Research papers

Comparative Protein Structure Modeling Using MODELLER

Narayanan Eswar, Ben Webb, Marc A. Martı́-Renom, M. S. Madhusudhan, David Eramian, Min‐Yi Shen, Ursula Pieper, Andrej Šali

Functional characterization of a protein sequence is a common goal in biology, and is usually facilitated by having an accurate three-dimensional (3-D) structure of the studied protein. In the absence of an experimentally determined structure, comparative or homology modeling can sometimes provide a useful 3-D model for a protein that is related to at least one known protein structure. Comparative modeling predicts the 3-D structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described.

Malignant astrocytic glioma: genetics, biology, and paths to treatment

Frank B. Furnari, Tim R. Fenton, Robert Bachoo, Akitake Mukasa, Jayne M. Stommel, Alexander H. Stegh, William C. Hahn, Keith…

Malignant astrocytic gliomas such as glioblastoma are the most common and lethal intracranial tumors. These cancers exhibit a relentless malignant progression characterized by widespread invasion throughout the brain, resistance to traditional and newer targeted therapeutic approaches, destruction of normal brain tissue, and certain death. The recent confluence of advances in stem cell biology, cell signaling, genome and computational science and genetic model systems have revolutionized our understanding of the mechanisms underlying the genetics, biology and clinical behavior of glioblastoma. This progress is fueling new opportunities for understanding the fundamental basis for development of this devastating disease and also novel therapies that, for the first time, portend meaningful clinical responses.

Deciding on the Number of Classes in Latent Class Analysis and Growth Mixture Modeling: A Monte Carlo Simulation Study

Karen Nylund‐Gibson, Tihomir Asparouhov, Bengt Muthén

Mixture modeling is a widely applied data analysis technique used to identify unobserved heterogeneity in a population. Despite mixture models' usefulness in practice, one unresolved issue in the application of mixture models is that there is not one commonly accepted statistical indicator for deciding on the number of classes in a study population. This article presents the results of a simulation study that examines the performance of likelihood-based tests and the traditionally used Information Criterion (ICs) used for determining the number of classes in mixture modeling. We look at the performance of these tests and indexes for 3 types of mixture models: latent class analysis (LCA), a factor mixture model (FMA), and a growth mixture models (GMM). We evaluate the ability of the tests and indexes to correctly identify the number of classes at three different sample sizes (n = 200, 500, 1,000). Whereas the Bayesian Information Criterion performed the best of the ICs, the bootstrap likelihood ratio test proved to be a very consistent indicator of classes across all of the models considered.

Mussel-Inspired Surface Chemistry for Multifunctional Coatings

Haeshin Lee, Shara M. Dellatore, William M. Miller, Phillip B. Messersmith

We report a method to form multifunctional polymer coatings through simple dip-coating of objects in an aqueous solution of dopamine. Inspired by the composition of adhesive proteins in mussels, we used dopamine self-polymerization to form thin, surface-adherent polydopamine films onto a wide range of inorganic and organic materials, including noble metals, oxides, polymers, semiconductors, and ceramics. Secondary reactions can be used to create a variety of ad-layers, including self-assembled monolayers through deposition of long-chain molecular building blocks, metal films by electroless metallization, and bioinert and bioactive surfaces via grafting of macromolecules.

A second generation human haplotype map of over 3.1 million SNPs

Sarah S. Murray, Dennis G. Ballinger, David R. Cox, David A. Hinds, Laura L. Stuvé, John W. Belmont, Suzanne M. Leal, David …

The Cauchy problem for a class of pseudodifferential equations over p-adic field

Nguyen Minh Chuong, Nguyen Van Co

Animated demonstrations and training wheels interfaces in a complex learning environment

Christian Spannagel, Raimund Girwidz, Herbert Löthe, Andreas Zendler, Ulrik Schroeder

Learning how to use a new software program can be a difficult and demanding task, especially for novices. There are several types of support for users exploring a software package. Animated demonstrations show how experts use an application, and training wheels interfaces offer a secure environment for exploration. To support different types of learners, external help should be adapted according to learner characteristics. The study presented in this article investigates effects of different support types in combination with the computer self-efficacy of learners. Young students (8th graders) were supported with text manuals, animated demonstrations, or animated demonstrations combined with a training wheels interface. In this context, they had to solve problems in physics and mathematics with a spreadsheet program. Results showed that animated demonstrations outperformed text manuals in many cases. Training wheels interfaces seemed to have disadvantages compared to unmodified user interfaces. In addition, motivational aspects have been investigated. Subjects with high computer self-efficacy scores were more motivated than their counterparts. Statistics (analysis of variance) revealed no interaction effects between the treatment and computer self-efficacy.

Greenhouse gas mitigation in agriculture

Pete Smith, Daniel Martino, Zucong Cai, D. M. Gwary, H. H. Janzen, Pushpam Kumar, Bruce A. McCarl, Stephen M. Ogle, F.P. O’M…

Agricultural lands occupy 37% of the earth's land surface. Agriculture accounts for 52 and 84% of global anthropogenic methane and nitrous oxide emissions. Agricultural soils may also act as a sink or source for CO2, but the net flux is small. Many agricultural practices can potentially mitigate greenhouse gas (GHG) emissions, the most prominent of which are improved cropland and grazing land management and restoration of degraded lands and cultivated organic soils. Lower, but still significant mitigation potential is provided by water and rice management, set-aside, land use change and agroforestry, livestock management and manure management. The global technical mitigation potential from agriculture (excluding fossil fuel offsets from biomass) by 2030, considering all gases, is estimated to be approximately 5500-6000Mt CO2-eq.yr-1, with economic potentials of approximately 1500-1600, 2500-2700 and 4000-4300Mt CO2-eq.yr-1 at carbon prices of up to 20, up to 50 and up to 100 US$ t CO2-eq.-1, respectively. In addition, GHG emissions could be reduced by substitution of fossil fuels for energy production by agricultural feedstocks (e.g. crop residues, dung and dedicated energy crops). The economic mitigation potential of biomass energy from agriculture is estimated to be 640, 2240 and 16 000Mt CO2-eq.yr-1 at 0-20, 0-50 and 0-100 US$ t CO2-eq.-1, respectively.

Use of mental health services for anxiety, mood, and substance disorders in 17 countries in the WHO world mental health surveys

Philip S. Wang, Sergio Aguilar‐Gaxiola, Jordi Alonso, Matthias C. Angermeyer, Guilherme Borges, Evelyn J. Bromet, Ronny Bruf…

Photogrammetric Engineering and Remote Sensing

John Nicol, B. King, Quattrochi, D, Dowman, I, Ehlers, M, Xiaoli, D

Quantum Computer Science

N. David Mermin

In the 1990's it was realized that quantum physics has some spectacular applications in computer science. This book is a concise introduction to quantum computation, developing the basic elements of this new branch of computational theory without assuming any background in physics. It begins with an introduction to the quantum theory from a computer-science perspective. It illustrates the quantum-computational approach with several elementary examples of quantum speed-up, before moving to the major applications: Shor's factoring algorithm, Grover's search algorithm, and quantum error correction. The book is intended primarily for computer scientists who know nothing about quantum theory, but will also be of interest to physicists who want to learn the theory of quantum computation, and philosophers of science interested in quantum foundational issues. It evolved during six years of teaching the subject to undergraduates and graduate students in computer science, mathematics, engineering, and physics, at Cornell University.

PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses

Shaun Purcell, Benjamin M. Neale, Katherine EO Todd-Brown, L. Odong Thomas, Manuel A. R. Ferreira, D.B. Bender, Julian Malle…

The English Lexicon Project

David A. Balota, Melvin J. Yap, Keith A. Hutchison, Michael J. Cortese, Brett Kessler, Bjorn Loftis, James H. Neely, Douglas…

Invasion biology and conservation biology: time to join forces to explore the links between species traits and extinction risk and invasiveness

Mark van Kleunen, David M. Richardson

Expansion and decline of species are natural phenomena (Levin, 2000). However, owing to the increasing infl uence of humans worldwide, the processes driving expansion and decline have speeded up dramatically. Hence, we have the current biodiversity crisis. Humanmediated forces are making some species rarer (ie, driving them towards extinction) while at the same time making some species expand their ranges (‘invasive’ sensu Richardson et al., 2000). Undisputedly, the immediate causes for extinction of native species and invasiveness of aliens are extrinsic factors, such as habitat destruction and climate change. However, the ultimate causes have to be ecological and life-history characteristics of species (Kotiaho et al., 2005). Therefore, important research directions in conservation biology and invasion biology are the analyses of species traits associated with rarity (Murray et al., 2002) and invasiveness (Pyšek and Richardson, 2007), respectively. The first are important for prioritizing conservation efforts, and the second are important for prioritizing eradication efforts and the development of screening protocols of potential invasiveness of species considered for introduction to other regions. Unravelling the links between species traits and extrinsic factors is highly complex, particularly because assessment of the causes of rarity and invasiveness relies mainly on retrospective analyses since large-scale controlled experiments are often not feasible (Richardson et al., 2004). However, with the increasing availability of large, widely accessible databases and analytical approaches (eg, Wilson et al., 2007), it is becoming easier to test which traits are associated with rarity and invasiveness, and under which conditions.

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

Yan Zhao, Donald G. Truhlar

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

The Bioecological Model of Human Development

Urie Bronfenbrenner, Pamela Morris

In this chapter, we undertake to present the ecological model of human development that has been introduced in a prior edition of this Handbook. The bioecological model is an evolving theoretical system for the scientific study of human development over time. The model presented in this chapter represents major theoretical innovations from the 1983 chapter in both form and content. The new model is not a paradigm shift, but rather represents a transition from a focus on the environment to a focus on proximal processes as engines of development. We begin with the defining properties of the model, which involves four principal components (process, person, context, and time), and the dynamic, interactive relationships among them. We then turn to the research designs required for testing the model. In doing so, we not only present the next stage in the evolution of an ecological theory of human development, but we also document the requirements for conducting developmental research in the discovery mode. We conclude with a look to the future—and what the bioecological model means for the future development of our species.

Postcolonial English

Edgar W. Schneider

The global spread of English has resulted in the emergence of a diverse range of postcolonial varieties around the world. Postcolonial English provides a clear and original account of the evolution of these varieties, exploring the historical, social and ecological factors that have shaped all levels of their structure. It argues that while these Englishes have developed new and unique properties which differ greatly from one location to another, their spread and diversification can in fact be explained by a single underlying process, which builds upon the constant relationships and communication needs of the colonizers, the colonized, and other parties. Outlining the stages and characteristics of this process, it applies them in detail to English in sixteen different countries across all continents as well as, in a separate chapter, to a history of American English. Of key interest to sociolinguists, dialectologists, historical linguists and syntacticians alike, this 2007 book provides a fascinating new picture of the growth and evolution of English around the globe.

Research Methods in Education

Louis Cohen, Lawrence Manion, Keith Morrison

This fully updated sixth edition of the international bestseller Research Methods in Education covers the whole range of methods currently employed by educational research at all stages. It is divided into five main parts: the context of educational research; planning educational research; styles of educational research; strategies for data collection and researching; and data analysis. The book also contains references to a comprehensive dedicated website of accompanying materials. The sixth edition includes new material on: complexity theory, ethics, sampling and sensitive educational research experimental research, questionnaire design and administration with practical guidance qualitative and quantitative data analysis, with practical examples internet based research. Research Methods in Education is essential reading for the professional researcher and continues to be the standard text for students and lecturers in educational research. To access the dedicated website of accompanying materials, please visit: www.routledge.com/textbooks/9780415368780.

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

Koichiro Tamura, Joel T. Dudley, M Nei, Sudhir Kumar

We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).

A survey of trust in computer science and the Semantic Web

Donovan Artz, Yolanda Gil

Ultracold atomic gases in optical lattices: mimicking condensed matter physics and beyond

Maciej Lewenstein, Anna Sanpera, V. Ahufinger, Bogdan Damski, Aditi Sen, Ujjwal Sen

We review recent developments in the physics of ultracold atomic and molecular gases in optical lattices. Such systems are nearly perfect realisations of various kinds of Hubbard models, and as such may very well serve to mimic condensed matter phenomena. We show how these systems may be employed as quantum simulators to answer some challenging open questions of condensed matter, and even high energy physics. After a short presentation of the models and the methods of treatment of such systems, we discuss in detail, which challenges of condensed matter physics can be addressed with (i) disordered ultracold lattice gases, (ii) frustrated ultracold gases, (iii) spinor lattice gases, (iv) lattice gases in “artificial” magnetic fields, and, last but not least, (v) quantum information processing in lattice gases. For completeness, also some recent progress related to the above topics with trapped cold gases will be discussed. Motto: There are more things in heaven and earth, Horatio, Than are dreamt of in your philosophy Citation1

An Overview of the Biology of the Desiccation-tolerant Resurrection Plant Myrothamnus flabellifolia

John P. Moore, George G. Lindsey, Jill M. Farrant, Wolf F. Brandt

BACKGROUND: Myrothamnus flabellifolia is unique as the only woody resurrection plant. It is an important plant in southern Africa because of its widespread occurrence and usage in African medicine and traditional culture. Many reports have investigated facets of its biology and the mechanisms associated with its desiccation tolerance. SCOPE: The general biology of the woody resurrection plant Myrothamnus flabellifolia is reviewed. The review focuses on the geography and ecology, systematic placement, evolution, morphology and reproductive ecology of M. flabellifolia as well as the wood anatomy and re-filling mechanism. In addition, the desiccation tolerance, ethnobotanical importance and medicinal properties of the plant are reviewed. Also, future research avenues are suggested, in particular the necessity to research the biogeography and systematics of the species and the role of the polyphenols present, as well as the molecular basis of the plant's desiccation tolerance.

Matplotlib: A 2D Graphics Environment

John D. Hunter

Matplotlib is a 2D graphics package used for Python for application development, interactive scripting,and publication-quality image generation across user interfaces and operating systems

Qualitative Research in Nursing: Advancing the Humanistic Imperative

Helen J. Streubert, Dona Rinaldi Carpenter

This text covers qualitative research methodologies and published literature in nursing education, administration and practice for each method. Other topics include publishing, conference presentation, grant writing and ethical concerns.