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1.  Wood Specific Gravity Variations and Biomass of Central African Tree Species: The Simple Choice of the Outer Wood 
PLoS ONE  2015;10(11):e0142146.
Wood specific gravity is a key element in tropical forest ecology. It integrates many aspects of tree mechanical properties and functioning and is an important predictor of tree biomass. Wood specific gravity varies widely among and within species and also within individual trees. Notably, contrasted patterns of radial variation of wood specific gravity have been demonstrated and related to regeneration guilds (light demanding vs. shade-bearing). However, although being repeatedly invoked as a potential source of error when estimating the biomass of trees, both intraspecific and radial variations remain little studied. In this study we characterized detailed pith-to-bark wood specific gravity profiles among contrasted species prominently contributing to the biomass of the forest, i.e., the dominant species, and we quantified the consequences of such variations on the biomass.
Radial profiles of wood density at 8% moisture content were compiled for 14 dominant species in the Democratic Republic of Congo, adapting a unique 3D X-ray scanning technique at very high spatial resolution on core samples. Mean wood density estimates were validated by water displacement measurements. Wood density profiles were converted to wood specific gravity and linear mixed models were used to decompose the radial variance. Potential errors in biomass estimation were assessed by comparing the biomass estimated from the wood specific gravity measured from pith-to-bark profiles, from global repositories, and from partial information (outer wood or inner wood).
Wood specific gravity profiles from pith-to-bark presented positive, neutral and negative trends. Positive trends mainly characterized light-demanding species, increasing up to 1.8 per meter for Piptadeniastrum africanum, and negative trends characterized shade-bearing species, decreasing up to 1 per meter for Strombosia pustulata. The linear mixed model showed the greater part of wood specific gravity variance was explained by species only (45%) followed by a redundant part between species and regeneration guilds (36%). Despite substantial variation in wood specific gravity profiles among species and regeneration guilds, we found that values from the outer wood were strongly correlated to values from the whole profile, without any significant bias. In addition, we found that wood specific gravity from the DRYAD global repository may strongly differ depending on the species (up to 40% for Dialium pachyphyllum).
Main Conclusion
Therefore, when estimating forest biomass in specific sites, we recommend the systematic collection of outer wood samples on dominant species. This should prevent the main errors in biomass estimations resulting from wood specific gravity and allow for the collection of new information to explore the intraspecific variation of mechanical properties of trees.
PMCID: PMC4640573  PMID: 26555144
2.  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
3.  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
4.  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
5.  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.
6.  A Method to Determine the Density of Foods using X-ray Imaging 
Journal of food engineering  2015;159:36-41.
Density of foods is an important physical property, which depends on structural properties of food. For porous foods such as baked foods, accurate measurement of density is challenging since traditional density measurement techniques are tedious, operator-dependent and incapable of precise volume measurement of foods. To overcome such limitations, a methodology was developed using both digital radiography(DR) and computed tomography(CT) x-ray imaging to directly determine density of foods. Apparent density was determined directly from x-ray linear attenuation coefficients by scanning at 40, 60, 80 kVp on DR and 45, 55, 70 kVp on CT. The apparent density can be directly determined using CT however sample thickness is needed to determine density using DR. No significant difference (p<0.05) was observed between density obtained from traditional methods, with density determined from x-ray linear attenuation coefficients. Density determined on CT for all foods with mean 0.579 g/cm3 had a standard deviation, SD = 0.0367 g/cm3. Density determination using x-ray linear attenuation was found to be a more efficient technique giving results comparable with conventional techniques.
PMCID: PMC4384159  PMID: 25848138
Apparent density; porous foods; x-ray imaging; digital radiography; computed tomography; x-ray linear attenuation coefficient
7.  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
8.  Broad Anatomical Variation within a Narrow Wood Density Range—A Study of Twig Wood across 69 Australian Angiosperms 
PLoS ONE  2015;10(4):e0124892.
Just as people with the same weight can have different body builds, woods with the same wood density can have different anatomies. Here, our aim was to assess the magnitude of anatomical variation within a restricted range of wood density and explore its potential ecological implications.
Twig wood of 69 angiosperm tree and shrub species was analyzed. Species were selected so that wood density varied within a relatively narrow range (0.38–0.62 g cm-3). Anatomical traits quantified included wood tissue fractions (fibres, axial parenchyma, ray parenchyma, vessels, and conduits with maximum lumen diameter below 15 μm), vessel properties, and pith area. To search for potential ecological correlates of anatomical variation the species were sampled across rainfall and temperature contrasts, and several other ecologically-relevant traits were measured (plant height, leaf area to sapwood area ratio, and modulus of elasticity).
Despite the limited range in wood density, substantial anatomical variation was observed. Total parenchyma fraction varied from 0.12 to 0.66 and fibre fraction from 0.20 to 0.74, and these two traits were strongly inversely correlated (r = -0.86, P < 0.001). Parenchyma was weakly (0.24 ≤|r|≤ 0.35, P < 0.05) or not associated with vessel properties nor with height, leaf area to sapwood area ratio, and modulus of elasticity (0.24 ≤|r|≤ 0.41, P < 0.05). However, vessel traits were fairly well correlated with height and leaf area to sapwood area ratio (0.47 ≤|r|≤ 0.65, all P < 0.001). Modulus of elasticity was mainly driven by fibre wall plus vessel wall fraction rather than by the parenchyma component.
Overall, there seem to be at least three axes of variation in xylem, substantially independent of each other: a wood density spectrum, a fibre-parenchyma spectrum, and a vessel area spectrum. The fibre-parenchyma spectrum does not yet have any clear or convincing ecological interpretation.
PMCID: PMC4408027  PMID: 25906320
9.  Numerical research on the anisotropic transport of thermal neutron in heterogeneous porous media with micron X-ray computed tomography 
Scientific Reports  2016;6:27488.
The anisotropic transport of thermal neutron in heterogeneous porous media is of great research interests in many fields. In this paper, it is the first time that a new model based on micron X-ray computed tomography (CT) has been proposed to simultaneously consider both the separation of matrix and pore and the distribution of mineral components. We apply the Monte Carlo method to simulate thermal neutrons transporting through the model along different directions, and meanwhile detect those unreacted thermal neutrons by an array detector on the other side of the model. Therefore, the anisotropy of pore structure can be imaged by the amount of received thermal neutrons, due to the difference of rock matrix and pore-filling fluids in the macroscopic reaction cross section (MRCS). The new model has been verified by the consistent between the simulated data and the pore distribution from X-ray CT. The results show that the evaluation of porosity can be affected by the anisotropy of media. Based on the research, a new formula is developed to describe the correlation between the resolution of array detectors and the quality of imaging. The formula can be further used to analyze the critical resolution and the suitable number of thermal neutrons emitted in each simulation. Unconventionally, we find that a higher resolution cannot always lead to a better image.
PMCID: PMC4897704  PMID: 27271330
10.  Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential 
IUCrJ  2015;2(Pt 4):464-474.
Neutron crystallography and sub-atomic X-ray crystallography complement each other in defining hydrogen positions in macromolecules. Significant advances have been made but much effort is still required if neutron crystallography is to become a mainstream activity.
The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c′, are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.
PMCID: PMC4491318  PMID: 26175905
neutron; X-ray; hydrogen; proton; protonation states; radiation damage; redox biology; proton coupling; electron transfer; X-ray laser; XFEL
11.  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
12.  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
13.  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
14.  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
15.  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
16.  High-resolution densitometry and elemental analysis of tropical wood 
Trees (Berlin, Germany : West)  2014;29(2):487-497.
Key message
Understanding the mobility and distribution of chemical elements in wood is necessary to apply dendrochemistry. Crystals are likely stable and could be used to analyze changes in nutrient supply.
Dendrochemistry uses the variation in wood chemical composition to infer about past environmental conditions and possible effects on tree growth. Elemental or isotopic variation might also help to identify annual growth where tree rings are anatomically not distinct. However, most elements are—to a certain degree—mobile within wood and may be related to anatomical structures. Therefore, understanding what affects elemental distribution is important to make use of and critically assess the potential of dendrochemistry. We studied the variation of wood density and elements at high spatial resolution in wood of six species with anatomically distinct to rather indistinct tree rings from a Thai monsoon forest. Many elements had a higher concentration in parenchyma than in fiber cells, and the co-variation of elements differed strongly between elements and also between species. Strong wood density changes along the ring boundary were found only in Melia azedarach. In all species, the X-ray images showed crystals. EDX spectra showed that these consist of calcium or silicon (in Chukrasia tabularis) as major elemental components. A high concentration of heavy metals (Fe, Cu and Zn) was found in Vitex peduncularis. We conclude that at least for the species studied the radial variation of elemental concentration is unlikely to reveal annual rings that anatomy could not. However, if elements in crystals are more stable than in cell walls or living protoplasts, analyzing the distribution of elements present in crystals may show environmental conditions that, in turn, influence crystal formation and are little known.
PMCID: PMC4480964  PMID: 26146458
Crystals; Dendrochemistry; Tropical wood; Wood anatomy; Wood chemical composition
17.  On the Chemistry and Physical Properties of Flux and Floating Zone Grown SmB6 Single Crystals 
Scientific Reports  2016;6:20860.
Recent theoretical and experimental findings suggest the long-known but not well understood low temperature resistance plateau of SmB6 may originate from protected surface states arising from a topologically non-trivial bulk band structure having strong Kondo hybridization. Yet others have ascribed this feature to impurities, vacancies, and surface reconstructions. Given the typical methods used to prepare SmB6 single crystals, flux and floating-zone procedures, such ascriptions should not be taken lightly. We demonstrate how compositional variations and/or observable amounts of impurities in SmB6 crystals grown using both procedures affect the physical properties. From X-ray diffraction, neutron diffraction, and X-ray computed tomography experiments we observe that natural isotope containing (SmB6) and doubly isotope enriched (154Sm11B6) crystals prepared using aluminum flux contain co-crystallized, epitaxial aluminum. Further, a large, nearly stoichiometric crystal of SmB6 was successfully grown using the float-zone technique; upon continuing the zone melting, samarium vacancies were introduced. These samarium vacancies drastically alter the resistance and plateauing magnitude of the low temperature resistance compared to stoichiometric SmB6. These results highlight that impurities and compositional variations, even at low concentrations, must be considered when collecting/analyzing physical property data of SmB6. Finally, a more accurate samarium-154 coherent neutron scattering length, 8.9(1) fm, is reported.
PMCID: PMC4759532  PMID: 26892648
18.  Inter- and intra-specific variation in drought sensitivity in Abies spec. and its relation to wood density and growth traits 
Agricultural and forest meteorology  2015;214-215:430-443.
Understanding drought sensitivity of tree species and its intra-specific variation is required to estimate the effects of climate change on forest productivity, carbon sequestration and tree mortality as well as to develop adaptive forest management measures. Here, we studied the variation of drought reaction of six European Abies species and ten provenances of Abies alba planted in the drought prone eastern Austria. Tree-ring and X-ray densitometry data were used to generate early- and latewood measures for ring width and wood density. Moreover, the drought reaction of species and provenances within six distinct drought events between 1970 and 2011, as identified by the standardized precipitation index, was determined by four drought response measures. The mean reaction of species and provenances to drought events was strongly affected by the seasonal occurrence of the drought: a short, strong drought at the beginning of the growing season resulted in growth reductions up to 50%, while droughts at the end of the growing season did not affect annual increment. Wood properties and drought response measures showed significant variation among Abies species as well as among A. alba provenances. Whereas A. alba provenances explained significant parts in the variation of ring width measures, the Abies species explained significant parts in the variation of wood density parameters. A consistent pattern in drought response across the six drought events was observed only at the inter-specific level, where A. nordmanniana showed the highest resistance and A. cephalonica showed the best recovery after drought. In contrast, differences in drought reaction among provenances were only found for the milder drought events in 1986, 1990, 1993 and 2000 and the ranking of provenances varied at each drought event. This indicates that genetic variation in drought response within A. alba is more limited than among Abies species. Low correlations between wood density parameters and drought response measures suggest that wood density is a poor predictor of drought sensitivity in Abies spec.
PMCID: PMC5049588  PMID: 27713591
Conifer; Silver fir; Drought response; Wood density; Growth reduction
19.  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
20.  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
21.  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
22.  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
23.  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
24.  Measurements of bone tunnel size in anterior cruciate ligament reconstruction: 2D versus 3D computed tomography model 
Revision anterior cruciate ligament (ACL) reconstruction requires a precise evaluation of previous tunnel locations and diameters. Enlargement of the tunnels, despite not usually affecting primary reconstruction outcomes, plays an important role in revision ACL management. Three dimensional (3D) computed tomography (CT) models are reported to be the most accurate method for identifying the tunnel position and possible conflicts with a revision tunnel placement. However, the ability of 3D CT to measure the tunnel size is still not proven. The goal of this study was to evaluate the ability of measuring the size of the bone tunnels in ACL reconstructed knees with 3D CT compared to the traditional two dimensional (2D) CT method.
Twenty-four patients had CT scans performed immediately following ACL reconstruction surgery. Their femoral tunnels size were measured by a standard 2D CT measurement and then compared with three novel 3D CT measuring methods: the best transverse section method, the best fit cylinder method and the wall thickness method. The drill size used during surgery was used as a control measure for the tunnel width. Intra-class correlation coefficients were obtained.
The intra-class correlation coefficient and respective 95% confidence interval range (ICC [95%CI]) for the three methods compared with the drill sizes were 0.899 [0.811-0.947] for the best transverse section method, 0.745 [0.553-0.862] for the best fit cylinder method, −0.004 [−0.081 to −0.12] for the wall thickness method and 0.922 [0.713-0.97] for the 2D CT method. The mean differences compared to the drill size were 0.02 mm for the best fit transverse section method, 0.01 mm for the best fit cylinder diameter method, 3.34 mm for the wall thickness method and 0.29 mm for the 2D CT method. The intra-rater agreement (ICC [95%CI]) was excellent for the best transverse section method 0.999 [0.998-0.999] and the 2D CT method 0.969 [0.941-0.984].
The 3D best transverse section method presented a high correlation to the drill sizes and high intra-rater agreement, and was the best method for ACL tunnel evaluation in a 3D CT based model.
PMCID: PMC4648836  PMID: 26914747
Anterior cruciate ligament; Tunnel enlargement; Revision ACL; 3D CT model
25.  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

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