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At least 271 records · Page 15Linked to original sources

Bioinformatics -- a patenting view.

The use of bioinformatics in the biological sciences has brought about a change in the way that biological inventions can be protected by patent laws. Using approaches developed in the fields of computer science and business, patent applicants now seek to protect certain aspects of their inventions, which include software, methods of doing business and uses of information as well as more traditional biotechnological products and processes. These approaches are useful in resolving some of the difficulties now faced in prosecuting patent applications directed to biological inventions that are claimed in more conventional terms.

Algorithms↗

Integrated expert systems and videodisc in surgical pathology: an overview.

We present an overview of our 6-year experience in the design of expert systems for anatomic pathology. Our practical goal is to help practicing pathologists with learning, teaching, and the task of diagnosis by providing them with dynamic expert knowledge by means of a personal computer. This project could only be undertaken by first addressing a scientific goal: to characterize the problem-solving strategies that expert pathologists use in making a diagnosis and to state them in the logical terms of computer science. Our approach has been to build systems first for experimentation and then for use. The result of our work is an integrated computer-based approach that handles expert knowledge as formal relationships and morphologic images and that uses a number of logical strategies to provide multiple perspectives on diagnostic tasks. Configured as a pathologist's workstation, this approach can be expected to enhance the performance of trained general pathologists and pathologists in training. Lymph node pathology has been used as the prototype domain for this research, but care has been taken to seek a generalized authoring and inference structure that can be applied to other areas of pathology by changing the contents but not the structure itself. Excursions into various surgical pathology specialties suggest that the ways the system is constructed and exercised is fundamentally robust. Such computer-based expert systems can be expected to generate a new standard in the practice of pathology--based on the "gold standard" of classical morphology, but including the coordinated use of new methods from immunology and molecular biology in a multidisciplinary approach to diagnosis when these techniques are relevant. The benefits from this technology can be expected to be widespread with the evolution, refinement, and diffusion of these systems.

Artificial Intelligence↗

Computational biology: toward deciphering gene regulatory information in mammalian genomes.

Computational biology is a rapidly evolving area where methodologies from computer science, mathematics, and statistics are applied to address fundamental problems in biology. The study of gene regulatory information is a central problem in current computational biology. This article reviews recent development of statistical methods related to this field. Starting from microarray gene selection, we examine methods for finding transcription factor binding motifs and cis-regulatory modules in coregulated genes, and methods for utilizing information from cross-species comparisons and ChIP-chip experiments. The ultimate understanding of cis-regulatory logic in mammalian genomes may require the integration of information collected from all these steps.

Animals↗

Performance characteristics of a Kodak computed radiography system.

The performance characteristics of a photostimulable phosphor based computed radiographic (CR) system were studied. The modulation transfer function (MTF), noise power spectra (NPS), and detective quantum efficiency (DQE) of the Kodak Digital Science computed radiography (CR) system (Eastman Kodak Co.-model 400) were measured and compared to previously published results of a Fuji based CR system (Philips Medical Systems-PCR model 7000). To maximize comparability, the same measurement techniques and analysis methods were used. The DQE at four exposure levels (30, 3, 0.3, 0.03 mR) and two plate types (standard and high resolution) were calculated from the NPS and MTF measurements. The NPS was determined from two-dimensional Fourier analysis of uniformly exposed plates. The presampling MTF was determined from the Fourier transform (FT) of the system's finely sampled line spread function (LSF) as produced by a narrow slit. A comparison of the slit type ("beveled edge" versus "straight edge") and its effect on the resulting MTF measurements was also performed. The results show that both systems are comparable in resolution performance. The noise power studies indicated a higher level of noise for the Kodak images (approximately 20% at the low exposure levels and 40%-70% at higher exposure levels). Within the clinically relevant exposure range (0.3-3 mR), the resulting DQE for the Kodak plates ranged between 20%-50% lower than for the corresponding Fuji plates. Measurements of the presampling MTF with the two slit types have shown that a correction factor can be applied to compensate for transmission through the relief edges.

Evaluation Studies as Topic↗

Design and use of clinical ontologies: curricular goals for the education of health-telematics professionals.

In computer science, the notion of a domain ontology--a formal specification of the concepts and of the relationships among concepts that characterize an application are a--has received considerable attention. In human-computer interaction, ontologies play a key role in defining the terms with which users and computer systems communicate. Such ontologies either implicitly or explicitly drive all dialogs between the computer and the user. In the construction of health-telematics applications, professionals need to understand how to design and apply domain ontologies to ensure effective communication with end-users. We currently are revising our training program in Medical Information Sciences at Stanford University to teach professional students in health telematics how to develop effective domain ontologies. Instruction concerning the construction and application of clinical domain ontologies should become an integral component of all health telematics curricula.

Attitude to Computers↗

Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets.

In order to improve our understanding of directly transmitted pathogens within host populations, epidemic models should take into account individual heterogeneities as well as stochastic fluctuations in individual parameters. The associated cost results in an increasing level of complexity of the mathematical models which generally lack consistent formalisms. In this paper, we demonstrate that complex epidemic models could be expressed as colored stochastic Petri nets (CSPN). CSPN is a mathematical tool developed in computer science. The concept is based on the Markov Chain theory and on a standard well codified graphical formalism. This approach presents an alternative to other computer simulation methods since it offers both a theoretical formalism and a graphical representation that facilitate the implementation, the understanding and thus the replication or modification of the model. We explain how common concepts of epidemic models--such as the incidence function--can be easily translated into an individual based point of view in the CSPN formalism. We then illustrate this approach by using the well documented susceptible-infected model with recruitment and death.

Animals↗

Picky: oligo microarray design for large genomes.

MOTIVATION: Many large genomes are getting sequenced nowadays. Biologists are eager to start microarray analysis taking advantage of all known genes of a species, but existing microarray design tools were very inefficient for large genomes. Also, many existing tools operate in a batch mode that does not assure best designs. RESULTS: Picky is an efficient oligo microarray design tool for large genomes. Picky integrates novel computer science techniques and the best known nearest-neighbor parameters to quickly identify sequence similarities and estimate their hybridization properties. Oligos designed by Picky are computationally optimized to guarantee the best specificity, sensitivity and uniformity under the given design constrains. Picky can be used to design arrays for whole genomes, or for only a subset of genes. The latter can still be screened against a whole genome to attain the same quality as a whole genome array, thereby permitting low budget, pathway-specific experiments to be conducted with large genomes. Picky is the fastest oligo array design tool currently available to the public, requiring only a few hours to process large gene sets from rice, maize or human.

Algorithms↗

Computer driven i.v. injection systems. State of the art, future developments.

The evolution of computer science is fast. New softwares and devices are proposed to physicians. We have designed and developed a complete guiding system build up around one personal computer, to assist the anesthetist to deliver simultaneously many drugs to a patient. This system is constituted of three modules. The first module SPINA is used to select the most appropriate IV drug from a data base considering patient's age, weight, disease state and surgery. It helps to evaluate its pharmacokinetic. The second module CINA is used to prepare the infusion sheet. The third module, MINA is used, for the start up and control of drug delivery and to synchronize the infusion pumps. It is also possible to interact on the preprogrammed infusion sequences. To achieve a closed loop regulation we have developed a fourth module PC-SCOPE; it manages the data acquisition. Some guidelines of our further developments are also presented.

Anesthesia Department, Hospital↗

Upper extremity pain and computer use among engineering graduate students.

BACKGROUND: The objective of this study was to investigate risk factors associated with persistent or recurrent upper extremity and neck pain among engineering graduate students. METHODS: A random sample of 206 Electrical Engineering and Computer Science (EECS) graduate students at a large public university completed an online questionnaire. RESULTS: Approximately 60% of respondents reported upper extremity or neck pain attributed to computer use and reported a mean pain severity score of 4.5 (+/-2.2; scale 0-10). In a final logistic regression model, female gender, years of computer use, and hours of computer use per week were significantly associated with pain. CONCLUSIONS: The high prevalence of upper extremity pain reported by graduate students suggests a public health need to identify interventions that will reduce symptom severity and prevent impairment.

Adult↗

Computer and the thought process.

Modelling of brain is an eternal problem and was revitalized by arrogant claims of some computer scientists. Several basic results of mathematics, especially in problems of uncertainty, computational complexity and logic prove limits of computation and indications that the brain works otherwise. The complexity of brain is not accessible by current electronic technology. However, brain research and computer science can learn a lot from each other by revealing relevant analogies.

Artificial Intelligence↗

Reinforcement learning control.

Reinforcement learning refers to improving performance through trial-and-error. Despite recent progress in developing artificial learning systems, including new learning methods for artificial neural networks, most of these systems learn under the tutelage of a knowledgeable 'teacher' able to tell them how to respond to a set of training stimuli. Learning under these conditions is not adequate, however, when it is costly, or even impossible, to obtain this kind of training information. Reinforcement learning is attracting increasing attention in computer science and engineering because it can be used by autonomous systems to learn from their experiences instead of from knowledgeable teachers, and it is attracting attention in computational neuroscience because it is consonant with biological principles. Recent research has improved the efficiency of reinforcement learning and has provided some striking examples of its capabilities.

Animals↗

Computational genomics.

We now know how to read the sequences of nucleotide letters that comprise the genome at a rather frightening speed--a several-million-base bacterial genome in several days is not a problem for one of the sequencing centers, and a billion-base eukaryotic genome can be done in less than a year. But reading a text and understanding it are two different things. So how well can we understand the genome sequences? The answer to this question is central to the whole enterprise of genomics, and this is where computational analysis of genomes takes the driver's seat. Here I will try to briefly outline some major goals, problems, challenges and approaches of computational genomics. Such a young field is already quite diverse, and in this short article I will concentrate on several issues that seen to be critical for deciphering biology from genome sequences, rather than mathematical and computer-science aspects that are well covered in several excellent books.

Adaptation, Biological↗

Will the digital computer transform classical mathematics?

Mathematics and machines have influenced each other for millennia. The advent of the digital computer introduced a powerfully new element that promises to transform the relation between them. This paper outlines the thesis that the effect of the digital computer on mathematics, already widespread, is likely to be radical and far-reaching. To articulate this claim, an abstract model of doing mathematics is introduced based on a triad of actors of which one, the 'agent', corresponds to the function performed by the computer. The model is used to frame two sorts of transformation. The first is pragmatic and involves the alterations and progressive colonization of the content and methods of enquiry of various mathematical fields brought about by digital methods. The second is conceptual and concerns a fundamental antagonism between the infinity enshrined in classical mathematics and physics (continuity, real numbers, asymptotic definitions) and the inherently real and material limit of processes associated with digital computation. An example which lies in the intersection of classical mathematics and computer science, the P=NP problem, is analysed in the light of this latter issue.

Artificial Intelligence↗

Craniofacial imaging informatics and technology development.

PURPOSE: 'Craniofacial imaging informatics' refers to image and related scientific data from the dentomaxillofacial complex, and application of 'informatics techniques' (derived from disciplines such as applied mathematics, computer science and statistics) to understand and organize the information associated with the data. METHOD: Major trends in information technology determine the progress made in craniofacial imaging and informatics. These trends include industry consolidation, disruptive technologies, Moore's law, electronic atlases and on-line databases. Each of these trends is explained and documented, relative to their influence on craniofacial imaging. RESULTS: Craniofacial imaging is influenced by major trends that affect all medical imaging and related informatics applications. The introduction of cone beam craniofacial computed tomography scanners is an example of a disruptive technology entering the field. An important opportunity lies in the integration of biologic knowledge repositories with craniofacial images. CONCLUSION: The progress of craniofacial imaging will continue subject to limitations imposed by the underlying technologies, especially imaging informatics. Disruptive technologies will play a major role in the evolution of this field.

Databases as Topic↗

Fifty years of research on self-replication: an overview.

The study of self-replicating structures or machines has been taking place now for almost half a century. My goal in this article is to present an overview of research carried out in the domain of self-replication over the past 50 years, starting from von Neumann's work in the late 1940s and continuing to the most recent research efforts. I shall concentrate on computational models, that is, ones that have been studied from a computer science point of view, be it theoretical or experimental. The systems are divided into four major classes, according to the model on which they are based: cellular automata, computer programs, strings (or strands), or an altogether different approach. With the advent of new materials, such as synthetic molecules and nanomachines, it is quite possible that we shall see this somewhat theoretical domain of study producing practical, real-world applications.

Biology↗

[Ecological forecasting: a frontier in ecology].

An evolving science of ecological forecasting is beginning to emerge, and could have an increasingly important role in policy-making and management of natural resources and environment. The progress in computer science, quantitative analysis and ecological theory, together with the application of new high technology, will increase our ability to forecast ecosystem change. The authors introduced the connotation of ecological forecasting, relevant research advances, and some typical examples. Ecological forecasting is an important frontier in ecology, and also, would be an important direction for future ecological study.

Decision Making↗

[The physical aspects of traditional radiology and of computed radiology compared].

In the last decade a new radiographic technique has been establishing itself which makes the most of technological progress in the fields of laser optics, of materials and of computer science and integrates conventional techniques introducing the digital image also into radiographic diagnosis. The authors, who have gained a wide experience in both the theory and the applications of Computed Radiography (CR), carefully reviewed Italian literature and found no review article on technical theoretical principles, while many such papers are found in international literature. Therefore, they took the lead for a review paper on this subject. For easier reading, the paper was divided into three parts: the first one is the necessary introduction to the physical parameters to understand radiographic images, i.e., the signal-to-noise ratio, the modulation transfer function, the Wiener spectrum and the detective quantum efficiency. The second part deals with the physical features of the formation of conventional radiographic images: the latest notions about the conversion of X-ray energy into light photons by intensifying screen phosphors are here reported. Finally, radiographic image readability is related to the characteristics of the screen-film system. The third part of the paper deals with CR, in particular with the problems related to image acquisition through the screens called imaging plates, to the laser reading technique and to image reconstruction. Finally, the different physical phenomena leading to radiant image degradation are examined sequentially, bearing in mind that the diagnostic yield of CR images can be improved with image processing, to obtain images which can be compared to conventional ones.

Algorithms↗

The Open System Interconnection as a building block in a health sciences information network.

The interconnection of integrated health sciences library systems with other health sciences computer systems to achieve information networks will require either custom linkages among specific devices or the adoption of standards that all systems support. The most appropriate standards appear to be those being developed under the Open System Interconnection (OSI) reference model, which specifies a set of rules and functions that computers must follow to exchange information. The protocols have been modularized into seven different layers. The lowest three layers are generally available as off-the-shelf interfacing products. The higher layers require special development for particular applications. This paper describes the OSI, its application in health sciences networks, and specific tasks that remain to be undertaken.

Computers↗