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PubMed2006

Direct aperture optimization for IMRT using Monte Carlo generated beamlets.

This work introduces an EGSnrc-based Monte Carlo (MC) beamlet does distribution matrix into a direct aperture optimization (DAO) algorithm for IMRT inverse planning. The technique is referred to as Monte Carlo-direct aperture optimization (MC-DAO). The goal is to assess if the combination of accurate Monte Carlo tissue inhomogeneity modeling and DAO inverse planning will improve the dose accuracy and treatment efficiency for treatment planning. Several authors have shown that the presence of small fields and/or inhomogeneous materials in IMRT treatment fields can cause dose calculation errors for algorithms that are unable to accurately model electronic disequilibrium. This issue may also affect the IMRT optimization process because the dose calculation algorithm may not properly model difficult geometries such as targets close to low-density regions (lung, air etc.). A clinical linear accelerator head is simulated using BEAMnrc (NRC, Canada). A novel in-house algorithm subdivides the resulting phase space into 2.5 X 5.0 mm2 beamlets. Each beamlet is projected onto a patient-specific phantom. The beamlet dose contribution to each voxel in a structure-of-interest is calculated using DOSXYZnrc. The multileaf collimator (MLC) leaf positions are linked to the location of the beamlet does distributions. The MLC shapes are optimized using direct aperture optimization (DAO). A final Monte Carlo calculation with MLC modeling is used to compute the final dose distribution. Monte Carlo simulation can generate accurate beamlet dose distributions for traditionally difficult-to-calculate geometries, particularly for small fields crossing regions of tissue inhomogeneity. The introduction of DAO results in an additional improvement by increasing the treatment delivery efficiency. For the examples presented in this paper the reduction in the total number of monitor units to deliver is approximately 33% compared to fluence-based optimization methods.

Algorithms↗
PubMed2006

Cone-beam mammo-computed tomography from data along two tilting arcs.

Over the past several years there has been an increasing interest in cone-beam computed tomography (CT) for breast imaging. In this article, we propose a new scheme for theoretically exact cone-beam mammo-CT and develop a corresponding Katsevich-type reconstruction algorithm. In our scheme, cone-beam scans are performed along two tilting arcs to collect a sufficient amount of information for exact reconstruction. In our algorithm, cone-beam data are filtered in a shift-invariant fashion and then weighted backprojected into the three-dimensional space for the final reconstruction. Our approach has several desirable features, including tolerance of axial data truncation, efficiency in sequential/parallel implementation, and accuracy for quantitative analysis. We also demonstrate the system performance and clinical utility of the proposed technique in numerical simulations.

Algorithms↗
PubMed2006

Towards a theory of a solution space for the biplane imaging geometry problem.

Biplane angiographic imaging is a primary method for visual and quantitative assessment of the vasculature. In order to reliably reconstruct the three-dimensional (3D) position, orientation, and shape of the vessel structure, a key problem is to determine the rotation matrix R and the translation vector t which relate the two coordinate systems. This so-called Imaging Geometry Determination problem is well studied in the medical imaging and computer vision communities and a number of interesting approaches have been reported. Each such technique determines a solution which yields 3D vasculature reconstructions with errors comparable to other techniques. From the literature, we see that different techniques with different optimization strategies yield reconstructions with equivalent errors. We have investigated this behavior, and it appears that the error in the input data leads to this equivalence effectively yielding what we call the solution space of feasible geometries, i.e., geometries which could be solutions given the error or uncertainty in the input image data. In this paper, we lay the theoretical framework for this concept of a solution space of feasible geometries using simple schematic constructions, deriving the underlying mathematical relationships, presenting implementation details, and discussing implications and applications of the proposed idea. Because the solution space of feasible geometries encompasses equivalent solutions given the input error, the solution space approach can be used to evaluate the precision of calculated geometries or 3D data based on known or estimated uncertainties in the input image data. We also use the solution space approach to calculate an imaging geometry, i.e., a solution.

Algorithms↗
PubMed1995

Guide to the Internet. The world wide web.

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals.

Computer Communication Networks↗
PubMedDate not supplied

A voice-enabled, structured medical reporting system.

Kurzweil Applied Intelligence received a research grant from the National Institute of Standards and Technology (NIST) Advanced Technology Program to develop a prototype voice-enabled, structured medical reporting system. In typical usage, the physician dictates to the system, which then uses automatic speech recognition and medical knowledge bases to produce a structured report. This report can then be formatted and viewed on a computer screen, stored in databases of patient information, transmitted to other systems, used to support outcome studies, or viewed on a Web browser. The output reports are structured according to two standard, platform-independent formats: SGML and CORBA. These formats represent the data in a way that can be read by both computers and humans, and efficiently communicated to a wide range of databases and communications protocols.

Information Storage and Retrieval↗
PubMedDate not supplied

Units of measure in clinical information systems.

The authors surveyed existing standard codes for units of measures, such as ISO 2955, ANSI X3.50, and Health Level 7's ISO+. Because these standards specify only the character representation of units, the authors developed a semantic model for units based on dimensional analysis. Through this model, conversion between units and calculations with dimensioned quantities become as simple as calculating with numbers. All atomic symbols for prefixes and units are defined in one small table. Huge permutated conversion tables are not required. This method is also simple enough to be widely implementable in today's information systems. To promote the application of the method the authors provide an open-source implementation of this method in JAVA. All existing code standards for units, however, are incomplete for practical use and require substantial changes to correct their many ambiguities. The authors therefore developed a code for units that is much more complete and free from ambiguities.

Mathematical Computing↗
PubMedDate not supplied

The shadow uniform resource locator: standardizing citations of electronically published materials.

Citation of scientific materials published on the Internet is often cumbersome because of unwieldy uniform resource locators (URLs). The authors describe a format for URLs that simplifies citation of scholarly materials. Its use depends on a simple HTML device, the "refresh page." Uniform citation would follow this format: [Author I. Title of article. http:// domain/year/month-day(e#).html]. The HTML code for such a page is: (HTML) (head) (meta HTTP-EQUIV="Refresh" CONTENT="0; URL= http://Actual-URL/ for-article/ referred-to/ incitation.html") (/head) (/HTML). The code instructs the browser to suppress the content of the refresh page and bring up the title page of the cited article instead. Citations would be succinct and predictable. An electronic journal would not need to alter its existing file hierarchy but would need to establish a distinct domain name and maintain a file of refresh pages. Utilization of the "shadow" URL would bring us one step closer to truly universal resource locators.

Hypermedia↗
PubMedDate not supplied

GeneClinics: a hybrid text/data electronic publishing model using XML applied to clinical genetic testing.

GeneClinics is an online genetic information resource consisting of descriptions of specific inherited disorders ("disease profiles") as well as information on the role of genetic testing in the diagnosis, management, and genetic counseling of patients with these inherited conditions. GeneClinics is intended to promote the use of genetic services in medical care and personal decision making by providing health care practitioners and patients with information on genetic testing for specific inherited disorders. GeneClinics is implemented as an object-oriented database containing a combination of data and semistructured text that is rendered as HTML for publishing a given "disease profile" on the Web. Content is acquired from authors via templates, converted to an XML document reflecting the underlying database schema (with tagging of embedded data), and then loaded into the database and subjected to peer review. The initial implementation of a production system and the first phase of population of the GeneClinics database content are complete. Further expansion of the content to cover more disease, significant scaling up of rate of content creation, and evaluation redesign are under way. The ultimate goal is to have an entry in GeneClinics for each entry in the GeneTests directory of medical genetics laboratories-that is, for each disease for which clinical genetic testing is available.

Causality↗
PubMedDate not supplied

GEM: a proposal for a more comprehensive guideline document model using XML.

OBJECTIVE: To develop a guideline document model that includes a sufficiently broad set of concepts to be useful throughout the guideline life cycle. DESIGN: Current guideline document models are limited in that they reflect the specific orientation of the stakeholder who created them; thus, developers and disseminators often provide few constructs for conceptualizing recommendations, while implementers de-emphasize concepts related to establishing guideline validity. The authors developed the Guideline Elements Model (GEM) using XML to better represent the heterogeneous knowledge contained in practice guidelines. Core constructs were derived from the Institute of Medicine's Guideline Appraisal Instrument, the National Guideline Clearinghouse, and the augmented decision table guideline representation. These were supplemented by additional concepts from a literature review. RESULTS: The GEM hierarchy includes more than 100 elements. Major concepts relate to a guideline's identity, developer, purpose, intended audience, method of development, target population, knowledge components, testing, and review plan. Knowledge components in guideline documents include recommendations (which in turn comprise conditionals and imperatives), definitions, and algorithms. CONCLUSION: GEM is more comprehensive than existing models and is expressively adequate to represent the heterogeneous information contained in guidelines. Use of XML contributes to a flexible, comprehensible, shareable, and reusable knowledge representation that is both readable by human beings and processible by computers.

Algorithms↗
PubMedDate not supplied

Domain-constrained generation of clinical condition sets to help test computer-based clinical guidelines.

The paper describes T/Gen, a prototype computer-based tool designed to help maintain the knowledge in a computer-based clinical practice guideline that provides patient-specific recommendations. T/Gen takes as input a set of clinical conditions to which a guideline must react, and allows the user to specify domain-specific constraints as to which combinations of conditions do not make sense or do not need to be exhaustively tested against one another. T/Gen automatically generates constrained sets of combinations of clinical conditions, each corresponding to a clinical case (or to several closely related clinical cases) that can be used to help test the computer-based guideline. The combinations can be used to test the guideline logic using T/Gen's built-in logic interpreter, or to generate a set of test cases for use in testing an operational guideline system. T/Gen has been developed and tested with five pilot guidelines, for two childhood immunization series, for influenza vaccination, for primary thyroid screening, and for embryo transplantation. The paper describes how T/Gen's approach is implemented for the five pilot guidelines, outlines the current status and future directions of the project, and discusses the design issues that arose in the course of carrying out the work.

Bacterial Capsules↗
PubMedDate not supplied

BrainImageJ: a Java-based framework for interoperability in neuroscience, with specific application to neuroimaging.

The Human Brain Project consortium continues to struggle with effective sharing of tools. To facilitate reuse of its tools, the Stanford Psychiatry Neuroimaging Laboratory (SPNL) has developed BrainImageJ, a new software framework in Java. The framework consists of two components-a set of four programming interfaces and an application front end. The four interfaces define extension pathways for new data models, file loaders and savers, algorithms, and visualization tools. Any Java class that implements one of these interfaces qualifies as a BrainImageJ plug-in-a self-contained tool. After automatically detecting and incorporating new plug-ins, the application front end transparently generates graphical user interfaces that provide access to plug-in functionality. New plug-ins interoperate with existing ones immediately through the front end. BrainImageJ is used at the Stanford Psychiatry Neuroimaging Laboratory to develop image-analysis algorithms and three-dimensional visualization tools. It is the goal of our development group that, once the framework is placed in the public domain, it will serve as an interlaboratory platform for designing, distributing, and using interoperable tools.

Algorithms↗
PubMed2005

Study of effect of drug lexicons on medication extraction from electronic medical records.

Extraction of relevant information from free-text clinical notes is becoming increasingly important in healthcare to provide personalized care to patients. The purpose of this dictionary-based NLP study was to determine the effects of using varying drug lexicons to automatically extract medication information from electronic medical records. A convenience training sample of 52 documents, each containing at least one medication, and a randomized test sample of 100 documents were used in this study. The training and test set documents contained a total of 681 and 641 medications respectively. Three sets of drug lexicons were used as sources for medication extraction: first, containing drug name and generic name; second with drug, generic and short names; third with drug, generic and short names followed by filtering techniques. Extraction with the first drug lexicon resulted in 83.7% sensitivity and 96.2% specificity for the training set and 85.2% sensitivity and 96.9% specificity for the test set. Adding the list of short names used for drugs resulted in increasing sensitivity to 95.0%, but decreased the specificity to 79.2% for the training set. Similar results of increased sensitivity of 96.4% and 80.1% specificity were obtained for the test set. Combination of a set of filtering techniques with data from the second lexicon increased the specificity to 98.5% and 98.8% for the training and test sets respectively while slightly decreasing the sensitivity to 94.1% (training) and 95.8% (test). Overall, the lexicon with filtering resulted in the highest precision, i.e., extracted the highest number of medications while keeping the number of extracted non-medications low.

Electronic Data Processing↗