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PubMed2006

Wall correction factors, Pwall, for parallel-plate ionization chambers.

The EGSnrc Monte Carlo user-code CSnrc is used to calculate wall correction factors, Pwall,, for parallel-plate ionization chambers in photon and electron beams. A set of Pwall values, computed at the reference depth in water, is presented for several commonly used parallel-plate chambers. These values differ from the standard assumption of unity used by dosimetry protocols by up to 1.7% for clinical electron beams. Calculations also show that Pwall is strongly dependent on the depth of measurement and can vary by as much as 6% for a 6 MeV beam in moving from a depth of dref to a depth of R50. In photon beams, where there is limited information available regarding Pwall for parallel-plate chambers, CSnrc calculations show Pwall values of up to 2.4% at the reference depth over a range of photon energies. The Pwall values for photon beams are in good agreement with previous estimates of the wall correction but have much lower statistical uncertainties and cover a wider range of photon beam energies.

Algorithms↗
PubMed2004

The management of type 2 diabetes in children and adolescents.

The medical community faces an emerging epidemic of type 2 diabetes (T2DM) in children and adolescents with a disproportionate increase among certain ethnic groups. T2DM represents one arm of the metabolic syndrome and parallels an increasing prevalence of obesity. The metabolic syndrome includes insulin resistance, hyperlipidemia, and hypertension with a consequent risk of early cardiovascular disease. Thus, treatment of T2DM and the metabolic syndrome pose a challenge for pediatric endocrinologists and represent an enormous public health issue. This review presents information about the treatment of childhood T2DM.

Adolescent↗
PubMed2006

A distributed environment for the integration of multiple high-performance decision support systems into clinical workflow.

Current studies conclude that clinical decision support systems can help reduce serious medical errors. The importance of Causal Probabilistic Networks (CPNs) for constructing such systems is already well-known. However, the computational complexity of probabilistic inference, which results in unacceptably high response times, can hinder acceptance and integration into clinician workflow. This paper investigates the optimization and parallelization potential of complex CPN-based medical decision support systems and evaluates the results of implementing a parallel, high performance version of an existing decision support system concerning proper antibiotic treatment therapy. Furthermore, it discusses distributed computing techniques for making multiple high performance decision support systems available at the time and location of decision making, by exploiting computing resources residing inside, as well as outside the hospital walls optimally.

Algorithms↗
PubMed2003

Computed tomography of acute pulmonary embolism.

Pulmonary embolism (PE) is a common condition in which diagnostic and therapeutic delays contribute to substantial morbidity and mortality. Advances in spiral computed tomography (CT) scanner technology over the past 10 years have been paralleled by progressive improvement in the ability to identify and accurately evaluate the pulmonary arteries for acute PE using CT pulmonary angiography (CTPA). Preliminary studies indicate multi-detector CT (MDCT) scanners offer improved accuracy for distal segmental and subsegmental PE. The ability to directly visualize emboli using CTPA has led to its widespread implementation. Published studies using optimal techniques have found sensitivity and specificity of approximately 90%. Clinical signs and symptoms are nonspecific. Only 20% to 30% of those patients evaluated for acute PE are found to harbor emboli. Previous imaging algorithms offered limited diagnostic value for the remaining 70% to 80% of patients who proved not to have PE. It has been shown that spiral CT identifies an alternate diagnosis in approximately 70% of these patients, which, along with its rapid and widespread availability, largely accounts for its popularity with referring clinicians. It is noted that meta-analysis studies of the existing data regarding spiral CT in acute PE have shown deficiencies in study designs, indicating that further research is required. However, at this time, spiral CT is being widely employed in the diagnostic work-up of patients with suspected acute PE. This review will discuss the use of spiral CT for acute PE, including scan acquisition parameters, radiation dose, diagnostic findings, interpretive pitfalls and the role of leg vein studies.

Acute Disease↗
PubMed2003

Reconstruction of current density distributions in axially symmetric cylindrical sections using one component of magnetic flux density: computer simulation study.

In magnetic resonance current density imaging (MRCDI), we inject current into a subject through surface electrodes and measure the induced magnetic flux density B inside the subject using an MRI scanner. Once we have obtained all three components of B, we can reconstruct the internal current density distribution J = inverted triangle x B/mu0). This technique, however, requires subject rotation since the MRI scanner can measure only one component of B that is parallel to the direction of its main magnetic field. In this paper, under the assumption that the out-of-plane current density Jz is negligible in an imaging slice belonging to the xy-plane, we developed an imaging technique of current density distributions using only Bz, the z-component of B. The technique described in this paper does not require a subject rotation but the quality of reconstructed images depends on the amount of out-of-plane current density Jz. From numerical simulations, we found that the new algorithm could be applied to subjects such as human limbs using longitudinal electrodes.

Algorithms↗
PubMed2005

Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-beta-lactamase by polarizable molecular mechanics. Validation on model binding sites by quantum chemistry.

Using the polarizable molecular mechanics method SIBFA, we have performed a search for the most stable binding modes of D- and L-thiomandelate to a 104-residue model of the metallo-beta-lactamase from B. fragilis, an enzyme involved in the acquired resistance of bacteria to antibiotics. Energy balances taking into account solvation effects computed with a continuum reaction field procedure indicated the D-isomer to be more stably bound than the L-one, conform to the experimental result. The most stably bound complex has the S(-) ligand bridging monodentately the two Zn(II) cations and one carboxylate O(-) H-bonded to the Asn193 side chain. We have validated the SIBFA energy results by performing additional SIBFA as well as quantum chemical (QC) calculations on small (88 atoms) model complexes extracted from the 104-residue complexes, which include the residues involved in inhibitor binding. Computations were done in parallel using uncorrelated (HF) as well as correlated (DFT, LMP2, MP2) computations, and the comparisons extended to corresponding captopril complexes (Antony et al., J Comput Chem 2002, 23, 1281). The magnitudes of the SIBFA intermolecular interaction energies were found to correctly reproduce their QC counterparts and their trends for a total of twenty complexes.

Algorithms↗
PubMed1996

Determination of spinal facet joint loads from extra articular strains--a theoretical validation.

Loads on the facet joints of the lumbar spine may play a role in low back pain. Abnormal loading of the facets, either primarily or as a consequence of disc degeneration, may accelerate their degeneration. Study of these phenomena is difficult, since here are few methods for a direct measure of facet forces occurring in vivo. The authors developed a method for the direct measure of facet forces in a canine animal model of spine disease using strain gages. The method used empirical calibration of the strain gages, which was used to reduce experimental strain output to facet force during function. In this Technical Note, a theoretical model is formulated, solved and validated which gives a theoretical basis for the data reduction method. The facet is modeled as a cantilevered plate and deformations, as function of applied normal load, solved for using a finite difference method. The model is validated by comparison with two experiments with strain-gaged facets. Results from the model show that a minimum of three strain gages is required to determine uniquely the location and magnitude of an applied load to the facet, and that at least two gages should be placed in the region where the cranial articular process joins the pedicle with the gage axis parallel to that of the process. Plate surface strains were found to be insensitive to changes in the area of the applied loads, for a given resultant force magnitude. The method may be useful in other applications in which resultant force magnitude and location need to be measured on plate-like structures.

Algorithms↗
PubMedDate not supplied

Hardware optimization and serial implementation of a novel spiking neuron model for the POEtic tissue.

In this paper we describe the hardware implementation of a spiking neuron model, which uses a spike time dependent plasticity (STDP) rule that allows synaptic changes by discrete time steps. For this purpose an integrate-and-fire neuron is used with recurrent local connections. The connectivity of this model has been set to 24 neighbours, so there is a high degree of parallelism. After obtaining good results with the hardware implementation of the model, we proceed to simplify this hardware description, trying to keep the same behaviour. Some experiments using dynamic grading patterns have been used in order to test the learning capabilities of the model. Finally, the serial implementation has been realized.

Action Potentials↗
PubMed1998

Local online learning of coherent information.

One of the goals of perception is to learn to respond to coherence across space, time and modality. Here we present an abstract framework for the local online unsupervised learning of this coherent information using multi-stream neural networks. The processing units distinguish between feedforward inputs projected from the environment and the lateral, contextual inputs projected from the processing units of other streams. The contextual inputs are used to guide learning towards coherent cross-stream structure. The goal of all the learning algorithms described is to maximize the predictability between each unit output and its context. Many local cost functions may be applied: e.g. mutual information, relative entropy, squared error and covariance. Theoretical and simulation results indicate that, of these, the covariance rule (1) is the only rule that specifically links and learns only those streams with coherent information, (2) can be robustly approximated by a Hebbian rule, (3) is stable with input noise, no pairwise input correlations, and in the discovery of locally less informative components that are coherent globally. In accordance with the parallel nature of the biological substrate, we also show that all the rules scale up with the number of streams.

Journal Article↗
PubMed2005

Noninvasive detection of coronary atherosclerotic plaque by multidetector row computed tomography.

BACKGROUND: Coronary artery disease continues to be one of the leading causes of death and disability around the globe, challenging the efficacy of currently applied schemes to predict the risk for future coronary events. In fact, algorithms such as the Framingham risk score that are based on traditional risk factors like hypertension and dyslipidemia are not very sensitive, leaving a majority of the population at intermediate risk. METHODS: Advances in multidetector computed tomography (MDCT) technology with submillimeter slice collimation (approximately 0.6 mm) and high temporal resolution now permit contrast-enhanced imaging of the coronary artery lumen and wall in a single breath hold. The current generation of MDCT provided in-plane resolution of 0.5 mm and a temporal resolution of 210 ms. The simultaneous acquisition of 16/64 parallel cross-sections reduces image acquisition time to about 10-20s using 60-80 ml of contrast agents to opacify the coronary artery lumen. CT imaging for coronary calcification is an established method with low radiation exposure. The amount of calcification is expressed as an Agatston Score (AS). RESULTS: The presence and amount of coronary calcification significantly increases the relative risk for future coronary events, independent from traditional risk factors (risk ratio 8.7 [95% Cl, 2.7-28.1]). Especially, individuals with a high AS (>400) who are at intermediate 10-y Framingham event risk may benefit from this additional risk stratification. However, calcification is rarely present in children and adolescents. However, there is a growing body of evidence suggesting that contrast-enhanced MDCT can detect both calcified and noncalcified plaques with high sensitivity and specificity for the detection of plaques > 0.5 mm when compared to intravascular ultrasound. Moreover, initial data suggest that plaque characteristics such as plaque area, volume, quantify and coronary plaque remodeling index can be quantified in good agreement with IVUS. The composition of noncalcified plaque may be further stratified into predominantly fibrous or lipid-rich plaque. Noncalcified plaque may be present already in children and adolescents with multiple risk factors. CONCLUSION: The available data indicate that high resolution MDCT can reliably detect, quantify and characterize calcified and noncalcified coronary atherosclerotic plaque. With MDCT, we now have a unique opportunity to study the natural history and response to therapy of noncalcified coronary plaques, which may be already present in obese children or children with multiple risk factors.

Adolescent↗
PubMed2005

The feasibility of spatial high-resolution magnetic resonance angiography (MRA) of the renal arteries at 3.0 T.

PURPOSE: To evaluate the feasibility of high-spatial resolution magnetic resonance angiography (MRA) of the renal arteries at 3.0 T. MATERIAL AND METHODS: Twelve healthy volunteers (mean age, 38.8 years) underwent renal MRA at 3.0 T. The application of parallel imaging with an acceleration factor of 3 allowed obtaining MR angiographic data with a voxel size of 0.9 x 0.8 x 0.9 mm in scan time of only 16 s. A dose of 0.2 mmol/kg body weight of 0.5-molar gadodiamide was administered at a flow rate of 2 ml/s. For image analysis, image quality, presence of artifacts, venous contamination and level of noise were rated by two radiologists in consensus. RESULTS: All examinations were of diagnostic quality. The image quality was rated good or very good in 91 % (11/12) of cases. Due to the high parallel imaging factor the level of noise was slightly increased without diagnostic impairment. Mild venous enhancement was found in 75 % (9/12) of the examinations. CONCLUSION: Renal MRA at 3.0 T is feasible with high spatial resolution and a short acquisition time.

Adult↗
PubMed1991

Molecular dynamics of phenol at the liquid-vapor interface of water.

Molecular dynamics results are presented for phenol at the water liquid-vapor interface at 300 K. The calculated excess free energy of phenol at the interface is -2.8 +/- 0.4 kcal/mol, in good agreement with the recent experimental results of Eisenthal and co-workers. The most probable orientation of the phenol molecule at the surface is such that the aromatic ring is perpendicular to the interface and the OH group is fully immersed in water. The hydroxyl substituent has a preferred orientation which is similar to the orientation of OH bonds of water at the pure water liquid-vapor interface. The transition between interfacial and bulk-like behavior of phenol is abrupt and occurs when the center of mass of the solute is located about 6 angstroms from the Gibbs surface of water. In this region the para carbon atom of the hydrophobic benzene ring can reach the interface and become partially dehydrated. This result suggests that the width of the interfacial region in which the behavior of a simple amphiphilic solute in water is influenced by the presence of the surface depends primarily on the size of its hydrophobic part. The role of the OH substituent was investigated by comparing phenol at the interface with two model systems: benzene with and without partial charges on carbon and hydrogen atoms. It is shown that in the absence of the hydrophilic substituent the solute is located further away from the liquid phase and is more likely to be oriented parallel to the interface. However, when the center of mass of the solute is moved into the interfacial region where the density of water approaches that of the bulk solvent, all three molecules become oriented perpendicularly to the surface. In this orientation the work of cavity formation needed to accommodate the hydrophobic ring in aqueous solvent is minimized.

Algorithms↗
PubMed2003

Interaction of cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine-cytosine base tetrads with K+, Na+ and Li+ ions -- a density functional study.

We have carried out B3LYP hybrid density functional studies of complexes formed by cyclic cytosine-, guanine-, thymine-, uracil- and mixed guanine cytosine-tetrads with Li+, Na+ and K+ ions to determine their structures and interaction energies. The conformations studied have been restricted to a hydrogen bond pattern closely related to the tetrads observed in experimental nucleic acid structures. A comparison of the alkali metal ion/tetrad complexes with the tetrads without cations indicates that alkali metal ions modulate the tetrad structures significantly and that even the hydrogen bond pattern may change. Guanine-tetrad cation complexes show the strongest interaction energy compared to other tetrads that occur less frequently in experimental structures. The most stable G-tetrad/metal ion structure adopts a nearly planar geometry that is especially suitable for tetraplex formation, which requires approximately parallel tetrad planes. In the cytosine-tetrad there is a very large central cavity suitable for cation recognition, but the complexes adopt a non-planar structure unsuitable for stacking, except possibly for ions with very large radii. Uracil and thymine tetrads show a significant different characteristics which may contribute to the differences between DNA and RNA

Algorithms↗
PubMed2005

JCat: a novel tool to adapt codon usage of a target gene to its potential expression host.

A novel method for the adaptation of target gene codon usage to most sequenced prokaryotes and selected eukaryotic gene expression hosts was developed to improve heterologous protein production. In contrast to existing tools, JCat (Java Codon Adaptation Tool) does not require the manual definition of highly expressed genes and is, therefore, a very rapid and easy method. Further options of JCat for codon adaptation include the avoidance of unwanted cleavage sites for restriction enzymes and Rho-independent transcription terminators. The output of JCat is both graphically and as Codon Adaptation Index (CAI) values given for the pasted sequence and the newly adapted sequence. Additionally, a list of genes in FASTA-format can be uploaded to calculate CAI values. In one example, all genes of the genome of Caenorhabditis elegans were adapted to Escherichia coli codon usage and further optimized to avoid commonly used restriction sites. In a second example, the Pseudomonas aeruginosa exbD gene codon usage was adapted to E.coli codon usage with parallel avoidance of the same restriction sites. For both, the degree of introduced changes was documented and evaluated. JCat is integrated into the PRODORIC database that hosts all required information on the various organisms to fulfill the requested calculations. JCat is freely accessible at http://www.prodoric.de/JCat.

Algorithms↗
PubMed2005

Steroid-resistant inflammation in a rat model of chronic obstructive pulmonary disease is associated with a lack of nuclear factor-kappaB pathway activation.

RATIONALE: Emphysema is one component of chronic obstructive pulmonary disease (COPD), a respiratory disease currently increasing in prevalence worldwide. The mainstay therapy adopted to treat patients with COPD is glucocorticoids; unfortunately, this treatment has limited impact on disease symptoms or underlying airway inflammation. OBJECTIVE: There is an urgent need to develop therapies that modify both the underlying inflammation, thought to be involved in disease progression, and the structural changes in the emphysematous lung. METHODS: We have characterized an elastase-driven model of experimental emphysema in the rat that demonstrates COPD-like airway inflammation and determined the impact of a clinically relevant glucocorticoid. MEASUREMENTS AND MAIN RESULTS: We observed an increase in lung neutrophils, lymphomononuclear cells, mucus production, and inflammatory cytokines. Also present were increases in average air space area, which are associated with emphysema-like changes in lung function, such as increased residual volume and decreased flow; these increases in area were maintained for up to 10 weeks. In addition, we observed that elastase-induced airway neutrophilia is steroid resistant. Interestingly, the inflammation observed after elastase administration was found to be temporally associated with a lack of nuclear factor-kappaB pathway activation. This apparent nuclear factor-kappaB-independent inflammation may explain why treatment with a glucocorticoid was ineffective in this preclinical model and could suggest parallels in the steroid-resistant human disease. CONCLUSION: We believe that this model, in addition to its suitability for testing therapies that may modify existing emphysema, could be useful in the search for new therapies to reduce the steroid-resistant airway inflammation evident in COPD.

Algorithms↗
PubMed2005

Near-infrared spectroscopic study of the physical and mechanical properties of wood with meso- and micro-scale anatomical observation.

Estimation of the density along with the tensile strength of wood within both the elastic and plastic deformation ranges, represented as modulus of elasticity (MOE) and ultimate tensile stress (UTS), respectively, were performed using near-infrared (NIR) spectroscopy. A partial least squares (PLS) analysis was applied to the measurements of density, MOE, and UTS, and resulted in a high accuracy of prediction, independent of wood species. The correlation coefficient between the NIR spectra and criterion variables, and the regression vector resulting from the PLS analysis, suggested that the characteristic absorption bands were strongly related to the predictability of each property. In the case of softwood, absorption bands due to intra-molecular hydrogen-bonded OH groups in the crystalline regions of cellulose, which are oriented preferentially in a direction parallel to the cellulose chain, might strongly affect the tensile strength of softwood. Hardwoods have much more complex and variable structures than softwoods; therefore, it was supposed that the key factor governing the tensile strength in hardwood would be the interaction between the three principal constituents (i. e., cellulose, hemicellulose, and lignin) of wood.

Algorithms↗
PubMed1992

Grand challenges in biomedical computing.

Advances in computing technology (both algorithms and hardware) over the next several years promise to make increasingly sophisticated computer modeling of biomedical phenomena a routine part of biomedical research. Improvements in both the absolute speed of processors and in their programming and graphics interfaces will allow nonexpert users to bring computing power equivalent to the supercomputers of a few years ago to bear on routine research problems and to display complex data in understandable ways (visualization). Although biomedical applications have traditionally not driven the leading edge of computing and supercomputing, such applications are increasingly being ported to advanced parallel and vector processors. This paper summarizes the current state of biomedical computing, citing examples of the best practice in research today. A number of projects enabled by advanced computing from various subdisciplines are described. Trends in technology for both inexpensive (workstation) and high-end computing (vector supercomputers and parallel processors) are cited; the implications of these for biomedical computing are discussed. "Grand challenges" in biomedical computing, i.e., computational problems of major scientific importance that are beyond our current capabilities but that might be achieved in a 5-year time frame, are outlined.

Attitude to Computers↗
PubMed2006

Quantification of lung tumor volume and rotation at 3D dynamic parallel MR imaging with view sharing: preliminary results.

The purpose of this study was to prospectively evaluate the volumes and rotations of pulmonary nodules during respiration by using three-dimensional fast low-angle shot dynamic magnetic resonance (MR) imaging (1.5/0.6 [repetition time msec/echo time msec], 3.8 x 3.8 x 3.8-mm voxel size, imaging time per three-dimensional data set of 1 second). The feasibility of the technique was verified by using 130-, 40-, and 12-cm3 phantoms made of meatballs and in five patients with solitary intrapulmonary tumors (four men, one woman; median age, 60 years) at computed tomography and histologic analysis. All patients provided written informed consent, and the study was institutional review board approved. It was proved that there were no substantial differences among the 21 algorithms used to correct partial volume effects. The most precise algorithm (r > 0.9, P < .01) used to correct partial volume effects--with which mean phantom volumes of 120.8 cm3 +/- 4.1, 36.1 cm3 +/- 3.98, and 13.1 cm3 +/- 1.5 were calculated--yielded a root mean square error of 14%. The MR imaging-derived nodule volume and rotation during respiration could be quantified by using oriented bounding box techniques.

Aged↗