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At least 1,801 records · Page 100Linked to original sources
PubMed2004

POSEIDON/RODOS models for radiological assessment of marine environment after accidental releases: application to coastal areas of the Baltic, Black and North Seas.

In the framework of the developments of the European system RODOS (Real-time On-line DecisiOn support System) for emergency response to nuclear accident, the computer code POSEIDON, that was developed to assess the radiological consequences of radioactive releases into marine environment, was adapted to cope with emergency conditions, in situations of radioactive discharges into the oceans from direct deposition from the atmosphere, sunken ships and containers, from discharges of rivers and estuaries and from coastal run-off. Based on the box model developed within the 'Marina' project, POSEIDON can calculate the dose effects from radionuclide releases in the coastal waters of Europe integrated over long time periods. A dynamic food chain model was implemented to deal with the short-term dynamical uptake of radioactivity by specific marine plants and organisms. POSEIDON has been installed on a UNIX platform to be fully compatible with RODOS input/output databases and on a Windows platform with an interface based on web technology. The 3D hydrodynamic model THREETOX is a part of the POSEIDON/RODOS system. It has been applied to coastal areas of the Baltic Sea, the Black Sea, and the North Sea. to derive the parameters for a flexible system of well-defined model compartments to be adapted to emergency conditions. The activity concentrations in water and in the marine food web were calculated by means of POSEIDON for radioactive fallout resulting from bomb testing, from the Chernobyl accident, and from routine discharges from nuclear facilities. POSEIDON's model results were compared with measurement data, and with calculation results from THREETOX. The model results agreed with the measurement data sufficiently.

Animals↗
PubMed2006

Quantum trajectory dynamics in arbitrary coordinates.

The quantum trajectory approach is generalized to arbitrary coordinate systems, including curvilinear coordinates. This allows one to perform an approximate quantum trajectory propagation, which scales favorably with system size, in the same framework as standard quantum wave packet dynamics. The trajectory formulation is implemented in Jacobi coordinates for a nonrotating triatomic molecule. Wave packet reaction probabilities are computed for the O(3P) + H2 --> OH + H reaction using the approximate quantum potential. The latter is defined by the nonclassical component of the momentum operator expanded in terms of linear and exponential functions. Unlike earlier implementations with linear functions, the introduction of the exponential function provides an accurate description of asymptotic dynamics for this system and gives good agreement of approximate reaction probabilities with accurate quantum calculations.

Journal Article↗
PubMed2002

Neural systems involved in "theory of mind".

What is the nature of our ability to understand and reason about the beliefs of others--the possession of a "theory of mind", or ToM? Here, we review findings from imaging and lesion studies indicating that ToM reasoning is supported by a widely distributed neural system. Some functional components of this system, such as language-related regions of the left hemisphere, the frontal lobes and the right temporal parietal cortex, are not solely dedicated to the computation of mental states. However, the system also includes a core, domain-specific component that is centred on the amygdala circuitry. We provide a framework in which impairments of ToM can be viewed in terms of abnormalities of the core system, the failure of a co-opted system that is necessary for performance on a particular set of tasks, or the absence of an experiential trigger for the emergence of ToM.

Amygdala↗
PubMed1998

Instability of signaling resolution models of parent-offspring conflict.

Recent signaling resolution models of parent-offspring conflict have provided an important framework for theoretical and empirical studies of communication and parental care. According to these models, signaling of need is stabilized by its cost. However, our computer simulations of the evolutionary dynamics of chick begging and parental investment show that in Godfray's model the signaling equilibrium is evolutionarily unstable: populations that start at the signaling equilibrium quickly depart from it. Furthermore, the signaling and nonsignaling equilibria are linked by a continuum of equilibria where chicks above a certain condition do not signal and we show that, contrary to intuition, fitness increases monotonically as the proportion of young that signal decreases. This result forces us to reconsider much of the current literature on signaling of need and highlights the need to investigate the evolutionary stability of signaling equilibria based on the handicap principle.

Animals↗
PubMed2004

Analyzing incomplete longitudinal clinical trial data.

Using standard missing data taxonomy, due to Rubin and co-workers, and simple algebraic derivations, it is argued that some simple but commonly used methods to handle incomplete longitudinal clinical trial data, such as complete case analyses and methods based on last observation carried forward, require restrictive assumptions and stand on a weaker theoretical foundation than likelihood-based methods developed under the missing at random (MAR) framework. Given the availability of flexible software for analyzing longitudinal sequences of unequal length, implementation of likelihood-based MAR analyses is not limited by computational considerations. While such analyses are valid under the comparatively weak assumption of MAR, the possibility of data missing not at random (MNAR) is difficult to rule out. It is argued, however, that MNAR analyses are, themselves, surrounded with problems and therefore, rather than ignoring MNAR analyses altogether or blindly shifting to them, their optimal place is within sensitivity analysis. The concepts developed here are illustrated using data from three clinical trials, where it is shown that the analysis method may have an impact on the conclusions of the study.

Antidepressive Agents↗
PubMed2026

CamK-DB: A k-mer MinHash fingerprint database for reference-free genotyping of Camellia accessions.

Tea (Camellia sinensis L.), a major global economic crop in Asia, poses challenges for genetic identification because its highly heterozygous, repetitive genome reduces the efficacy of conventional single-nucleotide polymorphism (SNP) and microsatellite markers, and interspecific hybridization further complicates the situation. To address these issues, CamK-DB was developed as a reference-free Camellia fingerprinting database built on MIKE MinHash sketches. We curated 418 candidate resequencing datasets, and built a database using standardized 5× genome-coverage fingerprints. Each accession is stored as a MIKE. jac fingerprint generated with k = 21 and recommended sketch/pre_cnt = 2000. CamK-DB provides a command-line interface for data management and a custom C++ query engine that computes top-10 matches using Jaccard similarity, complemented by a QT-based graphical interface for interactive analysis. This resource offers a robust and scalable framework for precise and routine germplasm identification, genomic phylogenetic inference, and strategic breeding program design. CamK-DB (database and code) is publicly available at https://github.com/sc-zhang/CamK-DB. CamK-DB binaries are provided for Windows 10/11 and Linux (x86_64, glibc ≥ 2.27).

Databases, Genetic↗
PubMed1986

Binomial regression in GLIM: estimating risk ratios and risk differences.

Although an estimate of the odds ratio adjusted for other covariates can be obtained by logistic regression, until now there has been no simple way to estimate other interesting parameters such as the risk ratio and risk difference multivariately for prospective binomial data. These parameters can be estimated in the generalized linear model framework by choosing different link functions or transformations of binomial or binary data. Macros for use with the program GLIM provide a simple method to compute parameters other than the odds ratio while adjusting for confounding factors. A data set presented previously is used as an example.

Biometry↗
PubMed2004

Network transitivity and matrix models.

This paper is a step towards a systematic theory of the transitivity (clustering) phenomenon in random networks. A static framework is used, with adjacency matrix playing the role of the dynamical variable. Hence, our model is a matrix model, where matrices are random, but their elements take values 0 and 1 only. Confusion present in some papers where earlier attempts to incorporate transitivity in a similar framework have been made is hopefully dissipated. Inspired by more conventional matrix models, analytic techniques to develop a static model with nontrivial clustering are introduced. Computer simulations complete the analytic discussion.

Cluster Analysis↗
PubMed1999

Alignment of adjacent picture frames captured by a CLSM.

Mosaicking a picture from its adjacent parts (called picture frames or tiles) is encountered in different fields of research and technology, e.g., photogrammetry, remote sensing, microscopy, etc. It is applied whenever the object of investigation is too large for the field of view of the sensor, e.g. a microscope. We describe mosaicking with a confocal laser-scanning microscope (CLSM) Bio-Rad, MRC 600 (U.K.). Aligning neighboring picture tiles was accomplished by registering the overlapped border areas of these tiles. Such registration procedures are constrained by: 1) the limited size of the registered samples (windows); 2) anisotropy of the form of the windows (usually narrow rectangles); and 3) the content of the windows, including changes of their intensity scale. Focusing on the latter problem, methods of registration were discussed and the robustness of the following three similarity based methods was studied with regard to the distortions of the intensity scales of the tiles to be registered: 1) the sum of absolute valued differences (SAVD); 2) normalized correlation coefficient (NCC); and 3) the mutual information function (MIF). Pilot experiments were extended to three-dimensional (3-D) stacks of pictures encountered in the framework of 3-D object rendering and visualization. MIF was found in most cases to be the most robust; however, it also demanded the most computational power. It is discussed how to choose a cost-effective method of the registration with regard to the content (texture, contrast, intensity scale distortion) of the tiles.

Microscopy, Confocal↗
PubMed2006

GVF-based anisotropic diffusion models.

In this paper, the gradient vector flow fields are introduced in image restoration. Within the context of flow fields, the shock filter, mean curvature flow, and Perona-Malik equation are reformulated. Many advantages over the original models can be obtained; these include numerical stability, large capture range, and high-order derivative estimation. In addition, a fairing process is introduced in the anisotropic diffusion, which contains a fourth-order derivative and is reformulated as the intrinsic Laplacian of curvature under the level set framework. By applying this fairing process, the shape boundaries will become more apparent. In order to overcome numerical errors, the intrinsic Laplacian of curvature is computed from the gradient vector flow fields instead of the observed images.

Algorithms↗
PubMed2005

Molecular modelling of the androgen receptor axis: rational basis for androgen receptor intervention in androgen-independent prostate cancer.

Androgen depletion in combination with antiandrogenic agents is initially highly effective for treating prostate cancer, and is the recommended treatment for more advanced or higher-grade tumours. However, many tumours eventually become insensitive to androgens, even though the androgen receptor (AR) continues to be expressed. Computational chemistry combined with structural analysis of nuclear receptors and determination of binding affinities of natural and designed coregulators (coactivators and corepressors) provides the theoretical framework for the rational design of novel therapeutic agents directed at the AR. Adding alternative groups to various sites throughout the receptor can alter the conformation of the molecule and its functional binding with coactivators or corepressors. Possible molecules can be identified thoroughly and systematically using intelligent high-throughput screening and FASTrack chemistry (three-dimensional crystallography). Applying these techniques should eventually result in therapeutic agents for androgen-independent prostate cancer that can block binding of AR coactivators while simultaneously increasing binding of AR corepressors.

Androgen Antagonists↗
PubMed1992

Gay and lesbian educators: past history/future prospects.

Although lesbians and gay men in education have been an invisible population, modern computer information retrieval techniques provided a mechanism to investigate the history of case law on gay and lesbian teacher dismissal and credential revocation. This legal framework was then augmented by social history gathered from newspapers and articles, and interviews with the parties involved in the legal or political debates. After presenting a history of the emergence of legal rights and political influence, the author discusses current trends in the employment rights and personal freedoms of gay and lesbian educators.

Adult↗
PubMed2003

Scattering mueller matrix of an ensemble of variously shaped small particles.

A description is given of an analytical solution to the scattering Mueller matrix of an ensemble of small particles that may be of different shape, size, composition, and structure. It is derived within the framework of the generalized multiparticle Mie solution (GMM). Provided that all individual T matrices of a group of particles are known analytically or can be computed accurately, light scattering by an arbitrary configuration of these particles can be predicted precisely for both fixed and random orientations. In practical implementations, the applicability of the solution is limited by the size of individual particles only, and there is no restriction on the overall dimension of an ensemble. This multiparticle-scattering formulation of the GMM has been implemented in several public-domain computer codes. In practical calculations, the maximum total number of particles in an ensemble that can be handled depends on the largest size of the individual components and the availability of computer memory.

Journal Article↗
PubMed2001

Mutation of a single conserved residue in VH complementarity-determining region 2 results in a severe Ig secretion defect.

During an immune response, somatic mutations are introduced into the VH and VL regions of Ig chains. The consequences of somatic mutation in highly conserved residues are poorly understood. Ile51 is present in 91% of murine VH complementarity-determining region 2 sequences, and we demonstrate that single Ile51-->Arg or Lys substitutions in the PCG1-1 Ab are sufficient to severely reduce Ig secretion (1-3% of wild-type (WT) levels). Mutant H chains, expressed in the presence of excess L chain, associate with Ig binding protein (BiP) and GRP94 and fail to form HL and H2L assembly intermediates efficiently. The mutations do not irreversibly alter the VH domain as the small amount of mutant H chain, which assembles with L chain as H2L2, is secreted. The secreted mutant Ab binds phosphocholine-protein with avidity identical with that of WT Ab, suggesting that the combining site adopts a WT conformation. A computer-generated model of the PCG1-1 variable region fragment of Ig (Fv) indicates that Ile51 is buried between complementarity-determining region 2 and framework 3 and does not directly contact the L chain. Thus, the Ile51-->Arg or Ile51-->Lys mutations impair association with the PCG1-1 L chain via indirect interactions. These interactions are in part dependent on the nature of the L chain as the PCG1-1 VH single Ile51-->Arg or Ile51-->Lys mutants were partially rescued when expressed with the J558L lambda1 L chain. These results represent the first demonstration that single somatic mutations in V(H) residues can impair Ig secretion and suggest one reason for the conservation of Ile51 in so many Ig VH.

Amino Acid Sequence↗
PubMed1983

Growing alternatives for computerized pharmacy.

HPI has chosen a unique approach in its computer project development and implementation. It has prioritized financial and distributive pharmacy services incorporated into a mainframe system. This system is intended as a national framework with high flexibility for addition of new services. It is referred to as Patient Records Electronically Prepared (PREP).

California↗
PubMed1995

Use of data abstraction methods to simplify monitoring.

I describe the Temporal Control System (TCS), a programming system designed for building intelligent temporal monitoring programs. The ICU data set provided as part of the 1994 AAAI Spring Symposium challenge is used to conduct several experiments. Empirical results from the ICU data set validate the scalable design of the TCS. The remaining experiments examine the computational problem of generating interval values from sample points through persistent assumptions. Using abstractions in combination with persistence assumptions makes the design of higher-level clinical reasoning programs simpler. Abstraction can be used to suppress clinically unimportant details, allowing an expert system to focus on the key information provided by clinical monitors. The TCS provides the framework for the implementation as well as a method of calculating the 'cost' of different approaches. To prevent the use of outdated information, it is often useful to limit the time span of a persistent interval. I show that such limitations can be very costly computationally and then show how the application of symbolic abstraction can help. Further performance improvements from switching from continuous to discrete step persistence are shown. These performance enhancing techniques have general applicability.

Abstracting and Indexing↗
PubMed1996

The computer-based record: patient moving from concept toward reality.

In 1991 the Institute of Medicine issued a report on improving patient records which has proven to be a landmark for the many individuals and institutions involved in the development of computer-based patient records (CPRs). The report called Computer-based Patient Records: An Essential Technology for Health Care, recommended that CPRs become the primary form for patient records, and urged widespread implementation of CPRs within a decade. It also provides a framework for reviewing the current status of CPRs. In reviewing progress that has been made toward CPRs since the Institute of Medicine (IOM) report was released, it is useful to look beyond the IOM report's major focus on efforts in the USA and include international activities related to CPR development and implementation. Looking forward, CPR efforts are likely to be expedited through greater collaboration.

Computer Communication Networks↗

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