Dealing with Missing Data: A Comparative Exploration of Approaches Using the Integrated City Sustainability Database

Studies of governments and local organizations using survey data have played a critical role in the development of urban studies and related disciplines. However, missing data pose a daunting challenge for this research. This article seeks to raise awareness about the treatment of missing data in urban studies research by comparing and evaluating three commonly used approaches to deal with missing data—listwise deletion, single imputation, and multiple imputation. Comparative analyses illustrate the relative performance of these approaches using the second-generation Integrated City Sustainability Database (ICSD). The results demonstrate the benefit of using an approach to missing data based on multiple imputation, using a theoretically informed and statistically supported set of predictor variables to develop a more complete sample that is free of issues raised by nonresponse in survey data. The results confirm the usefulness of the ICSD in the study of environmental and sustainability and other policy in U.S. cities. We conclude with a discussion of results and provide a set of recommendations for urban researcher scholars

Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216

Kineococcus radiotolerans SRS30216 was isolated from a high-level radioactive environment at the Savannah River Site (SRS) and exhibits γ-radiation resistance approaching that of Deinococcus radiodurans. The genome was sequenced by the U.S. Department of Energy's Joint Genome Institute which suggested the existence of three replicons, a 4.76 Mb linear chromosome, a 0.18 Mb linear plasmid, and a 12.92 Kb circular plasmid. Southern hybridization confirmed that the chromosome is linear. The K. radiotolerans genome sequence was examined to learn about the physiology of the organism with regard to ionizing radiation resistance, the potential for bioremediation of nuclear waste, and the dimorphic life cycle. K. radiotolerans may have a unique genetic toolbox for radiation protection as it lacks many of the genes known to confer radiation resistance in D. radiodurans. Additionally, genes involved in the detoxification of reactive oxygen species and the excision repair pathway are overrepresented. K. radiotolerans appears to lack degradation pathways for pervasive soil and groundwater pollutants. However, it can respire on two organic acids found in SRS high-level nuclear waste, formate and oxalate, which promote the survival of cells during prolonged periods of starvation. The dimorphic life cycle involves the production of motile zoospores. The flagellar biosynthesis genes are located on a motility island, though its regulation could not be fully discerned. These results highlight the remarkable ability of K radiotolerans to withstand environmental extremes and suggest that in situ bioremediation of organic complexants from high level radioactive waste may be feasible

Comparing Model Representations of Physiological Limits on Transpiration at a Semi-arid Ponderosa Pine Site

Mechanistic representations of biogeochemical processes in ecosystem models are rapidly advancing, requiring advancements in model evaluation approaches. Here we quantify multiple aspects of model functional performance to evaluate improved process representations in ecosystem models. We compare semi-empirical stomatal models with hydraulic constraints against more mechanistic representations of stomatal and hydraulic functioning at a semi-arid pine site using a suite of metrics and analytical tools. We find that models generally perform similarly under unstressed conditions, but performance diverges under atmospheric and soil drought. The more empirical models better capture synergistic information flows between soil water potential and vapor pressure deficit to transpiration, while the more mechanistic models are overly deterministic. Although models can be parameterized to yield similar functional performance, alternate parameterizations could not overcome structural model constraints that underestimate the unique information contained in soil water potential about transpiration. Additionally, both multilayer canopy and big-leaf models were unable to capture the magnitude of canopy temperature divergence from air temperature, and we demonstrate that errors in leaf temperature can propagate to considerable error in simulated transpiration. This study demonstrates the value of merging underutilized observational data streams with emerging analytical tools to characterize ecosystem function and discriminate among model process representations

Primary Health Care Potential Home for Family-Focused Preventive Interventions

Family-focused prevention programs have been shown to effectively reduce a range of negative behavioral health outcomes but have had limited reach. Three key barriers must be overcome to expand the reach of family-focused prevention programs and thereby achieve a significant public health impact. These barriers are (1) current social norms and perceptions of parenting programs; (2) concerns about the expertise and legitimacy of sponsoring organizations to offer parenting advice; and (3) a paucity of stable, sustainable funding mechanisms. Primary healthcare settings are well positioned to overcome these barriers. Recent changes within health care make primary care settings an increasingly favorable home for family-focused prevention and suggest possibilities for sustainable funding of family-focused prevention programs. This paper discusses the existing advantages of primary care settings and lays out a plan to move toward realizing the potential public health impact of family-focused prevention through widespread implementation in primary healthcare settings

ELemental abundances of Planets and brown dwarfs Imaged around Stars (ELPIS): I. Potential Metal Enrichment of the Exoplanet AF Lep b and a Novel Retrieval Approach for Cloudy Self-luminous Atmospheres

AF Lep A+b is a remarkable planetary system hosting a gas-giant planet that has the lowest dynamical mass among directly imaged exoplanets. We present an in-depth analysis of the atmospheric composition of the star and planet to probe the planet's formation pathway. Based on new high-resolution spectroscopy of AF Lep A, we measure a uniform set of stellar parameters and elemental abundances (e.g., [Fe/H] = $-0.27 \pm 0.31$ dex). The planet's dynamical mass ($2.8^{+0.6}_{-0.5}$ M$_{\rm Jup}$) and orbit are also refined using published radial velocities, relative astrometry, and absolute astrometry. We use petitRADTRANS to perform chemically-consistent atmospheric retrievals for AF Lep b. The radiative-convective equilibrium temperature profiles are incorporated as parameterized priors on the planet's thermal structure, leading to a robust characterization for cloudy self-luminous atmospheres. This novel approach is enabled by constraining the temperature-pressure profiles via the temperature gradient $(d\ln{T}/d\ln{P})$, a departure from previous studies that solely modeled the temperature. Through multiple retrievals performed on different portions of the $0.9-4.2$ $\mu$m spectrophotometry, along with different priors on the planet's mass and radius, we infer that AF Lep b likely possesses a metal-enriched atmosphere ([Fe/H] $> 1.0$ dex). AF Lep b's potential metal enrichment may be due to planetesimal accretion, giant impacts, and/or core erosion. The first process coincides with the debris disk in the system, which could be dynamically excited by AF Lep b and lead to planetesimal bombardment. Our analysis also determines $T_{\rm eff} \approx 800$ K, $\log{(g)} \approx 3.7$ dex, and the presence of silicate clouds and dis-equilibrium chemistry in the atmosphere. Straddling the L/T transition, AF Lep b is thus far the coldest exoplanet with suggested evidence of silicate clouds.Comment: AJ, in press. Main text: Pages 1-32, Figures 1-15, Tables 1-6. All figures and tables after References belong to the Appendix (Pages 32-58, Figures 16-20, Table 7). For supplementary materials, please refer to the Zenodo repository https://doi.org/10.5281/zenodo.826746

Promoter targeted small RNAs induce long-term transcriptional gene silencing in human cells

Small RNAs targeted to gene promoters in human cells can mediate transcriptional gene silencing (TGS) by directing silent state epigenetic modifications to targeted loci. Many mechanistic details of this process remain poorly defined, and the ability to stably modulate gene expression in this manner has not been explored. Here we describe the mechanisms of establishment and maintenance of long-term transcriptional silencing of the human ubiquitin C gene (UbC). Sustained targeting of the UbC promoter with a small RNA for a minimum of 3 days resulted in long-term silencing which correlated with an early increase in histone methylation and a later increase in DNA methylation at the targeted locus. Transcriptional silencing of UbC required the presence of a promoter-associated RNA. The establishment and maintenance of the TGS were shown to require distinct protein factors. Argonaute 1 (Ago1), DNA methyltransferase 3a (DNMT3a) and histone deacetylase 1 (HDAC1) were required for the initiation of silencing, and DNA methyltransferase 1 (DNMT1) was necessary for maintenance. Taken together the data presented here highlight the cellular pathway with which noncoding RNAs interact to epigenetically regulate gene expression in human cells

EZH2 Cooperates with BRD4-NUT to Drive NUT Carcinoma Growth by Silencing Key Tumor Suppressor Genes

NUT carcinoma (NC) is an aggressive carcinoma driven by the BRD4-NUT fusion oncoprotein, which activates chromatin to promote expression of pro-growth genes. BET bromodomain inhibitors (BETi) are a promising treatment for NC that can impede BRD4-NUT’s ability to activate genes, but the efficacy of BETi as monotherapy are limited. Here, we demonstrated that EZH2, which silences genes through establishment of repressive chromatin, is a dependency in NC. Inhibition of EZH2 with the clinical compound tazemetostat (taz) potently blocked growth of NC cells. Epigenetic and transcriptomic analysis revealed that taz reversed the EZH2-specific H3K27me3 silencing mark and restored expression of multiple tumor suppressor genes while having no effect on key oncogenic BRD4-NUT-regulated genes. Indeed, H3K27me3 and H3K27ac domains were found to be mutually exclusive in NC cells. CDKN2A was identified as the only gene among all taz-derepressed genes to confer resistance to taz in a CRISPR-Cas9 screen. Combined inhibition of EZH2 and BET synergized to downregulate cell proliferation genes resulting in more pronounced growth arrest and differentiation than either inhibitor alone. In pre-clinical models, combined taz and BETi synergistically blocked tumor growth and prolonged survival of NC-xenografted mice, with complete remission without relapse in one cohort. Identification of EZH2 as a dependency in NC substantiates the reliance of NC tumor cells on epigenetic dysregulation of functionally opposite, yet highly complementary, chromatin regulatory pathways to maintain NC growth

Smoke-free legislation and paediatric hospitalisations for acute respiratory tract infections:national quasi-experimental study with unexpected findings and important methodological implications

We investigated whether Scottish implementation of smoke-free legislation was associated with a reduction in unplanned hospitalisations or deaths ('events') due to respiratory tract infections (RTIs) among children. Interrupted time series (ITS). Children aged 0-12 years living in Scotland during 1996-2012. National comprehensive smoke-free legislation (March 2006). Acute RTI events in the Scottish Morbidity Record-01 and/or National Records of Scotland Death Records. 135 134 RTI events were observed over 155 million patient-months. In our prespecified negative binomial regression model accounting for underlying temporal trends, seasonality, sex, age group, region, urbanisation level, socioeconomic status and seven-valent pneumococcal vaccination status, smoke-free legislation was associated with an immediate rise in RTI events (incidence rate ratio (IRR)=1.24, 95% CI 1.20 to 1.28) and an additional gradual increase (IRR=1.05/year, 95% CI 1.05 to 1.06). Given this unanticipated finding, we conducted a number of post hoc exploratory analyses. Among these, automatic break point detection indicated that the rise in RTI events actually preceded the smoke-free law by 16 months. When accounting for this break point, smoke-free legislation was associated with a gradual decrease in acute RTI events: IRR=0.91/year, 95% CI 0.87 to 0.96. Our prespecified ITS approach suggested that implementation of smoke-free legislation in Scotland was associated with an increase in paediatric RTI events. We were concerned that this result, which contradicted published evidence, was spurious. The association was indeed reversed when accounting for an unanticipated antecedent break point in the temporal trend, suggesting that the legislation may in fact be protective. ITS analyses should be subjected to comprehensive robustness checks to assess consistency. [Abstract copyright: © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

'Riots engulfed the city':an experimental study investigating the legitimating effects of fire metaphors in discourses of disorder

In Cognitive Linguistic Critical Discourse Studies (CL-CDS), metaphor is identified as a key index of ideology and an important device in the legitimation of social action. From this perspective, metaphor is a cognitive-semiotic operation, invoked by metaphorical expressions in discourse, in which a source frame is mobilised to provide a template for sense-making inside a target frame, leading to particular framing effects. However, the extent to which metaphors in discourse genuinely activate an alternative frame and thereby achieve framing effects has recently been subject to question. Amid calls for more empirical forms of analysis in Critical Discourse Studies, the paper reports two experiments testing the legitimating framing effects of fire metaphors in discourses of disorder. Results show that images of fire and fire metaphors in the absence of competing images facilitate support for police use of water cannon in response to social unrest. The study not only justifies attention to metaphor in CL-CDS but similar effects across semiotic modalities are interpreted as evidence in support of simulation-based theories of metaphor