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PubMed2005

Star-branched polymers in an adsorbing slit: a Monte Carlo study.

A coarse-grained model of star-branched polymer chains confined in a slit was studied. The slit was formed by two parallel impenetrable surfaces, which were attractive for polymer beads. The polymer chains were flexible homopolymers built of identical united atoms whose positions in space were restricted to the vertices of a simple cubic lattice. The chains were regular star polymers consisted of f = 3 branches of equal length. The chains were modeled in good solvent conditions and, thus, there were no long-range specific interactions between the polymer beads-only the excluded volume was present. Monte Carlo simulations were carried out using the algorithm based on a chain's local changes of conformation. The influence of the chain length, the distances between the confining surfaces, and the strength of the adsorption on the properties of the star-branched polymers was studied. It was shown that the universal behavior found previously for the dimension of chains was not valid for some dynamic properties. The strongly adsorbed chains can change their position so that they swap between both surfaces with frequency depending on the size of the slit and on the temperature only.

Journal Article↗
PubMed2004

Who gets acknowledged: measuring scientific contributions through automatic acknowledgment indexing.

Acknowledgements in research publications, like citations, indicate influential contributions to scientific work. However, acknowledgements are different from citations; whereas citations are formal expressions of debt, acknowledgements are arguably more personal, singular, or private expressions of appreciation and contribution. Furthermore, many sources of research funding expect researchers to acknowledge any support that contributed to the published work. Just as citation indexing proved to be an important tool for evaluating research contributions, we argue that acknowledgements can be considered as a metric parallel to citations in the academic audit process. We have developed automated methods for acknowledgment extraction and analysis and show that combining acknowledgment analysis with citation indexing yields a measurable impact of the efficacy of various individuals as well as government, corporate, and university sponsors of scientific work.

Abstracting and Indexing↗
PubMedDate not supplied

Concept for an intelligent anaesthesia EEG monitor.

Considering the fundamental difficulties to define the term 'depth of anaesthesia', a more feasible concept for assessment of 'adequacy of anaesthesia' will be explained. The basic requirements for a monitoring index are definite response, gradual scaling and independence from the anaesthetic technique used. Additionally the index should be predictive for appearance of clinical signs of an inadequate anaesthesia. Different signal-processing methods will be discussed to extract the relevant information from both the spontaneous and the evoked brain electrical activity. In this context well established methods like spectral analysis are investigated in combination with new and more sophisticated methods like bispectral analysis or wavelet decomposition. Since no single-parameter index has been defined for monitoring depth of anaesthesia, a set of EEG parameters may be more useful to take into account intra- and interindividual variability. In parallel to the description of the monitor concept, the investigation of neural nets and fuzzy techniques, in addition to or in substitution of conventional statistical methods, will be introduced. Examples are given for data quality assessment, parameter extraction and re-classification.

Algorithms↗
PubMed2004

Sequence analysis and membrane partitioning energies of alpha-helical antimicrobial peptides.

Sequences of 221 alpha-helical antimicrobial peptides (alphaAMPs) were compared and 63-166 of them were selected and analyzed using Perl programs. The results showed that aliphatic amino acids Gly, Leu, Ala, Ile and two positively charged amino acids Lys and Arg were composed of more than 63% of the first 20 residues of alphaAMPs. The weighed mean membrane partitioning energies at positions from 1 to 25 of alphaAMPs were calculated. Profile of the partitioning energies suggests oblique membrane insertion and an amphipathic alpha-helical structure of the N-terminus of alphaAMP (residues from 1 to 13), a bend structure at positions 13 and 14, and a less structured C-terminus that parallels the surface of the membrane. These structural features are in good agreement with the experimentally determined membrane structure of hemagglutinin fusion peptide from influenza virus. We hypothesize that this (N-terminal oblique alpha-helix)-central bend-(C-terminus) could be a common structural motif of membrane-disruptive peptides.

Algorithms↗
PubMed2005

Intensity statistics in twinned crystals with examples from the PDB.

Entries deposited in the Protein Data Bank as of February 2004 for which both model and X-ray data were available were analysed to identify cases of twinning using such simple statistics as the R factor between potential twin-related reflections. Careful consideration of all identified twins showed that in many cases twinning was ignored during structure solution and refinement. Manual analysis of the models showed that twinning often occurs in association with rotational pseudosymmetry parallel to the twinning operator. The coexistence of these two phenomena complicates the detection and diagnostics of twinning using currently available twinning tests. It was concluded that a twinning-detection step should be incorporated in every stage of structure analysis from data acquisition to refinement and validation.

Algorithms↗
PubMed1999

Reliability of measurement of muscle fiber conduction velocity using surface EMG.

Cross-correlating two surface EMG signals detected at two different locations along the path of flow of action potential enables the measurement of the muscle fiber average conduction velocity in those active motor units monitored by the electrodes. The position of the peak of the cross-correlation function is the time delay between the two signals and hence the velocity may be deduced. The estimated velocity using this technique has been observed previously to depend on the location of the electrodes on the muscle surface. Different locations produced different estimates. In this paper we present a measurement system, analyze its inherent inaccuracies and use it for the purpose of investigating the reliability of measurement of conduction velocity from surface EMG. This system utilizes EMG signals detected at a number of locations on the biceps brachii, when under light tension, to look for any pattern of variations of velocity as a function of location and time. It consists of a multi-electrode unit and a set of eight parallel on-line correlators. The electrode unit and the parallel correlators ensure that these measurements are carried out under the same physical and physiological conditions of the muscle. Further, the same detected signals are used in different measurement configurations to try to understand the reasons behind the observed variations in the estimated velocity. The results obtained seem to suggest that there will always be an unpredictable random component superimposed on the estimated velocity, giving rise to differences between estimates at different locations and differences in estimates with time at the same location. Many factors contribute to this random component, such as the non-homogeneous medium between the muscle fibers and the electrodes, the non-parallel geometry and non-uniform conduction velocity of the fibers, and the physical and physiological conditions of the muscle. While it is not possible to remove this random component completely from the measurement, the user must be aware of its presence and how to reduce its effects.

Action Potentials↗
PubMed2000

Animat navigation using a cognitive graph.

This article describes a computational model of the hippocampus that makes it possible for a simulated rat to navigate in a continuous environment containing obstacles. This model views the hippocampus as a "cognitive graph", that is, a hetero-associative network that learns temporal sequences of visited places and stores a topological representation of the environment. Calling upon place cells, head direction cells, and "goal cells", it suggests a biologically plausible way of exploiting such a spatial representation for navigation that does not require complicated graph-search algorithms. Moreover, it permits "latent learning" during exploration, that is, the building of a spatial representation without the need of any reinforcement. When the rat occasionally discovers some rewarding place it may wish to rejoin subsequently, it simply records within its cognitive graph, through a series of goal and sub-goal cells, the direction in which to move from any given start place. Accordingly, the model implements a simple "place-recognition-triggered response" navigation strategy. Two implementations of place cell management are studied in parallel. The first one associates place cells with place fields that are given a priori and that are uniformly distributed in the environment. The second one dynamically recruits place cells as exploration proceeds and adjusts the density of such cells to the local complexity of the environment. Both implementations lead to identical results. The article ends with a few predictions about results to be expected in experiments involving simultaneous recordings of multiple cells in the rat hippocampus.

Animals↗
PubMed2002

Surveyance of disease frequency in a population by linkage to diagnostic laboratory databases. A system for monitoring the incidences of hyper- and hypothyroidism as part of the Danish iodine supplementation program.

UNLABELLED: In Denmark an increase in iodine intake through salt iodization has been introduced in 1998. In parallel a program for surveyance of thyroid diseases in the population was developed as recommended by UNICEF and WHO. OBJECTIVE: To develop and evaluate a computer based system to identify and register new cases of hyper- and hypothyroidism in a well defined cohort, by linkage to diagnostic laboratory databases. DESIGN AND RESULTS: (1) Two sub cohorts for monitoring were defined (n=535,859), and evaluated to minimize loss of new cases. Collaboration was established with laboratories covering thyroid hormone analyses in the cohort; (2) a diagnostic algorithm was defined and evaluated against clinical practice; (3) evaluation of the laboratory methods employed by the four participating laboratories, to ensure they would reach the same diagnosis in a patient; (4) a register database was developed which used data imported from the laboratory databases to automatically identify previously unknown cases of hyper- and hypothyroidism and record diagnostic activity in the area. All parts of the registration were carefully evaluated. CONCLUSION: We describe for the first time a computer based system for prospective measuring the incidence rate of hyper- and hypothyroidism. The system is particularly useful for monitoring of iodine supplementation programmes.

Databases, Factual↗
PubMed2006

Analysis of four-way two-dimensional liquid chromatography-diode array data: application to metabolomics.

Two-dimensional liquid chromatography (2D-LC) is rapidly gaining popularity for the analysis of very complex mixtures, including proteomic and metabolomic samples. It provides an effective strategy for separating such samples, because the resolving power of 2D-LC is far superior to that of traditional single-dimension separations. The present work focuses on the development of data analysis methods for the extremely large data sets, on the order of 10 million data points, generated by 2D-LC with diode-array detection (DAD). Specifically, we have applied and adapted chemometric methods to the analysis of maize seedling digests, focusing on compounds related to the biosynthetic pathways of indole-3-acetic acid, the primary growth regulator in plants. The chemometric techniques of window target testing factor analysis (WTTFA), along with parallel factor analysis - alternating least squares (PARAFAC-ALS) were used to analyze 2D-LC-DAD chromatograms of a sample composed of 26 indolic standards, 2 extracts of mutant orange pericarp maize seedlings, 2 extracts of wild-type maize seedlings, and a blank sample. The indolic compounds studied belonged to six spectrally unique groups, and WTTFA was able to specifically identify the presence or absence of any of the 26 indolic standards in the mutant and wild-type samples. A PARAFAC-ALS algorithm and an ALS algorithm with flexible constraints were successfully applied to resolve the spectrally rank deficient data and to demonstrate the quantitative potential of multivariate curve resolution methods. Using this procedure, 95 total peaks were resolved in the data set analyzed. Of those 95 peaks, 45 were found in both the mutant and wild-type maize samples, 16 peaks were unique to the mutant maize samples, 13 peaks were unique to the wild-type maize samples, and 15 peaks were unique to the standard chromatograms. Of the 26 standards included in the data set, several indole acetic acid conjugates were identified and quantified in the maize samples at levels of approximately 0.3-2 microg/g plant material.

Algorithms↗
PubMed2004

Vascular flow and perfusion imaging with ultrasound contrast agents.

Current techniques for imaging ultrasound (US) contrast agents (UCA) make no distinction between low-velocity microbubbles in the microcirculation and higher-velocity microbubbles in the larger vasculature. A combination of radiofrequency (RF) and Doppler filtering on a low mechanical index (MI) pulse inversion acquisition is presented that differentiates low-velocity microbubbles (on the order of mm/s) associated with perfusion, from the higher-velocity microbubbles (on the order of cm/s) in larger vessels. In vitro experiments demonstrate the ability to separate vascular flow using both harmonic and fundamental Doppler signals. Fundamental and harmonic Doppler signals from microbubbles using a low-MI pulse-inversion acquisition are compared with conventional color Doppler signals in vivo. Due to the lower transmit amplitude and enhanced backscatter from microbubbles, the in vivo signal to clutter ratios for both the fundamental (-11 dB) and harmonic (-4 dB) vascular flow signals were greater than with conventional power Doppler (-51 dB) without contrast agent. The processing investigated here, in parallel with conventional pulse-inversion processing, enables the simultaneous display of both perfusion and vascular flow. In vivo results demonstrating the feasibility and potential utility of the real-time display of both perfusion and vascular flow using US contrast agents are presented and discussed.

Algorithms↗
PubMed1992

Bacterial monitoring in vials using a spectrophotometric assimilation method.

Aseptic-filling processes are often used with fragile parenteral products that might be destroyed by terminal autoclaving. However, aseptic filling is not as effective as autoclaving in reducing contamination. As a result, time-consuming microbiological methods and turbidimetry are employed currently as product inspection techniques, but these processes can destroy the product and might not detect low levels of contamination. Thus, near-infrared (IR) light scattering was evaluated in this study as a new method for determining low levels of contamination noninvasively and nondestructively. A new parallel mathematical technique was used in conjunction with near-IR spectrophotometry to detect successfully contamination by several species of bacteria through intact glass vials. Using the near-IR method, products can be evaluated without introducing contamination, preserving the sample vial for dispensing or evaluation by another method.

Algorithms↗
PubMed2004

Comparison of the use of liver models for predicting drug clearance using in vitro kinetic data from hepatic microsomes and isolated hepatocytes.

PURPOSE: To compare three liver models (well-stirred, parallel tube, and dispersion) for the prediction of in vivo intrinsic clearance (CL(int)), hepatic clearance (CLh). and hepatic availability (Fh) of a wide range of drugs in the rat using in vitro data from two in vitro sources. METHODS: In vitro CL(int) was obtained from studies using isolated rat hepatocytes (35 drugs) or rat liver microsomes (52 drugs) and used to predict in vivo CL(int) using reported scaling factors, and subsequently CLh and Fh were predicted based on the three liver models. In addition, in vivo CL(int) values were calculated from the reported values of CLh based on each of the three models. RESULTS: For all of the parameters, predictions from hepatocyte data were consistently more accurate than those from microsomal data. Comparison of in vitro and in vivo CL(int) values demonstrated that the dispersion model and the parallel tube model were comparable and more accurate (less bias, more precise) than the well-stirred model. For CLh and Fh prediction, the three models performed similarly. CONCLUSIONS: Considering the statistics of the predictions for three liver models, the use of parallel tube model is recommended for the evaluation of in vitro CL(int) values both from microsomes and hepatocytes. However, for the prediction of the in vivo drug (hepatic) clearance from in vitro data, as there are minimal differences between the models, the use of the well-stirred liver model is recommended.

Algorithms↗
PubMed1997

Dynamics of a pair of spherical gravitating shells.

The dynamical N body problem for a system of mass points interacting solely through gravitational forces is not integrable. The difficulties which arise in constructing accurate numerical codes for simulating the motion over long time scales are legend. Thus, in order to test their theories, astronomers and astrophysicists resort to simpler, one-dimensional models which avoid the problems of binary formation, escape, and the singularity of the inverse square force law. To date, the most frequently employed "test" model consists of a system of parallel mass sheets moving perpendicular to their surface. While this system avoids all of the above problems, the time scale for reaching equilibrium is extremely long and probably arises from the system's weak ergodic properties, which become manifest even in the three sheet system. Here we consider a different one-dimensional gravitating system consisting of nonrotating concentric mass shells. For the case of two shells we investigate the structure of the phase space by studying the stability of periodic trajectories. By employing an event driven algorithm, we are able to directly investigate the influence of the singularity without having to resort to regularization of the force. Although stable structures are present at every energy, we find that the ergodic properties of this system are more robust than its planar counterpart. (c) 1997 American Institute of Physics.

Journal Article↗
PubMed1995

Laser profiling: a technique for the study of prosthetic heart valve leaflet motion.

A detailed understanding of the stresses and strains developed in functioning flexible-leaflet valves is necessary if a durable, non-thrombogenic heart valve replacement is to be realized. A new experimental tool, laser profiling, is presented for the study of flexible-leaflet heart valve dynamics. Profiles of moving leaflet surfaces are obtained by projecting parallel sheets of laser light onto valve leaflets as the valves open and close in a mock circulatory loop. Two versions of laser profiling have been developed. In two-dimensional mode multiple profiles are generated on a fixed plane in space but at discrete intervals in time, whereas in three-dimensional mode multiple profiles are generated across the leaflet surface at (effectively) a single instant in time. Highlighted leaflet profiles are captured by camera and transferred to an image processing system for analysis. A simple algorithm permits digitized profiles to be reconstructed within a computer-aided design software package, providing detailed visualization and quantification of valve motion. Extensive validation studies have been performed using the Medtronic-Hall mechanical prosthetic heart valve. Laser profiling enables computer reconstruction of the rigid occluder to an accuracy of +/- 200 microns from a 0.7 ms exposure taken during the period at which the occluder moves with greatest velocity. The technique has been applied to investigate the leaflet dynamics of a bovine pericardial heart valve prosthesis.

Acoustic Stimulation↗
PubMed2001

Magnetic fields with photon beams: use of circular current loops.

Strong transverse magnetic fields can produce very large dose enhancements and reductions in localized regions of a patient under irradiation by a photon beam. Through EGS4 Monte Carlo simulations, we have examined the effects of applying a magnetic field produced by a pair of circular current loops to a photon beam penetrating a water phantom of finite thickness. We have indeed found very substantial localized dose enhancements, albeit with no corresponding dose reduction just distal to the region of dose enhancement. (However, dose reduction does occur near the distal end of the phantom.) We have also observed two phenomena to be concerned with, for this configuration: significant broadening of the penumbra close to the current loop, and narrowness of the enhanced dose region in a plane parallel to the planes of the loops. We have also examined the use of a single current loop to produce the magnetic field, and have found great asymmetry in the dose distribution; this asymmetry appears to make it impossible to treat with a single circular magnet a tumor of large dimension extending below the application surface.

Algorithms↗
PubMed1992

Combining logistic regression and neural networks to create predictive models.

Neural networks are being used widely in medicine and other areas to create predictive models from data. The statistical method that most closely parallels neural networks is logistic regression. This paper outlines some ways in which neural networks and logistic regression are similar, shows how a small modification of logistic regression can be used in the training of neural network models, and illustrates the use of this modification for variable selection and predictive model building with neural networks.

Algorithms↗
PubMed1990

Intracellular signalling as a parallel distributed process.

Living cells respond to their environment by means of an interconnected network of receptors, second messengers, protein kinases and other signalling molecules. This article suggests that the performance of cell signalling pathways taken as a whole has similarities to that of the parallel distributed process networks (PDP networks) used in computer-based pattern recognition. Using the response of hepatocytes to glucagon as an example, a procedure is described by which a PDP network could simulate a cell signalling pathway. This procedure involves the following steps: (a) a bounded set of molecules is defined that carry the signals of interest; (b) each of these molecules is represented by a PDP-type of unit, with input and output functions and connection weights corresponding to specific biochemical parameters; (c) a "learning algorithm" is applied in which small random changes are made in the parameters of the cell signalling units and the new network is then tested by a selection procedure in favour of a specific input-output relationship. The analogy with PDP networks shows how living cells can recognize combinations of environmental influences, how cell responses can be stabilized and made resistant to damage, and how novel cell signalling pathways might appear during evolution.

Animals↗
PubMed2002

Evaluation of the EGSnrc Monte Carlo code for interface dosimetry near high-Z media exposed to kilovolt and 60Co photons.

High atomic number (Z) heterogeneities in tissue exposed to photons with energies of up to about 1 MeV can cause significant dose perturbations in their immediate vicinity. The recently released Monte Carlo (MC) code EGSnrc (Kawrakow 2000a Med. Phys. 27 485-98) was used to investigate the dose perturbation of high-Z heterogeneities in tissue in kilovolt (kV) and 60Co photon beams. Simulations were performed of measurements with a dedicated thin-window parallel-plate ion chamber near a high-Z interface in a 60Co photon beam (Nilsson et al 1992 Med. Phys. 19 1413-21). Good agreement was obtained between simulations and measurements for a detailed set of experiments in which the thickness of the ion chamber window, the thickness of the air gap between ion chamber and heterogeneity, the depth of the ion chamber in polystyrene and the material of the interface was varied. The EGSnrc code offers several improvements in the electron and photon production and transport algorithms over the older EGS4/PRESTA code (Nelson et al 1985 Stanford Linear Accelerator Center Report SLAC-265. Bielajew and Rogers 1987 Nucl. Instrum. Methods Phys. Res. B 18 165-81). The influence of the new EGSnrc features was investigated for simulations of a planar slab of a high-Z medium embedded in water and exposed to kV or 60Co photons. It was found that using the new electron transport algorithm in EGSnrc, including relativistic spin effects in elastic scattering, significantly affects the calculation of dose distribution near high-Z interfaces. The simulations were found to be independent of the maximum fractional electron energy loss per step (ESTEPE), which was often a cause for concern in older EGS4 simulations. Concerning the new features of the photon transport algorithm sampling of the photoelectron angular distribution was found to have a significant effect, whereas the effect of binding energies in Compton scatter was found to be negligible. A slight dose artefact very close to high-Z interfaces exposed to kilovolt x-rays was discovered when atomic relaxation processes following excitation were omitted.

Algorithms↗