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PubMedDate not supplied

Automated identification by computer of the mass spectra of drugs in urine or serum extracts.

Gas chromatography/mass spectrometry (GC/MS) is the method of choice for confirming the presence of drugs tentatively identified in urine or serum by thin-layer chromatography, gas chromatography, or immunoassay. One of the most widely used GC/MS systems is the Hewlett-Packard (HP) Model 5970 mass selective detector equipped with a work station programmed in Pascal. Searching of mass spectra after a GC/MS run must be done manually, and this can take hours, especially when there are many peaks in a chromatogram to check. I have developed software that allows the unattended searching of all peaks in a run, using a forward search algorithm with a custom-made drug library developed over a period of 5 years, and a reverse search with a 1600+ drug library from HP or another in-house drug library. Using these libraries with the two algorithms maximizes the chances of finding a drug peak and identifying it correctly. Individual searches take about 5 seconds each. Overall search time of nearly 200 mass spectra per run takes about 40 minutes, including printing time. This software has proven to be both labor saving and effective in positively identifying drugs.

Electronic Data Processing↗

PubMed2002

Benchmarking HIPAA compliance.

One of the nation's largest academic medical centers is benchmarking its operations using internally developed software to improve privacy/confidentiality of protected health information (PHI) and to enhance data security to comply with HIPAA regulations. It is also coordinating the development of a web-based interactive product that can help hospitals, physician practices, and managed care organizations measure their compliance with HIPAA regulations.

Academic Medical Centers↗

PubMed2001

Potential technology for studying dosimetry and response to airborne chemical and biological pollutants.

Advances in computational, and imaging techniques have enabled the rapid development of three-dimensional (3-D) models of biological systems in unprecedented detail. Using these advances, 3-D models of the lungs and nasal passages of the rat and human are being developed to ultimately improve predictions of airborne pollutant dosimetry. Techniques for imaging the respiratory tract by magnetic resonance imaging (MRI) were developed to improve the speed and accuracy of geometric data collection for mesh reconstruction. The MRI resolution is comparable to that obtained by manual measurements but at much greater speed and accuracy. Newly developed software (NWGrid) was utilized to translate imaging data from MR into 3-D mesh structures. Together, these approaches significantly reduced the time to develop a 3-D model. This more robust airway structure will ultimately facilitate modeling gas or vapor exchange between the respiratory tract and vasculature as well as enable linkages of dosimetry with cell response models. The 3-D, finite volume, viscoelastic mesh structures form the geometric basis for computational fluid dynamics modeling of inhalation, exhalation and the delivery of individual particles (or concentrations of gas or vapors) to discrete regions of the respiratory tract. The ability of these 3-D models to resolve dosimetry at such a high level of detail will require new techniques to measure regional airflows and particulate deposition for model validation.

Air Movements↗

PubMed2001

Overview of the tunable beamlines for protein crystallography at the EMBL Hamburg Outstation; an analysis of current and future usage and developments.

The EMBL Hamburg Outstation currently operates two tunable protein crystallography beamlines suitable for single and multiple anomalous diffraction (SAD/MAD) experiments. The first beamline, designated X31, is located on a bending magnet of the DORIS III storage ring whereas the second beamline, BW7A, is positioned at a multipole wiggler at the same storage ring. X31 is equipped with an energy stabilization device to ensure constant wavelength during longer data-collection periods. The in-house built crystallographic end-station is now equipped with a Mar345 imaging-plate scanner as a detector. The wiggler beamline BW7A features a novel sagitally focusing monochromator. The end-station used here has also been developed and built in-house. The beamline is currently operated with a Mar 165 CCD detector. In this paper the hardware and software developments of the last years will be summarized and the outlook for substantial upgrades will be given. The future plans include the design and construction of a third tunable beamline, designated X12, for protein crystallography. The development of automated beamlines for protein crystallography is of particular importance with respect to structural genomics initiatives. The analysis of the projects of the last years shows the wide range of anomalous scatterer used on the tunable beamlines thus demonstrating the need of a wide range of accessible energies and fast and reliable energy changes.

Crystallography↗

PubMed2004

The risky business of hiring stars.

With the battle for the best and brightest people heating up again, you're most likely out there looking for first-rate talent in the ranks of your competitors. Chances are, you're sold on the idea of recruiting from outside your organization, since developing people within the firm takes time and money. But the authors, who have tracked the careers of high-flying CEOs, researchers, software developers, and leading professionals, argue that top performers quickly fade after leaving one company for another. To study this phenomenon in greater detail, the authors analyzed the ups and downs of more than 1,000 star stock analysts, a well-defined group for which there are abundant data. The results were striking. After a star moves, not only does her performance plunge, but so does the effectiveness of the group she joins--and the market value of her new company. Moreover, transplanted stars don't stay with their new organizations for long, despite the astronomical salaries firms pay to lure them from rivals. Most companies that hire stars overlook the fact that an executive's performance is not entirely transferable because his personal competencies inevitably include company-specific skills. When the star leaves the old company for the new, he cannot take with him many of the resources that contributed to his achievements. As a result, he is unable to repeat his performance in another company--at least not until he learns to work the new system, which could take years. The authors conclude that companies cannot gain a competitive advantage or successfully grow by hiring stars from outside. Instead, they should focus on cultivating talent from within and do everything possible to retain the stars they create. Firms shouldn't fight the star wars, because winning could be the worst thing that happens to them.

Administrative Personnel↗

PubMed1999

Automated comet assay analysis.

BACKGROUND: Recently the "comet assay" or "single-cell gel electrophoresis assay" has been established as a sensitive method for the detection of DNA damage and repair. Most of the software now available to quantify various parameters for DNA damage requires the interaction of a human observer. In this report, we describe an automated analysis system that is based on self-developed software and hardware and needs minimal human interaction. METHODS: The image analysis is divided into two parts: 1) automatic cell recognition and comet classification and 2) quantification of desired comet parameters. Image preprocessing, segmentation, and feature classification were developed with algorithms based on mathematical morphology. To enhance evaluation speed, we have introduced parallel processing of data under the Windows NT operating system (Microsoft Corporation, Redmond, WA). Use of an analogue real-time autofocus unit (Böcker et al.: Phys Med Biol 1997;42:1981-1992) allows for faster analysis. RESULTS: Our recognition software shows a sensitivity of 95.2% and a specificity of 92.7% when tested on test samples from routine work with DNA damage by low-dose radiation (0-2 Gy). The parallel hardware and software concept enables us to analyze 100 comets on one slide in less than 15 min. CONCLUSIONS: A comparison of measurements made on the same samples by manual and automated analysis systems revealed that there are no significant differences. The slope of the dose-response curves and the repair kinetics are very similar and demonstrate that automatic comet assay analysis is possible.

Algorithms↗

PubMed1985

A computer-assisted electrocardiographic analysis system: methodology and potential application to cardiovascular toxicology.

An automated analysis of electrocardiographic (ECG) waveforms, based on a precise one-dimensional analysis of features within a generalized computer-enhanced ECG waveform, has been developed in our laboratory. ECG signals are monitored, amplified, and recorded using standard techniques. The recorder output signal is distributed to a microcomputer system. Software developed for the microcomputer slows the signal playback rate and permits operator review of the slowed signal for arrhythmia analysis. The analysis program identifies and superimposes 10-40 individual ECG complexes, depending on the heart rate, and generates an "ensembled" waveform. Operator interaction permits delineation of specific points on the displayed waveform and calculation of heart rate and duration of components within the ECG complex. The primary advantages of this system include (1) extensive automation--computer support decreases analytical time, increases precision, and permits rapid screening of large numbers of animals; (2) enhanced sensitivity--the use of functional parameters should provide a more sensitive index of toxicity than morphological parameters; (3) broad utility--this system provides the capability to utilize a variety of animals, both anesthetized and unanesthetized, ranging in age from fetuses to geriatrics, and permits studies of block as well as longitudinal design; and (4) ease of replication--standardization of equipment and techniques facilitates replication by other laboratories.

Animals↗

PubMed1986

BACOMP--database of bioactive compounds for structure-activity relationship.

BACOMP database is presented for structure-activity relationship (SAR) investigations; it was realized on a BK-1300 general purpose microcomputer using the MICRO-SETOR network database management system. Some general considerations of database design are given and the models and facilities for a development of a microcomputer-based SAR oriented database are described. The database contains the following information for the bioactive compounds: chemical structures, biological activities, trade names, reference numbers and information sources. For computer representation of chemical structures SAR oriented language is used. The database software includes: system software, data capture and data editing software, information retrieval and data processing applications. The software development is done in FORTRAN IV and MACRO assembly language. The programs are written in a completely interactive mode. The information retrieval software includes 12 functions giving an information for the database as a whole and for a single compound as well. The data processing software includes 8 functions for finding common structural fragments among compounds with similar biological activity and for estimating a structural similarity between different compounds. The functions are selected from corresponding screen MENUs. The function realization results are framed as appropriate screen formats and the receipt of hardcopies is available. The database can be used to develop predictive methods in respect of the investigated biological activity.

Drug Information Services↗

PubMed1997

The search for the elusive electronic medical record system--medical liability, the missing factor.

Over the past few years, the traditional paper-based medical record system has come under close scrutiny by every participant in the healthcare industry. Some groups, especially federal agencies such as Medicare and Medicaid, HMOs, and other third party payors, have begun to demand changes in medical record documentation, and have become very assertive as to what goals and objectives will be met. In contrast, the medical liability insurance industry has remained almost invisible during this period of transition. At a recent electronic medical records (EMR) conference participants attending a software development workshop were asked if they had their systems reviewed from a medicolegal standpoint by a malpractice insurance carrier. In response to this inquiry, not one software vendor raised their hand to indicate this had been accomplished, or was even contemplated. In the author's opinion, the key missing factor in the current quest for a paperless medical office system rests in the domain of those who represent the medical liability industry. All of these gate-keepers of medical loss and risk prevention will eventually be called upon, either by choice or necessity, to validate every working EMR system that is used in medical practices in the future. This article will explore the best information published from this currently silent sector of the industry, and proposes an active involvement by the medical liability industry in the current EMR design and development processes taking place. In addition, there are 10 minimum EMR design criteria contained in this article that are recommended for implementation based upon 16 years of medical malpractice experience and loss prevention input.

Humans↗

PubMed1992

Interactive video: an analysis of its value to nurse education.

This paper attempts to explain the emerging technology of interactive video and examine its possible place in nursing education. A brief description of the media is given with an exploration of the educational theory and justification underlying its use. A range of approaches to the evaluation of the technology itself and software available are given, which examine advantages and disadvantages for individual learners and for an organisation considering investment in this area. The possible role of interactive video in nurse education is discussed and a recommendation given that nurse educators need to keep up-to-date with developments in this type of educational technology and develop software suitable for the needs of nurses, rather than having to use packages developed for other purposes which have limited application for nursing.

Computer-Assisted Instruction↗

PubMed2003

New method for simultaneous anatomical and functional studies of articular joints and its application to the human knee.

In this paper a new methodology is described for the acquisition and computer elaboration of joint anatomy and motion data and the study of their correlation. The method uses a particular commercial electrogoniometer never used before for biomechanic investigations and software developed by the author for numerical interpolations and interactive display of the anatomical structures during joint motion. The original data acquisition protocol and computer elaboration software are described in detail, the theoretical and experimental accuracy of the method is reported and the original features and potential benefits of this approach in the field of joint biomechanics are discussed. Finally an experimental application for geometrical and functional analysis of the knee is presented as a practical example.

Biomechanical Phenomena↗

PubMedDate not supplied

Get a grip on patient safety: outcomes in the palm of your hand.

Documentation of what nurses do and the consequential impact on the care and safety of the patient is essential for the optimal use of intravascular devices. The University of Louisville Hospital's infection control department collaborated with the infusion therapy team on a project designed to provide an easier and more reliable way to quantify what the infusion therapy team did and the resultant patient outcomes. This project was based on software developed by the infection control department for use with the handheld personal digital assistant (PDA). This article will discuss how use of the PDA and software meet individual departmental needs and impact patient outcomes and patient safety by using evidence-based decision-making.

Documentation↗

PubMed1996

Three-dimensional prostate ultrasound and its application to cryosurgery.

Transrectal ultrasound (TRUS), despite its undeniable utility in prostate imaging, employs a spatially flexible and variable 2-dimensional (2-D) imaging technique to visualize a 3-dimensional (3-D) disease process and anatomy. To circumvent some of the limitations of 2-D TRUS, 3-D TRUS was developed. The system consists of a motorized assembly (to hold a standard ultrasound transducer) and a computer with a video frame grabber. The microcomputer, using software developed in our laboratory, rapidly reconstructs a series of linear ultrasound images into a 3-D image. The 3-D TRUS technology has been incorporated into our program for cryoablation of the prostate. With intraoperative 3-D TRUS providing a unique coronal view, cryoprobe placement is facilitated to detect malalignment and avoid subsequent suboptimal cryoablation. In our use of 3-D TRUS guidance, in all 21 initial patients, probe malalignment, otherwise not apparent on standard 2-D TRUS, was detected and corrected before cryosurgery. With median follow-up of just < 1 year, only 2 of 44 biopsy cores (from the same site of 1 patient) were positive at 3 and 6 months. 3-D TRUS appears to be a valuable adjunctive tool in prostate imaging, especially in providing guidance for cryoblation of prostate cancer.

Cryosurgery↗

PubMed1998

A software package for non-invasive, real-time beat-to-beat monitoring of stroke volume, blood pressure, total peripheral resistance and for assessment of autonomic function.

The goal of the present study was to develop and evaluate algorithms for non-invasive, real-time, beat-to-beat monitoring of stroke index (SI), blood pressure (BP) and total peripheral resistance index (TPRI) which has a menu-driven interface, suitable for routine use by unskilled staff. In addition, it was our aim to include a meta-analysis for the evaluation of autonomic function derived from the above haemodynamic data. This includes spectral analysis of heart rate (HR), BP, SI and TPRI and the automatic calculation of baroreceptor reflex sensitivity. Impedance cardiography was used for beat-to-beat SI determination, Finapres corrected by an oscillometric blood pressure measurement (Dinamap) on the upper arm for beat-to-beat BP measurement. We demonstrate noise free recordings during physiological (head up tilt) and pharmacological intervention (alpha 1-, beta 2-adrenoreceptor agonists, insulin induced hypoglycemia). The newly developed software should prove valuable for physiological, pharmacological and clinical studies.

Adult↗

PubMed2004

HDR quality assurance methods for personal digital assistants.

An important component of every clinical high-dose-rate (HDR) brachytherapy program is quality assurance (QA). One of the QA recommendations of the AAPM TG59 report is an independent verification on the results of treatment planning. It is desirable for the verification procedure to be as quick and easy to perform as possible and yet to have a high probability of detecting significant errors. The objective of this work is to describe the dosimetric methods and software developed to implement a departmental HDR QA program using personal digital assistants (PDAs). Verification of MammoSite treatment plans is presented as a practical example. PDAs that run the PalmOS were selected for their low cost and popularity among health care professionals. General-purpose applications were developed for linear sources, planar, and volume implants, that estimate the total dwell time of an HDR implant. This value can then be compared to the total dwell time calculated by the primary treatment planning system. The software incorporates the Paterson-Parker (PP) radium tables and the Greenfield-Tichman-Norman (GTN) version of the Quimby radium tables, which have been modified to a form more convenient for HDR calculations. A special purpose application based on the AAPM TG43 formalism was developed for the MammoSite breast applicator. For QA calculations perpendicular to the center of a single Iridium-192 (192I) HDR source, as exemplified by MammoSite treatments, linearly interpolating the PP or GTN tables is equivalent to applying the TG43 formalism at distances up to 5 cm from the source axis. The MammoSite-specific software also offers the option to calculate dosimetry based on the balloon volume. The PDA clock/calendar permits the software to automatically account for source decay. The touch-sensitive screen allows the familiar tabular format to be maintained while minimizing the effort required for calculations. The PP and GTN radium implant tables are easily modified to a form more convenient for HDR calculations. Deploying the HDR versions of the tables as PDA software makes general-purpose HDR QA effortless. For less conventional HDR applications such as MammoSite implants, a QA solution based on the TG43 formalism becomes practical when implemented on a small computer.

Brachytherapy↗

PubMed1988

Quality controlling interpretive reporting systems in clinical medicine--a changing responsibility.

This paper presents some observations on a number of topics which affect the quality of computer software and includes: current trends in software design, current levels of responsibilities for the various parties involved in bringing automation to clinical medicine, why software development is so difficult to quality control, and certain characteristics of system development which contribute most to the construction of inaccurate models.

Humans↗

PubMed2002

Large-scale gene expression analysis in molecular target discovery.

The evolution of simple arrays consisting of a few genes to ones composed of thousands of genes and/or ESTs has allowed investigators unprecedented views of the molecular mechanisms within cells. Due to the enormous quantities of information derived from microarray analysis, new types of problems have surfaced, such as where to store all of the data. The ability to solve database or statistical problems has required the bench biologist to collaborate with database developers, software designers and statisticians to determine solutions for storage, analysis and interpretation of microarray data. The collaborative effort between these extremely diverse disciplines has led to the development of creative database query and gene expression analysis tools, producing significant reductions in the time required by researchers to filter through the datasets and discover the key processes perturbed by the diseases of interest. Both unsupervised and supervised analysis methods have been applied to gene expression data leading to the discovery of novel therapeutic targets and diagnostic markers. Furthermore, tumor classification based on their respective molecular fingerprints has led to the classification of cancer subtypes and the discovery of novel molecular taxonomies that may eventually lead to improved patient stratification and superior therapeutic strategies.

Databases, Factual↗

PubMed2004

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

MOTIVATION: Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. RESULTS: Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. AVAILABILITY: http://www.molgenis.nl

Computational Biology↗