Showing papers by "University of Oregon published in 2007"

A caution regarding rules of thumb for variance inflation factors.

Abstract: The Variance Inflation Factor (VIF) and tolerance are both widely used measures of the degree of multi-collinearity of the ith independent variable with the other independent variables in a regression model. Unfortunately, several rules of thumb – most commonly the rule of 10 – associated with VIF are regarded by many practitioners as a sign of severe or serious multi-collinearity (this rule appears in both scholarly articles and advanced statistical textbooks). When VIF reaches these threshold values researchers often attempt to reduce the collinearity by eliminating one or more variables from their analysis; using Ridge Regression to analyze their data; or combining two or more independent variables into a single index. These techniques for curing problems associated with multi-collinearity can create problems more serious than those they solve. Because of this, we examine these rules of thumb and find that threshold values of the VIF (and tolerance) need to be evaluated in the context of several other factors that influence the variance of regression coefficients. Values of the VIF of 10, 20, 40, or even higher do not, by themselves, discount the results of regression analyses, call for the elimination of one or more independent variables from the analysis, suggest the use of ridge regression, or require combining of independent variable into a single index.

Research on Attention Networks as a Model for the Integration of Psychological Science

Abstract: As Titchener pointed out more than one hundred years ago, attention is at the center of the psychological enterprise. Attention research investigates how voluntary control and subjective experience arise from and regulate our behavior. In recent years, attention has been one of the fastest growing of all fields within cognitive psychology and cognitive neuroscience. This review examines attention as characterized by linking common neural networks with individual differences in their efficient utilization. The development of attentional networks is partly specified by genes, but is also open to specific experiences through the actions of caregivers and the culture. We believe that the connection between neural networks, genes, and socialization provides a common approach to all aspects of human cognition and emotion. Pursuit of this approach can provide a basis for psychology that unifies social, cultural, differential, experimental, and physiological areas, and allows normal development to serve as a baseline for understanding various forms of pathology. D.O. Hebb proposed this approach 50 years ago in his volume Organization of Behavior and continued with introductory textbooks that dealt with all of the topics of psychology in a common framework. Use of a common network approach to psychological science may allow a foundation for predicting and understanding human behavior in its varied forms.

The meaning of the body : aesthetics of human understanding

Abstract: In "The Meaning of the Body", Mark Johnson continues his pioneering work on the exciting connections between cognitive science, language, and meaning first begun in the classic "Metaphors We Live By". Johnson uses recent research into infant psychology to show how the body generates meaning even before self-consciousness has fully developed. From there he turns to cognitive neuroscience to further explore the bodily origins of meaning, thought, and language and examines the many dimensions of meaning - including images, qualities, emotions, and metaphors - that are all rooted in the body's physical encounters with the world. Drawing on the psychology of art and pragmatist philosophy, Johnson argues that all of these aspects of meaning-making are fundamentally aesthetic. He concludes that the arts are the culmination of human attempts to find meaning and that studying the aesthetic dimensions of our experience is crucial to unlocking meaning's bodily sources.Throughout, Johnson puts forth a bold new conception of the mind rooted in the understanding that philosophy will matter to nonphilosophers only if it is built on a visceral connection to the world.

Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers

Abstract: Restriction site associated DNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.

The role of ecological theory in microbial ecology

Abstract: Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.

Neural responses to taxation and voluntary giving reveal motives for charitable donations.

Abstract: Civil societies function because people pay taxes and make charitable contributions to provide public goods. One possible motive for charitable contributions, called "pure altruism," is satisfied by increases in the public good no matter the source or intent. Another possible motive, "warm glow," is only fulfilled by an individual's own voluntary donations. Consistent with pure altruism, we find that even mandatory, tax-like transfers to a charity elicit neural activity in areas linked to reward processing. Moreover, neural responses to the charity's financial gains predict voluntary giving. However, consistent with warm glow, neural activity further increases when people make transfers voluntarily. Both pure altruism and warm-glow motives appear to determine the hedonic consequences of financial transfers to the public good.

Do increases in patient activation result in improved self-management behaviors?

Abstract: Objective The purpose of this study is to determine whether patient activation is a changing or changeable characteristic and to assess whether changes in activation also are accompanied by changes in health behavior.

Ultralow Thermal Conductivity in Disordered, Layered WSe2 Crystals

Abstract: The cross-plane thermal conductivity of thin films of WSe2 grown from alternating W and Se layers is as small as 0.05 watts per meter per degree kelvin at room temperature, 30 times smaller than the c-axis thermal conductivity of single-crystal WSe2 and a factor of 6 smaller than the predicted minimum thermal conductivity for this material. We attribute the ultralow thermal conductivity of these disordered, layered crystals to the localization of lattice vibrations induced by the random stacking of two-dimensional crystalline WSe2 sheets. Disordering of the layered structure by ion bombardment increases the thermal conductivity.

Temperament, Development, and Personality:

Abstract: Understanding temperament is central to our understanding of development, and temperament constructs are linked to individual differences in both personality and underlying neural function. In this article, I review findings on the structure of temperament, its relation to the Big Five traits of personality, and its links to development and psychopathology. In addition, I discuss the relation of temperament to conscience, empathy, aggression, and the development of behavior problems, and describe the relation between effortful control and neural networks of executive attention. Finally, I present research on training executive attention.

If I Look at the Mass I Will Never Act: Psychic Numbing and Genocide

Abstract: Most people are caring and will exert great effort to rescue individual victims whose needy plight comes to their attention. These same good people, however, often become numbly indifferent to the plight of individuals who are “one of many” in a much greater problem. Why does this occur? The answer to this question will help us answer a related question that is the topic of this paper: Why, over the past century, have good people repeatedly ignored mass murder and genocide? Every episode of mass murder is unique and raises unique obstacles to intervention. But the repetitiveness of such atrocities, ignored by powerful people and nations, and by the general public, calls for explanations that may reflect some fundamental deficiency in our humanity — a deficiency that, once identified, might possibly be overcome. One fundamental mechanism that may play a role in many, if not all, episodes of mass-murder neglect involves the capacity to experience affect, the positive and negative feelings that combine with reasoned analysis to guide our judgments, decisions, and actions. I shall draw from psychological research to show how the statistics of mass murder or genocide, no matter how large the numbers, fail to convey the true meaning of such atrocities. The reported numbers of deaths represent dry statistics, “human beings with the tears dried off,” that fail to spark emotion or feeling and thus fail to motivate action. Recognizing that we cannot rely only upon our moral feelings to motivate proper action against genocide, we must look to moral argument and international law. The 1948 Genocide Convention was supposed to meet this need, but it has not been effective. It is time to examine this failure in light of the psychological deficiencies described here and design legal and institutional mechanisms that will enforce proper response to genocide and other forms of mass murder.

Visual Working Memory Represents a Fixed Number of Items Regardless of Complexity

Abstract: Does visual working memory represent a fixed number of objects, or is capacity reduced as object complexity increases? We measured accuracy in detecting changes between sample and test displays and found that capacity estimates dropped as complexity increased. However, these apparent capacity reductions were strongly correlated with increases in sample-test similarity (r= .97), raising the possibility that change detection was limited by errors in comparing the sample and test, rather than by the number of items that were maintained in working memory. Accordingly, when sample-test similarity was low, capacity estimates for even the most complex objects were equivalent to the estimate for the simplest objects (r= .88), suggesting that visual working memory represents a fixed number of items regardless of complexity. Finally, a correlational analysis suggested a two-factor model of working memory ability, in which the number and resolution of representations in working memory correspond to distinct dimensions of memory ability.

What a Drop Can Do: Dried Blood Spots as a Minimally Invasive Method for Integrating Biomarkers Into Population-Based Research

Abstract: Logistical constraints associated with the collection and analysis of biological samples in community-based settings have been a significant impediment to integrative, multilevel biodemographic and biobehavioral research. However, recent methodological developments have overcome many of these constraints and have also expanded the options for incorporating biomarkers into population-based health research in international as well as domestic contexts. In particular, using dried blood spot (DBS) samples—drops of whole blood collected on filter paper from a simple finger prick— provides a minimally invasive method for collecting blood samples in nonclinical settings. After a brief discussion of biomarkers more generally, we review procedures for collecting, handling, and analyzing DBS samples. Advantages of using DBS samples—compared with venipuncture—include the relative ease and low cost of sample collection, transport, and storage. Disadvantages include requirements for assay development and validation as well as the relatively small volumes of sample. We present the results of a comprehensive literature review of published protocols for analysis of DBS samples, and we provide more detailed analysis of protocols for 45 analytes likely to be of particular relevance to population-level health research. Our objective is to provide investigators with the information they need to make informed decisions regarding the appropriateness of blood spot methods for their research interests.

Toward a broader conception of creativity: A case for "mini-c" creativity.

Abstract: In this article the authors argue that a new category of creativity, called “mini-c” creativity, is needed to advance creativity theory and research. Mini-c creativity differs from little-c (everyday) or Big-C (eminent) creativity as it refers to the creative processes involved in the construction of personal knowledge and understanding. The authors discuss how the category of mini-c creativity addresses gaps in current conceptions of creativity, offers researchers a new and important unit of analysis, and helps to better frame the domain question in creativity research. Implications for creativity research are also discussed.

A two-color acid-free cartilage and bone stain for zebrafish larvae.

Abstract: Traditionally, cartilage is stained by alcian blue using acidic conditions to differentiate tissue staining. The acidic conditions are problematic when one wishes to stain the same specimen for mineralized bone with alizarin red, because acid demineralizes bone, which negatively affects bone staining. We have developed an acid-free method to stain cartilage and bone simultaneously in zebrafish larvae. This method has the additional advantage that PCR genotyping of stained specimens is possible.

Culture and Identity-Protective Cognition: Explaining the White Male Effect in Risk Perception

Abstract: Why do white men fear various risks less than women and minorities? Known as the white male effect, this pattern is well documented but poorly understood. This paper proposes a new explanation: identity-protective cognition. Putting work on the cultural theory of risk together with work on motivated cognition in social psychology suggests that individuals selectively credit and dismiss asserted dangers in a manner supportive of their preferred form of social organization. This dynamic, it is hypothesized, drives the white male effect, which reflects the risk skepticism that hierarchical and individualistic white males display when activities integral to their cultural identities are challenged as harmful. The article presents the results of an 1,800-person study that confirmed that cultural worldviews interact with the impact of gender and race on risk perception in patterns that suggest cultural-identity-protective cognition. It also discusses the implication of these findings for risk regulation and communication.

Culture and Identity-Protective Cognition: Explaining the White-Male Effect in Risk Perception

Abstract: Why do white men fear various risks less than women and minorities? Known as the “white-male effect,” this pattern is well documented but poorly understood. This article proposes a new explanation: identityprotective cognition. Putting work on the cultural theory of risk together with work on motivated cognition in social psychology suggests that individuals selectively credit and dismiss asserted dangers in a manner supportive of their cultural identities. This dynamic, it is hypothesized, drives the white-male effect, which reflects the risk skepticism that hierarchical and individualistic white males display when activities integral to their cultural identities are challenged as harmful. The article presents the results of an 1,800-person study that confirmed that cultural worldviews interact with the impact of gender and race on risk perception in patterns that suggest cultural-identity-protective cognition. It also discusses the implications of these findings for risk regulation and communication. Fear discriminates. Numerous studies show that risk perceptions are skewed across gender and race: women worry more than men, and minorities more than whites, about myriad dangers—from environmental pollution to

The Treatment for Adolescents with Depression Study (TADS): Long-term effectiveness and safety outcomes

Abstract: CONTEXT: The Treatment for Adolescents With Depression Study evaluates the effectiveness of fluoxetine hydrochloride therapy, cognitive behavior therapy (CBT), and their combination in adolescents with major depressive disorder. OBJECTIVE: To report effectiveness outcomes across 36 weeks of randomized treatment. DESIGN AND SETTING: Randomized, controlled trial conducted in 13 academic and community sites in the United States. Cognitive behavior and combination therapies were not masked, whereas administration of placebo and fluoxetine was double-blind through 12 weeks, after which treatments were unblinded. Patients assigned to placebo were treated openly after week 12, and the placebo group is not included in these analyses by design. PARTICIPANTS: Three hundred twenty-seven patients aged 12 to 17 years with a primary DSM-IV diagnosis of major depressive disorder. INTERVENTIONS: All treatments were administered per protocol. MAIN OUTCOME MEASURES: The primary dependent measures rated blind to treatment status by an independent evaluator were the Children's Depression Rating Scale-Revised total score and the response rate, defined as a Clinical Global Impressions-Improvement score of much or very much improved. RESULTS: Intention-to-treat analyses on the Children's Depression Rating Scale-Revised identified a significant time x treatment interaction (P Language: en

Generation and Photonic Guidance of Multi-Octave Optical-Frequency Combs

Abstract: Ultrabroad coherent comb-like optical spectra spanning several octaves are a chief ingredient in the emerging field of attoscience. We demonstrate generation and guidance of a three-octave spectral comb, spanning wavelengths from 325 to 2300 nanometers, in a hydrogen-filled hollow-core photonic crystal fiber. The waveguidance results not from a photonic band gap but from the inhibited coupling between the core and cladding modes. The spectrum consists of up to 45 high-order Stokes and anti-Stokes lines and is generated by driving the confined gas with a single, moderately powerful (10-kilowatt) infrared laser, producing 12-nanosecond-duration pulses. This represents a reduction by six orders of magnitude in the required laser powers over previous equivalent techniques and opens up a robust and much simplified route to synthesizing attosecond pulses.

Evidence for an extraterrestrial impact 12,900 years ago that contributed to the megafaunal extinctions and the Younger Dryas cooling

Abstract: A carbon-rich black layer, dating to ≈12.9 ka, has been previously identified at ≈50 Clovis-age sites across North America and appears contemporaneous with the abrupt onset of Younger Dryas (YD) cooling. The in situ bones of extinct Pleistocene megafauna, along with Clovis tool assemblages, occur below this black layer but not within or above it. Causes for the extinctions, YD cooling, and termination of Clovis culture have long been controversial. In this paper, we provide evidence for an extraterrestrial (ET) impact event at ≅12.9 ka, which we hypothesize caused abrupt environmental changes that contributed to YD cooling, major ecological reorganization, broad-scale extinctions, and rapid human behavioral shifts at the end of the Clovis Period. Clovis-age sites in North American are overlain by a thin, discrete layer with varying peak abundances of (i) magnetic grains with iridium, (ii) magnetic microspherules, (iii) charcoal, (iv) soot, (v) carbon spherules, (vi) glass-like carbon containing nanodiamonds, and (vii) fullerenes with ET helium, all of which are evidence for an ET impact and associated biomass burning at ≈12.9 ka. This layer also extends throughout at least 15 Carolina Bays, which are unique, elliptical depressions, oriented to the northwest across the Atlantic Coastal Plain. We propose that one or more large, low-density ET objects exploded over northern North America, partially destabilizing the Laurentide Ice Sheet and triggering YD cooling. The shock wave, thermal pulse, and event-related environmental effects (e.g., extensive biomass burning and food limitations) contributed to end-Pleistocene megafaunal extinctions and adaptive shifts among PaleoAmericans in North America.

Evolution of Animal Photoperiodism

Abstract: Photoperiodism is the ability of organisms to assess and use the day length as an anticipatory cue to time seasonal events in their life histories. Photoperiodism is especially important in initiating physiological and developmental processes that are typically irrevocable and that culminate at a future time or at a distant place; the further away in space or time, the more likely a seasonal event is initiated by photoperiod. The pervasiveness of photoperiodism across broad taxa, from rotifers to rodents, and the predictable changes of photoperiodic response with geography identify it as a central component of fitness in temperate and polar seasonal environments. Consequently, the role of day length cannot be disregarded when evaluating the mechanisms underlying life-historical events, range expansions, invasions of novel species, and response to climate change among animals in the temperate and polar regions of the world.

Less is more in presenting quality information to consumers.

Abstract: Much effort has been put into improving measures of health care quality. Although early research suggested that consumers made little use of quality reports, most reports were based on nonstandardized measures and were not user friendly. Information presentation approaches, however, will have a significant influence on what information is attended and used. The present research examines whether information presentation methods differentially influence consumers who differ in numeric skills. Results of three studies support the idea that "less is more" when presenting consumers with comparative performance information to make hospital choices. Results were particularly strong for those lower in numeracy, who had higher comprehension and made better choices when the information-presentation format was designed to ease the cognitive burden and highlight the meaning of important information. These findings have important implications for the sponsors of comparative quality reports designed to inform consumer decision making in health care.

Clathrate nanostructures for mass spectrometry

Abstract: The ability of mass spectrometry to generate intact biomolecular ions efficiently in the gas phase has led to its widespread application in metabolomics, proteomics, biological imaging, biomarker discovery and clinical assays (namely neonatal screens). Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization have been at the forefront of these developments. However, matrix application complicates the use of MALDI for cellular, tissue, biofluid and microarray analysis and can limit the spatial resolution because of the matrix crystal size (typically more than 10 mum), sensitivity and detection of small compounds (less than 500 Da). Secondary-ion mass spectrometry has extremely high lateral resolution (100 nm) and has found biological applications although the energetic desorption/ionization is a limitation owing to molecular fragmentation. Here we introduce nanostructure-initiator mass spectrometry (NIMS), a tool for spatially defined mass analysis. NIMS uses 'initiator' molecules trapped in nanostructured surfaces or 'clathrates' to release and ionize intact molecules adsorbed on the surface. This surface responds to both ion and laser irradiation. The lateral resolution (ion-NIMS about 150 nm), sensitivity, matrix-free and reduced fragmentation of NIMS allows direct characterization of peptide microarrays, direct mass analysis of single cells, tissue imaging, and direct characterization of blood and urine.

Numeracy Skill And The Communication, Comprehension, And Use Of Risk-Benefit Information

Abstract: Current health care policy emphasizes improving health outcomes and the efficacy of health care delivery by supporting informed consumer choices. At the same time, health information often involves uncertainty, and many people may lack the skills and knowledge to process this information, manage their health and health care, and make informed choices. Innumeracy, an element of poor health literacy, is associated with the comprehension and use of important health information. We review this literature and examine what can be done to help less numerate people act more effectively and take charge of their health.

Implicit theories of emotion: affective and social outcomes across a major life transition.

Abstract: The authors demonstrate that people differ systematically in their implicit theories of emotion: Some view emotions as fixed (entity theorists), whereas others view emotions as more malleable (incremental theorists). Using a longitudinal and multimethod design, the authors show that implicit theories of emotion, as distinct from intelligence, are linked to both emotional and social adjustment during the transition to college. Before entering college, individuals who held entity (vs. incremental) theories of emotion had lower emotion regulation self-efficacy and made less use of cognitive reappraisal (Part 1). Throughout their first academic term, entity theorists of emotion had less favorable emotion experiences and received decreasing social support from their new friends, as evidenced by weekly diaries (Part 2). By the end of freshman year, entity theorists of emotion had lower well-being, greater depressive symptoms, and lower social adjustment as indicated in both self- and peer-reports (Part 3). The emotional, but not the social, outcomes were partially mediated by individual differences in emotion regulation self-efficacy (Part 4). Together, these studies demonstrate that implicit theories of emotion can have important long-term implications for socioemotional functioning.

Crystal structure of an ancient protein: evolution by conformational epistasis.

Abstract: The structural mechanisms by which proteins have evolved new functions are known only indirectly. We report x-ray crystal structures of a resurrected ancestral protein-the approximately 450 million-year-old precursor of vertebrate glucocorticoid (GR) and mineralocorticoid (MR) receptors. Using structural, phylogenetic, and functional analysis, we identify the specific set of historical mutations that recapitulate the evolution of GR's hormone specificity from an MR-like ancestor. These substitutions repositioned crucial residues to create new receptor-ligand and intraprotein contacts. Strong epistatic interactions occur because one substitution changes the conformational position of another site. "Permissive" mutations-substitutions of no immediate consequence, which stabilize specific elements of the protein and allow it to tolerate subsequent function-switching changes-played a major role in determining GR's evolutionary trajectory.