Showing papers on "Context (language use) published in 2007"

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

Abstract: Whole-genome association studies (WGAS) bring new computational, as well as analytic, challenges to researchers. Many existing genetic-analysis tools are not designed to handle such large data sets in a convenient manner and do not necessarily exploit the new opportunities that whole-genome data bring. To address these issues, we developed PLINK, an open-source C/C++ WGAS tool set. With PLINK, large data sets comprising hundreds of thousands of markers genotyped for thousands of individuals can be rapidly manipulated and analyzed in their entirety. As well as providing tools to make the basic analytic steps computationally efficient, PLINK also supports some novel approaches to whole-genome data that take advantage of whole-genome coverage. We introduce PLINK and describe the five main domains of function: data management, summary statistics, population stratification, association analysis, and identity-by-descent estimation. In particular, we focus on the estimation and use of identity-by-state and identity-by-descent information in the context of population-based whole-genome studies. This information can be used to detect and correct for population stratification and to identify extended chromosomal segments that are shared identical by descent between very distantly related individuals. Analysis of the patterns of segmental sharing has the potential to map disease loci that contain multiple rare variants in a population-based linkage analysis.

Validation of the new Hipparcos reduction

Abstract: Context. A new reduction of the astrometric data as produced by the Hipparcos mission has been published, claiming accuracies for nearly all stars brighter than magnitude Hp = 8 to be better, by up to a factor 4, than in the original catalog ue. Aims. The new Hipparcos astrometric catalogue is checked for the quality of the data and the consistency of the formal errors as well as the possible presence of error correlations. The differences with the earlier publication are explained. Methods. The internal errors are followed through the reduction proc ess, and the external errors are investigated on the basis of a comparison with radio observations of a small selection of stars, and the distribution of negative parallaxes. Error co rrelation levels are investigated and the reduction by more than a factor 10 as obtained in the new catalogue is explained. Results. The formal errors on the parallaxes for the new catalogue are confirmed. The presence of a small amount of additional noise , though unlikely, cannot be ruled out. Conclusions. The new reduction of the Hipparcos astrometric data provides an improvement by a factor 2.2 in the total weight compared to the catalogue published in 1997, and provides much improved data for a wide range of studies on stellar luminosities and local galactic kinematics.

ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins.

Abstract: A major problem in structural biology is the recognition of errors in experimental and theoretical models of protein structures. The ProSA program (Protein Structure Analysis) is an established tool which has a large user base and is frequently employed in the refinement and validation of experimental protein structures and in structure prediction and modeling. The analysis of protein structures is generally a difficult and cumbersome exercise. The new service presented here is a straightforward and easy to use extension of the classic ProSA program which exploits the advantages of interactive web-based applications for the display of scores and energy plots that highlight potential problems spotted in protein structures. In particular, the quality scores of a protein are displayed in the context of all known protein structures and problematic parts of a structure are shown and highlighted in a 3D molecule viewer. The service specifically addresses the needs encountered in the validation of protein structures obtained from X-ray analysis, NMR spectroscopy and theoretical calculations. ProSA-web is accessible at https://prosa.services.came.sbg.ac.at.

Centering predictor variables in cross-sectional multilevel models: a new look at an old issue.

Abstract: Appropriately centering Level 1 predictors is vital to the interpretation of intercept and slope parameters in multilevel models (MLMs). The issue of centering has been discussed in the literature, but it is still widely misunderstood. The purpose of this article is to provide a detailed overview of grand mean centering and group mean centering in the context of 2-level MLMs. The authors begin with a basic overview of centering and explore the differences between grand and group mean centering in the context of some prototypical research questions. Empirical analyses of artificial data sets are used to illustrate key points throughout. The article provides a number of practical recommendations designed to facilitate centering decisions in MLM applications.

The Warwick-Edinburgh Mental Well-being Scale (WEMWBS): development and UK validation

Abstract: Background: There is increasing international interest in the concept of mental well-being and its contribution to all aspects of human life. Demand for instruments to monitor mental well-being at a population level and evaluate mental health promotion initiatives is growing. This article describes the development and validation of a new scale, comprised only of positively worded items relating to different aspects of positive mental health: the Warwick-Edinburgh Mental Well-Being Scale (WEMWBS). Methods: WEMWBS was developed by an expert panel drawing on current academic literature, qualitative research with focus groups, and psychometric testing of an existing scale. It was validated on a student and representative population sample. Content validity was assessed by reviewing the frequency of complete responses and the distribution of responses to each item. Confirmatory factor analysis was used to test the hypothesis that the scale measured a single construct. Internal consistency was assessed using Cronbach's alpha. Criterion validity was explored in terms of correlations between WEMWBS and other scales and by testing whether the scale discriminated between population groups in line with pre-specified hypotheses. Testretest reliability was assessed at one week using intra-class correlation coefficients. Susceptibility to bias was measured using the Balanced Inventory of Desired Responding. Results: WEMWBS showed good content validity. Confirmatory factor analysis supported the single factor hypothesis. A Cronbach's alpha score of 0.89 (student sample) and 0.91 (population sample) suggests some item redundancy in the scale. WEMWBS showed high correlations with other mental health and well-being scales and lower correlations with scales measuring overall health. Its distribution was near normal and the scale did not show ceiling effects in a population sample. It discriminated between population groups in a way that is largely consistent with the results of other population surveys. Testretest reliability at one week was high (0.83). Social desirability bias was lower or similar to that of other comparable scales. Conclusion: WEMWBS is a measure of mental well-being focusing entirely on positive aspects of mental health. As a short and psychometrically robust scale, with no ceiling effects in a population sample, it offers promise as a tool for monitoring mental well-being at a population level. Whilst WEMWBS should appeal to those evaluating mental health promotion initiatives, it is important that the scale's sensitivity to change is established before it is recommended in this context.

The Internationalization of Higher Education: Motivations and Realities

Abstract: Globalization and internationalization are related but not the same thing. Globalization is the context of economic and academic trends that are part of the reality of the 21st century. Internationalization includes the policies and practices undertaken by academic systems and institutions—and even individuals—to cope with the global academic environment. The motivations for internationalization include commercial advantage, knowledge and language acquisition, enhancing the curriculum with international content, and many others. Specific initiatives such as branch campuses, cross-border collaborative arrangements, programs for international students, establishing English-medium programs and degrees, and others have been put into place as part of internationalization. Efforts to monitor international initiatives and ensure quality are integral to the international higher education environment.

Cavity Opto-Mechanics

Abstract: The coupling of mechanical and optical degrees of freedom via radiation pressure has been a subject of early research in the context of gravitational wave detection. Recent experimental advances have allowed studying for the first time the modifications of mechanical dynamics provided by radiation pressure. This paper reviews the consequences of back-action of light confined in whispering-gallery dielectric micro-cavities, and presents a unified treatment of its two manifestations: notably the parametric instability (mechanical amplification and oscillation) and radiation pressure back-action cooling. Parametric instability offers a novel “photonic clock” which is driven purely by the pressure of light. In contrast, radiation pressure cooling can surpass existing cryogenic technologies and offers cooling to phonon occupancies below unity and provides a route towards cavity Quantum Optomechanics

Surface Enhanced Raman Scattering Enhancement Factors: A Comprehensive Study

Abstract: This paper presents an in-depth study of Surface Enhanced Raman Scattering (SERS) enhancement factors (EFs) and cross-sections, including several issues often overlooked. In particular, various possible rigorous definitions of the SERS EFs are introduced and discussed in the context of SERS applications, such as analytical chemistry and single molecule SERS. These definitions highlight the importance of a careful characterization of the non-SERS cross-sections of the probes under consideration. This aspect is illustrated by experimental results for the non-SERS cross-sections of representative SERS probes along with average SERS EFs for the same probes. In addition, the accurate experimental determination of single molecule enhancement factors is tackled with two recently developed techniques, namely: bi-analyte SERS (BiASERS) and temperature-dependent SERS vibrational pumping. We demonstrate that SERS EFs as low as 107, as opposed to the figure of 1014 often claimed in the literature, are sufficient for...

The Role of the Family Context in the Development of Emotion Regulation

Abstract: This article reviews current literature examining associations between components of the family context and children and adolescents' emotion regulation (ER). The review is organized around a tripartite model of familial influence. Firstly, it is posited that children learn about ER through observational learning, modeling and social referencing. Secondly, parenting practices specifically related to emotion and emotion management affect ER. Thirdly, ER is affected by the emotional climate of the family via parenting style, the attachment relationship, family expressiveness and the marital relationship. The review ends with discussions regarding the ways in which child characteristics such as negative emotionality and gender affect ER, how socialization practices change as children develop into adolescents, and how parent characteristics such as mental health affect the socialization of ER.

A survey on context-aware systems

Abstract: Context-aware systems offer entirely new opportunities for application developers and for end users by gathering context data and adapting systems behaviour accordingly. Especially in combination with mobile devices, these mechanisms are of high value and are used to increase usability tremendously. In this paper, we present common architecture principles of context-aware systems and derive a layered conceptual design framework to explain the different elements common to most context-aware architectures. Based on these design principles, we introduce various existing context-aware systems focusing on context-aware middleware and frameworks, which ease the development of context-aware applications. We discuss various approaches and analyse important aspects in context-aware computing on the basis of the presented systems.

What Do Laboratory Experiments Measuring Social Preferences Reveal About the Real World

Abstract: A critical question facing experimental economists is whether behavior inside the laboratory is a good indicator of behavior outside the laboratory. To address that question, we build a model in which the choices that individuals make depend not just on financial implications, but also on the nature and extent of scrutiny by others, the particular context in which a decision is embedded, and the manner in which participants and tasks are selected. We present empirical evidence demonstrating the importance of these various factors. To the extent that lab and naturally occurring environments systematically differ on any of these dimensions, the results obtained inside and outside the lab need not correspond. Focusing on experiments designed to measure social preferences, we discuss the extent to which the existing laboratory results generalize to naturally-occurring markets. We summarize cases where the lab may understate the importance of social preferences as well as instances in which the lab might exaggerate their importance. We conclude by emphasizing the importance of interpreting laboratory and field data through the lens of theory.

How habit limits the predictive power of intention: the case of information systems continuance

Abstract: Past research in the area of information systems acceptance has primarily focused on initial adoption under the implicit assumption that IS usage is mainly determined by intention. While plausible in the case of initial IS adoption, this assumption may not be as readily applicable to continued IS usage behavior since it ignores that frequently performed behaviors tend to become habitual and thus automatic over time. This paper is a step forward in defining and incorporating the "habit" construct into IS research. Specifically, the purpose of this study is to explore the role of habit and its antecedents in the context of continued IS usage. Building on previous work in other disciplines, we define habit in the context of IS usage as the extent to which people tend to perform behaviors (use IS) automatically because of learning. Using recent work on the continued usage of IS (IS continuance), we have developed a model suggesting that continued IS usage is not only a consequence of intention, but also of habit. In particular, in our research model, we propose IS habit to moderate the influence of intention such that its importance in determining behavior decreases as the behavior in question takes on a more habitual nature. Integrating past research on habit and IS continuance further, we suggest how antecedents of behavior/behavioral intention as identified by IS continuance research relate to drivers of habitualization. We empirically tested the model in the context of voluntary continued WWW usage. Our results support the argument that habit acts as a moderating variable of the relationship between intentions and IS continuance behavior, which may put a boundary condition on the explanatory power of intentions in the context of continued IS usage. The data also support that satisfaction, frequency of past behavior, and comprehensiveness of usage are key to habit formation and thus relevant in the context of IS continuance behavior. Implications of these findings are discussed and managerial guidelines presented.

Principles of QSAR models validation: internal and external

Abstract: The recent REACH Policy of the European Union has led to scientists and regulators to focus their attention on establishing general validation principles for QSAR models in the context of chemical regulation (previously known as the Setubal, nowadays, the OECD principles). This paper gives a brief analysis of some principles: unambiguous algorithm, Applicability Domain (AD), and statistical validation. Some concerns related to QSAR algorithm reproducibility and an example of a fast check of the applicability domain for MLR models are presented. Common myths and misconceptions related to popular techniques for verifying internal predictivity, particularly for MLR models (for instance crossvalidation, bootstrap), are commented on and compared with commonly used statistical techniques for external validation. The differences in the two validating approaches are highlighted, and evidence is presented that only models that have been validated externally, after their internal validation, can be considered reliable and applicable for both external prediction and regulatory purposes. (“Validation is one of those words...that is constantly used and seldom defined” as stated by A. R. Feinstein in the book Multivariate Analysis: An Introduction, Yale University Press, New Haven, 1996).

Longitudinal assessment of mental health problems among active and reserve component soldiers returning from the Iraq war.

Abstract: ContextTo promote early identification of mental health problems among combat veterans, the Department of Defense initiated population-wide screening at 2 time points, immediately on return from deployment and 3 to 6 months later. A previous article focusing only on the initial screening is likely to have underestimated the mental health burden.ObjectiveTo measure the mental health needs among soldiers returning from Iraq and the association of screening with mental health care utilization.Design, Setting, and ParticipantsPopulation-based, longitudinal descriptive study of the initial large cohort of 88 235 US soldiers returning from Iraq who completed both a Post-Deployment Health Assessment (PDHA) and a Post-Deployment Health Re-Assessment (PDHRA) with a median of 6 months between the 2 assessments.Main Outcome MeasuresScreening positive for posttraumatic stress disorder (PTSD), major depression, alcohol misuse, or other mental health problems; referral and use of mental health services.ResultsSoldiers reported more mental health concerns and were referred at significantly higher rates from the PDHRA than from the PDHA. Based on the combined screening, clinicians identified 20.3% of active and 42.4% of reserve component soldiers as requiring mental health treatment. Concerns about interpersonal conflict increased 4-fold. Soldiers frequently reported alcohol concerns, yet very few were referred to alcohol treatment. Most soldiers who used mental health services had not been referred, even though the majority accessed care within 30 days following the screening. Although soldiers were much more likely to report PTSD symptoms on the PDHRA than on the PDHA, 49% to 59% of those who had PTSD symptoms identified on the PDHA improved by the time they took the PDHRA. There was no direct relationship of referral or treatment with symptom improvement.ConclusionsRescreening soldiers several months after their return from Iraq identified a large cohort missed on initial screening. The large clinical burden recently reported among veterans presenting to Veterans Affairs facilities seems to exist within months of returning home, highlighting the need to enhance military mental health care during this period. Increased relationship problems underscore shortcomings in services for family members. Reserve component soldiers who had returned to civilian status were referred at higher rates on the PDHRA, which could reflect their concerns about their ongoing health coverage. Lack of confidentiality may deter soldiers with alcohol problems from accessing treatment. In the context of an overburdened system of care, the effectiveness of population mental health screening was difficult to ascertain.

Relativistic effects in homogeneous gold catalysis

Abstract: Transition-metal catalysts containing gold present new opportunities for chemical synthesis, and it is therefore not surprising that these complexes are beginning to capture the attention of the chemical community. Cationic phosphine-gold(i) complexes are especially versatile and selective catalysts for a growing number of synthetic transformations. The reactivity of these species can be understood in the context of theoretical studies on gold; relativistic effects are especially helpful in rationalizing the reaction manifolds available to gold catalysts. This Review draws on experimental and computational data to present our current understanding of homogeneous gold catalysis, focusing on previously unexplored reactivity and its application to the development of new methodology.

Increased acute myocardial infarction rates and cardiovascular risk factors among patients with human immunodeficiency virus disease.

Abstract: Context: Metabolic changes and smoking are common among HIV patients and may confer increased cardiovascular risk. Objective: The aim of the study was to determine acute myocardial infarction (AMI) rates and cardiovascular risk factors in HIV compared with non-HIV patients in two tertiary care hospitals. Design, Setting, and Participants: We conducted a health care system-based cohort study using a large data registry with 3,851 HIV and 1,044,589 non-HIV patients. AMI rates were determined among patients receiving longitudinal care between October 1, 1996, and June 30, 2004. Main Outcome Measures: The primary outcome was myocardial infarction, identified by International Classification of Diseases coding criteria. Results: AMI was identified in 189 HIV and 26,142 non-HIV patients. AMI rates per 1000 person-years were increased in HIV vs. non-HIV patients [11.13 (95% confidence interval [CI] 9.58–12.68) vs. 6.98 (95% CI 6.89–7.06)]. The HIV cohort had significantly higher proportions of hypertension (21.2 ...

Partial-Volume Effect in PET Tumor Imaging

Abstract: PET has the invaluable advantage of being intrinsically quantitative, enabling accurate measurements of tracer concentrations in vivo. In PET tumor imaging, indices characterizing tumor uptake, such as standardized uptake values, are becoming increasingly important, especially in the context of monitoring the response to therapy. However, when tracer uptake in small tumors is measured, large biases can be introduced by the partial-volume effect (PVE). The purposes of this article are to explain what PVE is and to describe its consequences in PET tumor imaging. The parameters on which PVE depends are reviewed. Actions that can be taken to reduce the errors attributable to PVE are described. Various PVE correction schemes are presented, and their applicability to PET tumor imaging is discussed.

Global reconstruction of the human metabolic network based on genomic and bibliomic data

Abstract: Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computational approaches are required to elucidate and understand metabolic genotype–phenotype relationships. We have manually reconstructed the global human metabolic network based on Build 35 of the genome annotation and a comprehensive evaluation of >50 years of legacy data (i.e., bibliomic data). Herein we describe the reconstruction process and demonstrate how the resulting genome-scale (or global) network can be used (i) for the discovery of missing information, (ii) for the formulation of an in silico model, and (iii) as a structured context for analyzing high-throughput biological data sets. Our comprehensive evaluation of the literature revealed many gaps in the current understanding of human metabolism that require future experimental investigation. Mathematical analysis of network structure elucidated the implications of intracellular compartmentalization and the potential use of correlated reaction sets for alternative drug target identification. Integrated analysis of high-throughput data sets within the context of the reconstruction enabled a global assessment of functional metabolic states. These results highlight some of the applications enabled by the reconstructed human metabolic network. The establishment of this network represents an important step toward genome-scale human systems biology.

Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework

Abstract: Species abundance distributions (SADs) follow one of ecologys oldest and most universal laws – every community shows a hollow curve or hyperbolic shape on a histogram with many rare species and just a few common species. Here, we review theoretical, empirical and statistical developments in the study of SADs. Several key points emerge. (i) Literally dozens of models have been proposed to explain the hollow curve. Unfortunately, very few models are ever rejected, primarily because few theories make any predictions beyond the hollow-curve SAD itself. (ii) Interesting work has been performed both empirically and theoretically, which goes beyond the hollow-curve prediction to provide a rich variety of information about how SADs behave. These include the study of SADs along environmental gradients and theories that integrate SADs with other biodiversity patterns. Central to this body of work is an effort to move beyond treating the SAD in isolation and to integrate the SAD into its ecological context to enable making many predictions. (iii) Moving forward will entail understanding how sampling and scale affect SADs and developing statistical tools for describing and comparing SADs. We are optimistic that SADs can provide significant insights into basic and applied ecological science.

N‐Heterocyclic Carbenes as Organocatalysts

Abstract: Organocatalyzed reactions represent an attractive alternative to metal-catalyzed processes notably because of their lower cost and benign environmental impact in comparison to organometallic catalysis. In this context, N-heterocyclic carbenes (NHCs) have been studied for their ability to promote primarily the benzoin condensation. Lately, dramatic progress in understanding their intrinsic properties and in their synthesis have made them available to organic chemists. This has resulted in a tremendous increase of their scope and in a true explosion of the number of papers reporting NHC-catalyzed reactions. Here, we highlight the ever-increasing number of reactions that can be promoted by N-heterocyclic carbenes.

Three-dimensional culture models of normal and malignant breast epithelial cells

Abstract: Extracellular matrix is a key regulator of normal homeostasis and tissue phenotype. Important signals are lost when cells are cultured ex vivo on two-dimensional plastic substrata. Many of these crucial microenvironmental cues may be restored using three-dimensional (3D) cultures of laminin-rich extracellular matrix (lrECM). These 3D culture assays allow phenotypic discrimination between nonmalignant and malignant mammary cells, as the former grown in a 3D context form polarized, growth-arrested acinus-like colonies whereas the latter form disorganized, proliferative and nonpolar colonies. Signaling pathways that function in parallel in cells cultured on plastic become reciprocally integrated when the cells are exposed to basement membrane-like gels. Appropriate 3D culture thus provides a more physiologically relevant approach to the analysis of gene function and cell phenotype ex vivo. We describe here a robust and generalized method for the culturing of various human breast cell lines in three dimensions and describe the preparation of cellular extracts from these cultures for molecular analyses. The procedure below describes the 3D 'embedded' assay, in which cells are cultured embedded in an lrECM gel (Fig. 1). By lrECM, we refer to the solubilized extract derived from the Engelbreth-Holm-Swarm mouse sarcoma cells. For a discussion of user options regarding 3D matrices, see Box 1. Alternatively, the 3D 'on-top' assay, in which cells are cultured on top of a thin lrECM gel overlaid with a dilute solution of lrECM, may be used as described in Box 2 (Fig. 1 and Fig. 2).

From the authors

Abstract: The members of the European Respiratory Society Task Force on Exercise Testing in Clinical Practice have read with interest the letter from J.E. Cotes and J.W. Reed and are of the opinion that any response to the points raised therein should be placed in the context of the purpose of a recently published Task Force 1. As stated in the introduction of this Task Force 1: “The purpose of this document is to present recommendations on the clinical use of exercise testing in patients with cardiopulmonary disease, with particular emphasis on the evidence base for functional evaluation, prognosis and assessment of interventions. While the scope of the document is broad, consideration will focus only on those indices which have demonstrable predictive power”. The key phrase here is “evidence base”, which represents a clear departure from the objectives of the 1997 Task Force 2. In recent years, there has been an accumulating body of evidence across a broad range of chronic lung and heart diseases ( e.g. chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), pulmonary vascular disease and chronic heart failure (CHF)) from studies using cycle ergometer protocols and field tests. It is upon this collective evidence base that the Task Force has formulated its recommendations for exercise testing in clinical practice. Furthermore, the Task Force was …

The Medicalization of Society: On the Transformation of Human Conditions into Treatable Disorders

Abstract: Medicalization : context, characteristics, and changes -- Extension : men and the medicalization of andropause, baldness, and erectile dysfunction -- Expansion : from hyperactive children to adult ADHD -- Enhancement : human growth hormone and the temptations of biomedical enhancement -- Continuity : homosexuality and the potential for remedicalization -- Measuring medicalization : categories, numbers, and treatment -- The shifting engines of medicalization -- Medicalization and its discontents.

Cell surface mechanics and the control of cell shape, tissue patterns and morphogenesis.

Abstract: Many signalling pathways have been shown to control cell shape and cell surface mechanics. Recent insights from diverse disciplines point to adhesion and cortical tension as regulators of cell shape and provide insights into how cell shape controls tissue geometry. Embryonic morphogenesis requires the execution of complex mechanisms that regulate the local behaviour of groups of cells. The orchestration of such mechanisms has been mainly deciphered through the identification of conserved families of signalling pathways that spatially and temporally control cell behaviour. However, how this information is processed to control cell shape and cell dynamics is an open area of investigation. The framework that emerges from diverse disciplines such as cell biology, physics and developmental biology points to adhesion and cortical actin networks as regulators of cell surface mechanics. In this context, a range of developmental phenomena can be explained by the regulation of cell surface tension.

Implicit Bias among Physicians and its Prediction of Thrombolysis Decisions for Black and White Patients

Abstract: Context Studies documenting racial/ethnic disparities in health care frequently implicate physicians’ unconscious biases. No study to date has measured physicians’ unconscious racial bias to test whether this predicts physicians’ clinical decisions.