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PubMed1980

Computer-assisted customized antimicrobial dosages.

The use of a computer-based consultation program to customize dosage regimens of antimicrobials for patients with meningitis or bacteremia is described. Using clinical and laboratory information entered by the user, the program determines causative organisms, recommends therapeutic regimens, and generates a graph depicting the expected blood level of each drug as a function of time. During therapy selection, the program considers the site of infection, the susceptibility of the organism to antibiotics, and the patient's clinical status and drug history. Individualized pharmacokinetic values allow for dosage adjustments in renal failure and estimation of blood levels. If renal impairment is present, dosage regimens for drugs excreted by the kidneys are adjusted to assure the desired steady-state blood levels. To help in selection of the optimal regimen, estimated blood levels for each regimen are graphed along with the minimum inhibitory concentration for the organism and the toxic level of the drug. A bulit-in knowledge base in conjunction with patient-specific information enables the computer program to determine appropriate treatment specific to a patient's age, renal function, and prior drug reactions.

Adult↗
PubMedDate not supplied

Using neural network predicted secondary structure information in automatic protein NMR assignment.

In CAPRI, an automated NMR assignment software package that was developed in our laboratory, both chemical shift values and coupling topologies of spin patterns are used in a procedure for amino acids recognition. By using a knowledge base of chemical shift distributions of the 20 amino acid types, fuzzy mathematics, and pattern recognition theory, the spin coupling topological graphs are mapped onto specific amino acid residues. In this work, we investigated the feasibility of using secondary structure information of proteins as predicted by neural networks in the automated NMR assignment. As the 1H and 13C chemical shifts of proteins are known to correlate to their secondary structures, secondary structure information is useful in improving the amino acid recognition. In this study, the secondary structures of proteins predicted by the PHD protein server and our own trained neural networks are used in the amino acid type recognition. The results show that the predicted secondary structure information can help to improve the accuracy of the amino acid recognition.

Algorithms↗
PubMed1998

Conceptual integration of information databases into an Intranet.

Large information systems handle massive volume of data stored in heterogeneous sources of information. Each server has its own model of concepts representation with regard to its aims. One of the main problems encountered by end-users when accessing different servers is to match their own viewpoint on biomedical concepts with their various representations that are made in the database servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet, and to propose a method to realize it. Moreover, this method provides designers of web sites with a powerful tool to manage them on the basis of an ontology of the biomedical domain. This method is based on the knowledge sources provided by the Unified Medical Language System project of the U.S. National Library of Medicine and exploits intensively the conceptual graphs theory.

Computer Communication Networks↗
PubMed1979

[Carl Heinrich Stratz (1858 to 1924), one of the first researchers in growth and development--chronological tables of his life and work (author's transl)].

Review of education, life and work of C.H. Stratz. First a clinical gynecologist and always earning his living from this profession, he was interested in the problems of somatic and regional anthropology. After 1900 he became more and more engaged in observations of the child's development from the new-born to the adolescent. His publications, especially his graphs and pictures of morphological changes in the childs body and the signs of puberty, have the following years deeply influenced our knowledge on "orthology" within the medical problems of youth.

Anthropology, Physical↗
PubMed1996

The project ARIANE: conceptual queries to information databases.

As information databases we consider all the collections of data records indexed by key-words, stored and delivered by computer systems. In previous research works we demonstrated the interest to design a conceptual model, in the conceptual graphs formalism, and to implement a computational model for information retrieval in large information databases. These models are based on the UMLS knowledge sources. This paper reminds briefly these models and describes tests done in querying a patients database and a bibliographical database.

Databases, Bibliographic↗
PubMedDate not supplied

Improving quality and performance practices using fiberoptic endoscopes in perioperative areas: a case study.

In response to the impact of healthcare reform, a re-engineering of problem areas within the University of Maryland's Medical System needed to be initiated. A critical issue to be addressed, within the perioperative areas of the hospital, was the delay in service because of the unavailability of functional fiberoptic endoscopes. This resulted in spiraling operating costs and compromised quality of care of patients. Analysis of the situation using fiberscope inventory data revealed unreliable quality-controlled reprocessing systems and lack of knowledge by the staff in handling and caring for the fiberscopes. A number of actions were taken to improve staff patterns of performance. Graphs, spreadsheets, and diagrams were used to pinpoint the problem areas for each perioperative area and were presented to the staff. These data were up-dated monthly to inform staff and inspire further improvements in performance. This re-engineering of the fiberoptic scope delivery system resulted in economic, operational, customers, and quality of care benefits. Fiberoptic endoscopes are increasingly used is surgical fields outside of the traditional endoscopy unit. Endoscopic nurses need to share expertise to improve the quality of performance in all areas of the hospital where fiberoptic scopes are used.

Academic Medical Centers↗
PubMed2026

Artificial Intelligence for Natural Products Discovery and Development.

Natural products (NPs) remain a cornerstone of modern drug discovery, offering stereochemical complexity and diverse bioactivities that precisely modulate therapeutic targets, refined through billions of years of evolution. However, their research has long been hindered by inefficient, empirical workflows, high resource consumption, structural complexity, and the "multicomponent, multi-target" nature of their mechanisms. The exponential growth of genomic, metabolomic, and spectral data has overwhelmed conventional analytical methods, exposing critical bottlenecks in handling high-dimensional, heterogeneous datasets that exceed human interpretive capacity. Artificial intelligence (AI) is emerging as a transformative paradigm to address these challenges, integrating multi-omics and chemical data to shift NP research from fragmented empiricism toward mechanism-driven, precision-oriented development. By leveraging deep learning architectures- including graph neural networks, Transformers, and diffusion-based generative models-AI enables systematic decoding of NP biosynthesis, automated structure elucidation, rational target identification, knowledge extraction from vast unstructured scientific literature, and de novo molecular design. This review comprehensively surveys recent advances in AI applications across the full NP discovery and development pipeline, encompassing genome mining, structure-based and ligand-based virtual screening, multimodal structural characterization, lead optimization, and biosynthetic pathway engineering. We further examine the emerging roles of protein-centric, molecule- centric, and multimodal foundation models, as well as large language models, in bridging genotype-to-chemotype gaps and unlocking unstructured scientific knowledge. Finally, we discuss critical challenges including data scarcity, representational limitations for complex stereochemistry, physical plausibility in generative models, and the urgent need for experimental validation, while outlining future directions toward autonomous experimentation, closed-loop optimization, and human-AI collaborative discovery.

Artificial intelligence↗
PubMed1979

Thermal conduction effects in human skin.

To determine the maximum permissible temperature any material may attain without causing pain or burn on contact with bare skin, over 2000 observations were made of pain threshold during contact with materials at elevated temperatures. Six materials were used representing the full range of thermal properties from good conductors to good insulators. Time to pain threshold was converted to time to threshold blister on the basis of the relationship between pain and burn established earlier for radiant and for convective heating. Calculated times to blister were used to predict the material temperatures causative of "touch-burn". Experimentally produced threshold blisters at the predicted temperature-times verified the predictions. Graphs and equations were generated for determining safe temperatures for any material in contact with bare skin for 1-5 s solely from a knowledge of its thermal properties. Conversely, the thermal inertia (k rho c) of the optimal material for a specific use and skin contact can be predicted from a knowledge of the maximum material temperature and length of contact time anticipated.

Aerospace Medicine↗
PubMed1990

Proposed methodology for knowledge acquisition: a study on congenital heart disease diagnosis.

This paper proposes a methodology for knowledge acquisition (KA) from multiple experts, in an attempt to elicit the heuristic rules followed by the physician in diagnosing twelve frequently occurring congenital heart diseases (CHD). Twenty-two pediatric cardiologists and twenty-three general cardiologists were interviewed with this technique; 274 interviews were conducted, 169 with the 22 experts, 105 with the 23 non-experts. A graph formalism was employed to represent their reasoning model, leading to the construction of a "mean reasoning model" for each diagnosis, separately for experts and non-experts. The results indicate that experts, compared to non-experts, tend to build knowledge representation models (KRM) that are smaller and less complex. Qualitative differences in information utilization between the two groups were also observed. Entropy analysis suggests a greater objectivity and cohesion of the experts' model.

Algorithms↗
PubMed1989

An AI-based communication system for motor and speech disabled persons: design methodology and prototype testing.

An intelligent communication device is developed to assist the nonverbal, motor disabled in the generation of written and spoken messages. The device is centered on a knowledge base of the grammatical rules and message elements. A "belief" reasoning scheme based on both the information from external sources and the embedded knowledge is used to optimize the process of message search. The search for the message elements is conceptualized as a path search in the language graph, and a special frame architecture is used to construct and to partition the graph. Bayesian "belief" reasoning from the Dempster-Shafer theory of evidence is augmented to cope with time-varying evidence. An "information fusion" strategy is also introduced to integrate various forms of external information. Experimental testing of the prototype system is discussed.

Artificial Intelligence↗
PubMed1995

A model for medical knowledge representation application to the analysis of descriptive pathology reports.

A new knowledge-representation system is presented, designed for medical knowledge-based applications and in particular for the analysis of descriptive medical reports. Knowledge is represented at two levels. A definitional level uses a concept-type hierarchy, a relation-type hierarchy, and a set of schematic graphs to define the concepts used and the relations between them, as well as different types of cardinality restrictions on these relations. A set of compositional hierarchies using the classic "has-part" relation as well as a new set-inclusion relation allows concept composition to be precisely defined. An assertional level allows the creation and manipulation of empirical data, in the form of graphs using the concepts, relations, and constraints defined at the definition level. The use of cardinality constraints in graph unification is considered in the context of descriptive medical discourse analysis.

Artificial Intelligence↗
PubMed1995

Visualization and comparison of molecular dynamics simulations of leukotriene C4, leukotriene D4, and leukotriene E4.

Molecular dynamics simulations of leukotriene C4 (LTC4), leukotriene D4 (LTD4), and leukotriene E4 (LTE4) were carried out, and the data were visualized in an animated video format. Three-dimensional ghost images show the positions of the heavy atoms of all three molecules throughout the simulations. The ghost images can be superimposed to give a single three-dimensional image in which the shapes of the most populated conformers of each molecule are apparent and can be compared. Leukotriene D4 was found to occupy mostly T-shaped conformations, while LTC4 occupied mostly cup-shaped conformations, and LTE4 occupied a wide range of conformations spanning the LTD4 and LTC4 types. Digital filtering and graphing of the internal geometries of the molecules as a function of time revealed differences in dynamic behavior. The results are discussed in light of current knowledge about leukotriene receptors.

Computer Graphics↗
PubMed1996

In vivo measurements of indwelling tracheo-oesophageal prostheses in alaryngeal speech.

Over the last 5 years, detailed air pressure, flow and voice measurements have been made on indwelling tracheo-oesophageal speaking valves whilst inserted in patients, using specially designed apparatus. This study was set up to investigate the relationship between speech and in vivo parameters. In vivo pressure measurements were generally lower for Groningen low resistance than Groningen high resistance, while flow and voice measurements were higher. A plot of opening pressure against pressure at maximum flow for all valves suggested a straight line relationship. A graph of maximum voice against composite parameter score for all valves showed a cluster of points between the composite score of 0-15. The advances in knowledge about these valves should be of use in the design of improved valves.

Aged↗
PubMed1996

New approaches in molecular structure prediction.

In the past years, much effort has been put on the development of new methodologies and algorithms for the prediction of protein secondary and tertiary structures from (sequence) data; this is reviewed in detail. New approaches for these predictions such as neural network methods, genetic algorithms, machine learning, and graph theoretical methods are discussed. Secondary structure prediction algorithms were improved mostly by considering families of related proteins; however, for the reliable tertiary structure modeling of proteins, knowledge-based techniques are still preferred. Methods and examples with more or less successful results are described. Also, programs and parameterizations for energy minimisations, molecular dynamics, and electrostatic interactions have been improved, especially with respect to their former limits of applicability. Other topics discussed in this review include the use of traditional and on-line databases, the docking problem and surface properties of biomolecules, packing of protein cores, de novo design and protein engineering, prediction of membrane protein structures, the verification and reliability of model structures, and progress made with currently available software and computer hardware. In summary, the prediction of the structure, function, and other properties of a protein is still possible only within limits, but these limits continue to be moved.

Chemical Phenomena↗
PubMed2001

Quantitative analysis of nucleic acid three-dimensional structures.

A new computer program to annotate DNA and RNA three-dimensional structures, MC-Annotate, is introduced. The goals of annotation are to efficiently extract and manipulate structural information, to simplify further structural analyses and searches, and to objectively represent structural knowledge. The input of MC-Annotate is a PDB formatted DNA or RNA three-dimensional structure. The output of MC-Annotate is composed of a structural graph that contains the annotations, and a series of HTML documents, one for each nucleotide conformation and base-base interaction present in the input structure. The atomic coordinates of all nucleotides and the homogeneous transformation matrices of all base-base interactions are stored in the structural graph. Symbolic classifications of nucleotide conformations, using sugar puckering modes and nitrogen base orientations around the glycosyl bond, and base-base interactions, using stacking and hydrogen bonding information, are introduced. Peculiarity factors of nucleotide conformations and base-base interactions are defined to indicate their marginalities with all other examples. The peculiarity factors allow us to identify irregular regions and possible stereochemical errors in 3-D structures without interactive visualization. The annotations attached to each nucleotide conformation include its class, its torsion angles, a distribution of the root-mean-square deviations with examples of the same class, the list of examples of the same class, and its peculiarity value. The annotations attached to each base-base interaction include its class, a distribution of distances with examples of the same class, the list of examples of the same class, and its peculiarity value. The distance between two homogeneous transformation matrices is evaluated using a new metric that distinguishes between the rotation and the translation of a transformation matrix in the context of nitrogen bases. MC-Annotate was used to build databases of nucleotide conformations and base-base interactions. It was applied to the ribosomal RNA fragment that binds to protein L11, which annotations revealed peculiar nucleotide conformations and base-base interactions in the regions where the RNA contacts the protein. The question of whether the current database of RNA three-dimensional structures is complete is addressed.

Base Pairing↗
PubMed1991

Determination of the etching surface of metal frameworks in resin-bonded prostheses.

The aim of electrolytic etching of the metal framework of resin bonded retainers is a microretentive surface. The results of metal etching depend on various factors such as metal alloy, casting conditions, etching solution, and constant electrolytical conditions. Precise knowledge of the inner metal surface is necessary for an exact setting of the current density per time unit. The indirect method of copying the contours from tinfoil to graph paper reduced the error rate to a mean value of +/- 2.3 mm2. This practical method of determining the metal surface before etching can be accomplished without complicated equipment.

Acid Etching, Dental↗
PubMed2026

Network methods for diagonal integration of unpaired single-cell multiomics data: a review.

MOTIVATION: Advances in single-cell sequencing have enabled multiomics profiling at unprecedented resolution; however, mass spectrometry-based single-cell proteomics (scMS) remains inherently destructive, precluding simultaneous transcriptomic capture. Unlike antibody-based methods such as CITE-seq, which permit paired profiling but are restricted to targeted protein panels, scMS provides unbiased, genome-scale coverage of the intracellular proteome yet necessitates post hoc integration of unpaired datasets. This diagonal integration challenge, where transcriptomes and proteomes are measured in separate cells lacking shared anchors, remains underserved by existing reviews, which focus predominantly on vertical integration strategies enabled by non-destructive assays. RESULTS: We survey the complete computational pipeline for constructing mechanistic proteogenomic networks from unpaired single-cell data, covering: (i) unimodal network inference such as knowledge-based approaches, probabilistic graphical models, temporal directionality inference, and generative and foundation model strategies that establish the transcriptomic scaffold; (ii) cross-modal integration architectures such as network propagation, graph neural networks (scMRDR, scmFormer, scCotag), and consensus frameworks designed explicitly for the unpaired proteomics setting; and (iii) benchmarking paradigms spanning network reconstruction (BEELINE, GRETA, CausalBench) and multi-task integration evaluation (scMultiBench, SCMMIB), with guidance on metric selection under network sparsity and class imbalance. We identify three principal axes of future development: generative proteomic translation from transcriptomic precursors, inductive prior embedding in next-generation architectures, and perturbation-based causal benchmarking. AVAILABILITY AND IMPLEMENTATION: This is a review article; no novel software is distributed. A curated benchmark resource table, methods starter guide, and per-method bottleneck annotations are provided in the Supplementary Material.

Multiomics↗
PubMed1975

[Radioisotopic examination and diagnosis of dryness of the mouth].

The clinical and sialographic opposition between true xerostomia (with continuous disorders) and paradoxical asialia (with inter-prandial disturbance, but sparing mealtime) led the authors to analyze these patient's scintigraphic scannings. A kinetic study of excretion was carried out with gamma-camera recording of intensity and glandular activity: the information thus obtained was set down in a numerical integration block and dealt with by computer. A graph of activity was plotted for each gland showing: - a phase of ascending concentration followed by a plateau corresponding to excretion at rest; - a phase of excretion provoked by a gustatory stimulus (physiological) with a very rapidly descending graph. It is possible to establish a ratio of glandular activity/blood activity at maximum concentration and maximum excretion. From the graphs thus obtained it is possible to perfectly differentiate true xerostomia (no excretion even with stimulation) from paradoxical asialia (no plateau of excretion at rest, but stimulus effective). A better knowledge of "dryness of the mouth" should enable better adapted therapy.

Diagnosis, Differential↗