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Current trends in mapping human genes.

The human is estimated to have at least 50,000 expressed genes (gene loci). Some information is available concerning about 5000 of these gene loci and about 1900 have been mapped, i.e., assigned to specific chromosomes (and in most instances particular chromosome regions). Progress has been achieved by a combination of physical mapping (e.g., study of somatic cell hybrids and chromosomal in situ hybridization) and genetic mapping (e.g., genetic linkage studies). New methods for both physical and genetic mapping are expanding the armamentarium. The usefulness of the mapping information is already evident; the spin-off from the Human Genome Project (HGP) begins immediately. The complete nucleotide sequence is the ultimate map of the human genome. Sequencing, although already under way for limited segments of the genome, will await further progress in gene mapping, and in particular creation of contig maps for each chromosome. Meanwhile the technology of sequencing and sequence information handling will be developed. It is argued that the HGP is a new form of coordinated, interdisciplinary science; that its primary objective must be seen as the creation of a tool for biomedical research--a source book that will be the basis of study of variation and function for a long time; that the impact on scientist training will be salutary by relieving graduate students of useless drudgery and by training scientists competent in both molecular genetics and computational science; and that the funding of the HGP will have an insignificant negative effect on science funding generally, and indeed may have a beneficial effect through economy of scale and a focusing of attention on the excitement of biology and medical science.

Chromosome Mapping

Polyploidy Arithmetic.

Polyploidy occurs in plants and animals, and is an important force in speciation and genome evolution. The main focus of this paper is the following fundamental question that was recently posed by Huber and Maher: Given the ploidy numbers of a collection of extant species, or their ploidy profile, what is the smallest number of hybridizations needed in any evolutionary history for these species to completely represent these numbers? In this paper, we shall show that this question can be rephrased in terms of addition chains and the closely related addition sequences, which have been studied for over a century in mathematics and computer science. These are sequences of natural numbers that start with 1, so that each number in the sequence larger than 1 is the sum of two other numbers arising earlier in the sequence. In our first main result, we show that finding the smallest number of hybridization events to explain a ploidy profile, or the hybrid number, is equivalent to solving the so-called addition sequence problem. This immediately implies that computing the hybridization number is computationally intractable. Even so, it also leads to new connections to representing polyploid evolution using networks. More specifically, in our second main result we show that ploidy profiles representable by tree-child networks are exactly the addition chains, implying a polynomial-time algorithm for identifying these profiles. We then consider beaded tree-child networks, which permit the representation of autopolyploidy events, and in our third main result we provide a greedy polynomial-time algorithm to decide whether a given profile can be realized by such a network. We expect that our results can be leveraged in future work through, for example, making use of known algorithms for computing short addition sequences to give bounds for the hybrid number, and in guiding network reconstruction for polyploid species.

Polyploidy

Fourier methods for biosequence analysis.

Novel methods are discussed for using fast Fourier transforms for DNA or protein sequence comparison. These methods are also intended as a contribution to the more general computer science problem of text search. These methods extend the capabilities of previous FFT methods and show that these methods are capable of considerable refinement. In particular, novel methods are given which (1) enable the detection of clusters of matching letters, (2) facilitate the insertion of gaps to enhance sequence similarity, and (3) accommodate to varying densities of letters in the input sequences. These methods use Fourier analysis in two distinct ways. (1) Fast Fourier transforms are used to facilitate rapid computation. (2) Fourier expansions are used to form an 'image' of the sequence comparison.

Amino Acid Sequence

Computer-assisted pathology encoding and reporting system (CAPER).

An on-line computer-assisted pathology encoding and reportying system (CAPER) has been developed by the Department of Pathology and Laboratory of Computer Science of the Massachusetts General Hospital for a department of surgical pathology that processes more than 25,000 specimens yearly. CAPER performs clerical functions, including the accessioning of specimens, monitoring their state of completion, production of log books, billing, statistics, and transfer of diagnoses to other hospital departments. It also permits instantaneous display of all diagnoses rendered within two years, printout within 24 hours of all older diagnoses for any patient, and retrieval of all specimens with any given diagnosis, further defined by any data item (e.g., age) stored in the computer file.

Computers

Automated recognition of corrupted arterial waveforms using neural network techniques.

A data acquisition system that automatically discards corrupted or undesirable signals would save untold hours of drudgery for researchers. Continuous recording of variables to provide detailed behavior patterns generates huge amounts of raw data. Unfortunately waveforms usually require visual inspection for isolating desired behavior or validating signal integrity. This tedious and time-consuming step can potentially be eliminated using a novel computer science technique. We have trained a simulated neural network to recognize corrupted arterial pressure waveforms. Our system can now evaluate the validity of the arterial waveform without human intervention with an average false positive error rate of 2.2% and an average false negative error rate of 12.6%.

Artifacts

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

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

Validating nursing theory for use within a computerized nursing information system.

Computerized nursing information systems (CNISs) exemplify the application of computer science to nursing knowledge. For nursing knowledge to be a basis for CNIS development, variable relationships must be clearly defined, thus allowing transformation of data into knowledge. Nursing theories define variable relationships; these definitions, however, often are not specific enough on which to base data-based nursing information systems. This article describes how a nursing process model was derived from Self-Care Deficit Nursing Theory, the process model validated, and data relationships established within the model prior to its use as a structure for a CNIS.

Computer Simulation

Noviceware: a model for learning the software development process.

Students and nursing faculty without formal computer science training can collaborate within an independent study structure to assist the student in gaining experience with the fundamentals of software development. The systems development life cycle approach provides an essential map to structure such independent studies. This article describes the development within an academic setting of a computerized research management system. The software builds a database of research case demographic data and data from a 65-item tool used in scoring videotapes of caregiver-infant interactions. For students and faculty contemplating similar projects, recommendations about planning software development experiences and securing hardware, software, and expert resources are provided.

Algorithms

Optical imaging of architecture and function in the living brain sheds new light on cortical mechanisms underlying visual perception.

Long standing questions related to brain mechanisms underlying perception can finally be resolved by direct visualization of the architecture and function of mammalian cortex. This advance has been accomplished with the aid of two optical imaging techniques with which one can literally see how the brain functions. The upbringing of this technology required a multi-disciplinary approach integrating brain research with organic chemistry, spectroscopy, biophysics, computer sciences, optics and image processing. Beyond the technological ramifications, recent research shed new light on cortical mechanisms underlying sensory perception. Clinical applications of this technology for precise mapping of the cortical surface of patients during neurosurgery have begun. Below is a brief summary of our own research and a description of the technical specifications of the two optical imaging techniques. Like every technique, optical imaging also suffers from severe limitations. Here we mostly emphasize some of its advantages relative to all alternative imaging techniques currently in use. The limitations are critically discussed in our recent reviews. For a series of other reviews, see Cohen (1989).

Brain

Expert systems as a diagnostic aid in otoneurology.

Expert systems (ES) are a new tool for information processing developed by the branch of computer science known as artificial intelligence. ES are capable of solving problems in a given domain by using the knowledge and emulating the behaviour of specialists in that field. ES can be used as powerful tools for education since they are able to justify their own conclusions and to make the underlying reasoning explicit. This paper presents 'Vertigo', an ES aimed at the classification and diagnosis of different forms of dizziness. It has been conceived mainly as a teaching tool in otoneurological departments. The rationale of this project, its development, the structure and the use of the system are described. So far, 'Vertigo' has been tested on more than 200 cases of dizziness and is presently being used by ENT residents during their otoneurology stage.

Diagnosis, Computer-Assisted

Proficiency of the Tradescantia-micronucleus image analysis system for scoring micronucleus frequencies and data analysis.

The Tradescantia-micronucleus (Trad-MCN) bioassay is an efficient short-term test for genotoxicity of pollutants. In order to increase the efficiency and to standardize the micronucleus (MCN) scoring process, an automated scoring system was developed using the principle of image analysis in computer science. This assemblage is called the Tradescantia-micronucleus image analysis (Trad-MCNIA) system. The MCN frequencies scored by this system were compared with those scored by human observation for its proficiency. A set of low MCN frequency (around 5 MCN/100 tetrads) slides prepared from a control group, a set of medium MCN frequency (around 20 MCN/100 tetrads) slides prepared from sodium azide treated plant cuttings and a set of high MCN frequency (around 50 MCN/100 tetrads) slides prepared from X-ray treated materials were used for this study. In the low MCN frequency slides, the Trad-MCNIA system scored about the same value as human observation. In the medium and high frequency slides, MCN frequencies scored by the system were lower than those scored by human observers. This discrepancy was corrected by increasing the power of the objective of the microscope in the system. The MCN frequencies scored by the system attained 90% congruity with those scored by human observers after the correction. The scoring speed of the system was about 3.5 times as fast as that by human observers, and the data could be statistically analyzed immediately after the data scores were recorded. Further improvements can be made by upgrading the video camera and the computer speed.

Azides

High-performance computing, high-speed networks, and configurable computing environments: progress toward fully distributed computing.

The next several years will see the maturing of a collection of technologies that will enable fully and transparently distributed computing environments. Networks will be used to configure independent computing, storage, and I/O elements into "virtual systems" that are optimal for solving a particular problem. This environment will make the most powerful computing systems those that are logically assembled from network-based components and will also make those systems available to a widespread audience. Anticipating that the necessary technology and communications infrastructure will be available in the next 3 to 5 years, we are developing and demonstrating prototype applications that test and exercise the currently available elements of this configurable environment. The Lawrence Berkeley Laboratory (LBL) Information and Computing Sciences and Research Medicine Divisions have collaborated with the Pittsburgh Supercomputer Center to demonstrate one distributed application that illuminates the issues and potential of using networks to configure virtual systems. This application allows the interactive visualization of large three-dimensional (3D) scalar fields (voxel data sets) by using a network-based configuration of heterogeneous supercomputers and workstations. The specific test case is visualization of 3D magnetic resonance imaging (MRI) data. The virtual system architecture consists of a Connection Machine-2 (CM-2) that performs surface reconstruction from the voxel data, a Cray Y-MP that renders the resulting geometric data into an image, and a workstation that provides the display of the image and the user interface for specifying the parameters for the geometry generation and 3D viewing. These three elements are configured into a virtual system by using several different network technologies. This paper reviews the current status of the software, hardware, and communications technologies that are needed to enable this configurable environment. These interdependent technologies include: (1) user interface and application program construction methodologies, (2) the interprocess communication (IPC) mechanisms used to connect the software modules of the application, (3) the network protocols and interface hardware used by the IPC for communicating between modules running on separate and independent computing system elements, (4) the telecommunications infrastructure that provides the low-level data transfer functions for the networks that connect the geographically distributed elements used by the application, and (5) the nature of the functional elements that will be connected to form virtual systems.

Computer Communication Networks

CSGL: chemical synthesis graph learning for molecule representation.

MOTIVATION: Molecule representation learning (MRL) translates molecules into a real vector space, serving as input to downstream tasks in biology, chemistry, and computer science. This article introduces a chemical synthesis graph learning (CSGL) framework, which enhances MRL by considering both the atomic structures of molecules and their roles in chemical reactions through a hierarchical graph representation. Specifically, molecules are first modeled based on their molecular graphs, which capture atomic-level structural information. They are then further refined using a chemical synthesis graph, where nodes represent reactant and product molecule sets, and edges encode chemical transformations between reactants and products (e.g. changes in molecular structures). CSGL optimizes molecular embeddings of reactant and product nodes in a fashion that ensures the embeddings conform to a chemical balance constraint. RESULTS: Experimental results show that our method CSGL achieves strong performance on a variety of tasks, including product prediction, reaction classification, and molecular property prediction. AVAILABILITY AND IMPLEMENTATION: https://github.com/li-2023/CSGL.

Machine Learning

A physician's workstation designed for NASA and earth-based applications.

One of the prime missions for NASA is the safety and care of astronauts. In addressing this challenge, a tool has been developed which has great potential for earth-based applications. The multimedia physician's workstation is the result of 13 years of planning and technical revolution in the field of computer science. Today, we have the hardware and the software to make a major change in the office-based practice of physicians. By offering the online features of a medical library as well as a complete multimedia medical record system, we are now in a position to introduce advance decision support technology that can be used on a daily basis for routine outpatient care. The system supports a new platform for patient education and offers the doctor an opportunity to share his expertise with his patient and their family. Although NASA will need several more years before this technology can be applied to a remote space environment, we plan to introduce this system into the doctor's office as an initial test of its feasibility. The basic design and general specifications of this multimedia workstation/office system are described and illustrated as they currently exist.

Aerospace Medicine

Who has the right to know the genetic constitution of a particular person?

Having conquered computer science, linguistics and aesthetics, the 'informational paradigm' has finally reached bioscience. In terms of information theory a human being's personal identity is defined by his/her unique combination of genetic information ('genetic fingerprint'). Any ethical analysis of the accessibility of individual genetic data must therefore be considered both from a medical ethics and from an information ethics point of view. As far as medical ethics is concerned it is obvious that certain medical activities relating to the physical and psychological integrity of human beings require informed consent. Since all activity involved in revealing a person's genetic constitution fulfils the requirements of informed consent, it goes without saying that only the person concerned has the right to determine who should have access to his/her genetic information. From an information ethics point of view, however, there is by definition no such thing as the natural right to private ownership of any kind of information. Information is in principle rather defined as a publicly shared good. We could therefore conclude from this that in principle everyone has the right to know everyone else's genetic constitution. The paper discusses some of the resulting problems by analysing different sets of arguments and confronting them with higher-order principles of modern ethics.

Confidentiality

Ca2+ imaging in single living cells: theoretical and practical issues.

The measurement of intracellular calcium ion concentrations [( Ca2+]i) in single living cells using quantitative fluorescence microscopy draws from a diverse set of disciplines, including cellular biology, optical physics, statistics and computer science. Over the last few years, we have devised and built a number of systems for measuring [Ca2+]i with Fura-2, and have applied them in the exploration of a wide range of biological processes controlled by Ca2+. In this report we discuss these systems and their advantages and limitations. We also describe the theoretical and practical problems associated with using Fura-2 to measure [Ca2+]i, and the solutions that we, and others, have developed to overcome them. The approaches described should provide useful guidance for others interested in imaging [Ca2+] distribution in living cells. The factors that limit current methods are discussed, and areas for future development are highlighted.

Animals

Insight into protein nuclear magnetic resonance research.

Nuclear magnetic resonance (NMR) is one of the most powerful techniques to investigate the geometry of molecules in solution. It has been widely applied, in recent years, to the study of protein conformation. However, full reconstruction of the 3-D structure of such macro-molecules, still constitutes a real challenge for the spectroscopist. Skills as diverse as biology, spectroscopy, signal processing, or computer sciences, are required. This paper presents various aspects of the research in that domain, and our contribution to it.

Algal Proteins