Accessing primary care Big Data: the development of a software algorithm to explore the rich content of consultation records

OBJECTIVE

To develop a natural language processing software inference algorithm to classify the content of primary care consultations using electronic health record Big Data and subsequently test the algorithm's ability to estimate the prevalence and burden of childhood respiratory illness in primary care.

DESIGN

Algorithm development and validation study. To classify consultations, the algorithm is designed to interrogate clinical narrative entered as free text, diagnostic (Read) codes created and medications prescribed on the day of the consultation.

SETTING

Thirty-six consenting primary care practices from a mixed urban and semirural region of New Zealand. Three independent sets of 1200 child consultation records were randomly extracted from a data set of all general practitioner consultations in participating practices between 1 January 2008-31 December 2013 for children under 18 years of age (n=754,242). Each consultation record within these sets was independently classified by two expert clinicians as respiratory or non-respiratory, and subclassified according to respiratory diagnostic categories to create three 'gold standard' sets of classified records. These three gold standard record sets were used to train, test and validate the algorithm.

OUTCOME MEASURES

Sensitivity, specificity, positive predictive value and F-measure were calculated to illustrate the algorithm's ability to replicate judgements of expert clinicians within the 1200 record gold standard validation set.

RESULTS

The algorithm was able to identify respiratory consultations in the 1200 record validation set with a sensitivity of 0.72 (95% CI 0.67 to 0.78) and a specificity of 0.95 (95% CI 0.93 to 0.98). The positive predictive value of algorithm respiratory classification was 0.93 (95% CI 0.89 to 0.97). The positive predictive value of the algorithm classifying consultations as being related to specific respiratory diagnostic categories ranged from 0.68 (95% CI 0.40 to 1.00; other respiratory conditions) to 0.91 (95% CI 0.79 to 1.00; throat infections).

CONCLUSIONS

A software inference algorithm that uses primary care Big Data can accurately classify the content of clinical consultations. This algorithm will enable accurate estimation of the prevalence of childhood respiratory illness in primary care and resultant service utilisation. The methodology can also be applied to other areas of clinical care.

Prevalence, natural course and predictors of depression 1 year following traumatic brain injury from a population-based study in New Zealand

OBJECTIVE

Depression is common post-TBI, yet has not been studied longitudinally, nor at a population level. This study examined prevalence of depression in a population-based sample across the first year post-TBI.

DESIGN AND METHODS

Prospective follow-up of 315 adults (>16 years) with assessments (Hospital Anxiety Depression Scale, DSM-IV criteria) at 1-, 6- and 12-months post-TBI. Demographic and injury-related predictors of depression at 1-year post-TBI were also explored.

RESULTS

The number of individuals identified as depressed reduced significantly between baseline and 12-months post-TBI from 21-12.4% using the HADS and 49-34% using DSM-IV criteria; with only 10 of the 28 individuals initially meeting criteria on the HADS continuing to do so at 12-month follow-up. Meeting HADS depression criteria was linked to pre-morbid depression and/or anxiety; while those meeting DSM-IV criteria were older, but not significantly so.

CONCLUSIONS

The findings suggest depression is common post-TBI and that clinicians/researchers use caution in its diagnosis, as existing criteria have significant overlap with common TBI sequels.

The association between health care professional attitudes and beliefs and the attitudes and beliefs, clinical management, and outcomes of patients with low back pain: a systematic review

BACKGROUND

It has been suggested that health care professional (HCP) attitudes and beliefs may negatively influence the beliefs of patients with low back pain (LBP), but this has not been systematically reviewed. This review aimed to investigate the association between HCP attitudes and beliefs and the attitudes and beliefs, clinical management, and outcomes of this patient population.

METHODS

Electronic databases were systematically searched for all types of studies. Studies were selected by predefined inclusion criteria. Methodological quality was appraised and strength of evidence was determined.

RESULTS

Seventeen studies from eight countries which investigated the attitudes and beliefs of general practitioners, physiotherapists, chiropractors, rheumatologists, orthopaedic surgeons and other paramedical therapists were included. There is strong evidence that HCP beliefs about back pain are associated with the beliefs of their patients. There is moderate evidence that HCPs with a biomedical orientation or elevated fear avoidance beliefs are more likely to advise patients to limit work and physical activities, and are less likely to adhere to treatment guidelines. There is moderate evidence that HCP attitudes and beliefs are associated with patient education and bed rest recommendations. There is moderate evidence that HCP fear avoidance beliefs are associated with reported sick leave prescription and that a biomedical orientation is not associated with the number of sickness certificates issued for LBP.

CONCLUSION

HCPs need to be aware of the association between their attitudes and beliefs and the attitudes and beliefs and clinical management of their patients with LBP.

Use of metabolic profiles for the assessment of dietary adequacy in UK dairy herds

Between April 1999 and March 2004, metabolic profile analyses were performed on individual blood samples from 35,506 dairy cattle in the UK. Assessment of the cows' energy status by the analysis of plasma samples for beta-hydroxybutyrate, glucose and non-esterified fatty acids showed that 70.4 per cent of the cows in early lactation (10 to 20 days calved), 57.1 per cent of the cows in mid-lactation (51 to 120 days calved) and 57.7 per cent of the dry cows within 10 days of their predicted calving date had one or more energy metabolites outside the optimum range; in addition, 16 per cent of the cows in early lactation, 5.6 per cent of those in mid-lactation and 20.5 per cent of the dry cows within 10 days of their predicted calving date had a low plasma urea nitrogen concentration, indicating poor intakes of effective rumen-degradable protein. Abnormalities in the concentrations of magnesium, inorganic phosphate, copper, selenium and iodine were relatively uncommon. The transitional period, particularly in late pregnancy, was commonly identified as a constraint on productivity. Nutritional problems were most commonly associated with poor feed intakes and poor feed management, rather than with the formulation of the rations.

A remote and highly conserved enhancer supports amygdala specific expression of the gene encoding the anxiogenic neuropeptide substance-P

The neuropeptide substance P (SP), encoded by the preprotachykinin-A (PPTA) gene, is expressed in the central and medial amygdaloid nucleus, where it plays a critical role in modulating fear and anxiety related behaviour. Determining the regulatory systems that support PPTA expression in the amygdala may provide important insights into the causes of depression and anxiety related disorders and will provide avenues for the development of novel therapies. In order to identify the tissue specific regulatory element responsible for supporting expression of the PPTA gene in the amygdala, we used long-range comparative genomics in combination with transgenic analysis and immunohistochemistry. By comparing human and chicken genomes, it was possible to detect and characterise a highly conserved long-range enhancer that supported tissue specific expression in SP expressing cells of the medial and central amygdaloid bodies (ECR1; 158.5 kb 5' of human PPTA ORF). Further bioinformatic analysis using the TRANSFAC database indicated that the ECR1 element contained multiple and highly conserved consensus binding sequences of transcription factors (TFs) such as MEIS1. The results of immunohistochemical analysis of transgenic lines were consistent with the hypothesis that the MEIS1 TF interacts with and maintains ECR1 activity in the central amygdala in vivo. The discovery of ECR1 and the in vivo functional relationship with MEIS1 inferred by our studies suggests a mechanism to the regulatory systems that control PPTA expression in the amygdala. Uncovering these mechanisms may play an important role in the future development of tissue specific therapies for the treatment of anxiety and depression.

Third sector primary care for vulnerable populations

This paper aims to describe and explain the development of third sector primary care organisations in New Zealand. The third sector is the non-government, non-profit sector. International literature suggests that this sector fulfils an important role in democratic societies with market-based economies, providing services otherwise neglected by the government and private for-profit sectors. Third sector organisations provided a range of social services throughout New Zealand's colonial history. However, it was not until the 1980s that third sector organisations providing comprehensive primary medical and related services started having a significant presence in New Zealand. In 1994 a range of union health centres, tribally based Mäori health providers, and community-based primary care providers established a formal network -- Health Care Aotearoa. While not representing all third sector primary care providers in New Zealand, Health Care Aotearoa was the best-developed example of a grouping of third sector primary care organisations. Member organisations served populations that were largely non-European and lived in deprived areas, and tended to adopt population approaches to funding and provision of services. The development of Health Care Aotearoa has been consistent with international experience of third sector involvement -- there were perceived "failures" in government policies for funding primary care and private sector responses to these policies, resulting in lack of universal funding and provision of primary care and continuing patient co-payments. The principal policy implication concerns the role of the third sector in providing primary care services for vulnerable populations as a partial alternative to universal funding and provision of primary care. Such an alternative may be convenient for proponents of reduced state involvement in funding and provision of health care, but may not be desirable from the point of view of equity and social cohesion insofar as the role of the welfare state is diminished.

New Zealand rural general practitioners 1999 survey--part 1: an overview of the rural doctor workforce and their concerns

AIMS

To obtain current information about New Zealand rural general practitioners (GPs) and their localitites.

METHODS

An anonymous postal questionnaire was mailed out to 559 rural and semi-rural GPs in November 1999, and non-responders were sent three reminders.

RESULTS

Of the 417 completed questionnaires returned (response rate 75%), 338 were from rural GPs(Rural Ranking Scale score > or = 35 points) and these formed the study group. The mean age was 44 years, 72% were male, and 93% were of New Zealand European ethnicity. Less than 50%had graduated from a New Zealand medical school with Britain (30%) and South Africa (11%) providing most of the foreign- trained rural GPs. Only 59% had received vocational training in general practice. The majority worked fulltime (79%) and owned their practice (78%), while 133 (39%) worked part time as rural hospital doctors and 72 (21%) provided intra-partum obstetric care. Over two thirds rated lack of locum relief, onerous oncall,and rural GP shortages as 'important' or 'very important' problems, with one third stating that more rural GPswere needed in their locality.

CONCLUSIONS

This, only the second national survey of rural GPs, provides a comprehensive overview of New Zealand rural general practice in November 1999. It confirms that the major current problem is an under supply of rural GPs, causing overwork and stress in those remaining.

The first sunrise: an experience of cultural immersion and community health needs assessment by undergraduate medical students in New Zealand

CONTEXT

Cultural factors in health and illness, and an awareness of community health needs analysis, are important issues for medical education. Both have received relatively little recognition in the medical education literature. This paper describes the development of an educational attachment to remote predominantly Maori rural communities in New Zealand. The twin purposes of the programme were to encourage students to adopt broad public health approaches in assessing the health needs of defined communities, and to increase their awareness of the importance of cultural issues.

METHODS

During a one week attachment, 51 students from the Wellington School of Medicine were hosted in six small communities in the East Cape region of New Zealand. Students gained an insight into the health needs of the communities and were encouraged to challenge their own attitudes, assumptions and thinking regarding the determinants of health and the importance of cultural factors in health and illness. The programme included both health needs assessment and cultural immersion. Students made visits with primary health care professionals and were also introduced to Maori history and cultural protocol, and participated in diverse activities ranging from the preparation of traditional medicines to performing their own songs in concert.

CONCLUSIONS

The students evaluated the course extremely highly. Attachments of this sort provide an opportunity for students to appreciate how cultural values have an impact on health care, and how they also make the teaching and learning of topics such as community health needs analysis an enjoyable and dynamic experience.

Utilisation rates in capitated primary care centres serving low income populations

AIM

To measure utilisation rates in capitated primary care organisations serving low income populations with low or zero co-payments, and to examine the relationship between utilisation rates and organisation, age group, sex, ethnicity, community services card (CSC) holding rates, high use health card (HUHC) holding rates and deprivation of area of residence (NZDep96).

METHODS

Data were collected during 1997/98, from eleven primary care organisations. Utilisation data were collected from practice computer information systems.

RESULTS

53.9% of registered patients were recorded as having consulted in a twelve-month period. Utilisation rates for doctor, nurse and midwife combined were higher amongst the young, elderly, and CSC holders. For males, they were higher amongst those living in the most socioeconomically deprived areas, but not for females. Utilisation rates were highest amongst the 'other' ethnic group, and lowest in the Pacific Island ethnic group. Organisation, age group, sex, ethnicity, CSC, HUHC and NZDep96 were independently predictive of total utilisation.

CONCLUSIONS

Utilisation rates in capitated practices tended to be lower than those in fee-for-service practices. If equitable needs-based capitation funding formulas are to be developed, utilisation data from capitated practices in a range of cultural and socioeconomic settings is urgently required.

The effect of doctor ethnicity and country of qualification on prescribing patterns: an ecological study

OBJECTIVE

To assess the effect of doctor ethnicity and country of qualification on prescribing patterns.

DESIGN

Ecological study.

SETTING

90 Family Health Services Authorities in the U.K.

RESULTS

Being an Asian doctor and qualifying from the Indian subcontinent contributes to 5% of the observed variation seen in the frequency of prescribing, but not the cost. The major determinant of variation in prescribing is deprivation, which accounts for 14% of the cost and 32% of the frequency of prescribing.

CONCLUSIONS

Being an Asian doctor and qualifying from the Indian subcontinent contributes to the frequency, but not the cost of prescribing variation. As this study was at the FHSA level, 'ecological fallacy' exists and further research is advocated at the individual doctor level.

A survey of job satisfaction, sources of stress and psychological symptoms among general practitioners in Leeds

BACKGROUND

The past seven years have seen rapid changes in general practice in the United Kingdom (UK), commencing with the 1990 contract. During the same period, concern about the health and morale of general practitioners (GPs) has increased and a recruitment crisis has developed.

AIM

To determine levels of psychological symptoms, job satisfaction, and subjective ill health in GPs and their relationship to practice characteristics, and to compare levels of job satisfaction since the introduction of the 1990 GP contract with those found before 1990.

METHOD

Postal questionnaire survey of all GP principals on the Leeds Health Authority list. The main outcome measures included quantitative measures of practice characteristics, job satisfaction, mental health (General Health Questionnaire), and general physical health. Qualitative statements about work conditions, job satisfaction, and mental health were collected.

RESULTS

A total of 285/406 GPs (70%) returned the questionnaires. One hundred and forty-eight (52%) scored 3 or more on the General Health Questionnaire (GHQ-12), which indicates a high level of psychological symptoms. One hundred and sixty GPs (56%) felt that work had affected their recent physical health. Significant associations were found between GHQ-12 scores, total job satisfaction scores, and GPs' perceptions that work had affected their physical health. Problems with physical and mental health were associated with several aspects of workload, including list size, number of sessions worked per week, amount of time spent on call, and use of deputizing services. In the qualitative part of the survey, GPs reported overwork and excessive hours, paperwork and administration, recent National Health Service (NHS) changes, and the 1990 GP contract as the most stressful aspects of their work.

CONCLUSIONS

Fifty-two per cent of GPs in Leeds who responded showed high levels of psychological symptoms. Job satisfaction was lower than in a national survey conducted in 1987, and GPs expressed the least satisfaction with their hours, recognition for their work, and rates of pay. Nearly 60% felt that their physical health had been affected by their work. These results point to a need to improve working conditions in primary care and for further research to determine the effect of any such changes.

Effect of doctors' ethnicity and country of qualification on prescribing patterns in single handed general practices: linkage of information collected by questionnaire and from routine data

OBJECTIVES

To test whether Asian general practitioners who qualified in the Indian subcontinent prescribe items more often, more expensive items, and fewer generic drugs than their British trained Asian and non-Asian counterparts.

DESIGN

Linkage study using data collected by questionnaire and from routine sources.

SETTING

General practices in England.

SUBJECTS

155 single handed general practitioners: 42 Asian doctors qualified in United Kingdom (group 1), 58 white doctors qualified in United Kingdom (group 2), and 55 Asian doctors qualified in Indian subcontinent (group 3).

MAIN OUTCOME MEASURES

Prescribing cost (cost per ASTRO-PU), prescribing frequency (number of items per ASTRO-PU), and generic prescribing (percentage of drugs prescribed that are generic).

RESULTS

Doctors in group 1 were significantly younger than those in the other groups and had a higher proportion of patients who were from deprived wards. There was no difference between the groups in the proportion of female doctors and total list size. After adjustment for confounding factors, there were no significant differences between the three groups for prescribing cost (16.58 (95% confidence interval 6.39 to 26.77) for group 1, 17.31 (6.92 to 27.69) for group 2, 17.80 (7.22 to 28.38) for group 3, P = 0.55); prescribing frequency (6.58 (4.60 to 8.40), 6.45 (4.70 to 8.30), 7.89 (6.16 to 9.64), P = 0.34); and generic prescribing (44.44 (38.95 to 49.93), 47.41 (42.12 to 52.70), 44.04 (38.75 to 49.33), P = 0.37).

CONCLUSIONS

Asian doctors qualified from the Indian subcontinent did not differ from British trained doctors in their prescribing practice. This study refutes the common belief that Asian doctors are high volume and high cost prescribers.

Can general practice provide useful information?--evaluation of a primary health care information project in northern England

OBJECTIVE

To develop a computerised primary care information gathering network capable of producing reliable risk factor and morbidity data from a wide diversity of general practice software systems.

METHOD

Fourteen practices from the Wakefield and Pontefract district collaborated in sharing information and solving technical difficulties associated with collecting data on coronary heart disease (CHD) risk factors, diabetes, and asthma. Practices also participated in rheumatology and mental health needs assessment projects.

RESULTS

Data could be transferred by diskette in only five of the systems and paper reports had to be used to post process the data into a standard format. Not all data were complete or comparable. Crude estimates only of smoking prevalence and smoking cessation interventions were possible, as well as of age and sex specific prevalences for asthma and diabetes. The rheumatology health needs assessment, using the prospective collection of consultation based data, highlighted an unmet need for rheumatology services in the community.

CONCLUSIONS

Although practices have been willing to devote considerable time and effort to the project, the diversity of software has precluded a simple methodology for data collection and analysis. The amount of useful information retrieved so far, has been limited but a number of important lessons have been learned which have implications for similar information projects and the use of primary care information in service planning.

Relationship among visible light source, composite resin polymerization shrinkage, and hygroscopic expansion

Composite resins contract during polymerization, and studies have shown that light-cured composite resins shrink toward the polymerizing light source. The purpose of this study was to investigate differences in the adaptation of composite resin to the axial wall in Class V restorations following light curing from the lingual or facial aspects. Polymerization contraction in relation to hygroscopic expansion of the restoration was also investigated. Results showed no statistically significant differences (P less than .05) in the adaptation of composite resin to the axial wall, regardless of the polymerization technique, the composite resin, or the effects of hygroscopic expansion.