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High performance computing and communications: potential applications in cancer research.

Application of high performance computing and communications (HPCC) in the health care system has begun to unfold. Computers are increasingly being used in data information flow, patient management, diagnosis and in estimating prognosis, treatment, drug design, and the education, and training of health professionals. The fast gigabit network, three-dimensional displays of medical images, automation of laboratory testings, linkage of large databases, computer-aided diagnosis, and interpretation have revolutionized medical care. These achievements have been possible in large part due to rapidly advancing fields of software algorithms, computational science, and communication technologies that have enabled the user to remotely access and share information in consistent and cost-effective way regardless of their geographical location. The present article introduces several facets of 'HPCC grand challenges' and discusses the role of HPCC in cancer prevention and control through accurate diagnosis and prognosis, image analysis and interpretation, and faster database linkage for evaluating outcome of the cancer-related health services research.

Computer Communication Networks↗

Probabilistic models of cognition: conceptual foundations.

Remarkable progress in the mathematics and computer science of probability has led to a revolution in the scope of probabilistic models. In particular, 'sophisticated' probabilistic methods apply to structured relational systems such as graphs and grammars, of immediate relevance to the cognitive sciences. This Special Issue outlines progress in this rapidly developing field, which provides a potentially unifying perspective across a wide range of domains and levels of explanation. Here, we introduce the historical and conceptual foundations of the approach, explore how the approach relates to studies of explicit probabilistic reasoning, and give a brief overview of the field as it stands today.

Algorithms↗

Understanding biology through bioinformatics.

During the journey from the discovery of DNA to be the source of genetic information and elucidation of double-helical nature of DNA molecule to the assembly of human genome sequence and there after, bioinformatics has become an integral part of modern biology. Bioinformatics relies substantially on significant contributions made by scientists in various fields, including but not limited to, linguistics, biology, mathematics, computer science, and statistics. There is an ever increasing amount of data to elucidate toxic mechanisms and/or adverse effects of xenobiotics in the field of toxicogenomics. Annotation in combination with various bioinformatics analytical tools can play a crucial role in the understanding of genes and proteins, and can potentially help draw meaningful conclusions from various data sources. This article attempts to present a simple overview of bioinformatics, and an effort is made to discuss annotation.

Computational Biology↗

Distance art groups for women with breast cancer: guidelines and recommendations.

To overcome barriers that prevent women with breast cancer from attending support groups, innovative formats and modes of delivery both need to be considered. The present study was part of an interdisciplinary program of research in which researchers from counseling psychology, psycho-oncology, nursing, computer science, and fine arts have explored art making as an innovative format and telehealth as a mode of delivery. For this study, we conducted focus groups and interviews with 25 people with expertise about breast cancer, art, art therapy, and distance delivery of mental health services to generate guidelines for distance art-based psychosocial support services to women with breast cancer. A qualitative analysis of the focus group and interview data yielded guidelines for developers and facilitators of distance art groups for women with breast cancer pertaining to (a) emotional expression, (b) emotional support, (c) emotional safety, and (d) accommodating individual differences, plus special considerations for art therapy groups. Further research is needed pertaining to the use of computers, involvement of art therapists, and screening out vulnerable clients.

Art Therapy↗

A microcomputer system for the practising cardiac surgeon.

The authors present a computer program designed for the practising cardiac surgeon who wishes to computerize patient data. The program is efficient, versatile and can be adapted to individual needs. It can be used with any IBM PC-compatible machine and requires little knowledge of computer science. More than 250 items on 30 000 patients can be stored and all this information analysed simultaneously. The program can chart a patient's profile and tabulate the information of the entire registry. It can generate lists of patients with their surgeons, cardiologists, diagnoses, operations and dates of intervention. It can also be used for mailing purposes.

Cardiac Surgical Procedures↗

An architecture for EEG signal processing and interpretation during sleep (ESPIS).

The project's aim is to develop a dedicated workstation in order to process multiple channels of electrophysiological signals in real-time during sleep. In ESPIS we are aiming to define both an architecture and an environment for EEG signal interpretation in medicine based on computer science gold standards (Unix, XWindow, Motif). Signal processing and pattern recognition analysis are provided by parallel processing on a specific developed acquisition architecture (DSP) based on transputers. The main result is a high performance prototype demonstrating signal interpretation during sleep which has already been tested in a medical environment. The overall specifications allow this biomedical device to be extended to other types of medical signals.

Algorithms↗

Application of automated bioacoustic identification in environmental education and assessment.

Developments in electronics and computer science have led to the introduction of an automated bioacoustic identification device used to resolve commonly encountered problems in the identification of animal species in the field. This technology aids our auditory observations, and also improves the quality of biological surveys and environmental monitoring. In this paper the future roles and possibilities of bioacoustics are discussed, providing some examples from the realm of environmental education and monitoring that focus on the use of nature sounds.

Acoustics↗

Advances in biomedical informatics for the management of cancer.

Increased access to health care, and advances in education and technology have resulted in a larger proportion of the population having longer life expectancy. The strong correlation between age and cancer has resulted in a major healthcare problem for this century, and until recently cancer has defied any long-lasting cure. However, progress, especially in the field of biomedical informatics, promises a successful prediction and possibly a permanent cure for cancer within the next two decades. Biomedical informatics-with its roots in computer science, biomedical engineering, biostatistics, and mathematics-helps to bring the patient closer to the physician, facilitates access to specialist information and knowledge bases across the world, and makes it possible to identify genetic expression profiles for malignant or cancerous cells. This paper reviews the new research findings in biomedical informatics, working toward the ultimate goal of successfully predicting cancer, solving complex problems in prevention and treatment of cancer, and perhaps completely curing the scourge of cancer.

Biometry↗

Online workbenches for neural network connections.

The nervous system is the most complex object we know of. It is a spatially distributed, functionally differentiated network formed by axonal connections between defined neuron populations and effector cells. Computer science provides exciting new tools for archiving, analyzing, synthesizing, and modeling on the Web vast amounts of frequently conflicting and incomplete qualitative and quantitative data about the organization and molecular mechanisms of neural networks. To optimize conceptual advances in systems neuroscience, it is important for the research and publishing communities to embrace three exercises: using defined nomenclatures; populating databases; and providing feedback to developers about improved design, performance, and functionality of knowledge management systems and associated visualization tools.

Animals↗

A review of content-based image retrieval systems in medical applications-clinical benefits and future directions.

Content-based visual information retrieval (CBVIR) or content-based image retrieval (CBIR) has been one on the most vivid research areas in the field of computer vision over the last 10 years. The availability of large and steadily growing amounts of visual and multimedia data, and the development of the Internet underline the need to create thematic access methods that offer more than simple text-based queries or requests based on matching exact database fields. Many programs and tools have been developed to formulate and execute queries based on the visual or audio content and to help browsing large multimedia repositories. Still, no general breakthrough has been achieved with respect to large varied databases with documents of differing sorts and with varying characteristics. Answers to many questions with respect to speed, semantic descriptors or objective image interpretations are still unanswered. In the medical field, images, and especially digital images, are produced in ever-increasing quantities and used for diagnostics and therapy. The Radiology Department of the University Hospital of Geneva alone produced more than 12,000 images a day in 2002. The cardiology is currently the second largest producer of digital images, especially with videos of cardiac catheterization ( approximately 1800 exams per year containing almost 2000 images each). The total amount of cardiologic image data produced in the Geneva University Hospital was around 1 TB in 2002. Endoscopic videos can equally produce enormous amounts of data. With digital imaging and communications in medicine (DICOM), a standard for image communication has been set and patient information can be stored with the actual image(s), although still a few problems prevail with respect to the standardization. In several articles, content-based access to medical images for supporting clinical decision-making has been proposed that would ease the management of clinical data and scenarios for the integration of content-based access methods into picture archiving and communication systems (PACS) have been created. This article gives an overview of available literature in the field of content-based access to medical image data and on the technologies used in the field. Section 1 gives an introduction into generic content-based image retrieval and the technologies used. Section 2 explains the propositions for the use of image retrieval in medical practice and the various approaches. Example systems and application areas are described. Section 3 describes the techniques used in the implemented systems, their datasets and evaluations. Section 4 identifies possible clinical benefits of image retrieval systems in clinical practice as well as in research and education. New research directions are being defined that can prove to be useful. This article also identifies explanations to some of the outlined problems in the field as it looks like many propositions for systems are made from the medical domain and research prototypes are developed in computer science departments using medical datasets. Still, there are very few systems that seem to be used in clinical practice. It needs to be stated as well that the goal is not, in general, to replace text-based retrieval methods as they exist at the moment but to complement them with visual search tools.

Databases, Factual↗

A biologically motivated associative memory architecture.

A synthesis of analytical techniques from the fields of biology, mathematics, computer science and engineering are used to model the information processing characteristics of the mammalian cerebellar cortex. By viewing anatomically different neurons as representing network elements whose input-output functions are different, a mechanism for distributing information throughout the memory is proposed. The functional circuitry developed to implement this feature is called the microcircuit. Overlapping microcircuit activity is used to describe the memory's read and write operations. Key features of the memory model include: (1) its use of a sparse interconnection network, (2) its ability to manipulate very large input patterns, (3) its distributed storage of input data patterns and (4) its statistical reconstruction of stored patterns during memory read operations. Quantitative measures for the memory's recall fidelity and storage capacity are derived and results of computer simulations are presented.

Animals↗

Intelligent systems: how can they help?

Expert systems are a branch of the computer science of artificial intelligence. Their ability to mimic experts by applying their domain knowledge has led to the construction of a number of medical applications. A brief resumé of the structure and the processes involved in constructing knowledge-based expert systems is given. Reasons are given for the failure of these successful programs to be widely implemented. It is to be expected that improvements in other areas of artificial intelligence will make them more widely acceptable to the non-expert.

Artificial Intelligence↗

Scientific bases of human-machine communication by voice.

The scientific bases for human-machine communication by voice are in the fields of psychology, linguistics, acoustics, signal processing, computer science, and integrated circuit technology. The purpose of this paper is to highlight the basic scientific and technological issues in human-machine communication by voice and to point out areas of future research opportunity. The discussion is organized around the following major issues in implementing human-machine voice communication systems: (i) hardware/software implementation of the system, (ii) speech synthesis for voice output, (iii) speech recognition and understanding for voice input, and (iv) usability factors related to how humans interact with machines.

Algorithms↗

Object-oriented biological system integration: a SARS coronavirus example.

MOTIVATION: The importance of studying biology at the system level has been well recognized, yet there is no well-defined process or consistent methodology to integrate and represent biological information at this level. To overcome this hurdle, a blending of disciplines such as computer science and biology is necessary. RESULTS: By applying an adapted, sequential software engineering process, a complex biological system (severe acquired respiratory syndrome-coronavirus viral infection) has been reverse-engineered and represented as an object-oriented software system. The scalability of this object-oriented software engineering approach indicates that we can apply this technology for the integration of large complex biological systems. AVAILABILITY: A navigable web-based version of the system is freely available at http://people.musc.edu/~zhengw/SARS/Software-Process.htm

Animals↗

A formal model for quality assurance in coloproctologic surgery.

In the last 30 years the advanced countries experienced a large growth of financial and social resources devoted to Health Care (HC) [1] The need of better co-ordinating activities of a composite large set of specialists, and the need of avoiding further growth of financial and social resources without reducing benefits, stimulated the growth of Health Care Evaluation (HCE) and Quality Assurance (QA) studies. In this paper we show how system analysis and precise assessment of the clinical process can be largely enhanced by using formal techniques. The proposed methodology takes advantage of positive experiences in computer science. It is based on a formal model of the clinical process that provides the physicians with support for assessing diagnostic procedures in a co-operative surgical environment [7]. Diagnostic, grading, and staging procedures are integrated in a single model that can be formally expressed and analyzed. The approach is exemplified by presenting an elementary model of the diagnosis, grading and staging procedures for the colo-rectal cancer and ulcerative colitis.

Colitis, Ulcerative↗

Towards the simulation of clinical cognition. Taking a present illness by computer.

Remarkably little is known about the cognitive processes which are employed in the solution of clinical problems. This paucity of information is probably accounted for in large part by the lack of suitable analytic tools for the study of the physician's thought processes. Here we report on the use of the computer as a laboratory for the study of clinical cognition. Our experimental approach has consisted of several elements. First, cognitive insights gained from the study of clinicians' behavior were used to develop a computer program designed to take the present illness of a patient with edema. The program was then tested with a series of prototypical cases, and the present illnesses generated by the computer were compared to those taken by the clinicians in our group. Discrepant behavior on the part of the program was taken as a stimulus for further refinement of the evolving cognitive theory of the present illness. Corresponding refinements were made in the program, and the process of testing and revision was continued until the program's behavior closely resembled that of the clinicians. The advances in computer science that made this effort possible include "goal-directed" programming, pattern-matching and a large associative memory, all of which are products of research in the field known as "artificial intelligence". The information used by the program is organized in a highly connected set of associations which is used to guide such activities as checking the validity of facts, generating and testing hypotheses, and constructing a coherent picture of the patient. As the program pursues its interrelated goals of information gathering and diagnosis, it uses knowledge of diseases and pathophysiology, as well as "common sense", to dynamically assemble many small problem-solving strategies into an integrated history-taking process. We suggest that the present experimental approach will facilitate accomplishment of the long-term goal of disseminating clinical expertise via the computer.

Computers↗

Artificial intelligence research in anesthesia and intensive care.

This article describes several research directions exploring the application of artificial intelligence techniques in anesthesia and intensive care. Artificial intelligence can be loosely defined as the discipline of designing computer systems that exhibit "intelligent" behavior. This article first introduces artificial intelligence and computer science research and discusses why medicine has proved to be a challenging domain for applying artificial intelligence techniques. A discussion of the central research themes that arise in medical artificial intelligence, many of which are common to different projects and to different medical settings, is followed by a description of specific research projects that apply artificial intelligence techniques in anesthesiology, ventilatory management, and cardiovascular management. Finally, further comments are made on the current state of the field.

Anesthesia↗

Brain-computer interfaces--the key for the conscious brain locked into a paralyzed body.

Brain-computer interfaces (BCIs) are systems that allow us to translate in real-time the electrical activity of the brain in commands to control devices. They do not rely on muscular activity and can therefore provide communication and control for those who are severely paralyzed (locked-in) due to injury or disease. It has been shown that locked-in patients are able to achieve EEG-controlled cursor or limb movement and patients have successfully communicated by means of a BCI. Current BCIs differ in how the neural activity of the brain is recorded, how subjects (humans and animals) are trained to produce a specific EEG response, how the signals are translated into device commands, and which application is provided to the user. The present review focuses on approaches to BCIs that process the EEG on-line and provide EEG feedback or feedback of results to the user. We regard online processing and feedback cornerstones for routine application of BCIs in the field. Because training patients in their home environment is effortful and personal and financial resources are limited, only few studies on BCI long-term use for communication with paralyzed patients are available. The need for multidisciplinary research, comprising computer science, engineering, neuroscience, and psychology is now being acknowledged by the BCI community. A standard BCI platform, referred to as BCI2000, has been developed, which allows us to better combine and compare the different BCI approaches of different laboratories. As BCI laboratories now also join to unify their expertise and collaborations are funded, we consider it realistic that within few years we will be able to offer a BCI, which will be easy to operate for patients and caregivers.

Animals↗