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1,332 papers found.
CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as 'Coot'.
DOI: 10.1107/s0907444904019158Sustainability is often poorly defined and difficult to measure. We describe several concepts from ecology, economics, and physics, that have contributed to sustainability indices, and discuss their positive and negative aspects. Indices range from mostly ecological (such as ecosystem resilience and global human carrying capacity), to those inspired by both economics and ecology (green income and maximum sustainable yield), to a mix of ecology and physics (exergy and emergy). Economic concepts such as substitutability of natural and human capital (the “weak” versus “strong” sustainability debate), and throughput of natural resources through an economic system, are the basis for several strictly economic indices. The second law of thermodynamics, which dictates the decrease in usable energy, has also had an increasing influence on sustainability discussions. The indices described here address different aspects of the interactions between human societies and ecosystems, and are therefore probably most effective when used in combination.
DOI: 10.2307/3868430Sustainability is often poorly defined and difficult to measure. We describe several concepts from ecology, economics, and physics, that have contributed to sustainability indices, and discuss their positive and negative aspects. Indices range from mostly ecological (such as ecosystem resilience and global human carrying capacity), to those inspired by both economics and ecology (green income and maximum sustainable yield), to a mix of ecology and physics (exergy and emergy). Economic concepts such as substitutability of natural and human capital (the “weak” versus “strong” sustainability debate), and throughput of natural resources through an economic system, are the basis for several strictly economic indices. The second law of thermodynamics, which dictates the decrease in usable energy, has also had an increasing influence on sustainability discussions. The indices described here address different aspects of the interactions between human societies and ecosystems, and are therefore probably most effective when used in combination.
DOI: 10.1890/1540-9295(2004)002[0419:tmiocs]2.0.co;2The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.
DOI: 10.1186/gb-2004-5-10-r80Existing evidence suggests that nursing students have high levels of stress and that counseling and other support services should be made available to them. However, the stressors and counseling needs of undergraduate nursing students in Nigeria have yet to be explored. This study used a questionnaire to investigate the stressors, counseling needs, and desired counseling facilities of undergraduate nursing students at the University of Ibadan. Common stressors included excessive schoolwork, financial problems, inadequate recreational facilities, and overcrowded accommodations. There was an association between reporting inconsiderate, insensitive lecturers as stressors and evidence of psychological distress. Nearly 60% of the respondents felt counseling would help them, and most desired counseling for academics, finances, and relationships. Most (78%) of the respondents preferred an independent facility with trained counselors. Desired characteristics for the services included accessibility, affordability, confidentiality, and a friendly atmosphere. Educators and administrators should use this information to design counseling facilities for students.
DOI: 10.3928/01484834-20040901-06We show that cosmic acceleration can arise due to very tiny corrections to the usual gravitational action of general relativity, of the form ${R}^{\ensuremath{-}n}$ with $n>0.$ This model eliminates the need for a nonzero cosmological constant or any other form of dark energy, attributing a purely gravitational origin to the acceleration of the universe.
DOI: 10.1103/physrevd.70.043528The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
DOI: 10.1002/jcc.20084The second edition features: a CD with all of the book's Amos, EQS, and LISREL programs and data sets; new chapters on importing data issues related to data editing and on how to report research; an updated introduction to matrix notation and programs that illustrate how to compute these calculations; many more computer program examples and chapter exercises; and increased coverage of factors that affect correlation, the 4-step approach to SEM and hypothesis testing, significance, power, and sample size issues. The new edition's expanded use of applications make this book ideal for advanced students and researchers in psychology, education, business, health care, political science, sociology, and biology. A basic understanding of correlation is assumed and an understanding of the matrices used in SEM models is encouraged.
DOI: 10.4324/9781410610904Understanding sources of sustained competitive advantage has become a major area of research in strategic management. Building on the assumptions that strategic resources are heterogeneously distributed across firms and that these differences are stable over time, this article examines the link between firm resources and sustained competitive advantage. Four empirical indicators of the potential of firm resources to generate sustained competitive advantage-value, rareness, imitability, and substitutability are discussed. The model is applied by analyzing the potential of several firm resources for generating sustained competitive advantages. The article concludes by examining implications of this firm resource model of sustained competitive advantage for other business disciplines.
DOI: 10.1016/s0742-3322(00)17018-4Neutron stars are some of the densest manifestations of massive objects in the universe. They are ideal astrophysical laboratories for testing theories of dense matter physics and provide connections among nuclear physics, particle physics, and astrophysics. Neutron stars may exhibit conditions and phenomena not observed elsewhere, such as hyperon-dominated matter, deconfined quark matter, superfluidity and superconductivity with critical temperatures near 10(10) kelvin, opaqueness to neutrinos, and magnetic fields in excess of 10(13) Gauss. Here, we describe the formation, structure, internal composition, and evolution of neutron stars. Observations that include studies of pulsars in binary systems, thermal emission from isolated neutron stars, glitches from pulsars, and quasi-periodic oscillations from accreting neutron stars provide information about neutron star masses, radii, temperatures, ages, and internal compositions.
DOI: 10.1126/science.1090720Objective methods for assessing perceptual image quality traditionally attempted to quantify the visibility of errors (differences) between a distorted image and a reference image using a variety of known properties of the human visual system. Under the assumption that human visual perception is highly adapted for extracting structural information from a scene, we introduce an alternative complementary framework for quality assessment based on the degradation of structural information. As a specific example of this concept, we develop a Structural Similarity Index and demonstrate its promise through a set of intuitive examples, as well as comparison to both subjective ratings and state-of-the-art objective methods on a database of images compressed with JPEG and JPEG2000.
DOI: 10.1109/tip.2003.819861This article examines health promotion and disease prevention from the perspective of social cognitive theory. This theory posits a multifaceted causal structure in which self-efficacy beliefs operate together with goals, outcome expectations, and perceived environmental impediments and facilitators in the regulation of human motivation, behavior, and well-being. Belief in one's efficacy to exercise control is a common pathway through which psychosocial influences affect health functioning. This core belief affects each of the basic processes of personal change--whether people even consider changing their health habits, whether they mobilize the motivation and perseverance needed to succeed should they do so, their ability to recover from setbacks and relapses, and how well they maintain the habit changes they have achieved. Human health is a social matter, not just an individual one. A comprehensive approach to health promotion also requires changing the practices of social systems that have widespread effects on human health.
DOI: 10.1177/1090198104263660Convex optimization problems arise frequently in many different fields. This book provides a comprehensive introduction to the subject, and shows in detail how such problems can be solved numerically with great efficiency. The book begins with the basic elements of convex sets and functions, and then describes various classes of convex optimization problems. Duality and approximation techniques are then covered, as are statistical estimation techniques. Various geometrical problems are then presented, and there is detailed discussion of unconstrained and constrained minimization problems, and interior-point methods. The focus of the book is on recognizing convex optimization problems and then finding the most appropriate technique for solving them. It contains many worked examples and homework exercises and will appeal to students, researchers and practitioners in fields such as engineering, computer science, mathematics, statistics, finance and economics.
DOI: 10.1017/cbo9780511804441We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.
DOI: 10.1093/nar/gkh340