Showing papers by "Michigan State University published in 2009"

The Seventh Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Seventh Data Release of the Sloan Digital Sky Survey (SDSS), marking the completion of the original goals of the SDSS and the end of the phase known as SDSS-II. It includes 11,663 deg^2 of imaging data, with most of the ~2000 deg^2 increment over the previous data release lying in regions of low Galactic latitude. The catalog contains five-band photometry for 357 million distinct objects. The survey also includes repeat photometry on a 120° long, 2°.5 wide stripe along the celestial equator in the Southern Galactic Cap, with some regions covered by as many as 90 individual imaging runs. We include a co-addition of the best of these data, going roughly 2 mag fainter than the main survey over 250 deg^2. The survey has completed spectroscopy over 9380 deg^2; the spectroscopy is now complete over a large contiguous area of the Northern Galactic Cap, closing the gap that was present in previous data releases. There are over 1.6 million spectra in total, including 930,000 galaxies, 120,000 quasars, and 460,000 stars. The data release includes improved stellar photometry at low Galactic latitude. The astrometry has all been recalibrated with the second version of the USNO CCD Astrograph Catalog, reducing the rms statistical errors at the bright end to 45 milliarcseconds per coordinate. We further quantify a systematic error in bright galaxy photometry due to poor sky determination; this problem is less severe than previously reported for the majority of galaxies. Finally, we describe a series of improvements to the spectroscopic reductions, including better flat fielding and improved wavelength calibration at the blue end, better processing of objects with extremely strong narrow emission lines, and an improved determination of stellar metallicities.

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

Abstract: The Ribosomal Database Project (RDP) provides researchers with quality-controlled bacterial and archaeal small subunit rRNA alignments and analysis tools. An improved alignment strategy uses the Infernal secondary structure aware aligner to provide a more consistent higher quality alignment and faster processing of user sequences. Substantial new analysis features include a new Pyrosequencing Pipeline that provides tools to support analysis of ultra high-throughput rRNA sequencing data. This pipeline offers a collection of tools that automate the data processing and simplify the computationally intensive analysis of large sequencing libraries. In addition, a new Taxomatic visualization tool allows rapid visualization of taxonomic inconsistencies and suggests corrections, and a new class Assignment Generator provides instructors with a lesson plan and individualized teaching materials. Details about RDP data and analytical functions can be found at http://rdp.cme.msu.edu/.

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.

Science for managing ecosystem services: Beyond the Millennium Ecosystem Assessment

Abstract: The Millennium Ecosystem Assessment (MA) introduced a new framework for analyzing social-ecological systems that has had wide influence in the policy and scientific communities. Studies after the MA are taking up new challenges in the basic science needed to assess, project, and manage flows of ecosystem services and effects on human well-being. Yet, our ability to draw general conclusions remains limited by focus on discipline-bound sectors of the full social-ecological system. At the same time, some polices and practices intended to improve ecosystem services and human well-being are based on untested assumptions and sparse information. The people who are affected and those who provide resources are increasingly asking for evidence that interventions improve ecosystem services and human well-being. New research is needed that considers the full ensemble of processes and feedbacks, for a range of biophysical and social systems, to better understand and manage the dynamics of the relationship between humans and the ecosystems on which they rely. Such research will expand the capacity to address fundamental questions about complex social-ecological systems while evaluating assumptions of policies and practices intended to advance human well-being through improved ecosystem services.

Personality and Subjective Well-Being

Abstract: Personality has been found to be more strongly associated with subjective well-being in many instances than are life circumstances. In part, this might be due to the fact that temperament and other individual differences can influence people’s feelings and evaluations of their lives, but also because people’s emotions are an inherent part of personality. This chapter discusses the heritability of “happiness,” that portion of subjective well-being that is due to genetic differences between individuals. The stability of subjective well-being over time is substantial, and this is likely due in part to the stability of personality. Specific personality traits are related to various types of well-being. For example, extroversion appears to be more strongly related to positive emotions, while neuroticism is more related to negative feelings. Although personality is an important correlate of subjective well-being, situations and life circumstances can in some cases have a considerable influence as well. Furthermore, personality can to some degree change over time, and with it, levels of subjective well-being can change.

Household actions can provide a behavioral wedge to rapidly reduce US carbon emissions

Abstract: Most climate change policy attention has been addressed to long-term options, such as inducing new, low-carbon energy technologies and creating cap-and-trade regimes for emissions. We use a behavioral approach to examine the reasonably achievable potential for near-term reductions by altered adoption and use of available technologies in US homes and nonbusiness travel. We estimate the plasticity of 17 household action types in 5 behaviorally distinct categories by use of data on the most effective documented interventions that do not involve new regulatory measures. These interventions vary by type of action and typically combine several policy tools and strong social marketing. National implementation could save an estimated 123 million metric tons of carbon per year in year 10, which is 20% of household direct emissions or 7.4% of US national emissions, with little or no reduction in household well-being. The potential of household action deserves increased policy attention. Future analyses of this potential should incorporate behavioral as well as economic and engineering elements.

Technological Pedagogical Content Knowledge (TPACK): The Development and Validation of an Assessment Instrument for Preservice Teachers

Abstract: Based in Shulman’s idea of Pedagogical Content Knowledge, Technological Pedagogical Content Knowledge (TPACK) has emerged as a useful frame for describing and understanding the goals for technology use in preservice teacher education. This paper addresses the need for a survey instrument designed to assess TPACK for preservice teachers. The paper describes survey development process and results from a pilot study on 124 preservice teachers. Data analysis procedures included Cronbach’s alpha statistics on the TPACK knowledge domains and factor analysis for each domain. Results suggest that, with the modification and/or deletion of 18 of the survey items, the survey is a reliable and valid instrument that will help educators design longitudinal studies to assess preservice teachers’ development of TPACK. (Keywords: TPACK, instrument development, preservice teachers) The purpose of this study was to develop and validate an instrument designed to measure preservice teachers’ self-assessment of their Technological Pedagogical Content Knowledge (TPACK) and related knowledge domains included in the framework. TPACK is a term used increasingly to describe what teachers need to know to effectively integrate technology into their teaching practices. In this article, we detail the steps used to develop and validate an instrument to measure preservice teachers’ development of TPACK. TheoreTICAl FrAmeworK

Genome evolution and adaptation in a long-term experiment with Escherichia coli

Abstract: The relationship between rates of genomic evolution and organismal adaptation remains uncertain, despite considerable interest. The feasibility of obtaining genome sequences from experimentally evolving populations offers the opportunity to investigate this relationship with new precision. Here we sequence genomes sampled through 40,000 generations from a laboratory population of Escherichia coli. Although adaptation decelerated sharply, genomic evolution was nearly constant for 20,000 generations. Such clock-like regularity is usually viewed as the signature of neutral evolution, but several lines of evidence indicate that almost all of these mutations were beneficial. This same population later evolved an elevated mutation rate and accumulated hundreds of additional mutations dominated by a neutral signature. Thus, the coupling between genomic and adaptive evolution is complex and can be counterintuitive even in a constant environment. In particular, beneficial substitutions were surprisingly uniform over time, whereas neutral substitutions were highly variable.

Nutrient Imbalances in agricultural development

Abstract: Nutrient cycles link agricultural systems to their societies and surroundings; inputs of nitrogen and phosphorus in particular are essential for high crop yields, but downstream and downwind losses of these same nutrients diminish environmental quality and human well-being. Agricultural nutrient balances differ substantially with economic development, from inputs that are inadequate to maintain soil fertility in parts of many developing countries, particularly those of sub-Saharan Africa, to excessive and environmentally damaging surpluses in many developed and rapidly growing economies. National and/or regional policies contribute to patterns of nutrient use and their environmental consequences in all of these situations ( 1 ). Solutions to the nutrient challenges that face global agriculture can be informed by analyses of trajectories of change within, as well as across, agricultural systems.

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.

Effective Practices for Developing Reading Comprehension

Abstract: Reading comprehension research has a long and rich history. There is much that we can say about both the nature of reading comprehension as a process and about effective reading comprehension instruction. Most of what we know has been learned since 1975. Why have we been able to make so much progress so fast? We believe that part of the reason behind this steep learning curve has been the lack of controversy about teaching comprehension. Unlike decoding, oral reading, and reading readiness, those who study reading comprehension instruction have avoided much of the acrimony characteristic of work in other aspects of reading. As it should be, much work on the process of reading comprehension has been grounded in studies of good readers. We know a great deal about what good readers do when they read:

Artificial bacterial flagella: Fabrication and magnetic control

Abstract: Inspired by the natural design of bacterial flagella, we report artificial bacterial flagella (ABF) that have a comparable shape and size to their organic counterparts and can swim in a controllable fashion using weak applied magnetic fields. The helical swimmer consists of a helical tail resembling the dimensions of a natural flagellum and a thin soft-magnetic “head” on one end. The swimming locomotion of ABF is precisely controlled by three orthogonal electromagnetic coil pairs. Microsphere manipulation is performed, and the thrust force generated by an ABF is analyzed. ABF swimmers represent the first demonstration of microscopic artificial swimmers that use helical propulsion. Self-propelled devices such as these are of interest in fundamental research and for biomedical applications.

Teachers' Technological Pedagogical Content Knowledge and Learning Activity Types: Curriculum-Based Technology Integration Reframed

Abstract: In this paper we critically analyze extant approaches to technology integration in teaching, arguing that many current methods are technocentric, often omitting sufficient consideration of the dynamic and complex relationships among content, technology, pedagogy, and context. We recommend using the technology, pedagogy, and content knowledge (TPACK) framework as a way to think about effective technology integration, recognizing technology, pedagogy, content and context as interdependent aspects of teachers’ knowledge necessary to teach content-based curricula effectively with educational technologies. We offer TPACK-based “activity types,” rooted in previous research about content-specific activity structures, as an alternative to existing professional development approaches and explain how this new way of thinking may authentically and successfully assist teachers’ and teacher educators’ technology integration efforts.

Developing a learning progression for scientific modeling: Making scientific modeling accessible and meaningful for learners

Abstract: Modeling is a core practice in science and a central part of scientific literacy. We present theoretical and empirical motivation for a learning progression for scientific modeling that aims to make the practice accessible and meaningful for learners. We define scientific modeling as including the elements of the practice (constructing, using, evaluating, and revising scientific models) and the metaknowledge that guides and motivates the practice (e.g., understanding the nature and purpose of models). Our learning progression for scientific modeling includes two dimensions that combine metaknowledge and elements of practice—scientific models as tools for predicting and explaining, and models change as understanding improves. We describe levels of progress along these two dimensions of our progression and illustrate them with classroom examples from 5th and 6th graders engaged in modeling. Our illustrations indicate that both groups of learners productively engaged in constructing and revising increasingly accurate models that included powerful explanatory mechanisms, and applied these models to make predictions for closely related phenomena. Furthermore, we show how students engaged in modeling practices move along levels of this progression. In particular, students moved from illustrative to explanatory models, and developed increasingly sophisticated views of the explanatory nature of models, shifting from models as correct or incorrect to models as encompassing explanations for multiple aspects of a target phenomenon. They also developed more nuanced reasons to revise models. Finally, we present challenges for learners in modeling practices—such as understanding how constructing a model can aid their own sensemaking, and seeing model building as a way to generate new knowledge rather than represent what they have already learned. 2009 Wiley Periodicals, Inc. J Res Sci Teach 46: 632-654, 2009

Is There a Latitudinal Gradient in the Importance of Biotic Interactions

Abstract: Biotic interactions are believed to play a role in the origin and maintenance of species diversity, and multiple hypotheses link the latitudinal diversity gradient to a presumed gradient in the importance of biotic interactions. Here we address whether biotic interactions are more important at low latitudes, finding support for this hypothesis from a wide range of interactions. Some of the best-supported examples are higher herbivory and insect predation in the tropics, and predominantly tropical mutualisms such as cleaning symbioses and ant-plant interactions. For studies that included tropical regions, biotic interactions were never more important at high latitudes. Although our results support the hypothesis that biotic interactions are more important in the tropics, additional research is needed, including latitudinal comparisons of rates of molecular evolution for genes involved in biotic interactions, estimates of gradients in interaction strength, and phylogenetic comparisons of the traits that med...

Innate immunity in plants : an arms race between pattern recognition receptors in plants and effectors in microbial pathogens

Abstract: For many years, research on a suite of plant defense responses that begin when plants are exposed to general microbial elicitors was underappreciated, for a good reason: There has been no critical experimental demonstration of their importance in mediating plant resistance during pathogen infection. Today, these microbial elicitors are named pathogen- or microbe-associated molecular patterns (PAMPs or MAMPs) and the plant responses are known as PAMP-triggered immunity (PTI). Recent studies provide an elegant explanation for the difficulty of demonstrating the role of PTI in plant disease resistance. It turns out that the important contribution of PTI to disease resistance is masked by pathogen virulence effectors that have evolved to suppress it.

Natural, Fibers, Biopolymers and Biocomposites

Abstract: Natural Fibers, Biopolymers, and Biocomposites: An Introduction A.K. Mohanty, M. Misra, L.T. Drzal, S.E. Selke, B.R. Harte, and G.Hinrichsen Plant Fibers as Reinforcement for Green Composites A. Bismarck, S. Mishra, and T. Lampke Processing of Bast Fiber Plants for Industrial Application F. Munder, C. Furll, and H.Hempel Recent Developments in Retting and Measurement of Fiber Quality in Natural Fibers: Pro and Cons R.B. Dodd and D.E. Akin Alternative Low-Cost Biomass for the Biocomposites Industry D.D. Stokke Fiber-Matrix Adhesion in Natural Fiber Composites P.J. Herrera Franco and A. Valadez-Gonzalez Natural Fiber Composites in Automotive Applications B.C. Suddell and W.J. Evans Natural Fiber Composites for Building Applications B. Singh and M. Gupta Thermoset Biocomposites D. Ray and J. Rout Thermoplastic Wood Fiber Composites S. Godavarti Bamboo-Based Ecocomposites and Their Potential Applications K. Kitagawa, U. S. Ishiaku, M. Mizoguchi, and H. Hamada Oil Palm Fiber-Thermoplastic Composites H.D. Rozman, Z.A. Mohd Ishak, and U.S. Ishiaku Natural Fiber-Rubber Composites and Their Applications S. Joseph, M. Jacob, and S. Thomas Straw-Based Biomass and Biocomposites X. Mo, D. Wang, and X.S. Sun Sorona(R)Polymer: Present Status and Future Perspectives J.V. Kurian Polylactic Acid Technology D.E. Henton, P. Gruber, J. Lunt, and J. Randall Polylactide-Based Biocomposites D. Plackett and A. Sodergard Bacterial Polyester-Based Biocomposites: A Review A. Hodzic Cellulose Fiber-Reinforced Cellulose Esters: Biocomposites for the Future G. Toriz, P. Gatenholm, B.D. Seiler, and D. Tindall Starch Polymers: Chemistry, Engineering, and Novel Products B.-S. Chiou, G.M. Glenn, S.H. Imam, M.K. Inglesby, D.F. Wood, and W.J. Orts Lignin-Based Polymer Blends and Biocomposite Materials S. Kubo, R.D. Gilbert, and J.F. Kadla Soy Protein-Based Plastics, Blends, and Composites A.K. Mohanty, W. Liu, P. Tummala, L.T. Drzal, M. Misra, and R.Narayan Synthesis, Properties, and Potential Applications of Novel Thermosetting Biopolymers from Soybean and Other Natural Oils F. Li and R.C. Larock Houses Using Soy Oil and Natural Fibers Biocomposites M.A. Dweib, A. O'Donnell, R.P. Wool, B. Hu, and H.W. Shenton III Biobased Polyurethanes and Their Composites: Present Status and Future Perspective J.-P. Latere Dwan'Isa, A.K. Mohanty, M. Misra, and L.T. Drzal Cellulose-Based Nanocomposites L. Berglund How Sustainable Are Biopolymers and Biobased Products? The Hope, the Doubts, and the Reality M. Patel and R. Narayan Index

Systematic measurements of identified particle spectra in pp, d+Au, and Au+Au collisions at the star detector.

Abstract: Identified charged-particle spectra of pi(+/-), K(+/-), p, and (p) over bar at midrapidity (vertical bar y vertical bar < 0.1) measured by the dE/dx method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for pp and d + Au collisions at root s(NN) = 200 GeV and for Au + Au collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/fm(3) for a formation time less than 1 fm/c. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in Au + Au collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral Au + Au collisions, to a value about 50% above the pp value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in pp, d + Au, and peripheral Au + Au collisions, drops significantly with centrality in Au + Au collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central Au + Au collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.

Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine.

Abstract: Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. Highthroughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples. The RDP-classifier was more efficient for the V4 than for the far less conserved and shorter V6 region, but differences in community structure also affected efficiency. Even when analyzing only 20% of the reads, the majority of the microbial diversity was captured in two samples tested. DNA from the four samples was hybridized against the Human Intestinal Tract (HIT) Chip, a phylogenetic microarray for community profiling. Comparison of clustering of genus counts from pyrosequencing and HITChip data revealed highly similar profiles. Furthermore, correlations of sequence abundance and hybridization signal intensities were very high for lower-order ranks, but lower at family-level, which was probably due to ambiguous taxonomic groupings. Conclusions: The RDP-classifier consistently assigned most V4 sequences from human intestinal samples down to genuslevel with good accuracy and speed. This is the deepest sequencing of single gastrointestinal samples reported to date, but microbial richness levels have still not leveled out. A majority of these diversities can also be captured with five times lower sampling-depth. HITChip hybridizations and resulting community profiles correlate well with pyrosequencing-based compositions, especially for lower-order ranks, indicating high robustness of both approaches. However, incompatible grouping schemes make exact comparison difficult.

The evolving concept of subjective well-being: The multifaceted nature of happiness.

Abstract: Subjective well-being, or what is popularly often called “happiness,” has been of intense interest throughout human history. We review research showing that it is not a single factor, but that subjective well-being is composed of a number of separable although somewhat related variables. For example, positive feelings, negative feelings, and life satisfaction are clearly separable. In understanding the various types of subjective well-being, it is important to remember that appraisals move from immediate situations to a later recall of feelings, and then to global evaluations of life. At each stage, from momentary feelings to large global life eval-uations, somewhat different processes are involved in what is called “happiness.” In order to understand how to measure subjective well-being, one must understand the time course and components of the phenomenon in question, and be clear about what is most important to assess. On-line feelings are very different from global evaluations of life, although both have been studied under the rubric of subjective well-being. Although debate has focused on which type of subjective well-being should be called “true happiness,” the goal of scientists is to understand each type, their relations with each other, and their causes. The future of the field depends on understanding the differences between various types of well-being, and the different and similar causes of each.

An ecological model of the impact of sexual assault on women's mental health.

Abstract: This review examines the psychological impact of adult sexual assault through an ecological theoretical perspective to understand how factors at multiple levels of the social ecology contribute to post-assault sequelae. Using Bronfenbrenner's (1979, 1986, 1995) ecological theory of human development, we examine how individual-level factors (e.g., sociodemographics, biological/genetic factors), assault characteristics (e.g., victim-offender relationship, injury, alcohol use), microsystem factors (e.g., informal support from family and friends), meso/ exosystem factors (e.g., contact with the legal, medical, and mental health systems, and rape crisis centers), macrosystem factors (e.g., societal rape myth acceptance), and chronosystem factors (e.g., sexual revictimization and history of other victimizations) affect adult sexual assault survivors' mental health outcomes (e.g., post-traumatic stress disorder, depression, suicidality, and substance use). Self-blame is conceptualized as meta-construct that stems from all levels of this ecological model. Implications for curbing and/or preventing the negative mental health effects of sexual assault are discussed.

Plant-microbes interactions in enhanced fertilizer-use efficiency.

Abstract: The continued use of chemical fertilizers and manures for enhanced soil fertility and crop productivity often results in unexpected harmful environmental effects, including leaching of nitrate into ground water, surface run-off of phosphorus and nitrogen run-off, and eutrophication of aquatic ecosystems. Integrated nutrient management systems are needed to maintain agricultural productivity and protect the environment. Microbial inoculants are promising components of such management systems. This review is a critical summary of the efforts in using microbial inoculants, including plant growth-promoting rhizobacteria and arbuscular mycorrhizal fungi for increasing the use efficiency of fertilizers. Studies with microbial inoculants and nutrients have demonstrated that some inoculants can improve plant uptake of nutrients and thereby increase the use efficiency of applied chemical fertilizers and manures. These proofs of concept studies will serve as the basis for vigorous future research into integrated nutrient management in agriculture.