Genomic aggregation effects and Simpson's paradox

A grant from the One-University Open Access Fund at the University of Kansas was used to defray the author’s publication fees in this Open Access journal. The Open Access Fund, administered by librarians from the KU, KU Law, and KUMC libraries, is made possible by contributions from the offices of KU Provost, KU Vice Chancellor for Research & Graduate Studies, and KUMC Vice Chancellor for Research. For more information about the Open Access Fund, please see http://library.kumc.edu/authors-fund.xml.Genomic studies have become commonplace, with thousands of gene expressions typically collected on single or multiple platforms and analyzed. Unaccounted time-ordered or epigenetic aspects of genetic expression may lead to a version of Simpson's paradox, ie, time-aggregated overall effects that do not reflect within strata patterns. Without clear functional models to motivate clustering and fitting algorithms, these confounding related issues require consideration. Several basic examples motivate discussion and more appropriate models for analysis of expression data are reviewed

Autism Spectrum Disorders and Identified Toxic Land Fills: Co-Occurrence Across States

It is believed that gene by environmental interactions contribute to the pathogenesis of autism spectrum disorders (ASD). We hypothesize that ASD are associated with early and repeated exposures to any of a number of toxicants or mixtures of toxicants. It is the cumulative effects of these repeated exposures acting upon genetically susceptible individuals that lead to the phenotypes of ASD. We report our initial observations of a considerable overlap of identified toxic landfills in the State of New Jersey and the residence of an ASD cohort, and a correlation between the identified toxic Superfund sites on each U.S. state and the total number of diagnosed cases of ASD in those states. The residence of 495 ASD patients in New Jersey by zip code and the toxic landfill sites were plotted on a map of Northern New Jersey. The area of highest ASD cases coincides with the highest density of toxic landfill sites while the area with lowest ASD cases has the lowest density of toxic landfill sites. Furthermore, the number of toxic Superfund sites and autism rate across 49 of the 50 states shows a statistically significant correlation (i.e. the number of identified superfund sites correlates with the rate of autism per 1000 residents in 49 of the states (p = 0.015; excluding the state of Oregon). These significant observations call for further organized studies to elucidate possible role(s) of environmental toxicants contributing to the pathogenesis of ASD

Using Teaching Excellence Surveys to Evaluate Improvements in Teaching Confidence

BACKGROUND: There are many surveys to assess teaching excellence, but few validated tools to assess improvements in teaching confidence among faculty over time. We hypothesized that previously validated surveys for learner evaluation of faculty teaching excellence also can be used as a self-evaluation tool to assess changes in faculty teaching skills confidence over time. METHODS: A cohort study was designed using a composite survey from two previously validated surveys (SETQ and CanMEDS) on teaching excellence. The composite survey was administered before and after a faculty development course on teaching excellence at the University of Kansas Medical Center in the Spring of 2012. Course “completers” attended more than 50% of the course and “non-completers” attended 50% or less of the course. RESULTS: The overall mean change in survey result scores on a five-point Likert scale was nearly one point for “completers” (mean difference = 0.92, SD = 0.41) as opposed to 0.34 for “non-completers” (SD = 0.34, p = 0.001). The Cronbach’s alpha coefficients for the pre-course surveys were 0.83 and 0.85 versus 0.88 and 0.83 for the post-course surveys, indicating a high internal consistency for both survey instruments. CONCLUSIONS: Measurable improvements in teaching skills confidence occur following faculty professional development courses. These improvements can be assessed more efficiently by using previously validated and reliable assessment tools in new and innovative ways

Creating Improved Communication Between Nursing and Physicians: Importance of Collaboration within a Hospital System

Background: Optimal communication between all members of the healthcare team is important to ensure safe and efficient patient care.Objective: To improve communication between nurses and resident physicians by developing and implementing a paging protocol.Methods: A resident-led workgroup was assembled to identify opportunities for improving communication. A survey was designed to assess current practices and perceptions related to resident and nurse communication. A facilitated focus group of residents and nurses met on two separate occasions to review the survey results and develop a set of mutually agreeable paging guidelines. The group chose to adopt the ISBARR communication tool and planned educational interventions accordingly. Residents and nurses were resurveyed roughly three months’ post-intervention.Results: The results indicated a 12.8% reduction (p=0.017) in the percentage of nurse respondents that “never” inquire whether or not another nurse on the unit needs to speak with the same physician prior to paging. A 10.3% increase (p=0.033) in resident respondents that “usually” receive grouped pages, and an 11% reduction (p=0.042) in the percentage of resident respondents that “never: receive grouped pages. However, only 53.3% (n=60) of nurse respondents and 44.1% (n=68) of resident respondents felt their ISBARR training was adequate. Moreover, only 38.4% and 30.9% of nurse and resident respondents, respectively felt the paging guidelines and ISBARR had improved overall communications between the two groups.Conclusions: While the follow-up survey results revealed some improvements in paging practices, the need for continued education was clear

Discovery and Early Evolution of ASASSN-19bt, the First TDE Detected by TESS

We present the discovery and early evolution of ASASSN-19bt, a tidal disruption event (TDE) discovered by the All-Sky Automated Survey for Supernovae (ASAS-SN) at a distance of $d\simeq115$ Mpc and the first TDE to be detected by TESS. As the TDE is located in the TESS Continuous Viewing Zone, our dataset includes 30-minute cadence observations starting on 2018 July 25, and we precisely measure that the TDE begins to brighten $\sim8.3$ days before its discovery. Our dataset also includes 18 epochs of Swift UVOT and XRT observations, 2 epochs of XMM-Newton observations, 13 spectroscopic observations, and ground data from the Las Cumbres Observatory telescope network, spanning from 32 days before peak through 37 days after peak. ASASSN-19bt thus has the most detailed pre-peak dataset for any TDE. The TESS light curve indicates that the transient began to brighten on 2019 January 21.6 and that for the first 15 days its rise was consistent with a flux $\propto t^2$ power-law model. The optical/UV emission is well-fit by a blackbody SED, and ASASSN-19bt exhibits an early spike in its luminosity and temperature roughly 32 rest-frame days before peak and spanning up to 14 days that has not been seen in other TDEs, possibly because UV observations were not triggered early enough to detect it. It peaked on 2019 March 04.9 at a luminosity of $L\simeq1.3\times10^{44}$ ergs s$^{-1}$ and radiated $E\simeq3.2\times10^{50}$ ergs during the 41-day rise to peak. X-ray observations after peak indicate a softening of the hard X-ray emission prior to peak, reminiscent of the hard/soft states in X-ray binaries.Comment: 23 pages, 14 figures, 5 tables. A machine-readable table containing the host-subtracted photometry presented in this manuscript is included as an ancillary fil

Effects of body plan evolution on the hydrodynamic drag and energy requirements of swimming in ichthyosaurs

Ichthyosaurs are an extinct group of fully marine tetrapods that were well adapted to aquatic locomotion. During their approximately 160 Myr existence, they evolved from elongate and serpentine forms into stockier, fish-like animals, convergent with sharks and dolphins. Here, we use computational fluid dynamics (CFD) to quantify the impact of this transition on the energy demands of ichthyosaur swimming for the first time. We run computational simulations of water flow using three-dimensional digital models of nine ichthyosaurs and an extant functional analogue, a bottlenose dolphin, providing the first quantitative evaluation of ichthyosaur hydrodynamics across phylogeny. Our results show that morphology did not have a major effect on the drag coefficient or the energy cost of steady swimming through geological time. We show that even the early ichthyosaurs produced low levels of drag for a given volume, comparable to those of a modern dolphin, and that deep ‘torpedo-shaped’ bodies did not reduce the cost of locomotion. Our analysis also provides important insight into the choice of scaling parameters for CFD applied to swimming mechanics, and underlines the great influence of body size evolution on ichthyosaur locomotion. A combination of large bodies and efficient swimming modes lowered the cost of steady swimming as ichthyosaurs became increasingly adapted to a pelagic existence

Offspring's Leukocyte Telomere Length, Paternal Age, and Telomere Elongation in Sperm

Leukocyte telomere length (LTL) is a complex genetic trait. It shortens with age and is associated with a host of aging-related disorders. Recent studies have observed that offspring of older fathers have longer LTLs. We explored the relation between paternal age and offspring's LTLs in 4 different cohorts. Moreover, we examined the potential cause of the paternal age on offspring's LTL by delineating telomere parameters in sperm donors. We measured LTL by Southern blots in Caucasian men and women (n=3365), aged 18–94 years, from the Offspring of the Framingham Heart Study (Framingham Offspring), the NHLBI Family Heart Study (NHLBI-Heart), the Longitudinal Study of Aging Danish Twins (Danish Twins), and the UK Adult Twin Registry (UK Twins). Using Southern blots, Q-FISH, and flow-FISH, we also measured telomere parameters in sperm from 46 young (<30 years) and older (>50 years) donors. Paternal age had an independent effect, expressed by a longer LTL in males of the Framingham Offspring and Danish Twins, males and females of the NHLBI-Heart, and females of UK Twins. For every additional year of paternal age, LTL in offspring increased at a magnitude ranging from half to more than twice of the annual attrition in LTL with age. Moreover, sperm telomere length analyses were compatible with the emergence in older men of a subset of sperm with elongated telomeres. Paternal age exerts a considerable effect on the offspring's LTL, a phenomenon which might relate to telomere elongation in sperm from older men. The implications of this effect deserve detailed study