Lightweight Knowledge Representations for Automating Data Analysis

The principal goal of data science is to derive meaningful information from data. To do this, data scientists develop a space of analytic possibilities and from it reach their information goals by using their knowledge of the domain, the available data, the operations that can be performed on those data, the algorithms/models that are fed the data, and how all of these facets interweave. In this work, we take the first steps towards automating a key aspect of the data science pipeline: data analysis. We present an extensible taxonomy of data analytic operations that scopes across domains and data, as well as a method for codifying domain-specific knowledge that links this analytics taxonomy to actual data. We validate the functionality of our analytics taxonomy by implementing a system that leverages it, alongside domain labelings for 8 distinct domains, to automatically generate a space of answerable questions and associated analytic plans. In this way, we produce information spaces over data that enable complex analyses and search over this data and pave the way for fully automated data analysis

Corneal perforation in ocular graft-versus-host disease

PURPOSE: Corneal perforation is a rare, vision-threatening complication of ocular graft-versus-host disease (GVHD) and is not well understood. Our objective was to examine the clinical disease course and histopathologic correlation in patients who progressed to this outcome. METHODS: This study is a retrospective case series from four academic centers in the United States. All patients received a hematopoietic stem cell transplant (HSCT) prior to developing ocular GVHD. Variables of interest included patient demographics, time interval between HSCT and ocular events, visual acuity throughout clinical course, corticosteroid and infection prophylaxis regimens at time of corneal perforation, medical/surgical interventions, and histopathology. RESULTS: Fourteen eyes from 14 patients were analyzed. Most patients were male (86%) and Caucasian (86%), and average age at time of hematopoietic stem cell transplant was 47 years. The mean interval between hematopoietic stem cell transplant and diagnosis of ocular graft-versus-host disease was 9.5 months, and between hematopoietic stem cell transplant and corneal perforation was 37 months. Initial best-corrected visual acuity was 20/40 or better in 9 eyes, and all eyes had moderate or poor visual outcomes despite aggressive management, including corneal gluing in all patients followed by keratoplasty in 8 patients. The mean follow-up after perforation was 34 months (range 2-140 months). Oral prednisone was used prior to perforation in 11 patients (79%). On histopathology, representative specimens in the acute phase demonstrated ulcerative keratitis with perforation but minimal inflammatory cells and no microorganisms, consistent with sterile corneal melt in the setting of immunosuppression; and in the healed phase, filling in of the perforation site with fibrous scar. CONCLUSIONS: In these patients, an extended time interval was identified between the diagnosis of ocular graft-versus-host disease and corneal perforation. This represents a critical window to potentially prevent this devastating outcome. Further study is required to identify those patients at greatest risk as well as to optimize prevention strategies

An exploration of the perceptions of caring held by students entering nursing programmes in the United Kingdom: A longitudinal qualitative study phase 1

In a climate of intense international scrutiny of healthcare and nursing in particular, there is an urgent need to identify, foster and support a caring disposition in student nurses worldwide. Yet relatively little is known about how core nursing values are shaped during education programmes and this warrants further investigation. This longitudinal study commencing in February 2013 examines the impact of an innovative nursing curriculum based on a humanising framework (Todres et al. 2009) and seeks to establish to what extent professional and core values are shaped over the duration of a three year nursing programme. This paper reports on Phase One which explores student nurses' personal values and beliefs around caring and nursing at the start of their programme. Undergraduate pre-registration nursing students from two discrete programmes (Advanced Diploma and BSc (Honours) Nursing with professional registration) were recruited to this study. Utilising individual semi-structured interviews, data collection commenced with February 2013 cohort (n = 12) and was repeated with February 2014 (n = 24) cohort. Findings from Phase One show that neophyte student nurses are enthusiastic about wanting to care and aspire to making a difference to patients and their families. This research promises to offer contributions to the debate around what caring means and in particular how it is understood by student nurses. Findings will benefit educators and students which will ultimately impact positively on those in receipt of healthcare

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Incidence, prevalence, and survival in patients with Langerhans cell histiocytosis: a national registry study from England, 2013-2019

This analysis is the largest population-based study to date to provide contemporary and comprehensive epidemiological estimates of all third edition of the International Classification of Diseases for Oncology (ICD-O-3) coded Langerhans cell histiocytosis (LCH) from England. People of all ages were identified from the National Cancer Registration Dataset using ICD-O-3 morphologies 9751–9754 for neoplasms diagnosed in 2013–2019. A total of 658 patients were identified, of whom 324 (49%) were children aged <15 years. The age-standardised incidence rate was 4.46 (95% confidence interval [CI] 3.99–4.98) per million children and 1.06 (95% CI 0.94–1.18) per million adults aged ≥15 years. Prevalence of LCH was 9.95 (95% CI 9.14–10.81) per million persons at the end of 2019. The 1-year overall survival (OS) was 99% (95% CI 97%–100%) for children and 90% (95% CI 87%–93%) for adults. Those aged ≥60 years had poorer OS than those aged <15 years (hazard ratio [HR] 22.12, 95% CI 7.10–68.94; p < 0.001). People in deprived areas had lower OS than those in the least deprived areas (HR 5.36, 95% CI 1.16–24.87; p = 0.03). There will inevitably be other environmental factors and associations yet to be identified, and the continued standardised data collection will allow further evaluation of data over time. This will be increasingly important with developments in LCH management following the large collaborative international trials such as LCH IV

Assessing team performance - Markers and methods

Optimal team performance in healthcare is vital to avoid error. Assessing teams improves their performance by providing accurate feedback to team members. To construct an assessment tool that is both valid and reliable, it is necessary to understand what should be measured, when it should be measured and the context of the team performance. Current assessment methods include observation of behavioural markers, self-assessment by team members, event-based coding, and narrative field notes. Future assessment tools should incorporate best practice elements such as having a theoretical or empirical basis for teamwork competencies, measuring process rather than outcomes, analysing rather than describing performance, capturing non-observable cognitions, distinguishing individual from collective team behaviours, using trained raters, and linking assessment to learning objectives

Identifying metabolite markers for preterm birth in cervicovaginal fluid by magnetic resonance spectroscopy

Introduction Preterm birth (PTB) may be preceded by changes in the vaginal microflora and metabolite profiles. Objectives We sought to characterise the metabolite profile of cervicovaginal fluid (CVF) of pregnant women by 1H NMR spectroscopy, and assess their predictive value for PTB. Methods A pair of high-vaginal swabs was obtained from pregnant women with no evidence of clinical infection and grouped as follows: asymptomatic low risk (ALR) women with no previous history of PTB, assessed at 20–22 gestational weeks, g.w., n = 83; asymptomatic high risk (AHR) women with a previous history of PTB, assessed at both 20–22 g.w., n = 71, and 26–28 g.w., n = 58; and women presenting with symptoms of preterm labor (PTL) (SYM), assessed at 24–36 g.w., n = 65. Vaginal secretions were dissolved in phosphate buffered saline and scanned with a 9.4 T NMR spectrometer. Results Six metabolites (lactate, alanine, acetate, glutamine/glutamate, succinate and glucose) were analysed. In all study cohorts vaginal pH correlated with lactate integral (r = -0.62, p\0.0001). Lactate integrals were higher in the term ALR compared to the AHR (20–22 g.w.) women (p = 0.003). Acetate integrals were higher in the preterm versus term women for the AHR (20–22 g.w.) (p = 0.048) and SYM (p = 0.003) groups; and was predictive of PTB\37 g.w. (AUC 0.78; 95 % CI 0.61–0.95), and delivery within 2 weeks of the index assessment (AUC 0.84; 95 % CI 0.64–1) in the SYM women, whilst other metabolites were not. Conclusion High CVF acetate integral of women with symptoms of PTL appears predictive of preterm delivery, as well as delivery within 2 weeks of presentation

Experimentally assessing the effect of search effort on snare detectability

Reducing threats to biodiversity is the key objective of ranger patrols in protected areas. However, efforts can be hampered by rangers' inability to detect threats, and poor understanding of threat abundance and distribution in a landscape. Snares are particularly problematic due to their cryptic nature and limited selectivity with respect to captured animals' species, sex, or age. Using an experimental approach, we investigated the effect of search effort, habitat, season, and team on rangers' detection of snares in a tropical forest landscape. We provide an effort-detection curve, and use our findings to make preliminary predictions about snare detection under different scenarios of patrol effort. Results suggest that the overall probability of a searcher detecting any given snare in a 0.25/km2 area, assuming 60 min (or approximately 2 km) of search effort is 20% (95% CI ± 15–25%), with no significant effect of season, habitat or team. Our models suggested this would increase by approximately 10% with an additional 30mins/1 km of search effort. Our preliminary predictions of the effectiveness of different patrolling scenarios show that detection opportunities are maximised at low effort levels by deploying multiple teams to a single area, but at high effort levels deploying single teams becomes more efficient. Our results suggest that snare detectability in tropical forest landscapes is likely to be low, and may not improve dramatically with increased search effort. Given this, managers need to consider whether intensive snare-removal efforts are the best use of limited resources; the answer will depend on their underlying objectives

Global wealth disparities drive adherence to COVID-safe pathways in head and neck cancer surgery

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