Learning to identify Protected Health Information by integrating knowledge- and data-driven algorithms: A case study on psychiatric evaluation notes.

De-identification of clinical narratives is one of the main obstacles to making healthcare free text available for research. In this paper we describe our experience in expanding and tailoring two existing tools as part of the 2016 CEGS N-GRID Shared Tasks Track 1, which evaluated de-identification methods on a set of psychiatric evaluation notes for up to 25 different types of Protected Health Information (PHI). The methods we used rely on machine learning on either a large or small feature space, with additional strategies, including two-pass tagging and multi-class models, which both proved to be beneficial.

Ethnicity and the first diagnosis of a wide range of cardiovascular diseases: Associations in a linked electronic health record cohort of 1 million patients.

Background: While the association of ethnic group with individual cardiovascular diseases has been studied, little is known about ethnic differences in the initial lifetime presentation of clinical cardiovascular disease in contemporary populations.

Methods And Results: We studied 1,068,318 people, aged ≥30 years and free from diagnosed CVD at baseline (90.9% White, 3.

The interaction between smoking and HLA genes in multiple sclerosis: replication and refinement.

Interactions between environment and genetics may contribute to multiple sclerosis (MS) development. We investigated whether the previously observed interaction between smoking and HLA genotype in the Swedish population could be replicated, refined and extended to include other populations. We used six independent case-control studies from five different countries (Sweden, Denmark, Norway, Serbia, United States).

Atrial fibrillation: the current epidemic.

Atrial fibrillation (AF) is the most common arrhythmia diagnosed in clinical practice. The consequences of AF have been clearly established in multiple large observational cohort studies and include increased stroke and systemic embolism rates if no oral anticoagulation is prescribed, with increased morbidity and mortality. With the worldwide aging of the population characterized by a large influx of "baby boomers" with or without risk factors for developing AF, an epidemic is forecasted within the next 10 to 20 years.

Trajectories of dementia-related cognitive decline in a large mental health records derived patient cohort.

Background: Modeling trajectories of decline can help describe the variability in progression of cognitive impairment in dementia. Better characterisation of these trajectories has significant implications for understanding disease progression, trial design and care planning.

Methods: Patients with at least three Mini-mental State Examination (MMSE) scores recorded in the South London and Maudsley NHS Foundation Trust Electronic Health Records, UK were selected (N = 3441) to form a retrospective cohort.

Long-term cardiovascular health in adult cancer survivors.

The number of cancer survivors has tremendously increased over the past decades as a result of aging of the population and improvements in early cancer detection and treatment. Ongoing successes in cancer treatment are expected to result in a further increase in the number of long-term survivors. However, cancer treatment can have detrimental cardiovascular side-effects that impact morbidity and mortality, reducing quality of life in cancer survivors.

Serious bacterial infections in neonates: improving reporting and case definitions.

Neonatal infections affect about 7 million neonates causing over 600 000 deaths every year. Estimating the burden is challenging as there are multiple reporting criteria and definitions for serious bacterial infections in neonates. Essential criteria for reporting serious neonatal bacterial infections have recently been published as the STROBE-NI checklist and, in the context of maternal vaccination, definitions have been published by the Brighton Collaboration Global Alignment of Immunization safety Assessment in pregnancy (GAIA) project.

β-Blockers and Mortality After Acute Myocardial Infarction in Patients Without Heart Failure or Ventricular Dysfunction.

Background: For acute myocardial infarction (AMI) without heart failure (HF), it is unclear if β-blockers are associated with reduced mortality.

Objectives: The goal of this study was to determine the association between β-blocker use and mortality in patients with AMI without HF or left ventricular systolic dysfunction (LVSD).

Methods: This cohort study used national English and Welsh registry data from the Myocardial Ischaemia National Audit Project.

Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype.

Background: Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Analysis (GSEA) aims to address this by identifying sets of genes or biological pathways contributing to a phenotype, through gene-gene interactions or other mechanisms, which are not the focus of conventional association methods.

Results: Approaches that utilize GSEA can now take input from array chips, either gene-centric or genome-wide, but are highly sensitive to study design, SNP selection and pruning strategies, SNP-to-gene mapping, and pathway definitions.

Trends in alcohol-related injury admissions in adolescents in Western Australia and England: population-based cohort study.

Background: Alcohol-related harm in young people is now a global health priority. We examined trends in hospital admissions for alcohol-related injuries for adolescents in Western Australia (WA) and in England, identified groups most at risk and determined causes of injuries.

Methods: Annual incidence rates for alcohol-related injury rates were calculated using population-level hospital admissions data for WA and England.

Genetic variation in the ADIPOQ gene, adiponectin concentrations and risk of colorectal cancer: a Mendelian Randomization analysis using data from three large cohort studies.

Higher levels of circulating adiponectin have been related to lower risk of colorectal cancer in several prospective cohort studies, but it remains unclear whether this association may be causal. We aimed to improve causal inference in a Mendelian Randomization meta-analysis using nested case-control studies of the European Prospective Investigation into Cancer and Nutrition (EPIC, 623 cases, 623 matched controls), the Health Professionals Follow-up Study (HPFS, 231 cases, 230 controls) and the Nurses' Health Study (NHS, 399 cases, 774 controls) with available data on pre-diagnostic adiponectin concentrations and selected single nucleotide polymorphisms in the ADIPOQ gene. We created an ADIPOQ allele score that explained approximately 3% of the interindividual variation in adiponectin concentrations.

Causal Associations of Adiposity and Body Fat Distribution With Coronary Heart Disease, Stroke Subtypes, and Type 2 Diabetes Mellitus: A Mendelian Randomization Analysis.

Background: The implications of different adiposity measures on cardiovascular disease etiology remain unclear. In this article, we quantify and contrast causal associations of central adiposity (waist-to-hip ratio adjusted for body mass index [WHRadjBMI]) and general adiposity (body mass index [BMI]) with cardiometabolic disease.

Methods: Ninety-seven independent single-nucleotide polymorphisms for BMI and 49 single-nucleotide polymorphisms for WHRadjBMI were used to conduct Mendelian randomization analyses in 14 prospective studies supplemented with coronary heart disease (CHD) data from CARDIoGRAMplusC4D (Coronary Artery Disease Genome-wide Replication and Meta-analysis [CARDIoGRAM] plus The Coronary Artery Disease [C4D] Genetics; combined total 66 842 cases), stroke from METASTROKE (12 389 ischemic stroke cases), type 2 diabetes mellitus from DIAGRAM (Diabetes Genetics Replication and Meta-analysis; 34 840 cases), and lipids from GLGC (Global Lipids Genetic Consortium; 213 500 participants) consortia.

Potential for mobile health (mHealth) prevention of cardiovascular diseases in Kerala: A population-based survey.

Background: India's southern state of Kerala stands at the forefront of India's epidemic of cardiovascular disease (CVD), among other non-communicable diseases (NCDs). Mobile phone use in healthcare (mHealth) has shown promise in India, including NCDs. However, suitability and acceptability of m-Health interventions is poorly researched, particularly in rural settings.

Functional Analysis of the Coronary Heart Disease Risk Locus on Chromosome 21q22.

. The coronary heart disease (CHD) risk locus on 21q22 (lead SNP rs9982601) lies within a "gene desert." The aim of this study was to assess if this locus is associated with CHD risk factors and to identify the functional variant(s) and gene(s) involved.

Mobile phone text messaging to improve medication adherence in secondary prevention of cardiovascular disease.

Background: Worldwide at least 100 million people are thought to have prevalent cardiovascular disease (CVD). This population has a five times greater chance of suffering a recurrent cardiovascular event than people without known CVD. Secondary CVD prevention is defined as action aimed to reduce the probability of recurrence of such events.

PCSK9 monoclonal antibodies for the primary and secondary prevention of cardiovascular disease.

Background: Despite the availability of effective drug therapies that reduce low-density lipoprotein (LDL)-cholesterol (LDL-C), cardiovascular disease (CVD) remains an important cause of mortality and morbidity. Therefore, additional LDL-C reduction may be warranted, especially for patients who are unresponsive to, or unable to take, existing LDL-C-reducing therapies. By inhibiting the proprotein convertase subtilisin/kexin type 9 (PCSK9) enzyme, monoclonal antibodies (PCSK9 inhibitors) may further reduce LDL-C, potentially reducing CVD risk as well.

Optimising spatial accessibility to inform rationalisation of specialist health services.

Background: In an era of budget constraints for healthcare services, strategies for provision of services that improve quality whilst saving costs are highly valued. A proposed means to achieve this is consolidation of services into fewer specialist centres, but this may lead to reduced spatial accessibility. We describe a methodology which includes implementing a combinatorial optimisation algorithm to derive combinations of services which optimise spatial accessibility in the context of service rationalisation, and demonstrate its use through the exemplar of tuberculosis clinics in London.

Development of a Web-Based Quality Dashboard Including a Toolbox to Improve Pain Management in Dutch Intensive Care.

Audit and feedback (A&F) is a common strategy to improve quality of care. Meta-analyses have indicated that A&F may be more effective in realizing desired change when baseline performance is low, it is delivered by a supervisor or colleague, it is provided frequently and in a timely manner, it is delivered in both verbal and written formats, and it includes specific targets and an action plan. However, there is little information to guide operationalization of these factors.

Learning Differentially Expressed Gene Pairs in Microarray Data.

To identify differentially expressed genes (DEGs) in analysis of microarray data, a majority of existing filter methods rank gene individually. Such a paradigm could overlook the genes with trivial individual discriminant powers but significant powers of discrimination in their combinations. This paper proposed an impurity metric in which the number of split intervals for each feature is considered as a parameter to be optimized for gaining maximal discrimination.

Maternal height and breast cancer risk: results from a study nested within the EPIC-Greece cohort.

The positive association of adult height with breast cancer (BC) risk has been hypothesized to be partly accounted for by an association of this risk with maternal height (operating in utero to modify hormone effects). In a case-control study (271 BC patients and 791 controls) nested within the EPIC-Greece cohort, we applied mediation analysis to calculate the direct and indirect (through the woman's own height) effect of maternal height on BC risk. Per 5 cm increase in maternal height and depending on its reference value: the indirect effect odds ratio ranges from 1.

Global Cardiovascular and Renal Outcomes of Reduced GFR.

The burden of premature death and health loss from ESRD is well described. Less is known regarding the burden of cardiovascular disease attributable to reduced GFR. We estimated the prevalence of reduced GFR categories 3, 4, and 5 (not on RRT) for 188 countries at six time points from 1990 to 2013.

Incentivised chronic disease management and the inverse equity hypothesis: findings from a longitudinal analysis of Scottish primary care practice-level data.

Background: The inverse equity hypothesis asserts that new health policies initially widen inequality, then attenuate inequalities over time. Since 2004, the UK's pay-for-performance scheme for chronic disease management (CDM) in primary care general practices (the Quality and Outcomes Framework) has permitted practices to except (exclude) patients from attending annual CDM reviews, without financial penalty. Informed dissent (ID) is one component of exception rates, applied to patients who have not attended due to refusal or non-response to invitations.

Exercise-based cardiac rehabilitation in heart transplant recipients.

Background: Heart transplantation is considered to be the gold standard treatment for selected patients with end-stage heart disease when medical therapy has been unable to halt progression of the underlying pathology. Evidence suggests that aerobic exercise training may be effective in reversing the pathophysiological consequences associated with cardiac denervation and prevent immunosuppression-induced adverse effects in heart transplant recipients.

Objectives: To determine the effectiveness and safety of exercise-based rehabilitation on the mortality, hospital admissions, adverse events, exercise capacity, health-related quality of life, return to work and costs for people after heart transplantation.