Facilitating Communication among Speech Pathologists Treating Children with Cleft Palate

An interactive web-based system was designed to facilitate communication between nonspecialist speech pathologists who provide therapy for individuals with speech disorders associated with cleft palate or craniofacial anomalies and specialist speech pathologists who provide physiologically based assessments of speech production. The web site includes instructional presentations, streaming video clips of endoscopic examinations, and exchange of information about the nature of therapy as recommended by the specialist and as provided by the nonspecialist. The approach demonstrates use of web-based computer facilities to improve the quality of communication among professionals with the goal of improving the outcomes of speech therapy. Information from the site can also be used in academic training programs as a teaching tool in courses on cleft palate speech.

Expanding access to high-quality plain-language patient education information through context-specific hyperlinks

Medical records, which are increasingly directly accessible to patients, contain highly technical terms unfamiliar to many patients. A federally qualified health center (FQHC) sought to help patients interpret their records by embedding context-specific hyperlinks to plain-language patient education materials in its portal. We assessed the impact of this innovation through a 3-year retrospective cohort study. A total of 12,877 (10% of all patients) in this safety net population had used the MPC links. Black patients, Latino patients comfortable using English, and patients covered by Medicaid were more likely to use the informational hyperlinks than other patients. The positive association with black race and Latino ethnicity remained statistically significant in multivariable models that controlled for insurance type. We conclude that many of the sociodemographic factors associated with the digital divide do not present barriers to accessing context-specific patient education information once in the portal. In fact, this type of highly convenient plain-language patient education may provide particular value to patients in traditionally disadvantaged groups.

Pupil Dilation and EEG Alpha Frequency Band Power Reveal Load on Executive Functions for Link-Selection Processes during Text Reading

Executive working memory functions play a central role in reading comprehension. In the present research we were interested in additional load imposed on executive functions by link-selection processes during computer-based reading. For obtaining process measures, we used a methodology of concurrent electroencephalographic (EEG) and eye-tracking data recording that allowed us to compare epochs of pure text reading with epochs of hyperlink-like selection processes in an online reading situation. Furthermore, this methodology allowed us to directly compare the two physiological load-measures EEG alpha frequency band power and pupil dilation. We observed increased load on executive functions during hyperlink-like selection processes on both measures in terms of decreased alpha frequency band power and increased pupil dilation. Surprisingly however, the two measures did not correlate. Two additional experiments were conducted that excluded potential perceptual, motor, or structural confounds. In sum, EEG alpha frequency band power and pupil dilation both turned out to be sensitive measures for increased load during hyperlink-like selection processes in online text reading.

Effects of hypermedia instruction on declarative, conditional and procedural knowledge in ADHD students

Two groups of students aged between 12 and 14 years--27 with attention deficit/hyperactivity disorder (ADHD) and 28 with both ADHD and learning problems--were compared to a sample of 29 typically developing students in terms of the acquisition and retention of declarative, conditional and procedural knowledge either in a hypermedia learning or in a traditional instructional setting. Hypermedia instruction produced better learning outcomes than traditional instruction did; the benefits concerned prevalently procedural knowledge and emerged mainly in the retention phase. Hypermedia instruction led ADHD students to reach achievement levels similar to those of typically developing students. Furthermore, hypermedia instruction contrasted the decay of knowledge from the acquisition to the retention phase in both clinical groups. On the basis of these findings, hypermedia instruction is proposed as an approach that may help ADHD learners to overcome attention deficits.

Integrating personalized medical test contents with XML and XSL-FO

BACKGROUND

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents.

METHODS

Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents.

RESULTS

The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion.

CONCLUSIONS

The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

The American Dental Association's Center for Evidence-Based Dentistry: a critical resource for 21st century dental practice

Through its website (http:// www.ada.org/prof/resources/ebd/index.asp), the American Dental Association's Center for Evidence-Based Dentistry offers dental health professionals access to systematic reviews of oral health-related research findings, as well as Clinical Recommendations, which summarize large bodies of scientific evidence in the form of practice recommendations, e.g., the use of professionally-applied topical fluoride and pit-and-fissure sealants. Another feature of the site of great practical importance to the practicing dentist is the Critical Summary, which is a concise review of an individual systematic review's methodology and findings, as well as the importance and context of the outcomes, and the strengths and weaknesses of the systematic review and its implications for dental practice.

Blended learning in orthodontic diagnosis: an interactive approach

Interactive multimedia programs can provide an opportunity for authentic learning both inside and outside the classroom. McGill University designed an interactive Orthodontic Diagnosis program on CD-ROM that has been used successfully in the faculty of dentistry to provide undergraduate students with interactive tutorials and exercises to help them recognize developing malocclusions. Key aspects of this multimedia program are the use of an outside-in approach to diagnosis as well as sound instructional design that provides practice opportunities and feedback to students. The goal is to bridge the gap between theoretical knowledge and the practical skills needed to be a successful dentist.

An update on Uniform Resource Locator (URL) decay in MEDLINE abstracts and measures for its mitigation

BACKGROUND

For years, Uniform Resource Locator (URL) decay or "link rot" has been a growing concern in the field of biomedical sciences. This paper addresses this issue by examining the status of the URLs published in MEDLINE abstracts, establishing current availability and estimating URL decay in these records from 1994 to 2006. We also reviewed the information provided by the URL to determine if the context that the author cited in writing the paper is the same information presently available in the URL. Lastly, with all the documented recommended methods to preserve URL links, we determined which among them have gained acceptance among authors and publishers.

METHODS

MEDLINE records from 1994 to 2006 from the National Library of Medicine in Extensible Mark-up Language (XML) format were processed yielding 10,208 URL addresses. These were accessed once daily at random times for 30 days. Titles and abstracts were also searched for the presence of archival tools such as WebCite, Persistent URL (PURL) and Digital Object Identifier (DOI).

RESULTS

Results showed that the average URL length ranged from 13 to 425 characters with a mean length of 35 characters [Standard Deviation (SD) = 13.51; 95% confidence interval (CI) 13.25 to 13.77]. The most common top-level domains were ".org" and ".edu", each with 34%. About 81% of the URL pool was available 90% to 100% of the time, but only 78% of these contained the actual information mentioned in the MEDLINE record. "Dead" URLs constituted 16% of the total. Finally, a survey of archival tool usage showed that since its introduction in 1998, only 519 of all abstracts reviewed had incorporated DOI addresses in their MEDLINE abstracts.

CONCLUSION

URL persistence parallels previous studies which showed approximately 81% general availability during the 1-month study period. As peer-reviewed literature remains to be the main source of information in biomedicine, we need to ensure the accuracy and preservation of these links.

A generic representation format of physiological experimental protocols for computer simulation using ontology

For computer simulations of physiological experiments using physiological models, a machine-readable format of experimental protocols is effective. Here, we propose an XML-based language, PEPML (Physiological Experimental Protocol Markup Language). In the PEPML, conditions and procedures of an experimental protocol are procedurally described as a list of events, each of which consists of a condition for execution and an action to be executed. Since variables used in a protocol can be specified using an ontology, the protocol can be applied to various models without editing tasks. The PEPML allows both application of multiple protocols to a single model and application of a single protocol to multiple models. This feature facilitates the efficient simulation for verifications, comparisons and utilizations of physiological models.

Hyperlink format, categorization abilities and memory span as contributors to deaf users hypertext access

Sixty deaf and hearing students were asked to search for goods in a Hypertext Supermarket with either graphical or textual links of high typicality, frequency, and familiarity. Additionally, they performed a picture and word categorization task and two working memory span tasks (spatial and verbal). Results showed that deaf students were faster in graphical than in verbal hypertext when the number of visited pages per search trial was blocked. Regardless of stimuli format, accuracy differences between groups did not appear, although deaf students were slower than hearing students in both Web search and categorization tasks (graphical or verbal). No relation between the two tasks was found. Correlation analyses showed that deaf students with higher spatial span were faster in graphical Web search, but no correlations emerged between verbal span and verbal Web search. A hypothesis of different strategies used by the two groups for searching information in hypertext is formulated. It is suggested that deaf users use a visual-matching strategy more than a semantic approach to make navigation decisions.

A web-based instruction module for interpretation of craniofacial cone beam CT anatomy

OBJECTIVES

To develop a web-based module for learner instruction in the interpretation and recognition of osseous anatomy on craniofacial cone-beam CT (CBCT) images.

METHODS

Volumetric datasets from three CBCT systems were acquired (i-CAT, NewTom 3G and AccuiTomo FPD) for various subjects using equipment-specific scanning protocols. The datasets were processed using multiple software to provide two-dimensional (2D) multiplanar reformatted (MPR) images (e.g. sagittal, coronal and axial) and three-dimensional (3D) visual representations (e.g. maximum intensity projection, minimum intensity projection, ray sum, surface and volume rendering). Distinct didactic modules which illustrate the principles of CBCT systems, guided navigation of the volumetric dataset, and anatomic correlation of 3D models and 2D MPR graphics were developed using a hybrid combination of web authoring and image analysis techniques. Interactive web multimedia instruction was facilitated by the use of dynamic highlighting and labelling, and rendered video illustrations, supplemented with didactic textual material. HTML coding and Java scripting were heavily implemented for the blending of the educational modules.

RESULTS

An interactive, multimedia educational tool for visualizing the morphology and interrelationships of osseous craniofacial anatomy, as depicted on CBCT MPR and 3D images, was designed and implemented.

CONCLUSIONS

The present design of a web-based instruction module may assist radiologists and clinicians in learning how to recognize and interpret the craniofacial anatomy of CBCT based images more efficiently.

[Learning vein puncture using digital educational material in a Nursing Undergraduate Course]

This exploratory descriptive study aimed at assessing the performance of undergraduate students in the fourth year of the Nursing course to carry out a vein puncture technique with the support of three digital educational materials--hypertext, educational games, and simulations. The sample consisted of 37 students, who had studied the digital material in an IT laboratory and had carried out the procedure of peripheral vein puncture in training laboratory. Ten stages considered essential for the accomplishment of the procedure were observed, and an assessment form of the educational materials was analyzed. Thirty three (89.19%) subjects had never done vein puncture, and 27 (72.97%) correctly performed five or more stages of the procedure. As to visualizing and saving the educational materials in the computer, 12 (32.44%) and 15 (40.54%) students, respectively, said to have had some kind of difficulty. According to 91.90% of the students, the material aided their learning process, which demonstrates this learning tool can be explored and more frequently used.

DEWEX: A system for designing and conducting Web-based experiments

DEWEX is a server-based environment for developing Web-based experiments. It provides many features for creating and running complex experimental designs on a local server. It is freeware and allows forboth using default features, for which only text input is necessary, and easy configurations that can be set up by the experimenter. The tool also provides log files on the local server that can be interpreted and analyzed very easily. As an illustration of how DEWEX can be used, a recent study is presented that demonstrates the system's most important features. This study investigated learning from multiple hypertext sources and shows the influences of task, source of information, and hypertext presentation format on the construction of mental representations of a hypertext about a historical event.

A multimethod approach to examining usability of Web privacy polices and user agents for specifying privacy preferences

Because all research methods have strengths and weaknesses, a multimethod approach often provides the best way to understand human behavior in applied settings. We describe how a multimethod approach was employed in a series of studies designed to examine usability issues associated with two aspects of online privacy: comprehension of privacy policies and configuration of privacy preferences for an online user agent. Archival research, user surveys, data mining, quantitative observations, and controlled experiments each yielded unique findings that, together, contributed to increased understanding of online-privacy issues for users. These findings were used to evaluate the accessibility of Web privacy policies to computer-literate users, determine whether people can configure user agents to achieve specific privacy goals, and discover ways in which the usability of those agents can be improved.

Open-source software for radiologists: a primer

There is a wide variety of free (open-source) software available via the Internet which may be of interest to radiologists. This article will explore the use of open-source software in radiology to help streamline academic workflow and improve general efficiency and effectiveness by highlighting a number of the most useful applications currently available. These include really simple syndication applications, e-mail management, spreadsheet, word processing, database and presentation packages, as well as image and video editing software. How to incorporate this software into radiological practice will also be discussed.

Expansion embedding techniques for reversible watermarking

Reversible watermarking enables the embedding of useful information in a host signal without any loss of host information. Tian's difference-expansion technique is a high-capacity, reversible method for data embedding. However, the method suffers from undesirable distortion at low embedding capacities and lack of capacity control due to the need for embedding a location map. We propose a histogram shifting technique as an alternative to embedding the location map. The proposed technique improves the distortion performance at low embedding capacities and mitigates the capacity control problem. We also propose a reversible data-embedding technique called prediction-error expansion. This new technique better exploits the correlation inherent in the neighborhood of a pixel than the difference-expansion scheme. Prediction-error expansion and histogram shifting combine to form an effective method for data embedding. The experimental results for many standard test images show that prediction-error expansion doubles the maximum embedding capacity when compared to difference expansion. There is also a significant improvement in the quality of the watermarked image, especially at moderate embedding capacities.

A semantic inheritance/inverse-inheritance mechanism for systematic bio-ontology construction

In this paper, we propose a semantic inheritance/inverse-inheritance mechanism for systematic bio-ontology construction. This mechanism allows domain experts to easily manage sophisticated bio-ontologies in which biological knowledge is encoded; it automatically captures semantics inferred from the ontology structure being constructed or already constructed. Based on the captured semantics it suggests appropriate recommendation to the experts. While inheritance enables them to consistently determine the semantics of relationships between ontology concepts (or classes), inverse-inheritance allows them to incrementally refine the semantics by exploiting a huge amount of relationships between the instances of the concepts. To demonstrate the feasibility of the mechanism, we also implement an OWL(Web Ontology Language)-based graphical bio-ontology management system. In the system, the mechanism is seamlessly applied to the ontology by well defined graphic notations based on OWL. OWL is adopted to fully express the subtle semantics inherently buried in the bio-ontology.

Advantages of combined touch screen technology and text hyperlink for the pathology grossing manual: a simple approach to access instructive information in biohazardous environments

Gross examination, encompassing description, dissection, and sampling, is a complex task and an essential component of surgical pathology. Because of the complexity of the task, standardized protocols to guide the gross examination often become a bulky manual that is difficult to use. This problem is further compounded by the high specimen volume and biohazardous nature of the task. As a result, such a manual is often underused, leading to errors that are potentially harmful and time consuming to correct-a common chronic problem affecting many pathology laboratories. To combat this problem, we have developed a simple method that incorporates complex text and graphic information of a typical procedure manual and yet allows easy access to any intended instructive information in the manual. The method uses the Object-Linking-and-Embedding function of Microsoft Word (Microsoft, Redmond, WA) to establish hyperlinks among different contents, and then it uses the touch screen technology to facilitate navigation through the manual on a computer screen installed at the cutting bench with no need for a physical keyboard or a mouse. It takes less than 4 seconds to reach any intended information in the manual by 3 to 4 touches on the screen. A 3-year follow-up study shows that this method has increased use of the manual and has improved the quality of gross examination. The method is simple and can be easily tailored to different formats of instructive information, allowing flexible organization, easy access, and quick navigation. Increased compliance to instructive information reduces errors at the grossing bench and improves work efficiency.

MASCOT HTML and XML parser: An implementation of a novel object model for protein identification data

Protein identification using MS is an important technique in proteomics as well as a major generator of proteomics data. We have designed the protein identification data object model (PDOM) and developed a parser based on this model to facilitate the analysis and storage of these data. The parser works with HTML or XML files saved or exported from MASCOT MS/MS ions search in peptide summary report or MASCOT PMF search in protein summary report. The program creates PDOM objects, eliminates redundancy in the input file, and has the capability to output any PDOM object to a relational database. This program facilitates additional analysis of MASCOT search results and aids the storage of protein identification information. The implementation is extensible and can serve as a template to develop parsers for other search engines. The parser can be used as a stand-alone application or can be driven by other Java programs. It is currently being used as the front end for a system that loads HTML and XML result files of MASCOT searches into a relational database. The source code is freely available at http://www.ccbm.jhu.edu and the program uses only free and open-source Java libraries.

Automated structure extraction and XML conversion of life science database flat files

In the light of the increasing number of biological databases, their integration is a fundamental prerequisite for answering complex biological questions. Database integration, therefore, is an important area of research in bioinformatics. Since most of the publicly available life science databases are still exclusively exchanged by means of proprietary flat files, database integration requires parsers for very different flat file formats. Unfortunately, the development and maintenance of database specific flat file parsers is a nontrivial and time-consuming task, which takes considerable effort in large-scale integration scenarios. This paper introduces heuristically based concepts for automatic structure extraction from life science database flat files. On the basis of these concepts the FlatEx prototype is developed for the automatic conversion of flat files into XML representations.

Reading strategies and prior knowledge in learning from hypertext

In two experiments, we identified two main strategies followed by hypertext readers in selecting their reading orders. The first consisted in selecting the text semantically related to the previously read section (coherence strategy), and the second in choosing the most interesting text, delaying reading of less interesting sections (interest strategy). Comprehension data revealed that these strategies affected learning differently as a function of the reader's prior knowledge. For low-knowledge readers, the coherence strategy supported better learning of the content. This effect seems to rely on the improvement of reading order coherence induced by this strategy. By contrast, for intermediate-knowledge readers the coherence and the interest strategies benefited comprehension equally. In both cases, learning was supported through the active processing induced by these strategies. Discussion focuses on resolving inconsistencies in the literature concerning whether or not hypertext supports better comprehension than does traditional linear texts.

Approaches to patient health information exchange and their impact on emergency medicine

Regional health information organizations and electronic health information exchange may have an important impact on the practice of emergency medicine in the United States. Regional health information organizations are local or regional information-sharing networks that enable electronic data interchange among stakeholders in a given geographic area. These stakeholders may include hospitals, skilled nursing facilities, clinics, private physicians' offices, pharmacies, laboratories, radiology facilities, health departments, payers, and possibly the patients themselves. Regional health information organizations are being formed across the country to improve the safety and efficiency of clinical care; improve public health efforts, biosurveillance, and disaster management response; and potentially create large databases of deidentified aggregate data for research. Because of the unique need for rapid access to information and the acuity of the clinical environment, few areas of the health care delivery system stand to change and benefit more from health information exchange than our nation's emergency departments. This article will explain the motivation for the development of regional health information organizations, identify some of the important issues in their formation, and discuss how their development might affect the practice of emergency medicine.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice

BACKGROUND

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database.

RESULTS

The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database.

CONCLUSION

Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Prediction in annotation based guideline encoding

The encoding of clinical practice guidelines into machine operable representations poses numerous challenges and will require considerable human intervention for the foreseeable future. To assist and potentially speed up this process, we have developed an incremental approach to guideline encoding which begins with the annotation of the original guideline text using markup techniques. A modular and flexible sequence of subtasks results in increasingly inter-operable representations while maintaining the connections to all prior source representations and supporting knowledge. To reduce the encoding bottleneck we also employ a number of machine-assisted learning and prediction techniques within a knowledge-based software environment. Promising results with a straightforward incremental learning algorithm illustrate the feasibility of such an approach.

Diffusion of innovations: Anatomical informatics and iPods

Over the course of many centuries, evolving scientific methods and technologies have advanced the study of anatomy. More recently, such dissemination of innovations has been formally studied in multidisciplinary psychosocial contexts, yielding useful knowledge about underlying principles and processes. We review these precepts and show how diffusion of innovations theory and principles apply to the development and dissemination of anatomical information methods and resources. We consider the factors affecting the late-20th-century dissemination of personal computers and World Wide Web hypermedia into widespread use in anatomical research and instruction. We report on the results of a small experiment in applied diffusion, the development and Internet-based distribution of learning resources for a popular, widely distributed personal media player. With these wearable microcomputer devices already in use by a variety of students, new opportunities exist for widespread dissemination of anatomical information. The continuing evolution of wearable computing devices underscores the need for maintaining anatomical information transportability via standardized data formats.

RuleEd, a web-based semantic network interface for constructing and revising computable eligibility rules

RuleEd is a web-based editing environment which enables clinical trial eligibility rules entered as free text to be represented as a series of terms mapped to unique concepts in a controlled vocabulary. RuleEd provides interfaces for creating and refining concept mappings for terms within rules and disambiguating multiply-mapped terms. A combination of inter-active and non-interactive methods enable authors to specify eligibility rule representations with a fine level of control.

Intelligent client for integrating bioinformatics services

MOTIVATION

In addition to existing bioinformatics software, a lot of new tools are being developed world wide to supply services for an ever growing, widely dispersed and heterogeneous collection of biological data. The integration of these resources under a common platform is a challenging task. To this end, several groups are developing integration technologies, in which services are usually registered in some sort of catalogue to allow novel discovering and accessing mechanisms to be implemented. However, each service demands specific interfaces to accommodate their parameters and it is a complicated task linking the different service inputs and outputs to solve a biological problem.

RESULTS

In this work we address the design and implementation of a versatile web client to access BioMOBY compatible services (a system by which a client can interact with multiple sources of biological data regardless of the underlying format or schema) using the service description stored in the BioMOBY catalogue. The automatic interface generator significantly reduces developing time and produces uniform service access mechanisms. The design and proof of concept (for such a client) including the generic interface generator have been developed and implemented in the National Institute for Bioinformatics in Spain.

AVAILABILITY

The INB (National Institute for Bioinformatics, Spain) platform is available at www.inab.org/MOWServ

Ergodic chaotic parameter modulation with application to digital image watermarking

This paper presents a novel technique for image watermarking based on chaos theory. Chaotic parameter modulation (CPM) is employed to modulate the copyright information into the bifurcating parameter of a chaotic system. The system output is a wideband signal and is used as a watermark to be inserted into the host image. In the detection, a novel method based on the ergodic property of chaotic signal is developed to demodulate the embedded copyright information. Compared to previous works on blind watermarking, the proposed technique can effectively remove the interference from the host image and, thus, improve the detection performance dramatically. Simulation results show that the ergodic CPM approach is effective for image watermarking in terms of noise performance, robustness against attacks, and payload. In addition, its implementation is very simple and the computation speed is fast. Compared to holographic transform domain method and the conventional spread spectrum watermarking scheme, the proposed technique is shown to be superior.

Congenital Melanocytic Nevus and the Internet: An Evaluation of Available Web-Based Resources

The Internet has become an increasingly used tool for patient education and the coordination of support groups. For families with children diagnosed with congenital melanocytic nevus, this is also the case. To evaluate the quality of congenital melanocytic nevus-related information on the Internet, a standardized assessment of web sites was used. The overall Internet informational and support resources regarding congenital melanocytic nevus were found to be accurate and user friendly but limited. The authors recommend practitioners direct patient families to www.nevusnetwork.org as a starting point, and supplement an interest in pictures and information regarding support groups with visits to www.dermatlas.org and http://groups.MSN.com/AussieNevusSupportGroup.

HTML and Web Site Design for the Radiologist: A Primer

A Web site has enormous potential as a medium for the radiologist to store, present, and share information in the form of text, images, and video clips. With a modest amount of tutoring and effort, designing a site can be as painless as preparing a Microsoft PowerPoint presentation. The site can then be used as a hub for the development of further offshoots (eg, Web-based tutorials, storage for a teaching library, publication of information about one's practice, and information gathering from a wide variety of sources). By learning the basics of hypertext markup language (HTML), the reader will be able to produce a simple and effective Web page that permits display of text, images, and multimedia files. The process of constructing a Web page can be divided into five steps: (a) creating a basic template with formatted text, (b) adding color, (c) importing images and multimedia files, (d) creating hyperlinks, and (e) uploading one's page to the Internet. This Web page may be used as the basis for a Web-based tutorial comprising text documents and image files already in one's possession. Finally, there are many commercially available packages for Web page design that require no knowledge of HTML.

Hypertext atlas of dermatopathology with expert system for epithelial tumors of the skin

BACKGROUND

Image resolution required for reference histological images is high. Obtaining high-resolution images requires a system, composing large image from individual smaller components. Such systems must thus be capable of automatically taking individual image parts, performing shading compensation and fusion of the image parts into one large image. Distribution of such images over the Internet requires developing a suitable user's interface with access to the image details.

METHODS

The ways of creating high-resolution images (virtual slides) and the interface enabling access to image details using Internet browser are described.

RESULTS

A collection of about 3200 dermatopathological, mostly histologic images is available at http://www.muni.cz/atlases: Hypertext atlas of dermatopathology. Methods of high-resolution image acquisition were used in digitizing the collection of skin lymphomas (Dermatology Institute, University Hospital, Zurich), which is a part of the atlas. The atlas is continuously maintained and upgraded; the number of contributors is growing.

The tissue microarray data exchange specification: a document type definition to validate and enhance XML data

BACKGROUND

The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness.

RESULTS

A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE).

CONCLUSION

ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data.

Forensic analysis of nonlinear collusion attacks for multimedia fingerprinting

Digital fingerprinting is a technology for tracing the distribution of multimedia content and protecting them from unauthorized redistribution. Unique identification information is embedded into each distributed copy of multimedia signal and serves as a digital fingerprint. Collusion attack is a cost-effective attack against digital fingerprinting, where colluders combine several copies with the same content but different fingerprints to remove or attenuate the original fingerprints. In this paper, we investigate the average collusion attack and several basic nonlinear collusions on independent Gaussian fingerprints, and study their effectiveness and the impact on the perceptual quality. With unbounded Gaussian fingerprints, perceivable distortion may exist in the fingerprinted copies as well as the copies after the collusion attacks. In order to remove this perceptual distortion, we introduce bounded Gaussian-like fingerprints and study their performance under collusion attacks. We also study several commonly used detection statistics and analyze their performance under collusion attacks. We further propose a preprocessing technique of the extracted fingerprints specifically for collusion scenarios to improve the detection performance.

The effectiveness of video support in the teaching of manual skills related to initial periodontal therapy tested on phantoms

INTRODUCTION

The teaching of manual skills and competencies is among the most time-consuming aspects of oral health-care education, especially when large groups of students are involved. Video has been repeatedly used as an educational tool with varying results.

PURPOSE

The present study aimed to investigate the effectiveness of a computer-based video support system during practical training of manual skills and competencies related to periodontal treatment.

MATERIALS AND METHODS

Eighty-four students were randomized into 9 groups: 5 experimental and 4 control groups. The control groups received instruction in the use of scaling and root planing instruments during a 7-hour seminar, and 2 hours of manual practice. The experimental groups received the same instruction, but in addition had access to a computer-based video support system, the Visual Training System (VTS), during practical training. During the 2-hour long practice session, all students practiced 21 different procedures, which were video recorded. The videos were later evaluated by an independent observer.

RESULTS

On the whole, the students in the experimental group performed significantly better than their colleagues in the control group. Specifically, the groups that utilized the VTS video support performed significantly better in 9 of the 21 procedures tested.

CONCLUSION

These results suggest that this computer-based video support can be an effective aid in the teaching of manual skills related to oral health care.

Wildfire: distributed, Grid-enabled workflow construction and execution

BACKGROUND

We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more scientists. The traditional solution to the problem of running workflows across multiple CPUs required programming, often in a scripting language such as perl. Programming places such solutions beyond the reach of many bioinformatics consumers.

RESULTS

We present Wildfire, a graphical user interface for constructing and running workflows. Wildfire borrows user interface features from Jemboss and adds a drag-and-drop interface allowing the user to compose EMBOSS (and other) programs into workflows. For execution, Wildfire uses GEL, the underlying workflow execution engine, which can exploit available parallelism on multiple CPU machines including Beowulf-class clusters and Grids.

CONCLUSION

Wildfire simplifies the tasks of constructing and executing bioinformatics workflows.

Using genomics to help predict drug interactions

This article proposes using genomic information to help tailor the output of a drug interaction program for a patient. This paper focuses on a particular CYP450 enzyme to illustrate adding genomic information to an existing drug interaction database. The data are formatted as an Extensible Markup Language (XML) document. The additional interaction information based on genomics for a patient is added to an XML document using XML tags. The suggestion is to combine specifics about a patient's genome with genomic information in the drug interactions database to increase the accuracy and details of a drug interaction program.

Design, implementation, use, and preliminary evaluation of SEBASTIAN, a standards-based Web service for clinical decision support

Despite their demonstrated ability to improve care quality, clinical decision support systems are not widely used. In part, this limited use is due to the difficulty of sharing medical knowledge in a machine-executable format. To address this problem, we developed a decision support Web service known as SEBASTIAN. In SEBASTIAN, individual knowledge modules define the data requirements for assessing a patient, the conclusions that can be drawn using that data, and instructions on how to generate those conclusions. Using standards-based XML messages transmitted over HTTP, client decision support applications provide patient data to SEBASTIAN and receive patient-specific assessments and recommendations. SEBASTIAN has been used to implement four distinct decision support systems; an architectural overview is provided for one of these systems. Preliminary assessments indicate that SEBASTIAN fulfills all original design objectives, including the re-use of executable medical knowledge across diverse applications and care settings, the straightforward authoring of knowledge modules, and use of the framework to implement decision support applications with significant clinical utility.

Image enhancement in the JPEG domain for people with vision impairment

An image enhancement algorithm for low-vision patients was developed for images compressed using the JPEG standard. The proposed algorithm enhances the images in the discrete cosine transform domain by weighting the quantization table in the decoder. Our specific implementation increases the contrast at all bands of frequencies by an equal factor. The enhancement algorithm has four advantages: 1) low computational cost; 2) suitability for real-time application; 3) ease of adjustment by end-users (for example, adjusting a single parameter); and 4) less severe block artifacts as compared with conventional (post compression) enhancements. Experiments with visually impaired patients show improved perceived image quality at moderate levels of enhancement but rejection of artifacts caused by higher levels of enhancement.

Design of signal-adapted multidimensional lifting scheme for lossy coding

This paper proposes a new method for the design of lifting filters to compute a multidimensional nonseparable wavelet transform. Our approach is stated in the general case, and is illustrated for the 2-D separable and for the quincunx images. Results are shown for the JPEG2000 database and for satellite images acquired on a quincunx sampling grid. The design of efficient quincunx filters is a difficult challenge which has already been addressed for specific cases. Our approach enables the design of less expensive filters adapted to the signal statistics to enhance the compression efficiency in a more general case. It is based on a two-step lifting scheme and joins the lifting theory with Wiener's optimization. The prediction step is designed in order to minimize the variance of the signal, and the update step is designed in order to minimize a reconstruction error. Application for lossy compression shows the performances of the method.

Robust image-adaptive data hiding using erasure and error correction

Information-theoretic analyses for data hiding prescribe embedding the hidden data in the choice of quantizer for the host data. In this paper, we propose practical realizations of this prescription for data hiding in images, with a view to hiding large volumes of data with low perceptual degradation. The hidden data can be recovered reliably under attacks, such as compression and limited amounts of image tampering and image resizing. The three main findings are as follows. 1) In order to limit perceivable distortion while hiding large amounts of data, hiding schemes must use image-adaptive criteria in addition to statistical criteria based on information theory. 2) The use of local criteria to choose where to hide data can potentially cause desynchronization of the encoder and decoder. This synchronization problem is solved by the use of powerful, but simple-to-implement, erasures and errors correcting codes, which also provide robustness against a variety of attacks. 3) For simplicity, scalar quantization-based hiding is employed, even though information-theoretic guidelines prescribe vector quantization-based methods. However, an information-theoretic analysis for an idealized model is provided to show that scalar quantization-based hiding incurs approximately only a 2-dB penalty in terms of resilience to attack.

A multiple-substream unequal error-protection and error-concealment algorithm for SPIHT-coded video bitstreams

This paper presents a coordinated multiple-substream unequal error-protection and error-concealment algorithm for SPIHT-coded bitstreams transmitted over lossy channels. In the proposed scheme, we divide the video sequence corresponding to a group of pictures into two subsequences and independently encode each subsequence using a three-dimensional SPIHT algorithm. We use two different partitioning schemes to generate the substreams, each of which offers some advantages under the appropriate channel condition. Each substream is protected by an FEC-based unequal error-protection algorithm, which assigns unequal forward error correction codes to each bit plane. Any information that is lost during the transmission for any substream is estimated at the receiver by using the correlation between the substreams and the smoothness of the video signal. Simulation results show that the proposed multiple-substream UEP algorithm is simple, fast, and robust in hostile network conditions, and that the proposed error-concealment algorithm can achieve 2-3-dB PSNR gain over the case when error concealment is not used at high packet-loss rates.

Locally optimum nonlinearities for DCT watermark detection

The issue of copyright protection of digital multimedia data has attracted a lot of attention during the last decade. An efficient copyright protection method that has been gaining popularity is watermarking, i.e., the embedding of a signature in a digital document that can be detected only by its rightful owner. Watermarks are usually blindly detected using correlating structures, which would be optimal in the case of Gaussian data. However, in the case of DCT-domain image watermarking, the data is more heavy-tailed and the correlator is clearly suboptimal. Nonlinear receivers have been shown to be particularly well suited for the detection of weak signals in heavy-tailed noise, as they are locally optimal. This motivates the use of the Gaussian-tailed zero-memory nonlinearity, as well as the locally optimal Cauchy nonlinearity for the detection of watermarks in DCT transformed images. We analyze the performance of these schemes theoretically and compare it to that of the traditionally used Gaussian correlator, but also to the recently proposed generalized Gaussian detector, which outperforms the correlator. The theoretical analysis and the actual performance of these systems is assessed through experiments, which verify the theoretical analysis and also justify the use of nonlinear structures for watermark detection. The performance of the correlator and the nonlinear detectors in the presence of quantization is also analyzed, using results from dither theory, and also verified experimentally.