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Results for “computational frameworks”

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At least 451 records · Page 25Linked to original sources
PubMed2003

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

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

Algorithms↗
PubMed2006

[Design of geometric models of the removable partial denture framework].

PURPOSE: The aim of this study was to introduce a method on computer aided design (CAD) of removable partial denture(RPD) framework based on domestic CAD/CAM software system, which contributes to the further research to develop the domestic software system applied in restorative dentistry. METHODS: Point cloud data of a partially edentulous cast, a mandibular Kennedy Class II modification 2 arch, was captured by an optical scanning system with projective grating and high-resolution digital camera. Using domestic CAD/CAM software system, the above point cloud data was reduced, digital surveying line and inserting path were determined. In terms of the principle of clinical design, the tissue surfaces and polishing surfaces of every component of RPD were built such as clasp, rest, lingual bar, and mesh construction, et al. As well as the characteristic structures of the framework, including the half-pear shaped cross section of lingual bar, the internal and external finish lines, the tissue stop at the tissue surface of mesh construction and so on, were fabricated on the base of reduced data model. 3-D surface model of the RPD framework was created. RESULTS: Geometric model of the RPD framework was fabricated successfully, which took on good fitting, high visibility and editing conveniently. And the data converted to STL file format that could be read by any other CAD/CAM software system and was in preparation for subsequent computer aided manufacture (CAM) of RPD framework. CONCLUSIONS: It is suggested that this method based on domestic software in CAD of RPD framework be feasible.

Computer-Aided Design↗
PubMed2004

Exact lattice calculations of dispersion coefficients in the presence of external fields and obstacles.

We present a study of the field-dependent dispersion coefficient of point-like particles in various 2D overdamped systems with obstructions (periodic, percolating, and trapping distributions of obstacles). These calculations profit from the synthesis of a newly proposed Monte Carlo algorithm--the first such algorithm that correctly reproduces the free dispersion coefficient in the presence of finite external fields--and an asymptotically exact calculation technique. The resulting method efficiently produces algebraic and numerical results without the need to actually perform Monte Carlo simulations. When compared to such simulations, our exact method features a negligible computational cost and exponentially small errors. Utilizing the power of this numerical method, we engage in comprehensive parametric analysis of several model systems, revealing very subtle effects that would otherwise be swamped by statistical errors or incur prohibitive computational costs. The unified framework presented here serves as a template for further applications of lattice random-walk models of biased diffusion.

Algorithms↗
PubMed2001

Epidemic spreading in scale-free networks.

The Internet has a very complex connectivity recently modeled by the class of scale-free networks. This feature, which appears to be very efficient for a communications network, favors at the same time the spreading of computer viruses. We analyze real data from computer virus infections and find the average lifetime and persistence of viral strains on the Internet. We define a dynamical model for the spreading of infections on scale-free networks, finding the absence of an epidemic threshold and its associated critical behavior. This new epidemiological framework rationalizes data of computer viruses and could help in the understanding of other spreading phenomena on communication and social networks.

Communication↗
PubMed1985

A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides.

Theoretical computations are performed on the structural and energetical factors involved in the sequence selective binding of daunomycin (DNM) to six representative self-complementary double-stranded hexanucleotides: d(CGTACG)2,d(CGATCG)2,d(CITACI)2, d(TATATA)2, d(CGCGCG)2 and d(TACGTA)2. The conformational angles of the hexanucleotides are fixed in values found in the representative crystal structure of the d(CGTACG)2-DNM complex. The intermolecular DNM-hexanucleotide interaction energies and the conformational energy changes of DNM upon binding are computed and optimized in the framework of the SIBFA procedure, which uses empirical formulas based on ab initio SCF computations. Among the two regularly alternating hexanucleotides, d(TATATA)2 and d(CGCGCG)2, a stronger binding is predicted for the former, in agreement with experimental results obtained with poly(dA-dT).poly(dA-dT) and poly(dG-dC).poly(dG-dC). Altogether, however, among the six investigated sequences, the strongest complexes are computed for the mixed hexanucleotides d(CGATCG)2 and d(CGTACG)2, containing the intercalation site between two CG base pairs and an adjacent TA base pair. This situation may be related to the increased affinity of DNM for GC rich DNA's and to the situation in the crystal structure of the DNM-d(CGTACG)2 complex. Analysis of the intrinsic base sequence preferences expressed by the individual constituents of DNM, namely the daunosamine side chain, the chromophore ring and its two 9-hydroxyl and 9-acetoxy substituents, reveals that the overall sequence preference found is the result of a rather intricate interplay of intrinsic sequence preferences, in particular at the level of daunosamine and the 9-hydroxyl substituent.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Sequence↗
PubMed1994

Structural features of the bradykinin receptor as determined by computer simulations, mutagenesis experiments, and conformationally constrained ligands: establishing the framework for the design of new antagonists.

1. In recent years, two classes of second generation bradykinin receptor antagonists have been reported. Both are of the general sequence D-Arg0-Arg1-Pro2-W3-Gly4-X5-Ser6-Y7-Z8+ ++-Arg9, where W is either Pro or Hyp, and X is an aromatic or aliphatic side chain-containing amino acid. Y and Z are unnatural amino acids, presumed to enforce a beta-turn structure. The de novo design of a non-peptide receptor antagonist (or the optimization of a lead discovered by random screening) will ultimately require knowledge about the receptor topology. In the absence of an experimentally determined structure of the bradykinin-bradykinin receptor complex, we have attempted to gain insights from other sources. 2. We have synthesized conformationally constrained ligands and completed extensive computer modeling on the bradykinin receptor. Moreover, using systematic synthetic modifications, we have explored the relative importances of selected amide bonds and side chains in second generation peptides and have made a series of C alpha- and/or N-methyl substitutions at positions four and five which led to the discovery of two new cyclic peptide antagonists. 3. Computational simulations led to a proposed model of bradykinin bound to its receptor which was found to be in good agreement with mutagenesis results. This model led ultimately to the design and synthesis of D-Arg0-Arg1-(12-aminododecanoyl)2-Ser3-D-Tic4-Oic5+ ++-Arg6. Consideration of this new lead compound, together with the extensive structure-activity relationship (SAR) which has been developed for peptide ligands and the receptor, represents a tangible framework for the design of more potent and longer-lasting antagonists of the bradykinin receptor.

Amino Acid Sequence↗
PubMed2003

Modelling intracellular H(+) ion diffusion.

Intracellular pH, an important modulator of cell function, is regulated by plasmalemmal proteins that transport H(+), or its equivalent, into or out of the cell. The pH(i) is also stabilised by high-capacity, intrinsic buffering on cytoplasmic proteins, oligopeptides and other solutes, and by the extrinsic CO(2)/HCO(3)(-) (carbonic) buffer. As mobility of these buffers is lower than for the H(+) ion, they restrict proton diffusion. In this paper we use computational approaches, based on the finite difference and finite element methods (FDM and FEM, respectively), for analysing the spatio-temporal behaviour of [H(+)] when it is locally perturbed. We analyse experimental data obtained for various cell-types (cardiac myocytes, duodenal enterocytes, molluscan neurons) where pH(i) has been imaged confocally using intracellular pH-sensitive dyes. We design mathematical algorithms to generate solutions for two-dimensional diffusion that fit data in terms of an apparent intracellular H(+) diffusion coefficient, D(H)(app). The models are used to explore how the spatial distribution of [H(+)](i) is affected by membrane H(+)-equivalent transport and by cell geometry. We then develop a mechanistic model, describing spatio-temporal changes of [H(+)](i) in a cardiac ventricular myocyte in terms of H(+)-shuttling on mobile buffers and H(+)-anchoring on fixed buffers. We also discuss how modelling may include the effects of extrinsic carbonic-buffering. Overall, our computational approach provides a framework for future analyses of the physiological consequences of pH(i) non-uniformity.

Animals↗
PubMed1994

Constructing regions for small area analysis: material deprivation and colorectal cancer.

BACKGROUND: This paper is about constructing small areas for the analysis of health data with the aims of health service delivery in mind. The areal framework should enable the analyst to link health data and census data and the areas should have large enough populations to ensure that rates are reliable and be homogeneous with respect to important socio-economic attributes. METHODS: An information-based statistic is used for the construction of regions in Sheffield based on the Townsend deprivation index. Enumeration districts are used as the geographical building blocks for the regions. The new regional framework is used for computing Bayes adjusted standardized incidence rates for colorectal cancer (CRC) across Sheffield. The paper then examines the statistical relationship between CRC incidence and deprivation across the set of regions using bivariate regression. RESULTS: The method yields regions that are considerably more homogeneous in terms of deprivation than wards, and using this framework it is shown that there is a (weak) statistical association at the regional scale between deprivation and CRC. CONCLUSION: We conclude that statistical tools can be employed to provide regions that meet the criteria for small area analysis of health data and the analyst does not have to be tied to large administrative units such as wards. There are some benefits to executing this work within a Geographic Informative System. The method should be of interest to those concerned with health service delivery and the identification of 'problem regions'.

Bayes Theorem↗
PubMed2006

Human errors and violations in computer and information security: the viewpoint of network administrators and security specialists.

This paper describes human errors and violations of end users and network administration in computer and information security. This information is summarized in a conceptual framework for examining the human and organizational factors contributing to computer and information security. This framework includes human error taxonomies to describe the work conditions that contribute adversely to computer and information security, i.e. to security vulnerabilities and breaches. The issue of human error and violation in computer and information security was explored through a series of 16 interviews with network administrators and security specialists. The interviews were audio taped, transcribed, and analyzed by coding specific themes in a node structure. The result is an expanded framework that classifies types of human error and identifies specific human and organizational factors that contribute to computer and information security. Network administrators tended to view errors created by end users as more intentional than unintentional, while errors created by network administrators as more unintentional than intentional. Organizational factors, such as communication, security culture, policy, and organizational structure, were the most frequently cited factors associated with computer and information security.

Computer Communication Networks↗
PubMed2004

Chemically feasible hypothetical crystalline networks.

Our systematic enumeration of 4-connected crystalline networks (that is, networks in which each atom is connected to exactly four neighbours) used recent advances in tiling theory to evolve over 900 topologies. The results are relevant to the structures of zeolites and other silicates, aluminophosphates (AlPOs), oxides, nitrides, chalcogenides, halides, carbon networks, and even to polyhedral bubbles in foams. Given their importance as molecular sieves, ion exchangers, catalysts and catalyst supports, we have applied the results to microporous aluminosilicates and aluminophosphates (zeolites). Zeolite chemistry has to date produced 152 distinct types of structure. However, it was always clear that although many further structures can be synthesised, only a fraction of the mathematically generated networks would be chemically feasible (many are 'strained' frameworks requiring unrealistic bond lengths and bond angles), and that an effective 'filtering' process is needed to identify the most plausible frameworks. Here, we describe the use of computational chemistry methods to calculate optimized structural parameters, framework energies relative to alpha-quartz, volumes accessible to sorption, and X-ray diffraction patterns for systematically enumerated hypothetical 4-connected crystalline frameworks. Structures were treated as silica polymorphs with the empirical formula SiO(2), and their energies were minimized.

Crystallization↗
PubMed2006

Computational modelling of cell spreading and tissue regeneration in porous scaffolds.

Improved biological and mechanical functionality of musculoskeletal tissue-engineered constructs is required for clinical application, which can only be achieved by comprehensive multidisciplinary research. This review focuses on the contribution of computational modelling as a framework for obtaining an integrated understanding of key processes, which include: nutrient transport and utilization, matrix formation, cell population dynamics, cell attachment and migration, and local cell-cell interactions. Such an integrated perspective of these key aspects will be critical to open up new directions in tissue engineering research, as significant progress can be made by combining existing computational and experimental methods. Furthermore, theoretical modelling has enormous potential in applications ranging from the interpretation of experimental results and the identification of the main governing processes, to the optimization of practical tissue engineering protocols with implications therein for an increasing ageing population.

Animals↗
PubMed1996

Theoretical neurobiology and schizophrenia.

This chapter addresses the idea that schizophrenia is a 'disconnection syndrome' from a theoretical and computational perspective. The distinction between anatomical and functional connectivity is reviewed and used as a framework to introduce empirical and computational evidence that schizophrenia involves, at some level, a disintegration of neuronal interactions. The chapter concludes with an example of computational neuroscience that relates observations on the dimensional complexity of neuronal dynamics in schizophrenia to the disconnection hypothesis.

Brain↗
PubMed2006

The interplay of the 3d9 and 3d10L electronic configurations in the copper K-edge XANES spectra of Cu(II) compounds.

A theoretical analysis of the X-ray absorption near-edge structure spectra at the Cu K-edge in several divalent copper [Cu(II)] compounds showing a distorted nearest-neighborhood around copper is presented. The experimental spectra of CuO and KCuF(3) have been compared with computations performed in the framework of the multiple-scattering theory. The results show that ab initio single-channel multiple-scattering calculations are not able to reproduce the experimental spectra. On the contrary, the experimental spectra can be accounted for by using two excitation channels and the sudden limit of the multichannel multiple-scattering theory. The comparison between experimental data and computations indicates that both 3d(9) and 3d(10)L electronic configurations are needed to account for the absorption process in these systems, suggesting that this is the general case for the K-edge XANES of divalent copper compounds.

Computer Simulation↗
PubMed2025

scnanoseq: an nf-core pipeline for Oxford Nanopore single-cell RNA-sequencing.

MOTIVATION: Recent advancements in long-read single-cell RNA sequencing (scRNA-seq) have facilitated the quantification of full-length transcripts and isoforms at the single-cell level. Historically, long-read data would need to be complemented with short-read single-cell data in order to overcome the higher sequencing errors to correctly identify cellular barcodes and unique molecular identifiers. Improvements in Oxford Nanopore sequencing, and development of novel computational methods have removed this requirement. Though these methods now exist, the limited availability of modular and portable workflows remains a challenge. RESULTS: Here, we present, nf-core/scnanoseq, a secondary analysis pipeline for long-read single-cell and single-nuclei RNA that delivers gene and transcript-level quantification. The scnanoseq pipeline is implemented using Nextflow and is built upon the nf-core framework, enabling portability across computational environments, scalability and reproducibility of results across pipeline runs. The nf-core/scnanoseq workflow follows best practices for analyzing single-cell and single-nuclei data, performing barcode detection and correction, genome and transcriptome read alignment, unique molecular identifier deduplication, gene and transcript quantification, and extensive quality control reporting. AVAILABILITY AND IMPLEMENTATION: The source code, and detailed documentation are freely available at https://github.com/nf-core/scnanoseq and https://nf-co.re/scnanoseq under the MIT License. Documentation for the version of nf-core/scnanoseq used for this paper, including default parameters and descriptions of output files are available at https://nf-co.re/scnanoseq/1.1.0.

Single-Cell Analysis↗
PubMed2004

The RUMBA software: tools for neuroimaging data analysis.

The enormous scale and complexity of data sets in functional neuroimaging makes it crucial to have well-designed and flexible software for image processing, modeling, and statistical analysis. At present, researchers must choose between general purpose scientific computing environments (e.g., Splus and Matlab), and specialized human brain mapping packages that implement particular analysis strategies (e.g., AFNI, SPM, VoxBo, FSL or FIASCO). For the vast majority of users in Human Brain Mapping and Cognitive Neuroscience, general purpose computing environments provide an insufficient framework for a complex data-analysis regime. On the other hand, the operational particulars of more specialized neuroimaging analysis packages are difficult or impossible to modify and provide little transparency or flexibility to the user for approaches other than massively multiple comparisons based on inferential statistics derived from linear models. In order to address these problems, we have developed open-source software that allows a wide array of data analysis procedures. The RUMBA software includes programming tools that simplify the development of novel methods, and accommodates data in several standard image formats. A scripting interface, along with programming libraries, defines a number of useful analytic procedures, and provides an interface to data analysis procedures. The software also supports a graphical functional programming environment for implementing data analysis streams based on modular functional components. With these features, the RUMBA software provides researchers programmability, reusability, modular analysis tools, novel data analysis streams, and an analysis environment in which multiple approaches can be contrasted and compared. The RUMBA software retains the flexibility of general scientific computing environments while adding a framework in which both experts and novices can develop and adapt neuroimaging-specific analyses.

Algorithms↗
PubMed2005

A risk-based approach to land-use planning.

The Seveso II-Directive requires that the objectives of preventing major accidents and limiting their consequences be taken into account by the Member States in their land-use policies and/or other relevant policies. This is to be achieved by ensuring adequate distances between industrial establishments and residential areas, areas of public use and areas of particular natural sensitivity or interest. A risk-based framework implemented in a computer program is presented which enables one to calculate adequate distances. The criterion used is a limit on the individual risk of death. The method is a simplified risk analysis which represents the plant, whose characteristics are normally unknown at the stage of land-use planning, by generic frequencies of release for process units and storage tanks. Their number depends on the size of the site to be allotted. The procedure is capable of addressing the siting of new establishments and, with due regard to the simplifications used, modifications to and new developments in the vicinity of existing establishments. Given the numerous assumptions, which have to be made, the framework represents a convention.

Accident Prevention↗
PubMed1999

A multi-differential neuromorphic approach to motion detection.

This paper presents a multi-differential neuromorphic approach to motion detection. The model is based evidence for a differential operators interpretation of the properties of the cortical motion pathway. We discuss how this strategy, which provides a robust measure of speed for a range of types of image motion using a single computational mechanism, forms a useful framework in which to develop future neuromorphic motion systems. We also discuss both our approaches to developing computational motion models, and constraints in the design strategy for transferring motion models to other domains of early visual processing.

Animals↗
PubMed1986

Computing with neural circuits: a model.

A new conceptual framework and a minimization principle together provide an understanding of computation in model neural circuits. The circuits consist of nonlinear graded-response model neurons organized into networks with effectively symmetric synaptic connections. The neurons represent an approximation to biological neurons in which a simplified set of important computational properties is retained. Complex circuits solving problems similar to those essential in biology can be analyzed and understood without the need to follow the circuit dynamics in detail. Implementation of the model with electronic devices will provide a class of electronic circuits of novel form and function.

Action Potentials↗