Development of a generalized method to allow the estimation of doses to the ICRP reference adults from CT, on the basis of normalized organ and CTDI dose data determined by Monte Carlo calculation for a range of contemporary scanners.

Objective. Development of a method to provide organ and effective dose coefficients to reference adults for any CT scanner based on values ofCTDImeasured both in air and in standard CT dosimetry phantoms.Approach. Results from previous Monte Carlo simulations for a range of contemporary CT scanners have been analyzed to provide linear models relating values of organ dose (normalized toCTDIfree-in-air), for each slab of 3 reference phantoms (ICRP Male/Female, and AH hermaphrodite), to similarly normalized values ofCTDIin standard CT dosimetry phantoms. Three methods have been investigated to apply the models to values ofCTDIfor a 'new' scanner not previously simulated: a Generic approach using averaged normalized organ dose profiles for whole body exposure of the phantoms; and two processes for matching the scanner, on the basis of normalized organ doses or effective dose (nE103,phan), to one of the 102 sets of dose coefficients previously calculated for 12 contemporary CT scanner models, from 4 manufacturers, operating under a range of conditions.Main results. The merit of each method has been quantitatively assessed when applied to both the present contemporary scanners with each test data set being excluded in turn during the matching process, and also to 3 previously-simulated older scanners. Whereas all three methods appear viable, with all doses being within 1% and 10% for the contemporary and old scanners respectively, matching tonE103,phanis overall the approach preferred in practice, yielding an uncertainty of around 6% in estimated values ofnE103,phan. The present methodology also provides superior performance when compared against some other common normalization factors forE103,phan.Significance. The CT dose model and the data sets will be incorporated into a new CT dosimetry tool that will be made available from UKHSA in support of facilitating improvements in patient protection.

CT scanner-specific organ dose coefficients generated by Monte Carlo calculation for the ICRP adult male and female reference computational phantoms.

Objective.Provide analyses of new organ dose coefficients (hereafter also referred to as normalized doses) for CT that have been developed to update the widely-utilized collection of data published 30 years ago in NRPB-SR250.Approach.In order to reflect changes in technology, and also ICRP recommendations concerning use of the computational phantoms adult male (AM) and adult female (AF), 102 series of new Monte Carlo simulations have been performed covering the range of operating conditions for 12 contemporary models of CT scanner from 4 manufacturers. Normalized doses (relative to free air on axis) have been determined for 39 organs, and for every 8 mm or 4.84 mm slab of AM and AF, respectively.Main results.Analyses of results confirm the significant influence (by up to a few tens of percent), on values of normalized organ (or contributions to effective dose (E103,phan)), for whole body exposure arising from selection of tube voltage and beam shaping filter. Use of partial (when available) rather than a Full fan beam reduced both organ and effective dose by up to 7%. Normalized doses to AF were larger than corresponding figures for AM by up to 30% for organs and by 10% forE103,phan. Additional simulations for whole body exposure have also demonstrated that: practical simplifications in the main modelling (point source, single slice thickness, neglect of patient couch and immobility of phantom arms) have sufficiently small (<5%) effect onE103,phan; mis-centring of the phantom away from the axis of rotation by 5 mm (in any direction) leads to changes in normalized organ dose andE103,phanby up to 20% and 6%, respectively; and angular tube current modulation can result in reductions by up to 35% and <15% in normalized organ dose andE103,phan, respectively, for 100% cosine variation.Significance.These analyses help advance understanding of the influence of operational scanner settings on organ dose coefficients for contemporary CT, in support of improved patient protection. The results will allow the future development of a new dose estimation tool.

Selection of bone dosimetry models for application in Monte Carlo simulations to provide CT scanner-specific organ dose coefficients.

This is the second paper arising from a project concerning the application of Monte Carlo simulations to provide scanner-specific organ dose coefficients for modern CT scanners. The present focus is centred on the bone dosimetry models that have been developed. Simulations have been performed in photon only transport mode, with the assumption of electron equilibrium. This approximation breaks down for doses to active marrow and endosteum since the target cells are localised within tens of micrometre from bone tissue and dose enhancement functions are necessary to correct for the additional dose from photoelectric electrons created in adjacent material. The dose enhancement models used previously in publications NRPB-SR250 (Jones and Shrimpton 1993 Software Report NRPB-SR250, National Radiological Protection Board, Chilton, UK) and ORNL-TM8381 (Cristy and Eckerman 1987 Technical Report Oak Ridge National Laboratory, Oak Ridge, TN) have been implemented and compared with the contemporary approaches of Johnson et al (2011 Phys. Med. Biol. 56 2347-65) and ICRP Publication 116 (ICRP 2010 Ann. ICRP 40 1-257) that are being adopted in the present project. In addition, the calculation of dose to endosteum in the medullary cavity is reviewed and updated using electron mode simulations. For the purposes of quality assurance and comparison, the various dose enhancement functions have been applied in relation to the NRPB18+DJ and HPA18+ stylised hermaphrodite phantoms and also the adult male and female voxel phantoms recommended in ICRP Publication 110 (ICRP 2009 Ann. ICRP 39 1-165), for exposure from three CT scanners modelled previously. Contemporary results for standard examinations on the head and trunk calculated for these latter phantoms demonstrate moderate increases (modal value +18%) in active marrow dose coefficients relative to values derived from data published in NRPB-SR250. A similar analysis in relation to endosteum dose coefficients shows larger reductions (modal value -46%), owing at least in part to changes in assumed location of the target cells. Even larger changes are apparent for both of these dose coefficients in relation to examination of the upper legs (-39% and -94%, respectively). However, resultant changes in any values of effective dose will be less owing to the low weighting factors applied for these tissues.

Development of Monte Carlo simulations to provide scanner-specific organ dose coefficients for contemporary CT.

The ImPACT (imaging performance assessment of CT scanners) CT patient dosimetry calculator is still used world-wide to estimate organ and effective doses (E) for computed tomography (CT) examinations, although the tool is based on Monte Carlo calculations reflecting practice in the early 1990's. Subsequent developments in CT scanners, definitions of E, anthropomorphic phantoms, computers and radiation transport codes, have all fuelled an urgent need for updated organ dose conversion factors for contemporary CT. A new system for such simulations has been developed and satisfactorily tested. Benchmark comparisons of normalised organ doses presently derived for three old scanners (General Electric 9800, Philips Tomoscan LX and Siemens Somatom DRH) are within 5% of published values. Moreover, calculated normalised values of CT Dose Index for these scanners are in reasonable agreement (within measurement and computational uncertainties of ±6% and ±1%, respectively) with reported standard measurements. Organ dose coefficients calculated for a contemporary CT scanner (Siemens Somatom Sensation 16) demonstrate potential deviations by up to around 30% from the surrogate values presently assumed (through a scanner matching process) when using the ImPACT CT Dosimetry tool for newer scanners. Also, illustrative estimates of E for some typical examinations and a range of anthropomorphic phantoms demonstrate the significant differences (by some 10's of percent) that can arise when changing from the previously adopted stylised mathematical phantom to the voxel phantoms presently recommended by the International Commission on Radiological Protection (ICRP), and when following the 2007 ICRP recommendations (updated from 1990) concerning tissue weighting factors. Further simulations with the validated dosimetry system will provide updated series of dose coefficients for a wide range of contemporary scanners.

Updated estimates of typical effective doses for common CT examinations in the UK following the 2011 national review.

OBJECTIVE: To investigate the impact of evolving International Commission on Radiological Protection (ICRP) recommendations concerning calculation of effective dose (E) and compare updated typical UK values for common CT examinations with previous data. METHODS: Monte Carlo simulations have provided normalized organ doses relating to 15 CT scanner models and 5 virtual reference adults. Series of representative E/dose-length product (DLP) coefficients were derived for common examinations on the separate bases of not only older stylized mathematical phantoms and voxel phantoms presently recommended by ICRP, but also the 1977, 1990 and 2007 formulations for E. Updated E/DLP coefficients were applied to typical values of DLP from the 2011 UK survey. RESULTS: Changes in ICRP recommendations that have arisen from improving evidence on stochastic risk, influence values of E by up to a factor two for CT examinations of the head and neck, although differences for the trunk typically amount to ±10%. Adoption of the voxel rather than the mathematical phantoms used previously can lead to further changes in E by a few tens of percent. Updated typical values of E for UK CT examinations range from 2 to 20 mSv. Increases by 20-400% since 2003 arise not only from increases by 30-160% in typical values of DLP, but also increases by 30-90% in relation to E/DLP coefficients for examinations of the trunk. CONCLUSION: Values of E, including updated typical data for UK CT, should be compared with caution in relation to their purpose and underlying factors concerning their calculation. ADVANCES IN KNOWLEDGE: Updated E/DLP coefficients and typical values of E for UK CT, and an appreciation of factors influencing these data.

The effect of angular and longitudinal tube current modulations on the estimation of organ and effective doses in x-ray computed tomography.

PURPOSE: Tube current modulation (TCM) is one of the recent developments in multislice CT that has proven to reduce the patient radiation dose without affecting the image quality. Presently established methods and published coefficients for estimating organ doses from the dose measured free in air on the axis of rotation or in the CT dose index (CTDI) dosimetry phantoms do not take into account this relatively new development in CT scanner design and technology. Based on these organ dose coefficients effective dose estimates can be made. The estimates are not strictly valid for CT scanning protocols utilizing TCM. In this study, the authors investigated the need to take TCM into account when estimating organ and effective dose values. METHODS: A whole-body adult anthropomorphic phantom (Alderson Rando) was scanned with a multislice CT scanner (Somatom Definition, Siemens, Forchheim, Germany) utilizing TCM (CareDose4D). Tube voltage was 120 kV, beam collimation 19.2 mm, and pitch 1. A voxelized patient model was used to define the tissues and organs in the phantom. Tube current values as a function of tube angle were obtained from the raw data for each individual tube rotation of the scan. These values were used together with the Monte Carlo dosimetry tool IMPACTMC (VAMP GmbH, Erlangen, Germany) to calculate organ dose values both with and without account of TCM. Angular and longitudinal modulations were investigated separately. Finally, corresponding effective dose conversion coefficients were determined for both cases according to the updated 2007 recommendations of the ICRP. RESULTS: TCM amplitude was greatest in the shoulder and pelvic regions. Consequently, dose distributions and organ dose values for particular cross sections changed considerably when taking angular modulation into account. The effective dose conversion coefficients were up to 11% lower for a single rotation in the shoulder region and 17% lower in the pelvis when taking angular TCM into account. In the head, neck, thorax, and upper abdominal regions, conversion coefficients changed similarly by only 5% or less. Conversion coefficients for estimating effective doses for scans of complete regions, e.g., chest or abdomen, were approximately 8% lower when taking angular and longitudinal TCMs into account. CONCLUSIONS: The authors conclude that for accurate organ and effective dose estimates in individual cross sections in the shoulder or pelvic regions, the angular tube current modulation should be taken into account. In general, using the average of the modulated tube current causes an overestimation of the effective dose.

Discovering rules for protein-ligand specificity using support vector inductive logic programming.

Structural genomics initiatives are rapidly generating vast numbers of protein structures. Comparative modelling is also capable of producing accurate structural models for many protein sequences. However, for many of the known structures, functions are not yet determined, and in many modelling tasks, an accurate structural model does not necessarily tell us about function. Thus, there is a pressing need for high-throughput methods for determining function from structure. The spatial arrangement of key amino acids in a folded protein, on the surface or buried in clefts, is often the determinants of its biological function. A central aim of molecular biology is to understand the relationship between such substructures or surfaces and biological function, leading both to function prediction and to function design. We present a new general method for discovering the features of binding pockets that confer specificity for particular ligands. Using a recently developed machine-learning technique which couples the rule-discovery approach of inductive logic programming with the statistical learning power of support vector machines, we are able to discriminate, with high precision (90%) and recall (86%) between pockets that bind FAD and those that bind NAD on a large benchmark set given only the geometry and composition of the backbone of the binding pocket without the use of docking. In addition, we learn rules governing this specificity which can feed into protein functional design protocols. An analysis of the rules found suggests that key features of the binding pocket may be tied to conformational freedom in the ligand. The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/.

Validation of a Monte Carlo tool for patient-specific dose simulations in multi-slice computed tomography.

Estimating the dose delivered to the patient in X-ray computed tomography (CT) examinations is not a trivial task. Monte Carlo (MC) methods appear to be the method of choice to assess the 3D dose distribution. The purpose of this work was to extend an existing MC-based tool to account for arbitrary scanners and scan protocols such as multi-slice CT (MSCT) scanners and to validate the tool in homogeneous and heterogeneous phantoms. The tool was validated by measurements on MSCT scanners for different scan protocols under known conditions. Quantitative CT Dose Index (CTDI) measurements were performed in cylindrical CTDI phantoms and in anthropomorphic thorax phantoms of various sizes; dose profiles were measured with thermoluminescent dosimeters (TLD) in the CTDI phantoms and compared with the computed dose profiles. The in-plane dose distributions were simulated and compared with TLD measurements in an Alderson-Rando phantom. The calculated dose values were generally within 10% of measurements for all phantoms and all investigated conditions. Three-dimensional dose distributions can be accurately calculated with the MC tool for arbitrary scanners and protocols including tube current modulation schemes. The use of the tool has meanwhile also been extended to further scanners and to flat-detector CT.

A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming.

Despite the increased recent use of protein-ligand and protein-protein docking in the drug discovery process due to the increases in computational power, the difficulty of accurately ranking the binding affinities of a series of ligands or a series of proteins docked to a protein receptor remains largely unsolved. This problem is of major concern in lead optimization procedures and has lead to the development of scoring functions tailored to rank the binding affinities of a series of ligands to a specific system. However, such methods can take a long time to develop and their transferability to other systems remains open to question. Here we demonstrate that given a suitable amount of background information a new approach using support vector inductive logic programming (SVILP) can be used to produce system-specific scoring functions. Inductive logic programming (ILP) learns logic-based rules for a given dataset that can be used to describe properties of each member of the set in a qualitative manner. By combining ILP with support vector machine regression, a quantitative set of rules can be obtained. SVILP has previously been used in a biological context to examine datasets containing a series of singular molecular structures and properties. Here we describe the use of SVILP to produce binding affinity predictions of a series of ligands to a particular protein. We also for the first time examine the applicability of SVILP techniques to datasets consisting of protein-ligand complexes. Our results show that SVILP performs comparably with other state-of-the-art methods on five protein-ligand systems as judged by similar cross-validated squares of their correlation coefficients. A McNemar test comparing SVILP to CoMFA and CoMSIA across the five systems indicates our method to be significantly better on one occasion. The ability to graphically display and understand the SVILP-produced rules is demonstrated and this feature of ILP can be used to derive hypothesis for future ligand design in lead optimization procedures. The approach can readily be extended to evaluate the binding affinities of a series of protein-protein complexes.

Protein motions during catalysis by dihydrofolate reductases.

Dihydrofolate reductase (DHFR) maintains the intracellular pool of tetrahydrofolate through catalysis of hydrogen transfer from reduced nicotinamide adenine dinucleotide to 7,8-dihydrofolate. We report results for pre-steady-state kinetic studies of the temperature dependence of the rates and the hydrogen/deuterium-kinetic isotope effects for the reactions catalysed by the enzymes from the mesophilic Escherichia coli and the hyperthermophilic Thermatoga maritima. We propose an evolutionary pattern in which catalysis progressed from a relatively rigid active site structure in the ancient thermophilic DHFR to a more flexible and kinetically more efficient structure in E. coli that actively promotes hydrogen transfer at physiological pH by modulating the tunnelling distance. The E. coli enzyme appeared relatively robust, in that kinetically severely compromised mutants still actively propagated the reaction. The reduced hydrogen transfer rates of the extensively studied Gly121Val mutant of DHFR from E. coli were most likely due to sterically unfavourable long-range effects from the introduction of the bulky isopropyl group.

Isolation of a small molecule inhibitor of DNA base excision repair.

The base excision repair (BER) pathway is essential for the removal of DNA bases damaged by alkylation or oxidation. A key step in BER is the processing of an apurinic/apyrimidinic (AP) site intermediate by an AP endonuclease. The major AP endonuclease in human cells (APE1, also termed HAP1 and Ref-1) accounts for >95% of the total AP endonuclease activity, and is essential for the protection of cells against the toxic effects of several classes of DNA damaging agents. Moreover, APE1 overexpression has been linked to radio- and chemo-resistance in human tumors. Using a newly developed high-throughput screen, several chemical inhibitors of APE1 have been isolated. Amongst these, CRT0044876 was identified as a potent and selective APE1 inhibitor. CRT0044876 inhibits the AP endonuclease, 3'-phosphodiesterase and 3'-phosphatase activities of APE1 at low micromolar concentrations, and is a specific inhibitor of the exonuclease III family of enzymes to which APE1 belongs. At non-cytotoxic concentrations, CRT0044876 potentiates the cytotoxicity of several DNA base-targeting compounds. This enhancement of cytotoxicity is associated with an accumulation of unrepaired AP sites. In silico modeling studies suggest that CRT0044876 binds to the active site of APE1. These studies provide both a novel reagent for probing APE1 function in human cells, and a rational basis for the development of APE1-targeting drugs for antitumor therapy.

Pivotal role of Gly 121 in dihydrofolate reductase from Escherichia coli: the altered structure of a mutant enzyme may form the basis of its diminished catalytic performance.

The structure and folding of dihydrofolate reductase (DHFR) from Escherichia coli and the mutant G121V-DHFR, in which glycine 121 in the exterior FG loop was replaced with valine, were studied by molecular dynamics simulations and CD and fluorescence spectroscopy. The importance of residue 121 for the chemical step during DHFR catalysis had been demonstrated previously. High-temperature MD simulations indicated that while DHFR and G121V-DHFR followed similar unfolding pathways, the strong contacts between the M20 loop and the FG loop in DHFR were less stable in the mutant. These contacts have been proposed to be involved in a coupled network of interactions that influence the protein dynamics and promote catalysis [Benkovic, S. J., and Hammes-Schiffer, S. (2003) Science 301, 1196-1202]. CD spectroscopy of DHFR and G121V-DHFR indicated that the two proteins existed in different conformations at room temperature. While the thermally induced unfolding of DHFR was highly cooperative with a midpoint at 51.6 +/- 0.7 degrees C, G121V-DHFR exhibited a gradual decrease in its level of secondary structure without a clear melting temperature. Temperature-induced unfolding and renaturation from the urea-denatured state revealed that both proteins folded via highly fluorescent intermediates. The formation of these intermediates occurred with relaxation times of 149 +/- 4.5 and 256 +/- 13 ms for DHFR and G121V-DHFR, respectively. The fluorescence intensity for the intermediates formed during refolding of G121V-DHFR was approximately twice that of the wild-type. While the fluorescence intensity then slowly decayed for DHFR toward a state representing the native protein, G121V-DHFR appeared to be trapped in a highly fluorescent state. These results suggest that the reduced catalytic activity of G121V-DHFR is the consequence of nonlocal structural effects that may result in a perturbation of the network of promoting motions.

Functional role for Tyr 31 in the catalytic cycle of chicken dihydrofolate reductase.

Despite much work, many key aspects of the mechanism of the dihydrofolate reductase (DHFR) catalyzed reduction of dihydrofolate remain unresolved. In bacterial forms of DHFR both substrate and water access to the active site are controlled by the conformation of the mobile M20 loop. In vertebrate DHFRs only one conformation of the residues corresponding to the M20 loop has been observed. Access to the active site was proposed to be controlled by residue 31. MD simulations of chicken DHFR complexed with substrates and cofactor revealed a closing of the side chain of Tyr 31 over the active site on binding of dihydrofolate. This conformational change was dependent on the presence of glutamate on the para-aminobenzoylamide moiety of dihydrofolate. In its absence, the conformation remained open. Although water could enter the active site and hydrogen bond to N5 of dihydrofolate, indicating the feasibility of water as the proton donor, this was not controlled by the conformation of Tyr 31. The water accessibility of the active site was low for both conformations of Tyr 31. However, when hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the average time during which water was found in hydrogen bonding distance to N5 of dihydrofolate in the active site increased almost fivefold. These results indicated that water can serve as the Broensted acid for the protonation of N5 of dihydrofolate during the DHFR catalyzed reduction.

Role of water in the catalytic cycle of E. coli dihydrofolate reductase.

Dihydrofolate reductase (DHFR) catalyzes the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of 7,8-dihydrofolate (H2F) to 5,6,7,8-tetrahydrofolate (H4F). Because of the absence of any ionizable group in the vicinity of N5 of dihydrofolate it has been proposed that N5 could be protonated directly by a water molecule at the active site in the ternary complex of the Escherichia coli enzyme with cofactor and substrate. However, in the X-ray structures representing the Michaelis complex of the E. coli enzyme, a water molecule has never been observed in a position that could allow protonation of N5. In fact, the side chain of Met 20 blocks access to N5. Energy minimization reported here revealed that water could be placed in hydrogen bonding distance of N5 with only minor conformational changes. The r.m.s. deviation between the conformation of the M20 loop observed in the crystal structures of the ternary complexes and the conformation adopted after energy minimization was only 0.79 A. We performed molecular dynamics simulations to determine the accessibility by water of the active site of the Michaelis complex of DHFR. Water could access N5 relatively freely after an equilibration time of approximately 300 psec during which the side chain of Met 20 blocked water access. Protonation of N5 did not increase the accessibility by water. Surprisingly the number of near-attack conformations, in which the distance between the pro-R hydrogen of NADPH and C6 of dihydrofolate was less than 3.5 A and the angle between C4 and the pro-R hydrogen of NADPH and C6 of dihydrofolate was greater than 120 degrees, did not increase after protonation. However, when the hydride was transferred from NADPH to C6 of dihydrofolate before protonation, the side chain of Met 20 moved away from N5 after approximately 100 psec thereby providing water access. The average time during which water was found in hydrogen bonding distance to N5 was significantly increased. These results suggest that hydride transfer might occur early to midway through the reaction followed by protonation. Such a mechanism is supported by the very close contact between C4 of NADP+ and C6 of folate observed in the crystal structures of the ternary enzyme complexes, when the M20 loop is in its closed conformation.