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Showing papers by "University of Virginia published in 2008"


Journal ArticleDOI
16 May 2008-Science
TL;DR: Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.
Abstract: Humans continue to transform the global nitrogen cycle at a record pace, reflecting an increased combustion of fossil fuels, growing demand for nitrogen in agriculture and industry, and pervasive inefficiencies in its use. Much anthropogenic nitrogen is lost to air, water, and land to cause a cascade of environmental and human health problems. Simultaneously, food production in some parts of the world is nitrogen-deficient, highlighting inequities in the distribution of nitrogen-containing fertilizers. Optimizing the need for a key human resource while minimizing its negative consequences requires an integrated interdisciplinary approach and the development of strategies to decrease nitrogen-containing waste.

5,249 citations


Journal ArticleDOI
TL;DR: The Compact Muon Solenoid (CMS) detector at the Large Hadron Collider (LHC) at CERN as mentioned in this paper was designed to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1)
Abstract: The Compact Muon Solenoid (CMS) detector is described. The detector operates at the Large Hadron Collider (LHC) at CERN. It was conceived to study proton-proton (and lead-lead) collisions at a centre-of-mass energy of 14 TeV (5.5 TeV nucleon-nucleon) and at luminosities up to 10(34)cm(-2)s(-1) (10(27)cm(-2)s(-1)). At the core of the CMS detector sits a high-magnetic-field and large-bore superconducting solenoid surrounding an all-silicon pixel and strip tracker, a lead-tungstate scintillating-crystals electromagnetic calorimeter, and a brass-scintillator sampling hadron calorimeter. The iron yoke of the flux-return is instrumented with four stations of muon detectors covering most of the 4 pi solid angle. Forward sampling calorimeters extend the pseudo-rapidity coverage to high values (vertical bar eta vertical bar <= 5) assuring very good hermeticity. The overall dimensions of the CMS detector are a length of 21.6 m, a diameter of 14.6 m and a total weight of 12500 t.

5,193 citations


Journal ArticleDOI
TL;DR: The approach taken in ADNI to standardization across sites and platforms of the MRI protocol, postacquisition corrections, and phantom‐based monitoring of all scanners could be used as a model for other multisite trials.
Abstract: Dementia, one of the most feared associates of increasing longevity, represents a pressing public health problem and major research priority. Alzheimer's disease (AD) is the most common form of dementia, affecting many millions around the world. There is currently no cure for AD, but large numbers of novel compounds are currently under development that have the potential to modify the course of the disease and slow its progression. There is a pressing need for imaging biomarkers to improve understanding of the disease and to assess the efficacy of these proposed treatments. Structural magnetic resonance imaging (MRI) has already been shown to be sensitive to presymptomatic disease (1-10) and has the potential to provide such a biomarker. For use in large-scale multicenter studies, however, standardized methods that produce stable results across scanners and over time are needed. The Alzheimer's Disease Neuroimaging Initiative (ADNI) study is a longitudinal multisite observational study of elderly individuals with normal cognition, mild cognitive impairment (MCI), or AD (11,12). It is jointly funded by the National Institutes of Health (NIH) and industry via the Foundation for the NIH. The study will assess how well information (alone or in combination) obtained from MRI, (18F)-fludeoyglucose positron emission tomography (FDG PET), urine, serum, and cerebrospinal fluid (CSF) biomarkers, as well as clinical and neuropsychometric assessments, can measure disease progression in the three groups of elderly subjects mentioned above. At the 55 participating sites in North America, imaging, clinical, and biologic samples will be collected at multiple time points in 200 elderly cognitively normal, 400 MCI, and 200 AD subjects. All subjects will be scanned with 1.5 T MRI at each time point, and half of these will also be scanned with FDG PET. Subjects not assigned to the PET arm of the study will be eligible for 3 T MRI scanning. The goal is to acquire both 1.5 T and 3 T MRI studies at multiple time points in 25% of the subjects who do not undergo PET scanning [R2C1]. CSF collection at both baseline and 12 months is targeted for 50% of the subjects. Sampling varies by clinical group. Healthy elderly controls will be sampled at 0, 6, 12, 24, and 36 months. Subjects with MCI will be sampled at 0, 6, 12, 18, 24, and 36 months. AD subjects will be sampled at 0, 6, 12, and 24 months. Major goals of the ADNI study are: to link all of these data at each time point and make this repository available to the general scientific community; to develop technical standards for imaging in longitudinal studies; to determine the optimum methods for acquiring and analyzing images; to validate imaging and biomarker data by correlating these with concurrent psychometric and clinical assessments; and to improve methods for clinical trials in MCI and AD. The ADNI study overall is divided into cores, with each core managing ADNI-related activities within its sphere of expertise: clinical, informatics, biostatistics, biomarkers, and imaging. The purpose of this report is to describe the MRI methods and decision-making process underlying the selection of the MRI protocol employed in the ADNI study.

3,611 citations


Journal ArticleDOI
TL;DR: On 13 October 1908, Fritz Haber filed his patent on the "synthesis of ammonia from its elements" for which he was later awarded the 1918 Nobel Prize in Chemistry as mentioned in this paper.
Abstract: On 13 October 1908, Fritz Haber filed his patent on the "synthesis of ammonia from its elements" for which he was later awarded the 1918 Nobel Prize in Chemistry. A hundred years on we live in a world transformed by and highly dependent upon Haber–Bosch nitrogen.

2,733 citations


Journal ArticleDOI
17 Jan 2008-Nature
TL;DR: With humans having an increasing impact on the planet, the interactions between the nitrogen cycle, the carbon cycle and climate are expected to become an increasingly important determinant of the Earth system.
Abstract: With humans having an increasing impact on the planet, the interactions between the nitrogen cycle, the carbon cycle and climate are expected to become an increasingly important determinant of the Earth system.

2,668 citations


Journal ArticleDOI
TL;DR: This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos and uses conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene.
Abstract: The in situ hybridization (ISH) technique allows the sites of expression of particular genes to be detected. This protocol describes ISH of digoxigenin-labeled antisense RNA probes to whole-mount zebrafish embryos. In our method, PCR-amplified sequence of a gene of interest is used as a template for the synthesis of an antisense RNA probe, which is labeled with digoxigenin-linked nucleotides. Embryos are fixed and permeabilized before being soaked in the digoxigenin-labeled probe. We use conditions that favor specific hybridization to complementary mRNA sequences in the tissue(s) expressing the corresponding gene. After washing away excess probe, hybrids are detected by immunohistochemistry using an alkaline phosphatase-conjugated antibody against digoxigenin and a chromogenic substrate. The whole procedure takes only 3 days and, because ISH conditions are the same for each probe tested, allows high throughput analysis of zebrafish gene expression during embryogenesis.

2,323 citations


Proceedings ArticleDOI
11 Aug 2008
TL;DR: Presents a collection of slides covering the following topics: CUDA parallel programming model; CUDA toolkit and libraries; performance optimization; and application development.
Abstract: The advent of multicore CPUs and manycore GPUs means that mainstream processor chips are now parallel systems. Furthermore, their parallelism continues to scale with Moore's law. The challenge is to develop mainstream application software that transparently scales its parallelism to leverage the increasing number of processor cores, much as 3D graphics applications transparently scale their parallelism to manycore GPUs with widely varying numbers of cores.

2,216 citations


Journal ArticleDOI
TL;DR: This activity describes the rationale for using carotid ultrasound to identify subclinical vascular disease and to evaluate cardiovascular disease risk, and explains the key components of interpreting carOTid ultrasound studies for cardiovascular Disease risk assessment.
Abstract: Continuing Medical Education Course for "Use of Carotid Ultrasound to Identify Subclinical Vascular Disease and Evaluate Cardiovascular Disease Risk: A Consensus Statement for the American Society of Echocardiography Carotid Intima-Media Thickness Task Force" Accreditation Statement The American Society of Echocardiography is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians. The American Society of Echocardiography designates this educational activity for a maximum of 1 AMA PRA Category 1 Credits ™. Physicians should only claim credit commensurate with the extent of their participation in the activity. ARDMS and CCI recognize ASE's certificates and have agreed to honor the credit hours toward their registry requirements for sonographers. The American Society of Echocardiography is committed to resolving all conflict of interest issues, and its mandate is to retain only those speakers with financial interests that can be reconciled with the goals and educational integrity of the educational program. Disclosure of faculty and commercial support sponsor relationships, if any, have been indicated. Target Audience 1. Physicians, physicians' assistants, and nurses with an interest in cardiac and vascular imaging, preventive cardiology, and cardiovascular disease risk assessment. 2. Ultrasonographers with interest in vascular imaging and cardiovascular disease risk assessment. Objectives Upon completing this activity, participants will be able to: 1. Describe the rationale for using carotid ultrasound to identify subclinical vascular disease and to evaluate cardiovascular disease risk. 2. Explain the application of carotid ultrasound to cardiovascular disease risk assessment. 3. Describe the scanning technique for identifying subclinical vascular disease using carotid ultrasound. 4. Explain the key components of interpreting carotid ultrasound studies for cardiovascular disease risk assessment. Authors Disclosures James H. Stein, MD, FASE: Research grants: Siemens Medical Solutions, Sonosite Intellectual property: listed as the inventor of Patent #US 6,730,0235 "Ultrasonic Apparatus and Method for Providing Quantitative Indication of Risk of Coronary Heart Disease." It has been assigned to the Wisconsin Alumni Research Foundation. Emile R. Mohler III, MD: Speakers bureau for Merck, BMS-Sanofi and AstraZeneca; Research grant support from BMS-Sanofi, Pfizer and GSK. Christopher M. Rembold, MD: Advisory Board for Sonosite. Estimated Time to Complete This Activity: 1 hour

2,097 citations


Posted Content
TL;DR: In this article, the authors present evidence from a survey of 872 employees of four firms that ethical cork climates are both multidimensional and multidetermined, and that there is variance in the ethical within organizations by position, tenure, and workgroup membership.
Abstract: Using a modification of a recently developed measure of ethical climates, this paper presents evidence from a survey of 872 employees of four firms that ethical cork climates are both multidimensional and multidetermined. The study demonstrates that organizations have distinct types of ethical climates and that there is variance in the ethical within organizations by position, tenure, and workgroup membership. Five empirically derived dimensions of ethical climate are described: law and code, caring, instrumentalism, independence, and rules. Analyses of variance reveal significant differences in ethical climates both across and within firms. A theory of ethical climates is developed from organizational and economic theory to describe the determinants of ethical climates in organizations. In particular, the sociocultural environment, organizational form, and organization-specific history are identified as determinants of ethical climates in organizations. The implications of ethical climate for organizational theory are also discussed.

2,000 citations


Journal ArticleDOI
04 Jan 2008-Science
TL;DR: This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments; acquisition of genes for tolerating terrestrial stresses; and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response.
Abstract: We report the draft genome sequence of the model moss Physcomitrella patens and compare its features with those of flowering plants, from which it is separated by more than 400 million years, and unicellular aquatic algae. This comparison reveals genomic changes concomitant with the evolutionary movement to land, including a general increase in gene family complexity; loss of genes associated with aquatic environments (e.g., flagellar arms); acquisition of genes for tolerating terrestrial stresses (e.g., variation in temperature and water availability); and the development of the auxin and abscisic acid signaling pathways for coordinating multicellular growth and dehydration response. The Physcomitrella genome provides a resource for phylogenetic inferences about gene function and for experimental analysis of plant processes through this plant's unique facility for reverse genetics.

1,749 citations


Journal ArticleDOI
TL;DR: Analysis of prekindergarten programs in 11 states suggests that policies, program development, and professional development efforts that improve teacher-child interactions can facilitate children's school readiness.
Abstract: This study examined development of academic, language, and social skills among 4-year-olds in publicly supported prekindergarten (pre-K) programs in relation to 3 methods of measuring pre-K quality, which are as follows: (a) adherence to 9 standards of quality related to program infrastructure and design, (b) observations of the overall quality of classroom environments, and (c) observations of teachers’ emotional and instructional interactions with children in classrooms. Participants were 2,439 children enrolled in 671 pre-K classrooms in 11 states. Adjusting for prior skill levels, child and family characteristics, program characteristics, and state, teachers’ instructional interactions predicted academic and language skills and teachers’ emotional interactions predicted teacher-reported social skills. Findings suggest that policies, program development, and professional development efforts that improve teacher–child interactions can facilitate children’s school readiness.

Journal ArticleDOI
Jan Schipper1, Jan Schipper2, Janice Chanson2, Janice Chanson1, Federica Chiozza3, Neil A. Cox1, Neil A. Cox2, Michael R. Hoffmann2, Michael R. Hoffmann1, Vineet Katariya1, John F. Lamoreux1, John F. Lamoreux4, Ana S. L. Rodrigues5, Ana S. L. Rodrigues6, Simon N. Stuart1, Simon N. Stuart2, Helen J. Temple1, Jonathan E. M. Baillie7, Luigi Boitani3, Thomas E. Lacher4, Thomas E. Lacher2, Russell A. Mittermeier, Andrew T. Smith8, Daniel Absolon, John M. Aguiar4, John M. Aguiar2, Giovanni Amori, Noura Bakkour9, Noura Bakkour2, Ricardo Baldi10, Ricardo Baldi11, Richard J. Berridge, Jon Bielby12, Jon Bielby7, Patricia Ann Black13, Julian Blanc, Thomas M. Brooks14, Thomas M. Brooks2, Thomas M. Brooks15, James Burton16, James Burton17, Thomas M. Butynski18, Gianluca Catullo, Roselle Chapman, Zoe Cokeliss7, Ben Collen7, Jim Conroy, Justin Cooke, Gustavo A. B. da Fonseca19, Gustavo A. B. da Fonseca20, Andrew E. Derocher21, Holly T. Dublin, J. W. Duckworth11, Louise H. Emmons22, Richard H. Emslie1, Marco Festa-Bianchet23, Matthew N. Foster, Sabrina Foster24, David L. Garshelis25, C. Cormack Gates26, Mariano Gimenez-Dixon, Susana González, José F. González-Maya, Tatjana C. Good27, Geoffrey Hammerson28, Philip S. Hammond29, D. C. D. Happold30, Meredith Happold30, John Hare, Richard B. Harris31, Clare E. Hawkins32, Clare E. Hawkins15, Mandy Haywood33, Lawrence R. Heaney34, Simon Hedges11, Kristofer M. Helgen22, Craig Hilton-Taylor1, Syed Ainul Hussain35, Nobuo Ishii36, Thomas Jefferson37, Richard K. B. Jenkins38, Charlotte H. Johnston8, Mark Keith39, Jonathan Kingdon40, David Knox2, Kit M. Kovacs41, Kit M. Kovacs42, Penny F. Langhammer8, Kristin Leus43, Rebecca L. Lewison44, Gabriela Lichtenstein, Lloyd F. Lowry45, Zoe Macavoy12, Georgina M. Mace12, David Mallon46, Monica Masi, Meghan W. McKnight, Rodrigo A. Medellín47, Patricia Medici48, G. Mills, Patricia D. Moehlman, Sanjay Molur, Arturo Mora1, Kristin Nowell, John F. Oates49, Wanda Olech, William R.L. Oliver, Monik Oprea22, Bruce D. Patterson34, William F. Perrin37, Beth Polidoro1, Caroline M. Pollock1, Abigail Powel50, Yelizaveta Protas9, Paul A. Racey38, Jim Ragle1, Pavithra Ramani24, Galen B. Rathbun51, Randall R. Reeves, Stephen B. Reilly37, John E. Reynolds52, Carlo Rondinini3, Ruth Grace Rosell-Ambal2, Monica Rulli, Anthony B. Rylands, Simona Savini, Cody J. Schank24, Wes Sechrest24, Caryn Self-Sullivan, Alan Shoemaker1, Claudio Sillero-Zubiri40, Naamal De Silva, David E. Smith24, Chelmala Srinivasulu53, P. J. Stephenson, Nico van Strien54, Bibhab Kumar Talukdar55, Barbara L. Taylor37, Rob Timmins, Diego G. Tirira, Marcelo F. Tognelli56, Marcelo F. Tognelli10, Katerina Tsytsulina, Liza M. Veiga57, Jean-Christophe Vié1, Elizabeth A. Williamson58, Sarah A. Wyatt, Yan Xie, Bruce E. Young28 
International Union for Conservation of Nature and Natural Resources1, Conservation International2, Sapienza University of Rome3, Texas A&M University4, University of Cambridge5, Instituto Superior Técnico6, Zoological Society of London7, Arizona State University8, Columbia University9, National Scientific and Technical Research Council10, Wildlife Conservation Society11, Imperial College London12, National University of Tucumán13, University of the Philippines Los Baños14, University of Tasmania15, University of Edinburgh16, Earthwatch Institute17, Drexel University18, Universidade Federal de Minas Gerais19, Global Environment Facility20, University of Alberta21, Smithsonian Institution22, Université de Sherbrooke23, University of Virginia24, Minnesota Department of Natural Resources25, University of Calgary26, James Cook University27, NatureServe28, University of St Andrews29, Australian National University30, University of Montana31, General Post Office32, University of Otago33, Field Museum of Natural History34, Wildlife Institute of India35, Tokyo Woman's Christian University36, National Oceanic and Atmospheric Administration37, University of Aberdeen38, University of the Witwatersrand39, University of Oxford40, Norwegian Polar Institute41, University Centre in Svalbard42, Copenhagen Zoo43, San Diego State University44, University of Alaska Fairbanks45, Manchester Metropolitan University46, National Autonomous University of Mexico47, University of Kent48, City University of New York49, Victoria University of Wellington50, California Academy of Sciences51, Mote Marine Laboratory52, Osmania University53, White Oak Conservation54, Aaranyak55, University of California, Davis56, Museu Paraense Emílio Goeldi57, University of Stirling58
10 Oct 2008-Science
TL;DR: In this paper, the authors present a comprehensive assessment of the conservation status and distribution of the world's mammals, including marine mammals, using data collected by 1700+ experts, covering all 5487 species.
Abstract: Knowledge of mammalian diversity is still surprisingly disparate, both regionally and taxonomically. Here, we present a comprehensive assessment of the conservation status and distribution of the world's mammals. Data, compiled by 1700+ experts, cover all 5487 species, including marine mammals. Global macroecological patterns are very different for land and marine species but suggest common mechanisms driving diversity and endemism across systems. Compared with land species, threat levels are higher among marine mammals, driven by different processes (accidental mortality and pollution, rather than habitat loss), and are spatially distinct (peaking in northern oceans, rather than in Southeast Asia). Marine mammals are also disproportionately poorly known. These data are made freely available to support further scientific developments and conservation action.

Journal ArticleDOI
TL;DR: The multistate Bennett acceptance ratio estimator (MBAR) as mentioned in this paper is an estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment.
Abstract: We present a new estimator for computing free energy differences and thermodynamic expectations as well as their uncertainties from samples obtained from multiple equilibrium states via either simulation or experiment. The estimator, which we call the multistate Bennett acceptance ratio estimator (MBAR) because it reduces to the Bennett acceptance ratio estimator (BAR) when only two states are considered, has significant advantages over multiple histogram reweighting methods for combining data from multiple states. It does not require the sampled energy range to be discretized to produce histograms, eliminating bias due to energy binning and significantly reducing the time complexity of computing a solution to the estimating equations in many cases. Additionally, an estimate of the statistical uncertainty is provided for all estimated quantities. In the large sample limit, MBAR is unbiased and has the lowest variance of any known estimator for making use of equilibrium data collected from multiple states. We illustrate this method by producing a highly precise estimate of the potential of mean force for a DNA hairpin system, combining data from multiple optical tweezer measurements under constant force bias.

Book
30 Mar 2008
TL;DR: Lave as discussed by the authors discusses the empirical and theoretical journey of effectuation and its relationship to performance in a business setting. But he does not address the problem of teaching effectiveness in a practical setting.
Abstract: Contents: Foreword by Lester Lave Preface Introduction Part I: The Empirical Journey - Entrepreneurial Expertise 1. What I Set Out to Study and Why 2. What I Found and How 3. Interpreting What I Found Part II: The Theoretical Journey - Effectuation 4. Understanding Effectuation: Problem Space and Solution Principles 5. Understanding Effectuation: Dynamics of the Effectual Process 6. Relating Effectuation to Performance Part III: Waypoint 7. Entrepreneurship as a Science of the Artificial 8. Competitive Advantages and Entrepreneurial Opportunities 9. Philosophy and Methodology of Effectual Economics 10. Markets in Human Hope Part IV: The Way Ahead 11. Teaching Effectuation 12. Research Works-in-Progress 13. New Research Ventures References Index

Journal ArticleDOI
TL;DR: In this article, the dependence of the strength of the electron-phonon coupling and the electron heat capacity on the electron temperature was investigated for eight representative metals, Al, Cu, Ag, Au, Ni, Pt, W, and Ti.
Abstract: The dependence of the strength of the electron-phonon coupling and the electron heat capacity on the electron temperature is investigated for eight representative metals, Al, Cu, Ag, Au, Ni, Pt, W, and Ti, for the conditions of strong electron-phonon nonequilibrium. These conditions are characteristic of metal targets subjected to energetic ion bombardment or short-pulse laser irradiation. Computational analysis based on first-principles electronic structure calculations of the electron density of states predicts large deviations (up to an order of magnitude) from the commonly used approximations of linear temperature dependence of the electron heat capacity and a constant electron-phonon coupling. These thermophysical properties are found to be very sensitive to details of the electronic structure of the material. The strength of the electron-phonon coupling can either increase (Al, Au, Ag, Cu, and W), decrease (Ni and Pt), or exhibit nonmonotonic changes (Ti) with increasing electron temperature. The electron heat capacity can exhibit either positive (Au, Ag, Cu, and W) or negative (Ni and Pt) deviations from the linear temperature dependence. The large variations of the thermophysical properties, revealed in this work for the range of electron temperatures typically realized in femtosecond laser material processing applications, have important implications for quantitative computational analysis of ultrafast processes associated with laser interaction with metals.

Journal ArticleDOI
TL;DR: In most subjects who had a hypersensitivity reaction to cetuximab, IgE antibodies against cetUXimab were present in serum before therapy, and the antibodies were specific for galactose-alpha-1,3-galactose.
Abstract: Background Cetuximab, a chimeric mouse–human IgG1 monoclonal antibody against the epidermal growth factor receptor, is approved for use in colorectal cancer and squamous-cell carcinoma of the head and neck. A high prevalence of hypersensitivity reactions to cetuximab has been reported in some areas of the United States. Methods We analyzed serum samples from four groups of subjects for IgE antibodies against cetuximab: pretreatment samples from 76 case subjects who had been treated with cetuximab at multiple centers, predominantly in Tennessee, Arkansas, and North Carolina; samples from 72 control subjects in Tennessee; samples from 49 control subjects with cancer in northern California; and samples from 341 female control subjects in Boston. Results Among 76 cetuximab-treated subjects, 25 had a hypersensitivity reaction to the drug. IgE antibodies against cetuximab were found in pretreatment samples from 17 of these subjects; only 1 of 51 subjects who did not have a hypersensitivity reaction had such ant...

Journal ArticleDOI
TL;DR: In this article, the authors present a framework to develop mainstream application software that transparently scales its parallelism to leverage the increasing number of processor cores, much as 3D graphics applications transparently scale their parallelism on manycore GPUs with widely varying numbers of cores.
Abstract: The advent of multicore CPUs and manycore GPUs means that mainstream processor chips are now parallel systems. Furthermore, their parallelism continues to scale with Moore’s law. The challenge is to develop mainstream application software that transparently scales its parallelism to leverage the increasing number of processor cores, much as 3D graphics applications transparently scale their parallelism to manycore GPUs with widely varying numbers of cores.

Journal ArticleDOI
TL;DR: Results from a test suite which includes problems in one-, two-, and three-dimensions for both hydrodynamics and MHD are given, not only to demonstrate the fidelity of the algorithms, but also to enable comparisons to other methods.
Abstract: A new code for astrophysical magnetohydrodynamics (MHD) is described. The code has been designed to be easily extensible for use with static and adaptive mesh refinement. It combines higher order Godunov methods with the constrained transport (CT) technique to enforce the divergence-free constraint on the magnetic field. Discretization is based on cell-centered volume averages for mass, momentum, and energy, and face-centered area averages for the magnetic field. Novel features of the algorithm include (1) a consistent framework for computing the time- and edge-averaged electric fields used by CT to evolve the magnetic field from the time- and area-averaged Godunov fluxes, (2) the extension to MHD of spatial reconstruction schemes that involve a dimensionally split time advance, and (3) the extension to MHD of two different dimensionally unsplit integration methods. Implementation of the algorithm in both C and FORTRAN95 is detailed, including strategies for parallelization using domain decomposition. Results from a test suite which includes problems in one-, two-, and three-dimensions for both hydrodynamics and MHD are given, not only to demonstrate the fidelity of the algorithms, but also to enable comparisons to other methods. The source code is freely available for download on the web.

Journal ArticleDOI
TL;DR: In this paper, a meta-analysis of thirty-nine study results published within the last ten years that directly compared Web and mail survey modes was conducted, showing that mail surveys have higher response rates than Web surveys in general.
Abstract: This study meta-analyzes thirty-nine study results published within last ten years that directly compared Web and mail survey modes. Although considerable variation exists across the studies, the authors’ findings show that mail surveys have higher response rates than Web surveys in general. Two study features (i.e., population types and follow-up reminders) are shown to contribute statistically to the variation of response rate differences between Web and paper surveys in the comparative studies. College respondents appear to be more responsive to Web surveys, while some other respondents (e.g., medical doctors, school teachers, and general consumers) appear to prefer traditional mail surveys. Follow-up reminders appear to be less effective for Web survey respondents than for mail survey respondents. Other study features (i.e., implementation of random assignment of survey respondents, incentives, and publication year) are not statistically useful in accounting for the variation of response rate differences between Web and mail surveys.

Journal ArticleDOI
TL;DR: Experiments 2-4 showed that the role of disgust in severity of moral judgments depends on participants' sensitivity to their own bodily sensations, indicating the importance—and specificity—of gut feelings in moral judgments.
Abstract: How, and for whom, does disgust influence moral judgment? In four experiments participants made moral judgments while experiencing extraneous feelings of disgust. Disgust was induced in Experiment 1 by exposure to a bad smell, in Experiment 2 by working in a disgusting room, in Experiment 3 by recalling a physically disgusting experience, and in Experiment 4 through a video induction. In each case, the results showed that disgust can increase the severity of moral judgments relative to controls. Experiment 4 found that disgust had a different effect on moral judgment than did sadness. In addition, Experiments 2-4 showed that the role of disgust in severity of moral judgments depends on participants' sensitivity to their own bodily sensations. Taken together, these data indicate the importance-and specificity-of gut feelings in moral judgments.

Journal ArticleDOI
TL;DR: The authors examined children's growth in school-related learning and social skills over the pre-Kindergarten (pre-K) year in state-funded programs designed to prepare children for kindergarten.

Journal ArticleDOI
16 May 2008-Science
TL;DR: Although ∼10% of the ocean's drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions.
Abstract: Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the ocean's external (nonrecycled) nitrogen supply and up to 3% of the annual new marine biological production, 0.3 petagram of carbon per year. This input could account for the production of up to 1.6 teragrams of nitrous oxide (N2O) per year. Although 10% of the ocean's drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions. The effects of increasing atmospheric nitrogen deposition are expected to continue to grow in the future.

Journal ArticleDOI
TL;DR: In this article, the authors investigate the association between aggressive tax and financial reporting and find a strong, positive relation, concluding that insufficient costs exist to offset financial and tax reporting incentives, such that nonconformity between financial accounting standards and tax law allows firms to manage book income upward and taxable income downward in the same reporting period.
Abstract: We investigate the association between aggressive tax and financial reporting and find a strong, positive relation. Our results suggest that insufficient costs exist to offset financial and tax reporting incentives, such that nonconformity between financial accounting standards and tax law allows firms to manage book income upward and taxable income downward in the same reporting period. To examine the relation between these aggressive reporting behaviors, we develop a measure of tax reporting aggressiveness that statistically detects tax shelter activity as least as well as, and often better than, other measures. In supplemental stock returns analyses, we confirm that the market overprices financial reporting aggressiveness. We also find that the market overprices tax reporting aggressiveness, but only for firms with the most aggressive financial reporting.

Journal ArticleDOI
21 Feb 2008-Nature
TL;DR: The analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations produces new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human- genetic studies in diverse worldwide populations.
Abstract: Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with increasing geographic distance from Africa, as expected under a serial founder effect for the out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected--including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas--the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.

Journal ArticleDOI
TL;DR: The guideline includes data on the epidemiology, clinical features, diagnosis, and treatment of many viral, bacterial, fungal, protozoal, and helminthic etiologies of encephalitis and provides information on when specific etiologic agents should be considered in individual patients with encephalopathy.
Abstract: Guidelines for the diagnosis and treatment of patients with encephalitis were prepared by an Expert Panel of the Infectious Diseases Society of America. The guidelines are intended for use by health care providers who care for patients with encephalitis. The guideline includes data on the epidemiology, clinical features, diagnosis, and treatment of many viral, bacterial, fungal, protozoal, and helminthic etiologies of encephalitis and provides information on when specific etiologic agents should be considered in individual patients with encephalitis.

Journal ArticleDOI
TL;DR: DNA delivery and successful tissue transfection are observed in the areas of the body where ultrasound is applied after intravascular administration of microbubbles and plasmid DNA.

Journal ArticleDOI
05 Sep 2008-Cell
TL;DR: The relationship between the circadian and metabolic systems and the implications for cardiovascular disease, obesity, and diabetes are reviewed.

Journal ArticleDOI
TL;DR: A model for adhesion assembly is developed that clarifies the relative contributions of myosin II and actin polymerization and organization and produces a model that shows that nascent adhesions assemble and are stable within the lamellipodium.
Abstract: Using two-colour imaging and high resolution TIRF microscopy, we investigated the assembly and maturation of nascent adhesions in migrating cells. We show that nascent adhesions assemble and are stable within the lamellipodium. The assembly is independent of myosin II but its rate is proportional to the protrusion rate and requires actin polymerization. At the lamellipodium back, the nascent adhesions either disassemble or mature through growth and elongation. Maturation occurs along an alpha-actinin-actin template that elongates centripetally from nascent adhesions. Alpha-Actinin mediates the formation of the template and organization of adhesions associated with actin filaments, suggesting that actin crosslinking has a major role in this process. Adhesion maturation also requires myosin II. Rescue of a myosin IIA knockdown with an actin-bound but motor-inhibited mutant of myosin IIA shows that the actin crosslinking function of myosin II mediates initial adhesion maturation. From these studies, we have developed a model for adhesion assembly that clarifies the relative contributions of myosin II and actin polymerization and organization.

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TL;DR: The initiation of atherosclerosis results from complex interactions of circulating factors and various cell types in the vessel wall, including endothelial cells, lymphocytes, monocytes, and smooth muscle cells (SMCs), which contribute to the initiation and propagation of the inflammatory response to lipid.
Abstract: The initiation of atherosclerosis results from complex interactions of circulating factors and various cell types in the vessel wall, including endothelial cells, lymphocytes, monocytes and smooth muscle cells (SMCs). Recent reviews highlight the role of activated endothelium and inflammatory cell recruitment in the initiation of and progression of early atherosclerosis. Yet, human autopsy studies, in vitro mechanistic studies and in vivo correlative data suggest an important role for SMCs in the initiation of atherosclerosis. SMCs are the major producers of extracellular matrix within the vessel wall and in response to atherogenic stimuli can modify the type of matrix proteins produced. In turn, the type of matrix present can affect the lipid content of the developing plaque and the proliferative index of the cells that are adherent to it. SMCs are also capable of functions typically attributed to other cell types. Like macrophages, SMCs can express a variety of receptors for lipid uptake and can form foam-like cells, thereby participating in the early accumulation of plaque lipid. Like endothelial cells, SMCs can also express a variety of adhesion molecules such as VCAM-1 and ICAM-1 to which monocytes and lymphocytes can adhere and migrate into the vessel wall. In addition, through these adhesion molecules, SMCs can also stabilize these cells against apoptosis, thus contributing to the early cellularity of the lesion. Like many cells within the developing plaque, SMCs also produce many cytokines such as PDGF, TGFβ, IFNγ; and MCP-1 all of which contribute to the initiation and propagation of the inflammatory response to lipid. Recent advances in SMC-specific gene modulation have enhanced our ability to determine the role of SMCs in early atherogenesis.

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TL;DR: Viral fusion proteins convert from a fusion-competent state to a membrane-embedded homotrimeric prehairpin, and then to a trimer-of-hairpins that brings the fusion peptide and the transmembrane domain into close proximity thereby facilitating the union of viral and target membranes.
Abstract: Recent work has identified three distinct classes of viral membrane fusion proteins based on structural criteria. In addition, there are at least four distinct mechanisms by which viral fusion proteins can be triggered to undergo fusion-inducing conformational changes. Viral fusion proteins also contain different types of fusion peptides and vary in their reliance on accessory proteins. These differing features combine to yield a rich diversity of fusion proteins. Yet despite this staggering diversity, all characterized viral fusion proteins convert from a fusion-competent state (dimers or trimers, depending on the class) to a membrane-embedded homotrimeric prehairpin, and then to a trimer-of-hairpins that brings the fusion peptide, attached to the target membrane, and the transmembrane domain, attached to the viral membrane, into close proximity thereby facilitating the union of viral and target membranes. During these conformational conversions, the fusion proteins induce membranes to progress through stages of close apposition, hemifusion, and then the formation of small, and finally large, fusion pores. Clearly, highly divergent proteins have converged on the same overall strategy to mediate fusion, an essential step in the life cycle of every enveloped virus.