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PubMed2005

Wine distillates: practical operating recipe formulation for stills.

Consumer perceptions of flavors are associated with the chemical composition of foods. However, consumer preferences change; therefore, it is necessary for food manufacturers to be able to adapt their products. Unlike in aged spirits, the chemical composition of young spirits is determined during distillation; therefore, this is where distillers must tailor their operating recipes to the new trends. Even for an experienced distiller, the complexity of the process makes adapting the operating recipe far from straightforward. In this study, we developed a methodology for generating practical recipes that makes use of computer simulations and optimization techniques. We used Pisco Brandy, a young Muscat wine distillate from Chile and Peru as our case study. Even so, because our methodology is independent of the chemical composition of the broth, it can be applied throughout the industry. Drawing on the experience and preferences of industry enologists, we designed a preferred distillate and used our methodology to obtain the appropriate recipe. This recipe was validated in lab scale experiments, and we obtained a much closer distillate to the desired prescription than commercial products.

Alcoholic Beverages↗
PubMedDate not supplied

Computer-assisted 3D analysis of cell distributions in the normal and epileptic cerebral cortex: description of a methodology in progress.

This paper describes software routines that (a) visualizes a stack of several thousands of aligned sequential photographic two-dimensional (2D) images stored in an image processing system; (b) creates a data base containing information about objects identified sequentially from the 2D images; (c) transfers the data base to a graphical terminal; (d) reconstructs a three-dimensional (3D) object space; and (e) supports on-line interaction between the image processing system and the graphical terminal. As an application example, the cell content of a prism of motor cerebral cortex of the cat is reconstructed. Preliminary results from reconstructing human epileptic temporal cortex (cortical microdysgenesia) are also reported.

Adult↗
PubMed1997

An Internet service for manipulating 3D models of human organs reconstructed from computer tomography and magnetic resonance imaging.

Our paper describes an integrated methodology addressing the development of an Internet service for medical professionals, medical students and generally, people interested in medicine. The service (currently developed in the framework of IAEVA, a Telematics Application Programme project of the European Union), incorporates a mechanism for retrieving from a relational database (reference library) 3D volumetric models of human organs reconstructed from computer tomography (CT) and/or magnetic resonance imaging (MRI). Retrieval is implemented in a way transparent to the actual physical location of the database. Prospective users are provided with a Solid Object Viewer that offers them manipulation (rotation, zooming, dissection etc.) of 3D volumetric models. The service constitutes an excellent foundation of understanding for medical professionals/students and a mechanism for broad and rapid dissemination of information related to particular pathological conditions; although pathological conditions of the knee and skin are supported currently, our methodology allows easy service extension into other human organs ultimately covering the entire human body. The service accepts most Internet browsers and supports MS-Windows 32 platforms; no graphics accelerators or any specialised hardware are necessary, thereby allowing service availability to the widest possible audience. Nevertheless, the service operates in near real-time not only over high speed expensive network lines but also over low/medium network connections.

Computer Communication Networks↗
PubMed2004

Assessment of pedicle screw placement utilizing conventional radiography and computed tomography: a proposed systematic approach to improve accuracy of interpretation.

STUDY DESIGN: This was a human cadaver study to determine the accuracy of conventional radiography and computed radiography in the evaluation of pedicle screw placement and to identify methodology for more precise reading of these examinations. OBJECTIVES: To determine the accuracy of conventional radiography and computed tomography in the evaluation of pedicle screw placement within lumbar vertebral pedicles and to develop methods to improve imaging interpretation. SUMMARY OF BACKGROUND DATA: Conventional radiography and computed tomography have been used in research and clinical settings to evaluate pedicle screw placement. This study evaluates the interpretative accuracy of readers blinded to the true position of screw placement using both imaging examinations. Furthermore, methodology was developed to improve accuracy of interpretation of these examinations. METHODS: Three cadaver lumbar spines were instrumented bilaterally with pedicle screws from L1 to L5. Thirty pedicles had 6.0 mm AO pedicle screws inserted using standard surgical technique. Seven directions of deliberate misplacement as well as correct placement of screws were performed at random levels for a total of eight possible screw positions. Conventional radiographs and computed tomography scans were obtained. A senior musculoskeletal radiologist and senior spine surgeon interpreted the images while blinded to screw placement. Examiners initially assessed the screws as in or out, followed by assessment of the eight possible types of screw position. Consensus interpretation was obtained regarding the placement of individual screws. The spines were then dissected to visualize the screws and their position related to the pedicle. After determining the true position of the screws, a systematic method was designed and applied to the interpretation of the imaging methods to identify screw positions. RESULTS: Using conventional radiographs, 63% of the screw placements were correctly identified as in or out of the pedicle. Computed tomography improved accuracy to 87%. Identifying the true directional component of screw position led to a decrease in accuracy (conventional radiographs 37% and computed tomography 47%). Using asystematic method to analyze imaging studies enabled detection of screw positions. CONCLUSION: Evaluation of pedicle screw placement is difficult even in experienced hands. A systematic approach to image interpretation should allow for an accurate assessment of pedicle screw placement.

Aged↗
PubMed2001

Computational neuroanatomy: new perspectives for neuroradiology.

Computational neuroanatomy is emerging as an exciting new methodology to characterise shape and neuroanatomical configuration of different brains. It encompasses a triad of techniques: Voxel-based morphometry (VBM), which compares neuroanatomical differences on a voxel by voxel basis, Deformation-based morphometry (DBM), which provides information about global differences in brain shape and Tensor-based morphometry (TBM) which provides information about local shape differences. This review will describe the methodology and clinical applications of these techniques.

Brain↗
PubMed1993

On the calculation of reference change values, with examples from a long-term study.

Reference change values (sometimes called critical differences) indicate statistically important changes between test values obtained on two occasions. They are commonly computed from the median (or mean) within-subject variance observed in repeated test measurements on a number of subjects. With this computational approach, all observed within-subject variances are assumed to be estimates of a constant true variance, the same for all individuals. Moreover, any possible correlation between successive values is almost always ignored. This simplified methodology differs from the method originally proposed for computing reference change values, which accounts for variability in true variances and for serial correlation. From data obtained from repeated measurements over 2 to 5 years in 72 physically healthy subjects, we computed and compared reference change values in 18 serum analytes, using the simplified method and the originally proposed procedure. Although the original method is more complicated and requires a computer program, we believe that it produces more-reliable reference change values than those obtained by the simplified approach. The former are generally larger, but remain sensitive to clinically important changes in the individual.

Adolescent↗
PubMed2006

A simple linear regression method for quantitative trait loci linkage analysis with censored observations.

Standard quantitative trait loci (QTL) mapping techniques commonly assume that the trait is both fully observed and normally distributed. When considering survival or age-at-onset traits these assumptions are often incorrect. Methods have been developed to map QTL for survival traits; however, they are both computationally intensive and not available in standard genome analysis software packages. We propose a grouped linear regression method for the analysis of continuous survival data. Using simulation we compare this method to both the Cox and Weibull proportional hazards models and a standard linear regression method that ignores censoring. The grouped linear regression method is of equivalent power to both the Cox and Weibull proportional hazards methods and is significantly better than the standard linear regression method when censored observations are present. The method is also robust to the proportion of censored individuals and the underlying distribution of the trait. On the basis of linear regression methodology, the grouped linear regression model is computationally simple and fast and can be implemented readily in freely available statistical software.

Chromosome Mapping↗
PubMed2005

Uncertainty analysis for computer model projections of hurricane losses.

Projecting losses associated with hurricanes is a complex and difficult undertaking that is wrought with uncertainties. Hurricane Charley, which struck southwest Florida on August 13, 2004, illustrates the uncertainty of forecasting damages from these storms. Due to shifts in the track and the rapid intensification of the storm, real-time estimates grew from 2 to 3 billion dollars in losses late on August 12 to a peak of 50 billion dollars for a brief time as the storm appeared to be headed for the Tampa Bay area. The storm hit the resort areas of Charlotte Harbor near Punta Gorda and then went on to Orlando in the central part of the state, with early poststorm estimates converging on a damage estimate in the 28 to 31 billion dollars range. Comparable damage to central Florida had not been seen since Hurricane Donna in 1960. The Florida Commission on Hurricane Loss Projection Methodology (FCHLPM) has recognized the role of computer models in projecting losses from hurricanes. The FCHLPM established a professional team to perform onsite (confidential) audits of computer models developed by several different companies in the United States that seek to have their models approved for use in insurance rate filings in Florida. The team's members represent the fields of actuarial science, computer science, meteorology, statistics, and wind and structural engineering. An important part of the auditing process requires uncertainty and sensitivity analyses to be performed with the applicant's proprietary model. To influence future such analyses, an uncertainty and sensitivity analysis has been completed for loss projections arising from use of a Holland B parameter hurricane wind field model. Uncertainty analysis quantifies the expected percentage reduction in the uncertainty of wind speed and loss that is attributable to each of the input variables.

Journal Article↗
PubMed2004

Using distributed partial memories to improve self-organizing collective movements.

Past self-organizing models of collectively moving "particles" (simulated bird flocks, fish schools, etc.) have typically been based on purely reflexive agents that have no significant memory of past movements. We hypothesized that giving such individual particles a limited distributed memory of past obstacles they encountered could lead to significantly faster travel between goal destinations. Systematic computational experiments using six terrains that had different arrangements of obstacles demonstrated that, at least in some domains, this conjecture is true. Furthermore, these experiments demonstrated that improved performance over time came not only from the avoidance of previously seen obstacles, but also (surprisingly) immediately after first encountering obstacles due to decreased delays in circumventing those obstacles. Simulations also showed that, of the four strategies we tested for removal of remembered obstacles when memory was full and a new obstacle was to be saved, none was better than random selection. These results may be useful in interpreting future experimental research on group movements in biological populations, and in improving existing methodologies for control of collective movements in computer graphics, robotic teams, particle swarm optimization, and computer games.

Algorithms↗
PubMed2006

Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions.

Predictions of the metabolic sites for new chemical entities, synthesized or only virtual, are important in the early phase of drug discovery to guide chemistry efforts in the synthesis of new compounds with reduced metabolic liability. This information can now be obtained from in silico predictions, and therefore, a thorough and unbiased evaluation of the computational techniques available is needed. Several computational methods to predict the metabolic hot spots are emerging. In this study, metabolite identification using MetaSite and a docking methodology, GLUE, were compared. Moreover, the published CYP3A4 crystal structure and computed CYP3A4 homology models were compared for their usefulness in predicting metabolic sites. A total of 227 known CYP3A4 substrates reported to have one or more metabolites adding up to 325 metabolic pathways were analyzed. Distance-based fingerprints and four-point pharmacophore derived from GRID molecular interaction fields were used to characterize the substrate and protein in MetaSite and the docking methodology, respectively. The CYP3A4 crystal structure and homology model with the reactivity factor enabled achieved a similar prediction success (78%) using the MetaSite method. The docking method had a relatively lower prediction success (approximately 57% for the homology model), although it still may provide useful insights for interactions between ligand and protein, especially for uncommon reactions. The MetaSite methodology is automated, rapid, and has relatively accurate predictions compared with the docking methodology used in this study.

Binding Sites↗
PubMed2005

Efficient, accurate calculation of rotational diffusion and NMR relaxation of globular proteins from atomic-level structures and approximate hydrodynamic calculations.

The calculation of the rotational diffusion tensor and NMR relaxation times of quasi-rigid macromolecular structures with atomic detail can be made by means of bead/shell models. The computing time required for calculation of these properties for a single structure using rigorous hydrodynamic methods requires a moderate computing time. In possible applications of the methodology in which such a calculation had to be repeated for many structures, a faster method would be welcome. We have studied the effect of introducing a simplifying approximation in the treatment of hydrodynamic interaction, comparing the rigorous and approximate results for a set of 30 globular proteins. When the NMR relaxation times are combined in some relative form, the rigorous and approximate results are practically coincident. For absolute quantities, such as the correlation time, we find that the bias introduced by the approximation can be closely predicted and corrected. The differences between the results of the approximate-corrected and rigorous procedures are not greater than usual experimental errors, and the typical computing time is reduced from 5 min to 1 s.

Nitrogen Isotopes↗
PubMed1977

Estimation of "safe doses" in carcinogenic experiments.

The statistical methodology for carcinogenic safety testing here developed has the following advantages: (1) Rather than making possibly unwarranted assumptions about a minimum slope in a dose response relationship, the present method represents an objective data based method of estimating "safe" doses. It is applicable to any specified permissible risk (of exceeding the spontaneous rate) and the latter must of course be specified by F.D.A. (2) Although the model which is used for the estimation of safe doses and their lower confidence points is parametric it comprises an adequately large number of parameters to allow for differences in the idiosyncracies of suspected carcinogens, host species and to a limited degree for variations in the experimental protocols. (3) The same computer program will cover the analysis of an experiments in which times to tumor have been recorded as well as experiments in which only tumor incidence rates have been recorded or mixtures of the two. "Better experimentation" is "rewarded" in that the lower confidence limits for the "safe doses" should be higher and more closely approach the true safe dose as the experimental effort increases. (4) The maximum likelihood estimation procedure is sophisticated and has asymptotic optimality properties. It utilizes the latest techniques of "convex programming" and the computer algorithm is straightforward and fast. The methodology proposed here also has the following shortcomings: (1) The model is (multi)parametric. However, it is of the form of the product model for age specific hazard rates which is now widely accepted. (2) Robustness studies on the effect of model breakdown on the estimated safe doses are as yet limited and should be followed up with more extensive studies. (3) Obviously no estimates of "safe doses" can be made if the spontaneous incidence rate is zero and the experimental dose levels have been chosen too small and no tumors have been observed. Similarly if the experimental doses are too small and the tumor incidence rates are all comparable with the spontaneous rate the estimation procedure is afflicted by extremely large errors. The situation improves slightly if the incidence for the highest dose level is higher than that of the lower dose levels which are all approximately equal. In such situations more satisfactory experimental data are needed. Some general recommendations are as follows: (1) Whenever possible it is preferable to record times to tumor and not just incidence rates. However, for experiments of sufficiently long duration necropsies following the varying times of death will provide adequate information on the time dependence of tumor incidence. It may also be advisable to deliberately vary the times of sacrifice to two or three different times. (2) Other considerations being equal it is preferable to have a large number of dose levels rather than more animals per dose level...

Animals↗
PubMed2004

Computer-aided tissue engineering: overview, scope and challenges.

Advances in computer-aided technology and its application with biology, engineering and information science to tissue engineering have evolved a new field of computer-aided tissue engineering (CATE). This emerging field encompasses computer-aided design (CAD), image processing, manufacturing and solid free-form fabrication (SFF) for modelling, designing, simulation and manufacturing of biological tissue and organ substitutes. The present Review describes some salient advances in this field, particularly in computer-aided tissue modeling, computer-aided tissue informatics and computer-aided tissue scaffold design and fabrication. Methodologies of development of CATE modelling from high-resolution non-invasive imaging and image-based three-dimensional reconstruction, and various reconstructive techniques for CAD-based tissue modelling generation will be described. The latest development in SFF to tissue engineering and a framework of bio-blueprint modelling for three-dimensional cell and organ printing will also be introduced.

Animals↗
PubMed2004

Dielectric spectroscopy and electrophoretic mobility measurements interpreted with the standard electrokinetic model.

We report results from complementary electrokinetic measurements-dielectric relaxation and electrophoretic mobility-undertaken to test the applicability of the standard electrokinetic theory with a model system. Dielectric spectra were obtained at frequencies between 1 kHz and 40 MHz with a new, two-electrode cell design [Hollingsworth and Saville, J. Colloid Interface Sci. 257 (2003) 65-76]; mobility data were acquired with an electrophoretic light scattering instrument. Data from the two-electrode cell were collected at different electrode separations and interpreted with newly developed procedures to remove the influence of electrode polarization. Methodology A employs extrapolation to infinite electrode separation to compute the dielectric constant and conductivity as functions of frequency. The contributions from suspended particles are reported in terms of dielectric constant and conductivity increments. Methodology B uses a theoretical model of electrode polarization and the standard electrokinetic model in a nonlinear regression scheme. Results are presented in several forms: frequency-dependent dielectric constant and conductivity increments, frequency-dependent dielectric constants and conductivities, and the complex dipole coefficient. It is shown that the standard model provides a consistent methodology for interpreting particle behavior; zeta-potentials inferred from mobility and dielectric relaxation agree to within experimental error. Moreover, the cell design and interpretation are straightforward and provide relatively simple ways to obtain complementary measurements over a wide frequency range. The results unambiguously show that electrokinetic character of this dispersion follows the standard model.

Journal Article↗
PubMed2004

Systematic review: computed tomography and ultrasonography to detect acute appendicitis in adults and adolescents.

BACKGROUND: Although clinicians commonly use computed tomography or ultrasonography to diagnose acute appendicitis, the accuracy of these imaging tests remains unclear. PURPOSE: To review the diagnostic accuracy of computed tomography and ultrasonography in adults and adolescents with suspected acute appendicitis. DATA SOURCES: The authors used MEDLINE, EMBASE, bibliographies, review articles, textbooks, and expert opinion to retrieve English- and non-English-language articles published from 1966 to December 2003. STUDY SELECTION: The authors included prospective studies evaluating computed tomography or ultrasonography followed by surgical confirmation or clinical follow-up in patients at least 14 years of age with suspected appendicitis. DATA EXTRACTION: One assessor (for non-English-language studies) or 2 assessors (for English-language studies) independently reviewed each article to abstract relevant study characteristics and results. DATA SYNTHESIS: Twelve computed tomography studies and 14 ultrasonography studies met inclusion criteria. Computed tomography had an overall sensitivity of 0.94 (95% CI, 0.91 to 0.95), a specificity of 0.95 (CI, 0.93 to 0.96), a positive likelihood ratio of 13.3 (CI, 9.9 to 17.9), and a negative likelihood ratio of 0.09 (CI, 0.07 to 0.12). Ultrasonography had an overall sensitivity of 0.86 (CI, 0.83 to 0.88), a specificity of 0.81 (CI, 0.78 to 0.84), a positive likelihood ratio of 5.8 (CI, 3.5 to 9.5), and a negative likelihood ratio of 0.19 (CI, 0.13 to 0.27). Verification bias and inappropriate blinding of reference standards were noted in all of the included studies. LIMITATIONS: The summary assessment of the diagnostic accuracy for both tests was limited by the small number of studies, heterogeneity among study samples, and poor methodologic quality in the original studies. CONCLUSIONS: Computed tomography is probably more accurate than ultrasonography for diagnosing appendicitis in adults and adolescents. Prospective studies that apply gold standard diagnostic testing to all study participants would more reliably estimate the true diagnostic accuracy of these tests.

Acute Disease↗
PubMed2003

Incorporation of variability into the modeling of viral delays in HIV infection dynamics.

We consider classes of functional differential equation models which arise in attempts to describe temporal delays in HIV pathogenesis. In particular, we develop methods for incorporating arbitrary variability (i.e., general probability distributions) for these delays into systems that cannot readily be reduced to a finite number of coupled ordinary differential equations (as is done in the method of stages). We discuss modeling from first principles, introduce several classes of non-linear models (including discrete and distributed delays) and present a discussion of theoretical and computational approaches. We then use the resulting methodology to carry out simulations and perform parameter estimation calculations, fitting the models to a set of experimental data. Results obtained confirm the statistical significance of the presence of delays and the importance of including delays in validating mathematical models with experimental data. We also show that the models are quite sensitive to the mean of the distribution which describes the delay in viral production, whereas the variance of this distribution has relatively little impact.

Computer Simulation↗
PubMed1999

What is the nature of increased Stroop interference in schizophrenia?

In comparison to controls, patients with schizophrenia classically display (1) an overall slowing in response times (RTs) and (2) a disproportionate slowing in RTs in the conflict condition of the Stroop color/word interference task. These two effects appear repeatedly in the card version of the Stroop task but were not replicated in a number of studies using a computer item-by-item version of the task. The present study was aimed at understanding the exact nature of the increased interference classically found in the performance of patients with schizophrenia in the card version of the Stroop task. We used a computer trial-by-trial version in which we investigated the effects of two major methodological differences between the two versions: (1) blocked (card version) versus mixed (computer version) presentation of the neutral, congruent and conflict conditions and (2) presence (card version) versus absence (computer version) of distractors in the spatial surrounding of the target. We found an overall slowing in performance and a disproportionate slowing in the conflict condition for patients with schizophrenia but only when the target was surrounded by distractors (in Experiments 2 and 3). The data are discussed in terms of a deficit in selective attention and inhibitory processes in schizophrenia.

Adult↗
PubMed1998

Optimization of the granulation process for designing tablets.

A computer optimization technique based on surface response methodology was applied to optimize the wet granulation process for designing tablets. Physical properties (mean granule size, granule size distribution, compressibility, granule strength) of a model granule formulation containing ethenzamide were accurately described by a second polynomial equation based on two independent variables (amounts of binder and binder solution). This regression equation also gave a good correlation for three physical properties of tablets (distintegration time, compactibility, compression force variance), but the correlation for tablet hardness and weight variation was poor. These results imply that not only the above physical properties of granules but also the rheological behavior and porous structure of granules are closely related to tablet properties. Using an optimization of five tablet properties using the generalized distance function, the predicted values of the physical properties of both granules and tablets agreed well with experimental values. This agreement indicates that the computer optimization technique is useful for optimizing the granulation process for designing tablets.

Computers↗