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At least 235 records · Page 13Linked to original sources
PubMed1993

The Müller-Lyer contrast illusion: a computational approach.

When a temporal delay is interposed between the contextual elements (wings) and the focal element (central axis) of the Müller-Lyer figures, the usual assimilation illusion changes to an illusion of contrast; that is, judged axis length is contrasted away from rather than assimilated toward the context provided by parallel extents between wings. Presentation time for the preceding contextual wings on the order of 1 sec or more was needed to produce contrast effects in judgments of the following focal axis (Experiment 3) and, given sufficient presentation time, these contrast effects were largely unaffected by the length of the temporal delay between contextual and focal elements, appearing equally strong for delays between 0 and 2 sec (Experiments 1 and 2). These results are consistent with a representational basis for these contrast effects that is high-level and long-lived. The Müller-Lyer contrast illusion may reflect the inadvertent error arising from basing judgments about particular objects on information about attribute differences among objects. Such judgmental errors may be the natural consequence of constrained computations that make explicit information required for certain common tasks, but at the expense of obscuring information required for less common tasks.

Adult↗
PubMed1975

Non-computer approach to structure-activity study. An expanded Fibonacci search applied to structurally diverse types of compounds.

The Fibonacci search technique, first applied to a structure-activity study by Bustard, has been expanded to allow the analysis of a broad class of structural types of compounds. The compounds are first arranged in order of increasing value of a molecular property of the analogs such as log P, Sigmapi, Sigmasigma, or Rm. A successful Fibonacci search of the compounds will find the most active analog in a small, predetermined number of steps. Examples are given where insight as to mechanism of action is indicated by the combination of various parameters such as log P and pKa. Additional examples illustrate the use of Fibonacci search to establish the parabolic dependence of the biological activity of lipophilicity and sigma, where such dependency had not been observed initially. This technique allows the treatment of a variety of structurally diverse types of compounds simultaneously. It is to be stressed that Fibonacci search can be applied to structure-activity studies without the use of a computer.

Antifungal Agents↗
PubMed2004

The effect of media perfusion on three-dimensional cultures of human chondrocytes: integration of experimental and computational approaches.

This work examines the effect of perfusion on human mature articular chondrocytes cultured on synthetic biodegradable scaffolds (DegraPol). Human chondrocytes were isolated, seeded on the scaffolds and subjected to perfused culture at a flow rate of 0.5 ml/min, corresponding to an average inlet fluid velocity of 44 microm/s, with flow inversion every 1 minute. The flow was imposed at the construct surface in some constructs, it was forced through the construct thickness in other constructs and was absent in the static controls. We compared cell viability and morphology and we evaluated material properties of the constructs at 1 month of culture. Thickness-perfused constructs showed significantly higher material properties and roughly a two-fold cell viability, when compared both to surface-perfused constructs and to static controls. Chondrocytes maintained a phenotypic morphology in all experiments, probably favoured by a limited cell-scaffold interaction. Biosynthetic activity could be demonstrated only in the bioreactor-cultured constructs. In this experimental model, a bi-directional flow of culture medium was applied to the cells at a macroscopic level and computational modelling was used to quantify the fluid-dynamic environment induced on the cells at a microscopic level. This method may be used to quantify the effects of fluid-dynamic shear on the growth modulation of tissue-engineered cartilage constructs, to potentially enhance tissue growth in vitro.

Biomechanical Phenomena↗
PubMed2005

A computational approach to predicting cell growth on polymeric biomaterials.

A predictive model that can correlate the chemical composition of a biomaterial with the biological response of cells that are in contact with that biomaterial would represent a major advance and would facilitate the rational design of new biomaterials. As a first step toward this goal, we report here on the use of Logical Analysis of Data (LAD) to model the effect of selected polymer properties on the growth of two different cell types, rat lung fibroblasts (RLF, a transformed cell line), and normal foreskin fibroblasts (NFF, nontransformed human cells), on 112 surfaces obtained from a combinatorially designed library of polymers. LAD is a knowledge extraction methodology, based on using combinatorics, optimization, and Boolean logic. LAD was trained on a subset of 62 polymers and was then used to predict cell growth on 50 previously untested polymers. Experimental validation indicated that LAD correctly predicted the high and low cell growth polymers and found optimal ranges for polymer chemical composition, surface chemistry, and bulk properties. Particularly noteworthy is that LAD correctly identified high-performing polymer surfaces, which surpassed commercial tissue culture polystyrene as growth substratum for normal foreskin fibroblasts. Our results establish the feasibility of using computational modeling of cell growth on flat polymeric surfaces to identify promising "lead" polymers for applications that require either high or low cell growth.

Animals↗
PubMed2006

Computational approach to estimating the effects of blood properties on changes in intra-stent flow.

In this study various blood rheological assumptions are numerically investigated for the hemodynamic properties of intra-stent flow. Non-newtonian blood properties have never been implemented in blood coronary stented flow investigation, although its effects appear essential for a correct estimation and distribution of wall shear stress (WSS) exerted by the fluid on the internal vessel surface. Our numerical model is based on a full 3D stent mesh. Rigid wall and stationary inflow conditions are applied. Newtonian behavior, non-newtonian model based on Carreau-Yasuda relation and a characteristic newtonian value defined with flow representative parameters are introduced in this research. Non-newtonian flow generates an alteration of near wall viscosity norms compared to newtonian. Maximal WSS values are located in the center part of stent pattern structure and minimal values are focused on the proximal stent wire surface. A flow rate increase emphasizes fluid perturbations, and generates a WSS rise except for interstrut area. Nevertheless, a local quantitative analysis discloses an underestimation of WSS for modelisation using a newtonian blood flow, with clinical consequence of overestimate restenosis risk area. Characteristic viscosity introduction appears to present a useful option compared to rheological modelisation based on experimental data, with computer time gain and relevant results for quantitative and qualitative WSS determination.

Animals↗
PubMedDate not supplied

Multipoint genomic scanning for quantitative loci: effects of map density, sibship size and computational approach.

Multipoint interval mapping (MIM) and the MAPMAKER/SIBS program (M/S) are two methods of mapping quantitative loci by examining identity by descent (IBD) sharing in a region spanned by multiple microsatellite DNA markers. For the purpose of comparison, we simulated a quantitative trait controlled by a two-locus model, and evaluated the power and genome-wide false positive rate of both approaches. Based on our simulation, we examined the effects of marker density (5 cM, 10 cM and 20 cM) and sibship size (2, 3, 4 and 5) on the power to detect linkage. Our results indicate that a 10 cM map provides the optimal trade-off between power and type I error, and that the power of MIM increases with sibship size and, in general, performs better than MAPMAKER/SIBS. Furthermore, we conclude that using a reasonable sample of randomly ascertained sibships, it is possible to map a quantitative trait locus (QTL) which accounts for 25% of the phenotypic variance.

Chromosome Mapping↗
PubMed2000

Probing structure-function relationships of the DNA polymerase alpha-associated zinc-finger protein using computational approaches.

We present the application of a method for protein structure prediction to aid the determination of structure-function relationships by experiment. The structure prediction method was rigourously tested by making blind predictions at the third meeting on the Critical Assessment of Protein Structure methods (CASP3). The method is a combined hierarchical approach involving exhaustive enumeration of all possible folds of a small protein sequence on a tetrahedral lattice. A set of filters, primarily in the form of discriminatory functions, are applied to these conformations. As the filters are applied, greater detail is added to the models resulting in a handful of all-atom "final" conformations. Encouraged by the results at CASP3, we used our approach to help solve a practical biological problem: the prediction of the structure and function of the 67-residue C-terminal zinc-finger region of the DNA polymerase alpha-associated zinc-finger (PAZ) protein. We discuss how the prediction points to a novel function relative to the sequence homologs, in conjunction with evidence from experiment, and how the predicted structure is guiding further experimental studies. This work represents a move from the theoretical realm to actual application of structure prediction methods for gaining unique insight to guide experimental biologists.

Amino Acid Sequence↗
PubMed2003

Neural stability and flexibility: a computational approach.

This paper addresses the issue of stability and flexibility of neural systems, and how a balance can be achieved. Assuming a close correspondence with cognitive and mental processes, we use a cortical neural network model to investigate how regulation of the neurodynamics can result in an efficient information processing, in terms of learning and associative memory. In particular, we use this model to investigate relations between structure, dynamics, and function of a neural system, and how the stability-flexibility dilemma may be solved by proper regulation. We focus on the complex neurodynamics and its modulation, and how this is related to the neural circuitry, where synaptic modification and network pruning are considered. Finally, we discuss the relevance of these results to clinical and experimental neuroscience and speculate on a link between neural instability and mental disorders.

Computational Biology↗
PubMed2004

The spacious active site of a Y-family DNA polymerase facilitates promiscuous nucleotide incorporation opposite a bulky carcinogen-DNA adduct: elucidating the structure-function relationship through experimental and computational approaches.

Y-family DNA polymerases lack some of the mechanisms that replicative DNA polymerases employ to ensure fidelity, resulting in higher error rates during replication of undamaged DNA templates and the ability to bypass certain aberrant bases, such as those produced by exposure to carcinogens, including benzo[a]pyrene (BP). A tumorigenic metabolite of BP, (+)-anti-benzo-[a]pyrene diol epoxide, attacks DNA to form the major 10S (+)-trans-anti-[BP]-N(2)-dG adduct, which has been shown to be mutagenic in a number of prokaryotic and eukaryotic systems. The 10S (+)-trans-anti-[BP]-N(2)-dG adduct can cause all three base substitution mutations, and the SOS response in Escherichia coli increases bypass of bulky adducts, suggesting that Y-family DNA polymerases are involved in the bypass of such lesions. Dpo4 belongs to the DinB branch of the Y-family, which also includes E. coli pol IV and eukaryotic pol kappa. We carried out primer extension assays in conjunction with molecular modeling and molecular dynamics studies in order to elucidate the structure-function relationship involved in nucleotide incorporation opposite the bulky 10S (+)-trans-anti-[BP]-N(2)-dG adduct by Dpo4. Dpo4 is able to bypass the 10S (+)-trans-anti-[BP]-N(2)-dG adduct, albeit to a lesser extent than unmodified guanine, and the V(max) values for insertion of all four nucleotides opposite the adduct by Dpo4 are similar. Computational studies suggest that 10S (+)-trans-anti-[BP]-N(2)-dG can be accommodated in the active site of Dpo4 in either the anti or syn conformation due to the limited protein-DNA contacts and the open nature of both the minor and major groove sides of the nascent base pair, which can contribute to the promiscuous nucleotide incorporation opposite this lesion.

Base Pairing↗
PubMed2003

Mechanobiology of soft skeletal tissue differentiation--a computational approach of a fiber-reinforced poroelastic model based on homogeneous and isotropic simplifications.

The material properties of multipotent mesenchymal tissue change dramatically during the differentiation process associated with skeletal regeneration. Using a mechanobiological tissue differentiation concept, and homogeneous and isotropic simplifications of a fiber-reinforced poroelastic model of soft skeletal tissues, we have developed a mathematical approach for describing time-dependent material property changes during the formation of cartilage, fibrocartilage, and fibrous tissue under various loading histories. In this approach, intermittently imposed fluid pressure and tensile strain regulate proteoglycan synthesis and collagen fibrillogenesis, assembly, cross-linking, and alignment to cause changes in tissue permeability (k), compressive aggregate modulus (H(A)), and tensile elastic modulus (E). In our isotropic model, k represents the permeability in the least permeable direction (perpendicular to the fibers) and E represents the tensile elastic modulus in the stiffest direction (parallel to the fibers). Cyclic fluid pressure causes an increase in proteoglycan synthesis, resulting in a decrease in k and increase in H(A) caused by the hydrophilic nature and large size of the aggregating proteoglycans. It further causes a slight increase in E owing to the stiffness added by newly synthesized type II collagen. Tensile strain increases the density, size, alignment, and cross-linking of collagen fibers thereby increasing E while also decreasing k as a result of an increased flow path length. The Poisson's ratio of the solid matrix, nu(s), is assumed to remain constant (near zero) for all soft tissues. Implementing a computer algorithm based on these concepts, we simulate progressive changes in material properties for differentiating tissues. Beginning with initial values of E=0.05 MPa, H(A)=0 MPa, and k=1 x 10(-13) m(4)/Ns for multipotent mesenchymal tissue, we predict final values of E=11 MPa, H(A)=1 MPa, and k=4.8 x 10(-15) m(4)/Ns for articular cartilage, E=339 MPa, H(A)=1 MPa, and k=9.5 x 10(-16) m(4)/Ns for fibrocartilage, and E=1,000 MPa, H(A)=0 MPa, and k=7.5 x 10(-16) m(4)/Ns for fibrous tissue. These final values are consistent with the values reported by other investigators and the time-dependent acquisition of these values is consistent with current knowledge of the differentiation process.

Algorithms↗
PubMed2006

A computational approach toward label-free protein quantification using predicted peptide detectability.

We propose here a new concept of peptide detectability which could be an important factor in explaining the relationship between a protein's quantity and the peptides identified from it in a high-throughput proteomics experiment. We define peptide detectability as the probability of observing a peptide in a standard sample analyzed by a standard proteomics routine and argue that it is an intrinsic property of the peptide sequence and neighboring regions in the parent protein. To test this hypothesis we first used publicly available data and data from our own synthetic samples in which quantities of model proteins were controlled. We then applied machine learning approaches to demonstrate that peptide detectability can be predicted from its sequence and the neighboring regions in the parent protein with satisfactory accuracy. The utility of this approach for protein quantification is demonstrated by peptides with higher detectability generally being identified at lower concentrations over those with lower detectability in the synthetic protein mixtures. These results establish a direct link between protein concentration and peptide detectability. We show that for each protein there exists a level of peptide detectability above which peptides are detected and below which peptides are not detected in an experiment. We call this level the minimum acceptable detectability for identified peptides (MDIP) which can be calibrated to predict protein concentration. Triplicate analysis of a biological sample showed that these MDIP values are consistent among the three data sets.

Algorithms↗
PubMed2026

In silico identification of DNMT1 inhibitors from the PlantCyc database through computational approach to assess the anti-cancer potential of nutraceutical compounds in breast cancer.

Breast cancer accounts for a disproportionate share of global cancer-related deaths, with 670,000 fatalities and 2.3 million new diagnoses recorded in women during 2022 alone. Existing treatment modalities carry considerable toxicity burdens, and resistance to available agents remains an unresolved clinical problem. DNA methyltransferase 1 (DNMT1), the enzyme chiefly responsible for maintaining genome-wide methylation patterns during DNA replication, has been mapped out as a high-value target in breast cancer because its dysregulation silences tumour suppressor genes through promoter hypermethylation. The present work involves hierarchical in silico workflow to screen 4549 plant-derived compounds from the PlantCyc database (v16.0.3) against the human DNMT1 catalytic domain (PDB ID: 4WXX). Ten top-scoring compounds were taken forward for molecular docking via AutoDock Vina; Quercetin and Kaempferol both recorded the highest binding affinities at -9.5 kcal/mol, Wogonin (-9.3 kcal/mol) and Xanthohumol (-8.1 kcal/mol) also emerged as strong binders. Pharmacokinetic evaluation using ADMET-AI confirmed that all 10 compounds met Lipinski's rule of five, with human intestinal absorption values at or above 0.98. Wogonin and Xanthohumol were selected for a 100 ns all-atom molecular dynamics (MD) simulation in GROMACS due to their well-rounded ADMET profiles and limited existing data on their specific interactions with DNMT1 in breast cancer. Across all measured trajectory metrics, backbone RMSD, residue fluctuation, radius of gyration, solvent-accessible surface area, and intermolecular hydrogen bond count, Wogonin formed a more stable, compact complex. These findings suggest that Wogonin and Xanthohumol are non-toxic nutraceutical candidates suitable for DNMT1 targeted epigenetic therapy, with computational foundation strong enough to facilitate future in vitro and in vivo validation work.

Humans↗
PubMedDate not supplied

Toward designing drug-like libraries: a novel computational approach for prediction of drug feasibility of compounds.

Prediction of the degree of drug-like character in small molecules is of great industrial interest. The major barrier, however, is the lack of a definition for drug-like character. We used the concept of the multilevel chemical compatibility (MLCC) between a compound and a drug library as a measure of the drug-like character of a compound. The rationale is that the local chemical environment of each atom or group of atoms in a compound largely contributes to the stability, toxicity, and metabolism in vivo. A systematic comparison of the local environments within a compound and those within the existing drugs provides a basis for determining whether and how much a compound is drug-like. We applied the MLCC calculations to four test sets: top selling drugs, compounds under biological testing prior to the preclinical test, anticancer drugs, and compounds known to have poor drug-like character. The following conclusions were obtained: (1) A convergent number of unique local structure types were found in the analysis of the library of the existing drugs. It suggests that the current drug library contains about 80% of all the viable types; therefore, discovery of a drug with new local structures is only an event of relatively small probability. (2) The method is highly selective in discerning drug-like compounds: most of the top drugs are predicted to be drug-like, about one-quarter of the biological testing compounds are drug-like, and about one-fifth of the anticancer drugs are drug-like. (3) The method also correctly predicted that none of the known problematic compounds are drug-like. (4) The method is fast enough for computational screening of virtual combinatorial chemistry libraries and databases of available compounds.

Combinatorial Chemistry Techniques↗
PubMed1995

Computational approaches to study protein unfolding: hen egg white lysozyme as a case study.

Four methods are compared to drive the unfolding of a protein: (1) high temperature (T-run), (2) high pressure (P-run), (3) by imposing a gradual increase in the mean radius of the protein using a penalty function added to the physical interaction function (F-run, radial force driven unfolding), and (4) by weak coupling of the difference between the temperature of the radially outward moving atoms and the radially inward moving atoms to an external temperature bath (K-run, kinetic energy driven unfolding). The characteristic features of the four unfolding pathways are analyzed in order to detect distortions due to the size or the type of the applied perturbation, as well as the features that are common to all of them. Hen egg white lysozyme is used as a test system. The simulations are analyzed and compared to experimental data like 1H-NMR amide proton exchange-folding competition, heat capacity, and compressibility measurements.

Amides↗
PubMed1999

A computational approach to simplifying the protein folding alphabet.

What is the minimal number of residue types required to form a structured protein? This question is important for understanding protein modeling and design. Recently, an experimental finding by Baker and coworkers suggested a five-residue solution to this problem. We were motivated by their results and by the arguments of Wolynes to study reductions of protein representation based on the concept of mismatch between a reduced interaction matrix and the Miyazawa and Jernigan (MJ) matrix. We find several possible simplified schemes from the relationship of minimized mismatch versus the number of residue types (N = approximately 2-20). As a specific case, an optimal reduction with five types of residues has the same form as the simplified palette of Baker and coworkers. Statistical and kinetic features of a number of sequences are tested. Comparison of results from sequences with 20 residue types and their reduced representations indicates that the reduction by mismatch minimization is successful. For example, sequences with five types of residues have good folding ability and kinetic accessibility in model studies.

Algorithms↗
PubMed2005

A computational approach to the inference of sphingolipid pathways from the genome of Aspergillus fumigatus.

A growing body of evidence suggests that sphingolipids are important bioactive molecules, in addition to being critical structural components of cellular membranes. These molecules have been implicated in regulating cell growth, differentiation, angiogenesis, apoptosis, and senescence. Many of the enzymes involved in sphingolipid biosynthesis are the targets of fungal toxins, thus underscoring the importance of this pathway. An international consortium has made considerable progress in sequencing the genome of Aspergillus fumigatus, one of the most common mold pathogens of humans; however, most genes have not yet been annotated. Here, we have identified genes involved in the sphingolipid pathway of A. fumigatus by comparative analysis with four other fungal species and the gene prediction program GlimmerM. Our results shows that A. fumigatus has most of the sphingolipid pathway genes found in other fungi, except for the CSG2 and IPT1 genes; the former is involved in the mannosylation of inositol phosphorylceramide (IPC) to mannose-inositol-phosphorylceramide and the latter involved in the synthesis of mannose-(inositol-P)(2)-ceramide from mannose-inositol-phosphorylceramide.

Aspergillus fumigatus↗
PubMed2000

A computational approach to modeling population differences.

Four experiments were conducted to determine whether the Hyperspace Analogue to Language (HAL) model of semantic memory could differentiate between two different populations. An analysis of the differences in densities (or average distances between word neighbors in semantic space) in HAL matrices--generated from text corpora derived from younger and older adults--confirmed that HAL was able to distinguish between the two age groups. This difference was again detected when structured interview data were used to build the corpora. A third experiment, designed to test the specificity of HAL in detecting differences between groups, did not detect any difference in the densities of the memory representations when older adults generated both the test corpora. The final experiment, conducted on the language of adults with Alzheimer's and normal adults, again demonstrated that HAL could discriminate between the two populations. These results suggest that HAL is capable of modeling, on the basis of changes in mean density, some of the differences between populations without modifying the model itself but, rather, by changing the text corpus from which the model creates its representations in semantic space.

Adult↗
PubMed2005

sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes.

Small non-coding bacterial RNAs (sRNAs) play important regulatory roles in a variety of cellular processes. Nearly all known sRNAs have been identified in Escherichia coli and most of these are not conserved in the majority of other bacterial species. Many of the E.coli sRNAs were initially predicted through bioinformatic approaches based on their common features, namely that they are encoded between annotated open reading frames and are flanked by predictable transcription signals. Because promoter consensus sequences are undetermined for most species, the successful use of bioinformatics to identify sRNAs in bacteria other than E.coli has been limited. We have created a program, sRNAPredict, which uses coordinate-based algorithms to integrate the respective positions of individual predictive features of sRNAs and rapidly identify putative intergenic sRNAs. Relying only on sequence conservation and predicted Rho-independent terminators, sRNAPredict was used to search for sRNAs in Vibrio cholerae. This search identified 9 of the 10 known or putative V.cholerae sRNAs and 32 candidates for novel sRNAs. Small transcripts for 6 out of 9 candidate sRNAs were observed by Northern analysis. Our findings suggest that sRNAPredict can be used to efficiently identify novel sRNAs even in bacteria for which promoter consensus sequences are not available.

Algorithms↗