Possible Sources of Bias in Primary Care Electronic Health Record Data Use and Reuse

Background - Enormous amounts of data are recorded routinely in health care as part of the care process, primarily for managing individual patient care. There are significant opportunities to use this data for other purposes, many of which would contribute to establishing a learning health system. This is particularly true for data recorded in primary care settings, as in many countries, these are the first place patients turn to for most health problems. Objective - In this paper, we discuss whether data that is recorded routinely as part of the health care process in primary care is actually fit to use for these other purposes, how the original purpose may affect the extent to which the data is fit for another purpose and the mechanisms behind these effects. In doing so, we want to identify possible sources of bias that are relevant for the (re-)use of this type of data. Methods –This discussion paper is based on the authors’ experience as users of electronic health records data, as a general practitioner, health informatics experts, and health services researchers. It is a product of the discussions they had during the TRANSFoRm project, which was funded by the EU and sought to develop, pilot and evaluate a core information architecture for the Learning Health System (LHS) in Europe, based on primary care electronic health records. Results – We first describe the different stages in the processing of EHR data, as well as the different purposes for which this data is used. Given the different data processing steps and purposes, we then discuss the possible mechanisms for each individual data processing step, that can generate biased outcomes. We identified thirteen possible sources of bias. Four of them are related to the organization of a health care system, some are of a more technical nature. Conclusions - There are a substantial number of possible sources of bias, and very little is known about the size and direction of their impact. However, any (re-)user of data that was recorded as part of the health care process (such as researchers and clinicians) should be aware of the associated data collection process and environmental influences that can affect the quality of the data. Our stepwise, actor and purpose oriented approach may help to identify these possible sources of bias. Unless data quality issues are better understood and unless adequate controls are embedded throughout the data lifecycle, data-driven healthcare will not live up to its expectations. We need a data quality research agenda to devise the appropriate instruments needed to assess the magnitude of each of the possible sources of bias, and then start measuring their impact. The possible sources of bias described in this paper serve as a starting point for this research agenda

The contribution of the Unresolved Extragalactic Radio Sources to the Brightness Temperature of the sky

The contribution of the Unresolved Extragalactic Radio Sources to the diffuse brightness of the sky was evaluated using the source number - flux measurements available in literature. We first optimized the fitting function of the data based on number counts distribution. We then computed the brightness temperature at various frequencies from 151 MHz to 8440 MHz and derived its spectral dependence. As expected the frequency dependence can be described by a power law with a spectral index $\gamma \simeq -2.7$, in agreement with the flux emitted by the {\it steep spectrum} sources. The contribution of {\it flat spectrum} sources becomes relevant at frequencies above several GHz. Using the data available in literature we improved our knowledge of the brightness of the unresolved extragalactic radio sources. The results obtained have general validity and they can be used to disentangle the various contributions of the sky brightness and to evaluate the CMB temperature.Comment: Accepted for publication in the Astrophysical Journa

Catalog of Radio Galaxies with z>0.3. I:Construction of the Sample

The procedure of the construction of a sample of distant ($z>0.3$) radio galaxies using NED, SDSS, and CATS databases for further application in statistical tests is described. The sample is assumed to be cleaned from objects with quasar properties. Primary statistical analysis of the list is performed and the regression dependence of the spectral index on redshift is found.Comment: 9 pages, 6 figures, 2 table

Radio Frequency Spectra of 388 Bright 74 MHz Sources

As a service to the community, we have compiled radio frequency spectra from the literature for all sources within the VLA Low Frequency Sky Survey (VLSS) that are brighter than 15 Jy at 74 MHz. Over 160 references were used to maximize the amount of spectral data used in the compilation of the spectra, while also taking care to determine the corrections needed to put the flux densities from all reference on the same absolute flux density scale. With the new VLSS data, we are able to vastly improve upon previous efforts to compile spectra of bright radio sources to frequencies below 100 MHz because (1) the VLSS flux densities are more reliable than those from some previous low frequency surveys and (2) the VLSS covers a much larger area of the sky (declination >-30 deg.) than many other low frequency surveys (e.g., the 8C survey). In this paper, we discuss how the spectra were constructed and how parameters quantifying the shapes of the spectra were derived. Both the spectra and the shape parameters are made available here to assist in the calibration of observations made with current and future low frequency radio facilities.Comment: Accepted to ApJ

Abattoir Factors Influencing the Incidence of Dark Cutting in Australian Grain-Fed Beef

The aim of this study was to evaluate the effect of carcass traits, lairage time and weather conditions during lairage and abattoir factors that impact the incidence of dark cutting in 142,228 grain-fed carcasses, as defined by Meat Standards Australia (MSA) guidelines. This study was conducted over a 12-month period analysing data from cattle that were supplied from seven feedlots and processed at three abattoirs. Abattoir data indicated that the average incidence of dark cutting within the study was 2.8%. Increased wind speeds (WSs) and rain during lairage at the abattoir was associated with an increased risk of dark cutting, whereas variation in ambient temperature and/or relative humidity did not influence dark cutting. Heavier carcasses with whiter fat, larger hump heights, more rib fat, higher marble scores and lower ossification had lower incidences of dark cutting. The factors abattoir, time in lairage, time to grading and grader within Abattoir had significant effects on the incidence of dark cutting. The results from this study suggest that reducing the time in lairage and increasing the time between slaughter and grading are the two major ways to reduce dark cutting in MSA carcasses

The philosopher of ambiguity: exploring stories of spirituality of people with aphasia through the lens of Merleau-Ponty

Spirituality as a concept has only recently begun to be considered in speech and language therapy research and practice, and phenomenology as a research methodology is also not widely used in SLT research. Yet, concepts propounded by the phenomenologist Maurice Merleau-Ponty arguably offer a useful theoretical framework from which to view certain aspects of SLT including the concept of spirituality and how this is expressed by people with a communication difficulty. In this project, eight people with aphasia were interviewed about their spirituality. The interviews were transcribed, themes identified and stories created. These stories were viewed using one of the concepts propounded by Merleau-Ponty, namely ambiguity

Fundamental properties of Fanaroff-Riley II radio galaxies investigated via Monte Carlo simulations

[Abridged] Radio galaxies and quasars are among the largest and most powerful single objects known and are believed to have had a significant impact on the evolving Universe and its large scale structure. We explore the intrinsic and extrinsic properties of the population of FRII objects (kinetic luminosities, lifetimes, and the central densities of their environments). In particular, the radio and kinetic luminosity functions of FRIIs are investigated using the complete, flux limited radio catalogues of 3CRR and Best et al. We construct multidimensional Monte Carlo simulations using semi-analytical models of FRII radio source growth to create artificial samples of radio galaxies. Unlike previous studies, we compare radio luminosity functions found with both the observed and simulated data to explore the fundamental source parameters. We allow the source physical properties to co-evolve with redshift, and we find that all the investigated parameters most likely undergo cosmological evolution. Strikingly, we find that the break in the kinetic luminosity function must undergo redshift evolution of at least (1+z)^3. The fundamental parameters are strongly degenerate, and independent constraints are necessary to draw more precise conclusions. We use the estimated kinetic luminosity functions to set constraints on the duty cycles of these powerful radio sources. A comparison of the duty cycles of powerful FRIIs with those determined from radiative luminosities of AGN of comparable black hole mass suggests a transition in behaviour from high to low redshifts, corresponding to either a drop in the typical black hole mass of powerful FRIIs at low redshifts, or a transition to a kinetically-dominated, radiatively-inefficient FRII population.Comment: Accepted to MNRAS. 30 pages, 18 figures, 4 tables + online material (in appendix): 9 pages, 14 figure

Extragalactic Peaked-Spectrum Radio Sources at Low Frequencies

This document is the Accepted Manuscript of the following article: J.R. Callingham, et al, 'Extragalactic Peaked-Spectrum Radio Sources at Low Frequencies', The Astrophysical Journal, 836 (2), (28pp), first published online 17 February 2017. DOI: https://doi.org/10.3847/1538-4357-836/2/174. © 2017, The American Astronomical Society. All rights reserved. Data tables, and the appendix containing all of the SEDs, are available from the journal and on request to the authorWe present a sample of 1,483 sources that display spectral peaks between 72 MHz and 1.4 GHz, selected from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey. The GLEAM survey is the widest fractional bandwidth all-sky survey to date, ideal for identifying peaked-spectrum sources at low radio frequencies. Our peaked-spectrum sources are the low frequency analogues of gigahertz-peaked spectrum (GPS) and compact-steep spectrum (CSS) sources, which have been hypothesized to be the precursors to massive radio galaxies. Our sample more than doubles the number of known peaked-spectrum candidates, and 95% of our sample have a newly characterized spectral peak. We highlight that some GPS sources peaking above 5 GHz have had multiple epochs of nuclear activity, and demonstrate the possibility of identifying high redshift ($z > 2$) galaxies via steep optically thin spectral indices and low observed peak frequencies. The distribution of the optically thick spectral indices of our sample is consistent with past GPS/CSS samples but with a large dispersion, suggesting that the spectral peak is a product of an inhomogeneous environment that is individualistic. We find no dependence of observed peak frequency with redshift, consistent with the peaked-spectrum sample comprising both local CSS sources and high-redshift GPS sources. The 5 GHz luminosity distribution lacks the brightest GPS and CSS sources of previous samples, implying that a convolution of source evolution and redshift influences the type of peaked-spectrum sources identified below 1 GHz. Finally, we discuss sources with optically thick spectral indices that exceed the synchrotron self-absorption limit.Peer reviewedFinal Accepted Versio

Competitive Performance of Transgenic Wheat Resistant to Powdery Mildew

Genetically modified (GM) plants offer an ideal model system to study the influence of single genes that confer constitutive resistance to pathogens on the ecological behaviour of plants. We used phytometers to study competitive interactions between GM lines of spring wheat Triticum aestivum carrying such genes and control lines. We hypothesized that competitive performance of GM lines would be reduced due to enhanced transgene expression under pathogen levels typically encountered in the field. The transgenes pm3b from wheat (resistance against powdery mildew Blumeria graminis) or chitinase and glucanase genes from barley (resistance against fungi in general) were introduced with the ubiquitin promoter from maize (pm3b and chitinase genes) or the actin promoter from rice (glucanase gene). Phytometers of 15 transgenic and non-transgenic wheat lines were transplanted as seedlings into plots sown with the same 15 lines as competitive environments and subject to two soil nutrient levels. Pm3b lines had reduced mildew incidence compared with control lines. Chitinase and chitinase/glucanase lines showed the same high resistance to mildew as their control in low-nutrient treatment and slightly lower mildew rates than the control in high-nutrient environment. Pm3b lines were weaker competitors than control lines. This resulted in reduced yield and seed number. The Pm3b line with the highest transgene expression had 53.2% lower yield than the control whereas the Pm3b line which segregated in resistance and had higher mildew rates showed only minor costs under competition. The line expressing both chitinase and glucanase genes also showed reduced yield and seed number under competition compared with its control. Our results suggest that single transgenes conferring constitutive resistance to pathogens can have ecological costs and can weaken plant competitiveness even in the presence of the pathogen. The magnitude of these costs appears related to the degree of expression of the transgenes