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At least 235 records · Page 13Linked to original sources
PubMed2026

Recent Advances in Multi-Omics of Systemic Lupus Erythematosus.

This comprehensive narrative review examines recent advances in multi-omics research for Systemic Lupus Erythematosus (SLE), emphasizing integrated approaches over single-omics studies. The review critically evaluates technological advancements, methodological innovations, and clinical applications while identifying current limitations and future research directions. We conducted a comprehensive narrative review following SANRA guidelines, searching PubMed, Web of Science, Scopus, and Embase, covering publications from January 2018 to June 2025. The review focuses on studies integrating two or more omics layers in SLE research, with emphasis on computational methods, biomarker validation, and clinical applications. Multi-omics integration has revealed critical insights into SLE pathogenesis, including immune cell heterogeneity, gene-environment interactions, and metabolic dysregulation. However, significant challenges remain in data integration methodologies, small sample sizes, and biomarker reproducibility. Current computational approaches include early integration (concatenation), intermediate integration (joint dimensionality reduction), and late integration (ensemble methods). While multi-omics approaches offer unprecedented insights into SLE complexity, standardized integration protocols and robust validation frameworks are urgently needed. Small sample sizes and heterogeneity issues limit reproducibility, particularly affecting biomarker discovery and clinical translation. Multi-omics integration represents a paradigm shift toward precision medicine in SLE, but realizing this potential requires addressing current methodological limitations, standardizing validation processes, and developing robust computational frameworks for reliable clinical applications.

Humans↗
PubMed1986

A theoretical study of the comparative binding affinities of daunomycin derivatives to a double-stranded oligomeric DNA. Proposal for new high affinity derivatives.

Theoretical computations were performed on the comparative binding affinities of daunomycin (DM, 1) and seven derivatives related to the double-stranded oligonucleotide d(CGATCG)2. The compounds investigated were 4-demethoxy DM (2), and its beta-anomer (3), 4-demethoxy-7,9-bis-epi DM (4) and its beta anomer (5), a derivative with glucosamine instead of daunosamine (6), and two additional hypothetical DM derivatives in which the cationic NH3+ group of the daunosamine moiety is replaced by either a CH2--NH3+ group (7) or a CH2CH2NH3+ group (8), so as to indicate the effect on the binding affinity of interposing one- or two-methylene groups between the sugar and the cationic charge. The conformational angles of the hexanucleotide are fixed in values found in the representative crystal structure of the d(CGTACG)2-DM complex. The intermolecular drug-hexanucleotide interaction energies and the conformational energy changes of the drug upon binding are computed and optimized in the framework of the SIBFA procedure (sum of interactions between fragments computed ab initio), which uses empirical formulas based on ab initio SCF computations. The overall binding affinity ordering of compounds 1-6 compares satisfactorily with the ordering of available experimental affinity constants. The binding affinities of compounds 7 and 8, for which no experimental results seem to be available yet, are predicted to be significantly higher than those of the parent compound DM, with the greatest affinity found for 7. Because of the overall correlation between binding affinity of anthracyclines to DNA and their antitumor activity, these last two compounds deserve an exploration of their chemotherapeutic efficiency.

DNA↗
PubMed1998

Computational models of neuromodulation.

Computational modeling of neural substrates provides an excellent theoretical framework for the understanding of the computational roles of neuromodulation. In this review, we illustrate, with a large number of modeling studies, the specific computations performed by neuromodulation in the context of various neural models of invertebrate and vertebrate preparations. We base our characterization of neuromodulations on their computational and functional roles rather than on anatomical or chemical criteria. We review the main framework in which neuromodulation has been studied theoretically (central pattern generation and oscillations, sensory processing, memory and information integration). Finally, we present a detailed mathematical overview of how neuromodulation has been implemented at the single cell and network levels in modeling studies. Overall, neuromodulation is found to increase and control computational complexity.

Animals↗
PubMed1978

Management policies and procedures needed for effective computer security.

Although many security issues are controlled by legislative ruling and social standards, or are constrained by technological limitations, many other important matters of operational computer security are directly or indirectly under managerial control. The author argues that the necessary control policies and procedures will become increasingly critical as our reliance upon computer-based information systems continues to increase. This article presents a comprehensive framework for understanding the various aspects of computer security. Through this framework, those areas controllable by management are identified, and possible actions are proposed.

Attitude↗
PubMed1999

Parieto-frontal coding of reaching: an integrated framework.

In the last few years, anatomical and physiological studies have provided new insights into the organization of the parieto-frontal network underlying visually guided arm-reaching movements in at least three domains. (1) Network architecture. It has been shown that the different classes of neurons encoding information relevant to reaching are not confined within individual cortical areas, but are common to different areas, which are generally linked by reciprocal association connections. (2) Representation of information. There is evidence suggesting that reach-related populations of neurons do not encode relevant parameters within pure sensory or motor "reference frames", but rather combine them within hybrid dimensions. (3) Visuomotor transformation. It has been proposed that the computation of motor commands for reaching occurs as a simultaneous recruitment of discrete populations of neurons sharing similar properties in different cortical areas, rather than as a serial process from vision to movement, engaging different areas at different times. The goal of this paper was to link experimental (neurophysiological and neuroanatomical) and computational aspects within an integrated framework to illustrate how different neuronal populations in the parieto-frontal network operate a collective and distributed computation for reaching. In this framework, all dynamic (tuning, combinatorial, computational) properties of units are determined by their location relative to three main functional axes of the network, the visual-to-somatic, position-direction, and sensory-motor axis. The visual-to-somatic axis is defined by gradients of activity symmetrical to the central sulcus and distributed over both frontal and parietal cortices. At least four sets of reach-related signals (retinal, gaze, arm position/movement direction, muscle output) are represented along this axis. This architecture defines informational domains where neurons combine different inputs. The position-direction axis is identified by the regular distribution of information over large populations of neurons processing both positional and directional signals (concerning the arm, gaze, visual stimuli, etc.) Therefore, the activity of gaze- and arm-related neurons can represent virtual three-dimensional (3D) pathways for gaze shifts or hand movement. Virtual 3D pathways are thus defined by a combination of directional and positional information. The sensory-motor axis is defined by neurons displaying different temporal relationships with the different reach-related signals, such as target presentation, preparation for intended arm movement, onset of movements, etc. These properties reflect the computation performed by local networks, which are formed by two types of processing units: matching and condition units. Matching units relate different neural representations of virtual 3D pathways for gaze or hand, and can predict motor commands and their sensory consequences. Depending on the units involved, different matching operations can be learned in the network, resulting in the acquisition of different visuo-motor transformations, such as those underlying reaching to foveated targets, reaching to extrafoveal targets, and visual tracking of hand movement trajectory. Condition units link these matching operations to reinforcement contingencies and therefore can shape the collective neural recruitment along the three axes of the network. This will result in a progressive match of retinal, gaze, arm, and muscle signals suitable for moving the hand toward the target.

Animals↗
PubMedDate not supplied

[Computer-assisted design in removable partial dentures. Expert system and software for framework tracing].

Stelligraph, a software program for designing the removable partial denture offers many possibilities in computer assisted technology. The design can be realized on any particular case, based on three different concepts. This software program can also provide on individual, manual and personalized design this offening complete freedom in the conception. This software program is an expert system in removable partial denture by providing the general practitioner with a rational design as well as clinical guidance for oral rehabilitation.

Denture Design↗
PubMedDate not supplied

Comparisons of precision of fit between cast and CNC-milled titanium implant frameworks for the edentulous mandible.

PURPOSE: The purpose of this study was to investigate and compare the precision of fabrication in repeatqdly produced computer numeric controlled (CNC)-milled frameworks with consventional castings, and to analyze the distortion from application of different veneering materials. MATERIALS AND METHODS: Twenty identical titanium frameworks were fabricated by means of a CNC milling technique for the same master model. Five conventional frameworks were cast as a control group to the same model. The frames were measured with regard to fit in a coordinate measuring machine linked to a computer. Measurements were made during different stages of handling of the titanium framework, and after veneering materials had been applied. RESULTS: The CNC frameworks showed a statistically better fit and precision of fabrication compared to conventional castings (P < .05). The application of veneering material did not statistically affect the fit of the titanium frameworks (P > .05). CONCLUSION: It is possible to fabricate implant-supported frameworks by means of the present CNC technique with a very high precision and repeatability.

Acrylic Resins↗
PubMed2026

Quantum computing-assisted validation of a conserved macrophage suppression module shared by ASFV and PEDV.

BACKGROUND: African swine fever virus (ASFV) and porcine epidemic diarrhea virus (PEDV) differ in viral biology and cellular tropism, yet both pathogens suppress macrophage-mediated immune responses in pigs. OBJECTIVE: To identify a conserved macrophage suppression module shared by ASFV and PEDV and evaluate quantum computing as an independent framework for biological network validation. METHODS: Integrated analysis of publicly available GEO datasets (GSE231435 for ASFV and GSE306895) identified 471 shared downregulated genes. A network- and multi-omics-informed 20-gene core was selected and encoded as a 20-qubit modularity-based Quadratic Unconstrained Binary Optimization (QUBO) problem. Community detection was benchmarked using the Quantum Approximate Optimization Algorithm (QAOA) on both the IBM Quantum Aer simulator and the 156-qubit IBM Fez (Heron r2) quantum processor and compared with brute-force enumeration and simulated annealing. RESULTS: A conserved macrophage suppression module shared by ASFV and PEDV was identified. For the STRING protein-protein interaction network, QAOA at circuit depth p&#x2009;=&#x2009;3 reproduced the brute-force optimum with an approximation ratio of 1.000. In contrast, performance progressively declined in the denser co-expression network with increasing circuit depth, consistent with noise accumulation under current Noisy Intermediate-Scale Quantum (NISQ) conditions. Multi-run consensus analysis identified stable hub genes, including MMP9 and SLA-DOA, as well as genes exhibiting variable community assignments. CONCLUSION: These findings reveal a conserved macrophage suppression module shared between ASFV and PEDV and demonstrate that quantum computing can serve as an independent validation framework for biologically meaningful host-response networks. Network topology emerged as a key determinant of QAOA performance on real NISQ hardware.

Animals↗
PubMed2003

Using patient-driven computers to provide cost-effective prevention in primary care: a conceptual framework.

This paper initially presents a rationale for the cost-effectiveness of using patient-driven computers in primary care services. It specifically defines the concepts of prevention and primary care, prior to outlining the advantages of promoting the implementation of prevention practices in primary care. It argues that greater use of computer technology represents one means of cost-effectively optimizing the integration of prevention into routine primary care, and identifies an apparent disjuncture between the potential of computers and the limited success with which attempts to integrate them into routine primary care services have been met, as evidenced in the published international literature. Among several possible explanations for this disjuncture, such as a possible lack of precision with which computers identify at-risk patients, perceived high costs associated with computers and physicians' concerns about the inflexibility and the more impersonal nature of computer interactions, is the apparent failure of researchers to utilize well designed and empirically tested models in the planning, implementation and evaluation of computerized care. An outline for such an approach, utilizing the Precede-Proceed model of health promotion planning and the Diffusion of Innovations theory, is presented.

British Columbia↗
PubMed1996

A Bayesian evolutionary distance for parametrically aligned sequences.

There is an inherent relationship between the process of pairwise sequence alignment and the estimation of evolutionary distance. This relationship is explored and made explicit. Assuming an evolutionary model and given a specific pattern of observed base mismatches, the relative probabilities of evolution at each evolutionary distance are computed using a Bayesian framework. The mean or the median of this probability distribution provides a robust estimate of the central value. The evolutionary distance has traditionally been computed as zero for an observed homology of 20 bases with no mismatches; we prove that it is highly probable that the distance is greater than 0.01. The mean of the distribution is 0.047, which is a better estimate of the evolutionary distance. Bayesian estimates of the evolutionary distance incorporate arbitrary prior information about variable mutation rates both over time and along sequence position, thus requiring only a weak form of the molecular-clock hypothesis. The endpoints of the similarity between genomic DNA sequences are often ambiguous. The probability of evolution at each evolutionary distance can be estimated over the entire set of alignments by choosing the best alignment at each distance and the corresponding probability of duplication at that evolutionary distance. A central value of this distribution provides a robust evolutionary distance estimate. We provide an efficient algorithm for computing the parametric alignment, considering evolutionary distance as the only parameter. These techniques and estimates are used to infer the duplication history of the genomic sequence in C. elegans and in S. cerevisiae. Our results indicate that repeats discovered using a single scoring matrix show a considerable bias in subsequent evolutionary distance estimates.

Animals↗
PubMed1986

A theoretical study of the binding of phenothiazine derivatives to residues 82-93 of calmodulin.

A theoretical study was performed of the interaction of four phenothiazine derivatives, promethazine, promazine, trifluopromazine, and trifluoperazine, with a fragment (82-93) of calmodulin, held in the alpha-helical conformation. The computations were performed in the framework of the SIBFA 2 procedure (sum of interactions between fragments computed ab initio), which uses analytical formulas based on ab initio self-consistent field computations. The interaction energy is the sum of the intermolecular phenothiazine-oligopeptide interaction energy and of the separate intramolecular energy variations of the phenothiazine and of the side chains of the oligopeptide upon complex formation. The ordering of interaction energies of the four investigated phenothiazines parallels the ordering of their experimentally measured affinities for calmodulin, with a maximum affinity for trifluoperazine. The principal features of the trifluoperazine complex are a short hydrogen bond between the piperazinium proton and one anionic oxygen of Glu 87, and hydrophobic interactions between the piperazinium ring and Val 91 and between the methylene chain and Ala 88, together with partial insertion of the phenothiazine ring and the--CF3 substituent between Phe 89 and Phe 92.

Calmodulin↗
PubMed1997

Visual space distortion.

We are surrounded by surfaces that we perceive by visual means. Understanding the basic principles behind this perceptual process is a central theme in visual psychology, psychophysics, and computational vision. In many of the computational models employed in the past, it has been assumed that a metric representation of physical space can be derived by visual means. Psychophysical experiments, as well as computational considerations, can convince us that the perception of space and shape has a much more complicated nature, and that only a distored version of actual, physical space can be computed. This paper develops a computational geometric model that explains why such distortion might take place. The basic idea is that, both in stereo and motion, we perceive the world from multiple views. Given the rigid transformation between the views and the properties of the image correspondence, the depth of the scene can be obtained. Even a slight error in the rigid transformation parameters causes distortion of the computed depth of the scene. The unified framework introduced here describes this distortion in computational terms. We characterize the space of distortions by its level sets, that is, we characterize the systematic distortion via a family of iso-distortion surfaces which describes the locus over which depths are distorted by some multiplicative factor. Given that humans' estimation of egomotion or estimation of the extrinsic parameters of the stereo apparatus is likely to be imprecise, the framework is used to explain a number of psychophysical experiments on the perception of depth from motion or stereo.

Cybernetics↗
PubMedDate not supplied

Precision of CNC-milled titanium frameworks for implant treatment in the edentulous jaw.

PURPOSE: The purpose of this report was to describe a new technique to fabricate one-piece, implant-supported titanium frameworks by means of a computer numeric-controlled (CNC) milling technique, and to compare the fit of these frameworks with conventional cast prostheses. MATERIALS AND METHODS: The study comprised 20 patients who were provided with 5 standard Brånemark implants each in the edentulous mandible. The fit of the first 10 prostheses with CNC-milled frameworks was measured by means of a 3-dimensional photogrammetric technique. The distortion of the center point of the framework cylinders was measured in relation to the master cast replicas. These measurements were compared with 10 randomly selected routine prostheses with cast frameworks. RESULTS: No significant differences were found between the 2 groups. The 3-dimensional distortion of the cylinders in the completed prostheses ranged from 3 to 80 microns; no passive framework was observed. More distortion was observed in the horizontal plane (x and y axes) as compared to the distortion in the vertical direction (z axis). CONCLUSION: The precision of fit of the first CNC-milled prostheses presented a comparable fit to the conventional cast frameworks. Consequently, this new technique could be a valid option for the routine fabrication of frameworks for implant prostheses.

Computer-Aided Design↗
PubMed2000

Statistical issues in toxicokinetic modeling: a bayesian perspective.

Determining the relationship between an exposure and the resulting target tissue dose is a critical issue encountered in quantitative risk assessment (QRA). Classical or physiologically based toxicokinetic (PBTK) models can be useful in performing that task. Interest in using these models to improve extrapolations between species, routes, and exposure levels in QRA has therefore grown considerably in recent years. In parallel, PBTK models have become increasingly sophisticated. However, development of a strong statistical foundation to support PBTK model calibration and use has received little attention. There is a critical need for methods that address the uncertainties inherent in toxicokinetic data and the variability in the human populations for which risk predictions are made and to take advantage of a priori information on parameters during the calibration process. Natural solutions to these problems can be found in a Bayesian statistical framework with the help of computational techniques such as Markov chain Monte Carlo methods. Within such a framework, we have developed an approach to toxicokinetic modeling that can be applied to heterogeneous human or animal populations. This approach also expands the possibilities for uncertainty analysis. We present a review of these efforts and other developments in these areas. Appropriate statistical treatment of uncertainty and variability within the modeling process will increase confidence in model results and ultimately contribute to an improved scientific basis for the estimation of occupational and environmental health risks.

Bayes Theorem↗
PubMed2026

Beyond antigen matching: compatibility intelligence theory for transfusion as an emergent biological system.

BACKGROUND: Despite major advances in serologic testing, extended phenotyping, and blood group genomics, clinically similar transfusion exposures may result in markedly different immune and clinical outcomes. Existing compatibility strategies do not fully explain this biological variability. OBJECTIVES: To examine transfusion compatibility as an emergent donor-recipient biological state and propose a systems-level conceptual framework that integrates established biological determinants into a testable model for future precision transfusion medicine. METHODS: This narrative review critically synthesizes current evidence from blood group genomics, recipient immunobiology, inflammation, disease-specific biology, transfusion medicine, and computational prediction. The proposed framework distinguishes Compatibility Intelligence Theory (CIT) as a biological interpretation from Precision Transfusion Intelligence (PTI) as its potential clinician-supervised translational application. RESULTS: The review argues that transfusion compatibility is shaped by interactions among donor genetics, recipient immune biology, inflammatory physiology, disease context, transfusion history, and longitudinal adaptation rather than by antigen matching alone. CIT provides an organizational framework for integrating these determinants, whereas PTI describes a possible clinician-supervised translation. To address current feasibility, the revised framework separates variables into routinely measurable, contextually available but incompletely standardized, and research-stage domains, and proposes a staged strategy for deriving rather than assuming their quantitative weights. Any clinical implementation would require comparative validation against current serologic, phenotypic, and genotype-based practice. CONCLUSIONS: Compatibility Intelligence Theory offers a testable systems-level framework for understanding transfusion compatibility without replacing established transfusion practices. The framework is not presented as a ready-to-use score: currently measurable variables can be organized for structured risk review, whereas inflammatory, immunogenetic, and multi-omic inputs require prospective standardization and validation. If future studies demonstrate incremental predictive and patient-centered benefit, CIT-informed PTI could support an adaptive, evidence-based extension of current precision transfusion practice.

Humans↗
PubMed2003

Human factors: imperative concepts for information systems in critical care.

This article provides an overview of human factors, ergonomics, human-computer interaction, and usability concepts as they relate to critical care settings. The use of these concepts can improve patient safety and the productivity of nurses, especially as they relate to the use of information systems. A framework for human-computer interaction is presented. Examples illustrate how the suite of human factors concepts is used to create intuitive, effective data presentations for use in critical care including an intensive care unit (ICU) summary display, an alternative graphic display, and modeling information sources of decision making in a neonatal ICU. The importance of integrating these concepts into advanced practice nurses' environments is made apparent.

Critical Care↗
PubMed2000

[Testing a computer-assisted bending machine for manufacturing orthodontic treatment elements].

The use of suitable orthodontic devices producing desired defined force systems is of importance for successful orthodontic treatment. Bending loops can be difficult and time-consuming. Computerised fabrication would enable very precise reproduction of individual loops. A bending machine has now been developed within the framework of a computer-assisted treatment concept. In this study, a prototype machine was used to fabricate U-, T- and delta loops made of stainless steel, cobalt chromium and titanium molybdenum wire. The various geometric parameters of each loop were measured to determine how precisely they had been produced. Furthermore, the force system of each loop were experimentally investigated during simulated activation in an orthodontic measurement and simulation system. The results indicate that the geometric parameters had an average error of 2.8 degrees for angles and 0.9 mm for lengths. Owing to the fabrication errors, loops of the same type produced different force systems. Overall, the new bending machine can fabricate different types of loop, but the requirements of very precise fabrication are currently not met. This fact, together with further limitations in terms of configuration, means that the machine cannot be used routinely at present. However, the machine can nevertheless be considered a good basis for further development.

Computer-Aided Design↗
PubMed2003

Inferring genetic networks and identifying compound mode of action via expression profiling.

The complexity of cellular gene, protein, and metabolite networks can hinder attempts to elucidate their structure and function. To address this problem, we used systematic transcriptional perturbations to construct a first-order model of regulatory interactions in a nine-gene subnetwork of the SOS pathway in Escherichia coli. The model correctly identified the major regulatory genes and the transcriptional targets of mitomycin C activity in the subnetwork. This approach, which is experimentally and computationally scalable, provides a framework for elucidating the functional properties of genetic networks and identifying molecular targets of pharmacological compounds.

Algorithms↗