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At least 1,387 records · Page 77Linked to original sources
PubMed2006

On the detection of simple points in higher dimensions using cubical homology.

Simple point detection is an important task for several problems in discrete geometry, such as topology preserving thinning in image processing to compute discrete skeletons. In this paper, the approach to simple point detection is based on techniques from cubical homology, a framework ideally suited for problems in image processing. A (d-dimensional) unitary cube (for a d-dimensional digital image) is associated with every discrete picture element, instead of a point in epsilon(d) (the d-dimensional Euclidean space) as has been done previously. A simple point in this setting then refers to the removal of a unitary cube without changing the topology of the cubical complex induced by the digital image. The main result is a characterization of a simple point p (i.e., simple unitary cube) in terms of the homology groups of the (3d - 1) neighborhood of p for arbitrary, finite dimensions

Algorithms↗
PubMed2006

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints.

BACKGROUND: We are interested in the problem of predicting secondary structure for small sets of homologous RNAs, by incorporating limited comparative sequence information into an RNA folding model. The Sankoff algorithm for simultaneous RNA folding and alignment is a basis for approaches to this problem. There are two open problems in applying a Sankoff algorithm: development of a good unified scoring system for alignment and folding and development of practical heuristics for dealing with the computational complexity of the algorithm. RESULTS: We use probabilistic models (pair stochastic context-free grammars, pairSCFGs) as a unifying framework for scoring pairwise alignment and folding. A constrained version of the pairSCFG structural alignment algorithm was developed which assumes knowledge of a few confidently aligned positions (pins). These pins are selected based on the posterior probabilities of a probabilistic pairwise sequence alignment. CONCLUSION: Pairwise RNA structural alignment improves on structure prediction accuracy relative to single sequence folding. Constraining on alignment is a straightforward method of reducing the runtime and memory requirements of the algorithm. Five practical implementations of the pairwise Sankoff algorithm - this work (Consan), David Mathews' Dynalign, Ian Holmes' Stemloc, Ivo Hofacker's PMcomp, and Jan Gorodkin's FOLDALIGN - have comparable overall performance with different strengths and weaknesses.

Algorithms↗
PubMed1988

The modelling of nucleophilic and electrophilic additions to organometallic complexes using molecular graphics techniques.

A new formalism has been developed in order to evaluate intermolecular interaction energies for inorganic and organometallic complexes in the framework of the extended Hückel method. In order to provide the shortest possible response time on an interactive computer graphics facility, this model should require the minimum amount of computer time, which explains why approximate procedures are used to evaluate electrostatic, charge transfer and exchange repulsion components. When applying this model to typical examples of electrophilic addition reactions to organometallic complexes, it is found that it is essential to take account of charge transfer interactions, the electrostatic component alone being not sufficient, even qualitatively, for a proper description of the reaction mechanism. The results, presented as color-coded dot molecular surfaces, show a very good agreement with experiment as to the site of attack, namely (i) on metal for the electrophilic attack on Fe(cp)2, Fe(CO)5 and X(cp)(CO)2, X = Co, Rh; (ii) on the cp ligand for the nucleophilic attack on Co(cp)2+ and Rh(cp)2+; (iii) on bz for the nucleophilic attack on Fe(cp)(bz)+. Finally, modellizations of the nucleophilic attack on a coordinated olefin and of the relation between structure and acidic properties of zeolites are presented and discussed.

Computer Graphics↗
PubMed2026

Machine learning-ready genomic biomarkers: ATF3 polymorphisms predict postoperative analgesic demand through AI-compatible phenotyping.

PURPOSE: To determine whether ATF3 polymorphisms can serve as genetic biomarkers for machine learning-based precision analgesia by establishing a genotype-phenotype association suitable for predictive modeling of postoperative opioid requirements. METHODS: In a prospective cohort of 167 adults undergoing abdominal surgery, ATF3 SNPs rs3122721 and rs3125293 were genotyped. A structured dataset architecture was developed to represent genetic profiles as input features for supervised learning models, enabling translational analysis of genotype‑dependent opioid consumption over 72 h. RESULTS: Patients with homozygous genotypes of the ATF3 SNPs had significantly higher opioid requirements than non‑carriers, despite reporting similar subjective pain scores. This consistent genotype‑dependent pattern provided a clinically relevant phenotype suitable for integration into predictive algorithms. CONCLUSION: ATF3 genotyping offers a promising biomarker for computationally informed precision analgesia. By linking genomic variability to clinically meaningful outcomes within a structured clinical and genomic framework, this approach supports the future development of risk-stratified clinical decision-support systems to optimize postoperative pain management.Trial registration ChiCTR1900021991, registered 30 April 2019. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s13755-026-00480-9.

ATF3↗
PubMed2005

Volumetric spatial decomposition of trabecular bone into rods and plates--a new method for local bone morphometry.

Bone microarchitecture is believed to play a key role in determining bone quality. We therefore present a new method for the volumetric spatial decomposition of trabecular bone samples into its basic elements (rods and plates). This new method is a framework for the element based description of bone microarchitecture. First, the newly developed algorithm was validated on computer-generated models. Then, it was applied to 328 human trabecular bone samples harvested from 70 donors at five different anatomical sites (calcaneus, femoral head, iliac crest, lumbar spine 2 and 4), which were previously scanned by microcomputed tomography. Standard three-dimensional morphometric algorithms were used to analyze the trabeculae on an individual basis with respect to their volume, surface, and thickness. The results were statistically compared for the five sites. In this study, it was possible for the first time to spatially decompose trabecular bone structures in its volumetric elements; rods and plates. The size of the largest element in the structures showed significant differences for the five compared sites. In samples from femoral head, we found that basically one "major element" was spanning through the whole structure whereas in lumbar spine and calcaneus, smaller elements dominate. From this, we suggest that the strength of strong, dense plate-like structures is determined by the major elements whereas in looser rod-like structures the strength is given by the arrangement, quality, and shape of a whole set of elements. Furthermore, we found that globally determined structural indices such as the mean curvature of the bone surface ( ) or related to this the structure model index (SMI) are almost exclusively explained by the arrangement of the plates. This also suggests that rods hold independent information characterizing trabecular bone quality, especially in the spine. These findings may improve the understanding of the site-specific role of bone microarchitecture in determining bone quality and in future studies the competence of bone.

Adult↗
PubMed2005

An efficient and generic extension to ITK to process arbitrary shaped regions of interest.

The paper describes a software method to extend ITK (Insight ToolKit, supported by the National Library of Medicine), leading to ITK++. This method, which is based on the extension of the iterator design pattern, allows the processing of regions of interest with arbitrary shapes, without modifying the existing ITK code. We experimentally evaluate this work by considering the practical case of the liver vessel segmentation from CT-scan images, where it is pertinent to constrain processings to the liver area. Experimental results clearly prove the interest of this work: for instance, the anisotropic filtering of this area is performed in only 16 s with our proposed solution, while it takes 52 s using the native ITK framework. A major advantage of this method is that only add-ons are performed: this facilitates the further evaluation of ITK++ while preserving the native ITK framework.

Algorithms↗
PubMed2005

Dopaminergic modulation of cognitive function-implications for L-DOPA treatment in Parkinson's disease.

It is well recognised that patients with Parkinson's disease exhibit cognitive deficits, even in the earliest disease stages. Whereas, L-DOPA therapy in early Parkinson's disease is accepted to improve the motor symptoms, the effects on cognitive performance are more complex: both positive and negative effects have been observed. The purpose of the present article is to review the effects of L-DOPA medication in Parkinson's disease on cognitive functions in the broad domains of cognitive flexibility and working memory. The review places the effects in Parkinson's disease within a framework of evidence from studies with healthy human volunteers, rodents and non-human primates as well as computational modeling work. It is suggested that beneficial or detrimental effects of L-DOPA are observed depending on task demands and basal dopamine levels in distinct parts of the striatum. The study of the beneficial and detrimental cognitive effects of L-DOPA in Parkinson's disease has substantial implications for the understanding and treatment development of cognitive abnormalities in Parkinson's disease as well as normal health.

Animals↗
PubMedDate not supplied

Modelling gastrointestinal bioelectric activity.

The development of an anatomically realistic biophysically based model of the human gastrointestinal (GI) tract is presented. A major objective of this work is to develop a modelling framework that can be used to integrate the physiological, anatomical and medical knowledge of the GI system. The anatomical model was developed by fitting derivative continuous meshes to digitised data taken from images of the visible man. Structural information, including fibre distributions of the smooth muscle layers and the arrangement of the networks of interstitial cells of Cajal, were incorporated using published information. A continuum modelling framework was used to simulate electrical activity from the single cell to the whole organ and body. Also computed was the external magnetic field generated from the GI electrical activity. The set of governing equations were solved using a combination of numerical techniques. Activity at the (continuum) cell level was solved using a high-resolution trilinear finite element procedure that had been defined from the previously fitted C1 continuous anatomical mesh. Multiple dipolar sources were created from the excitation waves which were embedded within a coupled C1 continuous torso model to produce both the cutaneous electrical field and the external magnetic field. Initial simulations were performed using a simplified geometry to test the implementation of the numerical solution procedure. The numerical procedures were shown to rapidly converge with mesh refinement. In the process of this testing, errors in a long standing analytic solution were identified and are corrected in Appendix B. Results of single cell activity were compared to published results illustrating that the key features of the slow wave activity were successfully replicated. Simulations using a two-dimensional slice through the gastric wall produced slow wave activity that agreed with the known frequency and propagation characteristics. Three-dimensional simulations were also performed using the full stomach mesh and results illustrated the slow wave propagation throughout the stomach musculature.

Animals↗
PubMedDate not supplied

A graph-based toy model of chemistry.

Large scale chemical reaction networks are a ubiquitous phenomenon, from the metabolism of living cells to processes in planetary atmospheres and chemical technology. At least some of these networks exhibit distinctive global features such as the "small world" behavior. The systematic study of such properties, however, suffers from substantial sampling biases in the few networks that are known in detail. A computational model for generating them is therefore required. Here we present a Toy Model that provides a consistent framework in which generic properties of extensive chemical reaction networks can be explored in detail and that at the same time preserves the "look-and-feel" of chemistry: Molecules are represented as labeled graphs, i.e., by their structural formulas; their basic properties are derived by a caricature version of the Extended Hückel MO theory that operates directly on the graphs; chemical reaction mechanisms are implemented as graph rewriting rules acting on the structural formulas; reactivities and selectivities are modeled by a variant of the Frontier Molecular Orbital Theory based on the Extended Hückel scheme. The approach is illustrated for two types of reaction networks: Diels-Alder reactions and the formose reaction implicated in prebiotic sugar synthesis.

Journal Article↗
PubMedDate not supplied

Toward an alternative hardness kernel matrix structure in the Electronegativity Equalization Method (EEM).

This study presents an alternative of the Electronegativity Equalization Method (EEM), where the usual Coulomb kernel has been transformed into a smooth function. The new framework, as the classical EEM, permits fast calculations of atomic charges in a given molecule for a small computational cost. The original EEM procedure needs to previously calibrate the different implied atomic hardness and electronegativity, using a chosen set of molecules. In the new EEM algorithm half the number of parameters needs to be calibrated, since a relationship between electronegativities and hardnesses has been found.

Algorithms↗
PubMed2001

Heterobuckybowls: a theoretical study on the structure, bowl-to-bowl inversion barrier, bond length alternation, structure-inversion barrier relationship, stability, and synthetic feasibility.

Hybrid density functional theory (DFT) calculations at the B3LYP/cc-pVDZ level have been performed on a series of heterobuckybowls, 3X, C(18)X(3)H(6) (X = O, NH, CH(2), BH, S, PH, PH(3), Si, SiH(2), and AlH). The minimum energy conformations and the transition states for bowl-to-bowl inversion, where the geometry is bowl shaped, are computed and characterized by frequency calculations. The geometries of heterotrindenes, 2X, C(12)X(3)H(6) (X = O, NH, CH(2), BH, S, PH, PH(3), Si, SiH(2), and AlH), were obtained, and the bond length alternation (Delta) in the central benzenoid ring shows remarkable sensitivity as a function of substituent with a wide range of fluctuations (-0.014 to +0.092 A). The Delta computed in 2BH was found to be comparable with the highest bond alternation reported to date in benzenoid frameworks. The inversion dynamics of these heterobowls and their bowl depths were fit to a mixed quartic/quadratic function. The size of the heteroatom seems to exclusively control the bowl depth and rigidity as well as the synthetic feasibility. In contrast, the bond length alternation seems to be controlled by electronic factors and not by the size of the substituted atom either in trindenes or in heterosumanenes. The thermodynamic stability of this class of compounds is very much comparable with trithiasumanene (3S), which has been synthesized recently. The chemical hardness (eta) was measured to assess the stability of the heterosumanenes. The strain energy buildup in a sequential ring closure strategy along two synthetic routes, namely a triphenylene route and a trindene route, were explored, and the trindene route was found to be highly favorable for making such compounds compared to the triphenylene route. However, in both routes the ease of the synthetic feasibility increases as the size of the heteroatom increases.

Journal Article↗
PubMed1994

The generic viewpoint assumption in a framework for visual perception.

A visual system makes assumptions in order to interpret visual data. The assumption of 'generic view' states that the observer is not in a special position relative to the scene. Researchers commonly use a binary decision of generic or accidental view to disqualify scene interpretations that assume accidental viewpoints. Here we show how to use the generic view assumption, and others like it, to quantify the likelihood of a view, adding a new term to the probability of a given image interpretation. The resulting framework better models the visual world and reduces the reliance on other prior assumptions. It may lead to computer vision algorithms of greater power and accuracy, or to better models of human vision. We show applications to the problems of inferring shape, surface reflectance properties, and motion from images.

Humans↗
PubMed2004

Modular epistasis in yeast metabolism.

Epistatic interactions, manifested in the effects of mutations on the phenotypes caused by other mutations, may help uncover the functional organization of complex biological networks. Here, we studied system-level epistatic interactions by computing growth phenotypes of all single and double knockouts of 890 metabolic genes in Saccharomyces cerevisiae, using the framework of flux balance analysis. A new scale for epistasis identified a distinctive trimodal distribution of these epistatic effects, allowing gene pairs to be classified as buffering, aggravating or noninteracting. We found that the ensuing epistatic interaction network could be organized hierarchically into function-enriched modules that interact with each other 'monochromatically' (i.e., with purely aggravating or purely buffering epistatic links). This property extends the concept of epistasis from single genes to functional units and provides a new definition of biological modularity, which emphasizes interactions between, rather than within, functional modules. Our approach can be used to infer functional gene modules from purely phenotypic epistasis measurements.

Algorithms↗
PubMed2002

Meat consumption in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohorts: results from 24-hour dietary recalls.

OBJECTIVE: To evaluate meat intake patterns in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohorts. DESIGN AND SETTING: 24-Hour dietary recalls were assessed within the framework of a prospective cohort study in 27 centres across 10 European countries by means of standardised computer-assisted interviews. SUBJECTS: In total, 22 924 women and 13 031 men aged 35-74 years. RESULTS: Mean total meat intake was lowest in the 'health-conscious' cohort in the UK (15 and 21 g day-1 in women and men, respectively) and highest in the north of Spain, especially in San Sebastian (124 and 234 g day-1, respectively). In the southern Spanish centres and in Naples (Italy), meat consumption was distinctly lower than in the north of these countries. Central and northern European centres/countries showed rather similar meat consumption patterns, except for the British and French cohorts. Differences in the intake of meat sub-groups (e.g. red meat, processed meat) across EPIC were even higher than found for total meat intake. With a few exceptions, the Mediterranean EPIC centres revealed a higher proportion of beef/veal and poultry and less pork or processed meat than observed in central or northern European centres. The highest sausage consumption was observed for the German EPIC participants, followed by the Norwegians, Swedish, Danish and Dutch. CONCLUSIONS: The results demonstrate distinct differences in meat consumption patterns between EPIC centres across Europe. This is an important prerequisite for obtaining further insight into the relationship between meat intake and the development of chronic diseases.

Adult↗
PubMed2006

Three-dimensional laryngeal model for planning of laryngeal framework surgery.

CONCLUSION: The three-dimensional prototype model was useful for planning of laryngeal framework surgery. OBJECTIVE: To discuss the usefulness of a three-dimensional laryngeal model for laryngeal framework surgery. MATERIALS AND METHODS: A three-dimensional laryngeal model was created based on the postoperative helical computed tomography (CT) data of the larynx (case 1) which underwent lateral cricoarytenoid muscle (LCA) pull surgery. LCA pull surgery is a kind of arytenoid adduction for unilateral vocal cord paralysis. A three-dimensional model of case 1 larynx was prototyped using a selective laser sintering method. In case 1, the patient's voice did not improve after LCA pull surgery. The three-dimensional model revealed that the original surgical procedure was not appropriate to obtain optimal arytenoid adduction. According to the analysis of this three-dimensional model, we changed the surgical approach and performed this new refined LCA pull surgery on another patient with unilateral vocal cord paralysis (case 2). RESULTS: We were able to pull LCA precisely in case 2. Three-dimensional CT of case 2 after refined LCA pull surgery allowed the correct pulling of LCA and complete adduction of arytenoid. The postoperative voice improved remarkably.

Aged↗
PubMed2002

A mathematical model of the stability control of human thorax and pelvis movements during walking.

A mathematical model is developed to study the human thorax and pelvis movements in the frontal plane during normal walking. The model comprises of two-link base-excited inverted pendulums with one-degree of rotational freedom for each link. Since the linear motion of the pelvis has a significant effect on the upper body stability, this effect is included in the model by having a base point moving in the frontal plane in a general way. Furthermore, because the postural stability is the primary requirement of normal human walking, the control law is developed based on Lyapunov's stability theory, which guarantees the stability of the pendulum system around the up-right position. To evaluate the model, the simulation results, including the angular displacement of each link and the torque applied on each link, are compared with those from gait measurements. It is shown that the simulation results match those from gait measurements closely. These results suggest that the proposed model can provide a useful framework for analysis of postural control mechanisms.

Algorithms↗
PubMed2005

A novel framework for sib pair linkage analysis.

Sib pair linkage analysis of a dichotomous trait is a popular method for narrowing the search for genes that influence complex diseases. Although the pedigree structures are uncomplicated and the underlying genetic principles straightforward, a surprising degree of complexity is involved in implementing a sib pair study and interpreting the results. Ascertainment may be based on affected, discordant, or unaffected sib pairs, as well as on pairs defined by threshold values for quantitative traits, such as extreme discordant sib pairs. To optimize power, various domain restrictions and null hypotheses have been proposed for each of these designs, yielding a wide array of choices for the analyst. To begin, we systematically classify the major sources of discretion in sib pair linkage analysis. Then, we extend the work of Kruglyak and Lander (1995), to bring the various forms into a unified framework and to facilitate a more general approach to the analysis. Finally, we describe a new, freely available computer program, Splat (Sib Pair Linkage Analysis Testing), that can perform any sib pair statistical test currently in use, as well as any user-defined test yet to be proposed. Splat uses the expectation maximization algorithm to calculate maximum-likelihood estimates of sharing (subject to user-specified conditions) and then plots LOD scores versus chromosomal position. It includes a novel grid-scanning capability that enables simultaneous visualization of multiple test statistics. This can lead to further insight into the genetic basis of the disease process under consideration. In addition, phenotype definitions can be modified without the recalculation of inheritance vectors, thereby providing considerable flexibility for exploratory analysis. The application of Splat will be illustrated with data from studies on the genetics of diabetic nephropathy.

Algorithms↗
PubMed2007

Nonlinear mechanics of soft fibrous networks.

Mechanical networks of fibres arise on a range of scales in nature and technology, from the cytoskeleton of a cell to blood clots, from textiles and felts to skin and collageneous tissues. Their collective response is dependent on the individual response of the constituent filaments as well as density, topology and order in the network. Here, we use the example of a low-density synthetic felt of athermal filaments to study the generic features of the mechanical response of such networks including strain stiffening and large effective Poisson ratios. A simple microscopic model allows us to explain these features of our observations, and provides us with a baseline framework to understand active biomechanical networks.

Biocompatible Materials↗