Dual-energy X-ray absorptiometry for measuring total bone mineral content in the rat: study of accuracy and precision

Sequential studies of osteopenic bone disease in small animals require the availability of non-invasive, accurate and precise methods to assess bone mineral content (BMC) and bone mineral density (BMD). Dual-energy X-ray absorptiometry (DXA), which is currently used in humans for this purpose, can also be applied to small animals by means of adapted software. Precision and accuracy of DXA was evaluated in 10 rats weighing 50-265 g. The rats were anesthetized with a mixture of ketamine-xylazine administrated intraperitoneally. Each rat was scanned six times consecutively in the antero-posterior incidence after repositioning using the rat whole-body software for determination of whole-body BMC and BMD (Hologic QDR 1000, software version 5.52). Scan duration was 10-20 min depending on rat size. After the last measurement, rats were sacrificed and soft tissues were removed by dermestid beetles. Skeletons were then scanned in vitro (ultra high resolution software, version 4.47). Bones were subsequently ashed and dissolved in hydrochloric acid and total body calcium directly assayed by atomic absorption spectrophotometry (TBCa[chem]). Total body calcium was also calculated from the DXA whole-body in vivo measurement (TBCa[DXA]) and from the ultra high resolution measurement (TBCa[UH]) under the assumption that calcium accounts for 40.5% of the BMC expressed as hydroxyapatite. Precision error for whole-body BMC and BMD (mean +/- S.D.) was 1.3% and 1.5%, respectively. Simple regression analysis between TBCa[DXA] or TBCa[UH] and TBCa[chem] revealed tight correlations (n = 0.991 and 0.996, respectively), with slopes and intercepts which were significantly different from 1 and 0, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Non-Maxwellian electron distributions in time-dependent simulations of low-Z materials illuminated by a high-intensity X-ray laser

The interaction of high intensity X-ray lasers with matter is modeled. A collisional-radiative timedependent module is implemented to study radiation transport in matter from ultrashort and ultraintense X-ray bursts. Inverse bremsstrahlung absorption by free electrons, electron conduction or hydrodynamic effects are not considered. The collisional-radiative system is coupled with the electron distribution evolution treated with a Fokker-Planck approach with additional inelastic terms. The model includes spontaneous emission, resonant photoabsorption, collisional excitation and de-excitation, radiative recombination, photoionization, collisional ionization, three-body recombination, autoionization and dielectronic capture. It is found that for high densities, but still below solid, collisions play an important role and thermalization times are not short enough to ensure a thermal electron distribution. At these densities Maxwellian and non-Maxwellian electron distribution models yield substantial differences in collisional rates, modifying the atomic population dynamics.

X-ray microtomography analysis of the damage micromechanisms in 3D woven composites under low-velocity impact

3D woven composites reinforced with either S2 glass, carbon or a hybrid combination of both and containing either polyethylene or carbon z-yarns were tested under low-velocity impact. Different impact energies (in the range of 21–316 J) were used and the mechanical response (in terms of the impact strength and energy dissipated) was compared with that measured in high-performance, albeit standard, 2D laminates. It was found that the impact strength in both 2D and 3D materials was mainly dependent on the in-plane fiber fracture. Conversely, the energy absorption capability was primarily influenced by the presence of z-yarns, having the 3D composites dissipated over twice the energy than the 2D laminates, irrespective of their individual characteristics (fiber type, compaction degree, porosity, etc.). X-ray microtomography revealed that this improvement was due to the z-yarns, which delayed delamination and maintained the structural integrity of the laminate, promoting energy dissipation by tow splitting, intensive fiber breakage under the tup and formation of a plug by out-of-plane shear.

Identification, retinoid binding, and x-ray analysis of a human retinol-binding protein

Two cellular retinol-binding proteins (CRBP I and II) with distinct tissue distributions and retinoid-binding properties have been recognized thus far in mammals. Here, we report the identification of a human retinol-binding protein resembling type I (55.6% identity) and type II (49.6% identity) CRBPs, but with a unique H residue in the retinoid-binding site and a distinctively different tissue distribution. Additionally, this binding protein (CRBP III) exhibits a remarkable sequence identity (62.2%) with the recently identified ι-crystallin/CRBP of the diurnal gecko Lygodactylus picturatus [Werten, P. J. L., Röll, B., van Alten, D. M. F. & de Jong, W. W. (2000) Proc. Natl. Acad. Sci. USA 97, 3282–3287 (First Published March 21, 2000; 10.1073/pnas.050500597)]. CRBP III and all-trans-retinol form a complex (Kd ≈ 60 nM), the absorption spectrum of which is characterized by the peculiar fine structure typical of the spectra of holo-CRBP I and II. As revealed by a 2.3-Å x-ray molecular model of apo-CRBP III, the amino acid residues that line the retinol-binding site in CRBP I and II are positioned nearly identically in the structure of CRBP III. At variance with the human CRBP I and II mRNAs, which are most abundant in ovary and intestine, respectively, the CRBP III mRNA is expressed at the highest levels in kidney and liver thus suggesting a prominent role for human CRBP III as an intracellular mediator of retinol metabolism in these tissues.

Circumstellar emission in Be/X-ray binaries of the Magellanic Clouds and the Milky Way

Aims. We study the optical and near-infrared colour excesses produced by circumstellar emission in a sample of Be/X-ray binaries. Our main goals are exploring whether previously published relations, valid for isolated Be stars, are applicable to Be/X-ray binaries and computing the distance to these systems after correcting for the effects of the circumstellar contamination. Methods. Simultaneous UBVRI photometry and spectra in the 3500−7000 Å spectral range were obtained for 11 optical counterparts to Be/X-ray binaries in the LMC, 5 in the SMC and 12 in the Milky Way. As a measure of the amount of circumstellar emission we used the Hα equivalent width corrected for photospheric absorption. Results. We find a linear relationship between the strength of the Hα emission line and the component of E(B − V) originating from the circumstellar disk. This relationship is valid for stars with emission lines weaker than EW ≈ −15   Å. Beyond this point, the circumstellar contribution to E(B − V) saturates at a value ≈0.17   mag. A similar relationship is found for the (V − I) near infrared colour excess, albeit with a steeper slope and saturation level. The circumstellar excess in (B − V) is found to be about five times higher for Be/X-ray binaries than for isolated Be stars with the same equivalent width EW(Hα), implying significant differences in the physical properties of their circumstellar envelopes. The distance to Be/X-ray binaries (with non-shell Be star companions) can only be correctly estimated by taking into account the excess emission in the V band produced by free-free and free-bound transitions in the circumstellar envelope. We provide a simple method to determine the distances that includes this effect.

Chandra and Suzaku observations of the Be/X-ray star HD110432

We present an analysis of a pointed 141 ks Chandra high-resolution transmission gratings observation of the Be X-ray emitting star HD110432, a prominent member of the γ Cas analogs. This observation represents the first high-resolution spectrum taken for this source as well as the longest uninterrupted observation of any γ Cas analog. The Chandra light curve shows a high variability but its analysis fails to detect any coherent periodicity up to a frequency of 0.05 Hz. Hardness ratio versus intensity analyses demonstrate that the relative contributions of the [1.5-3] Å, [3-6] Å, and [6-16] Å energy bands to the total flux change rapidly in the short term. The analysis of the Chandra High Energy Transmission Grating (HETG) spectrum shows that, to correctly describe the spectrum, three model components are needed. Two of those components are optically thin thermal plasmas of different temperatures (kT ≈ 8-9 and 0.2-0.3 keV, respectively) described by the models vmekal or bvapec. The Fe abundance in each of these two components appears equal within the errors and is slightly subsolar with Z ≈ 0.75 Z ☉. The bvapec model better describes the Fe L transitions, although it cannot fit well the Na XI Lyα line at 10.02 Å, which appears to be overabundant. Two different models seem to describe well the third component. One possibility is a third hot optically thin thermal plasma at kT = 16-21 keV with an Fe abundance Z ≈ 0.3 Z ☉, definitely smaller than for the other two thermal components. Furthermore, the bvapec model describes well the Fe K shell transitions because it accounts for the turbulence broadening of the Fe XXV and Fe XXVI lines with a v turb ≈ 1200 km s–1. These two lines, contributed mainly by the hot thermal plasma, are significantly wider than the Fe Kα line whose FWHM < 5 mÅ is not resolved by Chandra. Alternatively, the third component can be described by a power law with a photon index of Γ = 1.56. In either case, the Chandra HETG spectrum establishes that each one of these components must be modified by distinct absorption columns. The analysis of a noncontemporaneous 25 ks Suzaku observation shows the presence of a hard tail extending up to at least 33 keV. The Suzaku spectrum is described with the sum of two components: an optically thin thermal plasma at kT ≈ 9 keV and Z ≈ 0.74 Z ☉, and a very hot second plasma with kT ≈ 33 keV or, alternatively, a power law with photon index of Γ = 1.58. In either case, each one of the two components must be affected by different absorption columns. Therefore, the kT = 8-9 keV component is definitely needed while the nature of the harder emission cannot be unambiguously established with the present data sets. The analysis of the Si XIII and S XV He-like triplets present in the Chandra spectrum points to a very dense (ne ~ 1013 cm–3) plasma located either close to the stellar surface (r < 3R *) of the Be star or, alternatively, very close (r ~ 1.5R WD) to the surface of a (hypothetical) white dwarf companion. We argue, however, that the available data support the first scenario.

Accreting magnetars: a new type of high-mass X-ray binaries?

The discovery of very slow pulsations (Pspin =5560 s) has solved the long-standing question of the nature of the compact object in the high-mass X-ray binary 4U 2206+54 but has posed new ones. According to spin evolutionary models in close binary systems, such slow pulsations require a neutron star magnetic field strength larger than the quantum critical value of 4.4 × 1013 G, suggesting the presence of a magnetar. We present the first XMM–Newton observations of 4U 2206+54 and investigate its spin evolution. We find that the observed spin-down rate agrees with the magnetar scenario. We analyse Integral Spacecraft Gamma-Ray Imager (ISGRI)/INTErnational Gamma-RAy Laboratory (INTEGRAL) observations of 4U 2206+54 to search for the previously suggested cyclotron resonance scattering feature at ∼30 keV. We do not find a clear indication of the presence of the line, although certain spectra display shallow dips, not always at 30 keV. The association of these dips with a cyclotron line is very dubious because of its apparent transient nature. We also investigate the energy spectrum of 4U 2206+54 in the energy range 0.3–10 keV with unprecedented detail and report for the first time the detection of very weak 6.5 keV fluorescence iron lines. The photoelectric absorption is consistent with the interstellar value, indicating very small amount of local matter, which would explain the weakness of the florescence lines. The lack of matter locally to the source may be the consequence of the relatively large orbital separation of the two components of the binary. The wind would be too tenuous in the vicinity of the neutron star.

An XMM-Newton view of FeKα in high-mass X-ray binaries

We present a comprehensive analysis of the whole sample of available XMM-Newton observations of high-mass X-ray binaries (HMXBs) until August 2013, focusing on the FeKα emission line. This line is key to better understanding the physical properties of the material surrounding the X-ray source within a few stellar radii (the circumstellar medium). We collected observations from 46 HMXBs and detected FeKα in 21 of them. We used the standard classification of HMXBs to divide the sample into different groups. We find that (1) different classes of HMXBs display different qualitative behaviours in the FeKα spectral region. This is visible especially in SGXBs (showing ubiquitous Fe fluorescence but not recombination Fe lines) and in γ Cass analogues (showing both fluorescent and recombination Fe lines). (2) FeKα is centred at a mean value of 6.42 keV. Considering the instrumental and fits uncertainties, this value is compatible with ionization states that are lower than Fe xviii. (3) The flux of the continuum is well correlated with the flux of the line, as expected. Eclipse observations show that the Fe fluorescence emission comes from an extended region surrounding the X-ray source. (4) We observe an inverse correlation between the X-ray luminosity and the equivalent width of FeKα (EW). This phenomenon is known as the X-ray Baldwin effect. (5) FeKα is narrow (σline< 0.15 keV), reflecting that the reprocessing material does not move at high speeds. We attempt to explain the broadness of the line in terms of three possible broadening phenomena: line blending, Compton scattering, and Doppler shifts (with velocities of the reprocessing material V ~ 1000 km s-1). (6) The equivalent hydrogen column (NH) directly correlates to the EW of FeKα, displaying clear similarities to numerical simulations. It highlights the strong link between the absorbing and the fluorescent matter. (7) The observed NH in supergiant X-ray binaries (SGXBs) is in general higher than in supergiant fast X-ray transients (SFXTs). We suggest two possible explanations: different orbital configurations or a different interaction compact object – wind. (8) Finally, we analysed the sources IGR J16320-4751 and 4U 1700-37 in more detail, covering several orbital phases. The observed variation in NH between phases is compatible with the absorption produced by the wind of their optical companions. The results clearly point to a very important contribution of the donor’s wind in the FeKα emission and the absorption when the donor is a supergiant massive star.

Multiwavelength study of the fast rotating supergiant high-mass X-ray binary IGR J16465−4507

Context. Since its launch, the X-ray and γ-ray observatory INTEGRAL satellite has revealed a new class of high-mass X-ray binaries (HMXB) displaying fast flares and hosting supergiant companion stars. Optical and infrared (OIR) observations in a multi-wavelength context are essential to understand the nature and evolution of these newly discovered celestial objects. Aims. The goal of this multiwavelength study (from ultraviolet to infrared) is to characterise the properties of IGR J16465−4507, to confirm its HMXB nature and that it hosts a supergiant star. Methods. We analysed all OIR, photometric and spectroscopic observations taken on this source, carried out at ESO facilities. Results. Using spectroscopic data, we constrained the spectral type of the companion star between B0.5 and B1 Ib, settling the debate on the true nature of this source. We measured a high rotation velocity of v = 320 ± 8km s-1 from fitting absorption and emission lines in a stellar spectral model. We then built a spectral energy distribution from photometric observations to evaluate the origin of the different components radiating at each energy range. Conclusions. We finally show that, having accurately determined the spectral type of the early-B supergiant in IGR J16465−4507, we firmly support its classification as an intermediate supergiant fast X-ray transient (SFXT).

Crystallization and preliminary X-ray analysis of sulfite dehydrogenase from Stargeya novella

Crystals of purified heterodimeric sulfite dehydrogenase from Starkeya novella have been grown using vapour diffusion. X-ray diffraction data have been collected from crystals of the native protein at lambda=1.0 Angstrom and close to the iron absorption edge at lambda=1.737 Angstrom. The crystals belong to space group P2(1)2(1)2, with unit-cell parameters a=97.5, b=92.5, c=55.9 Angstrom. Native data have been recorded to 1.8 Angstrom resolution and Fe-edge data to 2.5 Angstrom.

IRAS 00183-7111: ALMA and X-ray view of an ultra luminous infrared galaxy

The aim of this Thesis work is to study the multi-frequency properties of the Ultra Luminous Infrared Galaxy (ULIRG) IRAS 00183-7111 (I00183) at z = 0.327, connecting ALMA sub-mm/mm observations with those at high energies in order to place constraints on the properties of its central power source and verify whether the gas traced by the CO may be responsible for the obscuration observed in X-rays. I00183 was selected from the so-called Spoon diagnostic diagram (Spoon et al. 2007) for mid-infrared spectra of infrared galaxies based on the equivalent width of the 6.2 μm Polycyclic Aromatic Hydrocarbon (PAH) emission feature versus the 9.7 μm silicate strength. Such features are a powerful tool to investigate the contribution of star formation and AGN activity in this class of objects. I00183 was selected from the top-left region of the plot where the most obscured sources, characterized by a strong Si absorption feature, are located. To link the sub-mm/mm to the X-ray properties of I00183, ALMA archival Cycle 0 data in Band 3 (87 GHz) and Band 6 (270 GHz) have been calibrated and analyzed, using CASA software. ALMA Cycle 0 was the Early Science program for which data reprocessing is strongly suggested. The main work of this Thesis consisted in reprocessing raw data to provide an improvement with respect to the available archival products and results, which were obtained using standard procedures. The high-energy data consists of Chandra, XMM-Newton and NuSTAR observations which provide a broad coverage of the spectrum in the energy range 0.5 − 30 keV. Chandra and XMM archival data were used, with an exposure time of 22 and 22.2 ks, respectively; their reduction was carried out using CIAO and SAS software. The 100 ks NuSTAR are still private and the spectra were obtained by courtesy of the PI (K. Iwasawa). A detailed spectral analysis was done using XSPEC software; the spectral shape was reproduced starting from simple phenomenological models, and then more physical models were introduced to account for the complex mechanisms that involve this source. In Chapter 1, an overview of the scientific background is discussed, with a focus on the target, I00183, and the Spoon diagnostic diagram, from which it was originally selected. In Chapter 2, the basic principles of interferometry are briefly introduced, with a description of the calibration theory applied to interferometric observations. In Chapter 3, ALMA and its capabilities, both current and future, are shown, explaining also the complex structure of the ALMA archive. In Chapter 4, the calibration of ALMA data is presented and discussed, showing also the obtained imaging products. In Chapter 5, the analysis and discussion of the main results obtained from ALMA data is presented. In Chapter 6, the X-ray observations, data reduction and spectral analysis are reported, with a brief introduction to the basic principle of X-ray astronomy and the instruments from which the observations were carried out. Finally, the overall work is summarized, with particular emphasis on the main obtained results and the possible future perspectives.

An X-ray study of the SNR G344.7-0.1 and the central object CXOU J170357.8-414302

Aims. We report results of an X-ray study of the supernova remnant (SNR) G344.7-0.1 and the point-like X-ray source located at the geometrical center of the SNR radio structure. Methods. The morphology and spectral properties of the remnant and the central X-ray point-like source were studied using data from the XMM-Newton and Chandra satellites. Archival radio data and infrared Spitzer observations at 8 and 24 mu m were used to compare and study its multi-band properties at different wavelengths. Results. The XMM-Newton and Chandra observations reveal that the overall X-ray emission of G344.7-0.1 is extended and correlates very well with regions of bright radio and infrared emission. The X-ray spectrum is dominated by prominent atomic emission lines. These characteristics suggest that the X-ray emission originated in a thin thermal plasma, whose radiation is represented well by a plane-parallel shock plasma model (PSHOCK). Our study favors the scenario in which G344.7-0.1 is a 6 x 10^3 year old SNR expanding in a medium with a high density gradient and is most likely encountering a molecular cloud on the western side. In addition, we report the discovery of a soft point-like X-ray source located at the geometrical center of the radio SNR structure. The object presents some characteristics of the so-called compact central objects (CCO). However, its neutral hydrogen absorption column (N_H) is inconsistent with that of the SNR. Coincident with the position of the source, we found infrared and optical objects with typical early-K star characteristics. The X-ray source may be a foreground star or the CCO associated with the SNR. If this latter possibility were confirmed, the point-like source would be the farthest CCO detected so far and the eighth member of the new population of isolated and weakly magnetized neutron stars.

Studies of Protein-Protein and Protein-Water Interactions by Small Angle X-Ray Scattering, Terahertz Spectroscopy, ASMOS, And Computer Simulation

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 µm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.