Centrale de mesure ambulatoire biomédicale sur PSoC

Improvement in quality and efficiency of health and medicine, at home and in hospital, has become of paramount importance. The solution to this problem would require the continuous monitoring of several key patient parameters, including the assessment of autonomic nervous system (ANS) activity using non-invasive sensors, providing information for emotional, sensorial, cognitive and physiological analysis of the patient. Recent advances in embedded systems, microelectronics, sensors and wireless networking enable the design of wearable systems capable of such advanced health monitoring. The subject of this article is an ambulatory system comprising of a small wrist device connected to several sensors for the detection of the autonomic nervous system activity. It affords monitoring of skin resistance, skin temperature and heart activity. It is also capable of recording the data on a removable media or sending it to computer via a wireless communication. The wrist device is based on a programmable system-on-chip (PSoC) from Cypress.     

T-wave Oversensing with Inappropriate Therapy in Remote Monitoring

T-wave oversensing can cause inappropriate implantable cardioverter-defibrillator (ICD) therapies that are difficult to correct. Remote monitoring allows follow-up of ICD patients without visiting the hospital and can help in early detection of any malfunctions. We describe the case of a patient who experienced inappropriate antitachycardia pacing therapy due to T-wave oversensing; the problem was promptly detected by remote monitoring and corrected by device reprogramming.     

Using Information from the Electronic Health Record to Improve Measurement of Unemployment in Service Members and Veterans with mTBI and Post-Deployment Stress

Objective

The purpose of this pilot study is 1) to develop an annotation schema and a training set of annotated notes to support the future development of a natural language processing (NLP) system to automatically extract employment information, and 2) to determine if information about employment status, goals and work-related challenges reported by service members and Veterans with mild traumatic brain injury (mTBI) and post-deployment stress can be identified in the Electronic Health Record (EHR).

Design

Retrospective cohort study using data from selected progress notes stored in the EHR.

Setting

Post-deployment Rehabilitation and Evaluation Program (PREP), an in-patient rehabilitation program for Veterans with TBI at the James A. Haley Veterans'' Hospital in Tampa, Florida.

Participants

Service members and Veterans with TBI who participated in the PREP program (N = 60).

Main Outcome Measures

Documentation of employment status, goals, and work-related challenges reported by service members and recorded in the EHR.

Results

Two hundred notes were examined and unique vocational information was found indicating a variety of self-reported employment challenges. Current employment status and future vocational goals along with information about cognitive, physical, and behavioral symptoms that may affect return-to-work were extracted from the EHR. The annotation schema developed for this study provides an excellent tool upon which NLP studies can be developed.

Conclusions

Information related to employment status and vocational history is stored in text notes in the EHR system. Information stored in text does not lend itself to easy extraction or summarization for research and rehabilitation planning purposes. Development of NLP systems to automatically extract text-based employment information provides data that may improve the understanding and measurement of employment in this important cohort.     

Remote monitoring in implantable defibrillator therapy

The major device manufacturers have introduced systems for remote patient monitoring. These remote monitoring systems promise more efficient patient management, especially in today’s clinical setting with the growing number of defibrillator implantations. The aim of this article is to present the role of remote patient monitoring in implantable cardioverter-defibrillator follow-up, its potential benefits and its barriers to widespread diffusion. (Neth Heart J 2008;16:53-6.)     

Remote monitoring and follow-up of cardiovascular implantable electronic devices in the Netherlands : An expert consensus report of the Netherlands Society of Cardiology

Remote monitoring of cardiac implanted electronic devices (CIED: pacemaker, cardiac resynchronisation therapy device and implantable cardioverter defibrillator) has been developed for technical control and follow-up using transtelephonic data transmission. In addition, automatic or patient-triggered alerts are sent to the cardiologist or allied professional who can respond if necessary with various interventions. The advantage of remote monitoring appears obvious in impending CIED failures and suspected symptoms but is less likely in routine follow-up of CIED. For this follow-up the indications, quality of care, cost-effectiveneness and patient satisfaction have to be determined before remote CIED monitoring can be applied in daily practice. Nevertheless remote CIED monitoring is expanding rapidly in the Netherlands without professional agreements about methodology, responsibilities of all the parties involved and that of the device patient, and reimbursement. The purpose of this consensus document on remote CIED monitoring and follow-up is to lay the base for a nationwide, uniform implementation in the Netherlands. This report describes the technical communication, current indications, benefits and limitations of remote CIED monitoring and follow-up, the role of the patient and device manufacturer, and costs and reimbursement. The view of cardiology experts and of other disciplines in conjunction with literature was incorporated in a preliminary series of recommendations. In addition, an overview of the questions related to remote CIED monitoring that need to be answered is given. This consensus document can be used for future guidelines for the Dutch profession.     

New method of monitoring remote wildlife via the Internet

A new system of monitoring remote wildlife via the Internet was developed. The system consists of a QuickTime streaming server with a digital PC camera and a recipient computer with monitoring software. Results of field experiments were fine. Wildlife (raccoon dogs and feral cats) inhabiting a forest remote from the observer were monitored and photographed automatically when detected. Data and frame rates were 35–300 kilobits per second and 3–14 frames per second, respectively, depending on the network traffic. This system is applicable wherever a broadband network is available and thus has great potential for ecological research.     

海洋保护区管理与保护成效评估的方法与进展

全球物种多样性的持续下降使得生物多样性保护面临巨大挑战, 海洋生物多样性的保护任务尤其艰巨。海洋保护区是保护生物多样性的有效方式之一, 如何对其成效进行评估是当前研究热点。然而, 目前针对海洋保护区的评估体系较少, 而且评估指标多侧重于管理成效。近年来随着全球生物多样性监测网络和数据库的建立, 以及多种新技术(如遥感、声呐系统、卫星追踪、基因组学等)在海洋生物多样性监测中的应用, 使得从生态系统到基因水平的多层次连续监测成为可能。基于此, 建议未来我国海洋保护区成效评估应在充分利用新技术方法的基础上, 加强长期科学监测, 建立并完善生物多样性监测数据库和信息共享机制, 发展跨学科的综合保护成效评估体系, 加强基于生物多样性监测的保护成效评估。     

生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

Project management system for structural and functional proteomics: Sesame

A computing infrastructure (Sesame) has been designed to manage and link individual steps in complex projects. Sesame is being developed to support a large-scale structural proteomics pilot project. When complete, the system is expected to manage all steps from target selection to data-bank deposition and report writing. We report here on the design criteria of the Sesame system and on results demonstrating successful achievement of the basic goals of its architecture. The Sesame software package, which follows the client/server paradigm, consists of a framework, which supports secure interactions among the three tiers of the system (the client, server, and database tiers), and application modules that carry out specific tasks. The framework utilizes industry standards. The client tier is written in Java2 and can be accessed anywhere through the Internet. All the development on the server tier is also carried out in Java2 so as to accommodate a wide variety of computer platforms. The database tier employs a commercial database management system. Each Sesame application module consists of a simple user interface in the client tier, corresponding objects in the server tier, and relevant data stored in the centralized database. For security, access to stored data is controlled by access privileges. The system facilitates both local and remote collaborations. Because users interact with the system using Java Web Start or through a web browser, access is limited only by the availability of an Internet connection. We describe several Sesame modules that have been developed to the point where they are being utilized routinely to support steps involved in structural and functional proteomics. This software is available to parties interested in using it and assisting to guide its further development.Deceased, 30 August 2000     

Electronic outbreak surveillance in Germany: a first evaluation for nosocomial norovirus outbreaks

Background

In Germany, surveillance for infectious disease outbreaks is integrated into an electronic surveillance system. For 2007, the national surveillance database contains case-based information on 201,224 norovirus cases, three-quarters of which are linked to outbreaks. We evaluated the data quality of the national database in reflecting nosocomial norovirus outbreak (NNO) data available in 19 Hessian local public health authorities (LPHAs) and the influence of differences between LPHA''s follow-up procedures for laboratory notifications of Norovirus positive stool samples on outbreak underascertainment.

Methods

Data on NNO beginning in 2007 and notified to the 19 LPHAs were extracted from the national database, investigated regarding internal validity and compared to data collected from LPHAs for a study on NNO control. LPHAs were questioned whether they routinely contacted all persons for whom a laboratory diagnosis of norovirus infection was notified. The number of outbreaks per 1,000 hospital beds and the number of cases within NNOs for acute care and rehabilitation hospitals were compared between counties with and without complete follow-up.

Results

The national database contained information on 155 NNOs, including 3,115 cases. Cases were missed in the national database in 58 (37%) of the outbreaks. Information on hospitalisation was incorrect for an estimated 47% of NNO cases. Information on county of infection was incorrect for 24% (199/820) of cases being forwarded between LPHAs for data entry. Reported NNO incidence and number of NNO cases in acute care hospitals was higher in counties with complete follow-up (incidence-rate ratio (IRR) 2.7, 95% CI 1.4–5.7, p-value 0.002 and IRR 2.1, 95% CI 1.9–2.4, p-value 0.001, respectively).

Conclusions

Many NNOs are not notified by hospitals and differences in LPHA procedures have an impact on the number of outbreaks captured in the surveillance system. Forwarding of case-by-case data on Norovirus outbreak cases from the local to the state and national level should not be required.     

A database system for fermentation processes

Data base management is needed in the whole industries, particularly in the fermentation industry, whose jobs are tedious yet require carefulness. The most important problem in the database system is not how to collect many informations, but how to handle the meaningful ones.The authors have recently developed an on-line monitoring and control system for the fermentation processes in co-operation with Fuji Facom Co. Ltd. and Komatsugawa Chemical Engineering Co. Ltd.This system enables us to measure directly those concentrations in fermentation systems which have been measured by offline so far, such as cell mass, substrate and metabolic products. The physiological activities of a microorganism, such as specific rate of cellular growth, that of substrate consumption, that of metabolites production, etc., became estimable precisely by eliminating the effect of noises.By enlarging the function of our monitoring and control system, we have developed a database system which is applicable in job scheduling not only in the laboratory but also in the production line, in automatic resource allocation and fault analyses of the fermentation processes.     

Critical evaluation of the JDO API for the persistence and portability requirements of complex biological databases

Background  

Complex biological database systems have become key computational tools used daily by scientists and researchers. Many of these systems must be capable of executing on multiple different hardware and software configurations and are also often made available to users via the Internet. We have used the Java Data Object (JDO) persistence technology to develop the database layer of such a system known as the SigPath information management system. SigPath is an example of a complex biological database that needs to store various types of information connected by many relationships.     

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.     

GENEUS, a computer system for DNA and protein sequence analysis containing an information retrieval system for the EMBL data library.

We describe a comprehensive computer system, GENEUS, for extensive DNA, RNA and protein sequence analysis. The analysis system is developed for the DEC VAX/VMS computer and uses the EMBL Nucleic Acid Sequence Data Library. Help information is available on-line on terminal screen. To speed up system handling, a qualifier oriented user communication is employed. All results are stored on files making them accessible to the computer editor. An information retrieval system for the EMBL Nucleotide Sequence Data Library is also described. A defined data-base interface allows connection to other analysis programs.+     

Evaluating Restoration Success on Lyell Island, British Columbia Using Oblique Videogrammetry

In degraded ecosystems where the impact on wildlife and the destruction of natural systems is high, restoration becomes a critical component of recovery. Monitoring restoration activities plays a key role in determining end points for restoration and assessing effectiveness. Appropriate monitoring of major systems, particularly in assessing vegetation reestablishment and slope stabilization, requires a long‐term commitment to annual assessment of change and improvement over time. However, intrinsic factors built into government or public management systems, such as budgeting and staffing limitations, limit the ability for long‐term monitoring of critical restoration projects. In the research reported in this article, we devised and assessed a new remote method for assessing restoration success and tested it on restoration and monitoring requirements in Lyell Island, British Columbia. We developed a system (the oblique data fusion system [ODFS]) to extract spatial information from oblique aerial video imagery. The ODFS enables low‐cost change detection and database updates at a range of operational scales. System tests show an absolute spatial accuracy on the order of ±2.1 m. The evaluation, based on digitized historical data, ground surveys, and the ODFS‐derived data, indicates that the landslide rate (new area/year) tapered off following treatment; after 5 years it had been reduced by a factor of 3 relative to the background rate. The recovery is deemed sufficient to initiate secondary restoration tasks. The evaluation demonstrates the accuracy and utility of the ODFS for long‐term monitoring of landscape restoration efforts, particularly in remote areas. In conclusion, this new innovative method shows considerable promise for park managers.     

Synchronization of APIIS based farm animal biodiversity systems

One of the major problems in the management of farm animal and biodiversity information is the exchange of data and keeping it up-to-date, an issue that is very common with distributed information systems consisting of number of databases. This article describes the synchronization protocol developed in APIIS (adaptable platform independent information system) framework and reviews the basic considerations required when building distributed information system that has to exchange information in a network of APIIS based systems. The protocol is designed to synchronize a common part of different database structures. It is developed without any intended use of proprietary database engine and can work with a variety of RDBMS (relational database management system). The main targets of the protocol are animal biodiversity information systems without permanently connected nodes. The EFABIS (European farm animal biodiversity information system) is reviewed as an example of the implementation.

Availability     

Design and realization of an on-line database for multidimensional microscopic images of biological specimens

The BioImage database is a new scientific database for multidimensional microscopic images of biological specimens, which is available through the World Wide Web (WWW). The development of this database has followed an iterative approach, in which requirements and functionality have been revised and extended. The complexity and innovative use of the data meant that technical and biological expertise has been crucial in the initial design of the data model. A controlled vocabulary was introduced to ensure data consistency. Pointers are used to reference information stored in other databases. The data model was built using InfoModeler as a database design tool. The database management system is the Informix Dynamic Server with Universal Data Option. This object-relational system allows the handling of complex data using features such as collection types, inheritance, and user-defined data types. Informix datablades are used to provide additional functionality: the Web Integration Option enables WWW access to the database; the Video Foundation Blade provides functionality for video handling.     

Freshwater Habitat Restoration Actions in the Pacific Northwest: A Decade's Investment in Habitat Improvement

Across the Pacific Northwest (PNW), both public and private agents are working to improve riverine habitat for a variety of reasons, including improving conditions for threatened and endangered salmon. These projects are moving forward with little or no knowledge of specific linkages between restoration actions and the responses of target species. Targeted effectiveness monitoring of these actions is required to redress this lack of mechanistic understanding, but such monitoring depends on detailed restoration information—that is, implementation monitoring. This article describes the process of assembling a database of restoration projects intended to improve stream and river habitat throughout the PNW. We designed the database specifically to address the needs of regional monitoring programs that evaluate the effectiveness of restoration actions. The database currently contains spatially referenced, project‐level data on over 23,000 restoration actions initiated at over 35,000 locations in the last 15 years (98% of projects report start or end dates between 1991 and 2005) in the states of Washington, Oregon, Idaho, and Montana. Data sources included federal, state, local, nongovernmental organization, and tribal contributors. The process of database production identified difficulties in the design of regional project tracking systems. The technical design issues range from low‐level information such as what defines a project or a location to high‐level issues that include data validation and legalities of interagency data sharing. The completed database will inform efficient monitoring design, effectiveness assessments, and restoration project planning.     

Local structure prediction with local structure-based sequence profiles

MOTIVATION: A large body of experimental and theoretical evidence suggests that local structural determinants are frequently encoded in short segments of protein sequence. Although the local structural information, once recognized, is particularly useful in protein structural and functional analyses, it remains a difficult problem to identify embedded local structural codes based solely on sequence information. RESULTS: In this paper, we describe a local structure prediction method aiming at predicting the backbone structures of nine-residue sequence segments. Two elements are the keys for this local structure prediction procedure. The first key element is the LSBSP1 database, which contains a large number of non-redundant local structure-based sequence profiles for nine-residue structure segments. The second key element is the consensus approach, which identifies a consensus structure from a set of hit structures. The local structure prediction procedure starts by matching a query sequence segment of nine consecutive amino acid residues to all the sequence profiles in the local structure-based sequence profile database (LSBSP1). The consensus structure, which is at the center of the largest structural cluster of the hit structures, is predicted to be the native state structure adopted by the query sequence segment. This local structure prediction method is assessed with a large set of random test protein structures that have not been used in constructing the LSBSP1 database. The benchmark results indicate that the prediction capacities of the novel local structure prediction procedure exceed the prediction capacities of the local backbone structure prediction methods based on the I-sites library by a significant margin. AVAILABILITY: All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia.edu/~ay1/.