The European Bioinformatics Institute (EMBL-EBI) in 2021

The European Bioinformatics Institute (EMBL-EBI) maintains a comprehensive range of freely available and up-to-date molecular data resources, which includes over 40 resources covering every major data type in the life sciences. This year's service update for EMBL-EBI includes new resources, PGS Catalog and AlphaFold DB, and updates on existing resources, including the COVID-19 Data Platform, trRosetta and RoseTTAfold models introduced in Pfam and InterPro, and the launch of Genome Integrations with Function and Sequence by UniProt and Ensembl. Furthermore, we highlight projects through which EMBL-EBI has contributed to the development of community-driven data standards and guidelines, including the Recommended Metadata for Biological Images (REMBI), and the BioModels Reproducibility Scorecard. Training is one of EMBL-EBI's core missions and a key component of the provision of bioinformatics services to users: this year's update includes many of the improvements that have been developed to EMBL-EBI's online training offering.

Neighborhood Socioeconomic Status and Stroke Incidence: A Systematic Review

OBJECTIVE

To summarize overall patterns of the impact of neighborhood socioeconomic status (nSES) on stroke incidence and uncover potential gaps in the literature, we conducted a systematic review of studies examining the association between nSES and stroke incidence, independent of individual SES.

METHODS

Four electronic databases and reference lists of included articles were searched, and corresponding authors were contacted to locate additional studies. A keyword search strategy included the 3 broad domains of neighborhood, SES, and stroke. Eight studies met our inclusion criteria (e.g., nSES as an exposure, individual SES as a covariate, and stroke incidence as an outcome). We coded study methodology and findings across the 8 studies.

RESULTS

The results provide evidence for the overall nSES and stroke incidence association in Sweden and Japan, but not within the United States. Findings were inconclusive when examining the nSES-stroke incidence association stratified by race. We found evidence for the mediating role of biological factors in the nSES-stroke incidence association.

CONCLUSIONS

Higher neighborhood disadvantage was found to be associated with higher stroke risk, but it was not significant in all the studies. The relationship between nSES and stroke risk within different racial groups in the United States was inconclusive. Inconsistencies may be driven by differences in covariate adjustment (e.g., individual-level sociodemographic characteristics and neighborhood-level racial composition). Additional research is needed to investigate potential intermediate and modifiable factors of the association between nSES and stroke incidence, which could serve as intervention points.

Latent Dirichlet allocation model for world trade analysis

International trade is one of the classic areas of study in economics. Its empirical analysis is a complex problem, given the amount of products, countries and years. Nowadays, given the availability of data, the tools used for the analysis can be complemented and enriched with new methodologies and techniques that go beyond the traditional approach. This new possibility opens a research gap, as new, data-driven, ways of understanding international trade, can help our understanding of the underlying phenomena. The present paper shows the application of the Latent Dirichlet allocation model, a well known technique in the area of Natural Language Processing, to search for latent dimensions in the product space of international trade, and their distribution across countries over time. We apply this technique to a dataset of countries’ exports of goods from 1962 to 2016. The results show that this technique can encode the main specialisation patterns of international trade. On the country-level analysis, the findings show the changes in the specialisation patterns of countries over time. As traditional international trade analysis demands expert knowledge on a multiplicity of indicators, the possibility of encoding multiple known phenomena under a unique indicator is a powerful complement for traditional tools, as it allows top-down data-driven studies.

Demographic and socioeconomic disparities of benign and malignant spinal meningiomas in the United States

INTRODUCTION

Spinal meningiomas constitute the majority of primary spinal neoplasms, yet their pathogenesis remains elusive. By investigating the distribution of these tumors across sociodemographic variables can provide direction in etiology elucidation and healthcare disparity identification.

METHODS

To investigate benign and malignant spinal meningioma incidences (per 100,000) with respect to sex, age, income, residence, and race/ethnicity, we queried the largest American administrative dataset (1997-2016), the National (Nationwide) Inpatient Sample (NIS), which surveys 20% of United States (US) discharges.

RESULTS

Annual national incidence was 0.62 for benign tumors and 0.056 for malignant. For benign meningiomas, females had an incidence of 0.81, larger (P=0.000004) than males at 0.40; yet for malignant meningiomas, males had a larger (P=0.006) incidence at 0.062 than females at 0.053. Amongst age groups, peak incidence was largest for those 65-84 years old (2.03) in the benign group, but 45-64 years old (0.083) for the malignant group. For benign and malignant meningiomas respectively, individuals with middle/high income had an incidence of 0.67 and 0.060, larger (P=0.000008; P=0.04) than the 0.48 and 0.046 of low income patients. Incidences were statistically similar (P=0.2) across patient residence communities. Examining race/ethnicity (P=0.000003) for benign meningiomas, incidences for Whites, Asian/Pacific Islanders, Hispanics, and Blacks were as follows, respectively: 0.83, 0.42, 0.28, 0.15.

CONCLUSIONS

Across sociodemographic strata, healthcare inequalities were identified with regards to spinal meningiomas. For benign spinal meningiomas, incidence was greatest for patients who were female, 65-84 years old, middle/high income, living in rural communities, White, and Asian/Pacific Islander. Meanwhile, for malignant spinal meningiomas incidence was greatest for males, those 45-65 years old, and middle/high income.

Economic Burden of Treatment-Resistant Depression in Privately Insured U.S. Patients with Physical Conditions

BACKGROUND

Little is known about the economic burden of treatment-resistant depression (TRD) in patients with physical conditions.

OBJECTIVE

To assess health care resource utilization (HRU) and costs, work loss days, and related costs in patients with TRD and physical conditions versus patients with the same conditions and non-TRD major depressive disorder (MDD) or without MDD.

METHODS

Adults aged < 65 years with MDD treated with antidepressants were identified in the OptumHealth Care Solutions database (July 2009-March 2017). Patients who received a diagnosis of MDD and initiated a third antidepressant regimen (index date) after 2 regimens of adequate dose and duration were defined as having TRD. Patients with non-TRD MDD and without MDD were assigned a random index date. Patients with < 6 months of continuous health plan eligibility pre- or post-index; a diagnosis of psychosis, schizophrenia, bipolar disorder/mania, dementia, and developmental disorders; and/or no baseline physical conditions (cardiovascular, metabolic, and respiratory disease or cancer) were excluded. Patients with TRD were matched 1:1 to each of the non-TRD MDD and non-MDD cohorts based on propensity scores. Per patient per year HRU, costs, and work loss outcomes were compared up to 24 months post-index date using negative binominal and ordinary least square regressions.

RESULTS

A total of 2,317 patients with TRD (mean age, 47.6 years; 63.1%, female; mean follow-up, 19.7 months) had ≥ 1 co-occurring key physical condition (cardiovascular, 52.5%; metabolic, 48.2%; respiratory, 16.4%; and cancer, 9.5%). Relative to non-TRD MDD and non-MDD cohorts, respectively, patients with TRD had 46% and 235% more inpatient admissions, 28% and 128% more emergency department visits, and 53% and 155% more outpatient visits (all P < 0.05). Health care costs were $22,541 in the TRD cohort, $17,450 in the non-TRD MDD cohort, and $10,047 in the non-MDD cohort, yielding cost differences of $5,091 (vs. non-TRD MDD) and $12,494 (vs. non-MDD; all P < 0.01). In patients with work loss data available (n = 278/cohort), those with TRD had 2.0 and 2.9 times more work loss as well as $8,676 and $10,323 higher work loss costs relative to those with non-TRD MDD and without MDD, respectively (all P < 0.001).

CONCLUSIONS

In patients with physical conditions, those with TRD had higher HRU and health care costs, work loss days, and associated costs compared with non-TRD MDD and non-MDD cohorts.

DISCLOSURES

This study was sponsored by Janssen Scientific Affairs (JSA), which was involved in all aspects of the research, including the design of the study; the collection, analysis, and interpretation of data; writing of the report; and the decision to submit the report for publication. Joshi and Daly are employed by JSA. Zhdanava, Pilon, Rossi, Morrison, and Lefebvre are employees of Analysis Group, which received funding from JSA for conducting this study and has received consulting fees from Novartis Pharmaceuticals and GSK, unrelated to this study. Kuvadia is employed by Integrated Resources, which has provided research services to JSA unrelated to this study; Joshi reports past employment by and stock ownership in Johnson & Johnson; Nelson reports advisory board, data and safety monitoring board, and consulting fees from Assurex, Eisai, FSV-7, JSA, Lundbeck, Otsuka, and Sunovion and royalties from UpToDate, unrelated to this study. This work was presented at AMCP Nexus 2019, held in National Harbor, MD, from October 29 to November 1, 2019.

Researchers' And Medical Student' Experience in Reference Management Software in a Low-Income Country

INTRODUCTION

Although the use of Reference Management Software (RMS) is increasing in developed countries, they seem to be unknown and less used in low-income countries.

AIM

To discover the major trends in the use of RMS among researchers and Ph.D. students in Tunisia, as a low-income country.

METHODS

A hardcopy survey was filled out by researchers and Ph.D. students during an educational seminar at the faculty of medicine of Sfax in 2016 with the aim to collect qualitative data to determine the participants' knowledge and use of RMS.

RESULTS

The survey collected 121 participants, among them, 53.7% know RMS. Mendeley proved to be the best-known software (41.5%), followed by Zotero (35.3%) and Endnote (23%). Training sessions in RMS were taken by 5% of participants. Among the 121 participants, 26.5%of them use RMS., Mendeley was the most used (46.9%), followed by EndNote (28.1%) and Zotero (25%). The most commonly popular feature in RMS is inserting citations (66.9%). Therefore, the analysis, of the reasons behind the choice of RMS proves that the software was used because it is convenient (38.4%),  most known (38.4%),  easy (30.7%), or suggested by colleagues (30.7%). The free and open-source software was preferred by 81% of the participants. g. However, 50.4% ignore the fact that Zotero is free. Several types and sources of captured citations were unknown by 53.8% and 59% of the rest of the participants.

CONCLUSION

The results clearly show that the lack of awareness about RMS in Tunisia is due to the absence of a formal training. As a result, the need for such training is highly important for researchers to be able to benefit from the different advantages of RMS while conducting their academic medical education.

Optimising medication data collection in a large-scale clinical trial

OBJECTIVE

Pharmaceuticals play an important role in clinical care. However, in community-based research, medication data are commonly collected as unstructured free-text, which is prohibitively expensive to code for large-scale studies. The ASPirin in Reducing Events in the Elderly (ASPREE) study developed a two-pronged framework to collect structured medication data for 19,114 individuals. ASPREE provides an opportunity to determine whether medication data can be cost-effectively collected and coded, en masse from the community using this framework.

METHODS

The ASPREE framework of type-to-search box with automated coding and linked free text entry was compared to traditional method of free-text only collection and post hoc coding. Reported medications were classified according to their method of collection and analysed by Anatomical Therapeutic Chemical (ATC) group. Relative cost of collecting medications was determined by calculating the time required for database set up and medication coding.

RESULTS

Overall, 122,910 participant structured medication reports were entered using the type-to-search box and 5,983 were entered as free-text. Free-text data contributed 211 unique medications not present in the type-to-search box. Spelling errors and unnecessary provision of additional information were among the top reasons why medications were reported as free-text. The cost per medication using the ASPREE method was approximately USD $0.03 compared with USD $0.20 per medication for the traditional method.

CONCLUSION

Implementation of this two-pronged framework is a cost-effective alternative to free-text only data collection in community-based research. Higher initial set-up costs of this combined method are justified by long term cost effectiveness and the scientific potential for analysis and discovery gained through collection of detailed, structured medication data.

Patients with Idiopathic Membranous Nephropathy: A Real-World Clinical and Economic Analysis of U.S. Claims Data

BACKGROUND

Membranous nephropathy (MN) is a common cause of nephrotic syndrome in nondiabetic adults. Approximately one third of patients with MN progress to end-stage renal disease (ESRD), while others may be successfully treated to remission. Patients with MN represent a high-risk population for whom management strategies can alter and improve outcomes. Currently, there is little real-world evidence regarding the burden of MN on health plans.

OBJECTIVES

To (a) characterize clinical and economic outcomes during a 1-year time frame among a prevalent cohort of patients with MN and (b) compare the 5% of patients incurring the highest cost with the remaining 95%.

METHODS

A retrospective analysis of commercially insured patients was conducted using MarketScan administrative health care claims data from January 1, 2012, to December 31, 2015. Patients were aged ≥ 18 years, enrolled In a fee-for-service plan, and had ≥ 2 medical claims for an MN diagnosis (ICD-9-CM codes 581.1, 582.1, and 583.1). Diagnoses indicating clear secondary causes were excluded wherever possible. Demographics were determined as of the first diagnosis date; clinical characteristics (e.g., MN-specific therapy, complications, and procedures), health care resource utilization (HCRU; inpatient, outpatient including other outpatient and emergency department [ED], and prescriptions), and costs were evaluated for 1 year following MN diagnosis. Total costs and cost distribution (2017 U.S. dollars) were examined using plan-paid and patient-paid amounts. The 95th percentile was used to categorize and compare the subcohorts: high-cost cohort (HCC) patients (top 5%) and non-high-cost cohort (NHCC) patients (the remaining 95%). Descriptive analyses, chi-square tests, and Wilcoxon rank-sum tests were conducted.

RESULTS

2,689 patients were identified (60.0% male, mean age = 46.4 years). Severity and advanced disease were observed In a higher proportion of HCC patients (n = 134) versus NHC patients (n = 2,555) via adverse health outcomes, procedures, and immunosuppressant use. HCC patients used significantly more resources on average than NHCC patients (additional use): 1.7 inpatient, 1.2 ED, and 4.8 outpatient office visits; 15 prescriptions; and 64.8 other outpatient visits (i.e., outpatient, hospital, and ESRD facilities). Total MN-related cost and mean (SD) cost per patient were $123.2 million and $45,814 ($101,353); HCC patients accounted for 43.7% of total costs for a mean cost per patient of $401,608 versus NHCC patients at 56.3% and mean cost per patient of $27,154. The greatest costs for both groups were related to outpatient visits (HCC = 46.7%; NHCC = 52.8%), inpatient visits (HCC = 27.7%; NHCC = 28.6%), and prescriptions (HCC = 25.7%; NHCC = 18.6%).

CONCLUSIONS

Patients with MN are significantly burdened with high disease severity and adverse health outcomes, resulting In substantial HCRU and costs. Health plan cost drivers for MN (HCC and NHCC patients) occurred primarily In the outpatient setting, followed by the inpatient setting and prescriptions. Modifiable aspects preceding progression to advanced renal disease and worse outcomes should be explored to Identify effective interventions and improve resource allocation earlier In the disease pathway, before ESRD.

DISCLOSURES

This study was funded by Mallinckrodt Pharmaceuticals. Kirkemo, Pavlova-Wolf, and Bartels-Peculis are employees and stockholders of Mallinckrodt Pharmaceuticals. Nazareth was an employee of Mallinckrodt Pharmaceuticals at the time of this study. Kariburyo, Xie, and Vaidya are employees of STATinMED Research, a paid consultant to Mallinckrodt Pharmaceuticals. Sim received an investigator-initiated research grant from Mallinkcrodt Pharmaceuticals. A portion of the study results were previously presented at the American Society of Nephrology (ASN) Kidney Week 2017; November 2, 2017; New Orleans, LA.

Model Comparisons of the Effectiveness and Cost-Effectiveness of Vaccination: A Systematic Review of the Literature

OBJECTIVES

To describe all published articles that have conducted comparisons of model-based effectiveness and cost-effectiveness results in the field of vaccination. Specific objectives were to 1) describe the methodologies used and 2) identify the strengths and limitations of the studies.

METHODS

We systematically searched MEDLINE and Embase databases for studies that compared predictions of effectiveness and cost-effectiveness of vaccination of two or more mathematical models. We categorized studies into two groups on the basis of their data source for comparison (previously published results or new simulation results) and performed a qualitative synthesis of study conclusions.

RESULTS

We identified 115 eligible articles (only 5% generated new simulations from the reviewed models) examining the effectiveness and cost-effectiveness of vaccination against 14 pathogens (69% of studies examined human papillomavirus, influenza, and/or pneumococcal vaccines). The goal of most of studies was to summarize evidence for vaccination policy decisions, and cost-effectiveness was the most frequent outcome examined. Only 33%, 25%, and 3% of studies followed a systematic approach to identify eligible studies, assessed the quality of studies, and performed a quantitative synthesis of results, respectively. A greater proportion of model comparisons using published studies followed a systematic approach to identify eligible studies and to assess their quality, whereas more studies using new simulations performed quantitative synthesis of results and identified drivers of model conclusions. Most comparative modeling studies concluded that vaccination was cost-effective.

CONCLUSIONS

Given the variability in methods used to conduct/report comparative modeling studies, guidelines are required to enhance their quality and transparency and to provide better tools for decision making.

The Mental Health Parity and Addiction Equity Act (MHPAEA) evaluation study: Did parity differentially affect substance use disorder and mental health benefits offered by behavioral healthcare carve-out and carve-in plans?

BACKGROUND

To assess whether implementation of the Mental Health Parity and Addiction Equity Act (MHPAEA) was associated with: 1. Reduced differences in financial requirements (i.e., copayments and coinsurance) for substance use disorder (SUD) versus specialty mental health (MH) care and 2. Reductions in the level of cost-sharing for SUD-specific services.

METHODS

MH and SUD copayments and coinsurance, 2008-2013, were obtained from benefits databases for carve-in and carve-out plans from Optum®. Linear regression was used to estimate the association of MHPAEA with differences between MH and SUD care financial requirements among carve-in and carve-out plans. A two-part regression model investigated whether MHPAEA was associated with changes in the use or level of financial requirements for SUD-specific services among carve-out plans.

RESULTS

MHPAEA was not associated with significant changes in the difference between SUD and MH copayments or coinsurance levels among either carve-in or carve-out plans. MHPAEA was associated with decreases in the levels of inpatient (in-network: -$51.17; out-of-network: -$34.39) and outpatient (in-network: -$10.26) detox copayments, but increases in the levels of in-network outpatient detox coinsurance (6 percentage points) among all carve-out plans.

CONCLUSION

Even if SUD benefits had been historically less generous than MH benefits, SUD financial requirements were already at parity with MH financial requirements by the time MHPAEA was passed, among Optum® plans. MHPAEA's SUD parity mandate reduced cost-sharing for detox services via copayments, but, for outpatient detox, the law simultaneously increased cost-sharing via coinsurance.

Patient Outcomes, Health Care Resource Use, and Costs Associated with High Versus Low HEDIS Asthma Medication Ratio

BACKGROUND

The Healthcare Effectiveness Data and Information Set (HEDIS) quality measures for asthma include the asthma medication ratio (AMR) as a marker of quality of care for patients with asthma. Few data are available to describe the association between health care use and costs in patients with high versus low AMR.

OBJECTIVE

To characterize health care use and costs associated with high versus low AMR in patients participating in commercial health plans.

METHODS

In a commercial claims database, this study retrospectively identified patients aged 5 to 64 years on December 31, 2011, who met the HEDIS definition of asthma in the premeasurement year (January 1, 2010-December 31, 2010) and the measurement year (January 1, 2011-December 31, 2011). Each patient was classified as having either high or low AMR based on the HEDIS definition. AMR was calculated as the ratio of controller to total asthma medications; high AMR was defined as ≥ 0.5. Annual per-patient health care use and costs were compared in patients with high versus low AMR using (a) multivariable linear regression models to estimate mean annual number of office visits, oral corticosteroids (OCS) bursts (≤ 15-day supply), and costs and (b) negative binomial models to estimate mean annual hospitalization and emergency department (ED) visits. All estimates were adjusted for age, sex, region, and Charlson Comorbidity Index score to control for differences between patients with high versus low AMR.

RESULTS

Patients were identified with high (30,575) and low (6,479) AMR. An average patient with high AMR had more all-cause office visits (14.1 vs. 11.0; P < 0.001), fewer all-cause hospitalizations (0.109 vs. 0.215; P < 0.001), fewer all-cause ED visits (0.321 vs. 0.768; P < 0.001), and fewer OCS bursts (0.83 vs. 1.33; P < 0.001) than an average patient with low AMR. An average patient with high AMR had fewer asthma-related hospitalizations (0.024 vs. 0.088; P < 0.001) and ED visits (0.060 vs. 0.304; P < 0.001) than an average patient with low AMR. Numbers of asthma-related annual office visits were similar between the high and low AMR groups (high 2.2 vs. low 2.2; not significant). The rate of poor asthma control events (≥ 6 short-acting beta-agonist dispensing events or ≥ 2 OCS bursts, asthma-related ED visits, or hospitalizations) was greater in patients with low AMR than in patients with high AMR (74.3% vs. 26.9%). An average patient with high AMR had lower annual nonmedication costs than an average patient with low AMR ($5,733 vs. $6,295; P = 0.011). Similar trends emerged for asthma-related costs. A patient with high AMR had higher average total annual health care costs than a patient with low AMR ($9,811 vs. $8,398; P < 0.001). These increased costs primarily resulted from increased medication costs for patients with high versus low AMR ($4,077 vs. $2,103; P < 0.001).

CONCLUSIONS

Although patients with high AMR had more office visits and higher medication (which resulted in higher overall health care) costs, their care was marked by fewer OCS bursts (indicating fewer instances of poor asthma control), fewer ED visits, and fewer hospitalizations and lower non-medication costs than those patients with low AMR. These findings support the use of AMR as a care quality measure for patients with persistent asthma.

DISCLOSURES

This study was funded by Genentech. Luskin has received consulting and lecture fees, research and travel support, and payment for developing educational presentations from Genentech and has received lecture fees from Merck. Raimundo and Solari are employees of Genentech. Antonova was employed by Genentech at the time of this study. Broder and Chang are employees of Partnership for Health Analytic Research, which received funding from Genentech to conduct this research. Study concept and design were contributed by all authors. Broder and Chang conducted analyses. All authors interpreted the data. Antonova wrote the manuscript with assistance from the other authors. All authors participated in manuscript review and revisions.

Beyond the EHR money pit: After investing big in health records, systems still face growing IT needs for upgrades, analytics and patient engagement

Demands for constant upgrades to already-installed electronic health record systems are slowing investment in other important digital technologies like telehealth, remote patient monitoring and online billing.

A Review of Nutritional Tracking Mobile Applications for Diabetes Patient Use

Diabetes, a prevalent disease in the United States, is greatly impacted by lifestyle choices, notably nutrition. The goal of this research was to determine which of the nutritional tracking applications (apps) available for Apple (Cupertino, CA) iOS, Android® (Google, Mountain View, CA), and Windows (Microsoft, Redmond, WA) platforms should be a first recommendation to diabetes patients searching for a smartphone app to aid in dietary logging and, for some apps, other varying lifestyle and health data. This project did so by identifying the smartphone apps available on the iTunes® (Apple), Google Play, and Microsoft stores that have nutritional tracking capabilities and are of potential benefit to a patient with diabetes based on certain criteria. Each of the individual apps was then evaluated to determine which would be of most benefit to a diabetes patient. The apps were assessed based on several parameters, such as their food databases, logging options, additional tracking options, interoperability with other devices and apps, and diabetes-specific resources. This information was then compiled and evaluated to determine which apps would be of most benefit for diabetes patients. This research provides valuable information for both patients and healthcare providers because the results of this study can be used as a reference for practitioners wishing to make app recommendations for diabetes patients who are implementing lifestyle change as an aspect of therapy.

[Systematic economic assessment and quality evaluation for traditional Chinese medicines]

To learn about the economic studies on traditional Chinese medicines in domestic literatures, in order to analyze the current economic assessment of traditional Chinese medicines and explore the existing problems. Efforts were made to search CNKI, VIP, Wanfang database and CBM by computer and include all literatures about economic assessment of traditional Chinese medicines published on professional domestic journals in the systematic assessment and quality evaluation. Finally, 50 articles were included in the study, and the systematic assessment and quality evaluation were made for them in terms of titles, year, authors' identity, expense source, disease type, study perspective, study design type, study target, study target source, time limit, cost calculation, effect indicator, analytical technique and sensitivity analysis. The finally quality score was 0.74, which is very low. The results of the study showed insufficient studies on economics of traditional Chinese medicines, short study duration and simple evaluation methods, which will be solved through unremitting efforts in the future.

Pharmaco-utilisation and related costs of drugs used to treat schizophrenia and bipolar disorder in Italy: the IBIS study

BACKGROUND

Schizophrenia and bipolar disorder (BD) are psychiatric diseases that are commonly managed with antipsychotics. Treatment pathways are highly variable and no universal treatment guidelines are available. The primary objective of the Italian Burden of Illness in Schizophrenia and BD (IBIS) study was to describe pharmaco-utilisation of antipsychotic treatments and characteristics of patients affected by schizophrenia or BD. A secondary objective was to describe costs of illness for patients with schizophrenia or BD.

METHODS

IBIS was a multicentre, real-world, retrospective, observational cohort study based on data obtained from administrative databases of 16 Local Health Units in Italy (~7.5 million individuals). Patients with schizophrenia or BD ≥18 years of age treated with antipsychotics between 1 January 2008 and 31 December 2009 were included in the primary analysis. Pharmaco-utilisation data were gathered over a follow-up period of 12 months.

RESULTS

Patients with schizophrenia and BD received a wide variety of antipsychotic medications. The proportion of patients on antipsychotic monotherapy was 68% in patients with schizophrenia and 70% in patients with BD. In patients with schizophrenia, ~1/3 of patients receiving antipsychotic monotherapy also received mood stabilisers and/or antidepressants (34.7%) compared with over half of those on antipsychotic polytherapy (52.2%). In patients with BD, use of mood stabilisers and/or antidepressants was even higher; 76.9% of patients receiving antipsychotic monotherapy also received mood stabilisers and/or antidepressants compared with 85.5% of patients on antipsychotic polytherapy. Switch therapy was more frequent in patients with BD than in patients with schizophrenia, whereas add-on therapy was more frequent in patients with schizophrenia than in patients with BD. The mean total disease-related cost per patient per annum was higher in patients with schizophrenia (€4,157) than in patients with BD (€3,301). The number and cost of hospitalisations was higher in patients with BD, whereas the number and cost of nursing home stays was higher in patients with schizophrenia.

CONCLUSION

Use of administrative databases has permitted retrieval of comprehensive information about therapeutic pathways, diagnostic history and costs in patients affected by schizophrenia or BD. A need for personalised treatment pathways has been described.

TRIAL REGISTRATION

clinicaltrials.gov: NCT01392482 ; first received June 29, 2011.

A Cost-Benefit Analysis: Electronic Clinical Procedural Resource Supporting Evidence-Based Practice

There are many benefits of having an electronic reference at the patient bedside. Because of the significant costs involved, it is important to first understand if staff will utilize the system. A cost-benefit analysis of such an electronic clinical procedural resource at one large, academic health system showed a significant savings of $360,899. Having an electronic reference system at the patient bedside increased standardization throughout the organization. Additionally, clinical and instructional experts are not needed to write standard policies and procedures. Ongoing education was needed to increase utilization of the system within the organization.

WHO essential medicines policies and use in developing and transitional countries: an analysis of reported policy implementation and medicines use surveys

BACKGROUND

Suboptimal medicine use is a global public health problem. For 35 years the World Health Organization (WHO) has promoted essential medicines policies to improve quality use of medicines (QUM), but evidence of their effectiveness is lacking, and uptake by countries remains low. Our objective was to determine whether WHO essential medicines policies are associated with better QUM.

METHODS AND FINDINGS

We compared results from independently conducted medicines use surveys in countries that did versus did not report implementation of WHO essential medicines policies. We extracted survey data on ten validated QUM indicators and 36 self-reported policy implementation variables from WHO databases for 2002-2008. We calculated the average difference (as percent) for the QUM indicators between countries reporting versus not reporting implementation of specific policies. Policies associated with positive effects were included in a regression of a composite QUM score on total numbers of implemented policies. Data were available for 56 countries. Twenty-seven policies were associated with better use of at least two percentage points. Eighteen policies were associated with significantly better use (unadjusted p<0.05), of which four were associated with positive differences of 10% or more: undergraduate training of doctors in standard treatment guidelines, undergraduate training of nurses in standard treatment guidelines, the ministry of health having a unit promoting rational use of medicines, and provision of essential medicines free at point of care to all patients. In regression analyses national wealth was positively associated with the composite QUM score and the number of policies reported as being implemented in that country. There was a positive correlation between the number of policies (out of the 27 policies with an effect size of 2% or more) that countries reported implementing and the composite QUM score (r=0.39, 95% CI 0.14 to 0.59, p=0.003). This correlation weakened but remained significant after inclusion of national wealth in multiple linear regression analyses. Multiple policies were more strongly associated with the QUM score in the 28 countries with gross national income per capita below the median value (US$2,333) (r=0.43, 95% CI 0.06 to 0.69, p=0.023) than in the 28 countries with values above the median (r=0.22, 95% CI -0.15 to 0.56, p=0.261). The main limitations of the study are the reliance on self-report of policy implementation and measures of medicine use from small surveys. While the data can be used to explore the association of essential medicines policies with medicine use, they cannot be used to compare or benchmark individual country performance.

CONCLUSIONS

WHO essential medicines policies are associated with improved QUM, particularly in low-income countries. Please see later in the article for the Editors' Summary.

A low computation cost method for seizure prediction

The dynamic changes of electroencephalograph (EEG) signals in the period prior to epileptic seizures play a major role in the seizure prediction. This paper proposes a low computation seizure prediction algorithm that combines a fractal dimension with a machine learning algorithm. The presented seizure prediction algorithm extracts the Higuchi fractal dimension (HFD) of EEG signals as features to classify the patient's preictal or interictal state with Bayesian linear discriminant analysis (BLDA) as a classifier. The outputs of BLDA are smoothed by a Kalman filter for reducing possible sporadic and isolated false alarms and then the final prediction results are produced using a thresholding procedure. The algorithm was evaluated on the intracranial EEG recordings of 21 patients in the Freiburg EEG database. For seizure occurrence period of 30 min and 50 min, our algorithm obtained an average sensitivity of 86.95% and 89.33%, an average false prediction rate of 0.20/h, and an average prediction time of 24.47 min and 39.39 min, respectively. The results confirm that the changes of HFD can serve as a precursor of ictal activities and be used for distinguishing between interictal and preictal epochs. Both HFD and BLDA classifier have a low computational complexity. All of these make the proposed algorithm suitable for real-time seizure prediction.

Construction and validation of a web-based epidemiological database for inflammatory bowel diseases in Europe An EpiCom study

BACKGROUND

The EpiCom-study investigates a possible East-West-gradient in Europe in the incidence of IBD and the association with environmental factors. A secured web-based database is used to facilitate and centralize data registration.

AIM

To construct and validate a web-based inception cohort database available in both English and Russian language.

METHOD

The EpiCom database has been constructed in collaboration with all 34 participating centers. The database was translated into Russian using forward translation, patient questionnaires were translated by simplified forward-backward translation. Data insertion implies fulfillment of international diagnostic criteria, disease activity, medical therapy, quality of life, work productivity and activity impairment, outcome of pregnancy, surgery, cancer and death. Data is secured by the WinLog3 System, developed in cooperation with the Danish Data Protection Agency. Validation of the database has been performed in two consecutive rounds, each followed by corrections in accordance with comments.

RESULTS

The EpiCom database fulfills the requirements of the participating countries' local data security agencies by being stored at a single location. The database was found overall to be "good" or "very good" by 81% of the participants after the second validation round and the general applicability of the database was evaluated as "good" or "very good" by 77%. In the inclusion period January 1st -December 31st 2010 1336 IBD patients have been included in the database.

CONCLUSION

A user-friendly, tailor-made and secure web-based inception cohort database has been successfully constructed, facilitating remote data input. The incidence of IBD in 23 European countries can be found at www.epicom-ecco.eu.

A comparison of the hospital costs of open vs. minimally invasive surgical management of necrotizing pancreatitis

BACKGROUND

Infected necrotizing pancreatitis is a major burden for both the patient and the health care system. Little is known about how hospital costs break down and how they may have shifted with the increasing use of minimally invasive techniques. The aim of this study was to analyse inpatient hospital costs associated with pancreatic necrosectomy.

METHODS

A prospective database was used to identify all patients who underwent an intervention for necrotizing pancreatitis. Costs of treatment were calculated using detailed information from the Decision Support Department. Costs for open and minimally invasive surgical modalities were compared.

RESULTS

Twelve open and 13 minimally invasive necrosectomies were performed in a cohort of 577 patients presenting over a 50-month period. One patient in each group died in hospital. Overall median stay was 3.8 days in the intensive care unit (ICU) and 44 days on the ward. The median overall treatment cost was US$ 56,674. The median largest contributors to this total were ward (26.3%), surgical personnel (22.3%) and ICU (17.0%) costs. These did not differ statistically between the two treatment modalities.

CONCLUSIONS

Pancreatic necrosectomy uses considerable health care resources. Minimally invasive techniques have not been shown to reduce costs. Any intervention that can reduce the length of hospital and, in particular, ICU stay by reducing the incidence of organ failure or by preventing secondary infection is likely to be cost-effective.

Trends in patient cost sharing for clinical services used as quality indicators

BACKGROUND

Patient copayments for all medical services have increased dramatically. There are few data available regarding how copayments have changed for services commonly considered to be quality indicators.

OBJECTIVE

Describe the relative change in copayments for services used as quality indicators and interventions subject to programs to control utilization.

DESIGN

A large claims database was used to assess copayment changes from 2001 to 2006 for selected drug and non-drug services in patient cohorts with specific chronic diseases.

SUBJECTS

Approximately 5 million commercially-insured individuals enrolled in a variety of fee-for-service and capitated health plans.

MEASUREMENTS

Copayment trends were calculated as the change in the average amount paid per unit service from 2001 to 2006.

RESULTS

Out-of-pocket payments for services targeted by quality improvement initiatives increased substantially [>50%] and in a similar magnitude to interventions subject to programs to control their use. For prescription drugs, the trend was driven more by copayment increases for branded medications [$10 per prescription] than for generic drugs [$2 per prescription]. Copayments for non-drug preventive services rose modestly.

CONCLUSIONS

Benefit designers should consider reversing the trend of copayment increases for services considered to be indicators of high quality care.

Healthcare resource utilization following switch or discontinuation in multiple sclerosis patients on disease modifying drugs

OBJECTIVE

The objective of this study was to explore the cost and utilization in the period following discontinuations or switches of disease modifying drugs (DMDs) for patients with multiple sclerosis (MS). Secondary objectives included an assessment of the time to switch or discontinuation from index DMD treatment.

METHODS

Cases were defined as a billed MS diagnosis in continuously enrolled patients initiated with interferon-beta1a IM, interferon-beta1b SC, glatiramer acetate, and interferon-beta1a SC found in the PharMetrics Patient-Centric Database. Information on patient demographics, diagnoses, procedures, pharmacy-dispensed drugs, and costs was extracted; reasons for discontinuation and expenses outside of the healthcare system were not available. Treatment discontinuations and switches between study drugs were defined using pharmacy prescription patterns and analyzed by descriptive and regression methods. The non-pharmacy medical costs in the 18 months following switching or discontinuation were compared to the costs in a randomly selected similar period for those patients who did not switch or discontinue these agents.

RESULTS

A total of 5,772 MS patients were continuously enrolled and were treated with one or more of the four drugs of interest, and about half of these patients switched drugs or discontinued treatment for at least 90 days. Patients initiated with interferon-beta1b SC were more likely to discontinue treatment compared to interferon-beta1a IM users. Non-pharmaceutical medical costs were highest for those switching treatments followed by those discontinuing DMDs in the 18 months following a switch or discontinuation, compared to persistent users of these drugs. Interferon beta1b SC initiators had higher costs following changes or discontinuations, while glatiramer acetate and interferon-beta1a SC users had lower subsequent costs compared to interferon-beta1a IM users.

LIMITATIONS

Unfortunately, the reasons for stopping the initial treatment cannot be determined from analysis of an administrative claims database. Also, the MS cases followed in this analysis are billing diagnostic events unconfirmed through a review of medical records or other data sources. The results are unstratified in terms of severity and thus while treatment patterns may vary for patients with different types of MS (e.g., progressive vs. relapsing-remitting), this cannot be examined in this analysis.

CONCLUSION

Changing or discontinuing DMDs is common among MS patients and is associated with higher non-pharmaceutical medical costs that vary based on the initiating drug and other demographics characteristics.

Development of a database for government-funded health/functional food research

The Korean Health/Functional Food Act of 2002 has led to the promotion of research on health/functional foods (HFFs). In order to track government-funded studies on HFFs, a free accessible database (National Research & Development on Functional Food, NaReaD(ff)) has been established by the Korea Food and Drug Administration. About 200 project reports funded by government agencies from 1993 through 2007 were retrieved, using existing government-wide online databases created by the Korea Institute Science and Technology, Evaluation and Planning and the Korea Institute of Science and Technology Information. In 2008, the database was released with information regarding individual projects and technological achievements for individual ingredients with a vision for HFF development. Overall, government-funded HFF research has primarily involved botanicals including herbs and food plants. The immune system, oxidant stress alleviation, and the cardiovascular system are the three leading health systems being investigated. With regard to the types of studies performed, the majority were in vitro studies and animal studies with limited numbers of human intervention studies. Government funds have been fragmented for many different ingredients, and this represents a major gap in HFF development. This database is most valuable for evaluating trends in government-funded HFF research. It is also useful to identify research overlaps and gaps and to help research scientists within academia and industry identify potential sources of government funding.

[Austrian haemophilia registry: up-date 2008 ]

The treatment of haemophilia requires continuous development of knowledge related to various aspects of diagnosis and therapy. It is, therefore, essential to collect valid and representative data, which are comparable on an international level. The Austrian Haemophilia Registry was set up by the Scientific Advisory Panel of the Austrian Haemophilia Society and by the patient organisation. For the design, it was decided to divide the registry into three sections, two concerning quality control and a third concerning scientific questions, the latter requiring written informed consent. A web-based software is used to collect data. Transfer and storage of data are secured and the server is situated in a computer center with video and access control. Data entry was initiated early 2008. Currently, only preliminary data are available. Our further focus is on continued data entry, which will further enable us to provide information concerning the characteristics of the haemophilia patient population in Austria and the actual treatment modalities used.

Educational attainment and smoking among women: risk factors and consequences for offspring

We examine the association between education and smoking by women in the population, including smoking during pregnancy, and identify risk factors for smoking and the consequences of smoking in pregnancy for children's smoking and behavioral problems. Secondary analyses of four national data sets were implemented: The National Survey of Drug Use and Health (2006), the National Longitudinal Survey of Youth (1979-2004); the National Longitudinal Survey of Adolescent Health (Wave III); National Health and Nutrition Examination Survey (2005-2006). The lower the level of education, the greater the risk of being a current smoker, smoking daily, smoking heavily, being nicotine dependent, starting to smoke at an early age, having higher levels of circulating cotinine per cigarettes smoked, and continuing to smoke in pregnancy. The educational gradient is especially strong in pregnancy. Educational level and smoking in pregnancy independently increase the risk of offspring smoking and antisocial and anxious/depressed behavior problems. These effects persist with control for other covariates, except maternal age at child's birth, which accounts for the impact of education on offspring smoking and anxious/depressed behavior problems. Women with low education should be the target of public health efforts toward reducing tobacco use. These efforts need to focus as much on social conditions that affect women's lives as on individual level interventions. These interventions would have beneficial effects not only for the women themselves but also for their offspring.

Validity of autism diagnoses using administrative health data

It is necessary to monitor autism prevalence in order to plan education support and health services for affected children. This study was conducted to assess the accuracy of administrative health databases for autism diagnoses. Three administrative health databases from the province of Nova Scotia were used to identify diagnoses of autism spectrum disorders (ASD): the Hospital Discharge Abstract Database, the Medical Services Insurance Physician Billings Database and the Mental Health Outpatient Information System database. Seven algorithms were derived from combinations of requirements for single or multiple ASD claims from one or more of the three administrative databases. Diagnoses made by the Autism Team of the IWK Health Centre, using state-of-the-art autism diagnostic schedules, were compared with each algorithm, and the sensitivity, specificity and C-statistic (i.e. a measure of the discrimination ability of the model) were calculated. The algorithm with the best test characteristics was based on one ASD code in any of the three databases (sensitivity=69.3%). Sensitivity based on an ASD code in either the hospital or the physician billing databases was 62.5%. Administrative health databases are potentially a cost efficient source for conducting autism surveillance, especially when compared to methods involving the collection of new data. However, additional data sources are needed to improve the sensitivity and accuracy of identifying autism in Canada.

Making health technology assessment information available for decision making: the development of a Thai database

In Thailand, there is an attempt to develop the Thai HTA database in order to improve the accessibility and usefulness of HTA information. At present, the database is available online at www.db.hitap.net. The database includes (1) economic evaluation studies i.e. cost-minimization analysis, cost-effectiveness analysis, cost-benefit analysis, and cost-utility analysis, (2) outcome assessment studies i.e. randomized controlled trials, and (3) quantitative measured quality of life studies. All HTA studies related to the Thai context, and published in either Thai or English from 1990 onward, are eligible for inclusion in the database. In addition, there is a quality evaluation for each economic evaluation study which will help readers, who have limited knowledge about the method, to understand and make appropriate use of the information in their own settings. This may also raise awareness among researchers, who will conduct economic evaluation studies in the future, to adhere to the standard methodological guidelines because the quality evaluation was developed based on the national guidelines published in this supplement journal.

[Use of geographical information systems in parasitic diseases and the importance of animal health economics]

In the world, economical losses due to the parasitic diseases reach enormous ratios in animal production. Both developed and developing countries set aside a considerable budget to control these parasitic diseases. This situation aids in the improvement of control methods of parasitic diseases. Also, it causes new ways of investigation that includes observation, evaluation and prevention of parasitic diseases. The Geographical Information System (GIS) has recently become one of the most common methods utilized to provide disease information technology with computer supported technology in many countries. The most important qualities of GIS are the formation of a powerful database, continual updating and rapid provision of coordination related to units. Many factors are evaluated at the same time by the system and also, results from analysis of data related to disease and their causes could reduce or prevent economical losses due to parasitic disease. In this study, possible uses of Geographical Information Systems against parasitic diseases and an approach in terms of animal health economics were presented.

Improving the quality of data entry in a low-budget head injury database

BACKGROUND

To assess the efficacy of a centralised review of a voluntary low-budget head injury database with a retrospective analysis of data before and after a centralised review.

METHOD

A computerised data collection (Neurolink) on traumatic brain injury cases admitted to three neuro-intensive care units in Milan (Italy): analysis of a three-year period (1999-2001). Data from 499 patients (epidemiology, type of lesion, clinical course, monitoring, treatment, complications and outcome). The audit involved a review of forms relating to patients enrolled in the three-year period, with the aim of improving the quality of data entry. Missing data in all empty fields were identified; evident errors and contradictory data were identified and corrected; missing and final data were analysed to test the efficacy of the review.

FINDINGS

The total post-review missing data rate was significantly lower than the paired pre-review missing data rate (p = 0.001). The same was confirmed for each of the 3 years (p = 0.001 for each year). The missing data rate significantly improved over the three-year period (p = 0.001). Data for the pre-hospitalisation period had the highest missing rates; data regarding the ICU stay showed the greatest improvement after the review. A total of 407 items (0.44%) were identified as errors.

CONCLUSIONS

Data quality is fundamental to avoid information bias in database analysis. This study indicates that it is possible to generate a serious data collection without significant resources. Audit seems to be an important tool before the final data is used for scientific projects.

National evaluation of US newborn screening system components

Newborn screening has existed as a state-based public health service since the early 1960s. Every state and most territorial jurisdictions have comprehensive newborn screening programs in place, but in the United States a national newborn screening policy does not exist. This results in different administrative infrastructures, screening requirements, laboratory and follow-up services, medical management approaches, and related activities across the country. Federal initiatives and support have contributed to limited evaluations of various aspects of individual newborn screening programs at the national level, but funding is an issue. The national evaluation strategies have taken various forms, all with the intent of improving the screening system through review of actions taken and suggestions for future improvements. While participation in the national evaluation effort for newborn screening laboratory practices includes all US programs, and this has aided in improving quality and harmonizing protocols, other national evaluation activities have been only moderately successful. National data reporting of quality indicators for various program elements must be comprehensive and timely, and the elements must be universally accepted in order to meet the evaluation and improvement needs of the national newborn screening system. A comprehensive real time national evaluation activity will likely require additional resources and enforcement incentives. Limited federal actions through grant incentives and selected reporting requirements provide a possible means of stimulating programs to participate in national harmonization efforts.

Morbidity and cost burden of methicillin-resistant Staphylococcus aureus in early onset ventilator-associated pneumonia

Introduction

To gain a better understanding of the clinical and economic outcomes associated with methicillin-resistant Staphylococcus aureus (MRSA) infection in patients with early onset ventilator-associated pneumonia (VAP), we retrospectively analyzed a multihospital US database to identify patients with VAP over a 24 month period (2002–2003).

Method

Data recorded included physiologic, laboratory, culture, and other clinical variables from 59 institutions. VAP was defined as new positive respiratory culture after at least 24 hours of mechanical ventilation (MV) and the presence of primary or secondary ICD-9-CM diagnosis codes of pneumonia. Outcomes measures included in-hospital morbidity and mortality for the population overall and after onset of VAP (duration of MV, intensive care unit [ICU] stay, in-hospital stay, and case mix and severity-adjusted operating cost). The overall cost was calculated at the hospital level using the Center for Medicare and Medicaid Services Cost/Charge Index for each calendar year.

Results

A total of 499 patients were identified as having VAP. S. aureus was the leading organism (31% of isolates). Patients with MRSA were significantly older than patients with methicillin-sensitive Staphylococcus aureus (MSSA; median age 74 versus 67 years, P < 0.05) and more likely to be medical patients. Compared with MSSA patients, MRSA patients on average consumed excess resources of 4.4 (95% confidence interval 0.6–8.2) overall MV days, 3.8 (-0.5 to +8.0) days of inpatient length of stay (LOS), 5.3 (1.0–9.7) ICU days, and US$7731 (-US$8393 to +US$23,856) total cost after controlling for case mix and other factors. Furthermore, MRSA patients needed excess resources after the onset of VAP (4.5 [95% confidence interval 1.0–8.1] MV days, 3.7 [-0.5 to +8.0] inpatient days, and 4.4 [0.4–8.4] ICU days) after controlling for the same case mix and admission severity covariates.

Conclusion

S. aureus remains a common cause of VAP. VAP due to MRSA was associated with increased overall LOS, ICU LOS, and attributable ICU LOS compared with MSSA-related VAP. Although not statistically significant because of small sample size and large variation, the attributable excess costs of MRSA amounted to approximately US$8000 per case after controlling for case mix and severity.

Data Standards: A Call to Action

Access to data is something that every molecular biologist takes for granted nowadays, but data alone is of little use unless it is made available in a useable form through the development and global uptake of data standards. The challenge of standards development has been taken up by grass-roots movements working within several different branches of the biomedical research community. Many of these initiatives are proving extremely successful; for example, the Gene Ontology, which provides a controlled vocabulary for describing the properties of gene products, the Microarray Gene Expression Data Society's standards for describing microarray experiments, and the emerging standards developed by the Proteomics Standards Initiative are gaining broad acceptance. Standards development now faces its greatest ever challenge--the integration of diverse data types to fulfill the goals of systems biology. Now is the time for the communities that are developing these standards, the funding bodies that have invested so heavily in high-throughput data generation, and the publishers of biomedical research papers to cooperate fully to make the goals of integrated data analysis a reality.