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PubMed1999

A software agent model of consciousness.

Baars (1988, 1997) has proposed a psychological theory of consciousness, called global workspace theory. The present study describes a software agent implementation of that theory, called "Conscious" Mattie (CMattie). CMattie operates in a clerical domain from within a UNIX operating system, sending messages and interpreting messages in natural language that organize seminars at a university. CMattie fleshes out global workspace theory with a detailed computational model that integrates contemporary architectures in cognitive science and artificial intelligence. Baars (1997) lists the psychological "facts that any complete theory of consciousness must explain" in his appendix to In the Theater of Consciousness; global workspace theory was designed to explain these "facts." The present article discusses how the design of CMattie accounts for these facts and thereby the extent to which it implements global workspace theory.

Cognition↗

PubMed1994

Evaluation of the exon predictions of the GRAIL software.

Identification of transcribed sequences within genomic regions has been a major rate-limiting step in the pursuit of genes. We have tested the ability of GRAIL 1 and GRAIL 2 to locate coding exons in the 41 longest human genomic sequences available in release 38 of the EMBL database. Of the total annotated exons GRAIL 1 correctly identified 68% of coding exons. GRAIL 2 correctly identified 71%. Of the 686 predictions made by GRAIL 1, 46.4% did not correspond to an annotated exon. The corresponding figures for GRAIL 2 were 556 and 30.5%. The GRAIL 2 software predicted as excellent a significantly higher proportion of the coding exons than did GRAIL 1, and also gave a significantly lower figure for false predictions. GRAIL 2 thus represents a significant improvement over GRAIL 1.

Exons↗

PubMed2001

Methodology used for "software for automated linkage in Italy" (SALI).

Linkage of epidemiological registries can provide cost-effective information on the associations between different diseases or exposures in the population under study and on completeness of surveillance system databases. We describe the program SALI (software for automated linkage in Italy) aimed at matching individual records from medium-sized registries (in the order of 100,000 records), where the desired outcome is to miss as few links as possible and, because of low link-likelihood (< 1%), a manual revision of matched pairs is feasible. SALI, developed in CA-Clipper language, uses registry files in dBase format. It requires only name, surname, and date of birth as key fields, and it allows for spelling errors in Italian or other Latin languages through a specific algorithm. Furthermore, a double-blind procedure ensures data confidentiality. The main linkage procedure is based on four stages, two automatic ones, and two where the operator can decide through specific windows whether to accept stage-selected matches. SALI takes into account possible errors in key fields thus reducing false negatives. It was used to solve the problem of linkage between AIDS and cancer registries in Italy. It can be used with every IBM-compatible computer system, assuring uniquely high portability.

Acquired Immunodeficiency Syndrome↗

PubMed1999

The SPORT-NMR software: a tool for determining relaxation times in unresolved NMR spectra.

A software package which allows the correct determination of individual relaxation times for all the nonequivalent nuclei in poorly resolved NMR spectra is described. The procedure used, based on the fitting of each spectrum in the series recorded in the relaxation experiment, should improve the analysis of relaxation data in terms of quantitative dynamic information, especially in anisotropic phases. Tests on simulated data and experimental examples concerning 1H and 13C T1rho measurement in a solid copolymer and 2H T1Z and T1Q measurement in a liquid crystal are shown and discussed.

Anisotropy↗

PubMed1999

Lineshape calculations on spreadsheet software.

Spectral lineshapes reflecting slow molecular reorientation are calculated by a simplified numeric approach based on the stochastic Liouville equation. The relevant reorientation process is described by a stationary Markov operator which is, using a finite grid point method, represented by a matrix with a dimension equivalent to the number of orientational sites. A differential equation for the time evolution of the density matrix allows the development of the overall magnetization to be calculated in consecutive time steps. For increased convenience and flexibility, the algorithm can be installed using commercial spreadsheet software on a regular personal computer.

Algorithms↗

PubMedDate not supplied

SUPRIM: easily modified image processing software.

A flexible, modular software package intended for the processing of electron microscopy images is presented. The system consists of a set of image processing tools or filters, written in the C programming language, and a command line style user interface based on the UNIX shell. The pipe and filter structure of UNIX and the availability of command files in the form of shell scripts eases the construction of complex image processing procedures from the simpler tools. Implementation of a new image processing algorithm in SUPRIM may often be performed by construction of a new shell script, using already existing tools. Currently, the package has been used for two- and three-dimensional image processing and reconstruction of macromolecules and other structures of biological interest.

Computer Simulation↗

PubMedDate not supplied

Automated software package for icosahedral virus reconstruction.

The three-dimensional reconstruction of icosahedral viruses from electron micrograph images has become an important tool for understanding virus structure, function, and pathogenesis. We have developed an integrated suite of software programs to automate most of the operations involved in producing these reconstructions from EM images. Our package combines the analytical capabilities of preexisting algorithms together with approaches we have developed to produce an interactive working environment which enhances the efficiency and usefulness of this approach to the structural analysis of icosahedral viruses.

Algorithms↗

PubMedDate not supplied

Software for 3-D reconstruction from images of oblique sections through 3-D crystals.

Oblique section reconstruction can produce a 3-D image from electron micrographs of a sectioned crystal when the orientation of the section plane is not aligned with the principal planes of the unit cell. We describe here the reconstruction protocol and the specialized computer software for a Fourier space method that can extract 3-D information from 2-D projection images of oblique sections. The protocol encompasses correction for image defects and image distortions, determination and refinement of reciprocal lattices, calculation of the crystal orientation in 3-D space, extraction of periodic information, alignment in Fourier space, determination and deconvolution of section thickness, and calculation of structure factors of the original crystal. A 3-D map of the unit cell can then be computed by standard crystallographic procedures. Oblique section reconstruction provides an alternative to tomography for 3-D imaging of crystalline objects with large unit cells. The method provides an excellent means of obtaining a 3-D transform using electron microscopy for comparison with X-ray diffraction data from native specimens.

Computer Simulation↗

PubMed1997

IRIS explorer software for radial-depth cueing reovirus particles and other macromolecular structures determined by cryoelectron microscopy and image reconstruction.

Structures of biological macromolecules determined by transmission cryoelectron microscopy (cryo-TEM) and three-dimensional image reconstruction are often displayed as surface-shaded representations with depth cueing along the viewed direction (Z cueing). Depth cueing to indicate distance from the center of virus particles (radial-depth cueing, or R cueing) has also been used. We have found that a style of R cueing in which color is applied in smooth or discontinuous gradients using the IRIS Explorer software is an informative technique for displaying the structures of virus particles solved by cryo-TEM and image reconstruction. To develop and test these methods, we used existing cryo-TEM reconstructions of mammalian reovirus particles. The newly applied visualization techniques allowed us to discern several new structural features, including sites in the inner capsid through which the viral mRNAs may be extruded after they are synthesized by the reovirus transcriptase complexes. To demonstrate the broad utility of the methods, we also applied them to cryo-TEM reconstructions of human rhinovirus, native and swollen forms of cowpea chlorotic mottle virus, truncated core of pyruvate dehydrogenase complex from Saccharomyces cerevisiae, and flagellar filament of Salmonella typhimurium. We conclude that R cueing with color gradients is a useful tool for displaying virus particles and other macromolecules analyzed by cryo-TEM and image reconstruction.

Animals↗

PubMed2026

High-Plex Tissue Imaging with Conventional Immunofluorescence Platforms and Open-Source Software via Iterative Bleaching Extends Multiplexity (IBEX).

Iterative bleaching extends multiplexity (IBEX) is an easy-to-use, highly multiplex immunofluorescent tissue imaging method that employs widely available microscopy platforms, commercial reagents, and open-source software. In this article, we describe how to implement this method in a laboratory that has minimal experience with immunohistochemistry.

Software↗

PubMed1998

Developing and testing integrated multicompartment models to describe a single-input multiple-output study using the SAAM II software system.

As measurement devices become more sophisticated, it is possible to design more complex input-output studies, i.e., studies where data are obtained from several sites in the system under study. To interpret the resulting data requires models which can integrate known information about the system under study while simultaneously describing the data. In this chapter, we will illustrate how to develop and test a model structure for a single-input multiple-output study using the SAAM II software system. This system has been designed to make the use of sound modeling principles easy. It will be assumed that a known amount of a radiolabeled substance was injected as a bolus into plasma, that this substance can bind to and be taken up by red cells, that its only route of elimination is through the urine, and that external measurements are possible over a target organ. The steps in developing a model structure will make use of SAAM II's forcing function capability to show how the system can be decoupled; this will permit us to postulate model structures for the various subsystems accessible to measurement. We will then show how to use this information to postulate a model describing all the data, and how to test this model structure. This will permit us to comment on those parts of the system not accessible for experimental measurement. We will end with a general discussion of how to test for goodness-of-fit and model order.

Computer Simulation↗

PubMed1998

Compartmental models: theory and practice using the SAAM II software system.

Understanding in vivo the functioning of metabolic systems at the whole-body or regional level requires one to make some assumptions on how the system works and to describe them mathematically, that is, to postulate a model of the system. Models of systems can have different characteristics depending on the properties of the system and the database available for their study; they can be deterministic or stochastic, dynamic or static, with lumped or distributed parameters. Metabolic systems are dynamic systems and we focus here on the most widely used class of dynamic (differential equation) models: compartmental models. This is a class of models for which the governing law is conservation of mass. It is a very attractive class to users because it formalizes physical intuition in a simple and reasonable way. Compartmental models are lumped parameter models, in that the events in the system are described by a finite number of changing variables, and are thus described by ordinary differential equations. While stochastic compartment models can also be defined, we discuss here the deterministic versions--those that can work with exact relationships between model variables. These are the models most widely used in discussions of endocrinology and metabolism. In this chapter, we will discuss the theory of compartmental models, and then discuss how the SAAM II software system, a system designed specifically to aid in the development and testing of multicompartmental models, can be used.

Blood Glucose↗

PubMed1994

Evaluation of an algorithm for the automated sequential assignment of protein backbone resonances: a demonstration of the connectivity tracing assignment tools (CONTRAST) software package.

The peptide sequential assignment algorithm presented here was implemented as a macro within the CONnectivity TRacing ASsignment Tools (CONTRAST) computer software package. The algorithm provides a semi- or fully automated global means of sequentially assigning the NMR backbone resonances of proteins. The program's performance is demonstrated here by its analysis of realistic computer-generated data for IIIGlc, a 168-residue signal-transducing protein of Escherichia coli [Pelton et al. (1991) Biochemistry, 30, 10043-10057]. Missing experimental data (19 resonances) were generated so that a complete assignment set could be tested. The algorithm produces sequential assignments from appropriate peak lists of nD NMR data. It quantifies the ambiguity of each assignment and provides ranked alternatives. A 'best first' approach, in which high-scoring local assignments are made before and in preference to lower scoring assignments, is shown to be superior (in terms of the current set of CONTRAST scoring routines) to approaches such as simulated annealing that seek to maximize the combined scores of the individual assignments. The robustness of the algorithm was tested by evaluating the effects of imposed frequency imprecision (scatter), added false signals (noise), missing peaks (incomplete data), and variation in user-defined tolerances on the performance of the algorithm.

Algorithms↗

PubMed1984

Software correction of scatter coincidence in positron CT.

This paper describes a software correction of scatter coincidence in positron CT which is based on an estimation of scatter projections from true projections by an integral transform. Kernels for the integral transform are projected distributions of scatter coincidences for a line source at different positions in a water phantom and are calculated by Klein-Nishina's formula. True projections of any composite object can be determined from measured projections by iterative applications of the integral transform. The correction method was tested in computer simulations and phantom experiments with Positologica. The results showed that effects of scatter coincidence are not negligible in the quantitation of images, but the correction reduces them significantly.

Models, Structural↗

PubMed1994

Software sensors for the monitoring of perfusion cultures: evaluation of the hybridoma density and the medium composition from glucose concentration measurements.

New software sensors based on the Extended Kalman Filter technique have been developed for the monitoring of animal cell perfusion cultures. They use a kinetic model describing the growth, death and metabolism of hybridoma cells as a function of the medium composition. The model was initially validated on a batch culture and found to correctly predict the continuous perfusion culture kinetics, except for the production of ammonia and lactate. Using the measurement of a single component in the culture medium, in this case glucose, the Extended Kalman Filter provides an excellent evaluation of the time variation of the concentrations of living and dead cells, of glutamine and antibodies, during the whole perfusion culture for a retained cell density rising from 1 to 11 x 10(6) cells.ml-1 inside the reactor.

Algorithms↗

PubMed1994

Postmortem validation of the automated coronary analysis (ACA) software package.

Goal of this study was to compare the quantitative coronary arteriographic (QCA) results obtained with the Philips DCI/ACA analytical software package with those from postmortem casts in an animal experimental setting. Standard digital coronary arteriograms were obtained from 6 mongrel dogs. After the imaging procedure, the dogs were sacrificed and casts were made of the coronary trees by filling the vessels with a mixture of radio-opaque barium and silicone gel at a fixed pressure of 100 mmHg. Vessel diameters were measured from the digital arteriograms at a total of 118 selected locations with the ACA package. Thin slices were cut from the casts at these same measurement locations and the areas of the cross sections were obtained by manual tracing of the outline of each slice in an approximately 40 x magnified image. From these cross-sectional areas, cast diameters were derived using the formula for circular cross-sections. Cast diameters ranged in size from 0.69 to 3.30 mm. The systematic error between the measurements was found to be 0.058 mm; (p < 0.015) and the standard deviation of the signed difference 0.255 mm; the correlation coefficient was r = 0.91. The largest error sources are supposed to be the slight differences in the selection of identical positions in the X-ray images and on the casts, and the 'out-of-plane' magnification for a number of vessel locations. This postmortem study demonstrates that the diameters of coronary vessels can be measured from digital arteriograms with the DCI/ACA package with a high degree of accuracy and precision.

Animals↗

PubMed1992

Real-time respiratory monitoring workstation--software and hardware engineering aspects.

We have applied advanced real-time techniques in software, that are intensively used in critical areas like space research and defence applications, to realise an Integrated Real-Time Respiratory Monitoring System at the Thorax Anesthesiology, Academic Hospital Rotterdam. The system is called the 'SERVO WINDOW'--a window to the servo ventilator. The heart of the system is a real-time kernel that uses preemptive scheduling to achieve multitasking on a IBM PC compatible hardware platform. To the clinician this means that he gets all relevant information from one source i.e. the Respiratory Workstation. The waveforms of the airway pressure, airway flow and the expired CO2 curve are displayed continuously on the screen. The Vector Loops like Pressure Volume, Flow Pressure and Flow Volume loops are also available in addition to the lung mechanics parameters like Expiratory and Inspiratory Resistances, Compliances, Peak Pressure, PEEP, etc. The Single Breath Diagram i.e. expired CO2 concentration versus volume and dead space ventilation is also calculated. The blood gas analysis data is plotted in convenient diagrams like the O2-CO2 diagram, Oxygen Chart, etc. The trend of all these parameters are available with a granularity of one minute. An industry standard laser printer is used for report generation to produce reports of the real-time waveforms, parameter values and the trends. User interface is through easy menus with the traditional keyboard, touchscreen including keyboard on screen for data entry and the mouse.

Computer Systems↗

PubMed1996

A complete computer monitoring and control system using commercially available, configurable software for laboratory and pilot plant Escherichia coli fermentations.

The advent of inexpensive computers and associated control and data acquisition software makes possible the development of sophisticated, configurable, integrated monitoring and control systems for small-scale laboratory and pilot-scale fermentors at low cost. We describe here the implementation of such a system, the interfacing of off-line instruments to enhance real time data analysis, low level process control and several substrate feeding protocols.

Ammonia↗