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PubMedDate not supplied

Computerized brain atlases as decision support systems: a methodological approach.

This paper deals with the development of computerized brain atlases addressing both research and clinical needs. The authors analyze in detail the potential of these systems and discuss the capabilities and limitations of the digital atlases currently being developed around the world. The authors propose to reconsider the concept of a brain atlas, regarding both its content, and the way it has to be used and managed in order to set up more effective cooperation between the user and the system. Particular emphasis is placed on extensibility and reuse issues. which are critical in this rapidly evolving field. These orientations result from both the authors' experience and the analysis of current trends in the field of neuroimaging. The general methodology is illustrated with examples related to computer aided surgical planning.

Artificial Intelligence↗
PubMed2005

Molecular simulations of aqueous electrolyte solubility: 1. The expanded-ensemble osmotic molecular dynamics method for the solution phase.

We have developed a molecular-level simulation technique called the expanded-ensemble osmotic molecular dynamics (EEOMD) method, for studying electrolyte solution systems. The EEOMD method performs simulations at a fixed number of solvent molecules, pressure, temperature, and overall electrolyte chemical potential. The method combines elements of constant pressure-constant temperature molecular dynamics and expanded-ensemble grand canonical Monte Carlo. The simulated electrolyte solution systems contain, in addition to solvent molecules, full and fractional ions and undissociated electrolyte molecular units. The fractional particles are coupled to the system via a coupling parameter that varies between 0 (no interaction between the fractional particle and the other particles in the system) and 1 (full interaction between the fractional particle and the other particles in the system). The time evolution of the system is governed by the constant pressure-constant temperature equations of motion and accompanied by random changes in the coupling parameter. The coupling-parameter changes are accepted with a probability derived from the expanded-ensemble osmotic partition function corresponding to the prescribed electrolyte chemical potential. The coupling-parameter changes mimic insertion/deletion of particles as in a crude grand canonical Monte Carlo simulation; if the coupling parameter becomes 0, the fractional particles disappear from the system, and as the coupling parameter reaches unity, the fractional particles become full particles. The method is demonstrated for a model of NaCl in water at ambient conditions. To test our approach, we first determine the chemical potential of NaCl in water by the thermodynamic integration technique and by the expanded-ensemble method. Then, we carry out EEOMD simulations for different specified values of the overall NaCl chemical potential and measure the concentration of ions resulting from the simulations. Both computations give consistent results, validating the EEOMD methodology.

Journal Article↗
PubMed1999

Development of a performance assessment capability in the waste management programs of the U.S. Nuclear Regulatory Commission.

The U.S. Nuclear Regulatory Commission (NRC) staff has developed a performance assessment capability to address three programmatic areas in nuclear waste management: high-level waste, low-level waste, and decommissioning of licensed facilities (license termination). The NRC capability consists of: (1) methodologies for performance assessment; (2) models and computer codes for estimating system performance; (3) regulatory guidance in various forms, such as regulations, Branch Technical Positions, and Standard Review Plans; and (4) a technical staff experienced in executing and evaluating performance assessments for a variety of waste systems. Although the tools and techniques are refined for each programmatic area, general approaches and similar issues are encountered in all areas.

Government Agencies↗
PubMed2006

Statistical mechanically averaged molecular properties of liquid water calculated using the combined coupled cluster/molecular dynamics method.

Liquid water is investigated theoretically using combined molecular dynamics (MD) simulations and accurate electronic structure methods. The statistical mechanically averaged molecular properties of liquid water are calculated using the combined coupled cluster/molecular mechanics (CC/MM) method for a large number of configurations generated from MD simulations. The method includes electron correlation effects at the coupled cluster singles and doubles level and the use of a large correlation consistent basis set. A polarizable force field has been used for the molecular dynamics part in both the CC/MM method and in the MD simulation. We describe how the methodology can be optimized with respect to computational costs while maintaining the quality of the results. Using the optimized method we study the energetic properties including the heat of vaporization and electronic excitation energies as well as electric dipole and quadrupole moments, the frequency dependent electric (dipole) polarizability, and electric-field-induced second harmonic generation first and second hyperpolarizabilities. Comparisons with experiments are performed where reliable data are available. Furthermore, we discuss the important issue on how to compare the calculated microscopic nonlocal properties to the experimental macroscopic measurements.

Journal Article↗
PubMed2006

Evaluation of low-scaling methods for calculation of phosphorescence parameters.

In order to find a methodology that is a compromise between favorable computational scaling and tolerable errors, a series of nonrelativistic approaches for the calculation of radiative phosphorescence lifetimes are benchmarked against fully relativistic four-component results. The study of the a 3A2-X 1A1 transition intensity in the series of H2CX molecules, where X is a chalcogene atom, X={O,S,Se,Te}, indicates a general good agreement between fully relativistic four-component and nonrelativistic perturbation-theoretical calculations. Among the nonrelativistic approaches, the scaled-charge spin-orbit operator approach is recognized as to provide transition matrix elements that are in good agreement with those obtained with the more elaborate Breit-Pauli and atomic mean field spin-orbit operators. This finding supports phosphorescence calculations using the available linear scaling technology for large complexes and, together with effective-core potentials, large complexes including heavy elements.

Journal Article↗
PubMed2005

Reliable prediction of transcription factor binding sites by phylogenetic verification.

We present a statistical methodology that largely improves the accuracy in computational predictions of transcription factor (TF) binding sites in eukaryote genomes. This method models the cross-species conservation of binding sites without relying on accurate sequence alignment. It can be coupled with any motif-finding algorithm that searches for overrepresented sequence motifs in individual species and can increase the accuracy of the coupled motif-finding algorithm. Because this method is capable of accurately detecting TF binding sites, it also enhances our ability to predict the cis-regulatory modules. We applied this method on the published chromatin immunoprecipitation (ChIP)-chip data in Saccharomyces cerevisiae and found that its sensitivity and specificity are 9% and 14% higher than those of two recent methods. We also recovered almost all of the previously verified TF binding sites and made predictions on the cis-regulatory elements that govern the tight regulation of ribosomal protein genes in 13 eukaryote species (2 plants, 4 yeasts, 2 worms, 2 insects, and 3 mammals). These results give insights to the transcriptional regulation in eukaryotic organisms.

Base Sequence↗
PubMed1999

Surface geochemistry of the clay minerals.

Clay minerals are layer type aluminosilicates that figure in terrestrial biogeochemical cycles, in the buffering capacity of the oceans, and in the containment of toxic waste materials. They are also used as lubricants in petroleum extraction and as industrial catalysts for the synthesis of many organic compounds. These applications derive fundamentally from the colloidal size and permanent structural charge of clay mineral particles, which endow them with significant surface reactivity. Unraveling the surface geochemistry of hydrated clay minerals is an abiding, if difficult, topic in earth sciences research. Recent experimental and computational studies that take advantage of new methodologies and basic insights derived from the study of concentrated ionic solutions have begun to clarify the structure of electrical double layers formed on hydrated clay mineral surfaces, particularly those in the interlayer region of swelling 2:1 layer type clay minerals. One emerging trend is that the coordination of interlayer cations with water molecules and clay mineral surface oxygens is governed largely by cation size and charge, similarly to a concentrated ionic solution, but the location of structural charge within a clay layer and the existence of hydrophobic patches on its surface provide important modulations. The larger the interlayer cation, the greater the influence of clay mineral structure and hydrophobicity on the configurations of adsorbed water molecules. This picture extends readily to hydrophobic molecules adsorbed within an interlayer region, with important implications for clay-hydrocarbon interactions and the design of catalysts for organic synthesis.

Journal Article↗
PubMed2005

Probabilistic assessment of clone overlaps in DNA fingerprint mapping via a priori models.

We construct a combinatorially exact probability distribution for the problem of a priori clone overlap assessment in DNA fingerprint mapping. It is implemented as a general enumeration methodology using Bell's exponential polynomials. Established computational metrics do not consider the conditional nature of the problem. They dramatically overpredict actual match probabilities as a consequence. This elevates the rate of false-negative overlap declarations, which is consistent with previous validation studies. Increased measurement resolution does not significantly improve accuracy. We describe general trends in error behavior for intermediate-size DNA clones and discuss corresponding limits on the ability to assess certain overlaps.

Chromosome Mapping↗
PubMed2002

Evaluation of the usefulness of percutaneous transhepatic portal catheterization for preoperatively diagnosing the localization of insulinomas.

INTRODUCTION: The precise intraoperative localization of insulinoma is essential for successful surgical management. AIMS: To assess the usefulness of measuring insulin levels by preoperative percutaneous transhepatic portal catheterization (PTPC) and intraoperative ultrasonography (US). METHODOLOGY: PTPC and other preoperative procedures (enhanced computed tomography [CT], arteriography, and US) were performed in eight patients with insulinoma based on our experience during the past 18 years. Intraoperative US was performed in six of the eight patients. RESULTS: PTPC was undertaken in all eight patients, and increased levels of insulin at the sites corresponding to tumors were observed in all patients. Intraoperative US was performed in six patients, which made it possible to detect insulinomas as hypoechoic masses in all of these patients. All tumors were found to exist as single entities. CONCLUSION: PTPC showed the highest diagnostic accuracy in detecting the number of and accurately localizing the tumors before surgery. Meanwhile, all findings from intraoperative US were identical to those of the resection samples, suggesting that this method is a highly reliable examination technique. We conclude that a combination of PTPC and intraoperative US may be essential for the successful surgical management of insulinomas.

Angiography↗
PubMed2002

Virtual center for renal support: technological approach to patient physiological image.

The patient physiological image (PPI) is a novel concept which manages the knowledge of the virtual center for renal support (VCRS), currently being developed by the Biomedical Engineering Group of the University of Seville. PPI is a virtual "replica" of the patient, built by means of a mathematical model, which represents several physiological subsystems of a renal patient. From a technical point of view, PPI is a component-oriented software module based on cutting-edge modeling and simulation technology. This paper provides a methodological and technological approach to the PPI. Computational architecture of PPI-based VCRS is also described. This is a multi-tier and multi-protocol system. Data are managed by several ORDBMS instances. Communications design is based on the virtual private network (VPN) concept. Renal patients have a minimum reliable access to the VCRS through a public switch telephone network--X.25 gateway. Design complies with the universal access requirement, allowing an efficient and inexpensive connection even in rural environments and reducing computational requirements in the patient's remote access unit. VCRS provides support for renal patients' healthcare, increasing the quality and quantity of monitored biomedical signals, predicting events as hypotension or low dialysis dose, assisting further to avoid them by an online therapy modification and easing diagnostic tasks. An online therapy adjustment experiment simulation is presented. Finally, the presented system serves as a computational aid for research in renal physiology. This is achieved by an open and reusable modeling and simulation architecture which allows the interaction among models and data from different scales and computer platforms, and a faster transference of investigation models toward clinical applications.

Aged↗
PubMed2000

UNWIRED E-MED: the next generation of wireless and internet telemedicine systems.

The movement of telemedicine to wireless and mobile Internet applications is imminent in the next few years. This migration from desktop platforms to wireless and mobile configurations will have a significant impact on future healthcare delivery systems and their globalization. Recent telecommunications and biomedical computing advances will significantly enhance the current methodologies of telemedicine and telecare systems. This editorial will present some of the evolutionary issues and important aspects that have to be considered in developing technologies for the next generation of Internet and third generation of mobile systems geared for future telemedical applications. These will provide new dimensions to existing medical services and areas of outreach that are not possible with the current generation that will have tremendous impact on how healthcare delivery will be shaped for the 21st century.

Internet↗
PubMed2004

Affine invariant features from the trace transform.

The trace transform is a generalization of the Radon transform that allows one to construct image features that are invariant to a chosen group of image transformations. In this paper, we propose a methodology and appropriate functionals that can be computed from the image function and which can be used to calculate features invariant to the group of affine transforms. We demonstrate the usefulness of the constructed image descriptors in retrieving images from an image database and compare it with relevant state-of-the-art object retrieval methods.

Algorithms↗
PubMed2000

False molecular clusters due to nonrandom association of IS6110 with Mycobacterium tuberculosis.

We sought to determine whether nonrandom association of IS6110 with Mycobacterium tuberculosis could result in false-positive clustering in unselected collections of isolates. We typed 196 strains of M. tuberculosis from an unselected community-based study in northern Tanzania by IS6110 and polymorphic GC-rich repetitive-sequence (PGRS) methodologies. The strains were analyzed by Gelcompar computer software. Analysis of 13 out of 25 groups showed that isolates with identical IS6110 and PGRS patterns were likely to be the same strain. Some IS6110 groups containing strains with identical PGRS patterns had similar IS6110 patterns that differed only by movement of the element. Isolates assigned to a single group (i.e., group 11) on the basis of sharing an identical IS6110 fingerprint pattern did not share identical PGRS fingerprint patterns. Six out of the nine bands in these isolates were in hot-spot locations, as previously defined. This indicates that nonrandom association may result in false-positive clustering in unselected community-based studies. Only strains with identical PGRS and IS6110 patterns are likely to be recently transmitted.

Bacterial Typing Techniques↗
PubMed1985

CT myelography for outpatients. An inpatient/outpatient pilot study to assess methodology.

The diagnostic usefulness, limitations, and adverse reactions associated with computed tomographic myelography using metrizamide were assessed for broad outpatient application. The initial approach was to examine inpatients (n = 38) with low-dose metrizamide (100 mgI/ml). This low dose was believed less likely to be associated with side effects. They were then treated as if they were outpatients, with the liberties this entailed. The consequences of needle puncture were minimized by using a 25-gauge disposable needle. Thirty-four (89%) patients remained free of side effects after the procedure. Subsequently, this technique was extended to 42 outpatients, 38 (90.5%) of whom remained asymptomatic. For comparison, 170 mgI/ml was used in another 25 outpatients, who evidenced more symptoms. The potential medical, economic, and therapeutic benefits of obviating hospitalization by safer outpatient CT myelography seem clear.

Ambulatory Care↗
PubMed1992

Longitudinal effects of passive smoking on pulmonary function in New Zealand children.

In this study we examined the longitudinal effects of smoke exposure on lung function in a cohort of New Zealand children observed from 9 to 15 yr of age. Possible exposures included in utero exposure from mothers smoking during pregnancy, passive smoke from parents, and active smoking by the children. Lung function measures of forced expiratory volume in one second (FEV1) and vital capacity (VC) were measured biennially and ratios (FEV1/VC) were computed. The data were analyzed using longitudinal methodology, and all subjects with at least one pulmonary function test and responses to the questions concerning smoke exposures were included (n = 634). Subjects reporting wheeze or asthma were examined as a separate subgroup. In the whole cohort, no significant detrimental effects were detected for absolute FEV1 or VC in either sex, related to active or passive smoke exposures. Parental smoking was, however, associated with persistent but mild and nonprogressive impairment of the FEV1/VC ratio in males, an effect that was present at the time lung function measurements were first made. This effect was not seen in females. In children with reported wheeze or asthma, parental smoking had progressive, more serious, and clinically significant effects on the FEV1/VC ratio among adolescents of both sexes, causing a mean reduction in FEV1/VC ratios by age 15 of 3.9% in males and 2.3% in females, in contrast to the observed increase in FEV1/VC ratios with age seen in nonexposed wheezing children. We conclude that passive smoking is a major contributing factor to the development and persistence of airflow limitation in wheezing children.

Adolescent↗
PubMed2002

Literature overview on artificial liver support in fulminant hepatic failure: a methodological approach.

Artificial liver support is a therapeutic option for subjects with fulminant hepatic failure. Results of these studies suggest a possible favourable effect on this condition. The aim of the present review is to evaluate not the results of the different artificial systems available but the methodology used to achieve these results. A computer and manual search of the literature was performed; 832 pertinent references were retrieved. Seventy-seven were full papers reporting the application of artificial liver support in animals or humans (15 RCTs (3 in humans, 12 in animals), 53 uncontrolled phase I trials, 9 case reports). The results of this review indicate that, although the rationale of artificial liver support as shown by animal studies is acceptable, the widespread use in clinical practice is not justified and a controlled design for the studies on artificial liver support systems is mandatory.

Animals↗
PubMed2000

Promoting good research practice.

Embarking on a new millennium provides the stimulus both to take stock and also to look forward. In the field of medical statistics there is much to make us feel proud and excited. Rapid methodological developments together with parallel developments in computer technology have enormously expanded our statistical repertoire. At the same time, the high profile attained by the evidence-based medicine movement means that the importance of our discipline is recognized more widely then ever before. However, any medical statistician who is involved in medical publishing, or who is even a regular reader of the medical literature, must be aware of the yawning chasm between what is recognized as good statistical practice and what is actually published. Poor study design, inappropriate analysis and selective reporting are commonplace. In my opinion the most important challenge currently facing our profession is the task of bridging this chasm.

Consensus Statements as Topic↗
PubMedDate not supplied

Dynamic simulation of pH in anaerobic processes.

With the objective of contributing to the buildup of mathematical tools for anaerobic process simulation, an algorithm for the dynamic simulation of pH was developed. The dynamic simulation of the gaseous phase variables was also considered. The pH algorithm was validated for a watery system, obtaining good agreement between predicted and experimental data. The applied methodology provides a differential equation that allows the inclusion of pH as a state variable of the system that can be easily included in a general mathematical model of anaerobic digestion using matrix notation. This methodology also allows a noticeable decrease in computing time in simulations. A dynamic anaerobic digestion model of complex substrates taken from the literature was completed with the developed algorithms, and it was used to predict the response of an anaerobic reactor against overloading and against the presence of pH-dependent inhibitors with satisfactory results.

Algorithms↗