PubMed HealthSearch

SEARCH · PubMed Health

Results for “Computational modeling”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2Linked to original sources

Effects of premature excitation and tachycardia on the spatial distribution of refractoriness and propagation of excitation in a computer model.

In this study, the spatial pattern of refractoriness and its effects on propagation of excitation during premature responses and tachycardia have been investigated using a computer model. The model simulated propagation, cycle length-dependent refractoriness, and slow propagation during the relative refractory period. Findings showed slow propagation near the origin of premature responses resulting in longer cycle lengths distal to the slowing. The nonuniform cycle lengths terminated by a premature response also represented the onset of the subsequent cycle, so the pattern of refractoriness was altered after both the premature and following cycle. This occurred even though cycle length affected only the immediately following refractory period in the model. The effect of nonuniform cycle lengths during a premature response on refractory periods after the subsequent response occurred with all cycle lengths of the later response. When the cycle length of that and further responses was sufficiently shortened to result in slowed propagation, changing spatial patterns of refractoriness and propagation occurred. The findings are evidence that responses with slow propagation during incomplete recovery of excitability can affect conduction velocity and refractoriness during multiple subsequent cycles. These effects are likely to occur in the heart but are modified by features such as sustained effects of cycle length on refractoriness, anisotropy, and electrotonic interactions.

Computer Simulation

A computer model of a cochlear-nucleus stellate cell: responses to amplitude-modulated and pure-tone stimuli.

A computer model of a ventral-cochlear-nucleus (VCN) stellate cell with chop-S type response properties is presented and evaluated. The model is based on a simplified model of spike generation preceded by a stage that simulates dendritic low-pass filtering. Input to the model is in the form of simulated auditory-nerve spikes produced by a model of the auditory periphery [Meddis and Hewitt, J. Acoust. Soc. Am. 89, 2866-2882 (1991)]. Outputs from the stellate-cell model are shown to qualitatively replicate a wide range of typical in vivo responses. These include: (a) realistic onset and steady-state rate-level functions, (b) "chopper"-type post-stimulus time histogram responses; (c) typical "chop-S"-type neuron responses characterized by a low coefficient of variance (CV less than 0.3) of interspike intervals as a function of time; (d) level-dependent amplitude-modulation transfer functions; (e) intrinsic oscillations in responses to pure-tone stimuli; (f) amplitude-modulation encoding over a wide dynamic range; and (g) frequency-limited phase locking to pure tones. It is shown that these responses can be explained primarily by the membrane properties of the cells. More specifically, how the model encodes signal amplitude modulation was studied and an explanation was suggested for the generation of the bandpass modulation transfer functions. Such functions are observed neurally in response to amplitude-modulated stimuli presented at moderate to high signal levels.

Animals

A computational model for bacteriophage ϕX174 gene expression.

Bacteriophage ϕX174 has been widely used as a model organism to study fundamental processes in molecular biology. However, several aspects of ϕX174 gene regulation are not fully resolved. Here we construct a computational model for ϕX174 and use the model to study gene regulation during the phage infection cycle. We estimate the relative strengths of transcription regulatory elements (promoters and terminators) by fitting the model to transcriptomics data. We show that the specific arrangement of a promoter followed immediately by a terminator, which occurs naturally in the ϕX174 genome, poses a parameter identifiability problem for the model, since the activity of one element can be partially compensated for by the other. We also simulate ϕX174 gene expression with two additional, putative transcription regulatory elements that have been proposed in prior studies. We find that the activities of these putative elements are estimated to be weak, and that variation in ϕX174 transcript abundances can be adequately explained without them. Overall, our work demonstrates that ϕX174 gene regulation is well described by the canonical set of promoters and terminators widely used in the literature.

Gene Expression Regulation, Viral

Computer modeling studies on the subsite interactions of ribonuclease T1.

The modes of binding of pGp,ApG,CpG and UpG to the enzyme ribonuclease T1 were determined by computer modeling. Essentially two binding modes are possible for all the four ligands--one with the 3'-phosphate group occupying the phosphate binding site (substrate mode of binding) and the second with the 5'-phosphate group occupying the phosphate binding site (inhibitor mode of binding). The latter binding mode is energetically favoured over the former and in this mode the base (G) and the 5'-phosphate moieties occupy the same sites on the enzyme as 5'-GMP when bound to RNase T1. The ribose moiety of pGp adopts a C3'-endo pucker form when bound to the enzyme and the glycosyl torsion angle will be in -syn range as 5'-GMP in the RNase T1-5'-GMP complex. Based on these results, a mechanism for the release of the product subsequent to cleavage of the substrate by the enzyme has been proposed. The amino acid residues Asn98 and Tyr45 are shown to form the subsites for the phosphate and the base respectively on the 5'-side of the guanine occupying the primary binding site. These studies also provide a stereochemical explanation for the specificity of the 1N subsite for adenine.

Asparagine

Addressing current challenges in cancer immunotherapy with mathematical and computational modelling.

The goal of cancer immunotherapy is to boost a patient's immune response to a tumour. Yet, the design of an effective immunotherapy is complicated by various factors, including a potentially immunosuppressive tumour microenvironment, immune-modulating effects of conventional treatments and therapy-related toxicities. These complexities can be incorporated into mathematical and computational models of cancer immunotherapy that can then be used to aid in rational therapy design. In this review, we survey modelling approaches under the umbrella of the major challenges facing immunotherapy development, which encompass tumour classification, optimal treatment scheduling and combination therapy design. Although overlapping, each challenge has presented unique opportunities for modellers to make contributions using analytical and numerical analysis of model outcomes, as well as optimization algorithms. We discuss several examples of models that have grown in complexity as more biological information has become available, showcasing how model development is a dynamic process interlinked with the rapid advances in tumour-immune biology. We conclude the review with recommendations for modellers both with respect to methodology and biological direction that might help keep modellers at the forefront of cancer immunotherapy development.

Computer Simulation

A computer model for the study of electrical current flow in the human thorax.

Electrocardiography has played an important role in the detection and characterization of heart function, both in normal and abnormal states. In this paper we present an inhomogeneous, anisotropic computer model of the human thorax for use in electrocardiography with emphasis on the calculation of transthoracic potential and current distributions. Knowledge of the current pathways in the thorax has many applications in electrocardiography and has direct utility in studies pertaining to cardiac defibrillation, forward and inverse problems, impedance tomography, and electrode placement in electrocardiography.

Computer Simulation

Metabolism of palmitate in perfused rat liver. Computer models of subcellular triacylglycerol metabolism.

1. In the preceding paper [Kondrup (1979) Biochem. J.184, 63-71] the separation of two major fractions of hepatic triacylglycerol was described. One fraction contained triacylglycerol from the endoplasmic reticulum and from the Golgi apparatus. The other fraction contained triacylglycerol from the cytoplasmic lipid droplets. In the present paper possible precursor-product relationships between the two fractions were investigated by means of computer models. 2. The fatty acids present in di- and tri-acylglycerol in the fractions isolated in the time studies were analysed by gas chromatography. From this analysis the relative specific radioactivities, and contents, of palmitate in acylglycerols in the two fractions at the various time points were calculated. 3. A computer was used to predict relative specific radioactivities of pools in defined models of hepatic triacylglycerol metabolism. The acceptability of the models was evaluated by comparing predicted with measured relative specific radioactivities. 4. It is suggested that triacylglycerol in cytoplasmic lipid droplets does not originate (a) directly from triacylglycerol in the endoplasmic reticulum, (b) from a sub-pool of it or (c) directly from non-esterified fatty acids entering the cell. Rather, it is formed from diacylglycerol (and acyl-CoA) in the endoplasmic reticulum. Diacylglycerol, on the other hand, is furnished in part by hydrolysis of triacylglycerol in the endoplasmic reticulum. 5. This suggestion is discussed in relation to previous models of hepatic fatty acid metabolism.

Animals

A computer model and a mechanical model of the circulation and their use in the evaluation of indices of myocardial blood flow.

Computer and mechanical models of the circulation have been made to study isotopic techniques of determining indices of myocardial blood flow. Parameters in the program and dimensions in the mechanical model have been scaled to represent the human circulation. Single rapid injections of 131I labelled human serum albumen were given into the venous line of the mechanical model and records obtained from collimated scintillation detectors positioned over the heart, lung and brain. Similar injections and recordings were simulated in the computer model. Two indices of myocardial flow have been studied. The first, described by Mena et al. is the ratio of the half time of the downslope of the left ventricular curve to the half time of the downslope of the brain curve. This index distinguished myocardial flows of 0,5% and 10% of total cardiac output but was also affected by changes in cerebral flow. A new index is proposed in which the half time of the left ventricular curve downslope is related to the half time of the downslope of the lung curve. This index can distinguish myocardial flows of 0,5% and 10% total flow but is not affected by changes in cerebral flow.

Blood Circulation

Integrating structure and experimental data annotations with computational modeling framework for predicting micro-nanoplastics toxicities.

The wide use of plastic materials leads to increased emissions of micro-nanoplastics (MNPs) into the environment, raising significant concerns about their impact on human health. Traditional experimental approaches for assessing MNPs toxicity are costly, time-consuming, and there are no experimental protocols that are universally acceptable. Computational modeling using machine learning (ML) approaches provides an efficient alternative to MNP toxicity assessment. However, most modeling studies of MNPs are limited due to the lack of high-quality data and there are few previous modeling studies considering complex structures of MNPs for model training. To address this challenge, we constructed three MNP datasets with popular toxicity endpoints from various resources and used nanostructure annotation techniques to create virtual MNPs (vMNPs) for all MNP structures. The MNP structures were digitalized from annotated vMNPs, and geometrical descriptors were calculated using the Delaunay Tessellation approach. Moreover, important experimental information, such as concentrations and cell lines, were transformed into extra training variables. Partial least squares regression (PLSR) models were built using both experimental and geometrical descriptors and validated through a leave-one-out cross validation procedure. The resulting models showed reasonable performance in predicting toxicity potentials of MNPs for the three endpoints in the present datasets. Moreover, an additional library of vMNPs with their predicted properties and bioactivities was constructed, directing further research of new MNPs. This study provides three novel ML models for MNPs by integrating geometrical and experimental descriptors, which have the potential to assess new MNPs for their toxicity. The modeling strategy developed in this study can be easily expanded to model other MNP toxicity endpoints and create promising new models for MNP toxicity assessments.

Data annotation

Preferred antagonist binding state of the NMDA receptor: synthesis, pharmacology, and computer modeling of (phosphonomethyl)phenylalanine derivatives.

A series of substituted [phosphono-, sulfo-, carboxy-, and (N-hydroxycarbamoyl)methyl]phenylalanines were synthesized as probes for the investigation of the preferred antagonist state of the NMDA receptor antagonists. The potency of these compounds was evaluated by measuring electrophysiological responses induced by NMDA in cultured mouse cortical neurons. 3-(Phosphonomethyl)phenylalanine [1(m)] a formal AP7 analogue, has been shown to be the most potent antagonist in this study with an IC50 of around 5 microM. The isomeric 2-(phosphonomethyl)phenylalanine [1(o)] was about half as active as 1(m) and as active as compound 5(3), a derivative which is cis-hydrogenated on the phenyl ring of 1(m). Replacement of a phosphono by a sulfo group led to a large reduction in the ability of these compounds to antagonize NMDA responses, although the ortho and meta isomers retained some activity in their reduced forms. In both series the para isomers were almost completely inactive at 100 microM. Introduction of a carboxyl or a bidentate HONHCO group in place of the phosphono moiety in the 3-position results in compounds devoid of activity. The active and inactive compounds of this study were used in conjunction with the most potent linear and cyclic phosphono-containing NMDA antagonists reported to date to determine, via computer modeling techniques, a three-dimensional model corresponding to a antagonist preferring state of the NMDA binding site. This structure defines a pharmacophore which is characterized by (i) well-defined distances between the central atoms of the polar groups PO3H-, NHn+, (n = 2, 3), and COO- (P-N = 5.89 +/- 0.12 A, P-C = 6.66 +/- 0.08 A, and N-C = 2.28 +/- 0.01 A), (ii) a sterically allowed region between the C5 methylene and the PO3H- group, and (iii) a molecular electrostatic field in which the positive, neutral, and negative potential zones are self-contained--with the negative potential zone connecting the PO3H- and COO- groups as the largest. We have compared our results to a preliminary model of the NMDA antagonist site by Hutchison et al. and to a topological model of the NMDA-glycine receptor site by Cordi et al. Our proposed steric-electrostatic pharmacophore which refines, simplifies, and improves these models has now to be validated by the design of new NMDA antagonists.

Animals

Electric pacing of intact and transected canine small intestine and its computer model.

In 10 conscious, fasted dogs with electrodes chronically implanted on the intestine, current pulses (8 mA, 50 ms) at frequencies the same as, or faster than, that of the natural intestinal pacemaker always entrained pacesetter potentials (PP) along the proximal frequency plateau, but not along the distal frequency gradient. As duodenal PP's were paced faster, the proximal plateau shortened by orad extension of the distal gradient. Entrained PP's propagated orally and aborally. Their velocity slowed caudally while varying inversely with their frequency. After midduodenal transection had reduced the frequency of the natural PP's distal to the cut, pacing entrained PP's in all areas of the bowel and restored the proximal plateau and distal gradient. But no area could be paced faster than before transection. PP's were not propagated across sites of transection. A digital computer model of coupled relaxation oscillators gave similar results. We conclude that the frequency of the natural pacemaker and the declining gradient of maximal driven frequency determine the frequency pattern of the small intestinal PP.

Animals

Application of discrete computer modeling to the dynamics of cell populations.

Computer simulation of the dynamics of cell populations is discussed in the paper. Fundamental features of CELLSIM simulation language are described. Acute leukemia cell population model was implemented on a digital computer using CELLSIM. Some of the computer outputs are shown. The results obtained so far are interesting and promissing for further research.

Acute Disease

Cross-sectional views of hemoglobin S fibers by electron microscopy and computer modeling.

Fibers of deoxyHb S have been investigated by thin-section electron microscopy, utilizing a tannic acid embedding procedure. On the basis of numerous measurements of cross-sectional center-to-center distances for adjacent fibers in pairs or arrays, fiber diameters (mean +/- SD) of 205 +/- 5 A in embedded cells and 212 +/- 8 A in embedded hemolysates were obtained. This is an agreement with values obtained by conventional embedding procedures [Crepeau, R. H., Dykes, G., Garrell, R. L. & Edelstein, S. J. (1978) Nature (London) 274, 616--617]. The use of tannic acid has resulted in improved resolution of fiber cross sections, revealing individual strands of Hb S molecules. Because the section thickness corresponds to approximately one-fifth of the fiber helical repeat distance, the strands in projection superimpose to form characteristic image patterns. Additional superposition patterns arise in sections taken at small deviations from perpendicularity to the longitudinal fiber axis. These patterns are consistent with the 14-strand structure for hemoglobin S fibers [Dykes, G., Crepeau, R. H. & Edelstein, S. J. (1978) Nature (London) 272, 506--510], as indicated by computer models of cross-sectional patterns for various thicknesses and angular deviations of sections.

Hemoglobin, Sickle

DNA -a computer model.

The model of the system DNA-histones functioning like a computer has the following elements: 1. The hydrogen bonds between the complementary nucleotide bases function as informational gates. When the pi electrons of a nucleotide base are excited, an exchange of protons is produced between the 2 complementary bases. The result is the displacement of the double conjugated bonds which facilitate the intermolecular transmission of the electronic wave of excitation by an electromagnetic coupling. 2. Each triplet of nucleotide bases of DNA fixes a certain amino acid (as in the genetic code). Between the nucleotide bases and the amino acids there are constituted informational gates, which ensure the circulation of the electronic wave of excitation.

Computers