Natural Language Processing in Electronic Health Records in Relation to Healthcare Decision-making: A Systematic Review

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification

The United Kingdom and British Empire: A Figurational Approach

Drawing upon the work of Norbert Elias and the process [figurational] sociology perspective, this article examines how state formation processes are related to, and, affected by, expanding and declining chains of international interdependence. In contrast to civic and ethnic conceptions, this approach focuses on the emergence of the nation/nation-state as grounded in broader processes of historical and social development. In doing so, state formation processes within the United Kingdom are related to the expansion and decline of the British Empire. That is, by focusing on the functional dynamics that are embedded in collective groups, one is able to consider how the UK’s ‘state’ and ‘imperial’ figurations were interdependently related to changes in both the UK and the former British Empire. Consequently, by locating contemporary UK relations in the historical context of former imperial relationships, nationalism studies can go ‘beyond’ the nation/nation-state in order to include broader processes of imperial expansion and decline. Here, the relationship between empire and nationalism can offer a valuable insight into contemporary political movements, especially within former imperial groups

A Randomised Trial Comparing Genotypic and Virtual Phenotypic Interpretation of HIV Drug Resistance: The CREST Study

OBJECTIVES: The aim of this study was to compare the efficacy of different HIV drug resistance test reports (genotype and virtual phenotype) in patients who were changing their antiretroviral therapy (ART). DESIGN: Randomised, open-label trial with 48-week followup. SETTING: The study was conducted in a network of primary healthcare sites in Australia and New Zealand. PARTICIPANTS: Patients failing current ART with plasma HIV RNA > 2000 copies/mL who wished to change their current ART were eligible. Subjects were required to be > 18 years of age, previously treated with ART, have no intercurrent illnesses requiring active therapy, and to have provided written informed consent. INTERVENTIONS: Eligible subjects were randomly assigned to receive a genotype (group A) or genotype plus virtual phenotype (group B) prior to selection of their new antiretroviral regimen. OUTCOME MEASURES: Patient groups were compared for patterns of ART selection and surrogate outcomes (plasma viral load and CD4 counts) on an intention-to-treat basis over a 48-week period. RESULTS: Three hundred and twenty seven patients completing > one month of followup were included in these analyses. Resistance tests were the primary means by which ART regimens were selected (group A: 64%, group B: 62%; p = 0.32). At 48 weeks, there were no significant differences between the groups for mean change from baseline plasma HIV RNA (group A: 0.68 log copies/mL, group B: 0.58 log copies/mL; p = 0.23) and mean change from baseline CD4+ cell count (group A: 37 cells/mm(3), group B: 50 cells/mm(3); p = 0.28). CONCLUSIONS: In the absence of clear demonstrated benefits arising from the use of the virtual phenotype interpretation, this study suggests resistance testing using genotyping linked to a reliable interpretive algorithm is adequate for the management of HIV infection

Role of the androgen receptor in breast cancer and preclinical analysis of enzalutamide

INTRODUCTION: The androgen receptor (AR) is widely expressed in breast cancers and has been proposed as a therapeutic target in estrogen receptor alpha (ER) negative breast cancers that retain AR. However, controversy exists regarding the role of AR, particularly in ER + tumors. Enzalutamide, an AR inhibitor that impairs nuclear localization of AR, was used to elucidate the role of AR in preclinical models of ER positive and negative breast cancer. METHODS: We examined nuclear AR to ER protein ratios in primary breast cancers in relation to response to endocrine therapy. The effects of AR inhibition with enzalutamide were examined in vitro and in preclinical models of ER positive and negative breast cancer that express AR. RESULTS: In a cohort of 192 women with ER + breast cancers, a high ratio of AR:ER (≥2.0) indicated an over four fold increased risk for failure while on tamoxifen (HR = 4.43). The AR:ER ratio had an independent effect on risk for failure above ER % staining alone. AR:ER ratio is also an independent predictor of disease-free survival (HR = 4.04, 95% CI: 1.68, 9.69; p = 0.002) and disease specific survival (HR = 2.75, 95% CI: 1.11, 6.86; p = 0.03). Both enzalutamide and bicalutamide inhibited 5-alpha-dihydrotestosterone (DHT)-mediated proliferation of breast cancer lines in vitro; however, enzalutamide uniquely inhibited estradiol (E2)-mediated proliferation of ER+/AR + breast cancer cells. In MCF7 xenografts (ER+/AR+) enzalutamide inhibited E2-driven tumor growth as effectively as tamoxifen by decreasing proliferation. Enzalutamide also inhibited DHT- driven tumor growth in both ER positive (MCF7) and negative (MDA-MB-453) xenografts, but did so by increasing apoptosis. CONCLUSIONS: AR to ER ratio may influence breast cancer response to traditional endocrine therapy. Enzalutamide elicits different effects on E2-mediated breast cancer cell proliferation than bicalutamide. This preclinical study supports the initiation of clinical studies evaluating enzalutamide for treatment of AR(+) tumors regardless of ER status, since it blocks both androgen- and estrogen- mediated tumor growth

Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

The Department of Energy site at Hanford, WA, has been historically impacted by U and Cr from the nuclear weapons industry. In an attempt to stimulate microbial remediation of these metals, in-situ lactate enrichment experiments are ongoing. In order to bridge the gap from the laboratory to the field, we inoculated triplicate anaerobic, continuous-flow glass reactors with groundwater collected from well Hanford 100-H in order to obtain a stable, enriched community while selecting for metal-reducing bacteria. Each reactor was fed from a single carboy containing defined media with 30 mM lactate at a rate of 0.223 ml/min under continuous nitrogen flow at 9 ml/min. Cell counts, organic acids, gDNA (for qPCR and pyrosequencing) and gases were sampled during the experiment. Cell counts remained low (less than 1x107 cells/ml) during the first two weeks of the experiment, but by day 20, had reached a density greater than 1x108 cells/ml. Metabolite analysis showed a decrease in the lactate concentrations over time. Pyruvate concentrations ranged from 20-40 uM the first week of the experiment then was undetectable after day 10. Likewise, formate appeared in the reactors during the first week with concentrations of 1.48-1.65 mM at day 7 then the concentrations decreased to 0.69-0.95 on day 10 and were undetectable on day 15. Acetate was present in low amounts on day 3 (0.15-0.33 mM) and steadily increased to 3.35-5.22 mM over time. Similarly, carbon dioxide was present in low concentrations early on and increased to 0.28-0.35 mM as the experiment progressed. We also were able to detect low amounts of methane (10-20 uM) during the first week of the experiment, but by day 10 the methane was undetectable. From these results and pyrosequencing analysis, we conclude that a shift in the microbial community dynamics occurred over time to eventually form a stable and enriched microbial community. Comprehensive investigations such as these allow for the examination of not only which nutrient source will accelerate site remediation, but also provide insight to evaluate remediation strategies through which enriched community members are important for bioremediation

High-resolution bathymetries and shorelines for the Great Lakes of the White Nile basin

This article is licensed under a Creative Commons Attribution 4.0 International License.HRBS-GLWNB 2020 presents the first open-source and high-resolution bathymetry, shoreline, and water level data for Lakes Victoria, Albert, Edward, and George in East Africa. For each Lake, these data have three primary products collected for this project. The bathymetric datasets were created from approximately 18 million acoustic soundings. Over 8,200 km of shorelines are delineated across the three lakes from high-resolution satellite systems and uncrewed aerial vehicles. Finally, these data are tied together by creating lake surface elevation models collected from GPS and altimeter measures. The data repository includes additional derived products, including surface areas, water volumes, shoreline lengths, lake elevation levels, and geodetic information. These data can be used to make allocation decisions regarding the freshwater resources within Africa, manage food resources on which many tens of millions of people rely, and help preserve the region’s endemic biodiversity. Finally, as these data are tied to globally consistent geodetic models, they can be used in future global and regional climate change models.ECU Open Access Publishing Support Fun

Serial killing and the postmodern self

© 2006 by SAGE PublicationsThe self has been a consistently central theme in philosophy and the social sciences and, in the last decades of the 20th century, the fragmentation of the modern self has engendered extensive academic commentary. In order to contribute to current discussions about self, it is perhaps most effective to map the transformation of a single representation of the self in contemporary culture. As a cultural ‘flashpoint’, the serial killer could provide an apposite analytical focus. Drawing critically on Mark Seltzer's work on serial killers this article interprets serial killing as a form of commodified transgression. In contrast to the modern self, established through state-institutionalized routines, serial killers establish their identities through ecstatic intercourse. These acts of bodily and ethical transgression are facilitated by the use of commodities. In this way, the serial killer represents a self which is consistent with the colonization of interpersonal relations by multinational capital. The serial killer signifies the appearance of a postmodern self

A Significantly off-center Ni56 Distribution for the Low-Luminosity Type Ia Supernova SN 2016brx from the 100IAS survey

We present nebular-phase spectra of the Type Ia supernova (SN Ia) 2016brx, a member of the 1991bg-like subclass that lies at the faint end of the SN Ia luminosity function. Nebular spectra are available for only three other 1991bg-like SNe, and their Co line centers are all within <~ 500 km/s of each other. In contrast, the nebular Co line center of SN 2016brx is blue-shifted by >1500 km/s compared to them and by ~1200 km/s compared to the rest frame. This is a significant shift relative to the narrow nebular line velocity dispersion of <~ 2000 km/s of these SNe. The large range of nebular line shifts implies that the Ni56 in the ejecta of SN 1991bg-like events is off-center by ~1000 km/s rather than universally centrally confined as previously suggested. With the addition of SN 2016brx, the Co nebular line shapes of 1991bg-like objects appear to connect with the brighter SNe Ia that show double-peak profiles, hinting at a continuous distribution of line profiles among SNe Ia. One class of models to produce both off-center and bi-modal Ni56 distributions is collisions of white dwarfs with unequal and equal masses.Comment: Minor Changes. Accepted by MNRAS Lette

The impact of a special school placement on self-perceptions of confidence and competence among prospective PE teachers

School-based placements are often used as a way of preparing prospective teachers for the demands of their future role. However, little is known about the impact of such situated learning experiences on prospective PE teachers’ confidence and competence. To the best of our knowledge, this article is the first of its kind to explore prospective teachers’ views of, and experiences within, special schools in order to identify the experiential mechanisms that shape self-perceptions of competence and confidence when teaching pupils with special educational needs and disabilities in PE. Thirty-two final year undergraduate students participated in focus group interviews and were selected on the basis that they: (1) were studying a Special Educational Needs and Disability in PE undergraduate module; (2) aspired to be a PE teacher; and (3) had attended six half-days of placement in a special school. All focus group transcripts were subjected to open, axial and selective coding in order to identify themes and sub-themes. The themes that were constructed from the analysis were: impact of placement role on confidence and competence; impact of knowing pupils’ needs and capabilities; conceptualising confidence and perceptions of its development; and conceptualising competence and perceptions of its development. We use these themes to discuss the usefulness of special school-based placements for preparing aspiring teachers for their role as inclusive educators

Updated standardized definitions for efficacy endpoints in adjuvant breast cancer clinical trials: STEEP Version 2.0

Purpose The Standardized Definitions for Efficacy End Points (STEEP) criteria, established in 2007, provide standardized definitions of adjuvant breast cancer clinical trial end points. Given the evolution of breast cancer clinical trials and improvements in outcomes, a panel of experts reviewed the STEEP criteria to determine whether modifications are needed.Methods We conducted systematic searches of ClinicalTrials.gov for adjuvant systemic and local-regional therapy trials for breast cancer to investigate if the primary end points reported met STEEP criteria. On the basis of common STEEP deviations, we performed a series of simulations to evaluate the effect of excluding non-breast cancer deaths and new nonbreast primary cancers from the invasive disease-free survival end point.Results Among 11 phase III breast cancer trials with primary efficacy end points, three had primary end points that followed STEEP criteria, four used STEEP definitions but not the corresponding end point names, and four used end points that were not included in the original STEEP manuscript. Simulation modeling demonstrated that inclusion of second nonbreast primary cancer can increase the probability of incorrect inferences, can decrease power to detect clinically relevant efficacy effects, and may mask differences in recurrence rates, especially when recurrence rates are low.Conclusion We recommend an additional end point, invasive breast cancer-free survival, which includes all invasive disease-free survival events except second nonbreast primary cancers. This end point should be considered for trials in which the toxicities of agents are well-known and where the risk of second primary cancer is small. Additionally, we provide end point recommendations for local therapy trials, low-risk populations, noninferiority trials, and trials incorporating patient-reported outcomes