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1.  Hirshfeld atom refinement 
IUCrJ  2014;1(Pt 5):361-379.
The new automated iterative Hirshfeld atom refinement method is explained and validated through comparison of structural models of Gly–l-Ala obtained from synchrotron X-ray and neutron diffraction data at 12, 50, 150 and 295 K. Structural parameters involving hydrogen atoms are determined with comparable precision from both experiments and agree mostly to within two combined standard uncertainties.
Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly–l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using Hartree–Fock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints – even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogen-atom ADPs differ by up to three combined standard uncertainties (csu’s), all other structural parameters agree within less than 2 csu’s. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements – an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å.
PMCID: PMC4174878  PMID: 25295177
aspherical atom partitioning; quantum mechanical molecular electron densities; X-ray structure refinement; hydrogen atom modelling; anisotropic displacement parameters
2.  Joint X-ray and neutron refinement with phenix.refine  
The implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.
Approximately 85% of the structures deposited in the Protein Data Bank have been solved using X-ray crystallography, making it the leading method for three-dimensional structure determination of macromolecules. One of the limitations of the method is that the typical data quality (resolution) does not allow the direct determination of H-atom positions. Most hydrogen positions can be inferred from the positions of other atoms and therefore can be readily included into the structure model as a priori knowledge. However, this may not be the case in biologically active sites of macromolecules, where the presence and position of hydrogen is crucial to the enzymatic mechanism. This makes the application of neutron crystallo­graphy in biology particularly important, as H atoms can be clearly located in experimental neutron scattering density maps. Without exception, when a neutron structure is determined the corresponding X-ray structure is also known, making it possible to derive the complete structure using both data sets. Here, the implementation of crystallographic structure-refinement procedures that include both X-ray and neutron data (separate or jointly) in the PHENIX system is described.
PMCID: PMC2967420  PMID: 21041930
structure refinement; neutrons; joint X-ray and neutron refinement; PHENIX
3.  Wood density and its radial variation in six canopy tree species differing in shade-tolerance in western Thailand 
Annals of Botany  2009;104(2):297-306.
Background and Aims
Wood density is a key variable for understanding life history strategies in tropical trees. Differences in wood density and its radial variation were related to the shade-tolerance of six canopy tree species in seasonally dry tropical forest in Thailand. In addition, using tree ring measurements, the influence of tree size, age and annual increment on radial density gradients was analysed.
Wood density was determined from tree cores using X-ray densitometry. X-ray films were digitized and images were measured, resulting in a continuous density profile for each sample. Mixed models were then developed to analyse differences in average wood density and in radial gradients in density among the six tree species, as well as the effects of tree age, size and annual increment on radial increases in Melia azedarach.
Key Results
Average wood density generally reflected differences in shade-tolerance, varying by nearly a factor of two. Radial gradients occurred in all species, ranging from an increase of (approx. 70%) in the shade-intolerant Melia azedarach to a decrease of approx. 13% in the shade-tolerant Neolitsea obtusifolia, but the slopes of radial gradients were generally unrelated to shade-tolerance. For Melia azedarach, radial increases were most-parsimoniously explained by log-transformed tree age and annual increment rather than by tree size.
The results indicate that average wood density generally reflects differences in shade-tolerance in seasonally dry tropical forests; however, inferences based on wood density alone are potentially misleading for species with complex life histories. In addition, the findings suggest that a ‘whole-tree’ view of life history and biomechanics is important for understanding patterns of radial variation in wood density. Finally, accounting for wood density gradients is likely to improve the accuracy of estimates of stem biomass and carbon in tropical trees.
PMCID: PMC2710901  PMID: 19454592
Radial gradients; shade-tolerance; tree biomass estimates; tree rings; tropical trees; wood density
4.  Fibre wall and lumen fractions drive wood density variation across 24 Australian angiosperms 
AoB Plants  2013;5:plt046.
Wood density is often considered to be a key plant functional trait. But it is not clear what actually wood density is? We rigorously quantified anatomical underpinnings of wood density variation. We found that density was mainly driven by properties of mechanical tissue such as fibre wall fraction and fibre lumen fraction. However, there was also a substantial anatomical variation independent of density. This variation suggests that different plant ecological strategies may be available to woods with the same density. Our results imply that density is a complex characteristic of wood rather than a straightforward indicator of plant ecological strategies.
Wood density is considered a key plant trait, affecting mechanical and physiological performance, yet its biological meaning is still rather unclear. Accordingly we investigated the anatomical underpinnings of wood density in trees and shrubs. We measured wood density and anatomical traits in distal stems 4–10 mm diameter under bark in 24 Australian species. Proportions of wood components that are functionally distinct were analysed, including fibre wall and lumen, vessel wall and lumen, and axial and ray parenchyma. Wood density was mainly driven by the density of wood outside vessel lumens (densityNV) rather than by vessel lumen fraction. In turn, densityNV variation was chiefly affected by fibre wall and lumen fractions. Considerable anatomical variation was observed at a given densityNV, especially among medium-densityNV species (0.60–0.85 g cm−3); this range of medium densityNV roughly translates to 0.50–0.75 g cm−3 of overall density. The anatomy of these species formed a continuum from low fibre lumen and medium parenchyma fractions to medium fibre lumen and low parenchyma fractions. Our data suggest that wood density is an emergent property influenced by a complex anatomy rather than an unambiguous functional trait, particularly in medium-density species. With much anatomical variation, they likely represent a wide range of ecological strategies.
PMCID: PMC4104653
Ecological strategies; fibres; parenchyma; rays; tissue fraction/proportion/percentage/volume; vessels; wood anatomy.
5.  Transcriptome profiling of radiata pine branches reveals new insights into reaction wood formation with implications in plant gravitropism 
BMC Genomics  2013;14(1):768.
Formation of compression (CW) and opposite wood (OW) in branches and bent trunks is an adaptive feature of conifer trees in response to various displacement forces, such as gravity, wind, snow and artificial bending. Several previous studies have characterized tracheids, wood and gene transcription in artificially or naturally bent conifer trunks. These studies have provided molecular basis of reaction wood formation in response to bending forces and gravity stimulus. However, little is known about reaction wood formation and gene transcription in conifer branches under gravity stress. In this study SilviScan® technology was used to characterize tracheid and wood traits in radiate pine (Pinus radiata D. Don) branches and genes differentially transcribed in CW and OW were investigated using cDNA microarrays.
CW drastically differed from OW in tracheids and wood traits with increased growth, thicker tracheid walls, larger microfibril angle (MFA), higher density and lower stiffness. However, CW and OW tracheids had similar diameters in either radial or tangential direction. Thus, gravity stress largely influenced wood growth, secondary wall deposition, cellulose microfibril orientation and wood properties, but had little impact on primary wall expansion. Microarray gene transcription revealed about 29% of the xylem transcriptomes were significantly altered in CW and OW sampled in both spring and autumn, providing molecular evidence for the drastic variation in tracheid and wood traits. Genes involved in cell division, cellulose biosynthesis, lignin deposition, and microtubules were mostly up-regulated in CW, conferring its greater growth, thicker tracheid walls, higher density, larger MFA and lower stiffness. However, genes with roles in cell expansion and primary wall formation were differentially transcribed in CW and OW, respectively, implicating their similar diameters of tracheid walls and different tracheid lengths. Interestingly, many genes related to hormone and calcium signalling as well as various environmental stresses were exclusively up-regulated in CW, providing important clues for earlier molecular signatures of reaction wood formation under gravity stimulus.
The first comprehensive investigation of tracheid characteristics, wood properties and gene transcription in branches of a conifer species revealed more accurate and new insights into reaction wood formation in response to gravity stress. The identified differentially transcribed genes with diverse functions conferred or implicated drastic CW and OW variation observed in radiata pine branches. These genes are excellent candidates for further researches on the molecular mechanisms of reaction wood formation with a view to plant gravitropism.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-14-768) contains supplementary material, which is available to authorized users.
PMCID: PMC4046691  PMID: 24209714
Compression wood; Tracheid; Conifers; Transcriptome; Microarray; Plant gravitropism; Microfibril angle (MFA); Wood stiffness
6.  Performance of Orbital Neutron Instruments for Spatially Resolved Hydrogen Measurements of Airless Planetary Bodies 
Astrobiology  2010;10(2):183-200.
Orbital neutron spectroscopy has become a standard technique for measuring planetary surface compositions from orbit. While this technique has led to important discoveries, such as the deposits of hydrogen at the Moon and Mars, a limitation is its poor spatial resolution. For omni-directional neutron sensors, spatial resolutions are 1–1.5 times the spacecraft's altitude above the planetary surface (or 40–600 km for typical orbital altitudes). Neutron sensors with enhanced spatial resolution have been proposed, and one with a collimated field of view is scheduled to fly on a mission to measure lunar polar hydrogen. No quantitative studies or analyses have been published that evaluate in detail the detection and sensitivity limits of spatially resolved neutron measurements. Here, we describe two complementary techniques for evaluating the hydrogen sensitivity of spatially resolved neutron sensors: an analytic, closed-form expression that has been validated with Lunar Prospector neutron data, and a three-dimensional modeling technique. The analytic technique, called the Spatially resolved Neutron Analytic Sensitivity Approximation (SNASA), provides a straightforward method to evaluate spatially resolved neutron data from existing instruments as well as to plan for future mission scenarios. We conclude that the existing detector—the Lunar Exploration Neutron Detector (LEND)—scheduled to launch on the Lunar Reconnaissance Orbiter will have hydrogen sensitivities that are over an order of magnitude poorer than previously estimated. We further conclude that a sensor with a geometric factor of ∼ 100 cm2 Sr (compared to the LEND geometric factor of ∼ 10.9 cm2 Sr) could make substantially improved measurements of the lunar polar hydrogen spatial distribution. Key Words: Planetary instrumentation—Planetary science—Moon—Spacecraft experiments—Hydrogen. Astrobiology 10, 183–200.
PMCID: PMC2956572  PMID: 20298147
7.  Correlative Nanoscale 3D Imaging of Structure and Composition in Extended Objects 
PLoS ONE  2012;7(11):e50124.
Structure and composition at the nanoscale determine the behavior of biological systems and engineered materials. The drive to understand and control this behavior has placed strong demands on developing methods for high resolution imaging. In general, the improvement of three-dimensional (3D) resolution is accomplished by tightening constraints: reduced manageable specimen sizes, decreasing analyzable volumes, degrading contrasts, and increasing sample preparation efforts. Aiming to overcome these limitations, we present a non-destructive and multiple-contrast imaging technique, using principles of X-ray laminography, thus generalizing tomography towards laterally extended objects. We retain advantages that are usually restricted to 2D microscopic imaging, such as scanning of large areas and subsequent zooming-in towards a region of interest at the highest possible resolution. Our technique permits correlating the 3D structure and the elemental distribution yielding a high sensitivity to variations of the electron density via coherent imaging and to local trace element quantification through X-ray fluorescence. We demonstrate the method by imaging a lithographic nanostructure and an aluminum alloy. Analyzing a biological system, we visualize in lung tissue the subcellular response to toxic stress after exposure to nanotubes. We show that most of the nanotubes are trapped inside alveolar macrophages, while a small portion of the nanotubes has crossed the barrier to the cellular space of the alveolar wall. In general, our method is non-destructive and can be combined with different sample environmental or loading conditions. We therefore anticipate that correlative X-ray nano-laminography will enable a variety of in situ and in operando 3D studies.
PMCID: PMC3501479  PMID: 23185554
8.  Global small-angle X-ray scattering data analysis for multilamellar vesicles: the evolution of the scattering density profile model 
Journal of Applied Crystallography  2013;47(Pt 1):173-180.
The high-resolution scattering length density analysis method has been generalized from unilamellar to multilamellar lipid vesicles. The method may be applied to X-ray data only, or to a joint analysis of X-ray and neutron data, yielding an improved refinement of the lipid backbone position.
The highly successful scattering density profile (SDP) model, used to jointly analyze small-angle X-ray and neutron scattering data from unilamellar vesicles, has been adapted for use with data from fully hydrated, liquid crystalline multilamellar vesicles (MLVs). Using a genetic algorithm, this new method is capable of providing high-resolution structural information, as well as determining bilayer elastic bending fluctuations from standalone X-ray data. Structural parameters such as bilayer thickness and area per lipid were determined for a series of saturated and unsaturated lipids, as well as binary mixtures with cholesterol. The results are in good agreement with previously reported SDP data, which used both neutron and X-ray data. The inclusion of deuterated and non-deuterated MLV neutron data in the analysis improved the lipid backbone information but did not improve, within experimental error, the structural data regarding bilayer thickness and area per lipid.
PMCID: PMC3937811  PMID: 24587787
small-angle X-ray scattering; scattering density profile model; genetic algorithms; liquid crystalline multilamellar vesicles
9.  A study to improve the image quality in low-dose computed tomography (SPECT) using filtration 
The output of the X-ray tube used in computed tomography (CT) provides a spectrum of photon energies. Low-energy photons are preferentially absorbed in tissue; the beam spectrum shifts toward the higher energy end as it passes through more tissue, thereby changing its effective attenuation coefficient and producing a variety of artifacts (beam-hardening effects) in images. Filtering of the beam may be used to remove low-energy photon component. The accuracy of attenuation coefficient calculation by bilinear model depends highly upon accuracy of Hounsfield units. Therefore, we have made an attempt to minimize the beam-hardening effects using additional copper filter in the X-ray beam. The quantitative evaluation were made to see the effect of additional filters on resulting CT images.
Materials and Methods:
This study was performed on dual-head SPECT (HAWKEYE 4, GE Healthcare) with low-dose CT which acquires images at peak voltages of 120/140 kV and a tube current of 2.5 mA. For the evaluation of image quality, we used CT QA Phantom (PHILIPS) having six different density pins of Water, Polyethylene, Nylon (Aculon), Lexan, Acrylic (Perspex) and Teflon. The axial images were acquired using copper filters of various thicknesses ranging from 1 to 5 mm in steps of 1 mm. The copper filter was designed in such a manner that it fits exactly on the collimator cover of CT X-ray tube. Appropriate fixation of the copper filter was ensured before starting the image acquisition. As our intention was only to see the effect of beam hardening on the attenuation map, no SPECT study was performed. First set of images was acquired without putting any filter into the beam. Then, successively, filters of different thicknesses were placed into the beam and calibration of the CT scanner was performed before acquiring the images. The X-ray tube parameters were kept the same as that of unfiltered X-ray beam. All the acquired image sets were displayed using Xeleris 2 (GE Healthcare) on a high-resolution monitor. Moreover, Jaszak's SPECT Phantom after removing the spheres was used to see the different contrast intensities by inserting the different contrast materials of iodine and bismuth in water as background media. Images were analyzed for visibility, spatial resolution and contrast.
Successive improvement in the image quality was noticed when we increased the filter thickness from 1 to 3 mm. The images acquired with 3-mm filter appeared almost with no artifacts and were visibly sharper. Lower energy photons from X-ray beam cause a number of artifacts, especially at bone–tissue interfaces. Additional filtrations removed lower energy photons and improved the image quality. Degradation in the image quality was noticed when we increased the filter thickness further to 4 and 5 mm. This degradation in image quality happened due to reduced photon flux of the resulting X-ray beam, causing high statistical noise. The spatial resolution for image matrix of 512 × 512 was found to be 1.29, 1.07, 0.64 and 0.54 mm for without filter, with 1, 2 and 3 mm filters, respectively. The image quality was further analyzed for signal-to-noise ratio (SNR). It was found to be 1.72, 1.78, 1.98 and 1.99 for open, with 1, 2 and 3 mm filters respectively. This shows that 3-mm filter results in an improvement of 15.7% in SNR.
On the basis of this study, we could conclude that use of 3-mm copper filter in the X-ray beam is optimal for removing the artifacts without causing any significant reduction in the photon flux of the resulting X-ray beam. We also propose that as artifacts have been removed from the images, the value of Hounsfield units will be more accurate and hence the value of attenuation coefficients lead to better contrast and visualization of SPECT images.
PMCID: PMC3180715  PMID: 21969774
Artifacts; attenuation correction; beam hardening; filtration; image quality; low-dose computed tomography
10.  Wood anatomical correlates with theoretical conductivity and wood density across China: evolutionary evidence of the functional differentiation of axial and radial parenchyma 
Annals of Botany  2013;112(5):927-935.
Background and Aims
In recent years considerable effort has focused on linking wood anatomy and key ecological traits. Studies analysing large databases have described how these ecological traits vary as a function of wood anatomical traits related to conduction and support, but have not considered how these functions interact with cells involved in storage of water and carbohydrates (i.e. parenchyma cells).
We analyzed, in a phylogenetic context, the functional relationship between cell types performing each of the three xylem functions (conduction, support and storage) and wood density and theoretical conductivity using a sample of approx. 800 tree species from China.
Key Results
Axial parenchyma and rays had distinct evolutionary correlation patterns. An evolutionary link was found between high conduction capacity and larger amounts of axial parenchyma that is probably related to water storage capacity and embolism repair, while larger amounts of ray tissue have evolved with increased mechanical support and reduced hydraulic capacity. In a phylogenetic principal component analysis this association of axial parenchyma with increased conduction capacity and rays with wood density represented orthogonal axes of variation. In multivariate space, however, the proportion of rays might be positively associated with conductance and negatively with wood density, indicating flexibility in these axes in species with wide rays.
The findings suggest that parenchyma types may differ in function. The functional axes represented by different cell types were conserved across lineages, suggesting a significant role in the ecological strategies of the angiosperms.
PMCID: PMC3747806  PMID: 23904446
Ecological strategies; evolutionary conservatism; hydraulic conductivity; parenchyma; water storage; wood anatomy; wood density
11.  Thermal and resonance neutrons generated by various electron and X-ray therapeutic beams from medical linacs installed in polish oncological centers 
High-energy photon and electron therapeutic beams generated in medical linear accelerators can cause the electronuclear and photonuclear reactions in which neutrons with a broad energy spectrum are produced. A low-energy component of this neutron radiation induces simple capture reactions from which various radioisotopes originate and in which the radioactivity of a linac head and various objects in the treatment room appear.
The aim of this paper is to present the results of the thermal/resonance neutron fluence measurements during therapeutic beam emission and exemplary spectra of gamma radiation emitted by medical linac components activated in neutron reactions for four X-ray beams and for four electron beams generated by various manufacturers’ accelerators installed in typical concrete bunkers in Polish oncological centers.
Materials and methods
The measurements of neutron fluence were performed with the use of the induced activity method, whereas the spectra of gamma radiation from decays of the resulting radioisotopes were measured by means of a portable high-purity germanium detector set for field spectroscopy.
The fluence of thermal neutrons as well as resonance neutrons connected with the emission of a 20 MV X-ray beam is ∼106 neutrons/cm2 per 1 Gy of a dose in water at a reference depth. It is about one order of magnitude greater than that for the 15 MV X-ray beams and about two orders of magnitude greater than for the 18–22 MeV electron beams regardless of the type of an accelerator.
The thermal as well as resonance neutron fluence depends strongly on the type and the nominal potential of a therapeutic beam. It is greater for X-ray beams than for electrons. The accelerator accessories and other large objects should not be stored in a treatment room during high-energy therapeutic beam emission to avoid their activation caused by thermal and resonance neutrons. Half-lives of the radioisotopes originating from the simple capture reaction (n,γ) (from minutes to hours) are long enough to accumulate radioactivity of components of the accelerator head. The radiation emitted by induced radioisotopes causes the additional doses to staff operating the accelerators.
PMCID: PMC3920349  PMID: 24669311
Thermal/resonance neutrons; Induce radioactivity; Medical linacs
12.  X-ray structure determination and deuteration of nattokinase 
Journal of Synchrotron Radiation  2013;20(Pt 6):875-879.
X-ray structure determination and deuteration of nattokinase were performed to facilitate neutron crystallographic analysis.
Nattokinase (NK) is a strong fibrinolytic enzyme, which is produced in abundance by Bacillus subtilis natto. Although NK is a member of the subtilisin family, it displays different substrate specificity when compared with other subtilisins. The results of molecular simulations predict that hydrogen arrangements around Ser221 at the active site probably account for the substrate specificity of NK. Therefore, neutron crystallographic analysis should provide valuable information that reveals the enzymatic mechanism of NK. In this report, the X-ray structure of the non-hydrogen form of undeuterated NK was determined, and the preparation of deuterated NK was successfully achieved. The non-hydrogen NK structure was determined at 1.74 Å resolution. The three-dimensional structures of NK and subtilisin E from Bacillus subtilis DB104 are near identical. Deuteration of NK was carried out by cultivating Bacillus subtilis natto in deuterated medium. The D2O resistant strain of Bacillus subtilis natto was obtained by successive cultivation rounds, in which the concentration of D2O in the medium was gradually increased. NK was purified from the culture medium and its activity was confirmed by the fibrin plate method. The results lay the framework for neutron protein crystallography analysis.
PMCID: PMC3795547  PMID: 24121331
nattokinase; Bacillus subtilis natto; deuteration; X-ray structure
13.  Multi-frequency characterization of the speed of sound and attenuation coefficient for longitudinal transmission of freshly excised human skulls 
Physics in medicine and biology  2010;56(1):219-250.
For medical applications of ultrasound inside the brain, it is necessary to understand the relationship between the apparent density of skull bone and its corresponding speed of sound and attenuation coefficient. Although there have been previous studies exploring this phenomenon, there is still a need to extend the measurements to cover more of the clinically relevant frequency range. The results of measurements of the longitudinal speed of sound and attenuation coefficient are presented for specimens of human calvaria. The study was performed for the frequencies of 0.27, 0.836, 1.402, 1.965 and 2.525 MHz. Specimens were obtained from fresh cadavers through a protocol with the Division of Anatomy of the University of Toronto. The protocol was approved by the Research Ethics Board of Sunnybrook Health Sciences Centre. The specimens were mounted in polycarbonate supports that were marked for stereoscopic positioning. Computer tomography (CT) scans of the skulls mounted on their supports were performed, and a three-dimensional skull surface was reconstructed. This surface was used to guide a positioning system to ensure the normal sound incidence of an acoustic signal. This signal was produced by a focused device with a diameter of 5 cm and a focal length of 10 cm. Measurements of delay in time of flight were carried out using a needle hydrophone. Measurements of effective transmitted energy were carried out using a radiation force method with a 10 μg resolution scale. Preliminary functions of speed of sound and attenuation coefficient, both of which are related to apparent density, were established using a multi-layer propagation model that takes into account speed of sound, density and thickness of the layer. An optimization process was executed from a large set of random functions and the best functions were chosen for those ones that closest reproduced the experimental observations. The final functions were obtained after a second pass of the optimization process was executed, but this time using a finite-difference time-difference solution of the Westervelt equation, which is more precise than the multi-layer model but much more time consuming for computation. For six of seven specimens, measurements were carried out on five locations on the calvaria, and for the other specimen three measurements were made. In total, measurements were carried out on 33 locations. Results indicated the presence of dispersion effects and that these effects are different according to the type of bone in the skull (cortical and trabecular). Additionally, both the speed of sound and attenuation showed dependence on the skull density that varied with the frequency. Using the optimal functions and the information of density from the CT scans, the average values (±s.d.) of the speed of sound for cortical bone were estimated to be 2384(±130), 2471(±90), 2504(±120), 2327(±90) and 2053(±40) m s−1 for the frequencies of 270, 836, 1402, 1965 and 2526 kHz, respectively. For trabecular bone, and in the same order of frequency values, the speeds of sound were 2140(±130), 2300(±100), 2219(±200), 2133(±130) and 1937(±40) m s−1, respectively. The average values of the attenuation coefficient for cortical bone were 33(±9), 240(±9) and 307(±30) Np m−1 for the frequencies of 270, 836, and 1402, respectively. For trabecular bone, and in the same order of frequency values, the average values of the attenuation coefficient were 34(±13), 216(±16) and 375(±30) Np m−1, respectively. For frequencies of 1.965 and 2.525 MHz, no measurable radiation force was detected with the setup used.
PMCID: PMC3166773  PMID: 21149950
14.  Radiocarbon Dating and Wood Density Chronologies of Mangrove Trees in Arid Western Australia 
PLoS ONE  2013;8(11):e80116.
Mangrove trees tend to be larger and mangrove communities more diverse in tropical latitudes, particularly where there is high rainfall. Variation in the structure, growth and productivity of mangrove forests over climatic gradients suggests they are sensitive to variations in climate, but evidence of changes in the structure and growth of mangrove trees in response to climatic variation is scarce. Bomb-pulse radiocarbon dating provides accurate dates of recent wood formation and tree age of tropical and subtropical tree species. Here, we used radiocarbon techniques combined with X-ray densitometry to develop a wood density chronology for the mangrove Avicennia marina in the Exmouth Gulf, Western Australia (WA). We tested whether wood density chronologies of A. marina were sensitive to variation in the Pacific Decadal Oscillation Index, which reflects temperature fluctuations in the Pacific Ocean and is linked to the instrumental rainfall record in north WA. We also determined growth rates in mangrove trees from the Exmouth Gulf, WA. We found that seaward fringing A. marina trees (∼10 cm diameter) were 48±1 to 89±23 years old (mean ± 1σ) and that their growth rates ranged from 4.08±2.36 to 5.30±3.33 mm/yr (mean ±1σ). The wood density of our studied mangrove trees decreased with increases in the Pacific Decadal Oscillation Index. Future predicted drying of the region will likely lead to further reductions in wood density and their associated growth rates in mangrove forests in the region.
PMCID: PMC3827189  PMID: 24265797
15.  A neutron track etch detector for electron linear accelerators in radiotherapy 
Radiology and Oncology  2010;44(1):62-66.
Electron linear accelerators in medical radiotherapy have replaced cobalt and caesium sources of radiation. However, medical accelerators with photon energies over 10 MeV generate undesired fast neutron contamination in a therapeutic X-ray photon beam. Photons with energies above 10 MeV can interact with the atomic nucleus of a high-Z material, of which the target and the head of an accelerator consist, and lead to the neutron ejection.
Results and conclusions.
Our neutron dosimeter, composed of the LR-115 track etch detector and boron foil BN-1 converter, was calibrated on thermal neutrons generated in the nuclear reactor of the Josef Stefan Institute (Slovenia), and applied to dosimetry of undesirable neutrons in photon radiotherapy by the linear accelerator 15 MV Siemens Mevatron. Having considered a high dependence of a cross-section between neutron and boron on neutron energy, and broad neutron spectrum in a photon beam, as well as outside the entrance door to maze of the Mevatron, we developed a method for determining the effective neutron detector response. A neutron dose rate in the photon beam was measured to be 1.96 Sv/h. Outside the Mevatron room the neutron dose rate was 0.62 μSv/h. PACS: 87.52. Ga; 87.53.St; 29.40.Wk.
PMCID: PMC3423670  PMID: 22933893
electron linear accelerator; photoneutron; track etch detector; neutron dose equivalent
16.  Bone mineral density in cone beam computed tomography: Only a few shades of gray 
World Journal of Radiology  2014;6(8):607-612.
Cone beam computed tomography (CBCT) has often been used to determine the quality of craniofacial bone structures through the determination of mineral density, which is based on gray scales of the images obtained. However, there is no consensus regarding the accuracy of the determination of the gray scales in these exams. This study aims to provide a literature review concerning the reliability of CBCT to determine bone mineral density. The gray values obtained with CBCT show a linear relationship with the attenuation coefficients of the materials, Hounsfield Units values obtained with medical computed tomography, and density values from dual energy X-ray absorciometry. However, errors are expected when CBCT images are used to define the quality of the scanned structures because these images show inconsistencies and arbitrariness in the gray values, particularly when related to abrupt change in the density of the object, X-ray beam hardening effect, scattered radiation, projection data discontinuity-related effect, differences between CBCT devices, changes in the volume of the field of view (FOV), and changes in the relationships of size and position between the FOV and the object evaluated. A few methods of mathematical correction of the gray scales in CBCT have been proposed; however, they do not generate consistent values that are independent of the devices and their configurations or of the scanned objects. Thus, CBCT should not be considered the examination of choice for the determination of bone and soft tissue mineral density at the current stage, particularly when values obtained are to be compared to predetermined standard values. Comparisons between symmetrically positioned structures inside the FOV and in relation to the exomass of the object, as it occurs with the right and left sides of the skull, seem to be viable because the effects on the gray scale in the regions of interest are the same.
PMCID: PMC4147441  PMID: 25170398
Tomography; Cone-Beam computed tomography; Bone mineral density; Reproducibility of results
17.  Hydraulic efficiency compromises compression strength perpendicular to the grain in Norway spruce trunkwood 
Trees (Berlin, Germany : West)  2011;25(2):289-299.
The aim of this study was to investigate bending stiffness and compression strength perpendicular to the grain of Norway spruce (Picea abies (L.) Karst.) trunkwood with different anatomical and hydraulic properties. Hydraulically less safe mature sapwood had bigger hydraulic lumen diameters and higher specific hydraulic conductivities than hydraulically safer juvenile wood. Bending stiffness (MOE) was higher, whereas radial compression strength lower in mature than in juvenile wood. A density-based tradeoff between MOE and hydraulic efficiency was apparent in mature wood only. Across cambial age, bending stiffness did not compromise hydraulic efficiency due to variation in latewood percent and because of the structural demands of the tree top (e.g. high flexibility). Radial compression strength compromised, however, hydraulic efficiency because it was extremely dependent on the characteristics of the “weakest” wood part, the highly conductive earlywood. An increase in conduit wall reinforcement of earlywood tracheids would be too costly for the tree. Increasing radial compression strength by modification of microfibril angles or ray cell number could result in a decrease of MOE, which would negatively affect the trunk’s capability to support the crown. We propose that radial compression strength could be an easily assessable and highly predictive parameter for the resistance against implosion or vulnerability to cavitation across conifer species, which should be topic of further studies.
PMCID: PMC3207224  PMID: 22058609
Compression strength perpendicular to the grain; Conduit wall reinforcement; Hydraulic efficiency; Modulus of elasticity in bending; Norway spruce; Structure–function relationships; Vulnerability to cavitation; Wood shrinkage
18.  Radial shrinkage and ultrasound acoustic emissions of fresh versus pre-dried Norway spruce sapwood 
Trees (Berlin, Germany : West)  2010;24(5):931-940.
Acoustic emission (AE) and radial shrinkage were compared between fully saturated fresh and pre-dried Norway spruce sapwood during dehydration at ambient temperature. Hydraulic conductivity measurements, anatomical investigations on bordered pits and X-ray computed tomography (CT) scans were done to search for possible AE sources other than the breakage of the water columns inside the tracheids. Both fresh and pre-dried specimens showed radial shrinkage due to drying surface layers right from the beginning of dehydration, which induced almost no AE. Whereas no dimensional changes occurred in pre-dried wood thereafter, fresh wood showed a rapid shrinkage increase starting at 25% relative water loss. This dimensional change ceased when further moisture got lost and was even partially reversed. AE of fresh wood showed much higher activity and energy, which is a waveform feature that describes the strength of the acoustic signal. Extremely high single AE energy events were detected at this critical stage of dehydration. After partial recovery from shrinkage, neither dimensional changes nor AE activity showed differences between fresh and pre-dried wood after more than 80% relative moisture loss. Our results suggested that fresh sapwood is more prone to dehydration stresses than pre-dried sapwood. Differences in AE and shrinkage behavior might be due to the weakening or distortion of the pit membranes (cavitation fatigue), pit aspiration, structural changes of the cell walls and micro-checks, which occurred during the first dehydration cycle.
PMCID: PMC3207202  PMID: 22064842
Bordered pits; Cavitation fatigue; Functional wood anatomy; Hydraulic conductance; Norway spruce (Picea abies); Acoustic emission testing; Wood shrinkage; X-ray computed tomography
19.  Radial shrinkage and ultrasound acoustic emissions of fresh versus pre-dried Norway spruce sapwood 
Trees (Berlin, Germany : West)  2010;24(5):931-940.
Acoustic emission (AE) and radial shrinkage were compared between fully saturated fresh and pre-dried Norway spruce sapwood during dehydration at ambient temperature. Hydraulic conductivity measurements, anatomical investigations on bordered pits and X-ray computed tomography (CT) scans were done to search for possible AE sources other than the breakage of the water columns inside the tracheids. Both fresh and pre-dried specimens showed radial shrinkage due to drying surface layers right from the beginning of dehydration, which induced almost no AE. Whereas no dimensional changes occurred in pre-dried wood thereafter, fresh wood showed a rapid shrinkage increase starting at 25% relative water loss. This dimensional change ceased when further moisture got lost and was even partially reversed. AE of fresh wood showed much higher activity and energy, which is a waveform feature that describes the strength of the acoustic signal. Extremely high single AE energy events were detected at this critical stage of dehydration. After partial recovery from shrinkage, neither dimensional changes nor AE activity showed differences between fresh and pre-dried wood after more than 80% relative moisture loss. Our results suggested that fresh sapwood is more prone to dehydration stresses than pre-dried sapwood. Differences in AE and shrinkage behavior might be due to the weakening or distortion of the pit membranes (cavitation fatigue), pit aspiration, structural changes of the cell walls and micro-checks, which occurred during the first dehydration cycle.
PMCID: PMC3207202  PMID: 22064842
Bordered pits; Cavitation fatigue; Functional wood anatomy; Hydraulic conductance; Norway spruce (Picea abies); Acoustic emission testing; Wood shrinkage; X-ray computed tomography
20.  Large crystal growth by thermal control allows combined X-ray and neutron crystallographic studies to elucidate the protonation states in Aspergillus flavus urate oxidase 
Journal of the Royal Society Interface  2009;6(Suppl 5):S599-S610.
Urate oxidase (Uox) catalyses the oxidation of urate to allantoin and is used to reduce toxic urate accumulation during chemotherapy. X-ray structures of Uox with various inhibitors have been determined and yet the detailed catalytic mechanism remains unclear. Neutron crystallography can provide complementary information to that from X-ray studies and allows direct determination of the protonation states of the active-site residues and substrate analogues, provided that large, well-ordered deuterated crystals can be grown. Here, we describe a method and apparatus used to grow large crystals of Uox (Aspergillus flavus) with its substrate analogues 8-azaxanthine and 9-methyl urate, and with the natural substrate urate, in the presence and absence of cyanide. High-resolution X-ray (1.05–1.20 Å) and neutron diffraction data (1.9–2.5 Å) have been collected for the Uox complexes at the European Synchrotron Radiation Facility and the Institut Laue-Langevin, respectively. In addition, room temperature X-ray data were also collected in preparation for joint X-ray and neutron refinement. Preliminary results indicate no major structural differences between crystals grown in H2O and D2O even though the crystallization process is affected. Moreover, initial nuclear scattering density maps reveal the proton positions clearly, eventually providing important information towards unravelling the mechanism of catalysis.
PMCID: PMC2843968  PMID: 19586953
urate oxidase; neutron and X-ray crystallography; crystal growth; phase diagram; H–D exchange; protonation states
21.  Automated simulation of areal bone mineral density assessment in the distal radius from high-resolution peripheral quantitative computed tomography 
Osteoporosis International  2009;20(12):2017-2024.
An automated image processing method is presented for simulating areal bone mineral density measures using high-resolution peripheral quantitative computed tomography (HR-pQCT) in the ultra-distal radius. The accuracy of the method is validated against clinical dual X-ray absorptiometry (DXA). This technique represents a useful reference to gauge the utility of novel 3D quantification methods applied to HR-pQCT in multi-center clinical studies and potentially negates the need for separate forearm DXA measurements.
Osteoporotic status is primarily assessed by measuring areal bone mineral density (aBMD) using 2D dual X-ray absorptiometry (DXA). However, this technique does not sufficiently explain bone strength and fracture risk. High-resolution peripheral quantitative computed tomography (HR-pQCT) has been introduced as a method to quantify 3D bone microstructure and biomechanics. In this study, an automated method is proposed to simulate aBMD measures from HR-pQCT distal radius images.
A total of 117 subject scans were retrospectively analyzed from two clinical bone quality studies. The distal radius was imaged by HR-pQCT and DXA on one of two devices (Hologic or Lunar). Areal BMD was calculated by simulation from HR-pQCT images (aBMDsim) and by standard DXA analysis (aBMDdxa).
The reproducibility of the simulation technique was 1.1% (root mean-squared coefficient of variation). HR-pQCT-based aBMDsim correlated strongly to aBMDdxa (Hologic: R2 = 0.82, Lunar: R2 = 0.87), though aBMDsim underestimated aBMDdxa for both DXA devices (p < 0.0001). Finally, aBMDsim predicted aBMD at the proximal femur and lumbar spine with equal power compared to aBMDdxa.
The results demonstrate that aBMD can be simulated from HR-pQCT images of the distal radius. This approach has the potential to serve as a surrogate forearm aBMD measure for clinical HR-pQCT studies when axial bone mineral density values are not required.
PMCID: PMC2777210  PMID: 19330422
Bone mineral density; DXA; HR-pQCT; Osteoporosis; Simulation
22.  Investigation of the possibility of gamma-ray diagnostic imaging of target compression at NIF 
The National Ignition Facility at Lawrence Livermore National Laboratory is the world’s leading facility to study the physics of igniting plasmas. Plasmas of hot deuterium and tritium, undergo d(t,n)α reactions that produce a 14.1 MeV neutron and 3.5 MeV a particle, in the center of mass. As these neutrons pass through the materials surrounding the hot core, they may undergo subsequent (n,x) reactions. For example, 12C(n,n’γ)12C reactions occur in remnant debris from the polymer ablator resulting in a significant fluence of 4.44 MeV gamma-rays. Imaging of these gammas will enable the determination of the volumetric size and symmetry of the ablation; large size and high asymmetry is expected to correlate with poor compression and lower fusion yield. Results from a gamma-ray imaging system are expected to be complimentary to a neutron imaging diagnostic system already in place at the NIF. This paper describes initial efforts to design a gamma-ray imaging system for the NIF using the existing neutron imaging system as a baseline for study. Due to the cross-section and expected range of ablator areal densities, the gamma flux should be approximately 10−3 of the neutron flux. For this reason, care must be taken to maximize the efficiency of the gamma-ray imaging system because it will be gamma starved. As with the neutron imager, use of pinholes and/or coded apertures are anticipated. Along with aperture and detector design, the selection of an appropriate scintillator is discussed. The volume of energy deposition of the interacting 4.44 MeV gamma-rays is a critical parameter limiting the imaging system spatial resolution. The volume of energy deposition is simulated with GEANT4, and plans to measure the volume of energy deposition experimentally are described. Results of tests on a pixellated LYSO scintillator are also presented.
PMCID: PMC3571118  PMID: 23420688
NIF; gamma; scintillator; GEANT4; energy deposition; ignition; fusion
23.  The radiosensitizing effect of Ku70/80 knockdown in MCF10A cells irradiated with X-rays and p(66)+Be(40) neutrons 
A better understanding of the underlying mechanisms of DNA repair after low- and high-LET radiations represents a research priority aimed at improving the outcome of clinical radiotherapy. To date however, our knowledge regarding the importance of DNA DSB repair proteins and mechanisms in the response of human cells to high-LET radiation, is far from being complete.
We investigated the radiosensitizing effect after interfering with the DNA repair capacity in a human mammary epithelial cell line (MCF10A) by lentiviral-mediated RNA interference (RNAi) of the Ku70 protein, a key-element of the nonhomologous end-joining (NHEJ) pathway. Following irradiation of control and Ku-deficient cell lines with either 6 MV X-rays or p(66)+Be(40) neutrons, cellular radiosensitivity testing was performed using a crystal violet cell proliferation assay. Chromosomal radiosensitivity was evaluated using the micronucleus (MN) assay.
RNAi of Ku70 caused downregulation of both the Ku70 and the Ku80 proteins. This downregulation sensitized cells to both X-rays and neutrons. Comparable dose modifying factors (DMFs) for X-rays and neutrons of 1.62 and 1.52 respectively were obtained with the cell proliferation assay, which points to the similar involvement of the Ku heterodimer in the cellular response to both types of radiation beams. After using the MN assay to evaluate chromosomal radiosensitivity, the obtained DMFs for X-ray doses of 2 and 4 Gy were 2.95 and 2.66 respectively. After neutron irradiation, the DMFs for doses of 1 and 2 Gy were 3.36 and 2.82 respectively. The fact that DMFs are in the same range for X-rays and neutrons confirms a similar importance of the NHEJ pathway and the Ku heterodimer for repairing DNA damage induced by both X-rays and p(66)+Be(40) neutrons.
Interfering with the NHEJ pathway enhanced the radiosensitivity of human MCF10A cells to low-LET X-rays and high-LET neutrons, pointing to the importance of the Ku heterodimer for repairing damage induced by both types of radiation. Further research using other high-LET radiation sources is however needed to unravel the involvement of DNA double strand break repair pathways and proteins in the cellular response of human cells to high-LET radiation.
PMCID: PMC2877562  PMID: 20423515
24.  First spin-resolved electron distributions in crystals from combined polarized neutron and X-ray diffraction experiments 
IUCrJ  2014;1(Pt 3):194-199.
A method to map spin-resolved electron distribution from combined polarized neutron and X-ray diffraction is described and applied for the first time to a molecular magnet and it is shown that spin up density is 5% more contracted than spin down density.
Since the 1980s it has been possible to probe crystallized matter, thanks to X-ray or neutron scattering techniques, to obtain an accurate charge density or spin distribution at the atomic scale. Despite the description of the same physical quantity (electron density) and tremendous development of sources, detectors, data treatment software etc., these different techniques evolved separately with one model per experiment. However, a breakthrough was recently made by the development of a common model in order to combine information coming from all these different experiments. Here we report the first experimental determination of spin-resolved electron density obtained by a combined treatment of X-ray, neutron and polarized neutron diffraction data. These experimental spin up and spin down densities compare very well with density functional theory (DFT) calculations and also confirm a theoretical prediction made in 1985 which claims that majority spin electrons should have a more contracted distribution around the nucleus than minority spin electrons. Topological analysis of the resulting experimental spin-resolved electron density is also briefly discussed.
PMCID: PMC4086435  PMID: 25075338
multipole refinement; charge and spin densities; joint refinement; molecular magnetic materials; magnetization density; polarized neutron diffraction
25.  Improved Contact X-Ray Microradiographic Method to Measure Mineral Density of Hard Dental Tissues 
Contact X-ray microradiography is the current gold standard for measuring mineral densities of partially demineralized tooth specimens. The X-ray sensitive film specified in the last J Res NIST publication on the subject is no longer commercially available.
Develop a new microradiographic method by identifying a commercially available film with greater than 3000 lines per millimeter resolution, which is sensitive to X rays, and develop correct film processing for X-ray microradiographic application.
A holographic film was identified as a potential replacement film. Proper exposure was determined utilizing a thick nickel plate to create test-strips. Film development was bracketed around manufacturer suggestions. Film linearity was determined with aluminum step-wedges. Microradiographs of 100 µm thick tooth sections, before and after acidic challenges, were a final test for film. Magnified images were captured with a digital microscope camera with 0.305 micrometers per pixel resolution.
The appropriate film exposure was 30 minutes at 80 kVp and 3 mA with a development time of 2 minutes. Step-wedge experiments show the system to be linear in terms of pixel intensities with respect to x-ray attenuation for normalized pixel intensity values that are 10% to 90% of full scale (r2 = 0.997) which encompasses the full exposure region of tooth tissue. Enamel sections were analyzed and show distinctive differences between erosion and demineralization. The image capture device resolution of 0.305 micrometers per pixel limits the system resolution.
Use of the identified holographic film when combined with the described processing modifications has resulted in an improved X-ray microradiographic method for the measurement of mineral density of dental hard tissues. The method described can be further improved by using a higher resolution digitization system. The method is appropriate for quantitatively measuring changes in mineral density and erosion.
PMCID: PMC3086209  PMID: 21546983

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