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This paper describes a new computer approach for chemotaxonomic studies. The methodology employed enables the search for chemical substructures as taxonomic descriptors using an expert system built with plant natural products. The operation of the system was tested with diterpenes as taxonomic markers in Lamiaceae.
As the number of complete genomes that have been sequenced keeps growing, unknown areas of the protein space are revealed and new horizons open up. Most of this information will be fully appreciated only when the structural information about the encoded proteins becomes available. The goal of structural genomics is to direct large-scale efforts of protein structure determination, so as to increase the impact of these efforts. This review focuses on current approaches in structural genomics aimed at selecting representative proteins as targets for structure determination. We will discuss the concept of representative structures/folds, the current methodologies for identifying those proteins, and computational techniques for identifying proteins which are expected to adopt new structural folds.
The emergence of a new field of science called complexity theory has made an impact on the community of scientists as well as the general public. This brief tutorial takes a very special view of this. The thesis is that complexity science has grown out of a general lack of satisfaction with traditional scientific practices and their failure to find a way of capturing anything but a shadow of complex reality. In spite of the many impressive advances from science and technology, it is clear that the picture delivered of the world is that of a surrogate world populated by machines and mechanisms. The nature of the real world demands more than traditional science can deliver. Yet traditional science has constraints and bounds on its universe of discourse. Complexity science, as presented here, demands that the barriers and constraints be removed in order to gain a more complete view of nature. This tutorial presents a summary of what is entailed by this new methodology.
Concerns about the variable natural history of untreated chronic hepatitis C and the costs and benefits of current therapy for this disease have been addressed by the techniques of cost-effectiveness analysis. The methodologies of decision analysis and Markov computer simulation, and available data on natural history, costs of care, and response to treatment, have been utilized to project the long-term costs and benefits of treatment. These models indicate that interferon monotherapy and combination therapy (interferon plus ribavirin) for previously untreated patients, for retreatment of patients who relapse after interferon treatment, and for retreatment of those who are non-responders to interferon monotherapy have calculated cost-effectiveness ratios that fall within the bounds of other widely accepted therapies or are cost-saving. Even empirical treatment, without liver biopsy, HCV RNA quantitation, or HCV genotyping, has an acceptable cost-effectiveness.
During the last decade, stereotactic radiotherapy has widely improved in France. Thus one should study the present situation and its future trend. QUANTITATIVE NEED: Considering single dose radiotherapy, there are about 900 to 1,000 cases treated per year. However, the trend towards more fractionated treatment will disturb this temporary equilibrium; thus more machine time will be necessary. QUALITATIVE NEED: Stereotactic radiotherapy is practiced by multi-disciplinary teams including physicians, physicists and scientific specialists. Radiotherapists and physicist are responsible for treatment planning and evaluation as well as for clinical and methodological research. Accordingly, they should possess computers, treatment planning systems, etc. Such teams are necessary to carry out complex irradiations. GENERAL EVOLUTION: Fractionation of irradiation nowadays seems mandatory for most intracranial tumors except metastases and small regular arteriovenous malformations. Heterogeneity of lesion dose is related to the geometry and the physics of convergent fixed or mobile beams. It can be improved and the healthy tissue irradiation can be diminished using the multi-isocentric planning for complex lesion or with micro multi leaf collimators. MODALITIES OF STEREOTACTIC RADIOTHERAPY ACCORDING TO LESION TYPE: For neurinomas of the acoustic nerve, fractionated stereotactic radiotherapy yields few of the complications published after single dose stereotactic radiotherapy. The same can be said for meningiomas although some series reported very few complications after single dose stereotactic radiotherapy. Solitary metastases without systemic evolution, not situated on the mid-line, are favorable candidates for palliative single dose stereotactic radiotherapy. The conjunction with total brain irradiation seems to be useful. Small arteriovenous malformations will be treated with single dose stereotactic radiotherapy, whereas voluminous and/or geometrically complex nidus could benefit from protons or photon beams modulated by micro multi leaf collimators and a few fractions. EXTRA-CRANIAL STEREOTACTIC RADIOTHERAPY: Single dose stereotactic radiotherapy and fractionated stereotactic radiotherapy will be used as boost in various situations such as massif facial and in all sorts of tumors in the body specially when lesions are close to critical organs.
A model-based methodology for optimal design of polymer-coated chemical sensors is developed and is illustrated for the example of infrared evanescent field chemical sensors. The methodology is based on rigorous and computationally efficient modeling of combined fluid mechanics and mass transfer, including transport of multiple analytes. A simple algebraic equation for the optimal size of the sensor flow cell is developed to guide sensor design and validated by extensive CFD simulations. Based upon these calculations, optimized geometries of the sensor flow cell are proposed to further improve the response time of chemical sensors.
New developments in clinical psychophysics allow a non-invasive assessment of visual function which may otherwise not be possible. Measurements of spatial and temporal contrast sensitivity functions, perimetric rod and cone sensitivity, colour vision testing, and newer tests such as hyperacuity thresholds may provide information about the mechanism of an abnormality, allow earlier detection of damage, determination of retinal function in the presence of ocular media disturbances, and allow more sensitive detection of the effects of treatment on visual function. Some methods are more effective in screening or monitoring patients over time while others can be used as research tools to investigate the underlying causes of visual dysfunction. Emerging technologies such as those based on video displays and computer generated graphics and advances in methodology provide potential for new applications. The selection of which aspect of visual function to test depends on the condition (e.g., retinal degeneration or glaucoma), the goals of the investigation, and the facilities available. These non-invasive methods can provide accurate information about retinal function and further improve our ability to quantify and document this most important aspect of the eye--its role in visual function.
The impressions of 200 patients (both medical and surgical) and 200 nursing staff (registered, enrolled and trainee enrolled nurses) in relation to two bed-bathing methods were compared by means of questionnaires and semi-structured interviews. Data regarding costs were obtained from appropriate cost centre managers. The results of the study found the soft towel bed-bathing method to be more cost effective and provide more patient and nurse satisfaction than the current bed-bathing method.
The Monte Carlo (MC) and molecular dynamics (MD) methodologies are now well established for computing equilibrium properties in homogeneous fluids. This is not yet the case for the direct simulation of two-phase systems, which exhibit nonuniformity of the density distribution across the interface. We have performed direct MC and MD simulations of the liquid-gas interface of n-pentane using a standard force-field model. We obtained density and pressure components profiles along the direction normal to the interface that can be very different, depending on the truncation and long range correction strategies. We discuss the influence on predicted properties of different potential truncation schemes implemented in both MC and MD simulations. We show that the MD and MC profiles can be made in agreement by using a Lennard-Jones potential truncated via a polynomial function that makes the first and second derivatives of the potential continuous at the cutoff distance. In this case however, the predicted thermodynamic properties (phase envelope, surface tension) deviate from experiments, because of the changes made in the potential. A further readjustment of the potential parameters is needed if one wants to use this method. We conclude that a straightforward use of bulk phase force fields in MD simulations may lead to some physical inconsistencies when computing interfacial properties.
We consider a multicenter clinical trial with treatments as fixed effects and centers and residuals as bivariate and univariate random effects, respectively. There exist situations where it is difficult to justify the conventional normality assumptions for the random components. Following Khatri and Patel (Commun. Stat.-Theory Methods 1992, 21, 21-39), we propose the weighted least-squares (WLS) method and two bootstrap methods, percentile and BCa, that are robust to the departure from normality. Through a simulation study, we compare WLS and bootstrap confidence intervals for the treatment difference. While all three methods give confidence intervals with desired coverage rates, the WLS method gives shorter intervals. We also propose a bootstrap method that is robust to outliers. A numerical example is given to illustrate the methodology.
This paper presents a methodology for three-dimensional (3D) computer modelling of the breast, using a combination of 3D geometrical primitives and voxel matrices that can be further subjected to simulated x-ray imaging, to produce synthetic mammograms. The breast phantom is a composite model of the breast and includes the breast surface, the duct system and terminal ductal lobular units. Cooper's ligaments, the pectoral muscle, the 3D mammographic background and breast abnormalities. A second analytical x-ray matter interaction modelling module is used to generate synthetic images from monoenergetic fan beams. Mammographic images of various synthesized breast models differing in size, shape and composition were produced. A preliminary qualitative assessment performed by three radiologists and a quantitative evaluation study using fractal and grey-level histogram analysis were conducted. A comparative study of extracted features with published data has also been performed. The evaluation results indicated good correlation of characteristics between synthetic and actual radiographs. Applications foreseen are not only in the area of breast imaging experimentation but also in education and training.
Simultaneous emission and transmission measurement is appealing in PET due to the matching of geometrical conditions between emission and transmission and reduced acquisition time for the study. A potential problem remains: when transmission statistics are low, attenuation correction could be very noisy. Although noise in the attenuation map can be controlled through regularization during statistical reconstruction, the selection of regularization parameters is usually empirical. In this paper, we investigate the use of discrete data consistency conditions (DDCC) to optimally select one or two regularization parameters. The advantages of the method are that the reconstructed attenuation map is consistent with the emission data and that it accounts for particularity in the emission reconstruction algorithm and acquisition geometry. The methodology is validated using a computer-generated whole-body phantom for both emission and transmission, neglecting random events and scattered radiation. MAP-TR was used for attenuation map reconstruction, while 3D OS-EM is used for estimating the emission image. The estimation of regularization parameters depends on the resolution of the emission image controlled by the number of iterations in OS-EM. The computer simulation shows that, on one hand, DDCC regularized attenuation map reduces propagation of the transmission scan noise to the emission image, while on the other hand DDCC prevents excessive attenuation map smoothing that could result in resolution mismatch artefacts between emission and transmission.
A nonlinear stochastic model of an AIDS epidemic with recruitment of infectives, susceptibles, and AIDS cases into a randomly mixing population of male homosexuals was formulated and studied from a methodological point of view through intensive computer experimentation. Probability generating functions were used to formulate a model for the monthly probability that a susceptible individual becomes infected with HIV, under the assumption that the probability of infection per sexual contact varies as a function of the duration of infection. A method for taking into account the use of condoms to prevent infection with HIV was also introduced. Nonlinear difference equations, resembling deterministic epidemic models, were embedded in the stochastic population process by iterating an initial conditional expectation. Examples of Monte Carlo experiments are presented, illustrating that solutions of these nonlinear difference equations are not always good measures of central tendency for variations in the sample functions of the process. Two important substantive conclusions drawn from the Monte Carlo experiments were that efforts should be made to collect quantitative information on the probability of infection per sexual contact as a function of duration of infection and the frequency of condom use within and among risk categories in a population.
The emotional impact of illness sustained by patients, their families, and friends is increasingly recognized as an important dimension of clinical evaluation and intervention. This study first attempted to extend a computerized technique of measuring the magnitude of mental events from a content analysis of speech initially designed for use on single verbal samples or verbal texts to the analysis of conversational interactions. The study then applied this method of extended measurement to conversations concerning seriously ill surgical patients. The authors' objective was to develop a graphic method that illustrates the neuropsychological interchanges occurring in these conversations. Speech samples were recorded during discussions among nurses, surgeons, intensivists, and family members involved in the care and treatment of seriously ill patients hospitalized in the surgical intensive care unit at Barnes-Jewish Hospitals associated with Washington University School of Medicine, St. Louis, Missouri. These samples then were transcribed into computer-readable text files and divided into utterances: uninterrupted speech by a single individual. The utterances were assigned numeric scores by a computer program on each of 14 validated content analysis scales measuring various neuropsychological dimensions. The scores are presented graphically in chronological sequence to illustrate the emotional interactions in these conversations. The graphic representations depicting sequences of computerized content analysis-derived scores for the mental reactions of the speakers in such conversations provide insights into the psychodynamics occurring in such stressful situations.
Healthcare errors among nurses are common because of the fast-paced work environment, in which extensive data must be analyzed and quick decision making is required. Assistive computing devices can help reduce nursing errors by providing timely access to client information and by assisting nurses with client monitoring, decision making, and bedside documentation. The purpose of this pilot study was to determine what assistive computing device features, functions, and input/output modalities nurses would find most useful as support for their nursing duties. Twenty nurses completed a questionnaire that examined their needs and preferences. Data analysis revealed a strong desire for capabilities related to facilitating information access and administering safe medication. The results of this study will be used to develop design criteria for an assistive computing device that will aim to improve the performance of nurses through appropriate information and data support.
One of the computational "grand challenges" is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. Here, a significant step forward is made by combining molecular dynamics with a novel variable transformation designed to enhance sampling by reducing barriers without introducing bias and, thus, to preserve, perfectly, equilibrium properties.
The first collaborative workshop on crystal structure prediction (CSP1999) has been followed by a second workshop (CSP2001) held at the Cambridge Crystallographic Data Centre. The 17 participants were given only the chemical diagram for three organic molecules and were invited to test their prediction programs within a range of named common space groups. Several different computer programs were used, using the methodology wherein a molecular model is used to construct theoretical crystal structures in given space groups, and prediction is usually based on the minimum calculated lattice energy. A maximum of three predictions were allowed per molecule. The results showed two correct predictions for the first molecule, four for the second molecule and none for the third molecule (which had torsional flexibility). The correct structure was often present in the sorted low-energy lists from the participants but at a ranking position greater than three. The use of non-indexed powder diffraction data was investigated in a secondary test, after completion of the ab initio submissions. Although no one method can be said to be completely reliable, this workshop gives an objective measure of the success and failure of current methodologies.
In image-guided therapy, high-quality preoperative images serve for planning and simulation, and intraoperatively as "background", onto which models of surgical instruments or radiation beams are projected. The link between a preoperative image and intraoperative physical space of the patient is established by image-to-patient registration. In this paper, we present a novel 3-D/2-D registration method. First, a 3-D image is reconstructed from a few 2-D X-ray images and next, the preoperative 3-D image is brought into the best possible spatial correspondence with the reconstructed image by optimizing a similarity measure (SM). Because the quality of the reconstructed image is generally low, we introduce a novel SM, which is able to cope with low image quality as well as with different imaging modalities. The novel 3-D/2-D registration method has been evaluated and compared to the gradient-based method (GBM) using standardized evaluation methodology and publicly available 3-D computed tomography (CT), 3-D rotational X-ray (3DRX), and magnetic resonance (MR) and 2-D X-ray images of two spine phantoms, for which gold standard registrations were known. For each of the 3DRX, CT, or MR images and each set of X-ray images, 1600 registrations were performed from starting positions, defined as the mean target registration error (mTRE), randomly generated and uniformly distributed in the interval of 0-20 mm around the gold standard. The capture range was defined as the distance from gold standard for which the final TRE was less than 2 mm in at least 95% of all cases. In terms of success rate, as the function of initial misalignment and capture range the proposed method outperformed the GBM. TREs of the novel method and the GBM were approximately the same. For the registration of 3DRX and CT images to X-ray images as few as 2-3 X-ray views were sufficient to obtain approximately 0.4 mm TREs, 7-9 mm capture range, and 80%-90% of successful registrations. To obtain similar results for MR to X-ray registrations, an image, reconstructed from at least 11 X-ray images was required. Reconstructions from more than 11 images had no effect on the registration results.