Statistical inference for the linear model with clustered data

Political scientists often confront clustered data, which can present problems for statistical inference. Through Monte Carlo simulation I examine the performance of standard error methods in clustered data for two linear estimators: Ordinary Least Squares (OLS) and Median Regression (MR). I consider changes to several parameters: sample size, number of clusters, intra-cluster correlation, and error term distribution (normal, which favors OLS as the most efficient estimator, and Student's t, which favors MR). Results indicate that conventional OLS and MR standard errors are often, but not always, biased downward in clustered data. Within OLS, the performance of the robust cluster standard errors (RCSE), which are designed for clustered data, is conditional on the level of covariate variation and the severity of cluster correlation. Regarding MR, two nonparametric methods perform well. I conclude that researchers should carefully examine the nature of the clustering in their data before choosing a standard error method

Multidimensional Democracy: The Supply and Demand of Political Representation

Research on representation in American politics typically examines the concept through only one of four dimensions: policy, service, allocation, or descriptive. Although scholars collectively provide a comprehensive view of representation, its multidimensional nature implies that any analysis of one dimension that does not account for the others is missing key elements of the process. Furthermore, most research focuses on the behavior of legislators. Less is known about the determinants of citizens' preferences. I unify the dimensions of representation in a theoretical model that accounts for both citizen demand and legislators' priorities (i.e., supply). I test this theory with three sources of original data: (1) survey experiments administered to a sample of American adults, (2) survey experiments administered to state legislators, and (3) a new archive of state legislators' websites. On the demand side, I posit that citizens' expectations about government's role in their lives drive preferences for representation. Using survey experiments from a nationally-representative sample, I provide empirical support by demonstrating that characteristics such as economic factors, ideology, and gender and race correspond as predicted with preferences for the four dimensions of representation and two role orientations. Next I turn to the supply of representation. I expect that, given the constraints of resources and costs, legislators systematically emphasize some dimensions over others to further the goal of re-election. Results from the survey experiments and legislator website data provide support; factors that alter resources, costs, and benefits---legislative institutions, district demand, and individual traits---structure legislators' strategic representational priorities. A critical finding in this research is evidence of a connection between demand for and supply of the dimensions of representation. For example, I find that disadvantaged constituents (e.g., the poor and racial minorities) prefer "district-centric" types of representation such as service and allocation, while the wealthy and whites prefer policy-based representation. Then I show evidence that legislators in relatively poor districts and/or those with large black populations emphasize service and allocation while legislators in wealthy and/or predominantly white districts focus more on policy. I conclude by discussing how this seemingly beneficial connection may ultimately contribute to inequality in American political representation.Doctor of Philosoph

A Diffusion Network Event History Estimator

Research on the diffusion of political decisions across jurisdictions typically accounts for units’ influence over each other with (1) observable measures or (2) by inferring latent network ties from past decisions. The former approach assumes that interdependence is static and perfectly captured by the data. The latter mitigates these issues but requires analytical tools that are separate from the main empirical methods for studying diffusion. As a solution, we introduce network event history analysis (NEHA), which incorporates latent network inference into conventional discrete-time event history models. We demonstrate NEHA’s unique methodological and substantive benefits in applications to policy adoption in the American states. Researchers can analyze the ties and structure of inferred networks to refine model specifications, evaluate diffusion mechanisms, or test new or existing hypotheses. By capturing targeted relationships unexplained by standard covariates, NEHA can improve models, facilitate richer theoretical development, and permit novel analyses of the diffusion process

Engineering bacteria to solve the Burnt Pancake Problem

<p>Abstract</p> <p>Background</p> <p>We investigated the possibility of executing DNA-based computation in living cells by engineering <it>Escherichia coli </it>to address a classic mathematical puzzle called the Burnt Pancake Problem (BPP). The BPP is solved by sorting a stack of distinct objects (pancakes) into proper order and orientation using the minimum number of manipulations. Each manipulation reverses the order and orientation of one or more adjacent objects in the stack. We have designed a system that uses site-specific DNA recombination to mediate inversions of genetic elements that represent pancakes within plasmid DNA.</p> <p>Results</p> <p>Inversions (or "flips") of the DNA fragment pancakes are driven by the <it>Salmonella typhimurium </it>Hin/<it>hix </it>DNA recombinase system that we reconstituted as a collection of modular genetic elements for use in <it>E. coli</it>. Our system sorts DNA segments by inversions to produce different permutations of a promoter and a tetracycline resistance coding region; <it>E. coli </it>cells become antibiotic resistant when the segments are properly sorted. Hin recombinase can mediate all possible inversion operations on adjacent flippable DNA fragments. Mathematical modeling predicts that the system reaches equilibrium after very few flips, where equal numbers of permutations are randomly sorted and unsorted. Semiquantitative PCR analysis of <it>in vivo </it>flipping suggests that inversion products accumulate on a time scale of hours or days rather than minutes.</p> <p>Conclusion</p> <p>The Hin/<it>hix </it>system is a proof-of-concept demonstration of <it>in vivo </it>computation with the potential to be scaled up to accommodate larger and more challenging problems. Hin/<it>hix </it>may provide a flexible new tool for manipulating transgenic DNA <it>in vivo</it>.</p

OSCE best practice guidelines—applicability for nursing simulations

Background: Objective structured clinical examinations (OSCEs) have been used for many years within healthcare programmes as a measure of students’ and clinicians’ clinical performance. OSCEs are a form of simulation and are often summative but may be formative. This educational approach requires robust design based on sound pedagogy to assure practice and assessment of holistic nursing care. As part of a project testing seven OSCE best practice guidelines (BPGs) across three sites, the BPGs were applied to an existing simulation activity. The aim of this study was to determine the applicability and value of the OSCE BPGs in an existing formative simulation. Methods: A mixed methods approach was used to address the research question: in what ways do OSCE BPGs align with simulations. The BPGs were aligned and compared with all aspects of an existing simulation activity offered to first-year nursing students at a large city-based university, prior to their first clinical placement in an Australian healthcare setting. Survey questions, comprised of Likert scales and free-text responses, used at other sites were slightly modified for reference to simulation. Students’ opinions about the refined simulation activity were collected via electronic survey immediately following the simulation and from focus groups. Template analysis, using the BPGs as existing or a priori thematic codes, enabled interpretation and illumination of the data from both sources.Results: Few changes were made to the existing simulation plan and format. Students’ responses from surveys (n = 367) and four focus groups indicated that all seven BPGs were applicable for simulations in guiding their learning, particularly in the affective domain, and assisting their perceived needs in preparing for upcoming clinical practice. Discussion: Similarities were found in the intent of simulation and OSCEs informed by the BPGs to enable feedback to students about holistic practice across affective, cognitive and psychomotor domains. The similarities in this study are consistent with findings from exploring the applicability of the BPGs for OSCEs in other nursing education settings, contexts, universities and jurisdictions. The BPGs also aligned with other frameworks and standards often used to develop and deliver simulations. Conclusions: Findings from this study provide further evidence of the applicability of the seven OSCE BPGs to inform the development and delivery of, in this context, simulation activities for nurses. The manner in which simulation is offered to large cohorts requires further consideration to meet students’ needs in rehearsing the registered nurse role

OSCE Best Practice Guidelines – applicability for nursing simulations

Background: Objective structured clinical examinations (OSCEs) have been used for many years within healthcare programmes as a measure of students’ and clinicians’ clinical performance. OSCEs are a form of simulation and are often summative but may be formative. This educational approach requires robust design based on sound pedagogy to assure practice and assessment of holistic nursing care. As part of a project testing seven OSCE best practice guidelines (BPGs) across three sites, the BPGs were applied to an existing simulation activity. The aim of this study was to determine the applicability and value of the OSCE BPGs in an existing formative simulation. Methods: A mixed methods approach was used to address the research question: in what ways do OSCE BPGs align with simulations. The BPGs were aligned and compared with all aspects of an existing simulation activity offered to first-year nursing students at a large city-based university, prior to their first clinical placement in an Australian healthcare setting. Survey questions, comprised of Likert scales and free-text responses, used at other sites were slightly modified for reference to simulation. Students’ opinions about the refined simulation activity were collected via electronic survey immediately following the simulation and from focus groups. Template analysis, using the BPGs as existing or a priori thematic codes, enabled interpretation and illumination of the data from both sources.Results: Few changes were made to the existing simulation plan and format. Students’ responses from surveys (n = 367) and four focus groups indicated that all seven BPGs were applicable for simulations in guiding their learning, particularly in the affective domain, and assisting their perceived needs in preparing for upcoming clinical practice. Discussion: Similarities were found in the intent of simulation and OSCEs informed by the BPGs to enable feedback to students about holistic practice across affective, cognitive and psychomotor domains. The similarities in this study are consistent with findings from exploring the applicability of the BPGs for OSCEs in other nursing education settings, contexts, universities and jurisdictions. The BPGs also aligned with other frameworks and standards often used to develop and deliver simulations. Conclusions: Findings from this study provide further evidence of the applicability of the seven OSCE BPGs to inform the development and delivery of, in this context, simulation activities for nurses. The manner in which simulation is offered to large cohorts requires further consideration to meet students’ needs in rehearsing the registered nurse role

Climate change considerations are fundamental to management of deep‐sea resource extraction

Climate change manifestation in the ocean, through warming, oxygen loss, increasing acidification, and changing particulate organic carbon flux (one metric of altered food supply), is projected to affect most deep‐ocean ecosystems concomitantly with increasing direct human disturbance. Climate drivers will alter deep‐sea biodiversity and associated ecosystem services, and may interact with disturbance from resource extraction activities or even climate geoengineering. We suggest that to ensure the effective management of increasing use of the deep ocean (e.g., for bottom fishing, oil and gas extraction, and deep‐seabed mining), environmental management and developing regulations must consider climate change. Strategic planning, impact assessment and monitoring, spatial management, application of the precautionary approach, and full‐cost accounting of extraction activities should embrace climate consciousness. Coupled climate and biological modeling approaches applied in the water and on the seafloor can help accomplish this goal. For example, Earth‐System Model projections of climate‐change parameters at the seafloor reveal heterogeneity in projected climate hazard and time of emergence (beyond natural variability) in regions targeted for deep‐seabed mining. Models that combine climate‐induced changes in ocean circulation with particle tracking predict altered transport of early life stages (larvae) under climate change. Habitat suitability models can help assess the consequences of altered larval dispersal, predict climate refugia, and identify vulnerable regions for multiple species under climate change. Engaging the deep observing community can support the necessary data provisioning to mainstream climate into the development of environmental management plans. To illustrate this approach, we focus on deep‐seabed mining and the International Seabed Authority, whose mandates include regulation of all mineral‐related activities in international waters and protecting the marine environment from the harmful effects of mining. However, achieving deep‐ocean sustainability under the UN Sustainable Development Goals will require integration of climate consideration across all policy sectors.This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2020 The Authors. Global Change Biology published by John Wiley & Sons Lt

Reviews and syntheses: The promise of big diverse soil data, moving current practices towards future potential

In the age of big data, soil data are more available and richer than ever, but – outside of a few large soil survey resources – they remain largely unusable for informing soil management and understanding Earth system processes beyond the original study. Data science has promised a fully reusable research pipeline where data from past studies are used to contextualize new findings and reanalyzed for new insight. Yet synthesis projects encounter challenges at all steps of the data reuse pipeline, including unavailable data, labor-intensive transcription of datasets, incomplete metadata, and a lack of communication between collaborators. Here, using insights from a diversity of soil, data, and climate scientists, we summarize current practices in soil data synthesis across all stages of database creation: availability, input, harmonization, curation, and publication. We then suggest new soil-focused semantic tools to improve existing data pipelines, such as ontologies, vocabulary lists, and community practices. Our goal is to provide the soil data community with an overview of current practices in soil data and where we need to go to fully leverage big data to solve soil problems in the next century

Nucleotides released by apoptotic cells act as a find-me signal to promote phagocytic clearance

Phagocytic removal of apoptotic cells occurs efficiently in vivo such that even in tissues with significant apoptosis, very few apoptotic cells are detectable1. This is thought to be due to the release of find-me signals by apoptotic cells that recruit motile phagocytes such as monocytes, macrophages, and dendritic cells, leading to the prompt clearance of the dying cells2. However, the identity and in vivo relevance of such find-me signals are not well understood. Here, through several lines of evidence, we identify extracellular nucleotides as a critical apoptotic cell find-me signal. We demonstrate the caspase-dependent release of ATP and UTP (in equimolar quantities) during the early stages of apoptosis by primary thymocytes and cell lines. Purified nucleotides at these concentrations were sufficient to induce monocyte recruitment comparable to apoptotic cell supernatants. Enzymatic removal of ATP and UTP (by apyrase or ectopic CD39 expression) abrogated the ability of apoptotic cell supernatants to recruit monocytes in vitro and in vivo. We then identified the ATP/UTP receptor P2Y2 as a critical sensor of nucleotides released by apoptotic cells using RNAi depletion studies in monocytes, and macrophages from P2Y2-null mice3. The in vivo relevance of nucleotides in apoptotic cell clearance was revealed by two approaches. First, in a murine air-pouch model, apoptotic cell supernatants induced a three-fold greater recruitment of monocytes and macrophages compared to supernatants from healthy cells; this recruitment was abolished by depletion of nucleotides and significantly decreased in P2Y2−/− mice. Second, clearance of apoptotic thymocytes was significantly impaired by either depletion of nucleotides or interference with P2Y receptor function (by pharmacological inhibition, or in P2Y2−/− mice). These results identify nucleotides as a critical find-me cue released by apoptotic cells to promote P2Y2-dependent phagocyte recruitment, and provide strong evidence for a clear relationship between a find-me signal and efficient corpse clearance in vivo

Judicial Review, Irrationality, and the Limits of Intervention by the Courts

When exercising judicial review, the courts, on occasions, have intervened in circumstances where administrative decisions were not irrational. However, these low standards of judicial intervention are arguably constitutional, especially since the enactment of the Human Rights Act 1998 (HRA). To this end, this article seeks to establish a zone of executive decision-making, for reasons of democracy, where the courts are clearly excluded. But it is unable to do so. Does this mean, therefore, that judicial intervention on the grounds of irrationality exists without limit? Assuming this to be the case, it is suggested that the courts should show greater respect to the administrative branch of the state where it has genuinely sought to engage with the legal process in arriving at its decisions