Using Syndromic Surveillance to Assess the Impact of Environmental Factors on Asthma- and COPD- Related ED Visits in Douglas County, Nebraska

Background: Asthma and chronic obstructive pulmonary disease (COPD) are chronic diseases associated with health disparities in Douglas County, Nebraska and in the United States. Currently there is a lack of information describing the impact of environmental factors in Nebraska on the burden of emergency department (ED) visits or hospitalizations related to these chronic respiratory (CR) diseases. The aim of this study was to determine if there is an association between the numbers of seasonal viral respiratory (SVR)- related ED visits, outdoor air pollutants, aeroallergens, or meteorological factors on the number of CR- related ED visits in Douglas County, Nebraska. Methods: We analyzed electronic health record (EHR) data from 8 of 9 hospitals in Douglas County, NE for ED visits from February 28, 2016 to December 29, 2018. Syndromic surveillance definitions were used to identify CR- and SVR- related ED visits in EHR ED data. Aeroallergen, outdoor air pollutant and temperature data were obtained. Descriptive statistics were performed on EHR and environmental data. Negative binomial models were used to determine the association between the number of CR- related weekly ED visits and the environmental factors of interest. These models were stratified to account for possible cofounding effect of patient age and season. Patient age was stratified into 3 age groups: \u3c 18 yrs., 18-39 yrs., ≥ 40 yrs. Results: Significant associations were observed between the number of CR- related weekly ED visits and the weekly number of SVR-related ED visits, mean weed pollen counts, mean mold spore counts, mean minimum temperature, mean carbon monoxide levels and mean fine particulate matter (PM2.5) levels. Discrepancies in significant associations between the CR- related weekly ED visits and the environmental variables were observed after stratifying the model by season and age groups. For instance, SVR-related weekly ED visits were significantly associated with an increase in CR-related weekly ED visits among the \u3c 18 yrs. and 18 to 39 yrs. age groups in the summer, the ≥ 40 yrs. age group in the fall, and the 18 to 39 yrs. and the ≥ 40 yrs. age groups in the winter. Minimum temperature was significantly associated with the increase in CR- related weekly ED visits among the \u3c 18 yrs. and 18 to 39 yrs. age groups in the fall. Significant associations with an increase in CR- related weekly ED visits were also observed for PM2.5 among the 18 to 39 yrs. and ≥ 40 yrs. age groups in the spring, and the \u3c 18 yrs. and ≥ 40 yrs. age groups in the fall. Weed pollen and mold spores were also significantly associated with an increase in CR- related weekly ED visits. While significant associations were observed for weed pollen during the summer among the \u3c 18 yrs. age group, significant associations were observed for mold spores among all age groups during spring, and among the ≥ 40 yrs. age group during summer. Carbon monoxide was associated with a decrease in CR-related weekly ED visits for the 18 to 39 yrs. age group in the fall. Conclusions: Results of this study indicate the association between environmental factors and CR- related ED visits in Douglas County, Nebraska could be affected by not only by SVR disease cycles, temperature and other environmental factors, but also by age. Additional analyses may be needed to further explore these associations

Gallus GBrowse: a unified genomic database for the chicken

Gallus GBrowse (http://birdbase.net/cgi-bin/gbrowse/gallus/) provides online access to genomic and other information about the chicken, Gallus gallus. The information provided by this resource includes predicted genes and Gene Ontology (GO) terms, links to Gallus In Situ Hybridization Analysis (GEISHA), Unigene and Reactome, the genomic positions of chicken genetic markers, SNPs and microarray probes, and mappings from turkey, condor and zebra finch DNA and EST sequences to the chicken genome. We also provide a BLAT server (http://birdbase.net/cgi-bin/webBlat) for matching user-provided sequences to the chicken genome. These tools make the Gallus GBrowse server a valuable resource for researchers seeking genomic information regarding the chicken and other avian species

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data

Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn from a high-throughput sequencing experiment. Here, the self-similar distributions appear as part of the evaluation of the error rate of the sequencing technology and the identification of tumorogenic genomic alterations. The other examples are obtained from risk factor evaluation and analysis of relative disease prevalence and co-mordbidity as these appear in electronic clinical data. The distributions are also relevant to identification of subclonal populations in tumors and the study of the evolution of infectious diseases, and more precisely the study of quasi-species and intrahost diversity of viral populations

Accurate Profiling of Microbial Communities from Massively Parallel Sequencing using Convex Optimization

We describe the Microbial Community Reconstruction ({\bf MCR}) Problem, which is fundamental for microbiome analysis. In this problem, the goal is to reconstruct the identity and frequency of species comprising a microbial community, using short sequence reads from Massively Parallel Sequencing (MPS) data obtained for specified genomic regions. We formulate the problem mathematically as a convex optimization problem and provide sufficient conditions for identifiability, namely the ability to reconstruct species identity and frequency correctly when the data size (number of reads) grows to infinity. We discuss different metrics for assessing the quality of the reconstructed solution, including a novel phylogenetically-aware metric based on the Mahalanobis distance, and give upper-bounds on the reconstruction error for a finite number of reads under different metrics. We propose a scalable divide-and-conquer algorithm for the problem using convex optimization, which enables us to handle large problems (with $\sim10^6$ species). We show using numerical simulations that for realistic scenarios, where the microbial communities are sparse, our algorithm gives solutions with high accuracy, both in terms of obtaining accurate frequency, and in terms of species phylogenetic resolution.Comment: To appear in SPIRE 1

The Preparation and Certification of School Librarians: Using Causal Educational Research About Teacher Characteristics to Probe Facets of Effectiveness

How do we define a high-quality school librarian? Decades of educational researchers have attempted to link teacher characteristics—such as how teachers are prepared, which credentials they carry, and years of experience—to student outcomes. These researchers have contended that individual educator attributes may have a direct effect on what and how much their students learn. School librarians are also teachers who have direct student contact, and although numerous studies have indicated that school librarian preparation, licensure, and other background characteristics are promising areas for further direct exploration, researchers have yet to examine if, how, and why school librarians’ certification or preparation positively impacts students’ learning outcomes. The purpose of this paper is to compare findings from causal educational research to findings from descriptive school librarianship research to discern possible areas of causal alignment that warrant further investigation. In this study, we present a subset of a larger mixed research synthesis of causal educational research related to student achievement, contextualized with existing school librarianship research, to draw relationships between classroom teacher and school librarian preparation and characteristics and to shape researchable conjectures about school librarians’ effects on learner outcomes