Showing papers by "Arizona State University published in 2007"

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).

Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystems.

Abstract: The cycles of the key nutrient elements nitrogen (N) and phosphorus (P) have been massively altered by anthropogenic activities. Thus, it is essential to understand how photosynthetic production across diverse ecosystems is, or is not, limited by N and P. Via a large-scale meta-analysis of experimental enrichments, we show that P limitation is equally strong across these major habitats and that N and P limitation are equivalent within both terrestrial and freshwater systems. Furthermore, simultaneous N and P enrichment produces strongly positive synergistic responses in all three environments. Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation.

Centering predictor variables in cross-sectional multilevel models: a new look at an old issue.

Abstract: Appropriately centering Level 1 predictors is vital to the interpretation of intercept and slope parameters in multilevel models (MLMs). The issue of centering has been discussed in the literature, but it is still widely misunderstood. The purpose of this article is to provide a detailed overview of grand mean centering and group mean centering in the context of 2-level MLMs. The authors begin with a basic overview of centering and explore the differences between grand and group mean centering in the context of some prototypical research questions. Empirical analyses of artificial data sets are used to illustrate key points throughout. The article provides a number of practical recommendations designed to facilitate centering decisions in MLM applications.

Required Sample Size to Detect the Mediated Effect

Abstract: Mediation models are widely used, and there are many tests of the mediated effect. One of the most common questions that researchers have when planning mediation studies is, "How many subjects do I need to achieve adequate power when testing for mediation?" This article presents the necessary sample sizes for six of the most common and the most recommended tests of mediation for various combinations of parameters, to provide a guide for researchers when designing studies or applying for grants.

The Constructive, Destructive, and Reconstructive Power of Social Norms

Abstract: Despite a long tradition of effectiveness in laboratory tests, normative messages have had mixed success in changing behavior in field contexts, with some studies showing boomerang effects. To test a theoretical account of this inconsistency, we conducted a field exper- iment in which normative messages were used to promote householdenergyconservation.Aspredicted,adescriptive normative message detailing average neighborhood usage produced either desirable energy savings or the undesir- able boomerang effect, depending on whether households were already consuming at a low or high rate. Also as predicted, adding an injunctive message (conveying social approval or disapproval) eliminated the boomerang effect. The results offer an explanation for the mixed success of persuasive appeals based on social norms and suggest how such appeals should be properly crafted.

Socioemotional Wealth and Business Risks in Family-controlled Firms: Evidence from Spanish Olive Oil Mills

Abstract: This paper challenges the prevalent notion that family-owned firms are more risk averse than publicly owned firms. Using behavioral theory, we argue that for family firms, the primary reference point is the loss of their socioemotional wealth, and to avoid those losses, family firms are willing to accept a significant risk to their performance; yet at the same time, they avoid risky business decisions that might aggravate that risk. Thus, we propose that the predictions of behavioral theory differ depending on family ownership. We confirm our hypotheses using a population of 1,237 family-owned olive oil mills in Southern Spain who faced the choice during a 54-year period of becoming a member of a cooperative, a decision associated with loss of family control but lower business risk, or remaining independent, which preserves the family's socioemotional wealth but greatly increases its performance hazard. As shown in this study, family firms may be risk willing and risk averse at the same time.

Negative Binomial Regression

Abstract: Preface 1. Introduction 2. The concept of risk 3. Overview of count response models 4. Methods of estimation and assessment 5. Assessment of count models 6. Poisson regression 7. Overdispersion 8. Negative binomial regression 9. Negative binomial regression: modeling 10. Alternative variance parameterizations 11. Problems with zero counts 12. Censored and truncated count models 13. Handling endogeneity and latent class models 14. Count panel models 15. Bayesian negative binomial models Appendix A. Constructing and interpreting interactions Appendix B. Data sets and Stata files References Index.

Complexity of coupled human and natural systems

Abstract: Integrated studies of coupled human and natural systems reveal new and complex patterns and processes not evident when studied by social or natural scientists separately. Synthesis of six case studies from around the world shows that couplings between human and natural systems vary across space, time, and organizational units. They also exhibit nonlinear dynamics with thresholds, reciprocal feedback loops, time lags, resilience, heterogeneity, and surprises. Furthermore, past couplings have legacy effects on present conditions and future possibilities.

Evolution of genes and genomes on the Drosophila phylogeny.

Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

Designed synthesis of 3D covalent organic frameworks.

Abstract: Three-dimensional covalent organic frameworks (3D COFs) were synthesized by targeting two nets based on triangular and tetrahedral nodes: ctn and bor. The respective 3D COFs were synthesized as crystalline solids by condensation reactions of tetrahedral tetra(4-dihydroxyborylphenyl) methane or tetra(4-dihydroxyborylphenyl)silane and by co-condensation of triangular 2,3,6,7,10,11-hexahydroxytriphenylene. Because these materials are entirely constructed from strong covalent bonds (C-C, C-O, C-B, and B-O), they have high thermal stabilities (400° to 500°C), and they also have high surface areas (3472 and 4210 square meters per gram for COF-102 and COF-103, respectively) and extremely low densities (0.17 grams per cubic centimeter).

Gesture Recognition: A Survey

Abstract: Gesture recognition pertains to recognizing meaningful expressions of motion by a human, involving the hands, arms, face, head, and/or body. It is of utmost importance in designing an intelligent and efficient human-computer interface. The applications of gesture recognition are manifold, ranging from sign language through medical rehabilitation to virtual reality. In this paper, we provide a survey on gesture recognition with particular emphasis on hand gestures and facial expressions. Applications involving hidden Markov models, particle filtering and condensation, finite-state machines, optical flow, skin color, and connectionist models are discussed in detail. Existing challenges and future research possibilities are also highlighted

Who are organic food consumers? A compilation and review of why people purchase organic food

Abstract: This paper integrates and synthesizes the findings of published research on organic food consumption. We identify several themes that reflect the various rationales used by consumers when deciding to purchase organic food. The literature clearly indicates that the word "organic" has many meanings, that consumers of organic foods are not homogeneous in demographics or in beliefs, and that further research could help better describe the various constituencies that are often lumped together as "organic food consumers". The organic and broader food industries must better understand the variety of motivations, perceptions, and attitudes consumers hold regarding organic foods and their consumption if their own long-term interests, as well as those of other stakeholders of food marketing, are to be best served. We conclude with implications and suggestions for further research.

Distribution of the product confidence limits for the indirect effect: Program PRODCLIN

Abstract: This article describes a program, PRODCLIN (distribution of the PRODuct Confidence Limits for INdirect effects), written for SAS, SPSS, and R, that computes confidence limits for the product of two normal random variables. The program is important because it can be used to obtain more accurate confidence limits for the indirect effect, as demonstrated in several recent articles (MacKinnon, Lockwood, & Williams, 2004; Pituch, Whittaker, & Stapleton, 2005). Tests of the significance of and confidence limits for indirect effects based on the distribution of the product method have more accurate Type I error rates and more power than other, more commonly used tests. Values for the two paths involved in the indirect effect and their standard errors are entered in the PRODCLIN program, and distribution of the product confidence limits are computed. Several examples are used to illustrate the PRODCLIN program. The PRODCLIN programs in rich text format may be downloaded from www.psychonomic.org/archive.

Diet and the evolution of human amylase gene copy number variation.

Abstract: Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Abstract: Species abundance distributions (SADs) follow one of ecologys oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.

Telomerase Mutations in Families with Idiopathic Pulmonary Fibrosis

Abstract: BACKGROUND Idiopathic pulmonary fibrosis is progressive and often fatal; causes of familial clustering of the disease are unknown. Germ-line mutations in the genes hTERT and hTR, encoding telomerase reverse transcriptase and telomerase RNA, respectively, cause autosomal dominant dyskeratosis congenita, a rare hereditary disorder associated with premature death from aplastic anemia and pulmonary fibrosis. METHODS To test the hypothesis that familial idiopathic pulmonary fibrosis may be caused by short telomeres, we screened 73 probands from the Vanderbilt Familial Pulmonary Fibrosis Registry for mutations in hTERT and hTR. RESULTS Six probands (8%) had heterozygous mutations in hTERT or hTR; mutant telomerase resulted in short telomeres. Asymptomatic subjects with mutant telomerase also had short telomeres, suggesting that they may be at risk for the disease. We did not identify any of the classic features of dyskeratosis congenita in five of the six families. CONCLUSIONS Mutations in the genes encoding telomerase components can appear as familial idiopathic pulmonary fibrosis. Our findings support the idea that pathways leading to telomere shortening are involved in the pathogenesis of this disease.

Hairpin vortex organization in wall turbulencea)

Abstract: Coherent structures in wall turbulence transport momentum and provide a means of producing turbulent kinetic energy. Above the viscous wall layer, the hairpin vortex paradigm of Theodorsen coupled with the quasistreamwise vortex paradigm have gained considerable support from multidimensional visualization using particle image velocimetry and direct numerical simulation experiments. Hairpins can autogenerate to form packets that populate a significant fraction of the boundary layer, even at very high Reynolds numbers. The dynamics of packet formation and the ramifications of organization of coherent structures (hairpins or packets) into larger-scale structures are discussed. Evidence for a large-scale mechanism in the outer layer suggests that further organization of packets may occur on scales equal to and larger than the boundary layer thickness.

The mid-infrared spectrum of star-forming galaxies: Global properties of polycyclic aromatic hydrocarbon emission

Abstract: We present a sample of low-resolution 5-38 μm Spitzer IRS spectra of the inner few square kiloparsecs of 59 nearby galaxies spanning a large range of star formation properties. A robust method for decomposing mid-infrared galaxy spectra is described and used to explore the behavior of PAH emission and the prevalence of silicate dust extinction. Evidence for silicate extinction is found in ~1/8 of the sample, at strengths that indicate that most normal galaxies undergo A_V ≲ 3 mag averaged over their centers. The contribution of PAH emission to the total infrared power is found to peak near 10% and extend up to ~20% and is suppressed at metallicities Z ≲ Z_☉/4, as well as in low-luminosity AGN environments. Strong interband PAH feature strength variations (2-5 times) are observed, with the presence of a weak AGN and, to a lesser degree, increasing metallicity shifting power to the longer wavelength bands. A peculiar PAH emission spectrum with markedly diminished 5-8 μm features arises among the sample solely in systems with relatively hard radiation fields harboring low-luminosity AGNs. The AGNs may modify the emitting grain distribution and provide the direct excitation source of the unusual PAH emission, which cautions against using absolute PAH strength to estimate star formation rates in systems harboring active nuclei. Alternatively, the low star formation intensity often associated with weak AGNs may affect the spectrum. The effect of variations in the mid-infrared spectrum on broadband infrared surveys is modeled and points to more than a factor of 2 uncertainty in results that assume a fixed PAH emission spectrum, for redshifts z = 0-2.5.

Organizational Predictors of Women on Corporate Boards

Abstract: Women are increasing in number among corporations' boards of directors, yet their representation is far from uniform across firms. In this study, we adopted a resource dependence theory lens to ide...

The Management of Organizational Justice

Abstract: Executive Overview Organizational justice has the potential to create powerful benefits for organizations and employees alike. These include greater trust and commitment, improved job performance, more helpful citizenship behaviors, improved customer satisfaction, and diminished conflict. We demonstrate the management of organizational justice with some suggestions for building fairness into widely used managerial activities. These include hiring, performance appraisal, reward systems, conflict management, and downsizing.

Relational Identity and Identification: Defining Ourselves Through Work Relationships

Abstract: We explore the meaning and significance of relational identity and relational identification, predicated on the role-relationship between two individuals. We argue that relational identity integrates person- and role-based identities and thereby the individual, interpersonal, and collective levels of self; contrast relational identity and relational identification with social identity and social identification; contend that relational identity and relational identification are each arranged in a cognitive hierarchy ranging from generalized to particularized schemas; and contrast relational identification with relational disidentification and ambivalent relational identification.

Spectral feature selection for supervised and unsupervised learning

Abstract: Feature selection aims to reduce dimensionality for building comprehensible learning models with good generalization performance. Feature selection algorithms are largely studied separately according to the type of learning: supervised or unsupervised. This work exploits intrinsic properties underlying supervised and unsupervised feature selection algorithms, and proposes a unified framework for feature selection based on spectral graph theory. The proposed framework is able to generate families of algorithms for both supervised and unsupervised feature selection. And we show that existing powerful algorithms such as ReliefF (supervised) and Laplacian Score (unsupervised) are special cases of the proposed framework. To the best of our knowledge, this work is the first attempt to unify supervised and unsupervised feature selection, and enable their joint study under a general framework. Experiments demonstrated the efficacy of the novel algorithms derived from the framework.

Riparian vegetation: Degradation, alien plant invasions, and restoration prospects

Abstract: Rivers are conduits for materials and energy; this, the frequent and intense disturbances that these systems experience, and their narrow, linear nature, create problems for conservation of biodiversity and ecosystem functioning in the face of increasing human influence. In most parts of the world, riparian zones are highly modified. Changes caused by alien plants — or environmental changes that facilitate shifts in dominance creating novel ecosystems — are often important agents of perturbation in these systems. Many restoration projects are underway. Objective frameworks based on an understanding of biogeographical processes at different spatial scales (reach, segment, catchment), the specific relationships between invasive plants and resilience and ecosystem functioning, and realistic endpoints are needed to guide sustainable restoration initiatives. This paper examines the biogeography and the determinants of composition and structure of riparian vegetation in temperate and subtropical regions and conceptualizes the components of resilience in these systems. We consider changes to structure and functioning caused by, or associated with, alien plant invasions, in particular those that lead to breached abiotic- or biotic thresholds. These pose challenges when formulating restoration programmes. Pervasive and escalating human-mediated changes to multiple factors and at a range of scales in riparian environments demand innovative and pragmatic approaches to restoration. The application of a new framework accommodating such complexity is demonstrated with reference to a hypothetical riparian ecosystem under three scenarios: (1) system unaffected by invasive plants; (2) system initially uninvaded, but with flood-generated incursion of alien plants and escalating invasion-driven alteration; and (3) system affected by both invasions and engineering interventions. The scheme has been used to derive a decision-making framework for restoring riparian zones in South Africa and could guide similar initiatives in other parts of the world.

A Whiff of Oxygen Before the Great Oxidation Event

Abstract: High-resolution chemostratigraphy reveals an episode of enrichment of the redox-sensitive transition metals molybdenum and rhenium in the late Archean Mount McRae Shale in Western Australia. Correlations with organic carbon indicate that these metals were derived from contemporaneous seawater. Rhenium/osmium geochronology demonstrates that the enrichment is a primary sedimentary feature dating to 2501 ± 8 million years ago (Ma). Molybdenum and rhenium were probably supplied to Archean oceans by oxidative weathering of crustal sulfide minerals. These findings point to the presence of small amounts of O 2 in the environment more than 50 million years before the start of the Great Oxidation Event.

Early human use of marine resources and pigment in South Africa during the Middle Pleistocene

Abstract: Genetic and anatomical evidence suggests that Homo sapiens arose in Africa between 200 and 100 thousand years (kyr) ago, and recent evidence indicates symbolic behaviour may have appeared approximately 135-75 kyr ago. From 195-130 kyr ago, the world was in a fluctuating but predominantly glacial stage (marine isotope stage MIS6); much of Africa was cooler and drier, and dated archaeological sites are rare. Here we show that by approximately 164 kyr ago (+/-12 kyr) at Pinnacle Point (on the south coast of South Africa) humans expanded their diet to include marine resources, perhaps as a response to these harsh environmental conditions. The earliest previous evidence for human use of marine resources and coastal habitats was dated to approximately 125 kyr ago. Coincident with this diet and habitat expansion is an early use and modification of pigment, probably for symbolic behaviour, as well as the production of bladelet stone tool technology, previously dated to post-70 kyr ago. Shellfish may have been crucial to the survival of these early humans as they expanded their home ranges to include coastlines and followed the shifting position of the coast when sea level fluctuated over the length of MIS6.