Data mining for heart failure : an investigation into the challenges in real life clinical datasets

Clinical data presents a number of challenges including missing data, class imbalance, high dimensionality and non-normal distribution. A motivation for this research is to investigate and analyse the manner in which the challenges affect the performance of algorithms. The challenges were explored with the help of a real life heart failure clinical dataset known as Hull LifeLab, obtained from a live cardiology clinic at the Hull Royal Infirmary Hospital. A Clinical Data Mining Workflow (CDMW) was designed with three intuitive stages, namely, descriptive, predictive and prescriptive. The naming of these stages reflects the nature of the analysis that is possible within each stage; therefore a number of different algorithms are employed. Most algorithms require the data to be distributed in a normal manner. However, the distribution is not explicitly used within the algorithms. Approaches based on Bayes use the properties of the distributions very explicitly, and thus provides valuable insight into the nature of the data.The first stage of the analysis is to investigate if the assumptions made for Bayes hold, e.g. the strong independence assumption and the assumption of a Gaussian distribution. The next stage is to investigate the role of missing values. Results found that imputation does not affect the performance as much as those records which are initially complete. These records are often not outliers, but contain problem variables. A method was developed to identify these. The effect of skews in the data was also investigated within the CDMW. However, it was found that methods based on Bayes were able to handle these, albeit with a small variability in performance. The thesis provides an insight into the reasons why clinical data often causes problems. Even the issue of imbalanced classes is not an issue, for Bayes is independent of this

What are the minimal sample size requirements for Mokken scaling? An empirical example with the Warwick-Edinburgh Mental Well-being Scale

PurposeSample size in Mokken scales is mostly studied on simulated data, reflected in the lack of consideration of sample size in most Mokken scaling studies. Recently, Straat et al. (2014) provided minimum sample size requirements for Mokken scale analysis based on simulation. Our study uses real data from the Warwick-Edinburgh Mental Well-Being Scale (N = 8463) to assess whether these hold.MethodsWe use per element accuracy to evaluate the impact of sample size, with scaling coefficients and confidence intervals around scale, item and item pair scalability coefficients.ResultsPer element accuracy, scalability coefficients, and confidence intervals around scalability coefficients are sensitive to sample size. The results from Straat et al. were not replicated; depending on the main goal of the research, sample sizes ranging from >250 to >1000 are needed.ConclusionsUsing our pragmatic approach, some practical recommendations are made regarding sample sizes for studies of Mokken scaling

How well do blood folate concentrations predict dietary folate intakes in a sample of Canadian lactating women exposed to high levels of folate? An observational study

<p>Abstract</p> <p>Background</p> <p>In 1998, mandatory folic acid fortification of white flour and select cereal grain products was implemented in Canada with the intention to increase dietary folate intakes of reproducing women. Folic acid fortification has produced a dramatic increase in blood folate concentrations among reproductive age women, and a reduction in neural tube defect (NTD)-affected pregnancies. In response to improved blood folate concentrations, many health care professionals are asking whether a folic acid supplement is necessary for NTD prevention among women with high blood folate values, and how reliably high RBC folate concentrations predict folate intakes shown in randomized controlled trials to be protective against NTDs. The objective of this study was to determine how predictive blood folate concentrations and folate intakes are of each other in a sample of well-educated lactating Canadian women exposed to high levels of synthetic folate.</p> <p>Methods</p> <p>The relationship between blood folate concentrations and dietary folate intakes, determined by weighed food records, were assessed in a sample of predominantly university-educated lactating women (32 ± 4 yr) at 4-(n = 53) and 16-wk postpartum (n = 55).</p> <p>Results</p> <p>Median blood folate concentrations of all participants were well above plasma and RBC folate cut-off levels indicative of deficiency (6.7 and 317 nmol/L, respectively) and all, except for 2 subjects, were above the cut-off for NTD-risk reduction (>906 nmol/L). Only modest associations existed between total folate intakes and plasma (r = 0.46, <it>P </it>< 0.001) and RBC (r = 0.36, <it>P </it>< 0.01) folate concentrations at 16-wk postpartum. Plasma and RBC folate values at 16-wk postpartum correctly identified the quartile of folate intake of only 26 of 55 (47%) and 18 of 55 (33%) of subjects, respectively. The mean RBC folate concentration of women consuming 151–410 μg/d of synthetic folate (2^ndquartile of intake) did not differ from that of women consuming >410 μg/d (3^rdand 4^thquartile).</p> <p>Conclusion</p> <p>Folate intakes, estimated by food composition tables, and blood folate concentrations are not predictive of each other in Canadian lactating women exposed to high levels of folate. Synthetic intakes > 151–410 μg/d in these women produced little additional benefit in terms of maximizing RBC content. More studies are needed to examine the relationship between blood folate concentration and NTD risk. Until data from such studies are available, women planning a pregnancy should continue to consume a daily folic acid supplement of 400 μg.</p

Aiming to increase birth weight: a randomised trial of pre-pregnancy information, advice and counselling in inner-urban Melbourne

BACKGROUND: In the 1980s there was substantial interest in early pregnancy and pre-pregnancy interventions to increase birth weight and reduce preterm birth. We developed an inter-pregnancy intervention, implemented in a randomised controlled trial, to be provided by midwives at home soon after women's first birth. METHODS: MCH nurses invited women to take part during their home visit to new mothers. Women's contact details, with their permission, were passed to the study midwife. She had a randomisation schedule to which women's names were added before she met the women or their partners. All women recruited had a home visit from the study midwife with a discussion of their first pregnancy, labour and birth and the postpartum experience. Women in the intervention arm received in addition a pre-pregnancy intervention with discussion of social, health or lifestyle problems, preparation and timing for pregnancy, family history, rubella immunisation, referrals for health problems, and a reminder card. The primary outcome was defined as a birth weight difference in the second birth of 100 g (one-sided) in favour of the intervention. Additional data collected were gestational age, perinatal deaths and birth defects. Analyses used EPI-INFO and STATA. RESULTS: Intervention and comparison groups were comparable on socioeconomic factors, prior reproductive history and first birth outcomes. Infant birth weight in the second birth was lower (-97.4 g,)) among infants in the intervention arm. There were no significant differences between intervention and comparison arms in the proportion of women having a preterm birth, an infant with low birthweight, or an infant with a birth weight <10(th )percentile. There were more adverse outcomes in the intervention arm: ten births <32 weeks), compared with one in standard care, and more infants with a birth weight <2000 g, 16 compared with two in standard care CONCLUSION: As the primary outcome was envisaged to be either improved birth weight or no effect, the study was not designed to identify the alternative outcome with confidence. Despite widespread support for pre-pregnancy interventions to improve maternal and perinatal health, this first randomised controlled trial of a multi-component intervention provided at home, did not have a beneficial outcome

118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects

<p>Abstract</p> <p>Background</p> <p>Folic acid taken in early pregnancy reduces risks for delivering offspring with several congenital anomalies. The mechanism by which folic acid reduces risk is unknown. Investigations into genetic variation that influences transport and metabolism of folate will help fill this data gap. We focused on 118 SNPs involved in folate transport and metabolism.</p> <p>Methods</p> <p>Using data from a California population-based registry, we investigated whether risks of spina bifida or conotruncal heart defects were influenced by 118 single nucleotide polymorphisms (SNPs) associated with the complex folate pathway. This case-control study included 259 infants with spina bifida and a random sample of 359 nonmalformed control infants born during 1983–86 or 1994–95. It also included 214 infants with conotruncal heart defects born during 1983–86. Infant genotyping was performed blinded to case or control status using a designed SNPlex assay. We examined single SNP effects for each of the 118 SNPs, as well as haplotypes, for each of the two outcomes.</p> <p>Results</p> <p>Few odds ratios (ORs) revealed sizable departures from 1.0. With respect to spina bifida, we observed ORs with 95% confidence intervals that did not include 1.0 for the following SNPs (heterozygous or homozygous) relative to the reference genotype: <it>BHMT </it>(rs3733890) OR = 1.8 (1.1–3.1), <it>CBS </it>(rs2851391) OR = 2.0 (1.2–3.1); <it>CBS </it>(rs234713) OR = 2.9 (1.3–6.7); <it>MTHFD1 </it>(rs2236224) OR = 1.7 (1.1–2.7); <it>MTHFD1 </it>(hcv11462908) OR = 0.2 (0–0.9); <it>MTHFD2 </it>(rs702465) OR = 0.6 (0.4–0.9); <it>MTHFD2 </it>(rs7571842) OR = 0.6 (0.4–0.9); <it>MTHFR </it>(rs1801133) OR = 2.0 (1.2–3.1); <it>MTRR </it>(rs162036) OR = 3.0 (1.5–5.9); <it>MTRR </it>(rs10380) OR = 3.4 (1.6–7.1); <it>MTRR </it>(rs1801394) OR = 0.7 (0.5–0.9); <it>MTRR </it>(rs9332) OR = 2.7 (1.3–5.3); <it>TYMS </it>(rs2847149) OR = 2.2 (1.4–3.5); <it>TYMS </it>(rs1001761) OR = 2.4 (1.5–3.8); and <it>TYMS </it>(rs502396) OR = 2.1 (1.3–3.3). However, multiple SNPs observed for a given gene showed evidence of linkage disequilibrium indicating that the observed SNPs were not individually contributing to risk. We did not observe any ORs with confidence intervals that did not include 1.0 for any of the studied SNPs with conotruncal heart defects. Haplotype reconstruction showed statistical evidence of nonrandom associations with <it>TYMS</it>, <it>MTHFR</it>, <it>BHMT </it>and <it>MTR </it>for spina bifida.</p> <p>Conclusion</p> <p>Our observations do not implicate a particular folate transport or metabolism gene to be strongly associated with risks for spina bifida or conotruncal defects.</p

Pharmacist and patient experiences of primary care during the COVID-19 pandemic: an interview study

Introduction: A number of significant changes designed to reduce the spread of COVID-19 were introduced in primary care during the COVID-19 pandemic. In Ireland, these included fundamental legislative and practice changes such as permitting electronic transfer of prescriptions, extending duration of prescription validity, and encouraging virtual consultations. Although such interventions served an important role in preventing the spread of infection, their impact on practice and patient care is not yet clear. The aim of this study was to investigate patient and healthcare professional (pharmacist and general practitioner) experiences to understand the impact of COVID-19 on primary care and medication safety during the first two years of the COVID-19 pandemic in Ireland. Methods: A qualitative study using semi-structured interviews was undertaken between October 2021 and January 2022. Participants included twelve patients, ten community pharmacists, and one general practitioner. Interviews were transcribed verbatim and analysed using thematic analysis. Only patient and pharmacist interviews were included. Findings: Themes from the interviews included: 1) Access to care, 2) Technological changes, 3) Experiences of care, and 4) Patient safety. Particular challenges identified included the difficulty faced by patients when accessing care, impacts on experiences of patient care, and extensive changes to pharmacy practice during the pandemic. Conclusions: This study found that COVID-19 countermeasures considerably impacted patient and pharmacist experiences of primary care in terms of care and medication safety. While many changes were welcomed, others such as virtual consultations were received more cautiously likely due to the rapid and unplanned nature of their introduction. Further research is needed to identify how to optimise these changes to improve pharmacist and patient experience, and to understand the impact on patient safety.</p

Medication safety incidents associated with the remote delivery of primary care: a rapid review

Objectives: The COVID-19 pandemic triggered rapid, fundamental changes, notably increased remote delivery of primary care. While the impact of these changes on medication safety is not yet fully understood, research conducted before the pandemic may provide evidence for possible consequences. To examine the published literature on medication safety incidents associated with the remote delivery of primary care, with a focus on telemedicine and electronic prescribing. Methods: A rapid review was conducted according to the Cochrane Rapid Reviews Methods Group guidance. An electronic search was carried out on Embase and Medline (via PubMed) using key search terms 'medication error', 'electronic prescribing', 'telemedicine' and 'primary care'. Identified studies were synthesised narratively; reported medication safety incidents were categorised according to the WHO Conceptual Framework for the International Classification for Patient Safety. Key findings: Fifteen studies were deemed eligible for inclusion. All 15 studies reported medication incidents associated with electronic prescribing; no studies were identified that reported medication safety incidents associated with telemedicine. The most commonly reported medication safety incidents were 'wrong label/instruction' and 'wrong dose/strength/frequency'. The frequency of medication safety incidents ranged from 0.89 to 81.98 incidents per 100 electronic prescriptions analysed. Summary: This review of medication safety incidents associated with the remote delivery of primary care identified common incident types associated with electronic prescriptions. There was a wide variation in reported frequencies of medication safety incidents associated with electronic prescriptions. Further research is required to determine the impact of the COVID-19 pandemic on medication safety in primary care, particularly the increased use of telemedicine.</p

Changes to primary care delivery during the COVID-19 pandemic and perceived impact on medication safety: a survey study

Introduction: The COVID-19 pandemic has had a profound impact on the delivery of primary care around the world. In Ireland, the use of technologies such as virtual consultations and the electronic transfer of prescriptions became widespread in order to deliver care to patients while minimising infection risk. The impact of these changes on medication safety is not yet known. Objectives: The aims of this survey study were to investigate 1) the changes that have occurred in Irish primary care since the start of the COVID-19 pandemic and 2) the impact of these changes on medication safety. Methods: Anonymous, online surveys were distributed to general practitioners (GPs) and pharmacists from August-September 2021. Surveys contained quantitative (multiple-choice, Likert scale) and qualitative (free-text) questions concerning workflow changes, medication safety incidents and near misses, and GP/pharmacist perspectives on medication safety and COVID-19. Reported medication safety incidents and near misses were categorised according to the WHO Conceptual Framework for the International Classification for Patient Safety. Results: In total, there were 251 responses to the survey, comprising of 211 pharmacists and 40 GPs. The most significant workflow changes during the pandemic were the widespread use of a secure clinical email service (Healthmail) that facilitates electronic prescription transfer and communication (75.3% of respondents) and the increased use of telephone consultations (49%). Overall, Healthmail was widely perceived to have had a positive impact on medication safety. Most GPs did not perceive a change in the frequency of medication safety incidents during the pandemic, while most pharmacists reported a slight increase in incidents. Survey participants highlighted pressure, patient expectations, and patient monitoring as significant challenges encountered during the pandemic. Conclusions: During the pandemic, a number of significant changes occurred in primary care in Ireland, particularly involving communication of healthcare information, with varying impacts on workflow and medication safety. Future research should focus on the optimisation of electronic prescribing and telemedicine services in Ireland, patient perspectives on the changes in primary care, and interventions to improve medication safety in primary care.</p