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At least 145 records · Page 8Linked to original sources

Integrating histology and histopathology teaching in practical classes using virtual slides.

The new medicine program at the University of New South Wales employs scenario-based learning with vertically integrated classes of year 1 and year 2 students, as well as horizontally integrated teaching with no discipline-specific courses. Coinciding with its introduction, we undertook comprehensive revision of the approach to teaching microscopic anatomy and pathology. We designed practical classes around virtual slides, which are high-magnification digital images of tissue sections stored in a multiresolution file format, viewable in a Web browser in a manner closely simulating conventional microscopy. In these classes, we integrated the teaching of histology and histopathology, introducing students to the microscopic features of tissues and organs, and giving them the opportunity to compare and contrast the normal with the abnormal in various disease states. Members of academic staff from both anatomy and pathology were present to promote discussion and respond to questions. Worksheets defined learning objectives and provided clinical cases as contexts for learning in each class. Evaluation revealed that students strongly supported the integrated approach. The efficiency of the teaching method meant that it was possible to work through 5-8 virtual slides per 2-hr class without difficulty. Students displayed considerable initiative in exploring the histological features of tissues, identifying the changes in various pathological states, and recognizing their relationship to clinical manifestations. We believe that the approach we have developed should help to minimize the potential adverse impact of curriculum reform on the teaching of morphology, while ensuring that learning remains both meaningful and interesting.

Computer Simulation↗

Comparing two-dimensional electrophoretic gel images across the Internet.

Scientists around the world often work on similar data so the need to share results and compare data arises periodically. We describe a method of comparing two two-dimensional (2-D) protein gels of similar samples created in different laboratories to help identify or suggest protein spot identification. Now that 2-D gels and associated databases frequently appear on the Internet, this opens up the possibility of visually comparing one's own experimental 2-D gel image data with data from another gel in a remote Internet database. In general, there are a few ways to compare images: (i) slide one gel (autoradiograph or stained gel) over the other while back-illuminated, or (ii) build a 2-D gel computer database from both gels after scanning and analyzing these gels. These are impractical since in the first case the gel from the Internet database is not locally available. In the second, the costs of building a multi-gel database solely to answer the question of whether a spot is the same spot may be excessive if only a single visual comparison is needed. We describe a distributed gel comparison program (URL: http://www-lmmb.ncifcrf.gov/flicker) which runs on any World Wide Web (WWW) connected computer and is invoked from a Java-capable web browser. One gel image is read from any Internet 2-D gel database (e.g. SWISS-2DPAGE) and the other may reside on the investigator's computer. Images may be more easily compared by first applying spatial warping or other transforms interactively on the user's computer. First, regions of interest are "landmarked" with several corresponding points in each gel image, then one gel image is warped to the geometry of the other. As the two gels are rapidly alternated, or flickered, in the same window, the user can slide one gel past the other to visually align corresponding spots by matching local morphology. This flicker-comparison technique may be applied to analyzing other types of one-dimensional and 2-D biomedical images.

Computer Communication Networks↗

Novel methodology for the archiving and interactive reading of clinical magnetic resonance spectroscopic imaging.

Archiving clinical magnetic resonance spectroscopic imaging (MRSI) data and presenting the data to specialists (e.g., neuroradiologists, neurosurgeons, neurologists, neuro-oncologists, and MR scientists) who work in different physical locations is a practical problem of significance. This communication describes a novel solution. The study hypothesis was that it is possible to use widely available distributed computing techniques to create a clinical MRSI user interface addressable from any personal computer with a suitable network connection. A worldwide web MRSI archive and interface system was created that permits the user to interactively view individual MRSI voxel spectra with correlation to MR images and to parametric spectroscopic images. Web browser software (i.e., Netscape and Internet Explorer) permits users in various physical locations to access centrally archived MRSI data using a variety of operating systems and client workstations. The system was used for archiving and displaying more than 1000 clinical MRSI studies performed at the authors' institution. The system also permits MRSI data to be viewed via the Internet from distant locations worldwide. The study illustrates that widely available software operating within highly distributed electronic networks can be used for archiving and interactive reading of large amounts of clinical MRSI data.

Humans↗

Defining extensible markup language standards for electromyography data transmission across the world-wide web.

Different electromyography (EMG) machines store their data in different formats that vary from manufacturer to manufacturer and even between different EMG machines from the same manufacturer. As advanced as these machines are today, it is necessary in most cases to use faxes, scanners, or a common interface such as Adobe's file format to exchange data between them. A possible solution to this problem is to translate the EMG machine's data output into a common format that can be read (and displayed) by commonly available programs or, even better, by a Web browser. We describe an EMG-extensible markup language (XML) translation program that takes proprietary data from an EMG machine and translates the data into XML, a common language format. Predefined extensible stylesheet language (XSL) style sheets allow the display of the data in user-defined formats for EMG machines, personal digital assistants such as Palm Pilots, and even cellular phones.

Electromyography↗

Virtual microscopy for learning and assessment in pathology.

Virtual slides are high-magnification digital images of tissue sections, stored in a multi-resolution file format. Using appropriate software, these slides can be viewed in a web browser in a manner that closely simulates examination of glass slides with a real microscope. We describe the successful implementation of teaching microscopic pathology with virtual slides and, for the first time, their use in summative assessment. Both students and teaching staff readily adapted to the use of virtual microscopy. Questionnaire feedback from students strongly indicated that virtual slides solved a number of problems in their learning, while providing good to excellent image quality. A deliberate policy of allocating two students per workstation promoted collaboration and helped to maintain interest in microscopic pathology. The use of a secure browser facilitated assessment using virtual slides, with no technical or security issues arising despite high peak demand. The new Medicine programme at the University of New South Wales will exclusively utilize virtual microscopy for the study of both histology and histopathology. We believe that the use of high-quality learning resources such as virtual slides can ensure that microscopic examination of tissues remains both meaningful and interesting.

Computer Simulation↗

Video on the Internet: An introduction to the digital encoding, compression, and transmission of moving image data.

In this paper, we seek to provide an introduction to the fast-moving field of digital video on the Internet, from the viewpoint of the biological microscopist who might wish to store or access videos, for instance in image databases such as the BioImage Database (http://www.bioimage.org). We describe and evaluate the principal methods used for encoding and compressing moving image data for digital storage and transmission over the Internet, which involve compromises between compression efficiency and retention of image fidelity, and describe the existing alternate software technologies for downloading or streaming compressed digitized videos using a Web browser. We report the results of experiments on video microscopy recordings and three-dimensional confocal animations of biological specimens to evaluate the compression efficiencies of the principal video compression-decompression algorithms (codecs) and to document the artefacts associated with each of them. Because MPEG-1 gives very high compression while yet retaining reasonable image quality, these studies lead us to recommend that video databases should store both a high-resolution original version of each video, ideally either uncompressed or losslessly compressed, and a separate edited and highly compressed MPEG-1 preview version that can be rapidly downloaded for interactive viewing by the database user.

Algorithms↗

A picture archiving and communications system featuring multiple monitors using Windows98.

We present an effective approach to manage, review, and distribute Digital Imaging and Communications in Medicine (DICOM) images with multiple monitors using Windows98 (Microsoft Corp, Redmond, WA) that can be implemented in an office-based setting. Computed tomography (CT), magnetic resonance imaging (MRI), and angiographic DICOM images were collected, compressed, and stored using Medweb (Medweb, Inc, San Francisco, CA) software. The Medweb server used the Linux/UNIX operating system on a Pentium 333-MHz processor with 128 MB of RAM. Short-term storage capacity was about 2 weeks with routine usage of an 11-GB hard drive. Images were presented for reading on a dual-monitor Windows98 Pentium display station with 160 MB of RAM using a Medweb/Netscape (Netscape Communications Corp, Mountain View, CA) viewer. There was no significant discrepancy in diagnosis between electronic and conventional film images. Mean reading time for 32 cases was 118 seconds. The Medweb JAVA plug-in viewer loaded the first image within 30 seconds of selecting the case for review. Full uncompressed 16-bit images allowed different window settings to better assess for pathology. Multiple monitors allowed viewing various hanging protocols. Cine viewing was also possible. Key diagnostic images were electronically transmitted to referring physicians. On-call radiologists were able to access images through the Internet. By combining Medweb, DICOM, and web-browser software using desktop personal computers (PCs), an easily accessible picture archiving and communications system (PACS) is available to radiologists and referring physicians. Multiple monitors are easily configured and managed using Windows98. This system can sustain changes and can be extended to provide variable functions using inexpensive PCs.

Angiography↗

Winter Flounder Expressed Sequence Tags: Establishment of an EST Database and Identification of Novel Fish Genes.

: An EST database of more than 900 sequences has been constructed from complementary DNAs from six different tissues (stomach, intestine, pyloric cecum, liver, spleen, and ovary) of the winter flounder Pleuronectes americanus. Template preparation and automated sequencing were optimized to generate high-quality information in an economic fashion. Using computer scripts developed in our laboratory, the sequences were automatically compared with sequences in the databases via a Web-browser interface, and significant returns were recorded and organized on user-friendly HTML pages. Half (453) of the ESTs had significant matches to database sequences of known function, 33 matched ESTs from other organisms, 34 matched ribosomal RNAs, and 24 matched hypothetical open reading frames of unknown function. Forty-one percent (374) of the ESTs had no matches to sequences in the database and presumably represent previously unidentified cDNAs. Several sequences are the first isolated from teleost fish, and should be of interest for gene mapping and studies of developmental biology.

Journal Article↗

[Digital teaching archive. Concept, implementation, and experiences in a university setting].

Film-based teaching files require a substantial investment in human, logistic, and financial resources. The combination of computer and network technology facilitates the workflow integration of distributing radiologic teaching cases within an institution (intranet) or via the World Wide Web (Internet). A digital teaching file (DTF) should include the following basic functions: image import from different sources and of different formats, editing of imported images, uniform case classification, quality control (peer review), a controlled access of different user groups (in-house and external), and an efficient retrieval strategy. The portable network graphics image format (PNG) is especially suitable for DTFs because of several features: pixel support, 2D-interlacing, gamma correction, and lossless compression. The American College of Radiology (ACR) "Index for Radiological Diagnoses" is hierarchically organized and thus an ideal classification system for a DTF. Computer-based training (CBT) in radiology is described in numerous publications, from supplementing traditional learning methods to certified education via the Internet. Attractiveness of a CBT application can be increased by integration of graphical and interactive elements but makes workflow integration of daily case input more difficult. Our DTF was built with established Internet instruments and integrated into a heterogeneous PACS/RIS environment. It facilitates a quick transfer (DICOM_Send) of selected images at the time of interpretation to the DTF and access to the DTF application at any time anywhere within the university hospital intranet employing a standard web browser. A DTF is a small but important building block in an institutional strategy of knowledge management.

Computer-Assisted Instruction↗

[The future of telepathology. An Internet "distributed system" with "open standards"].

With the availability of Internet, the interest in the possibilities of telepathology has increased considerably. In the foreground is thereby the need of the non-expert to bring in the opinions of experts on morphological findings by means of a fast and simple procedure. The new telepathology system iPath is in compliance with these needs. The system is based on small, but when possible independently working modules. This concept allows a simple adaptation of the system to the individual environment of the user (e.g. for different cameras, frame-grabbers, microscope steering tables etc.) and for individual needs. iPath has been in use for 6 months with various working groups. In telepathology a distinction is made between "passive" and "active" consultations but for both forms a non-expert brings in the opinion of an expert. In an active consultation both are in direct connection with each other (orally or via a chat-function), this is however not the case with a passive consultation. An active consultation can include the interactive discussion of the expert with the non-expert on images in an image database or the direct interpretation of images from a microscope by the expert. Four software modules are available for a free and as fast as possible application: (1) the module "Microscope control", (2) the module "Connector" (insertion of images directly from the microscope without a motorized microscope), (3) the module "Client-application" via the web-browser and (4) the module "Server" with a database. The server is placed in the internet and not behind a firewall. The server permanently receives information from the periphery and returns the information to the periphery on request. The only thing which the expert, the non-expert and the microscope have to know is how contact can made with the server.

Humans↗

Intranet and radiology: a critical appraisal of radiological applications of Intranet technology.

The World-Wide Web (WWW or Web) is the service which led to the huge popularity of the Internet by making it user friendly. Already in the early years of the Web, this technology was also used to make internal information systems easier to use and hospitals and departments set up "Intranets". An Intranet consists of a Web Server which is installed within a local area network (LAN) and allows information retrieval with a Web browser. This paper highlights the different fields of Intranet applications in radiology and in the hospital and focuses on systems for organisational issues as well as for patient data distribution. While an Intranet can be a solution for many problems, not only in radiology, it is accompanied by serious threats and common misunderstandings which are discussed.

Computer Communication Networks↗

Overview of acutely decompensated congestive heart failure (ADHF): a report from the ADHERE registry.

Acute decompensated heart failure (ADHF) has emerged as a major public health problem, and HF has become the leading cause of hospitalization in persons over 65 years of age. It is estimated that there are 6.5 million hospital days attributed to ADHF each year. Patients hospitalized with ADHF face a substantial risk of readmission, as high as 50% by 6 months after discharge. Despite the large number of patients hospitalized and this substantial risk, data on these patients have been limited and there has been little effort to improve the quality of care for patients hospitalized with ADHF. The Acute Decompensated Heart Failure National Registry (ADHERE) was designed to bridge this gap in knowledge and care by prospectively studying the characteristics, management, and outcomes of a broad spectrum of patients hospitalized with ADHF. Participating community and university hospitals identified patients with a primary or secondary discharge diagnosis of HF and collected medical history, management, treatments, and health outcomes via secure Web browser technology. As of October 2004, more than 160,000 patients from 281 hospitals have been enrolled. These patients differ substantially from those typically enrolled in randomized clinical trials. Initial data from the ADHERE registry have provided important insights into the clinical characteristics, patterns of care, and outcomes of patients with ADHF. ADHERE has documented significant delays in diagnosis and initiation of ADHF therapies as well as a substantial under-use of evidenced-based, guideline-recommended chronic HF therapies at hospital discharge. As such, there are substantial opportunities to improve the quality of care for ADHF patients in the nation's hospitals.

Acute Disease↗

Desirable attributes of public educational websites.

Certain attributes are particularly desirable for public educational websites, and websites for ethics education in particular. Among the most important of these attributes is wide accessibility through adherence to the World Wide Web Consortium (W3C) standards for HTML code. Adherence to this standard produces webpages that can be rendered by a full range of web browsers, including Braille and speech browsers. Although almost no academic websites, including ethics websites, and even fewer commercial websites are accessible by W3C standards, as illustrated by the Online Ethics Center for Engineering and Science , even websites created on limited budgets and with an undergraduate student staff can fulfill these standards. Other desirable attributes, such as provision of annotation for all links and the use of annotated links to give the user alternate ways of ordering and organizing content, are important for making full use of the educational possibilities of hypermedia for websites.

Computer-Assisted Instruction↗

Characteristics and outcomes of patients hospitalized for heart failure in the United States: rationale, design, and preliminary observations from the first 100,000 cases in the Acute Decompensated Heart Failure National Registry (ADHERE).

BACKGROUND: The ADHERE is designed to study characteristics, management, and outcomes in a broad sample of patients hospitalized with acute decompensated heart failure. Heart failure is a leading cause of hospitalization for adults older than 65 years in the United States. Most available data on these patients are limited by patient selection criteria and study design of clinical trials and single-center studies. METHODS: Participating hospitals identify patients with a primary or secondary discharge diagnosis of heart failure. Medical history, management, treatments, and health outcomes data are collected through review of medical records and entered into a database via secure web browser technology. RESULTS: As of January 2004, data on 107 362 patients have been received from 282 participating hospitals. Of enrollees with available analyzable data (N = 105 388 from 274 hospitals), the mean age was 72.4 (+/-14.0), and 52% were women. The most common comorbid conditions were hypertension (73%), coronary artery disease (57%), and diabetes (44%). Evidence of mild or no impairment of systolic function was found in 46% of patients. Inhospital mortality was 4.0% and the median hospital length of stay was 4.3 days. CONCLUSIONS: The ADHERE demonstrates both the feasibility and significant implications of gathering representative data on large numbers of patients hospitalized with heart failure. Initial data provided important insights into the clinical characteristics and patterns of care of these patients. Ongoing registry work will provide the framework for improved treatment strategies for patients hospitalized with decompensated heart failure.

Aged↗

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.

Organs and organelles represent core biological systems in mammals, but the diversity in protein composition remains unclear. Here, we combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria, and nuclei) in six organs (brain, heart, kidney, liver, lung, and placenta) of the laboratory mouse, Mus musculus. Using rigorous statistical filtering and machine-learning methods, the subcellular localization of 3274 of the 4768 proteins identified was determined with high confidence, including 1503 previously uncharacterized factors, while tissue selectivity was evaluated by comparison to previously reported mRNA expression patterns. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal.

Animals↗

PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.

Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method.

Algorithms↗

An online interactive simulation system for medical imaging education.

This report presents a recently developed web-based medical imaging simulation system for teaching students or other trainees who plan to work in the medical imaging field. The increased importance of computer and information technology widely applied to different imaging techniques in clinics and medical research necessitates a comprehensive medical imaging education program. A complete tutorial of simulations introducing popular imaging modalities, such as X-ray, MRI, CT, ultrasound and PET, forms an essential component of such an education. Internet technologies provide a vehicle to carry medical imaging education online. There exist a number of internet-based medical imaging hyper-books or online documentations. However, there are few providing interactive computational simulations. We focus on delivering knowledge of the physical principles and engineering implementation of medical imaging techniques through an interactive website environment. The online medical imaging simulation system presented in this report outlines basic principles underlying different imaging techniques and image processing algorithms and offers trainees an interactive virtual laboratory. For education purposes, this system aims to provide general understanding of each imaging modality with comprehensive explanations, ample illustrations and copious references as its thrust, rather than complex physics or detailed math. This report specifically describes the development of the tutorial for commonly used medical imaging modalities. An internet-accessible interface is used to simulate various imaging algorithms with user-adjustable parameters. The tutorial is under the MATLAB Web Server environment. Macromedia Director MX is used to develop interactive animations integrating theory with graphic-oriented simulations. HTML and JavaScript are used to enable a user to explore these modules online in a web browser. Numerous multiple choice questions, links and references for advanced study are provided in the tutorial for trainees to verify their understanding of each unit. It is expected that this tutorial will enhance medical imaging education, help trainees in subsequent analysis of image data, and form the basis for the development of more advanced technologies in the future.

Computer Simulation↗

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level.

The Silicon Cell initiative aims to understand cellular systems on the basis of the characteristics of their components. As a tool to achieve this, detailed kinetic models at the network reaction level are being constructed. Such detailed kinetic models are extremely useful for medical and biotechnological applications and form strong tools for fundamental studies. Several recently constructed detailed kinetic models on metabolism (glycolysis), signal transduction (EGF receptor), and the eukaryotic cell cycle (Saccharomyces cerevisiae) have been used to exemplify the Silicon Cell project. These models are stored and made accessible via the JWS Online Cellular Systems Modeling project, a web-based repository of kinetic models. Using a web-browser the models can be interrogated via a user-friendly graphical interface. The goal of the two projects is to combine models on parts of cellular systems and ultimately to construct detailed kinetic models at the cellular level.

Carbon↗