Instruments of Commerce and Knowledge: Probe Microscopy, 1980-2000

Longstanding debates about the role of the university in national culture and the global economy have entered a new phase in the past decade in most industrialized, and several industrializing, countries. One important focus of this debate is corporate involvement in academic scientific research. Proponents of the academic capitalism say that corporate involvement makes the university leaner, more agile, better able to respond to the needs of the day. Critics say that corporate involvement leaves society without the independent, critical voices traditionally lodged in universities. I argue that a science and technology studies perspective, using case studies of research communities, can push this debate in directions envisioned by neither proponents nor critics. I use the development and commercialization of the scanning tunneling microscope and the atomic force microscope as an example of how research communities continually redraw the line between corporate and academic institutions.

A MOSAIC of methods: Improving ortholog detection through integration of algorithmic diversity

Ortholog detection (OD) is a critical step for comparative genomic analysis of protein-coding sequences. In this paper, we begin with a comprehensive comparison of four popular, methodologically diverse OD methods: MultiParanoid, Blat, Multiz, and OMA. In head-to-head comparisons, these methods are shown to significantly outperform one another 12-30% of the time. This high complementarity motivates the presentation of the first tool for integrating methodologically diverse OD methods. We term this program MOSAIC, or Multiple Orthologous Sequence Analysis and Integration by Cluster optimization. Relative to component and competing methods, we demonstrate that MOSAIC more than quintuples the number of alignments for which all species are present, while simultaneously maintaining or improving functional-, phylogenetic-, and sequence identity-based measures of ortholog quality. Further, we demonstrate that this improvement in alignment quality yields 40-280% more confidently aligned sites. Combined, these factors translate to higher estimated levels of overall conservation, while at the same time allowing for the detection of up to 180% more positively selected sites. MOSAIC is available as python package. MOSAIC alignments, source code, and full documentation are available at http://pythonhosted.org/bio-MOSAIC

Cluster-Robust Variance Estimation for Dyadic Data

Dyadic data are common in the social sciences, although inference for such settings involves accounting for a complex clustering structure. Many analyses in the social sciences fail to account for the fact that multiple dyads share a member, and that errors are thus likely correlated across these dyads. We propose a nonparametric sandwich-type robust variance estimator for linear regression to account for such clustering in dyadic data. We enumerate conditions for estimator consistency. We also extend our results to repeated and weighted observations, including directed dyads and longitudinal data, and provide an implementation for generalized linear models such as logistic regression. We examine empirical performance with simulations and applications to international relations and speed dating

Historical Racism and the Daily Show: Catching racism clip

This article is featured in the journal Tapestries: Interwoven voices of local and global identities, volume 4

Executive Nursing Leadership: Change and Conflict related to the Triple Aim

Executive nurses work at the top of organizations and face unique challenges in today’s healthcare system. This qualitative study investigated the lived experiences of executive nurses to better understand their leadership journey. This study explored the professional development of executive nurses navigating change and conflict. The study used phenomenological inquiry and gathered data through individual semi-structured interviews, workplace observations, and document reviews. Based on the collected data experiential themes were identified. The study focused on executive nursing and the Institute for Healthcare Improvement’s (IHI) “Triple Aim” of creating better patient experiences, reducing system cost, and improving population health. The study interpreted critical turning points in executive nurses’ careers and triangulated data to identify, then, analyze central themes. Through the analysis of themes, new insights were created which connected current executive nurse functioning and future healthcare design. As a result, this study informed future thinking. The semi-structured interviews uncovered points of major change and conflict; particularly, related to fundamental organizational transformation, strategic goals, and the “Triple Aim”. Six key themes affecting executive nurse leadership emerged. The six key themes included: Focusing on population health, relationships, knowledge of the healthcare environment, technical leadership and change management skills, defined professional competencies, and central business skills. To provoke innovation and thought leadership, the six themes were interpreted using Zweig’s (2012) Class Theory, Shiva’s (2005) Perceptions of Corporate Power, and Plato’s Allegory of the Cave (Duarte, 2012)