Research papers

Model Selection and Estimation in Regression with Grouped Variables

Ming Yuan, Yi Lin

Summary We consider the problem of selecting grouped variables (factors) for accurate prediction in regression. Such a problem arises naturally in many practical situations with the multifactor analysis-of-variance problem as the most important and well-known example. Instead of selecting factors by stepwise backward elimination, we focus on the accuracy of estimation and consider extensions of the lasso, the LARS algorithm and the non-negative garrotte for factor selection. The lasso, the LARS algorithm and the non-negative garrotte are recently proposed regression methods that can be used to select individual variables. We study and propose efficient algorithms for the extensions of these methods for factor selection and show that these extensions give superior performance to the traditional stepwise backward elimination method in factor selection problems. We study the similarities and the differences between these methods. Simulations and real examples are used to illustrate the methods.

Foundations for engineering biology

Drew Endy

Acceptance and Commitment Therapy: Model, processes and outcomes

Steven C. Hayes, Jason B. Luoma, Frank W. Bond, Akihiko Masuda, Jason Lillis

Generalized Linear Models

Physics of thin-film ferroelectric oxides

Matthew Dawber, Karin M. Rabe, J. F. Scott

This review covers important advances in recent years in the physics of thin-film ferroelectric oxides, the strongest emphasis being on those aspects particular to ferroelectrics in thin-film form. The authors introduce the current state of development in the application of ferroelectric thin films for electronic devices and discuss the physics relevant for the performance and failure of these devices. Following this the review covers the enormous progress that has been made in the first-principles computational approach to understanding ferroelectrics. The authors then discuss in detail the important role that strain plays in determining the properties of epitaxial thin ferroelectric films. Finally, this review ends with a look at the emerging possibilities for nanoscale ferroelectrics, with particular emphasis on ferroelectrics in nonconventional nanoscale geometries.

Microfluidics: Fluid physics at the nanoliter scale

Todd M. Squires, Stephen R. Quake

Microfabricated integrated circuits revolutionized computation by vastly reducing the space, labor, and time required for calculations. Microfluidic systems hold similar promise for the large-scale automation of chemistry and biology, suggesting the possibility of numerous experiments performed rapidly and in parallel, while consuming little reagent. While it is too early to tell whether such a vision will be realized, significant progress has been achieved, and various applications of significant scientific and practical interest have been developed. Here a review of the physics of small volumes (nanoliters) of fluids is presented, as parametrized by a series of dimensionless numbers expressing the relative importance of various physical phenomena. Specifically, this review explores the Reynolds number Re, addressing inertial effects; the P\'eclet number Pe, which concerns convective and diffusive transport; the capillary number Ca expressing the importance of interfacial tension; the Deborah, Weissenberg, and elasticity numbers De, Wi, and El, describing elastic effects due to deformable microstructural elements like polymers; the Grashof and Rayleigh numbers Gr and Ra, describing density-driven flows; and the Knudsen number, describing the importance of noncontinuum molecular effects. Furthermore, the long-range nature of viscous flows and the small device dimensions inherent in microfluidics mean that the influence of boundaries is typically significant. A variety of strategies have been developed to manipulate fluids by exploiting boundary effects; among these are electrokinetic effects, acoustic streaming, and fluid-structure interactions. The goal is to describe the physics behind the rich variety of fluid phenomena occurring on the nanoliter scale using simple scaling arguments, with the hopes of developing an intuitive sense for this occasionally counterintuitive world.

Three Approaches to Qualitative Content Analysis

Hsiu-Fang Hsieh, Sarah E. Shannon

Content analysis is a widely used qualitative research technique. Rather than being a single method, current applications of content analysis show three distinct approaches: conventional, directed, or summative. All three approaches are used to interpret meaning from the content of text data and, hence, adhere to the naturalistic paradigm. The major differences among the approaches are coding schemes, origins of codes, and threats to trustworthiness. In conventional content analysis, coding categories are derived directly from the text data. With a directed approach, analysis starts with a theory or relevant research findings as guidance for initial codes. A summative content analysis involves counting and comparisons, usually of keywords or content, followed by the interpretation of the underlying context. The authors delineate analytic procedures specific to each approach and techniques addressing trustworthiness with hypothetical examples drawn from the area of end-of-life care.

Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

Aravind Subramanian, Pablo Tamayo, Vamsi K. Mootha, Sayan Mukherjee, Benjamin L. Ebert, Michael A. Gillette, Amanda G. Paulo…

Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.

Contribution of Primary Care to Health Systems and Health

Bárbara Starfield, Leiyu Shi, James Macinko

Evidence of the health-promoting influence of primary care has been accumulating ever since researchers have been able to distinguish primary care from other aspects of the health services delivery system. This evidence shows that primary care helps prevent illness and death, regardless of whether the care is characterized by supply of primary care physicians, a relationship with a source of primary care, or the receipt of important features of primary care. The evidence also shows that primary care (in contrast to specialty care) is associated with a more equitable distribution of health in populations, a finding that holds in both cross-national and within-national studies. The means by which primary care improves health have been identified, thus suggesting ways to improve overall health and reduce differences in health across major population subgroups.

Niche Conservatism: Integrating Evolution, Ecology, and Conservation Biology

John J. Wiens, Catherine H. Graham

▪ Abstract Niche conservatism is the tendency of species to retain ancestral ecological characteristics. In the recent literature, a debate has emerged as to whether niches are conserved. We suggest that simply testing whether niches are conserved is not by itself particularly helpful or interesting and that a more useful focus is on the patterns that niche conservatism may (or may not) create. We focus specifically on how niche conservatism in climatic tolerances may limit geographic range expansion and how this one type of niche conservatism may be important in (a) allopatric speciation, (b) historical biogeography, (c) patterns of species richness, (d) community structure, (e) the spread of invasive, human-introduced species, (f) responses of species to global climate change, and (g) human history, from 13,000 years ago to the present. We describe how these effects of niche conservatism can be examined with new tools for ecological niche modeling.

Maximum entropy modeling of species geographic distributions

Steven J. Phillips, Robert P. Anderson, Robert E. Schapire

Stress, Health, and the Life Course: Some Conceptual Perspectives

Leonard I. Pearlin, Scott Schieman, Elena M. Fazio, Stephen C. Meersman

This article proposes several conceptual perspectives designed to advance our understanding of the material and experiential conditions contributing to persistent disparities in rates of morbidity and mortality among groups unequal in their social and economic statuses. An underlying assumption is that these disparities, which are in clear evidence at mid- and late life, may be anchored to earlier circumstances of the life course. Of particular interest are those circumstances resulting in people with the least privileged statuses having the greatest chances of exposure to health-related stressors. Among the stressors closely linked to status and status attainment are those that continue or are repeated across the life course, such as enduring economic strain and discriminatory experiences. Also taking a long-range toll on health are circumstances of stress proliferation, a process that places people exposed to a serious adversity at risk for later exposure to additional adversities. We suggest that this process can be observed in instances of trauma, in early out-of-sequence transitions, and in the case of undesired changes that disrupt behaviors and relationships in established roles. Effective effort to close the systemic health gaps must recognize their structural underpinnings.

Understanding Interaction Models: Improving Empirical Analyses

Thomas Brambor, William R. Clark, Matt Golder

Multiplicative interaction models are common in the quantitative political science literature. This is so for good reason. Institutional arguments frequently imply that the relationship between political inputs and outcomes varies depending on the institutional context. Models of strategic interaction typically produce conditional hypotheses as well. Although conditional hypotheses are ubiquitous in political science and multiplicative interaction models have been found to capture their intuition quite well, a survey of the top three political science journals from 1998 to 2002 suggests that the execution of these models is often flawed and inferential errors are common. We believe that considerable progress in our understanding of the political world can occur if scholars follow the simple checklist of dos and don'ts for using multiplicative interaction models presented in this article. Only 10% of the articles in our survey followed the checklist.

Case-based tutoring systems for procedural problem solving on the www

Seokmin Han, Sangmin Lee, Geun‐Sik Jo

Phytochemical constituents of some Nigerian medicinal plants

H. O. Edeoga, D. E. Okwu, B. O. Mbaebie

Alkaloids, tannins, saponins, steroid, terpenoid, flavonoids, phlobatannin and cardic glycoside distribution in ten medicinal plants belonging to different families were assessed and compared. The medicinal plants investigated were Cleome nutidosperma, Emilia coccinea, Euphorbia heterophylla, Physalis angulata, Richardia bransitensis, Scopania dulcis, Sida acuta, Spigelia anthelmia, Stachytarpheta cayennensis and Tridax procumbens. All the plants were found to contain alkaloids, tannins and flavonoids except for the absence of tannins in S. acuta and flavonoids in S. cayennsis respectively. The significance of the plants in traditional medicine and the importance of the distribution of these chemical constituents were discussed with respect to the role of these plants in ethnomedicine in Nigeria. Key words: Medicinal plants, ethnomedicine, phytochemical constituents.

The Cambridge Grammar of the English Language

Rodnry Huddleston, Geqffrry Pullum

Publisher description: This book presents a new and comprehensive descriptive grammar of English, written by the principal authors in collaboration with an international research team of a dozen linguists in five countries. It represents a major advance over previous grammars by virtue of drawing systematically on the linguistic research carried out on English during the last forty years. It incorporates insights from the theoretical literature but presents them in a way that is accessible to readers without formal training in linguistics. It is based on a sounder and more consistent descriptive framework than previous large-scale grammars, and includes much more explanation of grammatical terms and concepts, together with justification for the ways in which the analysis differs from traditional grammar. The book contains twenty chapters and a guide to further reading. Its usefulness is enhanced by diagrams of sentence structure, cross-references between sections, a comprehensive index, and user-friendly design and typography throughout.

Proceedings of the 19th International Joint Conference on Artificial Intelligence

Josep M. Pujol, Jordi Delgado, Ramón Sangüesa, Andreas Flache

Principles and Practice of Structural Equation Modeling

Rex B. Kline

Emphasizing concepts and rationale over mathematical minutiae, this is the most widely used, complete, and accessible structural equation modeling (SEM) text. Continuing the tradition of using real data examples from a variety of disciplines, the significantly revised fourth edition incorporates recent developments such as Pearl's graphing theory and the structural causal model (SCM), measurement invariance, and more. Readers gain a comprehensive understanding of all phases of SEM, from data collection and screening to the interpretation and reporting of the results. Learning is enhanced by exercises with answers, rules to remember, and topic boxes. The companion website supplies data, syntax, and output for the book's examples--now including files for Amos, EQS, LISREL, Mplus, Stata, and R (lavaan). New to This Edition •Extensively revised to cover important new topics: Pearl's graphing theory and the SCM, causal inference frameworks, conditional process modeling, path models for longitudinal data, item response theory, and more. •Chapters on best practices in all stages of SEM, measurement invariance in confirmatory factor analysis, and significance testing issues and bootstrapping. •Expanded coverage of psychometrics. •Additional computer tools: online files for all detailed examples, previously provided in EQS, LISREL, and Mplus, are now also given in Amos, Stata, and R (lavaan). •Reorganized to cover the specification, identification, and analysis of observed variable models separately from latent variable models. Pedagogical Features •Exercises with answers, plus end-of-chapter annotated lists of further reading. •Real examples of troublesome data, demonstrating how to handle typical problems in analyses. •Topic boxes on specialized issues, such as causes of nonpositive definite correlations. •Boxed rules to remember. •Website promoting a learn-by-doing approach, including syntax and data files for six widely used SEM computer tools.

Bioinformatics and Computational Biology Solutions Using R and Bioconductor

Robert Gentleman, Vincent J. Carey, Wolfgang Huber, Rafael A. Irizarry, Sandrine Dudoit

Hyberbolic Conservation Laws in Continuum Physics

Constantine M. Dafermos

The Language of Evaluation: Appraisal in English

James R. Martin, Peter Robert Rupert White

List of Figures List of Tables Acknowledgements Preface Introduction Attitude: Ways of Feeling Engagement and Graduation: Alignment, Solidarity and the Construed Reader Evaluative Key: Taking a Stance Enacting Appraisal: Text Analysis References Index

Balancing Family and Career

Aba Bentil Andam

In essentially all countries, responsibilities for child care, cooking, cleaning, and other homemaking tasks fall predominantly on the wife and mother. In addition, the childbearing years come during the period when a physicist must study hard, work long hours on research, and take temporary positions, often abroad. Thus, balancing family and career has long been one of the major barriers to women’s participation in science and engineering fields, including physics. While many young women believe that they must choose between having children and having a science career, the fact is that the majority of women physicists in both developing and developed countries have successfully done both. This paper summarizes some ideas and recommendations raised in discussions, especially focused on easing the challenges of having children while in temporary jobs, returning to physics after a career break, the need for “family‐friendly” working conditions, and the dual‐career problem facing couples where both are scientists.

Women in Physics in Ghana: Improvement on the Horizon

Aba Bentil Andam

A bonded-particle model for rock

D.O. Potyondy, Peter Cundall