Showing papers by "University of Oregon published in 2002"

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Abstract: Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences These are clustered into 33,409 'transcriptional units', contributing 901% of a newly established mouse transcriptome database Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome 41% of all transcriptional units showed evidence of alternative splicing In protein-coding transcripts, 79% of splice variations altered the protein product Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics

Kelp forest ecosystems: biodiversity, stability, resilience and future

Abstract: Kelp forests are phyletically diverse, structurally complex and highly productive components of coldwater rocky marine coastlines. This paper reviews the conditions in which kelp forests develop globally and where, why and at what rate they become deforested. The ecology and long archaeological history of kelp forests are examined through case studies from southern California, the Aleutian Islands and the western North Atlantic, well-studied locations that represent the widest possible range in kelp forest biodiversity. Global distribution of kelp forests is physiologically constrained by light at high latitudes and by nutrients, warm temperatures and other macrophytes at low latitudes. Within mid-latitude belts (roughly 40–60° latitude in both hemispheres) well-developed kelp forests are most threatened by herbivory, usually from sea urchins. Overfishing and extirpation of highly valued vertebrate apex predators often triggered herbivore population increases, leading to widespread kelp deforestation. Such deforestations have the most profound and lasting impacts on species-depauperate systems, such as those in Alaska and the western North Atlantic. Globally urchin-induced deforestation has been increasing over the past 2–3 decades. Continued fishing down of coastal food webs has resulted in shifting harvesting targets from apex predators to their invertebrate prey, including kelp-grazing herbivores. The recent global expansion of sea urchin harvesting has led to the widespread extirpation of this herbivore, and kelp forests have returned in some locations but, for the first time, these forests are devoid of vertebrate apex predators. In the western North Atlantic, large predatory crabs have recently filled this void and they have become the new apex predator in this system. Similar shifts from fish- to crab-dominance may have occurred in coastal zones of the United Kingdom and Japan, where large predatory finfish were extirpated long ago. Three North American case studies of kelp forests were examined to determine their long history with humans and project the status of future kelp forests to the year 2025. Fishing impacts on kelp forest systems have been both profound and much longer in duration than previously thought. Archaeological data suggest that coastal peoples exploited kelp forest organisms for thousands of years, occasionally resulting in localized losses of apex predators, outbreaks of sea urchin populations and probably small-scale deforestation. Over the past two centuries, commercial exploitation for export led to the extirpation of sea urchin predators, such as the sea otter in the North Pacific and predatory fishes like the cod in the North Atlantic. The large-scale removal of predators for export markets increased sea urchin abundances and promoted the decline of kelp forests over vast areas. Despite southern California having one of the longest known associations with coastal kelp forests, widespread deforestation is rare. It is possible that functional redundancies among predators and herbivores make this most diverse system most stable. Such biodiverse kelp forests may also resist invasion from non-native species. In the species-depauperate western North Atlantic, introduced algal competitors carpet the benthos and threaten future kelp dominance. There, other non-native herbivores and predators have become established and dominant components of this system. Climate changes have had measurable impacts on kelp forest ecosystems and efforts to control the emission of greenhouse gasses should be a global priority. However, overfishing appears to be the greatest manageable threat to kelp forest ecosystems over the 2025 time horizon. Management should focus on minimizing fishing impacts and restoring populations of functionally important species in these systems.

Molecular bonding and interactions at aqueous surfaces as probed by vibrational sum frequency spectroscopy.

Abstract: Aqueous surfaces and interfaces are important in many physical, chemical, and biological processes in our world. The adsorption, dissolution, and reaction of atmospheric gases at the surfaces of atmospheric aerosols and oceanic waters play a key role in the composition of our atmosphere and the sustainability of plant and animal species in land waters. The transport and exchange of ions and solutes across the interface between an aqueous phase and hydrophobic biomolecular assemblies underlies some of the most important processes in living plants and animals. Membrane formation, protein folding, and micelle formation all involve, and are often controlled by, bonding interactions with water molecules at their surfaces. The unique physical, chemical, and biological properties of aqueous surfaces arise from the strong hydrogen bonding that occurs between water molecules and the asymmetry in this otherwise tetrahedral bonding coordination that results from the termination of the bulk water phase. Although there has been increased experimental and theoretical effort in recent years focused on developing a molecular picture of the structure and bonding of water layers to other solid, liquid, and gaseous media, consensus on the details of interfacial bonding has been slow or nonexistent in many areas. The adsorption of ions, surfactants, and solute molecules at these interfaces adds a level of complexity to the Geraldine Richmond holds the Richard M. and Patricia H. Noyes Professor of Chemistry position at the University of Oregon. She received her Ph.D. degree under the mentorship of George Pimentel at the University of California, Berkeley, in 1980. From 1980 to 1985 she was on the faculty at Bryn Mawr College and moved to the University of Oregon in 1985 as an associate professor. Richmond is recognized for her fundamental studies of the structure, dynamics, and bonding characteristics of surfaces and interfaces. Her research group uses a combination of linear and nonlinear optical methods, thermodynamic measurements, and theory to characterize interactions at aqueous surfaces, metal and semiconductor surfaces in contact with liquids and adsorbates, and liquid/liquid interfaces. Richmond has received several recent honors for these studies including the 2002 ACS Spectrochemical Analysis Award, the 2001 Oregon Scientist of the Year, and the 1996 Olin-Garvan Medal of the ACS and has been a Fellow of the American Physical Society since 1993. 2693 Chem. Rev. 2002, 102, 2693−2724

Positive Behavior Support: Evolution of an Applied Science

Abstract: Positive behavior support (PBS) is an applied science that uses educational and systems change methods (environmental redesign) to enhance quality of life and minimize problem behavior. PBS initial...

The Evolution of Discipline Practices: School-Wide Positive Behavior Supports

Abstract: SUMMARY In response to public requests to improve the purpose and structure of discipline systems, schools have increased their emphases on “school-wide” positive behavior support. The thesis of this paper is that the current problem behavior of students in elementary and middle schools requires a preventive, whole-school approach. The foundation for such an approach lies in the emerging technology of positive behavior support. The features of positive behavior support are defined, and their application to whole-school intervention articulated. Finally, the steps that have been used to implement school-wide positive behavior support in over 500 schools across the nation are described.

The Promise and Perils of Wnt Signaling Through β-Catenin

Abstract: Wnt pathways are involved in the control of gene expression, cell behavior, cell adhesion, and cell polarity. In addition, they often operate in combination with other signaling pathways. The Wnt/beta-catenin pathway is the best studied of the Wnt pathways and is highly conserved through evolution. In this pathway, Wnt signaling inhibits the degradation of beta-catenin, which can regulate transcription of a number of genes. Some of the genes regulated are those associated with cancer and other diseases (for example, colorectal cancer and melanomas). As a result, components of the Wnt/beta-catenin pathway are promising targets in the search for therapeutic agents. Information about Wnt pathways is available both in canonical terms and at the species level. In addition to the canonical Wnt/beta-catenin pathway, information is now available for Drosophila, Caenorhabditis elegans, and Xenopus. The STKE Connections Maps for these pathways provide an important tool in accessing this large body of complex information.

Cross-modal plasticity: where and how?

Abstract: Animal studies have shown that sensory deprivation in one modality can have striking effects on the development of the remaining modalities. Although recent studies of deaf and blind humans have also provided convincing behavioural, electrophysiological and neuroimaging evidence of increased capabilities and altered organization of spared modalities, there is still much debate about the identity of the brain systems that are changed and the mechanisms that mediate these changes. Plastic changes across brain systems and related behaviours vary as a function of the timing and the nature of changes in experience. This specificity must be understood in the context of differences in the maturation rates and timing of the associated critical periods, differences in patterns of transiently existing connections, and differences in molecular factors across brain systems.

Young tracks of hotspots and current plate velocities

Abstract: SUMMARY Plate motions relative to the hotspots over the past 4 to 7 Myr are investigated with a goal of determining the shortest time interval over which reliable volcanic propagation rates and segment trends can be estimated. The rate and trend uncertainties are objectively determined from the dispersion of volcano age and of volcano location and are used to test the mutual consistency of the trends and rates. Ten hotspot data sets are constructed from overlapping time intervals with various durations and starting times. Our preferred hotspot data set, HS3, consists of two volcanic propagation rates and eleven segment trends from four plates. It averages plate motion over the past ≈5.8 Myr, which is almost twice the length of time (3.2 Myr) over which the NUVEL-1A global set of relative plate angular velocities is estimated. HS3-NUVEL1A, our preferred set of angular velocities of 15 plates relative to the hotspots, was constructed from the HS3 data set while constraining the relative plate angular velocities to consistency with NUVEL-1A. No hotspots are in significant relative motion, but the 95 per cent confidence limit on motion is typically ±20 to ±40 km Myr −1 and ranges up to ±145 km Myr −1 . The uncertainties of the new angular velocities of plates relative to the hotspots are smaller than those of previously published HS2-NUVEL1 (Gripp & Gordon 1990), while being averaged over a shorter and much more uniform time interval. Nine of the fourteen HS2-NUVEL1 angular velocities lie outside the 95 per cent confidence region of the corresponding HS3NUVEL1A angular velocity, while all fourteen of the HS3-NUVEL1A angular velocities lie inside the 95 per cent confidence region of the corresponding HS2-NUVEL1 angular velocity. The HS2-NUVEL1 Pacific Plate angular velocity lies inside the 95 per cent confidence region of the HS3-NUVEL1A Pacific Plate angular velocity, but the 0 to 3 Ma Pacific Plate angular velocity of Wessel & Kroenke (1997) lies far outside the confidence region. We show that the change in trend of the Hawaiian hotspot over the past 2 to 3 Myr has no counterpart on other chains and therefore provides no basis for inferring a change in Pacific Plate motion relative to global hotspots. The current angular velocity of the Pacific Plate can be shown to differ from the average over the past 47 Myr in rate but not in orientation, with the current rotation being about 50 per cent faster (1.06 ± 0.10 deg Myr −1 ) than the average (0.70 deg Myr −1 ) since the 47-Myr-old bend in the Hawaiian‐Emperor chain.

Gene expression during the life cycle of Drosophila melanogaster.

Abstract: Molecular genetic studies of Drosophila melanogaster have led to profound advances in understanding the regulation of development. Here we report gene expression patterns for nearly one-third of all Drosophila genes during a complete time course of development. Mutations that eliminate eye or germline tissue were used to further analyze tissue-specific gene expression programs. These studies define major characteristics of the transcriptional programs that underlie the life cycle, compare development in males and females, and show that large-scale gene expression data collected from whole animals can be used to identify genes expressed in particular tissues and organs or genes involved in specific biological and biochemical processes.

Charcoal as a Fire Proxy

Abstract: Charcoal analysis of lake sediments is used to reconstruct long-term variations in fire occurrence that can complement and extend reconstructions provided by dendrochronological and historical records In the last 15 years, several papers have reviewed the methods for charcoal analysis of lake-sediment cores and its use as a tool for studying fire history (eg, Tolonen, 1986; Patterson et al, 1987; MacDonald et al, 1991; J S Clark, 1988a; J S Clark et al, 1998; Long et al, 1998; Whitlock & Anderson, in review) In most cases, pollen and charcoal data from the same cores are used to examine the linkages among climate, vegetation, fire, and sometimes anthropogenic activities in the past The growing use of charcoal analysis reflects a heightened interest within the paleoecological community to consider fire as an ecosystem process operating on long and short time scales, as well as an increasing need on the part of forest managers to understand prehistoric fire regimes In this chapter, we discuss issues of site selection, chronology, and methodology in charcoal analysis, based on recent advances in the discipline We also review the theoretical and empirical basis for charcoal analysis, including assumptions about the charcoal source area and the processes that transport and deposit charcoal into lakes Fire reconstructions based on lake-sediment records are derived from three primary data sources: particulate charcoal that provides direct evidence of burning; pollen evidence of fluctuations in vegetation that can be tied to disturbance; and lithologic evidence of watershed adjustments to fire, such as erosion or the formation of fire-altered minerals Charcoal analysis quantifies the accumulation of charred particles in sediments during and following a fire event Stratigraphic levels with abundant charcoal (so-called charcoal

The BABAR detector

Abstract: BABAR, the detector for the SLAC PEP-II asymmetric e+e- B Factory operating at the upsilon 4S resonance, was designed to allow comprehensive studies of CP-violation in B-meson decays. Charged particle tracks are measured in a multi-layer silicon vertex tracker surrounded by a cylindrical wire drift chamber. Electromagentic showers from electrons and photons are detected in an array of CsI crystals located just inside the solenoidal coil of a superconducting magnet. Muons and neutral hadrons are identified by arrays of resistive plate chambers inserted into gaps in the steel flux return of the magnet. Charged hadrons are identified by dE/dx measurements in the tracking detectors and in a ring-imaging Cherenkov detector surrounding the drift chamber. The trigger, data acquisition and data-monitoring systems, VME- and network-based, are controlled by custom-designed online software. Details of the layout and performance of the detector components and their associated electronics and software are presented.

How specific is the relation between executive function and theory of mind? Contributions of inhibitory control and working memory

Abstract: The relation between executive function (EF) and theory of mind (ToM) may involve specific processes of inhibition and/or working memory capacity contributing to ToM, or it might be a reflection of general intellectual ability. To differentiate these alternatives, we administered task batteries measuring inhibitory control (IC), working memory, and ToM, as well as measures of verbal and performance intelligence, to 47 typically developing preschool children. Inhibitory control tasks in which a dominant response needed to be suppressed while a subdominant response was activated (Conflict IC) significantly predicted performance on false belief tasks over and above working memory, the intelligence measures, a simple delay task (Delay IC), and age. In contrast, working memory, Delay IC, and intelligence were not significant in this analysis. Conflict IC, but not Delay IC, was related to working memory. Together, these findings suggest that the combination of inhibition and working memory (as reflected in Conflict IC tasks) may be central to the relation between EF and false belief understanding. Copyright © 2002 John Wiley & Sons, Ltd.

Headwaters of the zebrafish — emergence of a new model vertebrate

Abstract: The understanding of vertebrate development has advanced considerably in recent years, primarily due to the study of a few model organisms. The zebrafish, the newest of these models, has risen to prominence because both genetic and experimental embryological methods can be easily applied to this animal. The combination of approaches has proven powerful, yielding insights into the formation and function of individual tissues, organ systems and neural networks, and into human disease mechanisms. Here, we provide a personal perspective on the history of zebrafish research, from the assembly of the first genetic and embryological tools through to sequencing of the genome.

A Meta-Study of Algorithm Visualization Effectiveness

Abstract: Algorithm visualization (AV) technology graphically illustrates how algorithms work. Despite the intuitive appeal of the technology, it has failed to catch on in mainstream computer science education. Some have attributed this failure to the mixed results of experimental studies designed to substantiate AV technology's educational effectiveness. However, while several integrative reviews of AV technology have appeared, none has focused specifically on the software's effectiveness by analyzing this body of experimental studies as a whole. In order to better understand the effectiveness of AV technology, we present a systematic meta-study of 24 experimental studies. We pursue two separate analyses: an analysis ofindependent variables , in which we tie each study to a particular guiding learning theory in an attempt to determine which guiding theory has had the most predictive success; and an analysis of dependent variables, which enables us to determine which measurement techniques have been most sensitive to the learning benefits of AV technology. Our most significant finding is that how students use AV technology has a greater impact on effectiveness than what AV technology shows them. Based on our findings, we formulate an agenda for future research into AV effectiveness.

A Synthesis of Research on Effective Interventions for Building Reading Fluency with Elementary Students with Learning Disabilities

Abstract: Fluent reading, often defined as speed and accuracy, is an important skill for all readers to develop Students with learning disabilities (LD) often struggle to read fluently, leading to difficulties in reading comprehension Despite recent attention to reading fluency and ways to improve fluency, it is not clear which features of interventions that are designed to enhance fluency are beneficial for the most struggling readers The purpose of this study is to synthesize research on interventions that are designed primarily to build reading fluency for students with LD The search yielded 24 published and unpublished studies that reported findings on intervention features, including repeated reading with and without a model, sustained reading, number of repetitions, text difficulty, and specific improvement criteria Our findings suggest that effective interventions for building fluency include an explicit model of fluent reading, multiple opportunities to repeatedly read familiar text independently and with corrective feedback, and established performance criteria for increasing text difficulty

Reexamining the empirical evidence for an environmental kuznets curve

Abstract: This paper uses an updated and revised panel data set on ambient air pollution in cities worldwide to examine the robustness of the evidence for the existence of an inverted U-shaped relationship between national income and pollution. We test the sensitivity of the pollution-income relationship to functional forms, to additional covariates, and to changes in the nations, cities, and years sampled. We find that the results are highly sensitive to these changes, and conclude that there is little empirical support for an inverted U-shaped relationship between several important air pollutants and national income in these data.

The Determinants of the Flow of Funds of Managed Portfolios: Mutual Funds vs. Pension Funds

Abstract: This study compares the relations between asset flow and performance in the retail mutual fund and fiduciary pension fund segments of the money management industry, and relates empirical differences to fundamental differences in the clientele they serve. A striking difference is the shape of the flow-performance relation. In contrast to mutual fund investors, pension clients punish poorly performing managers by withdrawing assets under management and do not flock disproportionately to recent winners. We interpret these and other empirical differences in the context of the manager evaluation procedures typical in each segment. We conclude that pension managers have little incentive to engage in the risk-shifting behavior previously identified among mutual fund managers.

Problem Behavior Interventions for Young Children with Autism: A Research Synthesis

Abstract: This paper provides a summary of research on behavioral interventions for children with autism 8 years of age or younger published between 1996 and 2000. The analysis is divided into four sections: (1) emerging themes in the technology of behavior support, (2) a review of existing research syntheses focusing on behavioral interventions, (3) a new literature review of current pertinent research, and (4) an evaluative discussion of the synthesis results and the field's future needs to develop effective behavioral interventions for young children with autism. The authors offer recommendations for strengthening the existing research base and advancing behavioral technology to meet the needs of the defined target population.

Collaborative Planning: Building Consensus and Building a Distinct Model for Practice

Abstract: Collaborative planning is an interactive process of consensus building and implementation using stakeholder and public involvement. Based on research of twenty case studies in the United States and...

Cardiac troponin T is essential in sarcomere assembly and cardiac contractility.

Abstract: Mutations of the gene (TNNT2) encoding the thin-filament contractile protein cardiac troponin T are responsible for 15% of all cases of familial hypertrophic cardiomyopathy, the leading cause of sudden death in young athletes. Mutant proteins are thought to act through a dominant-negative mode that impairs function of heart muscle. TNNT2 mutations can also lead to dilated cardiomyopathy, a leading cause of heart failure. Despite the importance of cardiac troponin T in human disease, its loss-of-function phenotype has not been described. We show that the zebrafish silent heart (sih) mutation affects the gene tnnt2. We characterize two mutated alleles of sih that severely reduce tnnt2 expression: one affects mRNA splicing, and the other affects gene transcription. Tnnt2, together with alpha-tropomyosin (Tpma) and cardiac troponins C and I (Tnni3), forms a calcium-sensitive regulatory complex within sarcomeres. Unexpectedly, in addition to loss of Tnnt2 expression in sih mutant hearts, we observed a significant reduction in Tpma and Tnni3, and consequently, severe sarcomere defects. This interdependence of thin-filament protein expression led us to postulate that some mutations in tnnt2 may trigger misregulation of thin-filament protein expression, resulting in sarcomere loss and myocyte disarray, the life-threatening hallmarks of TNNT2 mutations in mice and humans.

Institutional change in large law firms: a resource dependency and institutional perspective

Abstract: We integrate resource dependency and institutional theory to argue that resource scarcity drives, and legitimacy enables, institutional change. Building on a historical account, we examine the sources and timing of innovation departing from standard human resource practices using event history analysis of over 200 principal offices of large law firms. Offices with human resource scarcity innovated to acquire alternative resources; highly prestigious offices had the legitimacy to be first or early adopters. Our findings highlight the value of looking to the resource side and to the notion of legitimacy in building an institutional theory of change.

Comparative quantitative genetics : evolution of the G matrix

Abstract: Quantitative genetics provides one of the most promising frameworks with which to unify the fields of macroevolution and microevolution. The genetic variance–covariance matrix ( G ) is crucial to quantitative genetic predictions about macroevolution. In spite of years of study, we still know little about how G evolves. Recent studies have been applying an increasingly phylogenetic perspective and more sophisticated statistical techniques to address G matrix evolution. We propose that a new field, comparative quantitative genetics, has emerged. Here we summarize what is known about several key questions in the field and compare the strengths and weaknesses of the many statistical and conceptual approaches now being employed. Past studies have made it clear that the key question is no longer whether G evolves but rather how fast and in what manner. We highlight the most promising future directions for this emerging field.

On fusion categories

Abstract: Using a variety of methods developed in the literature (in particular, the theory of weak Hopf algebras), we prove a number of general results about fusion categories in characteristic zero. We show that the global dimension of a fusion category is always positive, and that the S-matrix of any modular category (not necessarily hermitian) is unitary. We also show that the category of module functors between two module categories over a fusion category is semisimple, and that fusion categories and tensor functors between them are undeformable (generalized Ocneanu rigidity). In particular the number of such categories (functors) realizing a given fusion datum is finite. Finally, we develop the theory of Frobenius-Perron dimensions in an arbitrary fusion category and classify categories of prime dimension.

Structural organization of the endoplasmic reticulum

Abstract: The endoplasmic reticulum (ER) is a continuous membrane system but consists of various domains that perform different functions. Structurally distinct domains of this organelle include the nuclear envelope (NE), the rough and smooth ER, and the regions that contact other organelles. The establishment of these domains and the targeting of proteins to them are understood to varying degrees. Despite its complexity, the ER is a dynamic structure. In mitosis it must be divided between daughter cells and domains must be re-established, and even in interphase it is constantly rearranged as tubules extend along the cytoskeleton. Throughout these rearrangements the ER maintains its basic structure. How this is accomplished remains mysterious, but some insight has been gained from in vitro systems.

Geochemical Climofunctions from North American Soils and Application to Paleosols across the Eocene‐Oligocene Boundary in Oregon

Abstract: The degree of chemical weathering in soils increases with mean annual precipitation (P; mm) and mean annual temperature (T; C). We have quantified these relationships using a database of major-element chemical analyses of 126 North American soils. The most robust relationship found was between P and the chemical index of alteration without potash (CIA-K): with . Another strong relationship was found between P and

Online Research Methodology

Abstract: The Internet’s potential for quantitative data collection has been debated by researchers for many years. For advertising academics and practitioners, the Internet allows for the assessment of consumer opinions and attitudes toward a range of topics. However, the accessibility of online populations and the generalizability of data collected online are uncertain. The author discusses a range of online techniques and what we still need to learn about such techniques in order to harness the potential of the Internet for quantitative research.The author wishes to acknowledge the insights provided by Mariea Hoy, Angela Mak, and Tad O’Dell during the preparation of this manuscript.