Using machine learning to standardize medication records in a pan-Canadian electronic medical record database: a data-driven algorithm study focused on antibiotics prescribed in primary care.

BACKGROUND: Most antibiotics dispensed by community pharmacies in Canada are prescribed by family physicians, but using the prescribing information contained within primary care electronic medical records (EMRs) for secondary purposes can be challenging owing to variable data quality. We used antibiotic medications as an exemplar to validate a machine-learning approach for cleaning and coding medication data in a pan-Canadian primary care EMR database. METHODS: The Canadian Primary Care Sentinel Surveillance Network database contained an estimated 42 million medication records, which we mapped to an Anatomic Therapeutic Chemical (ATC) code by applying a semisupervised classification model developed using reference standard labels derived from the Health Canada Drug Product Database. We validated the resulting ATC codes in a subset of antibiotic records (16 119 unique strings) to determine whether the algorithm correctly classified the medication according to manual review of the original medication record. RESULTS: In the antibiotic subset, the algorithm showed high validity (sensitivity 99.5%, specificity 92.4%, positive predictive value 98.6%, negative predictive value 97.0%) in classifying whether the medication was an antibiotic. INTERPRETATION: Our machine-learning algorithm classified unstructured antibiotic medication data from primary care with a high degree of accuracy. Access to cleaned EMR data can support important secondary uses, including community-based antibiotic prescribing surveillance and practice improvement.

The What and the How: A pilot study of feedback from service providers and consumers about service development in new urban mental health hub.

OBJECTIVE: An inner-city hospital purchased a local hotel to provide support, digital engagement, skill development groups and referrals to partner agencies. Being aware of the hotel's importance to the local community, we sought feedback on a model of care relevant to perceived gaps and needs in support for mental health. METHODS: Four online focus groups included healthcare professionals, nominated opinion leaders from local Non-Government Organisations (NGOs), consumers and carers to reflect a range of views. Focus group data were qualitatively analysed. RESULTS: Participants made useful suggestions about WHAT educational, preventative and therapeutic services were needed. They emphasised the importance of HOW people engage with the service, the balance between accessibility and security. Other themes included targeting people with limited health literacy, integration with existing services, building on site heritage and ongoing evaluation of objectives and needs. CONCLUSIONS: This pilot study demonstrated clear support for providing safe and welcoming access to services, with resources and access to services to improve their health and wellbeing built on principles of social justice and inclusion. Participants had constructive ideas of what was needed, and ongoing patient and public research is anticipated.

Fluid Optimisation in Emergency Laparotomy (FLO-ELA) Trial: study protocol for a multi-centre randomised trial of cardiac output-guided fluid therapy compared to usual care in patients undergoing major emergency gastrointestinal surgery.

INTRODUCTION: Postoperative morbidity and mortality in patients undergoing major emergency gastrointestinal surgery are a major burden on healthcare systems. Optimal management of perioperative intravenous fluids may reduce mortality rates and improve outcomes from surgery. Previous small trials of cardiac-output guided haemodynamic therapy algorithms in patients undergoing gastrointestinal surgery have suggested this intervention results in reduced complications and a modest reduction in mortality. However, this existing evidence is based mainly on elective (planned) surgery, with little evaluation in the emergency setting. There are fundamental clinical and pathophysiological differences between the planned and emergency surgical setting which may influence the effects of this intervention. A large definitive trial in emergency surgery is needed to confirm or refute the potential benefits observed in elective surgery and to inform widespread clinical practice. METHODS: The FLO-ELA trial is a multi-centre, parallel-group, open, randomised controlled trial. 3138 patients aged 50 and over undergoing major emergency gastrointestinal surgery will be randomly allocated in a 1:1 ratio using minimisation to minimally invasive cardiac output monitoring to guide protocolised administration of intra-venous fluid, or usual care without cardiac output monitoring. The trial intervention will be carried out during surgery and for up to 6 h postoperatively. The trial is funded through an efficient design call by the National Institute for Health and Care Research Health Technology Assessment (NIHR HTA) programme and uses existing routinely collected datasets for the majority of data collection. The primary outcome is the number of days alive and out of hospital within 90 days of randomisation. Participants and those delivering the intervention will not be blinded to treatment allocation. Participant recruitment started in September 2017 with a 1-year internal pilot phase and is ongoing at the time of publication. DISCUSSION: This will be the largest contemporary randomised trial examining the effectiveness of perioperative cardiac output-guided haemodynamic therapy in patients undergoing major emergency gastrointestinal surgery. The multi-centre design and broad inclusion criteria support the external validity of the trial. Although the clinical teams delivering the trial interventions will not be blinded, significant trial outcome measures are objective and not subject to detection bias. TRIAL REGISTRATION: ISRCTN 14729158. Registered on 02 May 2017.

A Multimodal Approach to Training Coronavirus Disease (COVID-19) Processes Across Four Intensive Care Units.

Background: Coronavirus disease (COVID-19) required innovative training strategies for emergent aerosol generating procedures in intensive care units. This manuscript summarizes institutional operationalization of COVID-specific training, standardized across four intensive care units. Methods & Results: An interdisciplinary team collaborated with the Simulator Program and OpenPediatrics refining logistics using process maps, walkthroughs and simulation. A multimodal approach to information dissemination, high-volume team training in modified resuscitation practices and technical skill acquisition included instructional videos, training superusers, small-group simulation using a flipped classroom approach with rapid cycle deliberate practice, interactive webinars, and cognitive aids. Institutional data on application of this model are presented. Conclusion: Success was founded in interdisciplinary collaboration, resource availability and institutional buy in.

Asymbiotic in vitro seed germination, in vitro seedling development, and ex vitro acclimatization of Spiranthes.

Premise: Reproducible seed propagation and production protocols were developed for Spiranthes and related taxa to facilitate ex situ conservation practices. Methods and Results: Spiranthes seeds were scarified for 3- and 10-min intervals in 10% sodium hypochlorite solution, then cultured on three seed germination media. After germination, seedlings were given one of the three photoperiod treatments, and then planted in one of four greenhouse substrates. Seed germination ranged from 0% to 90% and occurred on all three media only after the 3-min scarification. Seedlings in the 24/0-h light/dark and 16/8-h light/dark photoperiods on P723 medium had significantly higher fresh weight than those in the dark treatment group. Ex vitro survival ranged from 55% to 95% across substrates. Conclusions: Results show that Spiranthes seeds are damaged by extended chemical scarification, are adaptable to a variety of culture media, and require light for optimal development. Further experimentation showed that the propagation protocols described here can be applied broadly within the genus.

Nasal high flow therapy use in wards in patients with chronic obstructive pulmonary disease may spare ICU resources.

Nasal high flow therapy has been previously studied for the management of acute hypoxic respiratory failure in patients with chronic obstructive pulmonary disease but the data regarding its use outside of the intensive care unit are sparse. We aimed to evaluate safety and efficacy of nasal high flow therapy outside of the intensive care unit in patients with acute hypoxic respiratory failure and known chronic obstructive pulmonary disease. We conducted a retrospective matched historic cohort study of adult patients with diagnosed chronic obstructive pulmonary disease presenting with acute hypoxic respiratory failure between December 2017 to June 2019, after the initiation of a new protocol, which allowed patients to be managed with nasal high flow therapy on the medical/surgical wards instead of transferring them to the ICU per prior standard of care. Nasal high flow therapy was initiated either in the emergency department or on the medical/surgical wards. Patients were matched with historical cohorts who were managed with prior standard of care based on age, body mass index, comorbidities, and home oxygen use. Primary outcome of interest was difference in rates of mechanical ventilation. Secondary outcomes included hospital length of stay, total number of days spent in the intensive care unit, and in-hospital mortality. A total of 90 patients met study inclusion criteria and were matched to 90 historical control patients. Among the study group, 8% required mechanical ventilation versus 9% in the control group (p = 0.79). Hospital length of stay was 7 days in study group versus 6 days in control group (p = 0.02), and in-hospital mortality was the same in both study and control groups at 12% (p = 0.99). Nineteen percent of study group patients required ICU level of care at any time during the admission compared with 49% of control group (p < 0.001). Nasal high flow therapy use in patients with acute hypoxic respiratory failure and underlying chronic obstructive pulmonary disease outside of the intensive care unit may spare ICU resources and cost without delay in definitive care such as mechanical ventilation.

Pelvic floor disorders in women who consult primary care clinics: development and validation of case definitions using primary care electronic medical records.

BACKGROUND: To date, there has been no validated method to identify cases of pelvic floor disorders in primary care electronic medical record (EMR) data. We aimed to develop and validate symptom-based case definitions for urinary incontinence, fecal incontinence and pelvic organ prolapse in women, for use in primary care epidemiologic or clinical research. METHODS: Our retrospective study used EMR data from the Southern Alberta Primary Care Research Network (SAPCReN) and the Canadian Primary Care Sentinel Surveillance Network (CPCSSN) in southern Alberta. Trained researchers remotely reviewed a random sample of EMR charts of women aged 18 years or older from 6 rural and urban clinics to validate case definitions for urinary incontinence, fecal incontinence and pelvic organ prolapse. We calculated sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), and estimated SAPCReN prevalence as appropriate. RESULTS: Charts of 900 women were included. Sensitivity was 81.9% (95% confidence interval [CI] 75.1-87.2) for urinary incontinence, 61.2% (95% CI 46.2-74.5) for fecal incontinence, and 51.8% (95% CI 40.6-62.8) for pelvic organ prolapse. Corresponding specificity values were 71.9% (95% CI 68.4-75.1), 99.2% (95% CI 98.2-99.6) and 98.8% (95% CI 97.7-99.4), PPVs 40.6% (95% CI 35.4-46.0), 81.1% (95% CI 64.3-91.4) and 81.1% (95% CI 67.6-90.1), and NPVs 94.4% (95% CI 92.1-96.1), 97.8% (95% CI 96.5-98.6) and 95.3% (95% CI 93.6-96.6). The SAPCReN-observed prevalence for urinary incontinence was 29.7% (95% CI 29.3-30.0), but the adjusted prevalence was 2.97%. INTERPRETATION: The case definition for urinary incontinence met our standard for validity (sensitivity and specificity > 70%), and the case definitions for fecal incontinence and pelvic organ prolapse had PPVs greater than 80%. The urinary incontinence definition may be used in epidemiologic research, and those for fecal incontinence and pelvic organ prolapse may be used in quality-improvement studies or creation of disease registries. Our symptom-based case definitions could also be adapted for research in other EMR settings.

Emotional capture during emotion-induced blindness is not automatic.

The present research used behavioral and event-related brain potentials (ERP) measures to determine whether emotional capture is automatic in the emotion-induced blindness (EIB) paradigm. The first experiment varied the priority of performing two concurrent tasks: identifying a negative or neutral picture appearing in a rapid serial visual presentation (RSVP) stream of pictures and multiple object tracking (MOT). Results showed that increased attention to the MOT task resulted in decreased accuracy for identifying both negative and neutral target pictures accompanied by decreases in the amplitude of the P3b component. In contrast, the early posterior negativity (EPN) component elicited by negative pictures was unaffected by variations in attention. Similarly, there was a decrement in MOT performance for dual-task versus single task conditions but no effect of picture type (negative vs neutral) on MOT accuracy which isn't consistent with automatic emotional capture of attention. However, the MOT task might simply be insensitive to brief interruptions of attention. The second experiment used a more sensitive reaction time (RT) measure to examine this possibility. Results showed that RT to discriminate a gap appearing in a tracked object was delayed by the simultaneous appearance of to-be-ignored distractor pictures even though MOT performance was once again unaffected by the distractor. Importantly, the RT delay was the same for both negative and neutral distractors suggesting that capture was driven by physical salience rather than emotional salience of the distractors. Despite this lack of emotional capture, the EPN component, which is thought to reflect emotional capture, was still present. We suggest that the EPN doesn't reflect capture but rather downstream effects of attention, including object recognition. These results show that capture by emotional pictures in EIB can be suppressed when attention is engaged in another difficult task. The results have important implications for understanding capture effects in EIB.

From a small local audit to a regional quality improvement project - Improving lung protective ventilation.

BACKGROUND: Lung protective ventilation with tidal volumes (VT) of 6-8 ml per kg ideal body weight have been shown to reduce mortality in patients with acute respiratory distress syndrome and reduce post-operative pulmonary complications in major abdominal surgery. Following a local audit on weight recording, the Southcoast Perioperative Audit and Research Collaboration (SPARC) conducted a regional multi-disciplinary survey on the current practice in lung protective ventilation in the Wessex region. This resulted in a quality improvement project improving lung protective ventilation across these intensive care units. METHODS: Over one-week period in January over two consecutive years, lung protective ventilation parameters of mandatory ventilated patients (above the age of 18 years) were audited in intensive care units in the Wessex region. RESULTS: A total 1843 hours of mandatory ventilation were audited. The quality improvement project led to an improvement of lung protective ventilation with an average of 30% higher duration of ventilation with VT < 8 ml/kg ideal body weight. There was a suggestion that documentation of height and weight on admission to intensive care units improved compliance with lung protective ventilation. CONCLUSIONS: Adherence to lung protective ventilation is variable across intensive care units but can be improved by recording patient's weight and height accurately and using simple chart to help calculate the appropriate tidal volume. Additionally, this project demonstrates how a regional audit and quality improvement network can help to facilitate regional quality improvement.

Nitrogen losses to the environment following food-based digestate and compost applications to agricultural land.

The anaerobic digestion of food waste for energy recovery produces a nutrient-rich digestate which is a valuable source of crop available nitrogen (N). As with any 'new' material being recycled to agricultural land it is important to develop best management practices that maximise crop available N supply, whilst minimising emissions to the environment. In this study, ammonia (NH3) and nitrous oxide (N2O) emissions to air and nitrate (NO3-) leaching losses to water following digestate, compost and livestock manure applications to agricultural land were measured at 3 sites in England and Wales. Ammonia emissions were greater from applications of food-based digestate (c.40% of total N applied) than from livestock slurry (c.30% of total N applied) due to its higher ammonium-N content (mean 5.6 kg/t compared with 1-2 kg/t for slurry) and elevated pH (mean 8.3 compared with 7.7 for slurry). Whilst bandspreading was effective at reducing NH3 emissions from slurry compared with surface broadcasting it was not found to be an effective mitigation option for food-based digestate in this study. The majority of the NH3 losses occurred within 6 h of spreading highlighting the importance of rapid soil incorporation as a method for reducing NH3 emissions. Nitrous oxide losses from food-based digestates were low, with emission factors all less than the IPCC default value of 1% (mean 0.45 ± 0.15%). Overwinter NO3- leaching losses from food-based digestate were similar to those from pig slurry, but much greater than from pig farmyard manure or compost. Both gaseous N losses and NO3- leaching from green and green/food composts were low, indicating that, in these terms, compost can be considered as an 'environmentally benign' material. These findings have been used in the development of best practice guidelines which provide a framework for the responsible use of digestates and composts in agriculture.

Cometary science after Rosetta.

The European Space Agency's Rosetta mission ended operations on 30 September 2016 having spent over 2 years in close proximity to its target comet, 67P/Churyumov-Gerasimenko. Shortly before this, in summer 2016, a discussion meeting was held to examine how the results of the mission could be framed in terms of cometary and solar system science in general. This paper provides a brief history of the Rosetta mission, and gives an overview of the meeting and the contents of this associated special issue.This article is part of the themed issue 'Cometary science after Rosetta'.

Development of a validated algorithm for the diagnosis of paediatric asthma in electronic medical records.

An accurate estimation of the prevalence of paediatric asthma in Alberta and elsewhere is hampered by uncertainty regarding disease definition and diagnosis. Electronic medical records (EMRs) provide a rich source of clinical data from primary-care practices that can be used in better understanding the occurrence of the disease. The Canadian Primary Care Sentinel Surveillance Network (CPCSSN) database includes cleaned data extracted from the EMRs of primary-care practitioners. The purpose of the study was to develop and validate a case definition of asthma in children 1-17 who consult family physicians, in order to provide primary-care estimates of childhood asthma in Alberta as accurately as possible. The validation involved the comparison of the application of a theoretical algorithm (to identify patients with asthma) to a physician review of records included in the CPCSSN database (to confirm an accurate diagnosis). The comparison yielded 87.4% sensitivity, 98.6% specificity and a positive and negative predictive value of 91.2% and 97.9%, respectively, in the age group 1-17 years. The algorithm was also run for ages 3-17 and 6-17 years, and was found to have comparable statistical values. Overall, the case definition and algorithm yielded strong sensitivity and specificity metrics and was found valid for use in research in CPCSSN primary-care practices. The use of the validated asthma algorithm may improve insight into the prevalence, diagnosis, and management of paediatric asthma in Alberta and Canada.

Feasibility of Using Low-Cost Motion Capture for Automated Screening of Shoulder Motion Limitation after Breast Cancer Surgery.

OBJECTIVE: To determine if a low-cost, automated motion analysis system using Microsoft Kinect could accurately measure shoulder motion and detect motion impairments in women following breast cancer surgery. DESIGN: Descriptive study of motion measured via 2 methods. SETTING: Academic cancer center oncology clinic. PARTICIPANTS: 20 women (mean age = 60 yrs) were assessed for active and passive shoulder motions during a routine post-operative clinic visit (mean = 18 days after surgery) following mastectomy (n = 4) or lumpectomy (n = 16) for breast cancer. INTERVENTIONS: Participants performed 3 repetitions of active and passive shoulder motions on the side of the breast surgery. Arm motion was recorded using motion capture by Kinect for Windows sensor and on video. Goniometric values were determined from video recordings, while motion capture data were transformed to joint angles using 2 methods (body angle and projection angle). MAIN OUTCOME MEASURE: Correlation of motion capture with goniometry and detection of motion limitation. RESULTS: Active shoulder motion measured with low-cost motion capture agreed well with goniometry (r = 0.70-0.80), while passive shoulder motion measurements did not correlate well. Using motion capture, it was possible to reliably identify participants whose range of shoulder motion was reduced by 40% or more. CONCLUSIONS: Low-cost, automated motion analysis may be acceptable to screen for moderate to severe motion impairments in active shoulder motion. Automatic detection of motion limitation may allow quick screening to be performed in an oncologist's office and trigger timely referrals for rehabilitation.

Helminth parasites--masters of regulation.

Immune regulation by parasites is a global concept that includes suppression, diversion, and conversion of the host immune response to the benefit of the pathogen. While many microparasites escape immune attack by antigenic variation or sequestration in specialized niches, helminths appear to thrive in exposed extracellular locations, such as the lymphatics, bloodstream, or gastrointestinal tract. We review here the multiple layers of immunoregulation that have now been discovered in helminth infection and discuss both the cellular and the molecular interactions involved. Key events among the host cell population are dominance of the T-helper 2 cell (Th2) phenotype and the selective loss of effector activity, against a background of regulatory T cells, alternatively activated macrophages, and Th2-inducing dendritic cells. Increasingly, there is evidence of important effects on other innate cell types, particularly mast cells and eosinophils. The sum effect of these changes to host reactivity is to create an anti-inflammatory environment, which is most favorable to parasite survival. We hypothesize therefore that parasites have evolved specific molecular strategies to induce this conducive landscape, and we review the foremost candidate immunomodulators released by helminths, including cytokine homologs, protease inhibitors, and an intriguing set of novel products implicated in immune suppression.

Use of the ProSeal Laryngeal Mask Airway to initiate ventilation during intensive care and subsequent percutaneous tracheostomy.

The ProSeal Laryngeal Mask Airway is a supraglottic airway that aims to provide improved airway seal and separation of the gastrointestinal and respiratory tracts. We report two cases in which the ProSeal Laryngeal Mask Airway was used to initiate controlled ventilation in the intensive care unit and subsequently provide airway maintenance during percutaneous dilational tracheostomy. The first case involved a patient with a known difficult airway who had previously been impossible to intubate conventionally. In both cases, airway management and subsequent tracheostomy were performed without complication.