Showing papers by "University of Oregon published in 2000"

The evolutionary fate and consequences of duplicate genes

Abstract: Gene duplication has generally been viewed as a necessary source of material for the origin of evolutionary novelties, but it is unclear how often gene duplicates arise and how frequently they evolve new functions. Observations from the genomic databases for several eukaryotic species suggest that duplicate genes arise at a very high rate, on average 0.01 per gene per million years. Most duplicated genes experience a brief period of relaxed selection early in their history, with a moderate fraction of them evolving in an effectively neutral manner during this period. However, the vast majority of gene duplicates are silenced within a few million years, with the few survivors subsequently experiencing strong purifying selection. Although duplicate genes may only rarely evolve new functions, the stochastic silencing of such genes may play a significant role in the passive origin of new species.

Predicting the probability for falls in community-dwelling older adults using the Timed Up & Go Test.

Abstract: Background and Purpose. This study examined the sensitivity and specificity of the Timed Up & Go Test (TUG) under single-task versus dual-task conditions for identifying elderly individuals who are prone to falling. Subjects. Fifteen older adults with no history of falls (mean age578 years, SD56, range565‐ 85) and 15 older adults with a history of 2 or more falls in the previous 6 months (mean age586.2 years, SD56, range576 ‐95) participated. Methods. Time taken to complete the TUG under 3 conditions (TUG, TUG with a subtraction task [TUG cognitive], and TUG while carrying a full cup of water [TUG manual]) was measured. A multivariate analysis of variance and discriminant function and logistic regression analyses were performed. Results. The TUG was found to be a sensitive (sensitivity587%) and specific (specificity587%) measure for identifying elderly individuals who are prone to falls. For both groups of older adults, simultaneous performance of an additional task increased the time taken to complete the TUG, with the greatest effect in the older adults with a history of falls. The TUG scores with or without an additional task (cognitive or manual) were equivalent with respect to identifying fallers and nonfallers. Conclusions and Discussion. The results suggest that the TUG is a sensitive and specific measure for identifying communitydwelling adults who are at risk for falls. The ability to predict falls is not enhanced by adding a secondary task when performing the TUG. [Shumway-Cook A, Brauer S, Woollacott M. Predicting the probability for falls in community-dwelling older adults using the Timed Up & Go Test. Phys Ther. 2000;80:896 ‐903.]

The probability of duplicate gene preservation by subfunctionalization.

Abstract: It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 10 5 or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.

Temperament and personality: origins and outcomes.

Abstract: This article reviews how a temperament approach emphasizing biological and developmental processes can integrate constructs from subdisciplines of psychology to further the study of personality Basic measurement strategies and findings in the investigation of temperament in infancy and childhood are reviewed These include linkage of temperament dimensions with basic affective-motivational and attentional systems, including positive affecl/approach, fear, frustration/anger, and effortful control Contributions of biological models that may support these processes are then reviewed Research indicating how a temperament approach can lead researchers of social and personality development to investigate important person-environment interactions is also discussed Lastly, adult research suggesting links between temperament dispositions and the Big Five personality factors is described Temperament arises from our genetic endowment It influences and is influenced by the experience of each individual, and one of its outcomes is the adult personality An important goal of our research has been to specify processes at the levels of biology and social development that may link a child's early endowment to its later expression as an adult In this article, we suggest that understanding temperament is central to understanding personality Individual differences in temperament have implications for development in infancy and childhood, and they form the core of personality as it develops Temperament also provides processoriented models that are often lacking in trait theories of personality, by establishing links between individual differences in behavior and their psychological and biological substrates Temperament also can be used to relate human individual differences, through evolutionary models, to individual differences in nonhuman animals The purpose of this article is to review our approach to temperament research, indicating ways in which thinking about temperament can illuminate the understanding of individual differences Many of the guiding principles of this approach are already familiar to personality researchers, because they were laid out by those who helped to develop modern conceptions of personality Other principles may be less familiar, because they derive more heavily

Developing mechanisms of self-regulation

Abstract: Child development involves both reactive and self-regulatory mechanisms that children develop in conjunction with social norms. A half-century of research has uncovered aspects of the physical basis of attentional networks that produce regulation, and has given us some knowledge of how the social environment may alter them. In this paper, we discuss six forms of developmental plasticity related to aspects of attention. We then focus on effortful or executive aspects of attention, reviewing research on temperamental individual differences and important pathways to normal and pathological development. Pathologies of development may arise when regulatory and reactive systems fail to reach the balance that allows for both self-expression and socially acceptable behavior. It remains a challenge for our society during the next millennium to obtain the information necessary to design systems that allow a successful balance to be realized by the largest possible number of children.

Applying Positive Behavior Support and Functional Behavioral Assessment in Schools

Abstract: Positive behavior support (PBS) and functional behavioral assessment (FBA) are two significant concepts of the 1997 amendments to the Individuals with Disabilities Education Act. These two concepts...

Financing Policy, Basis Risk, and Corporate Hedging: Evidence from Oil and Gas Producers

Abstract: This paper studies the hedging policies of oil and gas producers between 1992 and 1994. My evidence shows that the extent of hedging is related to financing costs: In particular, companies with greater financial leverage manage price risks more extensively. My evidence also shows that the likelihood of hedging is related to economies of scale in hedging costs and to the basis risk associated with hedging instruments. Larger companies and companies whose production is located primarily in regions where prices have a high correlation with the prices on which exchangetraded derivatives are based are more likely to manage risks. DESPITE THE PREVALENCE OF CORPORATE RISK MANAGEMENT and the effort that has been devoted to developing theoretical rationales for hedging, there are no widely accepted explanations for risk management as a corporate policy. Important questions remain regarding the determinants of the extent to which a company hedges, the impact of risk management on a firm's value, and the interaction between a firm's hedging policy and its other policy decisions. To address some of these questions, I examine the risk management activities of 100 oil and gas producers for 1992 to 1994. In particular, I investigate whether the fraction of production an oil and gas producer hedges against price fluctuations is related to its financing policy, tax status, compensation policy, ownership structure, and operating characteristics. I document a wide variation in hedging policies among oil and gas producers. My tests find that this variation is associated with several differences in the firms' characteristics. The fraction of production hedged is positively related to the differences in financial leverage, measured as the ratio of total debt to total assets, and it is greater for oil and gas producers

The Baryonic Tully-Fisher Relation.

Abstract: We explore the Tully-Fisher relation over five decades in stellar mass in galaxies with circular velocities ranging over 30 Vc 300 km s-1. We find a clear break in the optical Tully-Fisher relation: field galaxies with Vc 90 km s-1 fall below the relation defined by brighter galaxies. These faint galaxies, however, are very rich in gas; adding in the gas mass and plotting the baryonic disk mass Md = M* + Mgas in place of luminosity restores the single linear relation. The Tully-Fisher relation thus appears fundamentally to be a relation between rotation velocity and total baryonic mass of the form Md ∝ V.

Zebrafish Comparative Genomics and the Origins of Vertebrate Chromosomes

Abstract: To help understand mechanisms of vertebrate genome evolution, we have compared zebrafish and tetrapod gene maps. It has been suggested that translocations are fixed more frequently than inversions in mammals. Gene maps showed that blocks of conserved syntenies between zebrafish and humans were large, but gene orders were frequently inverted and transposed. This shows that intrachromosomal rearrangements have been fixed more frequently than translocations. Duplicated chromosome segments suggest that a genome duplication occurred in ray-fin phylogeny, and comparative studies suggest that this event happened deep in the ancestry of teleost fish. Consideration of duplicate chromosome segments shows that at least 20% of duplicated gene pairs may be retained from this event. Despite genome duplication, zebrafish and humans have about the same number of chromosomes, and zebrafish chromosomes are mosaically orthologous to several human chromosomes. Is this because of an excess of chromosome fissions in the human lineage or an excess of chromosome fusions in the zebrafish lineage? Comparative analysis suggests that an excess of chromosome fissions in the tetrapod lineage may account for chromosome numbers and provides histories for several human chromosomes.

The Baryonic Tully-Fisher Relation

Abstract: We explore the Tully-Fisher relation over five decades in stellar mass in galaxies with circular velocities ranging over 30 < Vc < 300 km/s. We find a clear break in the optical Tully-Fisher relation: field galaxies with Vc < 90 km/s fall below the relation defined by brighter galaxies. These faint galaxies are however very gas rich; adding in the gas mass and plotting baryonic disk mass Md = M* + Mg in place of luminosity restores a single linear relation. The Tully-Fisher relation thus appears fundamentally to be a relation between rotation velocity and total baryonic mass of the form Md = A Vc^4.

Parenting Practices and Child Disruptive Behavior Problems in Early Elementary School

Abstract: Examined the hypothesis that distinct parenting practices may be associated with type and profile of a child's disruptive behavior problems (e.g., oppositional, aggressive, hyperactive). Parents of 631 behaviorally disruptive children described the extent to which they experienced warm and involved interactions with their children and the extent to which their discipline strategies were inconsistent and punitive and involved spanking and physical aggression. As expected from a developmental perspective, parenting practices that included punitive interactions were associated with elevated rates of all child disruptive behavior problems. Low levels of warm involvement were particularly characteristic of parents of children who showed elevated levels of oppositional behaviors. Physically aggressive parenting was linked more specifically with child aggression. In general, parenting practices contributed more to the prediction of oppositional and aggressive behavior problems than to hyperactive behavior proble...

Dimensions of Privacy Concern Among Online Consumers

Abstract: The Federal Trade Commission (FTC) is one of many organizations studying influences on consumer privacy online. The authors investigate these influences, taking into consideration the current body of literature on privacy and the Internet and the FTC’s core principles of fair information practice. The authors analyze these influences to assess the underlying factors of privacy concern online. The authors examine the current recommendations and actions of the FTC in light of the results of an e-mail survey of online consumers in the United States that assessed their attitudes toward privacy online. The authors find that the FTC’s core principles address many of online consumers’ privacy concerns. However, two factors not directly incorporated in the five principles, the relationships between entities and online users and the exchange of information for appropriate compensation, may influence consumers’ privacy concerns.

Turbulent convection at very high Rayleigh numbers

Abstract: Turbulent convection occurs when the Rayleigh number (Ra)--which quantifies the relative magnitude of thermal driving to dissipative forces in the fluid motion--becomes sufficiently high. Although many theoretical and experimental studies of turbulent convection exist, the basic properties of heat transport remain unclear. One important question concerns the existence of an asymptotic regime that is supposed to occur at very high Ra. Theory predicts that in such a state the Nusselt number (Nu), representing the global heat transport, should scale as Nu proportional to Ra(beta) with beta = 1/2. Here we investigate thermal transport over eleven orders of magnitude of the Rayleigh number (10(6) < or = Ra < or = 10(7)), using cryogenic helium gas as the working fluid. Our data, over the entire range of Ra, can be described to the lowest order by a single power-law with scaling exponent beta close to 0.31. In particular, we find no evidence for a transition to the Ra(1/2) regime. We also study the variation of internal temperature fluctuations with Ra, and probe velocity statistics indirectly.

Mood, personality, and self-monitoring: negative affect and emotionality in relation to frontal lobe mechanisms of error monitoring.

Abstract: A fundamental question in frontal lobe function is how motivational and emotional parameters of behavior apply to executive processes. Recent advances in mood and personality research and the technology and methodology of brain research provide opportunities to address this question empirically. Using event-related-potentials to track error monitoring in real time, the authors demonstrated that variability in the amplitude of the error-related negativity (ERN) is dependent on mood and personality variables. College students who are high on negative affect (NA) and negative emotionality (NEM) displayed larger ERN amplitudes early in the experiment than participants who are low on these dimensions. As the high-NA and -NEM participants disengaged from the task, the amplitude of the ERN decreased. These results reveal that affective distress and associated behavioral patterns are closely related with frontal lobe executive functions.

Statistical control of artifacts in dense array EEG/MEG studies

Abstract: With the advent of dense sensor arrays (64-256 channels) in electroencephalography and magnetoencephalography studies, the probability increases that some recording channels are contaminated by artifact. If all channels are required to be artifact free, the number of acceptable trials may be unacceptably low. Precise artifact screening is necessary for accurate spatial mapping, for current density measures, for source analysis, and for accurate temporal analysis based on single-trial methods. Precise screening presents a number of problems given the large datasets. We propose a procedure for statistical correction of artifacts in dense array studies (SCADS), which (1) detects individual channel artifacts using the recording reference, (2) detects global artifacts using the average reference, (3) replaces artifact-contaminated sensors with spherical interpolation statistically weighted on the basis of all sensors, and (4) computes the variance of the signal across trials to document the stability of the averaged waveform. Examples from 128-channel recordings and from numerical simulations illustrate the importance of careful artifact review in the avoidance of analysis errors.

The Study of Groups: Past, Present, and Future:

Abstract: A century of research on small groups has yielded bountiful findings about many specific features and processes in groups. Much of that work, in line with a positivist epistemology that emphasizes control and precision and favors the laboratory experiment over other data collection strategies, has also tended to treat groups as though they were simple, isolated, static entities. Recent research trends that treat groups as complex, adaptive, dynamic systems open up new approaches to studying groups. In line with those trends, a theory of groups as complex systems is offered and some methodological and conceptual issues raised by this theory are identified. A 3-pronged research strategy based on theory development, computational modeling, and empirical research that holds promise for illuminating the dynamic processes underlying the emergence of complexity and the ongoing balance of continuity and change in groups is proposed.

Violence risk assessment and risk communication: the effects of using actual cases, providing instruction, and employing probability versus frequency formats.

Abstract: This article describes studies designed to inform policy makers and practitioners about factors influencing the validity of violence risk assessment and risk communication. Forensic psychologists and psychiatrists were shown case summaries of patients hospitalized with mental disorder and were asked to judge the likelihood that the patient would harm someone within six months after discharge from the hospital. They also judged whether the patient posed a high risk, medium risk, or low risk of harming someone after discharge. Studies 1 and 2 replicated, with real case summaries as stimuli, the response-scale effects found by Slovic and Monahan (1995). Providing clinicians with response scales allowing more discriminability among smaller probabilities led patients to be judged as posing lower probabilities of committing harmful acts. This format effect was not eliminated by having clinicians judge relative frequencies rather than probabilities or by providing them with instruction in how to make these types of judgments. In addition, frequency scales led to lower mean likelihood judgments than did probability scales, but, at any given level of likelihood, a patient was judged as posing higher risk if that likelihood was derived from a frequency scale (e.g., 10 out of 100) than if it was derived from a probability scale (e.g., 10%). Similarly, communicating a patient's dangerousness as a relative frequency (e.g., 2 out of 10) led to much higher perceived risk than did communicating a comparable probability (e.g., 20%). The different reactions to probability and frequency formats appear to be attributable to the more frightening images evoked by frequencies. Implications for risk assessment and risk communication are discussed.

Preventing school violence: The use of office discipline referrals to assess and monitor school-wide discipline interventions.

Abstract: Confronted by increasing incidents of violent behavior in schools, educators are being asked to make schools safer. Schools, however, receive little guidance or assistance in their attempts to establish and sustain proactive discipline systems. One area of need lies in directions for use of existing discipline information to improve school-wide behavior support. In this article, we describe how office discipline referrals might be used as an information source to provide an indicator of the status of school-wide discipline and to improve the precision with which schools manage, monitor, and modify their universal interventions for all students and their targeted interventions for students who exhibit the most severe problem behaviors.

Single-molecule studies of the effect of template tension on T7 DNA polymerase activity

Abstract: T7 DNA polymerase1,2 catalyses DNA replication in vitro at rates of more than 100 bases per second and has a 3′→5′ exonuclease (nucleotide removing) activity at a separate active site. This enzyme possesses a ‘right hand’ shape which is common to most polymerases with fingers, palm and thumb domains3,4. The rate-limiting step for replication is thought to involve a conformational change between an ‘open fingers’ state in which the active site samples nucleotides, and a ‘closed’ state in which nucleotide incorporation occurs3,5. DNA polymerase must function as a molecular motor converting chemical energy into mechanical force as it moves over the template. Here we show, using a single-molecule assay based on the differential elasticity of single-stranded and double-stranded DNA, that mechanical force is generated during the rate-limiting step and that the motor can work against a maximum template tension of ∼34 pN. Estimates of the mechanical and entropic work done by the enzyme show that T7 DNA polymerase organizes two template bases in the polymerization site during each catalytic cycle. We also find a force-induced 100-fold increase in exonucleolysis above 40 pN.

Improving Graduation and Employment Outcomes of Students with Disabilities: Predictive Factors and Student Perspectives

Abstract: This article reports on findings from two studies that examined secondary and transition practices. The first study examined student and program factors that predicted participants' graduation with a standard high school diploma and placement in employment and continuing education. The second study examined participants' perceptions of the program and staff characteristics that were most important in helping them achieve their education and transition goals. Findings from these studies indicate that career-related work experience and completion of student-identified transition goals were highly associated with improved graduation and employment outcomes. Individualization of services around student goals and personalized attention from staff were highly valued by participants. Recommendations for policy and practice are discussed.

Medial Frontal Cortex in Action Monitoring

Abstract: Effective behavior requires continuous action monitoring. Electrophysiological studies in both monkeys and humans have shown activity in the medial frontal cortex that reflects dynamic control and monitoring of behavioral acts. In humans, the centromedial frontal cortex shows an electrical response within 100 msec of an error, the error-related negativity (ERN). The ERN occurs only when subjects are aware of making an error, suggesting that a critical factor may be self-monitoring of the action process. In the present study, we examined late responses in a deadline reaction time task, in which the subject becomes increasingly aware of making an error as the response becomes increasingly late. We found evidence of response conflict before errors defined by late responses but not before errors defined by incorrect responses. The results also show a linear increase in the amplitude of the ERN with increasingly late responses. These data suggest that frontal networks provide dynamic representations that monitor and evaluate the unfolding action plan.

Retrieval-induced forgetting: evidence for a recall-specific mechanism.

Abstract: Previous work has shown that recalling information from long-term memory can impair the long-term retention of related representations—a phenomenon known as retrieval-induced forgetting (Anderson, Bjork, & Bjork, 1994). We report an experiment in which the question of whether retrieval is necessary to induce this form of impairment was examined. All the subjects studied six members from each of eight taxonomic categories (e.g.,fruit orange). In the competitive practice condition, the subjects practiced recalling three of the six members, using category-stem cues (e.g.,fruit or____). In the noncompetitive practice condition, the subjects were reexposed to these same members for the same number of repetitions but were asked to recall the category name by using the exemplar and a stem as cues (e.g.,fr____orange). Despite significant and comparable facilitation of practiced items in both conditions, only the competitive practice subjects were impaired in their ability to recall the nonpracticed members on a delayed cued-recall test. These findings argue that retrieval-induced forgetting is not caused by increased competition arising from the strengthening of practiced items, but by inhibitory processes specific to the situation of recall.

CYK-4: A Rho family gtpase activating protein (GAP) required for central spindle formation and cytokinesis.

Abstract: During cytokinesis of animal cells, the mitotic spindle plays at least two roles. Initially, the spindle positions the contractile ring. Subsequently, the central spindle, which is composed of microtubule bundles that form during anaphase, promotes a late step in cytokinesis. How the central spindle assembles and functions in cytokinesis is poorly understood. The cyk-4 gene has been identified by genetic analysis in Caenorhabditis elegans. Embryos from cyk-4(t1689ts) mutant hermaphrodites initiate, but fail to complete, cytokinesis. These embryos also fail to assemble the central spindle. We show that the cyk-4 gene encodes a GTPase activating protein (GAP) for Rho family GTPases. CYK-4 activates GTP hydrolysis by RhoA, Rac1, and Cdc42 in vitro. RNA-mediated interference of RhoA, Rac1, and Cdc42 indicates that only RhoA is essential for cytokinesis and, thus, RhoA is the likely target of CYK-4 GAP activity for cytokinesis. CYK-4 and a CYK-4:GFP fusion protein localize to the central spindle and persist at cell division remnants. CYK-4 localization is dependent on the kinesin-like protein ZEN-4/CeMKLP1 and vice versa. These data suggest that CYK-4 and ZEN-4/CeMKLP1 cooperate in central spindle assembly. Central spindle localization of CYK-4 could accelerate GTP hydrolysis by RhoA, thereby allowing contractile ring disassembly and completion of cytokinesis.

Adolescent Growth in New Forms of Problem Behavior: Macro- and Micro-Peer Dynamics

Abstract: Longitudinal data from an at-risk sample were used to analyze individual linear trend scores for each of three new forms of problem behavior that emerges during the interval from age 10 through 18 years. Growth in substance use, health-risking sexual behavior and police arrests defined a latent construct for growth in adolescent problem behavior. A structural equation model (SEM) showed a significant path from early involvement with deviant peers to a latent construct for growth in new forms of antisocial behavior. A second SEM showed that the contribution of early involvement to later growth was mediated by a latent construct for deviancy training assessed at age 14 years. The relative rates of reinforcement for deviancy, amount of time spent with deviant peers, and deviancy level of the peer network defined a deviancy training construct that accounted for 53% of the variance in later growth in new forms.

What We Know about Effective Instructional Practices for English-Language Learners

Abstract: This research synthesis, using a qualitative multivocal method (Ogawa & Malen, 1991), investigates the knowledge base of effective instruction for English-language learners in elementary and middle school grades. Interviews with professional educators and researchers around the country in a series of five work groups were conducted. Findings from the work groups were enhanced by a review of the literature consisting of 9 intervention studies (8 group studies and 1 single-subject study) and 15 descriptive studies. Major themes and implications for conducting future research and improving current practice are discussed.

Glucose depletion causes haploid invasive growth in yeast

Abstract: Haploid yeast invades solid agar in response to nutrient limitation. To decipher the cues that underlie invasion, we have developed a single cell invasive growth assay. Using this assay, as well as the traditional plate-washing assay, we show that invasive growth occurs in response to glucose depletion. In the absence of glucose (or other fermentable sugar), individual cells adopted a nonaxial budding pattern and elongated morphology within the first cell divisions, and invasion into the agar was observed in microcolonies containing as few as 10 cells. In support of this observation, we found that glucose suppressed the hyperinvasive growth morphology of STE11-4, pbs2, hsl7, and RAS2V19 mutations. In addition, removal of glucose from YPD medium caused constitutive invasion in wild-type cells. We tested glucose control proteins for a role in invasion and found that Snf1, a protein required for derepression of glucose-repressed genes, was required for invasive growth. The transcription factor Sip4, which interacts with Snf1 and is induced during the diauxic shift, had an inhibitory role on invasive growth, suggesting that multiple mechanisms are required for glucose depletion-dependent invasion.