Development of a customised data management system for a COVID-19-adapted colorectal cancer pathway

Objectives A customised data management system was required for a rapidly implemented COVID-19-adapted colorectal cancer pathway in order to mitigate the risks of delayed and missed diagnoses during the pandemic. We assessed its performance and robustness.Methods A system was developed using Microsoft Excel (2007) to retain the spreadsheets’ intuitiveness of direct data entry. Visual Basic for Applications (VBA) was used to construct a user-friendly interface to enhance efficiency of data entry and segregate the data for operational tasks.Results Large data segregation was possible using VBA macros. Data validation and conditional formatting minimised data entry errors. Computation by the COUNT function facilitated live data monitoring.Conclusion It is possible to rapidly implement a makeshift database system with clinicians’ regular input. Large-volume data management using a spreadsheet system is possible with appropriate data definition and VBA-programmed data segregation. The described concept is applicable to any data management system construction requiring speed and flexibility in a resource-limited situation

Implementation of a risk mitigating COVID-adapted colorectal cancer pathway

No abstract available

Descriptive and Inferential Statistics in Undergraduate Data Science Research Projects

Undergraduate data science research projects form an integral component of the Wesley College science and mathematics curriculum. In this chapter, we provide examples for hypothesis testing, where statistical methods or strategies are coupled with methodologies using interpolating polynomials, probability and the expected value concept in statistics. These are areas where real-world critical thinking and decision analysis applications peak a student’s interest

CfAIR2: Near Infrared Light Curves of 94 Type Ia Supernovae

CfAIR2 is a large homogeneously reduced set of near-infrared (NIR) light curves for Type Ia supernovae (SN Ia) obtained with the 1.3m Peters Automated InfraRed Imaging TELescope (PAIRITEL). This data set includes 4607 measurements of 94 SN Ia and 4 additional SN Iax observed from 2005-2011 at the Fred Lawrence Whipple Observatory on Mount Hopkins, Arizona. CfAIR2 includes JHKs photometric measurements for 88 normal and 6 spectroscopically peculiar SN Ia in the nearby universe, with a median redshift of z~0.021 for the normal SN Ia. CfAIR2 data span the range from -13 days to +127 days from B-band maximum. More than half of the light curves begin before the time of maximum and the coverage typically contains ~13-18 epochs of observation, depending on the filter. We present extensive tests that verify the fidelity of the CfAIR2 data pipeline, including comparison to the excellent data of the Carnegie Supernova Project. CfAIR2 contributes to a firm local anchor for supernova cosmology studies in the NIR. Because SN Ia are more nearly standard candles in the NIR and are less vulnerable to the vexing problems of extinction by dust, CfAIR2 will help the supernova cosmology community develop more precise and accurate extragalactic distance probes to improve our knowledge of cosmological parameters, including dark energy and its potential time variation.Comment: 31 pages, 15 figures, 10 tables. Accepted to ApJS. v2 modified to more closely match journal versio

Primary care biomarkers and dementia in people of the Torres Strait, Australia: extended data analysis

Objective: Dementia disproportionately affects First Nations populations. Biomarkers collected in primary care may assist with determining dementia risk. Our previous underpowered study showed some suggestive associations between baseline biomarkers with follow-up dementia or cognitive impairment. The current study extended this work with a larger linked dataset. Study design and setting: Probabilistic data linkage was used to combine four baseline datasets with one follow-up assessment of dementia status 0–20 years later in a First Nations population in Australia. Mixed Effects Generalized Linear Regression models were used to test associations between baseline measures and follow-up status, accounting for repeated measures within individuals. Results: Linked data were available for 88 individuals, with 101–279 baseline observations, depending on the type of measure. Higher urinary albumin to creatine ratio was associated with greater risk of cognitive impairment/dementia, whereas body weight and key lipid markers were negatively associated. There was no clear trend when these associations were examined by timing of measurement (i.e., ≤10 years or >10 years before a dementia assessment). Conclusions: The results of this study support findings from our previous work and indicate that microalbuminuria can be an early indicator of dementia risk in this population. The weight and lipid profile findings reflect the mixed results in the published literature and require further investigation and interpretation

Post-stroke inhibition of induced NADPH oxidase type 4 prevents oxidative stress and neurodegeneration

Ischemic stroke is the second leading cause of death worldwide. Only one moderately effective therapy exists, albeit with contraindications that exclude 90% of the patients. This medical need contrasts with a high failure rate of more than 1,000 pre-clinical drug candidates for stroke therapies. Thus, there is a need for translatable mechanisms of neuroprotection and more rigid thresholds of relevance in pre-clinical stroke models. One such candidate mechanism is oxidative stress. However, antioxidant approaches have failed in clinical trials, and the significant sources of oxidative stress in stroke are unknown. We here identify NADPH oxidase type 4 (NOX4) as a major source of oxidative stress and an effective therapeutic target in acute stroke. Upon ischemia, NOX4 was induced in human and mouse brain. Mice deficient in NOX4 (Nox4(-/-)) of either sex, but not those deficient for NOX1 or NOX2, were largely protected from oxidative stress, blood-brain-barrier leakage, and neuronal apoptosis, after both transient and permanent cerebral ischemia. This effect was independent of age, as elderly mice were equally protected. Restoration of oxidative stress reversed the stroke-protective phenotype in Nox4(-/-) mice. Application of the only validated low-molecular-weight pharmacological NADPH oxidase inhibitor, VAS2870, several hours after ischemia was as protective as deleting NOX4. The extent of neuroprotection was exceptional, resulting in significantly improved long-term neurological functions and reduced mortality. NOX4 therefore represents a major source of oxidative stress and novel class of drug target for stroke therapy

Three Dimensional Numerical General Relativistic Hydrodynamics I: Formulations, Methods, and Code Tests

This is the first in a series of papers on the construction and validation of a three-dimensional code for general relativistic hydrodynamics, and its application to general relativistic astrophysics. This paper studies the consistency and convergence of our general relativistic hydrodynamic treatment and its coupling to the spacetime evolutions described by the full set of Einstein equations with a perfect fluid source. The numerical treatment of the general relativistic hydrodynamic equations is based on high resolution shock capturing schemes. These schemes rely on the characteristic information of the system. A spectral decomposition for general relativistic hydrodynamics suitable for a general spacetime metric is presented. Evolutions based on three different approximate Riemann solvers coupled to four different discretizations of the Einstein equations are studied and compared. The coupling between the hydrodynamics and the spacetime (the right and left hand side of the Einstein equations) is carried out in a treatment which is second order accurate in {\it both} space and time. Convergence tests for all twelve combinations with a variety of test beds are studied, showing consistency with the differential equations and correct convergence properties. The test-beds examined include shocktubes, Friedmann-Robertson-Walker cosmology tests, evolutions of self-gravitating compact (TOV) stars, and evolutions of relativistically boosted TOV stars. Special attention is paid to the numerical evolution of strongly gravitating objects, e.g., neutron stars, in the full theory of general relativity, including a simple, yet effective treatment for the surface region of the star (where the rest mass density is abruptly dropping to zero).Comment: 45 pages RevTeX, 34 figure

The mental health expert patient: findings from a pilot study of a generic chronic condition self-management programme for people with mental illness

Author version made available in accordance with the publisher's policyBackground Less than optimal outcomes and escalating costs for chronic conditions including mental illness have prompted calls for innovative approaches to chronic illness management. Aims This study aimed to test the feasibility and utility of combining a generic, clinician administered and peer-led self-management group approach for people with serious mental illness. Method General practitioners and mental health case managers used a patient-centered care model (the Flinders Model) to assist 38 patients with serious mental illness to identify their self-management needs, and match these with interventions including Stanford peer-led, self-management groups and one-to-one peer support. Self-management and quality of life outcomes were measured and qualitative evaluation elicited feedback from all participants. Results Collaborative care planning, combined with a problems and goals focused approach, resulted in improved self-management and mental functioning at 3 to 6 months follow up. The Stanford self-management course was applicable and acceptable to patients with serious mental illnesses. Qualitative feedback was highly supportive of this approach. Conclusions Generic, structured assessment and care planning approaches, resulting in self-management education targeted to the individual, improved self-management and quality of life. Patients and service providers reported considerable gains despite the challenges associated with introducing a generic model within the mental health and general practice sector

The mental health expert patient: findings from a pilot study of a generic chronic condition self-management programme for people with mental illness

Author version made available in accordance with the publisher's policyBackground Less than optimal outcomes and escalating costs for chronic conditions including mental illness have prompted calls for innovative approaches to chronic illness management. Aims This study aimed to test the feasibility and utility of combining a generic, clinician administered and peer-led self-management group approach for people with serious mental illness. Method General practitioners and mental health case managers used a patient-centered care model (the Flinders Model) to assist 38 patients with serious mental illness to identify their self-management needs, and match these with interventions including Stanford peer-led, self-management groups and one-to-one peer support. Self-management and quality of life outcomes were measured and qualitative evaluation elicited feedback from all participants. Results Collaborative care planning, combined with a problems and goals focused approach, resulted in improved self-management and mental functioning at 3 to 6 months follow up. The Stanford self-management course was applicable and acceptable to patients with serious mental illnesses. Qualitative feedback was highly supportive of this approach. Conclusions Generic, structured assessment and care planning approaches, resulting in self-management education targeted to the individual, improved self-management and quality of life. Patients and service providers reported considerable gains despite the challenges associated with introducing a generic model within the mental health and general practice sector