Showing papers by "Washington State University published in 2009"

The B73 Maize Genome: Complexity, Diversity, and Dynamics

Abstract: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

The Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution

Abstract: To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.

Defects in ZnO

Abstract: Zinc oxide (ZnO) is a wide band gap semiconductor with potential applications in optoelectronics, transparent electronics, and spintronics. The high efficiency of UV emission in this material could be harnessed in solid-state white lighting devices. The problem of defects, in particular, acceptor dopants, remains a key challenge. In this review, defects in ZnO are discussed, with an emphasis on the physical properties of point defects in bulk crystals. As grown, ZnO is usually n-type, a property that was historically ascribed to native defects. However, experiments and theory have shown that O vacancies are deep donors, while Zn interstitials are too mobile to be stable at room temperature. Group-III (B, Al, Ga, and In) and H impurities account for most of the n-type conductivity in ZnO samples. Interstitial H donors have been observed with IR spectroscopy, while substitutional H donors have been predicted from first-principles calculations but not observed directly. Despite numerous reports, reliable p-t...

Big 4 Office Size and Audit Quality

Abstract: Larger offices of Big 4 auditors are predicted to have higher quality audits for SEC registrants due to greater in‐house experience in administering such audits. We test this prediction b...

Jasmonate passes muster: a receptor and targets for the defense hormone.

Abstract: The oxylipin jasmonate (JA) regulates many aspects of growth, development, and environmental responses in plants, particularly defense responses against herbivores and necrotrophic pathogens. Mutants of Arabidopsis helped researchers define the biochemical pathway for synthesis of jasmonoyl-isoleucine (JA-Ile), the active form of JA hormone, and demonstrated that JA is required for plant survival of insect and pathogen attacks and for plant fertility. Transcriptional profiling led to the discovery of the JASMONATE ZIM-DOMAIN (JAZ) proteins, which are repressors of JA signaling. JA-Ile relieves repression by promoting binding of the JAZ proteins to the F-box protein CORONATINE INSENSITIVE1 (COI1) and their subsequent degradation by the ubiquitination/26S-proteasome pathway. Although we now have a much better understanding of the molecular mechanism of JA action, many questions remain. Experimental answers to these questions will expand our knowledge of oxylipin signaling in plants and animals and will also...

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

Abstract: The uneven distribution of species richness is a fundamental and unexplained pattern of vertebrate biodiversity. Although species richness in groups like mammals, birds, or teleost fishes is often attributed to accelerated cladogenesis, we lack a quantitative conceptual framework for identifying and comparing the exceptional changes of tempo in vertebrate evolutionary history. We develop MEDUSA, a stepwise approach based upon the Akaike information criterion for detecting multiple shifts in birth and death rates on an incompletely resolved phylogeny. We apply MEDUSA incompletely to a diversity tree summarizing both evolutionary relationships and species richness of 44 major clades of jawed vertebrates. We identify 9 major changes in the tempo of gnathostome diversification; the most significant of these lies at the base of a clade that includes most of the coral-reef associated fishes as well as cichlids and perches. Rate increases also underlie several well recognized tetrapod radiations, including most modern birds, lizards and snakes, ostariophysan fishes, and most eutherian mammals. In addition, we find that large sections of the vertebrate tree exhibit nearly equal rates of origination and extinction, providing some of the first evidence from molecular data for the importance of faunal turnover in shaping biodiversity. Together, these results reveal living vertebrate biodiversity to be the product of volatile turnover punctuated by 6 accelerations responsible for >85% of all species as well as 3 slowdowns that have produced “living fossils.” In addition, by revealing the timing of the exceptional pulses of vertebrate diversification as well as the clades that experience them, our diversity tree provides a framework for evaluating particular causal hypotheses of vertebrate radiations.

Measuring Narrative Engagement

Abstract: Research indicates that the extent to which one becomes engaged, transported, or immersed in a narrative influences the narrative's potential to affect subsequent story-related attitudes and beliefs. Explaining narrative effects and understanding the mechanisms responsible depends on our ability to measure narrative engagement in a theoretically meaningful way. This article develops a scale for measuring narrative engagement that is based on a mental models approach to narrative processing. It distinguishes among four dimensions of experiential engagement in narratives: narrative understanding, attentional focus, emotional engagement, and narrative presence. The scale is developed and validated through exploratory and confirmatory factor analyses with data from viewers of feature film and television, in different viewing situations, and from two different countries. The scale's ability to predict enjoyment and story-consistent attitudes across different programs is presented. Implications for conceptualiz...

When Customer Love Turns into Lasting Hate:The Effects of Relationship Strength and Time on Customer Revenge and Avoidance

Abstract: This article explores the effects of time and relationship strength on the evolution of customer revenge and avoidance in online public complaining contexts. First, the authors examine whether online complainers hold a grudge—in terms of revenge and avoidance desires—over time. They find that time affects the two desires differently: Although revenge decreases over time, avoidance increases over time, indicating that customers indeed hold a grudge. Second, the authors examine the moderation effect of a strong relationship on how customers hold this grudge. They find that firms' best customers have the longest unfavorable reactions (i.e., a longitudinal love-becomes-hate effect). Specifically, over time, the revenge of strong-relationship customers decreases more slowly and their avoidance increases more rapidly than that of weak-relationship customers. Third, the authors explore a solution to attenuate this damaging effect—namely, the firm offering an apology and compensation after the online com...

The Importance of a General Measure of Brand Engagement on Market Behavior: Development and Validation of a Scale

Abstract: Brand engagement in self-concept (BESC) is a generalized view of brands in relation to the self, with consumers varying in their tendency to include important brands as part of their self-concepts. The authors develop an eight-item scale to measure BESC and demonstrate that it captures a consumer's general engagement with brands. This scale successfully predicts consumers' differential attention to, memory of, and preference for their favorite brands. Brand engagement in self-concept is also related to differential brand loyalty, with high-BESC consumers being less price and time sensitive regarding their favorite brands than low-BESC consumers. The authors discuss the usefulness of this construct for marketing research.

The Influence of Website Characteristics on a Consumer's Urge to Buy Impulsively

Abstract: With the proliferation of e-commerce, there is growing evidence that online impulse buying is occurring, yet relatively few researchers have studied this phenomenon. This paper reports on two studies that examine how variations in a website influence online impulse buying. The results reveal some relevant insights about this phenomenon. Specifically, although many participants had the urge to buy impulsively, regardless of website quality, this behavior's likelihood and magnitude was directly influenced by varying the quality of task-relevant and mood-relevant cues. Task-relevant cues include characteristics, such as navigability, that help in the attainment of the online consumer's shopping goal. Conversely, mood-relevant cues refer to the characteristics, such as visual appeal, that affect the degree to which a user enjoys browsing a website but that do not directly support a particular shopping goal. The implications of the results for both future research and the design of human-computer interfaces are discussed.

The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

Abstract: We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species.

Development and implementation of high-throughput SNP genotyping in barley

Abstract: High density genetic maps of plants have, nearly without exception, made use of marker datasets containing missing or questionable genotype calls derived from a variety of genic and non-genic or anonymous markers, and been presented as a single linear order of genetic loci for each linkage group. The consequences of missing or erroneous data include falsely separated markers, expansion of cM distances and incorrect marker order. These imperfections are amplified in consensus maps and problematic when fine resolution is critical including comparative genome analyses and map-based cloning. Here we provide a new paradigm, a high-density consensus genetic map of barley based only on complete and error-free datasets and genic markers, represented accurately by graphs and approximately by a best-fit linear order, and supported by a readily available SNP genotyping resource. Approximately 22,000 SNPs were identified from barley ESTs and sequenced amplicons; 4,596 of them were tested for performance in three pilot phase Illumina GoldenGate assays. Data from three barley doubled haploid mapping populations supported the production of an initial consensus map. Over 200 germplasm selections, principally European and US breeding material, were used to estimate minor allele frequency (MAF) for each SNP. We selected 3,072 of these tested SNPs based on technical performance, map location, MAF and biological interest to fill two 1536-SNP "production" assays (BOPA1 and BOPA2), which were made available to the barley genetics community. Data were added using BOPA1 from a fourth mapping population to yield a consensus map containing 2,943 SNP loci in 975 marker bins covering a genetic distance of 1099 cM. The unprecedented density of genic markers and marker bins enabled a high resolution comparison of the genomes of barley and rice. Low recombination in pericentric regions is evident from bins containing many more than the average number of markers, meaning that a large number of genes are recombinationally locked into the genetic centromeric regions of several barley chromosomes. Examination of US breeding germplasm illustrated the usefulness of BOPA1 and BOPA2 in that they provide excellent marker density and sensitivity for detection of minor alleles in this genetically narrow material.

The ACS Fornax Cluster Survey. V. Measurement and Recalibration of Surface Brightness Fluctuations and a Precise Value of the Fornax-Virgo Relative Distance

Abstract: We present (g 475 – z 850) color and z 850-band surface brightness fluctuations (SBFs) measurements for 43 early-type galaxies in the Fornax cluster imaged with the Hubble Space Telescope Advanced Camera for Surveys. These are combined with our earlier measurements for Virgo cluster galaxies to derive a revised, nonlinear calibration of the z 850-band SBF absolute magnitude as a function of (g 475 – z 850) color, valid for the AB color range 0.8 1.02, but it is about twice as large for bluer galaxies. We also present an alternative SBF calibration based on the "fluctuation count" parameter , a proxy for galaxy mass. This gives a consistent relative distance but with larger intrinsic scatter, and we adopt the result from the calibration on (g 475 – z 850) because of its basis in stellar population properties alone. Finally, we find no evidence for systematic trends of the galaxy distances with position or velocity (e.g., no current infall); the Fornax cluster appears both compact and well virialized.

Ca 2+ /calmodulin regulates salicylic-acid-mediated plant immunity

Abstract: Intracellular calcium transients during plant-pathogen interactions are necessary early events leading to local and systemic acquired resistance. Salicylic acid, a critical messenger, is also required for both of these responses, but whether and how salicylic acid level is regulated by Ca(2+) signalling during plant-pathogen interaction is unclear. Here we report a mechanism connecting Ca(2+) signal to salicylic-acid-mediated immune response through calmodulin, AtSR1 (also known as CAMTA3), a Ca(2+)/calmodulin-binding transcription factor, and EDS1, an established regulator of salicylic acid level. Constitutive disease resistance and elevated levels of salicylic acid in loss-of-function alleles of Arabidopsis AtSR1 suggest that AtSR1 is a negative regulator of plant immunity. This was confirmed by epistasis analysis with mutants of compromised salicylic acid accumulation and disease resistance. We show that AtSR1 interacts with the promoter of EDS1 and represses its expression. Furthermore, Ca(2+)/calmodulin-binding to AtSR1 is required for suppression of plant defence, indicating a direct role for Ca(2+)/calmodulin in regulating the function of AtSR1. These results reveal a previously unknown regulatory mechanism linking Ca(2+) signalling to salicylic acid level.

Networks-on-Chip in a Three-Dimensional Environment: A Performance Evaluation

Abstract: The Network-on-Chip (NoC) paradigm has emerged as a revolutionary methodology for integrating a very high number of intellectual property (IP) blocks in a single die. The achievable performance benefit arising out of adopting NoCs is constrained by the performance limitation imposed by the metal wire, which is the physical realization of communication channels. With technology scaling, only depending on the material innovation will extend the lifetime of conventional interconnect systems a few technology generations. According to International Technology Roadmap for Semiconductors (ITRS) for the longer term, new interconnect paradigms are in need. The conventional two dimensional (2D) integrated circuit (IC) has limited floor-planning choices, and consequently it limits the performance enhancements arising out of NoC architectures. Three dimensional (3D) ICs are capable of achieving better performance, functionality, and packaging density compared to more traditional planar ICs. On the other hand, NoC is an enabling solution for integrating large numbers of embedded cores in a single die. 3D NoC architectures combine the benefits of these two new domains to offer an unprecedented performance gain. In this paper we evaluate the performance of 3D NoC architectures and demonstrate their superior functionality in terms of throughput, latency, energy dissipation and wiring area overhead compared to traditional 2D implementations.

Aquatic therapy: scientific foundations and clinical rehabilitation applications

Abstract: The aquatic environment has broad rehabilitative potential, extending from the treatment of acute injuries through health maintenance in the face of chronic diseases, yet it remains an underused modality. There is an extensive research base supporting aquatic therapy, both within the basic science literature and clinical literature. This article describes the many physiologic changes that occur during immersion as applied to a range of common rehabilitative issues and problems. Because of its wide margin of therapeutic safety and clinical adaptability, aquatic therapy is a very useful tool in the rehabilitative toolbox. Through a better understanding of the applied physiology, the practitioner may structure appropriate therapeutic programs for a diverse patient population.

Implications of global climate change for snowmelt hydrology in the twenty-first century.

Abstract: For most of the global land area poleward of about 40° latitude, snow plays an important role in the water cycle. The (seasonal) timing of runoff in these areas is especially sensitive to projected losses of snowpack associated with warming trends, whereas projected (annual) runoff volume changes are primarily associated with precipitation changes, and to a lesser extent, with changes in evapotranspiration (ET). Regional studies in the USA (and especially the western USA) suggest that hydrologic adjustments to a warming climate have been ongoing since the mid-twentieth century. We extend the insights extracted from the western USA to the global scale using a physically based hydrologic model to assess the effects of systematic changes in precipitation and temperature on snow-affected portions of the global land area as projected by a suite of global climate models. While annual (and in some cases seasonal) changes in precipitation are a key driver of projected changes in annual runoff, we find, as in the western USA, that projected warming produces strong decreases in winter snow accumulation and spring snowmelt over much of the affected area regardless of precipitation change. Decreased snowpack produces decreases in warm-season runoff in many mid- to high-latitude areas where precipitation changes are either moderately positive or negative in the future projections. Exceptions, however, occur in some high-latitude areas, particular in Eurasia, where changes in projected precipitation are large enough to result in increased, rather than decreased, snow accumulation. Overall, projected changes in snowpack and the timing of snowmelt-derived runoff are largest near the boundaries of the areas that currently experience substantial snowfall, and at least qualitatively, they mirror the character of observed changes in the western USA. Copyright © 2008 John Wiley & Sons, Ltd.

Keeping the Resident in the Loop: Adapting the Smart Home to the User

Abstract: Advancements in supporting fields have increased the likelihood that smart-home technologies will become part of our everyday environments. However, many of these technologies are brittle and do not adapt to the user's explicit or implicit wishes. Here, we introduce CASAS, an adaptive smart-home system that utilizes machine learning techniques to discover patterns in resident's daily activities and to generate automation polices that mimic these patterns. Our approach does not make any assumptions about the activity structure or other underlying model parameters but leaves it completely to our algorithms to discover the smart-home resident's patterns. Another important aspect of CASAS is that it can adapt to changes in the discovered patterns based on the resident implicit and explicit feedback and can automatically update its model to reflect the changes. In this paper, we provide a description of the CASAS technologies and the results of experiments performed on both synthetic and real-world data.

Quorum Sensing: A New Biofouling Control Paradigm in a Membrane Bioreactor for Advanced Wastewater Treatment

Abstract: Bacteria regulate specific group behaviors such as biofilm formation in response to population density using small signal molecules called autoinducers (quorum sensing, QS). In this study, the concept of bacterial QS was applied to membrane bioreactors (MBRs) for advanced wastewater treatment as a new biofouling control paradigm. The research was conducted in three phases: (1) demonstrate the presence of the autoinducer signal in MBRs, (2) correlate QS activity and membrane biofouling, (3) apply QS-based membrane biofouling control. A bioassay with Agrobacterium tumefaciens reporter strain proved that N-acyl homoserine lactone (AHL) autoinducers were produced in the MBR. Furthermore, thin-layer chromatographic analysis identified at least three different AHLs in the biocake, of which N-octanoyl-homoserine lactone was the most abundant. During continuous MBR operation, the biocake showed strong AHL activity simultaneously with abrupt increase in the transmembrane pressure, which implies that QS is in close...

Interdisciplinarity: A Critical Assessment

Abstract: This article draws together disparate research and theorizing on interdisciplinarity. We first describe widespread efforts to promote interdisciplinarity in U.S. universities and critically examine the assumptions underlying these initiatives. Next, we present a cross-sectional view of interdisciplinary communication, knowledge diffusion, research assessment, and interdisciplinary research centers. We then describe research and theories that provide historical perspectives on the disciplinary system, interdiscipline formation, applied and professional fields, and institutional fragmentation. We present original findings on the prevalence of research centers, faculty hiring patterns in hybrid fields, and the diffusion of research across disciplines in the humanities and social sciences. The review concludes with a critical summary and suggestions for future research.

Assessing the Quality of Activities in a Smart Environment

Abstract: Objectives: Pervasive computing technology can provide valuable health monitoring and assistance technology to help individuals live independent lives in their own homes. As a critical part of this technology, our objective is to design software algorithms that recognize and assess the consistency of activities of daily living that individuals perform in their own homes. Methods: We have designed algorithms that automatically learn Markov models for each class of activity. These models are used to recognize activities that are performed in a smart home and to identify errors and inconsistencies in the performed activity. Results: We validate our approach using data collected from 60 volunteers who performed a series of activities in our smart apartment testbed. The results indicate that the algorithms correctly label the activities and successfully assess the completeness and consistency of the performed task. Conclusions: Our results indicate that activity recognition and assessment can be automated using machine learning algorithms and smart home technology. These algorithms will be useful for automating remote health monitoring and interventions.

An upper limit on the stochastic gravitational-wave background of cosmological origin

Abstract: A stochastic background of gravitational waves is expected to arise from a superposition of a large number of unresolved gravitational-wave sources of astrophysical and cosmological origin. It should carry unique signatures from the earliest epochs in the evolution of the Universe, inaccessible to standard astrophysical observations. Direct measurements of the amplitude of this background are therefore of fundamental importance for understanding the evolution of the Universe when it was younger than one minute. Here we report limits on the amplitude of the stochastic gravitational-wave background using the data from a two-year science run of the Laser Interferometer Gravitational-wave Observatory (LIGO). Our result constrains the energy density of the stochastic gravitational-wave background normalized by the critical energy density of the Universe, in the frequency band around 100 Hz, to be <6.9 times 10-6 at 95% confidence. The data rule out models of early Universe evolution with relatively large equation-of-state parameter, as well as cosmic (super)string models with relatively small string tension that are favoured in some string theory models. This search for the stochastic background improves on the indirect limits from Big Bang nucleosynthesis and cosmic microwave background at 100 Hz.

Social Value Orientation and Cooperation in Social Dilemmas: A Meta-Analysis

Abstract: This article reports a meta-analysis of 82 studies assessing the relationship between social value orientation (SVO) and cooperation in social dilemmas. A significant and small to medium effect size was found (r = .30). Results supported a hypothesis that the effect size was larger when participants were not paid (r = .39) than when they were paid (r = .23). The effect size was also larger in give-some (r = .29) as opposed to take-some (r = .22) games. However, contrary to expectations, the effect was not larger in one-shot, as opposed to iterated games. Findings are discussed in the context of theory on SVO and directions for future research are outlined.

The regional and global significance of nitrogen removal in lakes and reservoirs

Abstract: Human activities have greatly increased the transport of biologically available nitrogen (N) through watersheds to potentially sensitive coastal ecosystems. Lentic water bodies (lakes and reservoirs) have the potential to act as important sinks for this reactive N as it is transported across the landscape because they offer ideal conditions for N burial in sediments or permanent loss via denitrification. However, the patterns and controls on lentic N removal have not been explored in great detail at large regional to global scales. In this paper we describe, evaluate, and apply a new, spatially explicit, annual-scale, global model of lentic N removal called NiRReLa (Nitrogen Retention in Reservoirs and Lakes). The NiRReLa model incorporates small lakes and reservoirs than have been included in previous global analyses, and also allows for separate treatment and analysis of reservoirs and natural lakes. Model runs for the mid-1990s indicate that lentic systems are indeed important sinks for N and are conservatively estimated to remove 19.7 Tg N year−1 from watersheds globally. Small lakes (<50 km2) were critical in the analysis, retaining almost half (9.3 Tg N year−1) of the global total. In model runs, capacity of lakes and reservoirs to remove watershed N varied substantially at the half-degree scale (0–100%) both as a function of climate and the density of lentic systems. Although reservoirs occupy just 6% of the global lentic surface area, we estimate they retain ~33% of the total N removed by lentic systems, due to a combination of higher drainage ratios (catchment surface area:lake or reservoir surface area), higher apparent settling velocities for N, and greater average N loading rates in reservoirs than in lakes. Finally, a sensitivity analysis of NiRReLa suggests that, on-average, N removal within lentic systems will respond more strongly to changes in land use and N loading than to changes in climate at the global scale.