Impacts of phosphorus amendments on legacy soil contamination from lead-based paint on a California, USA university campus.

Lead (Pb) is one of the most common heavy metal urban soil contaminants with well-known toxicity to humans. This incubation study (2-159 d) compared the ability of bone meal (BM), potassium hydrogen phosphate (KP), and triple superphosphate (TSP), at phosphorus:lead (P:Pb) molar ratios of 7.5:1, 15:1, and 22.5:1, to reduce bioaccessible Pb in soil contaminated by Pb-based paint relative to control soil to which no P amendment was added. Soil pH and Mehlich 3 bioaccessible Pb and P were measured as a function of incubation time and amount and type of P amendment. XAS assessed Pb speciation after 30 and 159 d of incubation. The greatest reductions in bioaccessible Pb at 159 d were measured for TSP at the 7.5:1 and 15:1 P:Pb molar ratios. The 7.5:1 KP treatment was the only other treatment with significant reductions in bioaccessible Pb compared to the control soil. It is unclear why greater reductions of bioaccessible Pb occurred with lower P additions, but it strongly suggests that the amount of P added was not a controlling factor in reducing bioaccessible Pb. This was further supported because Pb-phosphates were not detected in any samples using XAS. The most notable difference in the effect of TSP versus other amendments was the reduction in pH. However, the relationship between increasing TSP additions, resulting in decreasing pH and decreasing Pb bioaccessibility was not consistent. The 22.5:1 P:Pb TSP treatment had the lowest pH but did not significantly reduce bioaccessible Pb compared to the control soil. The 7.5:1 and 15:1 P:Pb TSP treatments significantly reduced bioaccessible Pb relative to the control and had significantly higher pH than the 22.5:1 P:Pb treatment. Clearly, impacts of P additions and soil pH on Pb bioaccessibility require further investigation to decipher mechanisms governing Pb speciation in Pb-based paint contaminated soils.

Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution.

BACKGROUND: Transcriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species' ability to interbreed and generate hybrid individuals. RESULTS: We generated transcriptomes of the Rakov Skocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F1 hybrids between cave and surface individuals. RNAseq of F2 hybrids, as well as genotyping of a backcross, allowed for positional information of multiple candidate genes from the differential expression and allele-specific analyses. CONCLUSIONS: As expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F1 hybrids identified genes with cave-biased (cave allele has higher mRNA levels than the surface allele) and surface-biased expression (surface allele has higher mRNA levels than the cave allele). RNAseq of F2 hybrids allowed for multiple genes to be placed to previously mapped genomic regions responsible for eye and pigmentation phenotypes. In the future, these transcriptomic resources will guide prioritization of candidates for functional analysis.

Identification and classification of cis-regulatory elements in the amphipod crustacean Parhyale hawaiensis.

Emerging research organisms enable the study of biology that cannot be addressed using classical 'model' organisms. New data resources can accelerate research in such animals. Here, we present new functional genomic resources for the amphipod crustacean Parhyale hawaiensis, facilitating the exploration of gene regulatory evolution using this emerging research organism. We use Omni-ATAC-seq to identify accessible chromatin genome-wide across a broad time course of Parhyale embryonic development. This time course encompasses many major morphological events, including segmentation, body regionalization, gut morphogenesis and limb development. In addition, we use short- and long-read RNA-seq to generate an improved Parhyale genome annotation, enabling deeper classification of identified regulatory elements. We discover differential accessibility, predict nucleosome positioning, infer transcription factor binding, cluster peaks based on accessibility dynamics, classify biological functions and correlate gene expression with accessibility. Using a Minos transposase reporter system, we demonstrate the potential to identify novel regulatory elements using this approach. This work provides a platform for the identification of novel developmental regulatory elements in Parhyale, and offers a framework for performing such experiments in other emerging research organisms.

Spatial Clustering of Hookah Lounges, Vape Shops, and All Tobacco Retailers Near Colleges.

INTRODUCTION: US college students smoke hookah and vape nicotine at higher rates than other young adults. Density and/or proximity of hookah lounges and vape shops near colleges has been described, but this study is the first to test whether tobacco retailers spatially cluster near college campuses. AIMS AND METHODS: We created and linked spatial shapefiles for community colleges and 4-year colleges in California with lists of hookah lounges, vape shops, and licensed tobacco retailers. We simulated 100 datasets, placing hookah lounges, vape shops, and tobacco retailers randomly in census tracts in proportion to population density. A modified version of Ripley's K-function was computed using the radius (r) from each retailer within retail category. RESULTS: In 2018-2019, 50.5% of hookah lounges (n = 479), 42.5% of vape shops (n = 2467), and 42.0% of all tobacco retailers (n = 31 100) were located within 3 miles of a community college. Spatial clustering was significant (p < .05) from at least 0.4 miles for hookah lounges, 0.1 mile for vape shops, and 0.3 miles for all tobacco retailers. For 4-year colleges, approximately 46.8% of hookah lounges, 31.3% of vape shops, and 31.6% of all tobacco retailers were located within 3 miles. Clustering was significant from 0.2 miles for hookah lounges and 1.3 miles for all tobacco retailers but was not significant for vape shops. CONCLUSIONS: Evidence that some types of tobacco retailers cluster near community colleges and 4-year colleges implies greater accessibility and exposure to advertising for students. It is also concerning because a higher probability of underage tobacco sales presumably exists near colleges. IMPLICATIONS: Prior studies infer that hookah lounges and vape shops cluster near colleges from the density and closer proximity to campuses. This study modified a traditional test of spatial clustering and considered community colleges separately from 4-year universities. Spatial clustering of hookah lounges and all licensed tobacco retailers was evident near both types of campuses, but vape shops clustered only near community colleges. Place-based strategies to limit tobacco retail density could expand state and local laws that prohibit tobacco sales near schools to include retailers near college campuses. In addition, college environments should be a target for reducing hookah smoking and nicotine vaping.

Repurposing existing medications for coronavirus disease 2019: protocol for a rapid and living systematic review.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has no confirmed specific treatments. However, there might be in vitro and early clinical data as well as evidence from severe acute respiratory syndrome and Middle Eastern respiratory syndrome that could inform clinicians and researchers. This systematic review aims to create priorities for future research of drugs repurposed for COVID-19. METHODS: This systematic review will include in vitro, animal, and clinical studies evaluating the efficacy of a list of 34 specific compounds and 4 groups of drugs identified in a previous scoping review. Studies will be identified both from traditional literature databases and pre-print servers. Outcomes assessed will include time to clinical improvement, time to viral clearance, mortality, length of hospital stay, and proportions transferred to the intensive care unit and intubated, respectively. We will use the GRADE methodology to assess the quality of the evidence. DISCUSSION: The challenge posed by COVID-19 requires not just a rapid review of drugs that can be repurposed but also a sustained effort to integrate new evidence into a living systematic review. TRIAL REGISTRATION: PROSPERO 2020 CRD42020175648.

Repurposing Existing Medications for Coronavirus Disease 2019: Protocol for a Rapid and Living Systematic Review.

BACKGROUND: Coronavirus Disease 2019 (COVID-19) has no known specific treatments. However, there might be in vitro and early clinical data as well as evidence from Severe Acute Respiratory Syndrome and Middle Eastern Respiratory Syndrome that could inform clinicians and researchers. This systematic review aims to create priorities for future research of drugs repurposed for COVID-19. METHODS: This systematic review will include in vitro, animal, and clinical studies evaluating the efficacy of a list of 34 specific compounds and four groups of drugs identified in a previous scoping review. Studies will be identified both from traditional literature databases and pre-print servers. Outcomes assessed will include time to clinical improvement, time to viral clearance, mortality, length of hospital stay, and proportions transferred to the intensive care unit and intubated, respectively. We will use the GRADE methodology to assess the quality of the evidence. DISCUSSION: The challenge posed by COVID-19 requires not just a rapid review of drugs that can be repurposed but also a sustained effort to integrate new evidence into a living systematic review. SYSTEMATIC REVIEW REGISTRATION: PROSPERO 2020 CRD42020175648.

The amphipod crustacean Parhyale hawaiensis: An emerging comparative model of arthropod development, evolution, and regeneration.

Recent advances in genetic manipulation and genome sequencing have paved the way for a new generation of research organisms. The amphipod crustacean Parhyale hawaiensis is one such system. Parhyale are easy to rear and offer large broods of embryos amenable to injection, dissection, and live imaging. Foundational work has described Parhyale embryonic development, while advancements in genetic manipulation using CRISPR-Cas9 and other techniques, combined with genome and transcriptome sequencing, have enabled its use in studies of arthropod development, evolution, and regeneration. This study introduces Parhyale development and life history, a catalog of techniques and resources for Parhyale research, and two case studies illustrating its power as a comparative research system. This article is categorized under: Comparative Development and Evolution > Evolutionary Novelties Adult Stem Cells, Tissue Renewal, and Regeneration > Regeneration Comparative Development and Evolution > Model Systems Comparative Development and Evolution > Body Plan Evolution.

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus.

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.

Neighborhood Variation in the Price of Cheap Tobacco Products in California: Results From Healthy Stores for a Healthy Community.

BACKGROUND: Retail marketing surveillance research highlights concerns about lower priced cigarettes in neighborhoods with a higher proportion of racial/ethnic minorities but focuses almost exclusively on premium brands. To remedy this gap in the literature, the current study examines neighborhood variation in prices for the cheapest cigarettes and a popular brand of cigarillos in a large statewide sample of licensed tobacco retailers in a low-tax state. METHODS: All 61 local health departments in California trained data collectors to conduct observations in a census of eligible licensed tobacco retailers in randomly selected zip codes (n = 7393 stores, completion rate=91%). Data were collected in 2013, when California had a low and stagnant tobacco tax. Two prices were requested: the cheapest cigarette pack regardless of brand and a single, flavored Swisher Sweets cigarillo. Multilevel models (stores clustered in tracts) examined prices (before sales tax) as a function of neighborhood race/ethnicity and proportion of school-age youth (aged 5-17). Models adjusted for store type and median household income. RESULTS: Approximately 84% of stores sold cigarettes for less than $5 and a Swisher Sweets cigarillo was available for less than $1 in 74% of stores that sold the brand. The cheapest cigarettes cost even less in neighborhoods with a higher proportion of school-age residents and Asian/Pacific Islanders. CONCLUSIONS: Neighborhood disparities in the price of the cheapest combustible tobacco products are a public health threat. Policy changes that make all tobacco products, especially combustible products, less available and more costly may reduce disparities in their use and protect public health. IMPLICATIONS: Much of what is known about neighborhood variation in the price of combustible tobacco products focuses on premium brand cigarettes. The current study extends this literature in two ways, by studying prices for the cheapest cigarette pack regardless of brand and a popular brand of flavored cigarillos and by reporting data from the largest statewide sample of licensed tobacco retailers. Significantly lower prices in neighborhoods with a higher proportion of youth and of racial/ethnic groups with higher smoking prevalence are a cause of concern. The study results underscore the need for policies that reduce availability and increase price of combustible tobacco products, particularly in states with low, stagnant tobacco taxes.

Inequalities in tobacco outlet density by race, ethnicity and socioeconomic status, 2012, USA: results from the ASPiRE Study.

BACKGROUND: Evidence of racial/ethnic inequalities in tobacco outlet density is limited by: (1) reliance on studies from single counties or states, (2) limited attention to spatial dependence, and (3) an unclear theory-based relationship between neighbourhood composition and tobacco outlet density. METHODS: In 97 counties from the contiguous USA, we calculated the 2012 density of likely tobacco outlets (N=90 407), defined as tobacco outlets per 1000 population in census tracts (n=17 667). We used 2 spatial regression techniques, (1) a spatial errors approach in GeoDa software and (2) fitting a covariance function to the errors using a distance matrix of all tract centroids. We examined density as a function of race, ethnicity, income and 2 indicators identified from city planning literature to indicate neighbourhood stability (vacant housing, renter-occupied housing). RESULTS: The average density was 1.3 tobacco outlets per 1000 persons. Both spatial regression approaches yielded similar results. In unadjusted models, tobacco outlet density was positively associated with the proportion of black residents and negatively associated with the proportion of Asian residents, white residents and median household income. There was no association with the proportion of Hispanic residents. Indicators of neighbourhood stability explained the disproportionate density associated with black residential composition, but inequalities by income persisted in multivariable models. CONCLUSIONS: Data from a large sample of US counties and results from 2 techniques to address spatial dependence strengthen evidence of inequalities in tobacco outlet density by race and income. Further research is needed to understand the underlying mechanisms in order to strengthen interventions.

Peer Assessment Enhances Student Learning: The Results of a Matched Randomized Crossover Experiment in a College Statistics Class.

Feedback has a powerful influence on learning, but it is also expensive to provide. In large classes it may even be impossible for instructors to provide individualized feedback. Peer assessment is one way to provide personalized feedback that scales to large classes. Besides these obvious logistical benefits, it has been conjectured that students also learn from the practice of peer assessment. However, this has never been conclusively demonstrated. Using an online educational platform that we developed, we conducted an in-class matched-set, randomized crossover experiment with high power to detect small effects. We establish that peer assessment causes a small but significant gain in student achievement. Our study also demonstrates the potential of web-based platforms to facilitate the design of high-quality experiments to identify small effects that were previously not detectable.