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At least 199 records · Page 11Linked to original sources
PubMed2004

Modulation of septo-hippocampal Theta activity by GABAA receptors: an experimental and computational approach.

Theta frequency oscillation of the septo-hippocampal system has been considered as a prominent activity associated with cognitive function and affective processes. It is well documented that anxiolytic drugs diminish septo-hippocampal oscillatory Theta activity contributing to their either therapeutic or unwanted side effects. In the present experiments we applied a combination of computational and physiological techniques to explore the functional role of GABAA receptors in Theta oscillation. In electrophysiological experiments extracellular single unit recordings were performed from medial septum/diagonal band of Broca with simultaneous hippocampal (CA1) electroencephalogram (EEG) recordings from anesthetized rats. Neurotransmission at GABAA receptors were modulated by means of pharmacological tools: the actions of the GABAA receptor positive allosteric modulator diazepam and inverse agonist/negative allosteric modulator FG-7142 were evaluated on septo-hippocampal activity. Systemic administration of diazepam inhibited, whereas FG-7142 enhanced Theta oscillation of septal neurons and hippocampal EEG Theta activity. In parallel to these experimental observations, a computational model has been constructed by implementing a septal GABA neuron model with a CA1 hippocampal model containing three types of neurons (including oriens and basket interneurons and pyramidal cells; latter modeled by multicompartmental techniques; for detailed model description with network parameters see online addendum: http://geza.kzoo.edu/theta). This connectivity made the network capable of simulating the responses of the septo-hippocampal circuitry to the modulation of GABAA transmission, and the presently described computational model proved suitable to reveal several aspects of pharmacological modulation of GABAA receptors. In addition, computational findings indicated different roles of distinctively located GABAA receptors in theta generation.

Animals↗
PubMed2001

Predicting anti-HIV activity: computational approach using a novel topological descriptor.

The discriminating power of a novel topological descriptor termed as eccentric adjacency index in the estimation of anti-HIV activity, for a data set of 107 1-[(2-hydroxyethoxy)methyl]-6-(phenylthio)thymine (HEPT) derivatives was investigated in the present study. The value of eccentric adjacency index of each derivative was computed and active range was identified using moving average analysis. Subsequently, each derivative was assigned a biological activity which was then compared with the reported anti-HIV activity. The accuracy of prediction was found to be more than ninety percent in the active range using eccentric adjacency index. The proposed index offers a vast potential for structure-activity/property studies.

Anti-HIV Agents↗
PubMed2006

Identification of a novel putative mitogen-activated kinase cascade on human chromosome 21 by computational approaches.

UNLABELLED: Down syndrome (DS) is the most frequent form of mental retardation and is caused by chromosome 21 (HSA21) trisomy. Despite the number of known genes involved in DS and its high therapeutic interest, biological mechanisms leading to the DS phenotype are not fully clear. We present a functional hypothesis based on fold recognition and hidden Markov model techniques for four HSA21 genes located in the DS Candidate Region (DSCR). More specifically, we propose that they are members of a novel mitogen-activated protein kinase pathway with DYRK1A, SNF1LK and RIPK4 gene products being elements of the kinase cascade and the DSCR3 acting as structural scaffold for their interaction. This hypothesis finds support in various biochemical studies concerning the biological behavior and features of the involved HSA21 proteins. Our analysis calls for specifically designed experiments to validate our prediction and establish its relevance in terms of therapeutic approaches to the disease. CONTACT: anna.tramontano@uniroma1.it SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Amino Acid Sequence↗
PubMed2004

From a spin-off to the advantageous use in Diels-Alder reactions: a combined synthetic, spectroscopic and computational approach to N-(dienyl)acylamines.

The acid-catalyzed condensation of aldehydes and acetamide has been shown to provide a pool of diverse equilibrating species. For the first time, the synthesis of substituted 1-N-acylamino-1,3-butadienes has been accomplished directly in moderate yields upon telomerization of two molecules of aldehyde with one molecule of carboxamide. Detailed spectroscopic and computational investigations establish the favourable formation of all-trans aminodienes under the reaction conditions. Employment thereof as diene building blocks in Diels-Alder reactions allows for the synthesis of carbocyclic molecules with high stereocontrol.

Journal Article↗
PubMed2005

Parametric optimization of a model-based segmentation algorithm for cardiac MR image analysis: a grid-computing approach.

In this work we present a Grid-based optimization approach performed on a set of parameters that affects both the geometric and grey-level appearance properties of a three-dimensional model-based algorithm for cardiac MRI segmentation. The search for optimal values was assessed by a Monte Carlo procedure using computational Grid technology. A series of segmentation runs were conducted on an evaluation database comprising 30 studies at two phases of the cardiac cycle (60 datasets), using three shape models constructed by different methods. For each of these model-patient combinations, six parameters were optimized in two steps: those which affect the grey-level properties of the algorithm first and those relating to the geometrical properties, secondly. Two post-processing tasks (one for each stage) collected and processed (in total) more than 70000 retrieved result files. Qualitative and quantitative validation of the fitting results indicates that the segmentation performance was greatly improved with the tuning. Based on the experienced benefits with the use of our middleware, and foreseeing the advent of large-scale tests and applications in cardiovascular imaging, we strongly believe that the use of Grid computing technology in medical image analysis constitutes a real necessity.

Algorithms↗
PubMed2001

Identification and analysis of eukaryotic promoters: recent computational approaches.

The DNA sequence of several higher eukaryotes is now complete, and we know the expression patterns of thousands of genes under a variety of conditions. This gives us the opportunity to identify and analyze the parts of a genome believed to be responsible for most transcription control--the promoters. This article gives a short overview of the state-of-the-art techniques for computational promoter localization and analysis, and comments on the most recent advances in the field.

Base Sequence↗
PubMed1998

Taking a computational approach to aging: the SPAN theory of working memory.

The decline of working memory capacity associated with normal adult aging is well-known. What is less well established is the cause of this decline. One prominent proposal is that working memory decline is caused by a reduction in basic information-processing speed, but this account has lacked a demonstration that general slowing is computationally sufficient to produce a decrease in working memory capacity. This article presents a production system theory of working memory (SPAN) based on established mechanisms: slowing, decay, and displacement. Models of 2 tasks--digit symbol and computation span--which have been prominent in research on slowing, are presented in detail. These models demonstrate that slowing is sufficient to produce differences in these tasks, and they provide a quantitative match to observed young-old differences as well. This advance for slowing theory also demonstrates the viability of computational tools in aging research.

Adult↗
PubMed2003

Computational approach for modeling intra- and extracellular dynamics.

We introduce a phase-field approach for diffusion inside and outside a closed cell with damping and with source terms at the stationary interface. The method is compared to exact solutions (where possible) and the more traditional finite element method. It is shown to be very accurate, easy to implement, and computationally inexpensive. We apply our method to a recently introduced model for chemotaxis by Rappel et al. [Biophys. J. 83, 1361 (2002)].

Journal Article↗
PubMed2003

Computational approaches to identify promoters and cis-regulatory elements in plant genomes.

The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5'-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.

Computational Biology↗
PubMed2026

Phage bioinformatics tools: a review of computational approaches for bacteriophage research.

Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection, and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 in identification tasks and, through structure-informed prediction, raise functional annotation to over half of phage genes. Furthermore, we map the upstream components, namely, gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalizable strain-level host predictor exists for phage therapy; varying true-positive rates (0%-97%) underscore the absence of standardized community benchmarks analogous to Critical Assessment of Structure Prediction or Critical Assessment of Metagenome Interpretation. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.

Computational Biology↗
PubMed1995

Patient education: an innovative computer approach.

Patient teaching has always been a part of quality nursing care. It is now more important than ever in order to ensure quality care and safety after discharge from the hospital. Nursing managers must develop cost-effective strategies for patient education in the current atmosphere of cost-containment and constant changes in health care. One method of accomplishing this is to utilize a hospital computer system to provide teaching materials and a documentation tool.

Computer-Assisted Instruction↗
PubMed1999

The role of neuronal death during the development of topographically ordered projections: a computational approach.

At the time of synaptogenesis typically 50% of the neurons die. The biological role of this is still unclear, but there is evidence in the visual system that many neurons projecting to topographically inappropriate parts of their target are eliminated to improve the accuracy of the mapping. The signaling that determines neuronal survival involves electrical activity and trophic factors. Based on these observations, we have elaborated a computational model for the self-organization of a two-layered neural network. We observe changes in the topographical organization between the two layers. In layer 1, a traveling wave of electrical activity is used as input. Activity transmission to layer 2 can generate, according to a Hebbian rule, a retrograde death signal that is compensated by a trophic survival signal generated by the target cells. Approximately 50% of the neurons die, and we observe refinement in the topography between the two layers. In alternative versions of the model, we show that an equivalent reorganization can occur through Hebbian synaptic modification alone, but with less precision and efficiency. When the two mechanisms are combined, synaptic modification provides no further improvement over that produced by neuronal death alone. This computational study supports the hypothesis that neuronal death during development can play a role in the refinement of topographical projections in the nervous system.

Animals↗
PubMed2006

Computational approaches for the prediction of protein function in the mitochondrion.

Understanding a complex biological system, such as the mitochondrion, requires the identification of the complete repertoire of proteins targeted to the organelle, the characterization of these, and finally, the elucidation of the functional and physical interactions that occur within the mitochondrion. In the last decade, significant developments have contributed to increase our understanding of the mitochondrion, and among these, computational research has played a significant role. Not only general bioinformatics tools have been applied in the context of the mitochondrion, but also some computational techniques have been specifically developed to address problems that arose from within the mitochondrial research field. In this review the contribution of bioinformatics to mitochondrial biology is addressed through a survey of current computational methods that can be applied to predict which proteins will be localized to the mitochondrion and to unravel their functional interactions.

Computational Biology↗
PubMed2003

Discussion on the reverberatory model of short-term memory: a computational approach.

Up to now a number of models have been proposed to underlie memory formation in the central nervous system. Two of these models are the reverberatory circuit model and the other one the self-feedback loop model. This paper considers these two models regarding their ability to preserve neural activity and to hold information. In the self-feedback loop model, the activity level of the loop output is computed regarding the short lasting initial input. In the reverberatory circuit model, the activity levels of the proposed two-layer network outputs were computed regarding the short lasting initial inputs of the network. In the self-feedback loop model, the activity level of the loop output changes with each reverberation until it reaches a specific limit and then remains at that level. In the reverberatory circuit model, the activity levels of the proposed two-layer network outputs display an oscillatory behavior. These models can preserve the input activity, but they change its level with each reverberation. Information carried by a single neuron is related to its activity level. Therefore these models change the information during the reverberation. Short-term memory must hold the information for a certain period of time, so these models cannot be proposed to underlie short-term memory formation.

Humans↗
PubMedDate not supplied

Simplified computational approach for dual-probe heat-pulse method.

Two equations are currently available for estimating soil volumetric heat capacity (pc) with the dual-probe heat-pulse (DPHP) method. One is simple but gives only approximate results because it assumes that the DPHP sensor releases an impulse of heat instantaneously. The other explicitly accounts for the finite duration of heating and gives exact results. Unfortunately, the equation that gives exact results involves the exponential integral function, which is not available in most computer spreadsheet software packages or data logger function libraries. In this note we introduce an approximation of the exact equation that contains only simple algebraic functions. The approximation consists of the first five terms of a Taylor series, which are written as a telescoped polynomial for computational purposes. For most applications of the DPHP method, the polynomial approximation gives estimates of pc that are at least an order of magnitude more accurate than estimates obtained from the simple equation based on instantaneous heating.

Algorithms↗
PubMed2003

Computational approaches to protein-protein interaction.

The interactions between proteins allow the cell's life. A number of experimental, genome-wide, high-throughput studies have been devoted to the determination of protein-protein interactions and the consequent interaction networks. Here, the bioinformatics methods dealing with protein-protein interactions and interaction network are overviewed. 1. Interaction databases developed to collect and annotate this immense amount of data; 2. Automated data mining techniques developed to extract information about interactions from the published literature; 3. Computational methods to assess the experimental results developed as a consequence of the finding that the results of high-throughput methods are rather inaccurate; 4. Exploitation of the information provided by protein interaction networks in order to predict functional features of the proteins; and 5. Prediction of protein-protein interactions.

Algorithms↗
PubMedDate not supplied

Predicting anticonvulsant activity of benzamides/benzylamines: computational approach using topological descriptors.

The relationship of Wiener's index (a distance-based topological descriptor), Zagreb group parameter (an adjacency-based topological descriptor) and eccentric connectivity index (an adjacency-cum-distance-based topological descriptor) with the anticonvulsant activity of a series of substituted benazamides/benzylamines has been investigated. A training set comprising 41 analogues of substituted benazamides/benzylamines was selected for the present investigations. The values of the Wiener's index, Zagreb group parameter and eccentric connectivity index and of each of 41 analogues comprising the data set were computed and active ranges were identified. Subsequently, a biological activity was assigned to each analogue involved in the data set which was then compared with the reported anticonvulsant activity. An exceptionally high accuracy of predictions ranging from a minimum of approximately 88% for the Zagreb group parameter to a maximum of approximately 97% for Wiener's index were obtained.

Anticonvulsants↗
PubMed2002

Computational approaches to cellular rhythms.

Oscillations arise in genetic and metabolic networks as a result of various modes of cellular regulation. In view of the large number of variables involved and of the complexity of feedback processes that generate oscillations, mathematical models and numerical simulations are needed to fully grasp the molecular mechanisms and functions of biological rhythms. Models are also necessary to comprehend the transition from simple to complex oscillatory behaviour and to delineate the conditions under which they arise. Examples ranging from calcium oscillations to pulsatile intercellular communication and circadian rhythms illustrate how computational biology contributes to clarify the molecular and dynamical bases of cellular rhythms.

Animals↗