Modeling Disease Severity in Multiple Sclerosis Using Electronic Health Records

Objective

To optimally leverage the scalability and unique features of the electronic health records (EHR) for research that would ultimately improve patient care, we need to accurately identify patients and extract clinically meaningful measures. Using multiple sclerosis (MS) as a proof of principle, we showcased how to leverage routinely collected EHR data to identify patients with a complex neurological disorder and derive an important surrogate measure of disease severity heretofore only available in research settings.

Methods

In a cross-sectional observational study, 5,495 MS patients were identified from the EHR systems of two major referral hospitals using an algorithm that includes codified and narrative information extracted using natural language processing. In the subset of patients who receive neurological care at a MS Center where disease measures have been collected, we used routinely collected EHR data to extract two aggregate indicators of MS severity of clinical relevance multiple sclerosis severity score (MSSS) and brain parenchymal fraction (BPF, a measure of whole brain volume).

Results

The EHR algorithm that identifies MS patients has an area under the curve of 0.958, 83% sensitivity, 92% positive predictive value, and 89% negative predictive value when a 95% specificity threshold is used. The correlation between EHR-derived and true MSSS has a mean R² = 0.38±0.05, and that between EHR-derived and true BPF has a mean R² = 0.22±0.08. To illustrate its clinical relevance, derived MSSS captures the expected difference in disease severity between relapsing-remitting and progressive MS patients after adjusting for sex, age of symptom onset and disease duration (p = 1.56×10⁻¹²).

Conclusion

Incorporation of sophisticated codified and narrative EHR data accurately identifies MS patients and provides estimation of a well-accepted indicator of MS severity that is widely used in research settings but not part of the routine medical records. Similar approaches could be applied to other complex neurological disorders.     

Electronic Medical Records and Electronic Health Records: Overview for Nurse Practitioners

Electronic medical records (EMRs) and electronic health records (EHRs) have become essential systems by which nurse practitioners (NPs) communicate vital patient information to other members of the health care team as well as to patients. In this article we examine the important distinctions between EMRs and EHRs; review the genesis of these types of records; summarize applicable provisions of the Health Insurance Portability and Accountability Act from a recent legal case centered around NP utilization of EMRs and EHRs; address open patient access to medical information; and examine threats to security. Suggestions are offered on ways in which NPs can safeguard confidential patient information.     

A Quantitative Assessment Method for Ascaris Eggs on Hands

The importance of hands in the transmission of soil transmitted helminths, especially Ascaris and Trichuris infections, is under-researched. This is partly because of the absence of a reliable method to quantify the number of eggs on hands. Therefore, the aim of this study was to develop a method to assess the number of Ascaris eggs on hands and determine the egg recovery rate of the method. Under laboratory conditions, hands were seeded with a known number of Ascaris eggs, air dried and washed in a plastic bag retaining the washing water, in order to determine recovery rates of eggs for four different detergents (cationic [benzethonium chloride 0.1% and cetylpyridinium chloride CPC 0.1%], anionic [7X 1% - quadrafos, glycol ether, and dioctyl sulfoccinate sodium salt] and non-ionic [Tween80 0.1% -polyethylene glycol sorbitan monooleate]) and two egg detection methods (McMaster technique and FLOTAC). A modified concentration McMaster technique showed the highest egg recovery rate from bags. Two of the four diluted detergents (benzethonium chloride 0.1% and 7X 1%) also showed a higher egg recovery rate and were then compared with de-ionized water for recovery of helminth eggs from hands. The highest recovery rate (95.6%) was achieved with a hand rinse performed with 7X 1%. Washing hands with de-ionized water resulted in an egg recovery rate of 82.7%. This washing method performed with a low concentration of detergent offers potential for quantitative investigation of contamination of hands with Ascaris eggs and of their role in human infection. Follow-up studies are needed that validate the hand washing method under field conditions, e.g. including people of different age, lower levels of contamination and various levels of hand cleanliness.     

A Full Color System for Quantitative Assessment of Histochemical and Immunohistochemical Staining Patterns

Quantitative measures of staining distributions are important to compare the presence and patterns of cells or macromolecules. Typically, achromatic thresholding systems are used to compare staining distributions. Achromatic video signals, however, lack sufficient resolution to identify and compare chromatic changes. The purpose of this study is to describe a full color system for analysis of chromatic staining distributions. The hardware system includes a Leitz Diaplan microscope, video camera, GVP videoboard and Amiga 3000 computer. Software was developed in “C” to partition the video signal into hue (H), saturation (S) and value (V). Also, percentage of stained area was determined. Kodak color filters were used to assess the accuracy and precision of the system. Craniofacial tissues were stained with varying concentrations of toluidine blue and primary anti-Brdll antibodies. HSV and the percentage of stained areas were determined and displayed low coefficients of error. HSV values also performed as expected for standard filters as well as cellular staining concentrations. This system is easily implemented and should be useful for comparing chromatic changes with any color resulting from histochemical or immunohistochemical procedures.     

电子健康档案符合性测试的提出与设计

卫生信息化建设已然成为世界各国推进卫生服务可及性过程中重要的关注点。在审视我国以电子健康档案和电子病历为核心的卫生信息化建设理论研究和实践探索的基础上,阐述电子健康档案符合性测试的内涵和基本特征,深入探讨电子健康档案符合性测试点要求和用例设计,并提出电子健康档案符合性测试的基本思路、技术路线和测试管理流程。     

卫生信息化背景下电子健康档案建设的法律思考

在卫生信息化日快速发展的背景下, 电子健康档案日益被重视并开始逐步推广,但是其中存在的法律问题也同时显现。在分析我国电子健康档案信息安全的基础上,对电子健康档案的法律地位、患者的隐私权、医师注意义务以及政府的公共行政权利等方面进行了探讨。     

A Method for the Quantitative Assessment of Wound-induced Chitinase Activity in Potato Tubers

A method for the quantitative assessment of chitinase activity was developed. Dilution series of crude potato tuber chitinase extracts were assayed with a colorimetric microtitre plate assay. using CM-chitin-RBV as enzyme substrate. Linearity between absorbance values mea-sured (540 nm) and enzyme concentration was found to be limited to the low concentration range. where depletion of the substrate was no longer limiting. As as absorbance of 0.1 always fell within the concentration range for which absorbance-concentration linearity was valid. one unit of enzyme activity was defined as the amount of enzyme needed to yield and A of 0.1. A more reliable method for the assessment of chitinase activity was established by basing the difinition of enzyme, activity on a concentration rather than on as absorbance value. as was done previously. Using this method, differences in the rate of chitinase induction upon wounding were demonstrated for six commercial potato cultivars.     

Chapter 13: Mining Electronic Health Records in the Genomics Era

Abstract: The combination of improved genomic analysis methods, decreasing genotyping costs, and increasing computing resources has led to an explosion of clinical genomic knowledge in the last decade. Similarly, healthcare systems are increasingly adopting robust electronic health record (EHR) systems that not only can improve health care, but also contain a vast repository of disease and treatment data that could be mined for genomic research. Indeed, institutions are creating EHR-linked DNA biobanks to enable genomic and pharmacogenomic research, using EHR data for phenotypic information. However, EHRs are designed primarily for clinical care, not research, so reuse of clinical EHR data for research purposes can be challenging. Difficulties in use of EHR data include: data availability, missing data, incorrect data, and vast quantities of unstructured narrative text data. Structured information includes billing codes, most laboratory reports, and other variables such as physiologic measurements and demographic information. Significant information, however, remains locked within EHR narrative text documents, including clinical notes and certain categories of test results, such as pathology and radiology reports. For relatively rare observations, combinations of simple free-text searches and billing codes may prove adequate when followed by manual chart review. However, to extract the large cohorts necessary for genome-wide association studies, natural language processing methods to process narrative text data may be needed. Combinations of structured and unstructured textual data can be mined to generate high-validity collections of cases and controls for a given condition. Once high-quality cases and controls are identified, EHR-derived cases can be used for genomic discovery and validation. Since EHR data includes a broad sampling of clinically-relevant phenotypic information, it may enable multiple genomic investigations upon a single set of genotyped individuals. This chapter reviews several examples of phenotype extraction and their application to genetic research, demonstrating a viable future for genomic discovery using EHR-linked data.

What to Learn in This Chapter

• Describe the types of information available in Electronic Health Records (EHRs), and the relative sensitivity and positive predictive value of each
• Describe the difference between unstructured and structured information in the EHR
• Describe methods for developing accurate phenotype algorithms that integrate structured and unstructured EHR information, and the roles played by billing codes, laboratory values, medication data, and natural language processing
• Describe recent uses of EHR-derived phenotypes to study genome-phenome relationships
• Describe the cost advantages unique to EHR-linked biobanks, and the ability to reuse genetic data for many studies
• Understand the role of EHRs to enable phenome-wide association studies of genetic variants

This article is part of the “Translational Bioinformatics” collection for PLOS Computational Biology.

     

A Qualitative Exploration of Workarounds Related to the Implementation of National Electronic Health Records in Early Adopter Mental Health Hospitals

Aims

To investigate the perceptions and reported practices of mental health hospital staff using national hospital electronic health records (EHRs) in order to inform future implementations, particularly in acute mental health settings.

Methods

Thematic analysis of interviews with a wide range of clinical, information technology (IT), managerial and other staff at two early adopter mental health National Health Service (NHS) hospitals in London, UK, implementing national EHRs.

Results

We analysed 33 interviews. We first sought out examples of workarounds, such as delayed data entry, entering data in wrong places and individuals using the EHR while logged in as a colleague, then identified possible reasons for the reported workarounds. Our analysis identified four main categories of factors contributing to workarounds (i.e., operational, cultural, organisational and technical). Operational factors included poor system integration with existing workflows and the system not meeting users'' perceived needs. Cultural factors involved users'' competence with IT and resistance to change. Organisational factors referred to insufficient organisational resources and training, while technical factors included inadequate local technical infrastructure. Many of these factors, such as integrating the EHR system with day-to-day operational processes, staff training and adequate local IT infrastructure, were likely to apply to system implementations in various settings, but we also identified factors that related particularly to implementing EHRs in mental health hospitals, for example: EHR system incompatibility with IT systems used by mental health–related sectors, notably social services; the EHR system lacking specific, mental health functionalities and options; and clinicians feeling unable to use computers while attending to distressed psychiatric patients.

Conclusions

A better conceptual model of reasons for workarounds should help with designing, and supporting the implementation and adoption of, EHRs for use in hospital mental health settings.     

Approaches to Recording Drug Allergies in Electronic Health Records: Qualitative Study

Background

Drug allergy represent an important subset of adverse drug reactions that is worthy of attention because many of these reactions are potentially preventable with use of computerised decision support systems. This is however dependent on the accurate and comprehensive recording of these reactions in the electronic health record. The objectives of this study were to understand approaches to the recording of drug allergies in electronic health record systems.

Materials and Methods

We undertook a case study comprising of 21 in-depth interviews with a purposefully selected group of primary and secondary care clinicians, academics, and members of the informatics and drug regulatory communities, observations in four General Practices and an expert group discussion with 15 participants from the Allergy and Respiratory Expert Resource Group of the Royal College of General Practitioners.

Results

There was widespread acceptance among healthcare professionals of the need for accurate recording of drug allergies and adverse drug reactions. Most drug reactions were however likely to go unreported to and/or unrecognised by healthcare professionals and, even when recognised and reported, not all reactions were accurately recorded. The process of recording these reactions was not standardised.

Conclusions

There is considerable variation in the way drug allergies are recorded in electronic health records. This limits the potential of computerised decision support systems to help alert clinicians to the risk of further reactions. Inaccurate recording of information may in some instances introduce new problems as patients are denied treatments that they are erroneously believed to be allergic to.     

美国电子健康档案发展策略及启示

美国是电子健康档案建设的先行者,经过40余年的发展,取得了显著进展,并在电子健康档案的组织建设、标准制定、资金筹集、隐私与安全保护、利益相关者协调方面积累了丰富的经验。主要论述了美国电子健康档案的发展历程及具体策略,以期为我国电子健康档案建设提供借鉴。     

A Deterministic Method for Deriving Site-Specific Human Health Assessment Criteria for Contaminants in Soil

A method for deriving Site-Specific Assessment Criteria (SSAC) for use when considering risk to human health from chronic exposure to heavy metals (except lead), metalloids, and organic substances in soil, with application to the United Kingdom (UK), is described. The SSAC represents the soil concentration above which an unacceptable risk to human health may be indicated.

The method considers the UK standard land uses (residential with and without plant uptake, allotment gardens, and commercial/industrial) by applying the default exposure factors and algorithms provided. Non-standard land uses can be also considered. Site-specific determinations of contaminant bioaccessibility or of plant-to-soil concentration factors may be used if available.

The method adopts the risk-based source-pathway-receptor pollutant linkage framework and a deterministic methodology. Exposure pathways considered are direct ingestion of soil and dust, consumption of home grown or allotment vegetables, ingestion of soil attached to such vegetables, inhalation of soil vapors outdoors and inhalation of soil vapors indoors. A test for the significance of the dermal pathway is also included.

It is not intended that the method be used to generate or replace UK Soil Guideline Values, because this can only be done by the appropriate authoritative bodies within the UK (Department of the Environment, Food and Rural Affairs and the Environment Agency).     

转基因大豆MON89788芯片式数字PCR定量方法的建立

针对抗虫耐除草剂大豆转基因品系MON89788,从转基因植物基因组DNA的提取、核酸模板的质量和浓度控制、引物探针的筛选、PCR反应过程的建立等方面建立了一套完整的转基因大豆芯片式dPCR定量检测方法。本实验也对该方法的重复性和定量检测限进行考察。10组5%转基因品系大豆MON89788样品定量重复性RSD在1.17%-9.97%之间,均满足国际上转基因定量结果RSD小于25%的要求。用该方法对转基因含量为5%、1%、0.1%的大豆MON89788进行定量检测,其定量结果为5.20%、0.94%和0.11%,RSD分别为6.2%、3.6%和15.2%。该检测方法的定量限达到0.1%,能满足欧盟对转基因定量标识0.9%的要求。将本实验建立的方法用于转基因大豆的定量检测,能为规范我国转基因监管工作的实施提供强有力的技术支撑。     

European Electronic Personal Health Records initiatives and vulnerable migrants: A need for greater ethical,legal and social safeguards

The effective collection and management of personal data of rapidly migrating populations is important for ensuring adequate healthcare and monitoring of a displaced peoples’ health status. With developments in ICT data sharing capabilities, electronic personal health records (ePHRs) are increasingly replacing less transportable paper records. ePHRs offer further advantages of improving accuracy and completeness of information and seem tailored for rapidly displaced and mobile populations. Various emerging initiatives in Europe are seeking to develop migrant‐centric ePHR responses. This paper highlights their importance and benefits, but also identifies a number of significant ethical, legal and social issues (ELSI) and challenges to their design and implementation, regarding (1) the kind of information that should be stored, (2) who should have access to information, and (3) potential misuse of information. These challenges need to be urgently addressed to make possible the beneficial use of ePHRs for vulnerable migrants in Europe.     

A Novel Method for Assessment of Natural Killer Cell Cytotoxicity Using Image Cytometry

Natural killer (NK) cells belong to the innate arm of the immune system and though activated NK cells can modulate immune responses through the secretion of cytokines, their primary effector function is through target cell lysis. Accordingly, cytotoxicity assays are central to studying NK cell function. The ⁵¹Chromium release assay, is the “gold standard” for cytotoxicity assay, however, due to concerns over toxicity associated with the use and disposal of radioactive compounds there is a significant interest in non-radioactive methods. We have previously used the calcein release assay as a non-radioactive alternative for studying NK cell cytotoxicity. In this study, we show that the calcein release assay varies in its dynamic range for different tumor targets, and that the entrapped calcein could remain unreleased within apoptotic bodies of lysed tumor targets or incompletely released resulting in underestimation of percent specific lysis. To overcome these limitations, we developed a novel cytotoxicity assay using the Cellometer Vision Image Cytometer and compared this method to standard calcein release assay for measuring NK cell cytotoxicity. Using tumor lines K562, 721.221, and Jurkat, we demonstrate here that image cytometry shows significantly higher percent specific lysis of the target cells compared to the standard calcein release assay within the same experimental setup. Image cytometry is able to accurately analyze live target cells by excluding dimmer cells and smaller apoptotic bodies from viable target cell counts. The image cytometry-based cytotoxicity assay is a simple, direct and sensitive method and is an appealing option for routine cytotoxicity assay.     

Signs of the 2009 Influenza Pandemic in the New York-Presbyterian Hospital Electronic Health Records

Background

In June of 2009, the World Health Organization declared the first influenza pandemic of the 21^st century, and by July, New York City''s New York-Presbyterian Hospital (NYPH) experienced a heavy burden of cases, attributable to a novel strain of the virus (H1N1pdm).

Methods and Results

We present the signs in the NYPH electronic health records (EHR) that distinguished the 2009 pandemic from previous seasonal influenza outbreaks via various statistical analyses. These signs include (1) an increase in the number of patients diagnosed with influenza, (2) a preponderance of influenza diagnoses outside of the normal flu season, and (3) marked vaccine failure. The NYPH EHR also reveals distinct age distributions of patients affected by seasonal influenza and the pandemic strain, and via available longitudinal data, suggests that the two may be associated with distinct sets of comorbid conditions as well. In particular, we find significantly more pandemic flu patients with diagnoses associated with asthma and underlying lung disease. We further observe that the NYPH EHR is capable of tracking diseases at a resolution as high as particular zip codes in New York City.

Conclusion

The NYPH EHR permits early detection of pandemic influenza and hypothesis generation via identification of those significantly associated illnesses. As data standards develop and databases expand, EHRs will contribute more and more to disease detection and the discovery of novel disease associations.