Becoming a Reading Specialist: Surveying the Possibilities

The terrain of graduate programs is changing, especially in light of preparing highly qualified teachers (NCLB, 2001) and standards-based accreditation (IRA, 2004a, NCATE, 2008). This changing terrain is noticed as many institutions of higher learning undergo program reviews through self-studies required by the institution, by state departments of education, by specialized professional associations, or by national accreditation entities. This project sought to explore the nature of reading specialists master’s programs by examining their websites in light of the shift towards standards-based accreditation of programs and the influence of federal legislation. Specific objectives for this descriptive study included: (a) reviewing master’s programs that lead to reading specialist certification at institutions of varying purpose, size, and location; (b) examining program configurations, including but not limited to programs of study, requirements, and special features; and (c) exploring features of institutions’ websites offering information about becoming a certified reading specialist

Viability of brown trout embryos positively linked to melanin-based but negatively to carotenoid-based colours of their fathers

‘Good-genes’ models of sexual selection predict significant additive genetic variation for fitness-correlated traits within populations to be revealed by phenotypic traits. To test this prediction, we sampled brown trout (Salmo trutta) from their natural spawning place, analysed their carotenoid-based red and melanin-based dark skin colours and tested whether these colours can be used to predict offspring viability. We produced half-sib families by in vitro fertilization, reared the resulting embryos under standardized conditions, released the hatchlings into a streamlet and identified the surviving juveniles 20 months later with microsatellite markers. Embryo viability was revealed by the sires' dark pigmentation: darker males sired more viable offspring. However, the sires' red coloration correlated negatively with embryo survival. Our study demonstrates that genetic variation for fitness-correlated traits is revealed by male colour traits in our study population, but contrary to predictions from other studies, intense red colours do not signal good genes

Damping of Tensor Modes in Cosmology

An analytic formula is given for the traceless transverse part of the anisotropic stress tensor due to free streaming neutrinos, and used to derive an integro-differential equation for the propagation of cosmological gravitational waves. The solution shows that anisotropic stress reduces the squared amplitude by 35.6 % for wavelengths that enter the horizon during the radiation-dominated phase, independent of any cosmological parameters. This decreases the tensor temperature and polarization correlation functions for these wavelengths by the same amount. The effect is less for wavelengths that enter the horizon at later times. At the longest wavelengths the decrease in the tensor correlation functions due to neutrino free streaming ranges from 10.7% for $\Omega_Mh^2=0.1$ to 9.0% for $\Omega_Mh^2=0.15$. An Appendix gives a general proof that tensor as well as scalar modes satisfy a conservation law for perturbations outside the horizon, even when the anisotropic stress tensor is not negligible.Comment: 14 pages. The original version of this paper has been expanded to deal with perturbations of any wavelength. While for wavelengths short enough to enter the horizon during radiation dominance, temperature and polarization correlations are damped by 35.6%, at the longest wavelengths the damping is from 9.0% to 11%. An added Appendix gives a general proof that tensor as well as scalar modes satisfy a conservation law outside the horizon, even during neutrino decoupling. Some references are also adde

Discovery of a Redox Thiol Switch: Implications for Cellular Energy Metabolism

The redox-based modifications of cysteine residues in proteins regulate their function in many biological processes. The gas molecule H2S has been shown to persulfidate redox sensitive cysteine residues resulting in an H2S-modified proteome known as the sulfhydrome. Tandem Mass Tags (TMT) multiplexing strategies for large-scale proteomic analyses have become increasingly prevalent in detecting cysteine modifications. Here we developed a TMT-based proteomics approach for selectively trapping and tagging cysteine persulfides in the cellular proteomes. We revealed the natural protein sulfhydrome of two human cell lines, and identified insulin as a novel substrate in pancreatic beta cells. Moreover, we showed that under oxidative stress conditions, increased H2S can target enzymes involved in energy metabolism by switching specific cysteine modifications to persulfides. Specifically, we discovered a Redox Thiol Switch, from protein S-glutathioinylation to S-persulfidation (RTSGS). We propose that the RTSGS from S-glutathioinylation to S-persulfidation is a potential mechanism to fine tune cellular energy metabolism in response to different levels of oxidative stress

Hairy Black Holes in String Theory

Solutions of bosonic string theory are constructed which correspond to four-dimensional black holes with axionic quantum hair. The basic building blocks are the renormalization group flows of the CP1 model with a theta term and the SU(1,1)/U(1) WZW coset conformal field theory. However the solutions are also found to have negative energy excitations, and are accordingly expected to decay to the vacuum.Comment: 14 pages (References added

Observations of Phytoplankton and Nutrients from a Lagrangian Drifter off Northern California

A Lagrangian drifter was deployed in a cold filament off northern California as part of the Coastal Transition Zone program. The drifter was equipped with an optical package (consisting of a spectroradiometer, a fluorometer, and a beam transmissometer) suspended at 8.5-m depth and a water sampler suspended at 16.3-m depth. The drifter was recovered after 8 days. Optical, chemical, and biological properties changed considerably as the drifter moved offshore in the cold filament. Concentrations of phytoplankton chlorophyll increased rapidly in the first 2 days, in parallel with the disappearance of nitrate and nitrite. After this initial period, chlorophyll decreased gradually over the next 6 days with prominent diurnal fluctuations present in the last 3 days. Water transparency also showed similar long-term as well as diurnal fluctuations. The phytoplankton community became increasingly dominated by large centric diatoms throughout the deployment. Although total cell volume was higher towards the middle of the deployment, this increase occurred without a parallel increase in chlorophyll. In addition, total particulate concentrations were highest nearshore. Although the drifter slippage was approximately 1 cm/s, the biological, chemical, and physical characteristics of the water were affected by both in situ changes and vertical motions of the water. These results are generally consistent with results from other upwelling studies

Scientific review by the marine science advisory panel of Oregon University System scientists of the US Commission on ocean policy preliminary report for Governor Kulongoski's Oregon response

The U.S. Commission on Ocean Policy (USCOP) has articulated a set of overarching Guiding Principles to frame the creation of a new national ocean policy. When taken collectively, these principles provide a careful, circumspect, and ambitious context from which to develop policies that will promote vibrant coastal communities, healthy and resilient ecosystems, abundant wildlife, sustainable fisheries, clean and safe shorelines, and enjoyable and inspirational recreational opportunities—in short, the visions that Oregonians articulate for their coast and ocean. The Guiding Principles align closely with Oregon’s Statewide Planning Goals, policies, and values. In fact, they underscore the importance of weighing long-term interests more heavily than short-term ones in the balance of competing uses. They are holistic in geographic scope, rather than focused on a single component of a complex ecosystem. The USCOP Guiding Principles were conceived to foster an atmosphere of objective scientific inquiry to form the basis of policy and decision-making to reconcile the diverse needs of all Oregonians.Keywords: Estuary, Shellfish, Beach, Fish, Kelp, Estuarine, Habitat, Algae, Marine, Indicators, Freshwater, Mammal

Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid nematode genomes

Portland\u27s Changing Landscape

Occasional Papers in Geography Publication No. 4 What is the nature and character of Portland? What are the conditions, changes and developments that have made it what it is? How does Portland compare with other places? What makes it unique? These are some of the question pursued in this volume. This book contains thirteen chapters discussing various facets of Portland\u27s environmental, economy, and character. It is an up-to-date and comprehensive analysis of dynamics and change in the landscape. An overview is provided of Portland as a city and place to live, as well as its functional significance on a national and international basis. Two threads are woven through the tapestry of these essays. One is that Portland is a big city but with many attributes of a small town. The other is the closeness and accessibility of city and nature. The challenge is how to nurture and maintain both - to have our cake and eat it too. The evidence is clear that most American cities have not been able to achieve this. Only the future can tell how Portland will fare. The authors are all professional geographers or work in closely related fields. All have been involved with the Portland scene for a number of years and are uniquely qualified to write about these topics. While each approaches problems from his or her own perspective, the net result is a summing up, a taking stock of where we have been and where we are going. When considered as a whole the book should provide a better view than we have had of the nature and character of this special place.https://pdxscholar.library.pdx.edu/geog_occasionalpaper/1000/thumbnail.jp

Upper limits on the strength of periodic gravitational waves from PSR J1939+2134

The first science run of the LIGO and GEO gravitational wave detectors presented the opportunity to test methods of searching for gravitational waves from known pulsars. Here we present new direct upper limits on the strength of waves from the pulsar PSR J1939+2134 using two independent analysis methods, one in the frequency domain using frequentist statistics and one in the time domain using Bayesian inference. Both methods show that the strain amplitude at Earth from this pulsar is less than a few times $10^{-22}$.Comment: 7 pages, 1 figure, to appear in the Proceedings of the 5th Edoardo Amaldi Conference on Gravitational Waves, Tirrenia, Pisa, Italy, 6-11 July 200