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PubMed2025

Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.

The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying noninvasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g., gut, oral, and skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and Artificial Intelligence-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and generate robust and testable hypotheses. This article is part of a special series: Driving Cancer Discoveries with Computational Research, Data Science, and Machine Learning/AI .

Humans↗
PubMed2002

A methodology for incorporating web technologies into a computer-based patient record, with contributions from cognitive science.

Cognitive science is a rich source of insight for creative use of new Web technologies by medical informatics workers. I outline a project to Web-enable an existing computer-based patient record (CPR) in the context of ideas from philosophy, linguistics, artificial intelligence, and cognitive psychology. Web prototypes play an important role (a) because Web technology lends itself to rapid prototype development, and (b) because prototypes help team members bridge among disparate medical, computing, and business ontologies. Six Web-enabled CPR prototypes were created and ranked. User scenarios were generated using a user communication matrix. Resulting prototypes were compared according to the degree to which they satisfied medical, computing, and business constraints. In a different organization, or at different time, candidate prototypes and their ranking might have been different. However, prototype generation and comparison are fundamentally influenced by factors usefully understood in a cognitive science framework.

Cognitive Science↗
PubMed1993

The Human Brain Project: an international resource.

As the amount of basic neuroscientific information increases dramatically, its day-to-day integration and application becomes an increasing difficulty. Technological advances, particularly in computer and information sciences, should allow this information 'explosion' to become more manageable. To this end, the Human Brain Project, an initiative of several NIH Institutes and other United States Government agencies, is being developed to provide a computer database that will allow neuroscientists access to information at all levels of integration, from genes to behavior. In this article Michael Huerta, Stephen Koslow and Alan Leshner outline the genesis and ideas behind the initiative and discuss its future development.

Brain↗
PubMed1992

The integrated health-care system: reflection and projection.

This paper presents a personal view of the development of integrated, comprehensive health-care systems in the United States. The influence of Federal legislation is described, beginning with the 1950-60s policy objective of Hill-Burton Program administrators to create a number of community-based regional medical centers, each consisting of a range of health services organized by and around community hospitals. Later variations of the concept appeared in such programs as Medicare-Medicaid, Comprehensive Health Planning, the Regional Medical Programs, and the new Agency for Health Care Policy and Research. Based on the cumulative experience of the past, the economic, professional and social climate of the present, with its increasing involvement of the patient/payer/consumer in decisions, and the enhanced inter-organizational coordination emerging from technologies of computers and communication science, the goal of creating comprehensive integrated systems as conceived in the 1950s and 60s may finally be achieved in the 1990s, but in a different form from that envisioned earlier. By judicious exploitation of computer and communication capabilities and the massive knowledge bases evolving from research, the way is eased for patient-centered integration and coordination of services without demanding integration in the sense of ownership or formal control of all the providers within a central organization.

Comprehensive Health Care↗
PubMed2006

Re-engineering Colles: form, function and fragility fractures.

Of the twenty nine anatomy professors in the Royal College of Surgeons in Ireland, primus inter pares is Abraham Colles. In his 1811 book A Treatise on Surgical Anatomy he revolutionised the subject by teaching it topographically, seeking "to describe the relative position of the parts and to point out the subservience of anatomical knowledge to surgical practice". Today we have extended this to 'clinical practice' and, in the Anatomy Room, students are guided through each region by clinically trained staff, from surface anatomy via three-dimensional dissection to radiological images. This is augmented by online histology and radiology courses and DVDs in which dissection footage, edited by a content analysis engine, is used to preview and review practical classes. In the same book, Colles also wrote that 'the fixed and immutable laws of mathematics are little applicable to the science of medicine'. Computer-aided learning argues against this. So does research which links fatigue microdamage to bone remodelling and the development of algorithms to predict, and thus prevent, osteoporotic fractures. Mechanical principles are being used to develop scaffolds for tissue engineering and to optimise the mechanical environment of seeded mesenchymal stem cells. While Colles' teaching approach holds true, in biomechanics, tissue engineering and computing, mathematical laws are now being successfully applied to medical science.

Anatomy↗
PubMed1986

Origins of medical informatics.

Medical informatics is a new knowledge domain of computer and information science, engineering and technology in all fields of health and medicine, including research, education and practice. Medical informatics has evolved over the past 30 years as medicine learned to exploit the extraordinary capabilities of the electronic digital computer to better meet its complex information needs. The first articles on this subject appeared in the 1950s, the number of publications rapidly increased in the 1960s and medical informatics was identified as a new specialty in the 1970s.

History, 20th Century↗
PubMed1985

User involvement in the development and use of computer based systems for the health and rehabilitation sciences: reducing protocol test errors.

In this study an attempt was made to clarify conflicting results in the learner control literature. The learner control concept was redefined in order to include both choice and self investment variables. The combined effects of choice and self investment variables were considered in this study to be motivational variables which affect the learner's attitudes and performance on a computer assisted instructional task. The results of this investigation indicated overall differences in performance among treatment groups. An interaction effect between choice and self investment was found for the performance measure. The expected interaction and perceived control measures were not found. Various analyses of the postexperimental test protocol scoring errors were conducted in order to investigate the effectiveness of the computer assisted instruction (CAI) task. Completion of the CAI task seemed to decrease the number of scoring errors made on subsequent test protocols as compared to those who did not use the CAI task. Implications for the health and rehabilitation sciences are discussed.

Attitude↗
PubMed1999

Wildcat World: simulation programs for teaching basic concepts in psychological science.

A series of computer programs is described that allows beginning psychology students to design, conduct, analyze, and interpret virtual (computer-simulated) psychological studies. This technique allows the instructor more control over the outcome of student experiments, increases the scope of experiments that can be done by students, decreases the amount of class time that must be devoted to conducting experiments, and eliminates concerns about student experimenters using human or animal subjects.

Computer-Assisted Instruction↗
PubMed1995

Temperature prediction of space flight experiments by computer thermal analysis.

Life sciences experiments are especially sensitive to temperature. A small temperature difference between otherwise identical samples can cause various differences in biological reaction rates. Knowledge of experimental temperatures and temperature histories help to distinguish the effects of microgravity and temperature on spaceflight experiments compared to ground based studies, and allow appropriate controls and sensitivity tests. Up to the present time, the Orbiter (Space Shuttle) has not generally provided temperature measurement instrumentation inside ambient lockers located in the Mid-deck of the Orbiter, or inside similar facilities such as Spacehab and Spacelab, but many pieces of hardware do have temperature recording capability. Most of these temperatures, however, have only been roughly measured or estimated. Such reported experimental temperatures, while accurate within a range of several degrees Celsius, are of limited utility to biological researchers. The temperature controlled lockers used in spaceflight, such as Commercial-Refrigeration Incubation Modules (C-R/IMs), severely reduce the mass and volume available for test samples and do not necessarily provide uniform thermal environments. While these test carriers avoid some of the experimental temperature variations of the ambient lockers, the number of samples which can be accommodated in these temperature controlled units is limited. In the present work, improved models of thermal prediction and control were sought. Temperatures are predicted by thermal analysis software using empirical temperatures recorded during STS-57. These temperatures are compared to data recorded throughout the mission using Ambient Temperature Recorders (ATRs) located within several payload lockers. Additional test cases are undertaken using controlled ground experiments to more precisely determine the reliability of the thermal model. The approach presented should increase the utility of various spaceflight carriers in the support of biological and material science research and ground control studies done in preparation for flight.

Air Conditioning↗
PubMed2003

Computational approaches to motor learning by imitation.

Movement imitation requires a complex set of mechanisms that map an observed movement of a teacher onto one's own movement apparatus. Relevant problems include movement recognition, pose estimation, pose tracking, body correspondence, coordinate transformation from external to egocentric space, matching of observed against previously learned movement, resolution of redundant degrees-of-freedom that are unconstrained by the observation, suitable movement representations for imitation, modularization of motor control, etc. All of these topics by themselves are active research problems in computational and neurobiological sciences, such that their combination into a complete imitation system remains a daunting undertaking-indeed, one could argue that we need to understand the complete perception-action loop. As a strategy to untangle the complexity of imitation, this paper will examine imitation purely from a computational point of view, i.e. we will review statistical and mathematical approaches that have been suggested for tackling parts of the imitation problem, and discuss their merits, disadvantages and underlying principles. Given the focus on action recognition of other contributions in this special issue, this paper will primarily emphasize the motor side of imitation, assuming that a perceptual system has already identified important features of a demonstrated movement and created their corresponding spatial information. Based on the formalization of motor control in terms of control policies and their associated performance criteria, useful taxonomies of imitation learning can be generated that clarify different approaches and future research directions.

Humans↗
PubMed2003

A preliminary analysis of the dental informatics literature.

Dental informatics is an emerging discipline applying computer and information science to dental practice, research, education, and management. To date, the dental informatics research literature has not been comprehensively reviewed. This study reports an initial analysis of the dental informatics literature. We developed an initial, comprehensive retrieval strategy to locate dental informatics citations in MEDLINE (1966-April 2003), including three concepts: dentistry, computers, and research. After refinement of the search, we manually classified the final set into four categories: (1) non-dental; (2) dental, but neither dental informatics nor IT-related; (3) dental informatics; and (4) IT in dentistry. We analyzed informatics and IT-related citations regarding their distribution across journals, growth rate, the number of authors and their publication frequency, and content as expressed by Medical Subject Headings (MeSH). The final set of citations (n = 3872) consisted of: 12% non-dental articles; 59% dental, but not informatics- or IT-related articles; 16% informatics-related articles; and 13% IT-related articles. Informatics-related citations appeared in 176 journals, and IT-related citations in 206 journals. Approximately 50 papers are currently published in both categories yearly. While a great many authors have contributed to this literature, very few have published more than three papers. Main topics of articles included "Imaging and Image Processing", "Computer-aided Diagnosis and Therapy", "Computer-aided Instruction", and "Other". The dental informatics literature is small, but growing. Imaging and image processing predominate as research topics.

Bibliographies as Topic↗
PubMed2002

Applications of computer software for the interpretation and management of mass spectrometry data in pharmaceutical science.

The rapid growth of mass spectrometry (MS)-based computer software applications has been fueled by the unprecedented need to capture and analyze MS data and provide the information necessary for decision-making. Shorter timelines and a significantly greater number of samples has resulted in a tremendous focus on streamlined approaches that provide scientists, managers, and executives the capability to readily obtain, or even request, the necessary information that leads to accelerated product development. The generation of analytical data using roboticized high-throughput hardware has produced a bottleneck since data can be generated faster than it can be analyzed. New techniques including MS/MS and accurate mass experiments are feasible only using computers to capture and manage the enormous amounts of data necessary to perform the experiments. Whatever the nature of the experiments conducted, the MS analysis strategy is to extract the appropriate information required for decision-making in as facile a manner as possible. We will review here a survey of the creation of commercial and laboratory specific reference databases and associated searching algorithms and also recent efforts to introduce advancedprocessing and analysis algorithms to the hands of the masses, specifically as an aid to structure elucidation.

Chemistry, Pharmaceutical↗