Boston College

SUMMARY: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. AVAILABILITY: http://samtools.sourceforge.net.

The present article presents a meta-analytic test of intergroup contact theory. With 713 independent samples from 515 studies, the meta-analysis finds that intergroup contact typically reduces intergroup prejudice. Multiple tests indicate that this finding appears not to result from either participant selection or publication biases, and the more rigorous studies yield larger mean effects. These contact effects typically generalize to the entire outgroup, and they emerge across a broad range of outgroup targets and contact settings. Similar patterns also emerge for samples with racial or ethnic targets and samples with other targets. This result suggests that contact theory, devised originally for racial and ethnic encounters, can be extended to other groups. A global indicator of Allport's optimal contact conditions demonstrates that contact under these conditions typically leads to even greater reduction in prejudice. Closer examination demonstrates that these conditions are best conceptualized as an interrelated bundle rather than as independent factors. Further, the meta-analytic findings indicate that these conditions are not essential for prejudice reduction. Hence, future work should focus on negative factors that prevent intergroup contact from diminishing prejudice as well as the development of a more comprehensive theory of intergroup contact.

By characterizing the geographic and functional spectrum of human genetic variation, the 1000 Genomes Project aims to build a resource to help to understand the genetic contribution to disease. Here we describe the genomes of 1,092 individuals from 14 populations, constructed using a combination of low-coverage whole-genome and exome sequencing. By developing methods to integrate information across several algorithms and diverse data sources, we provide a validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. We show that individuals from different populations carry different profiles of rare and common variants, and that low-frequency variants show substantial geographic differentiation, which is further increased by the action of purifying selection. We show that evolutionary conservation and coding consequence are key determinants of the strength of purifying selection, that rare-variant load varies substantially across biological pathways, and that each individual contains hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites. This resource, which captures up to 98% of accessible single nucleotide polymorphisms at a frequency of 1% in related populations, enables analysis of common and low-frequency variants in individuals from diverse, including admixed, populations. This report from the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations; hundreds of rare non-coding variants at conserved sites, such as motif-disrupting changes in transcription-factor-binding sites, can be found in each individual. This report by the 1000 Genomes Project describes the genomes of 1,092 individuals from 14 human populations, providing a resource for common and low-frequency variant analysis in individuals from diverse populations. Integrative analyses reveal profiles of rare and common variants in different populations. The frequencies of rare variants vary across biological pathways, and hundreds of rare, non-coding variants at conserved sites — such as changes disrupting transcription-factor motifs — can be established for each individual.

The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms. We undertook three projects: low-coverage whole-genome sequencing of 179 individuals from four populations; high-coverage sequencing of two mother–father–child trios; and exon-targeted sequencing of 697 individuals from seven populations. We describe the location, allele frequency and local haplotype structure of approximately 15 million single nucleotide polymorphisms, 1 million short insertions and deletions, and 20,000 structural variants, most of which were previously undescribed. We show that, because we have catalogued the vast majority of common variation, over 95% of the currently accessible variants found in any individual are present in this data set. On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders. We demonstrate how these results can be used to inform association and functional studies. From the two trios, we directly estimate the rate of de novo germline base substitution mutations to be approximately 10−8 per base pair per generation. We explore the data with regard to signatures of natural selection, and identify a marked reduction of genetic variation in the neighbourhood of genes, due to selection at linked sites. These methods and public data will support the next phase of human genetic research. This issue of Nature contains the first publication from The 1000 Genomes Project, an international collaboration that will produce an extensive public catalogue of human genetic variation. The plan, in fact, is to sequence about 2,000 unidentified individuals from 20 populations around the world. This first paper presents the results from the project's pilot phase, testing three different strategies for genome-wide sequencing with high-throughput platforms: low-coverage whole-genome sequencing of 179 individuals in three population groups, high-coverage sequencing of two mother–father–child trios, and exon-targeted sequencing of 697 individuals from seven populations. The goal of the 1000 Genomes Project is to provide in-depth information on variation in human genome sequences. In the pilot phase reported here, different strategies for genome-wide sequencing, using high-throughput sequencing platforms, were developed and compared. The resulting data set includes more than 95% of the currently accessible variants found in any individual, and can be used to inform association and functional studies.

We present the design for an absorbing metamaterial (MM) with near unity absorbance A(omega). Our structure consists of two MM resonators that couple separately to electric and magnetic fields so as to absorb all incident radiation within a single unit cell layer. We fabricate, characterize, and analyze a MM absorber with a slightly lower predicted A(omega) of 96%. Unlike conventional absorbers, our MM consists solely of metallic elements. The substrate can therefore be optimized for other parameters of interest. We experimentally demonstrate a peak A(omega) greater than 88% at 11.5 GHz.

Strategic managers are consistently faced with the decision of how to allocate scarce corporate resources in an environment that is placing more and more pressures on them. Recent scholarship in strategic management suggests that many of these pressures come directly from sources associated with social issues in management, rather than traditional arenas of strategic management. Using a greatly improved source of data on corporate social performance, this paper reports the results of a rigorous study of the empirical linkages between financial and social performance. Corporate social performance (CSP) is found to be positively associated with prior financial performance, supporting the theory that slack resource availability and CSP are positively related. CSP is also found to be positively associated with future financial performance, supporting the theory that good management and CSP are positively related.© 1997 by John Wiley & Sons, Ltd

At the heart of emotion, mood, and any other emotionally charged event are states experienced as simply feeling good or bad, energized or enervated. These states--called core affect--influence reflexes, perception, cognition, and behavior and are influenced by many causes internal and external, but people have no direct access to these causal connections. Core affect can therefore be experienced as free-floating (mood) or can be attributed to some cause (and thereby begin an emotional episode). These basic processes spawn a broad framework that includes perception of the core-affect-altering properties of stimuli, motives, empathy, emotional meta-experience, and affect versus emotion regulation; it accounts for prototypical emotional episodes, such as fear and anger, as core affect attributed to something plus various nonemotional processes.

The dimensionless thermoelectric figure of merit (ZT) in bismuth antimony telluride (BiSbTe) bulk alloys has remained around 1 for more than 50 years. We show that a peak ZT of 1.4 at 100 degrees C can be achieved in a p-type nanocrystalline BiSbTe bulk alloy. These nanocrystalline bulk materials were made by hot pressing nanopowders that were ball-milled from crystalline ingots under inert conditions. Electrical transport measurements, coupled with microstructure studies and modeling, show that the ZT improvement is the result of low thermal conductivity caused by the increased phonon scattering by grain boundaries and defects. More importantly, ZT is about 1.2 at room temperature and 0.8 at 250 degrees C, which makes these materials useful for cooling and power generation. Cooling devices that use these materials have produced high-temperature differences of 86 degrees , 106 degrees , and 119 degrees C with hot-side temperatures set at 50 degrees, 100 degrees, and 150 degrees C, respectively. This discovery sets the stage for use of a new nanocomposite approach in developing high-performance low-cost bulk thermoelectric materials.

Looking Back, Looking Forward Constructing Narratives for Research Thematic Analysis Structural Analysis Dialogic Performance Analysis Visual Analysis Truths and Cautions

Understanding customer experience and the customer journey over time is critical for firms. Customers now interact with firms through myriad touch points in multiple channels and media, and customer experiences are more social in nature. These changes require firms to integrate multiple business functions, and even external partners, in creating and delivering positive customer experiences. In this article, the authors aim to develop a stronger understanding of customer experience and the customer journey in this era of increasingly complex customer behavior. To achieve this goal, they examine existing definitions and conceptualizations of customer experience as a construct and provide a historical perspective of the roots of customer experience within marketing. Next, they attempt to bring together what is currently known about customer experience, customer journeys, and customer experience management. Finally, they identify critical areas for future research on this important topic.

Media discourse and public opinion are treated as two parallel systems of constructing meaning. This paper explores their relationship by analyzing the discourse on nuclear power in four general audience media: television news coverage, newsmagazine accounts, editorial cartoons, and syndicated opinion columns. The analysis traces the careers of different interpretive packages on nuclear power from 1945 to the present. This media discourse, it is argued, is an essential context for understanding the formation of public opinion on nuclear power. More specifically, it helps to account for such survey results as the decline in support for nuclear power before Three Mile Island, a rebound after a burst of media publicity has died out, the gap between general support for nuclear power and support for a plant in one's own community, and the changed relationship of age to support for nuclear power from 1950 to the present.

The authors report a study of the effects of price, brand, and store information on buyers’ perceptions of product quality and value, as well as their willingness to buy. Hypotheses are derived fro...

Abstract Many of the recent advances in enhancing the thermoelectric figure of merit are linked to nanoscale phenomena found both in bulk samples containing nanoscale constituents and in nanoscale samples themselves. Prior theoretical and experimental proof‐of‐principle studies on quantum‐well superlattice and quantum‐wire samples have now evolved into studies on bulk samples containing nanostructured constituents prepared by chemical or physical approaches. In this Review, nanostructural composites are shown to exhibit nanostructures and properties that show promise for thermoelectric applications, thus bringing together low‐dimensional and bulk materials for thermoelectric applications. Particular emphasis is given in this Review to the ability to achieve 1) a simultaneous increase in the power factor and a decrease in the thermal conductivity in the same nanocomposite sample and for transport in the same direction and 2) lower values of the thermal conductivity in these nanocomposites as compared to alloy samples of the same chemical composition. The outlook for future research directions for nanocomposite thermoelectric materials is also discussed.

Theory indicates that resilient individuals "bounce back" from stressful experiences quickly and effectively. Few studies, however, have provided empirical evidence for this theory. The broaden-and-build theory of positive emotions (B. L. Fredrickson, 1998, 2001) is used as a framework for understanding psychological resilience. The authors used a multimethod approach in 3 studies to predict that resilient people use positive emotions to rebound from, and find positive meaning in, stressful encounters. Mediational analyses revealed that the experience of positive emotions contributed, in part, to participants' abilities to achieve efficient emotion regulation, demonstrated by accelerated cardiovascular recovery from negative emotional arousal (Studies 1 and 2) and by finding positive meaning in negative circumstances (Study 3). Implications for research on resilience and positive emotions are discussed.

We examined how aspects of intellectual capital influenced various innovative capabilities in organizations. In a longitudinal, multiple-informant study of 93 organizations, we found that human, organizational, and social capital and their interrelationships selectively influenced incremental and radical innovative capabilities. As anticipated, organizational capital positively influenced incremental innovative capability, while human capital interacted with social capital to positively influence radical innovative capability. Counter to our expectations, however, human capital by itself was negatively associated with radical innovative capability. Interestingly, social capital played a significant role in both types of innovation, as it positively influenced incremental and radical innovative capabilities.

Through qualitative and empirical research, the authors find that the service quality construct conforms to the structure of a third-order factor model that ties service quality perceptions to distinct and actionable dimensions: outcome, interaction, and environmental quality. In turn, each has three subdimensions that define the basis of service quality perceptions. The authors further suggest that for each of these subdimensions to contribute to improved service quality perceptions, the quality received by consumers must be perceived to be reliable, responsive, and empathetic. The authors test and support this conceptualization across four service industries. They consider the research and managerial implications of the study and its limitations.

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.

Despite the importance to researchers, managers, and policy makers of how information technology (IT) contributes to organizational performance, there is uncertainty and debate about what we know and don’t know. A review of the literature reveals that studies examining the association between information technology and organizational performance are divergent in how they conceptualize key constructs and their interrelationships. We develop a model of IT business value based on the resource-based view of the firm that integrates the various strands of research into a single framework. We apply the integrative model to synthesize what is known about IT business value and guide future research by developing propositions and suggesting a research agenda. A principal finding is that IT is valuable, but the extent and dimensions are dependent upon internal and external factors, including complementary organizational resources of the firm and its trading partners, as well as the competitive and macro environment. Our analysis provides a blueprint to guide future research and facilitate knowledge accumulation and creation concerning the organizational performance impacts of information technology.

In this paper, we review and analyze the emerging network paradigm in organizational research. We begin with a conventional review of recent research organized around recognized research streams. Next, we analyze this research, developing a set of dimensions along which network studies vary, including direction of causality, levels of analysis, explanatory goals, and explanatory mechanisms. We use the latter two dimensions to construct a 2-by-2 table cross-classifying studies of network consequences into four canonical types: structural social capital, social access to resources, contagion, and environmental shaping. We note the rise in popularity of studies with a greater sense of agency than was traditional in network research.

This paper develops a resource model of political participation. The resources considered are time, money, and civic skills—those communications and organizational capacities that are essential to political activity. These skills are not only acquired early in life but developed in the nonpolitical institutional settings of adult life: the workplace, organizations, and churches and synagogues. These resources are distributed differentially among groups defined by socioeconomic status. A two-stage least squares analysis shows these resources have powerful effects on overall political activity, thus explaining why socioeconomic status has traditionally been so powerful in predicting participation. We disaggregate overall activity into three kinds of acts: those that involve giving time, those that entail donating money, and voting. Each requires a different configuration of resources resulting in different patterns of stratification across various political acts.