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PubMed1995

An inventory of computer resources for the medical application of virtual reality.

Within the framework of the scientific community, we could define virtual reality (VR) as an effective simulation of complex environmental aspects related to both interaction-dependent and high-risk operations, where mistakes will lead to unacceptable consequences. Surgeons performing open surgery, endoscopists working on the intestine or neurologists working on the brain-all are impressive examples where the VR approach looks potentially quite interesting. In fact the risk of unsatisfactory implementations, too poor with respect to the complexity of the real world, coming from the unsatisfactory performance of the present-day technology, is quite high. Typically, the loss of the real time requirement for the operator interactions can remove much of the effectiveness of what has been built. Some questions about the real need for high performance computational resources and high level graphic resolution need to be answered. This paper presents and discusses an inventory of computational resources used in real applications.

CD-ROM↗
PubMed1975

Physical basis of charge pairing in mitochondria.

The postulate of charge pairing in the mitochondrial inner membrane is justified by applying a formula due to Fuoss to calculate the probability density for the distance between a positive and a negative charge. For dielectric constants 10 or less pairing is absolute, for 20 there is some tendency towards pairing, and at 78 it is nonexistent. Pairing, partner exchange or charge substitution, inhibition, and antiport uncoupling can be rationalized within this framework.

Computers↗
PubMed1980

Modern methods of investigation in speech production.

Methodologies of speech research with respect to the production processes are discussed, with an emphasis on the recent development of new instrumental techniques. It is argued that systematic studies of large amounts of speech data are necessary to understand the basic characteristics of speech. The traditional notion of phoneme-size segments seems inappropriate for interpreting multidimensional articulatory movements by a concatenative model. Experimental means such as a computer-controlled X-ray microbeam technique and advanced statistical processing, in combination with a new theoritical framework of phonetic description, promise future development.

Computers↗
PubMed1989

Decision analysis: a framework for critical care decision assistance.

The ultimate goal of medical computer systems is to help clinicians make good decisions. Such systems must be based on sound principles. Decision analysis is a 25-year-old discipline that provides the needed rigorous foundation for decision assistance. Decision analysis comprises the philosophy, procedures, and tools that can correct the flaws in existing critical care decision-making practice. Intelligent decision systems--computer-based systems that automate decision analysis--make it practical to apply decision analysis to critical care. Orchestra is a pilot intelligent decision system (now under development) that coordinates the efforts of the critical care specialist, the bedside physician, and the bedside nurse in building decision models that can provide recommendations and insight for ventilator management decisions. Decision analysis delivered by intelligent decision systems has great potential for improving critical care decision-making.

Algorithms↗
PubMed2026

AI-genomics synergy for drug repurposing in breast cancer: an interpretability-driven framework.

Breast cancer's genomic heterogeneity complicates drug discovery, making repurposing an attractive but challenging strategy. Advances in artificial intelligence now enable integration of multi-omics data to reveal drug-gene-disease relationships and generate subtype-specific repurposing hypotheses. In this Review, we examine AI-driven computational approaches from signature-based to multi-modal frameworks and propose an integrated interpretability-driven framework linking mechanistic validation with clinical translation toward more transparent and actionable precision oncology.

Journal Article↗
PubMed2026

Comparative and Subtractive Genomics Analysis of Multidrug-Resistant Klebsiella pneumoniae Strains for Novel Target Identification and Drug Repurposing Strategies.

The rapid rise of multidrug-resistant (MDR) Klebsiella pneumoniae has created a major global health challenge due to the limited availability of conserved therapeutic targets effective across diverse resistant strains. In this study, an integrative computational target-discovery and drug-repurposing framework was applied to six clinically relevant K. pneumoniae strains. Comparative genomic analysis identified 3012 conserved genes, which were subsequently filtered to nine essential, non-host homologous proteins. Among these, three conserved cytoplasmic proteins (accD, cpxR, and mraZ) were prioritized for functional analysis, with acetyl-CoA carboxylase subunit beta (accD) emerging as the most promising therapeutic target based on sequence conservation, predicted essentiality, subcellular localization, and pathway association. Structural assessment supported the reliability of the predicted accD model, whereas consensus binding-site analysis identified key residues suitable for ligand interaction. Virtual screening of FDA-approved drugs followed by molecular docking identified several compounds with favorable binding profiles toward accD. Subsequent molecular dynamics simulations, including root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), hydrogen-bond occupancy, principal component analysis (PCA), and PCA-based free energy landscape (FEL) analyses, consistently identified tenapanor, micafungin, deferoxamine, and cobicistat as the most stable protein-ligand complexes, with tenapanor exhibiting the most favorable overall structural and thermodynamic stability profile. These findings identify accD as a promising therapeutic target in MDR K. pneumoniae and suggest several FDA-approved compounds as potential candidates for drug repurposing. Although experimental validation is needed to confirm their biological activity and therapeutic potential, this study demonstrates the potential of integrating comparative genomics with molecular dynamics analyses to support antimicrobial target identification and drug repurposing against MDR bacterial pathogens.

Klebsiella pneumoniae↗
PubMed1992

Cluster analysis and related techniques in medical research.

In this paper we review methods of cluster analysis in the context of classifying patients on the basis of clinical and/or laboratory type observations. Both hierarchical and non-hierarchical methods of clustering are considered, although the emphasis is on the latter type, with particular attention devoted to the mixture likelihood-based approach. For the purposes of dividing a given data set into g clusters, this approach fits a mixture model of g components, using the method of maximum likelihood. It thus provides a sound statistical basis for clustering. The important but difficult question of how many clusters are there in the data can be addressed within the framework of standard statistical theory, although theoretical and computational difficulties still remain. Two case studies, involving the cluster analysis of some haemophilia and diabetes data respectively, are reported to demonstrate the mixture likelihood-based approach to clustering.

Algorithms↗
PubMed1982

Assessment of left ventricular function using an angiographic method.

Angiographic methods are by far the most frequently used for calculation of left ventricular volume, mass, forces acting within the ventricular wall or for analysis of contractile performance and diastolic property of the overall ventricle, as well as regional myocardial function in the presence of ischemia. A critical review of the theoretical basis and practical methods of calculation of these variables is presented. The left ventricular pressure-volume diagram is constructed which allows for an assessment of the inotropic state of the ventricle from the similar tension-length framework as obtained in the isolated papillary muscle. Computer technology of digital filtering and subtraction provides for an enhancement of the contrast of the ventricular image obtained with minimal doses of contrast medium. On-line methods for edge tracing and subsequent data processing are alleviating much of the tedious and laborious work of manual analysis of angiograms and accuracy of the calculation has been enhanced. Left ventriculography is most useful in diagnosing the presence of abnormal wall motion. Methods of assessing the magnitude and extent of the relative area of localized myocardial dysfunction are discussed. Quantitative information is crucial for evaluating prognosis and determining the application of therapeutic interventions.

Angiocardiography↗
PubMed1986

Mosaic architecture of the somatic sensory-recipient sector of the cat's striatum.

The striatum is known to have a compartmental organization in which histochemically defined zones called striosomes form branched 3-dimensional labyrinths embedded within the surrounding matrix. We explored how fiber projections from cortical somatic sensory areas representing cutaneous and deep-receptor inputs are organized in relation to this striatal architecture. Areas SI and 3a were mapped electrophysiologically, and distinguishable anterograde tracers (wheat germ agglutinin-HRP and 35S-methionine) were injected into physiologically identified loci. Primary somatic sensory corticostriatal projections were confined to a small, well-defined sector in the dorsolateral corner of the ipsilateral striatum. The somatic sensory afferents were arranged according to a coherent global body map in which rostral body parts were represented more laterally than caudal body parts. Single cortical loci innervated branched and clustered striatal zones that were reminiscent of the striosomes in their range of sizes and shapes yet lay strictly within the extrastriosomal matrix. In contrast to the global orderliness of the striatal body map, there were clear examples of locally complex patterns in which functionally distinct inputs interdigitated with each other. These patterns were often, but not always, produced when corticostriatal afferents carrying different submodality types were labeled. These findings demonstrate the existence of striosome-like striatal compartments within the seemingly uniform extrastriosomal matrix. The principle of mosaic organization thus holds throughout the tissue of the somatic sensory striatum. The striatal architecture delineated here could provide the anatomical substrate for computations requiring cross-modality comparisons within the framework of an overall somatotopy. If a similar multicompartmental architecture also characterizes other striatal regions, as seems likely, it may set general constraints on the nature of associative processing within the striatum as a whole.

Afferent Pathways↗
PubMed1982

Topological aspects of ion transport in complex epithelia (frog skin).

A weak point of the current concept of the kinetics of ion flow in complex epithelial tissue membranes, such as frog skin, is the supposition that these tissue membranes and their exterior environments can be looked upon as a "three compartment system." In the present study a new and more realistic conceptual framework, a "multicompartment system," is applied to a computer assisted kinetic analysis of experimental data. These deal with Na+ flows in "tight" and "leaky" frog skins, prior to and after the treatment with the Na+-blocking drug amiloride. It is shown by numerical examples that unpredictable Na+ flux patterns in frog skin arise from two diverse contributing factors: 1) The constitutive physical relationships which govern the local events at the level of the plasma membranes, and 2) the much neglected topology, i.e., the "connectedness" of the heterogeneous compartments.

Animals↗
PubMed1995

An optimized parsing algorithm well suited to RNA folding.

The application of stochastic context-free grammars to the determination of RNA foldings allows a simple description of the sub-class of sought secondary structures, but it needs efficient parsing algorithms. The more classic thermodynamic model of folding, popularized by Zuker under the framework of dynamic programming algorithms, allows an easy computation of foldings but its use is delicate when constraints have to be introduced on sought secondary structures. We show here that S-attribute grammars unify these two models and we introduce a parsing algorithm whose efficiency enables us to handle problems until then too difficult or too large to deal with. As a matter of fact, our algorithm is as efficient as a standard dynamic programming one when applied to the thermodynamic model (yet it offers a greater flexibility for the expression of constraints) and it is faster and saves more space than other parsing algorithms used so far for stochastic grammars.

Algorithms↗
PubMed1992

Generalized linear models with random effects; salamander mating revisited.

In recent years much effort has been devoted to extending regression methodology to non-Gaussian data, where responses are not independent. These methods for dependent responses are suitable for data from longitudinal studies or nested designs. However, use of these methods for crossed designs seems to have serious limitations due to the intensive computations involved because of the intractable nature of the joint distribution. In this paper, we cast the problem in a Bayesian framework and use a Monte Carlo method, the Gibbs sampler, to avoid current computational limitations. The flexibility of this approach is illustrated by analyzing the interesting salamander mating data reported by McCullagh and Nelder (1989, Generalized Linear Models, 2nd edition, London: Chapman and Hall).

Analysis of Variance↗
PubMed1990

[Deviation and rotation of the larynx in computer tomography].

Many authors described the clinical importance of asymmetry of the laryngeal framework. However, its pathogenesis is generally unknown. In this study, CT images of 315 Japanese subjects were investigated to define the laryngeal position relative to the midline of the cervical vertebra. The CT slice of each subject within 5 mm cephalad of the cricoarytenoid joint was traced. Then, the deviation and rotation angles were measured using our method. Seventy one percent of the subjects' larynges deviated and/or rotated to the right side, while 17% to the left side. Six percent showed neither deviation nor rotation. As to the rest of 6%, deviation and rotation were in opposite directions. Besides, the length of the thyroid alae were measured in 282 subjects. Left ala was longer in 55%, and right was in 23%, and almost equal in 22%. The conclusions are as follows, 1. The majority of the subjects' CT images showed deviation and/or rotation of the laryngeal framework to the right side. 2. So called idiopathic laryngeal deviation is a case which observed in those cases with remarkable deviation and/or rotation of the laryngeal framework. 3. Aging seemed to be an important factor in acceleration of the laryngeal deviation and rotation. 4. The type of diseases and the side of mass lesions had no statistical significance in deviation and rotation of the larynx.

Adult↗
PubMed2026

A scalable HPC framework for bioinformatics in resource-limited settings: design principles, implementation, and sustainability from the UVRI experience.

MOTIVATION: Building and sustaining High-Performance Computing (HPC) infrastructure for bioinformatics research in resource-limited settings presents significant technical, financial and operational challenges. Institutions in low-and middle-income regions often face constraints such as limited technical expertise, unstable infrastructure and restricted funding which can hinder the deployment of large-scale computational platforms necessary for modern genomics and bioinformatics analyses. RESULTS: We present a scalable and modular HPC framework developed at the Uganda Virus Research Institute (UVRI) to support large-scale genomics and other omics data analyses in resource-limited settings. The framework integrates open-source HPC management tools, infrastructure automation, and reproducible configuration management to enable reliable deployment and maintenance. Optimized storage and networking configurations combined with a phased capacity-building strategy support high-throughput genomic workflows while strengthening local technical expertise. From our implementation experience, we derive ten practical design and operational rules that provide a transferable methodology for establishing and sustaining in-house HPC infrastructure. These rules emphasize strategic investment in human capacity, structured planning, leveraging collaborations, adoption of open-source technologies and service management practices to improve operational resilience and long-term sustainability. AVAILABILITY: The design principles, automation strategies and implementation guidelines described in this work are applicable to institutions seeking to establish sustainable HPC resources for bioinformatics research in resource-constrained environments.

Computational Biology↗
PubMedDate not supplied

Information technology and computer-based decision support in diabetic management.

This paper describes the application of computer-based techniques within an intelligent, knowledge-based framework to the management of diabetes. The objectives are to structure data collection and storage so that the relevant patient-specific data are collected and made accessible as needed, and to provide clinical decision support on either a day-by-day or longer timescale as appropriate; these objectives relating to both hospital clinic and general practice. For longer-term management, a prototype rule set (greater than 500 rules) has been developed (coded in Sigma PROLOG), validated and tested on patient data. The data collection programs (written in SCULPTOR) to feed the ruleset have been tested in the hospital clinic and compared with the resident data collection system for usability, and impact on the running of the clinic. Links between the data collection programs and the ruleset program have been written and tested. The computer system will also incorporate a module, combining knowledge-based advisory system and glucose/insulin model as patient simulator, that can be tested as a potential decision aid for adjusting insulin dosage on a daily basis.

Data Collection↗
PubMed2026

Collective posterior inference from highly variable empirical replicates.

High-throughput experimental platforms now routinely generate data from dozens or hundreds of independent observations. Simulation-based inference (SBI) offers a powerful framework for estimating model parameters from such complex datasets, but standard methods struggle to scale to the noisy multiple-replicates regime without incurring prohibitive computational costs or careful hyperparameter tuning. Here, we introduce a new method for fast and robust collective posterior inference from multiple independent replicates using a robust product-of-experts aggregation scheme that automatically mitigates the influence of outliers. Evaluating it on synthetic and empirical evolutionary datasets, we find it achieves state-of-the-art estimation accuracy and computational efficiency, including inference from noisy observations. Our method is compatible with any SBI framework, providing a scalable, plug-and-play solution for inference from noisy multiple-replicate datasets.

Computational Biology↗
PubMed2026

FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.

MOTIVATION: Since the introduction of single-cell RNA sequencing (scRNA-seq), numerous computational approaches have been developed to reconstruct dynamic cellular processes from static transcriptional profiles. These methods order cells along continuous trajectories by assessing their similarity in the gene-expression space. However, they rely on several assumptions, such as prior knowledge of the structure and directionality of the expected genealogy. These assumptions can limit their application to complex cellular systems with poorly understood developmental paths. RESULTS: To address this challenge, we introduce FIERCE (Framework for InfERence of the veloCity of Entropy), a novel computational pipeline designed to predict the changes in the differentiation potency of single cells during dynamic processes. Through a fully unsupervised approach, FIERCE enables the inference of cell lineages directly on the differentiation landscape of the biological system, thus eliminating the need for prior specification of developmental parameters. We demonstrate the efficacy of FIERCE by reconstructing three well-known mouse differentiation systems and by quantifying its accuracy on simulated data. AVAILABILITY AND IMPLEMENTATION: The FIERCE R package is available on GitHub at https://github.com/bicciatolab/FIERCE.

Cell Differentiation↗