded. IBDWS population genetics analysis software is hosted at http://phage.sdsu.edu/~jensen/ and documentation is available at http://www.bio.sdsu.edu/pub/andy/IBD.html . The source code has been made available on Source Forge at http://sourceforge.net/projects/ibdws/ .

Evidence and implications of recent climate change in northern Alaska and other arctic regions.

Abstract: The Arctic climate is changing. Permafrost is warming, hydrological processes are chang- ing and biological and social systems are also evolving in response to these changing conditions. Knowing how the structure and function of arctic terrestrial ecosystems are responding to recent and persistent climate change is paramount to understanding the future state of the Earth system and how humans will need to adapt. Our holistic review presents a broad array of evidence that illustrates con- vincingly; the Arctic is undergoing a system-wide response to an altered climatic state. New extreme and seasonal surface climatic conditions are being experienced, a range of biophysical states and pro- cesses influenced by the threshold and phase change of freezing point are being altered, hydrological and biogeochemical cycles are shifting, and more regularly human sub-systems are being affected. Importantly, the patterns, magnitude and mechanisms of change have sometimes been unpredictable or difficult to isolate due to compounding factors. In almost every discipline represented, we show

Social exclusion impairs self-regulation.

Abstract: Six experiments showed that being excluded or rejected caused decrements in self-regulation. In Experiment 1, participants who were led to anticipate a lonely future life were less able to make themselves consume a healthy but bad-tasting beverage. In Experiment 2, some participants were told that no one else in their group wanted to work with them, and these participants later ate more cookies than other participants. In Experiment 3, excluded participants quit sooner on a frustrating task. In Experiments 4-6, exclusion led to impairment of attention regulation as measured with a dichotic listening task. Experiments 5 and 6 further showed that decrements in self-regulation can be eliminated by offering a cash incentive or increasing self-awareness. Thus, rejected people are capable of self-regulation but are normally disinclined to make the effort.

Healthy nutrition environments: concepts and measures.

Abstract: The authors provide a conceptual model of a healthy nutrition environment, then review the types of measures required to assess various aspects of this environment. Measures fall into priority categories of consumer and community environments.

Rapid acidification of the ocean during the Paleocene-Eocene thermal maximum.

Abstract: The Paleocene-Eocene thermal maximum (PETM) has been attributed to the rapid release of ∼2000 × 10 9 metric tons of carbon in the form of methane. In theory, oxidation and ocean absorption of this carbon should have lowered deep-sea pH, thereby triggering a rapid ( 100,000 years). These findings indicate that a large mass of carbon (»2000 × 10 9 metric tons of carbon) dissolved in the ocean at the Paleocene-Eocene boundary and that permanent sequestration of this carbon occurred through silicate weathering feedback.

Understanding organization-customer links in service settings.

Abstract: We develop a framework of service-unit behavior that begins with a unit's leader's service-focused behavior and progresses through intermediate links (service climate and customer-focused organizat...

Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards.

Abstract: Partitioned Bayesian analyses of approximately 2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean -lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2 ln Bayes factor > 10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.

RNA Viral Community in Human Feces: Prevalence of Plant Pathogenic Viruses

Abstract: The human gut is known to be a reservoir of a wide variety of microbes, including viruses. Many RNA viruses are known to be associated with gastroenteritis; however, the enteric RNA viral community present in healthy humans has not been described. Here, we present a comparative metagenomic analysis of the RNA viruses found in three fecal samples from two healthy human individuals. For this study, uncultured viruses were concentrated by tangential flow filtration, and viral RNA was extracted and cloned into shotgun viral cDNA libraries for sequencing analysis. The vast majority of the 36,769 viral sequences obtained were similar to plant pathogenic RNA viruses. The most abundant fecal virus in this study was pepper mild mottle virus (PMMV), which was found in high concentrations—up to 109 virions per gram of dry weight fecal matter. PMMV was also detected in 12 (66.7%) of 18 fecal samples collected from healthy individuals on two continents, indicating that this plant virus is prevalent in the human population. A number of pepper-based foods tested positive for PMMV, suggesting dietary origins for this virus. Intriguingly, the fecal PMMV was infectious to host plants, suggesting that humans might act as a vehicle for the dissemination of certain plant viruses.

Fetal alcohol spectrum disorders: an overview with emphasis on changes in brain and behavior.

Abstract: Fetal alcohol spectrum disorders constitute a major public health problem. This article presents an overview of important issues that surround these disorders and emphasizes the structural and neurobehavioral consequences associated with prenatal exposure to alcohol. Diagnostic criteria are discussed, and possible moderating factors for the range of outcomes are mentioned. In addition, the prevalence of fetal alcohol spectrum disorders is described, and estimates of the financial impact of these disorders are given. Heavy prenatal alcohol exposure can severely affect the physical and neurobehavioral development of a child. Autopsy and brain imaging studies indicate reductions and abnormalities in overall brain size and shape, specifically in structures such as the cerebellum, basal ganglia, and corpus callosum. A wide range of neuropsychological deficits have been found in children prenatally exposed to alcohol, including deficits in visuospatial functioning, verbal and nonverbal learning, attention, and ...

Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations.

Abstract: The oceanic cyanobacteria Prochlorococcus are globally important, ecologically diverse primary producers. It is thought that their viruses (phages) mediate population sizes and affect the evolutionary trajectories of their hosts. Here we present an analysis of genomes from three Prochlorococcus phages: a podovirus and two myoviruses. The morphology, overall genome features, and gene content of these phages suggest that they are quite similar to T7-like (P-SSP7) and T4-like (P-SSM2 and P-SSM4) phages. Using the existing phage taxonomic framework as a guideline, we examined genome sequences to establish “core” genes for each phage group. We found the podovirus contained 15 of 26 core T7-like genes and the two myoviruses contained 43 and 42 of 75 core T4-like genes. In addition to these core genes, each genome contains a significant number of “cyanobacterial” genes, i.e., genes with significant best BLAST hits to genes found in cyanobacteria. Some of these, we speculate, represent “signature” cyanophage genes. For example, all three phage genomes contain photosynthetic genes (psbA, hliP) that are thought to help maintain host photosynthetic activity during infection, as well as an aldolase family gene (talC) that could facilitate alternative routes of carbon metabolism during infection. The podovirus genome also contains an integrase gene (int) and other features that suggest it is capable of integrating into its host. If indeed it is, this would be unprecedented among cultured T7-like phages or marine cyanophages and would have significant evolutionary and ecological implications for phage and host. Further, both myoviruses contain phosphate-inducible genes (phoH and pstS) that are likely to be important for phage and host responses to phosphate stress, a commonly limiting nutrient in marine systems. Thus, these marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments.

A review and critique of emotional intelligence measures.

Abstract: Summary Emotional intelligence measures vary widely in both their content and in their method of assessment. In particular, emotional intelligence measures tend to use either a self-report personality-based approach, an informant approach, or an ability-based assessment procedure. In this paper, the measurement and psychometric properties of four of the major emotional intelligence measures (Emotional Competence Inventory, Emotional Quotient Inventory, Multifactor Emotional Intelligence Scale, Mayer–Salovey–Caruso Emotional Intelligence Test) are reviewed, the comparability of these measures is examined, and some conclusions and suggestions for future research on emotional intelligence measures are provided. Copyright # 2005 John Wiley & Sons, Ltd.

Robust decision‐making under severe uncertainty for conservation management

Abstract: In conservation biology it is necessary to make management decisions for endangered and threatened species under severe uncertainty. Failure to acknowledge and treat uncertainty can lead to poor decisions. To illustrate the importance of considering uncertainty, we reanalyze a decision problem for the Sumatran rhino, Dicerorhinus sumatrensis, using information-gap theory to propagate uncertainties and to rank management options. Rather than requiring information about the extent of parameter uncertainty at the outset, information-gap theory addresses the question of how much uncertainty can be tolerated before our decision would change. It assesses the robustness of decisions in the face of severe uncertainty. We show that different management decisions may result when uncertainty in utilities and probabilities are considered in decision-making problems. We highlight the importance of a full assessment of uncertainty in conservation management decisions to avoid, as much as possible, undesirable outcomes.

Imputation of Missing Data When Measuring Physical Activity by Accelerometry

Abstract: Within the past several years, accelerometry has emerged as an important means of assessing the duration and intensity of physical activity and has served to define primary outcome measures in several observational (1,4,20) and experimental studies (6,7,11,15,17). It is currently being used in the large group-randomized Trial of Activity in Adolescent Girls (TAAG) to examine the effect of a school- and community-based intervention on physical activity in middle-school girls. The uniaxial accelerometer considered in this trial, the ActiGraph, formerly known as the Computer Science and Applications (CSA) and Manufacturing Technologies Inc. (MTI) (ActiGraph, LLC, Fort Walton Beach, FL) is a small (5 × 4 × 1.5 cm) and lightweight (45 g) device that captures vertical acceleration. Acceleration is sampled 10× s−1, and the data are summed over a user-specified time interval (e.g., 30 s, 1 min) and the summed value or activity “count” is stored in memory. Although the measurement protocols vary, most studies involve monitoring physical activity over several days to ensure reliable estimates of usual physical activity behavior and to account for potentially important differences in activity patterns on weekdays versus weekend days (19). Participants are typically instructed to wear the accelerometer during waking hours, except when bathing and showering. Data from accelerometers are summarized in numerous ways, including the mean total count per day (11) and the mean minutes per day spent in moderate or vigorous physical activity (using established count cut points to distinguish specific intensity levels). The analysis is complicated in that 1) activity levels vary among days of the week and times of day and 2) over multiple days of monitoring, missing data arising from removal of the monitor are a common occurrence. Although participant noncompliance accounts for a large fraction of the missing data, legitimate reasons for removing the monitor, such as complying with mandated sports league safety regulations or participation in water-related activity (for monitors that are not waterproof), also contribute to data loss. Thus, the timing and amount of data contributed by each individual vary. If summary statistics are computed using the observed data only, these statistics have the potential to be biased. For example, the total count for a given day clearly underestimates the true level of activity on days in which the monitor is worn only part of a day. Some researchers have tried to minimize this bias by computing summary statistics after excluding accelerometer data on days in which the monitor is worn only part of the day. These are called incomplete days of observation. This strategy, however, is not without issues. First, even after excluding days with, say, less than 8 h of wearing time, the number of hours the monitor is worn is still likely to vary. Moreover, if included days have intervals when the subject was awake but not wearing the monitor, then total activity will be underestimated. Second, this approach ignores possible differences in activity levels on complete days and incomplete days, making the estimated summary statistics from complete days subject to selection bias. This paper proposes an analytical approach whereby the observed data are used to help predict activity levels for segments of the day in which the monitor is not worn. The resultant data set is pseudo-complete in the sense that each individual will have either observed or imputed data for all segments of each day in which the monitor was intended to be worn. Summary statistics are then estimated from this pseudo-complete data set. This imputation strategy is analogous to imputing missing item responses on multi-item questionnaires. The literature contains numerous examples in which this treatment of item nonresponse has been found to reduce bias effectively (5,21). In the following section, accelerometer data collected during the feasibility phase of the TAAG trial are used to demonstrate the potential for bias in estimating physical activity when all observed data are used as well as when a subset of data that excludes incomplete days of monitoring is used. We then describe procedures for filling in missing data using single imputation through expectation maximization (EM) and multiple imputation (MI) (9,14). The remaining sections of the paper describe the design of a simulation study to assess the effectiveness of the imputation approaches, present its results, and discuss the effectiveness of imputation as a strategy for dealing with missing data in the context of accelerometry.

Hylid frog phylogeny and sampling strategies for speciose clades

Abstract: How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families We sampled 81 species (54 hylids and 27 outgroups) for two mitochondrial genes (12S, ND1), two nuclear genes (POMC, c-myc), and morphology (144 characters) in an attempt to resolve higher-level relationships We then added 117 taxa to the combined data set, many of which were sampled for only one gene (12S) Despite the relative incompleteness of the majority of taxa, the resulting trees placed all taxa in the expected higher-level clades with strong support, despite some taxa being > 90% incomplete Furthermore, we found no relationship between the completeness of a taxon and the support (parsimony bootstrap or Bayesian posterior probabilities) for its localized placement on the tree Separate analysis of the data set with the most taxa (12S) gives a somewhat problematic estimate of higher-level relationships, suggesting that data sets scored only for some taxa (ND1, nuclear genes, morphology) are important in determining the outcome of the combined analysis The results show that hemiphractine hylids are not closely related to other hylids and should be recognized as a distinct family They also show that the speciose genus Hyla is polyphyletic, but that its species can be arranged into three monophyletic genera A new classification of hylid frogs is proposed Several potentially misleading signals in the morphological data are discussed

Environmental marketing strategy and firm performance: Effects on new product performance and market share

Abstract: Recent studies on marketing and the natural environment have called for research that links environmental marketing strategies to the performance of the firm. This research operationalizes the enviropreneurial marketing (EM) construct and examines its relationship with firm performance. It is the first empirical research to operationalize the EM construct. The new scale, albeit a first attempt, demonstrates encouraging psychometric properties. According to the resource-based view of the firm, a resource such as EM should directly influence firms’ capabilities (e.g., new product development success) but not competitive advantage (e.g., change in market share). A nationwide study of top-level marketing managers supports this perspective. In addition, although market turbulence also affects new product development success, it does not have an impact on EM. This suggests that EM formation is driven by internal rather than external forces.

Regional convergence, inequality, and space

Abstract: The study of regional income convergence continues to attract enormous attention. Recent emphasis has been placed on the underlying spatial dimensions of regional growth processes both from theoretical and empirical perspectives, as well as from exploratory and confirmatory methodological stances. This paper provides a critical review of empirical approaches and methodological advances with an emphasis on the treatment of spatial effects, namely spatial dependence, spatial heterogeneity, and spatial scale. A number of areas that have been overlooked are highlighted, and the paper suggests a research agenda on regional growth empirics. Copyright 2005, Oxford University Press.

Site‐level evaluation of satellite‐based global terrestrial gross primary production and net primary production monitoring

Abstract: Operational monitoring of global terrestrial gross primary production (GPP) and net primary production (NPP) is now underway using imagery from the satellite-borne Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. Evaluation of MODIS GPP and NPP products will require site-level studies across a range of biomes, with close attention to numerous scaling issues that must be addressed to link ground measurements to the satellite-based carbon flux estimates. Here, we report results of a study aimed at evaluating MODIS NPP/GPP products at six sites varying widely in climate, land use, and vegetation physiognomy. Comparisons were made for twenty-five 1km 2 cells at each site, with 8-day averages for GPP and an annual value for NPP. The validation data layers were made with a combination of ground measurements, relatively high resolution satellite data (Landsat Enhanced Thematic Mapper Plus at � 30m resolution), and process-based modeling. There was strong seasonality in the MODIS GPP at all sites, and mean NPP ranged from 80gCm � 2 yr � 1 at an arctic tundra site to 550gCm � 2 yr � 1 at a temperate deciduous forest site. There was not a consistent over- or underprediction of NPP across sites relative to the validation estimates. The closest agreements in NPP and GPP were at the temperate deciduous forest, arctic tundra, and boreal forest sites. There was moderate underestimation in the MODIS products at the agricultural field site, and strong overestimation at the desert grassland and at the dry coniferous forest sites. Analyses of specific inputs to the MODIS NPP/ GPP algorithm ‐ notably the fraction of photosynthetically active radiation absorbed by the vegetation canopy, the maximum light use efficiency (LUE), and the climate data ‐ revealed the causes of the over- and underestimates. Suggestions for algorithm improvement include selectively altering values for maximum LUE (based on observations at eddy covariance flux towers) and parameters regulating autotrophic respiration.

The relationship between quality of life and self-determination: an international study.

Abstract: Background The aim of this study was to evaluate the relationship between self-determination and quality of life (QOL) of persons with intellectual disabilities (ID) living in four countries (Canada, United States, Belgium and France). Method Participants were 182 adults with mild ID living in community settings (with families, living independently or in supported living environments). QOL was measured with the Quality of Life Questionnaire. Self-determination was measured using the Adult version of The Arc's Self-Determination Scale. Discriminant function and correlational analyses were conducted. Results Discriminant function analysis indicated that essential characteristics of self-determination predicted membership in the high QOL group and that overall self-determination and QOL were significantly correlated, as were sub-scale scores. Conclusions The study replicates findings from a previous study with an international sample and confirms the importance of self-determination to enhance QOL. Subsequent research should examine the direction of the relationship between self-determination and QOL and examine the relationship of essential characteristics of self-determined behaviour and core domains of QOL in greater detail.

Comparison of finite difference and boundary integral solutions to three-dimensional spontaneous rupture

Abstract: The spontaneously propagating shear crack on a frictional interface has proven to be a useful idealization of a natural earthquake. The corresponding boundary value problems are nonlinear and usually require computationally intensive numerical methods for their solution. Assessing the convergence and accuracy of the numerical methods is challenging, as we lack appropriate analytical solutions for comparison. As a complement to other methods of assessment, we compare solutions obtained by two independent numerical methods, a finite difference method and a boundary integral (BI) method. The finite difference implementation, called DFM, uses a traction-at-split-node formulation of the fault discontinuity. The BI implementation employs spectral representation of the stress transfer functional. The three-dimensional (3-D) test problem involves spontaneous rupture spreading on a planar interface governed by linear slip-weakening friction that essentially defines a cohesive law. To get a priori understanding of the spatial resolution that would be required in this and similar problems, we review and combine some simple estimates of the cohesive zone sizes which correspond quite well to the sizes observed in simulations. We have assessed agreement between the methods in terms of the RMS differences in rupture time, final slip, and peak slip rate and related these to median and minimum measures of the cohesive zone resolution observed in the numerical solutions. The BI and DFM methods give virtually indistinguishable solutions to the 3-D spontaneous rupture test problem when their grid spacing Δx is small enough so that the solutions adequately resolve the cohesive zone, with at least three points for BI and at least five node points for DFM. Furthermore, grid-dependent differences in the results, for each of the two methods taken separately, decay as a power law in Δx, with the same convergence rate for each method, the calculations apparently converging to a common, grid interval invariant solution. This result provides strong evidence for the accuracy of both methods. In addition, the specific solution presented here, by virtue of being demonstrably grid-independent and consistent between two very different numerical methods, may prove useful for testing new numerical methods for spontaneous rupture problems.

Best practices for physical activity programs and behavior counseling in older adult populations.

Abstract: Physical activity offers one of the greatest opportunities for people to extend years of active independent life and reduce functional limitations. The article identifies key practices for promoting physical activity in older adults, with a focus on those with chronic disease or low fitness and those with low levels of physical activity. Key practices identified: (a) A multidimensional activity program that includes endurance, strength, balance, and flexibility training is optimal for health and functional benefits; (b) principles of behavior change including social support, self-efficacy, active choices, health contracts, assurances of safety, and positive reinforcement enhance adherence; (c) manage risk by beginning at low intensity but gradually increasing to moderate physical activity, which has a better risk:benefit ratio and should be the goal for older adults; (d) an emergency procedure plan is prudent for community-based programs; and (e) monitoring aerobic intensity is important for progression and motivation. Selected content review of physical activity programming from major organizations and institutions is provided.