Knitting Statistics Notes: Creating Teaching Materials with Data Analysis Code and Results Embedded

R is a widely used, free, open source software package for data analysis and graphics. Along with core functionality, there are many additional packages to enable specialist usage. One of these packages knitr' allows the integration of R and LaTeX code. This means that code, output and narrative are all included in one source document. Output is generated automatically from the code. If any changes are made to the data, all output is updated automatically. From a teaching perspective, this is particularly useful if you want to create notes with various graphs, statistics etc and you also want to provide the code that shows the student how to do this analysis in R. It is possible to hide either the code or the output. For example, if you are making introduction to statistics worksheets for non-statistics students, you might not want to include R code. If you are including exercises for students, you might not want to include the output and instead have them answer some questions. You can also set these options globally then by changing one option, create two versions of the document - one with solutions, one without, just from one source document

Demonstration of a novel technique to quantitatively assess inflammatory mediators and cells in rat knee joints

<p>Abstract</p> <p>Background</p> <p>The inflammation that accompanies the pain and swelling associated with osteo- and rheumatoid arthritis is mediated by complex interactions of inflammatory mediators. Cytokines play a pivotal role in orchestrating many of these processes, including inflammatory cell recruitment, adhesion and activation. In addition, prostaglandins are secreted into the synovial cavity and are involved in perpetuation of local inflammation, vasodilatation and vasoconstriction, and also with bone resorption. Pre-clinical models have been developed in order to correlate to the human disease and principle among these is the adjuvant-induced arthritis model in the rat.</p> <p>Methods</p> <p>We have developed a technique to quantitatively assess the contents of synovial fluid samples from rat joints. Two needles joined together are inserted into the knee joint of anaesthetised rats and connected to a Watson-Marlow perfusion pump. Sterile saline is infused and withdrawn at 100 μl min^-1until a 250 μl sample is collected.</p> <p>Results</p> <p>Our results demonstrate up to 125 fold increases in synovial IL1α and IL1β concentrations, approximately 30 fold increases in levels of IL6 and IL10 and a 200–300 fold elevation in synovial concentrations of TNFα during FCA-induced experimental arthritis. Finally, this novel technique has demonstrated a dose-response relationship between FCA and the total cell counts of synovial perfusates.</p> <p>Conclusion</p> <p>In summary, this new technique provides a robust method for quantifying inflammatory mediators and cells from the synovial cavity itself, thereby detailing the inflammatory processes from within the capsule and excluding those processes occurring in other tissues surrounding the entire articulation.</p

A questionnaire-based study of Paediatric Dentists’ knowledge of teething signs, symptoms and management

Introduction Signs and symptoms attributed to erupting primary teeth are commonly known as “teething”. Its existence is controversial with concern that overusing this term might mask other illnesses and some treatments may be unnecessary or harmful. Parents/carers can access over-the-counter remedies and may seek professional advice. This survey-based investigation explored gaps in knowledge, training, perceptions and experiences of UK Paediatric Dentists (PDs) regarding teething in young children. Method Cross-sectional study with a convenience sample of PDs with different training levels, accessed through the British Society for Paediatric Dentistry membership lists. A 10-item questionnaire explored participants’ knowledge of teething-related issues and management. Responses are presented using descriptive statistics. Results Of 80 responding PDs (response rate 27%), 62–74% suggested drooling, irritability, oral fixation and flushed cheeks were attributed to primary tooth eruption. Fifty-eight (72%) participants were unaware of guidelines, yet 53 (66%) felt guidance was needed. Conclusion Signs and symptoms of teething might mask underlying conditions so it should be a diagnosis of exclusion. PDs attributed similar signs and symptoms to teething, as have been reported in the literature, although some commented that they did not think teething was a condition. There was a lack of awareness over guidelines

Risk of bleeding amongst warfarin and direct oral anticoagulant users prescribed immediate antibiotics for respiratory tract infection: cohort study

Purpose: Incidence of bleeding amongst warfarin and direct oral anticoagulant (DOAC) users is greater following a respiratory tract infection (RTI). It is unclear whether immediate antibiotics modify this association. We estimated the risk of bleeding amongst warfarin and DOAC users with RTI by antibiotic treatment. Methods: This retrospective cohort study used data from the Clinical Practice Research Datalink (CPRD) GOLD for adults in England prescribed warfarin or a DOAC, who sought primary care for an RTI between 1st January 2011 and 31st December 2019. Outcomes were major bleeding (hospital admission for intracranial or gastrointestinal bleeding), and non‐major bleeding (hospital admission or General Practice consult for epistaxis, haemoptysis, or haematuria). Cox models derived hazard ratios (HRs) and 95% confidence intervals (CIs) for each outcome, adjusting for confounders using inverse probability of treatment weighting. Results: Of 14 817 warfarin and DOAC users consulting for an RTI, 8768 (59%) were prescribed immediate antibiotics and 6049 (41%) were not. Approximately 49% were female, and median age was 76 years. Antibiotics were associated with reduced risk of major bleeding (adjusted HR 0.38, 95% CI 0.25 to 0.58). This was consistent across several sensitivity analyses. Antibiotics were also associated with a reduced risk of non‐major bleeding (adjusted HR 0.78, 95% CI 0.61 to 0.99). Conclusions: Immediate antibiotics were associated with reduced risk of bleeding amongst warfarin and DOAC users with an RTI. Further work is needed to understand mechanisms and confirm whether a lower threshold for antibiotic use for RTI in this population may be beneficial

Where there is no hospital: improving the notification of community deaths

Globally, an estimated two-thirds of all deaths occur in the community, the majority of which are not attended by a physician and remain unregistered. Identifying and registering these deaths in civil registration and vital statistics (CRVS) systems, and ascertaining the cause of death, is thus a critical challenge to ensure that policy benefits from reliable evidence on mortality levels and patterns in populations. In contrast to traditional processes for registration, death notification can be faster and more efficient at informing responsible government agencies about the event and at triggering a verbal autopsy for ascertaining cause of death. Thus, innovative approaches to death notification, tailored to suit the setting, can improve the availability and quality of information on community deaths in CRVS systems.; Here, we present case studies in four countries (Bangladesh, Colombia, Myanmar and Papua New Guinea) that were part of the initial phases of the Bloomberg Data for Health Initiative at the University of Melbourne, each of which faces unique challenges to community death registration. The approaches taken promote improved notification of community deaths through a combination of interventions, including integration with the health sector, using various notifying agents and methods, and the application of information and communication technologies. One key factor for success has been the smoothing of processes linking notification, registration and initiation of a verbal autopsy interview. The processes implemented champion more active notification systems in relation to the passive systems commonly in place in these countries.; The case studies demonstrate the significant potential for improving death reporting through the implementation of notification practices tailored to a country's specific circumstances, including geography, cultural factors, structure of the existing CRVS system, and available human, information and communication technology resources. Strategic deployment of some, or all, of these innovations can result in rapid improvements to death notification systems and should be trialled in other settings

Myocardial infarction and stroke subsequent to urinary tract infection (MISSOURI): protocol for a self-controlled case series using linked electronic health records

Introduction: There is increasing interest in the relationship between acute infections and acute cardiovascular events. Most previous research has focused on understanding whether the risk of acute cardiovascular events increases following a respiratory tract infection. The relationship between urinary tract infections (UTIs) and acute cardiovascular events is less well studied. Therefore, the aim of this study is to determine whether there is a causal relationship between UTI and acute myocardial infarction (MI) or stroke. Methods and analysis: We will undertake a self-controlled case series study using linked anonymised general practice, hospital admission and microbiology data held within the Secure Anonymised Information Linkage (SAIL) Databank. Self-controlled case series is a relatively novel study design where individuals act as their own controls, thereby inherently controlling for time-invariant confounders. Only individuals who experience an exposure and outcome of interest are included. We will identify individuals in the SAIL Databank who have a hospital admission record for acute MI or stroke during the study period of 2010–2020. Individuals will need to be aged 30–100 during the study period and be Welsh residents for inclusion. UTI will be identified using general practice, microbiology and hospital admissions data. We will calculate the incidence of MI and stroke in predefined risk periods following an UTI and in ‘baseline’ periods (without UTI exposure) and use conditional Poisson regression models to derive incidence rate ratios. Ethics and dissemination: Data access, research permissions and approvals have been obtained from the SAIL independent Information Governance Review Panel, project number 0972. Findings will be disseminated through conferences, blogs, social media threads and peer-reviewed journals. Results will be of interest internationally to primary and secondary care clinicians who manage UTIs and may inform future clinical trials of preventative therapy

Developing and testing a measure of consultation-based reassurance for people with low back pain in primary care:a cross-sectional study

BACKGROUND: Reassurance from physicians is commonly recommended in guidelines for the management of low back pain (LBP), but the process of reassurance and its impact on patients is poorly researched. We aimed to develop a valid and reliable measure of the process of reassurance during LBP consultations. METHODS: Items representing the data-gathering stage of the consultation and affective and cognitive reassurance were generated from literature on physician-patient communication and piloted with expert researchers and physicians, a Patient and Public Involvement group, and LBP patients to form a questionnaire. Patients presenting for LBP at 43 General Practice surgeries were sent the questionnaire. The questionnaire was analysed with Rasch modelling, using two samples from the same population of recent LBP consultations: the first (n = 157, follow-up n = 84) for exploratory analysis and the second (n = 162, follow-up n = 74) for confirmatory testing. Responses to the questionnaire were compared with responses to satisfaction and enablement scales to assess the external validity of the items, and participants completed the questionnaire again one-week later to assess test-retest reliability. RESULTS: The questionnaire was separated into four subscales: data-gathering, relationship-building, generic reassurance, and cognitive reassurance, each containing three items. All subscales showed good validity within the Rasch models, and good reliability based on person- and item-separations and test-retest reliability. All four subscales were significantly positively correlated with satisfaction and enablement for both samples. The final version of the questionnaire is presented here. CONCLUSIONS: Overall, the measure has demonstrated a good level of validity and generally acceptable reliability. This is the first measure to focus specifically on reassurance for LBP in primary care settings, and will enable researchers to further understanding of what is reassuring within the context of low back pain consultations, and how outcomes are affected by different types of reassurance. Additionally, the measure may provide a useful training and audit tool for physicians. The new measure requires testing in prospective cohorts, and would benefit from further validation against ethnographic observation of consultations in real time