Using synchrotron radiation inline phase‐contrast imaging computed tomography to visualize three‐dimensional printed hybrid constructs for cartilage tissue engineering

Synchrotron radiation inline phase‐contrast imaging combined with computed tomography (SR‐inline‐PCI‐CT) offers great potential for non‐invasive characterization and three‐dimensional visualization of fine features in weakly absorbing materials and tissues. For cartilage tissue engineering, the biomaterials and any associated cartilage extracellular matrix (ECM) that is secreted over time are difficult to image using conventional absorption‐based imaging techniques. For example, three‐dimensional printed polycaprolactone (PCL)/alginate/cell hybrid constructs have low, but different, refractive indices and thicknesses. This paper presents a study on the optimization and utilization of inline‐PCI‐CT for visualizing the components of three‐dimensional printed PCL/alginate/cell hybrid constructs for cartilage tissue engineering. First, histological analysis using Alcian blue staining and immunofluorescent staining assessed the secretion of sulfated glycosaminoglycan (GAGs) and collagen type II (Col2) in the cell‐laden hybrid constructs over time. Second, optimization of inline PCI‐CT was performed by investigating three sample‐to‐detector distances (SDD): 0.25, 1 and 3 m. Then, the optimal SDD was utilized to visualize structural changes in the constructs over a 42‐day culture period. The results showed that there was progressive secretion of cartilage‐specific ECM by ATDC5 cells in the hybrid constructs over time. An SDD of 3 m provided edge‐enhancement fringes that enabled simultaneous visualization of all components of hybrid constructs in aqueous solution. Structural changes that might reflect formation of ECM also were evident in SR‐inline‐PCI‐CT images. Summarily, SR‐inline‐PCI‐CT images captured at the optimized SDD enables visualization of the different components in hybrid cartilage constructs over a 42‐day culture period.     

Full‐energy peak efficiency of Si drift and Si(Li) detectors for photons with energies above the Si K binding energy

We studied the full‐energy peak efficiency of a Si drift detector (SDD) and a Si(Li) detector (SLD) using the formalisms proposed by Seltzer [Nucl. Instrum. Meth. 188 (1981) 133] and O'Meara and Campbell [X‐Ray Spectrom. 33 (2004) 146]. The respective adjustable parameters were fitted to full‐energy peak efficiencies measured with certified point radioactive sources. Seltzer's model was able to reproduce the experimental data for the SDD and the SLD in the 6–40 keV and 6–100 keV energy ranges, respectively. In turn, O'Meara and Campbell's formula also performed well for the SDD between 6 and 40 keV and proved to fit satisfactorily in the energy interval 6–60 keV for the SLD. Copyright © 2016 John Wiley & Sons, Ltd.     

Determination of kernel emission spectrum of a mini X‐ray tube for EDXRF applications

Knowing the spectrum near the output of the relatively new mini X‐ray tube (MXRT) commercial models is fundamentally important in energy‐dispersive X‐ray fluorescence scan images, especially in the in vivo applications. This information is relevant for determining the absorbed dose during a measurement and for absolute quantification by a fundamental parameter method. However, it is not possible to measure it directly using a silicon drift detector (SDD) given the high saturation in the counts. In this work, an experimental methodology is developed for determining the kernel spectrum emitted by the MXRT, enabling the quantification of its energy flux density over short distances. Different distances were used: source–detector, solid emission angle (collimation), attenuation characteristics of the medium (air), and in a vacuum, within an energy range of 1–40 keV, to determine the X‐ray tube spectrum. The spectrum is measured by an SDD, taking its efficiency and dead time into account. In order to verify the method, a spectrum that is rebuilt starting with the kernel is compared, under the same conditions, with a reference spectrum that is directly measured in air and with a theoretical spectrum obtained by the Ebel model. The results are consistent and validate the methodology employed in this work. Additionally, low‐energy peaks were detected, corresponding to the tube material's L lines, which are not present in the original spectrum reported by the manufacturer. Copyright © 2015 John Wiley & Sons, Ltd.     

Single‐crystal diffraction at the Extreme Conditions beamline P02.2: procedure for collecting and analyzing high‐pressure single‐crystal data

Fast detectors employed at third‐generation synchrotrons have reduced collection times significantly and require the optimization of commercial as well as customized software packages for data reduction and analysis. In this paper a procedure to collect, process and analyze single‐crystal data sets collected at high pressure at the Extreme Conditions beamline (P02.2) at PETRA III, DESY, is presented. A new data image format called `Esperanto' is introduced that is supported by the commercial software package CrysAlis^Pro (Agilent Technologies UK Ltd). The new format acts as a vehicle to transform the most common area‐detector data formats via a translator software. Such a conversion tool has been developed and converts tiff data collected on a Perkin Elmer detector, as well as data collected on a MAR345/555, to be imported into the CrysAlis^Pro software. In order to demonstrate the validity of the new approach, a complete structure refinement of boron‐mullite (Al₅BO₉) collected at a pressure of 19.4 (2) GPa is presented. Details pertaining to the data collections and refinements of B‐mullite are presented.     

A 3 × 6 arrayed CCD X‐ray detector for continuous rotation method in macromolecular crystallography

A 3 × 6 arrayed charge‐coupled device (CCD) X‐ray detector has been developed for the continuous‐rotation method in macromolecular crystallography at the Photon Factory. The detector has an area of 235.9 mm × 235.9 mm and a readout time of 1.9 s. The detector is made of a 3 × 6 array of identical modules, each module consisting of a fiber‐optic taper (FOT), a CCD sensor and a readout circuit. The outputs from 18 CCDs are read out in parallel and are then digitized by 16‐bit analog‐to‐digital converters. The advantage of this detector over conventional FOT‐coupled CCD detectors is the unique CCD readout scheme (frame transfer) which enables successive X‐ray exposures to be recorded without interruption of the sample crystal rotation. A full data set of a lysozyme crystal was continuously collected within 360 s (180° rotation, 3 s/1.5° frame). The duty‐cycle ratio of the X‐ray exposure to the data collection time was almost 100%. The combination of this detector and synchrotron radiation is well suited to rapid and continuous data collection in macromolecular crystallography.     

Novel high‐resolution silicon drift detectors

Silicon drift detectors (SDDs) are used as energy‐dispersive detectors for x‐ray fluorescence analysis in commercial systems. Because of the low capacitance of the readout anode, achieved by the device topology and by the integration of the first FET on the chip, noise contributions are very small, allowing good energy resolution at low shaping times and high count rates. Typical energy resolution is better than 147 eV FWHM at 5.9 keV (Mn Kα), at ?10°C. This allows the chips to be cooled with a thermoelectric element, avoiding the use of liquid nitrogen. SDD chips are produced at MPI‐Halbleiterlabor in Munich with different geometries and areas. Recently, a new SDD has been developed which places the anode and the integrated JFET at the margin of the chip where it can easily be shielded from direct irradiation with the use of a collimator. The new layout allows the design of a readout anode with smaller area and therefore reduces the capacitance to values of about 120 fF compared with 200–250 fF with standard SDDs. The result is an improvement in energy resolution down to 128 eV at ?15°C. A second effect is the enhancement of the peak‐to‐background values to 6000 homogeneously across the active area of the detector. Copyright © 2004 John Wiley & Sons, Ltd.     

High‐energy X‐ray diffraction using the Pixium 4700 flat‐panel detector

The Pixium 4700 detector represents a significant step forward in detector technology for high‐energy X‐ray diffraction. The detector design is based on digital flat‐panel technology, combining an amorphous Si panel with a CsI scintillator. The detector has a useful pixel array of 1910 × 2480 pixels with a pixel size of 154 µm × 154 µm, and thus it covers an effective area of 294 mm × 379 mm. Designed for medical imaging, the detector has good efficiency at high X‐ray energies. Furthermore, it is capable of acquiring sequences of images at 7.5 frames per second in full image mode, and up to 60 frames per second in binned region of interest modes. Here, the basic properties of this detector applied to high‐energy X‐ray diffraction are presented. Quantitative comparisons with a widespread high‐energy detector, the MAR345 image plate scanner, are shown. Other properties of the Pixium 4700 detector, including a narrow point‐spread function and distortion‐free image, allows for the acquisition of high‐quality diffraction data at high X‐ray energies. In addition, high frame rates and shutterless operation open new experimental possibilities. Also provided are the necessary data for the correction of images collected using the Pixium 4700 for diffraction purposes.     

Picosecond time‐resolved laser pump/X‐ray probe experiments using a gated single‐photon‐counting area detector

The recent developments in X‐ray detectors have opened new possibilities in the area of time‐resolved pump/probe X‐ray experiments; this article presents the novel use of a PILATUS detector to achieve X‐ray pulse duration limited time‐resolution at the Advanced Photon Source (APS), USA. The capability of the gated PILATUS detector to selectively detect the signal from a given X‐ray pulse in 24 bunch mode at the APS storage ring is demonstrated. A test experiment performed on polycrystalline organic thin films of α‐perylene illustrates the possibility of reaching an X‐ray pulse duration limited time‐resolution of 60 ps using the gated PILATUS detector. This is the first demonstration of X‐ray pulse duration limited data recorded using an area detector without the use of a mechanical chopper array at the beamline.     

Performance of a four‐element Si drift detector for X‐ray absorption fine‐structure spectroscopy: resolution, maximum count rate,and dead‐time correction with incorporation into the ATHENA data analysis software

The performance of a four‐element Si drift detector for energy‐dispersive fluorescence‐yield X‐ray absorption fine‐structure measurements is reported, operating at the National Institute of Standards and Technology beamline X23A2 at the National Synchrotron Light Source. The detector can acquire X‐ray absorption fine‐structure spectra with a throughput exceeding 4 × 10⁵ counts per second per detector element (>1.6 × 10⁶ total counts per second summed over all four channels). At this count rate the resolution at 6 keV is approximately 220 eV, which adequately resolves the Mn Kα and Kβ fluorescence lines. Accurate dead‐time correction is demonstrated, and it has been incorporated into the ATHENA data analysis program. To maintain counting efficiency and high signal to background, it is suggested that the incoming count rate should not exceed ～70% of the maximum throughput.     

Micro‐beam x‐ray fluorescence analysis of individual particles with correction for absorption effects

A method of correction for absorption effects in micro‐beam x‐ray fluorescence analysis is described. A fast, energy‐dispersive, silicon drift detector (SDD) was used to measure the primary x‐ray beam transmitted through the sample. The absorption factors were calculated using the data acquired with the SDD. The possibility of using the coherently, incoherently and multiple scattered primary radiation for determining the mass of individual particles was examined. The proposed methods were validated with the use of NIST K3089 glass micro‐spheres of known composition. Copyright © 2006 John Wiley & Sons, Ltd.     

A flow‐through reaction cell for in situ X‐ray diffraction and absorption studies of heterogeneous powder–liquid reactions and phase transformations

A portable powder–liquid high‐corrosion‐resistant reaction cell has been designed to follow in situ reactions by X‐ray powder diffraction (XRD) and X‐ray absorption spectroscopy (XAS) techniques. The cell has been conceived to be mounted on the experimental stations for diffraction and absorption of the Spanish CRG SpLine‐BM25 beamline at the European Synchrotron Radiation Facility. Powder reactants and/or products are kept at a fixed position in a vertical geometry in the X‐ray pathway by a porous membrane, under forced liquid reflux circulation. Owing to the short pathway of the X‐ray beam through the cell, XRD and XAS measurements can be carried out in transmission configuration/mode. In the case of the diffraction technique, data can be collected with either a point detector or a two‐dimensional CCD detector, depending on specific experimental requirements in terms of space or time resolution. Crystallization processes, heterogeneous catalytic processes and several varieties of experiments can be followed by these techniques with this cell. Two experiments were carried out to demonstrate the cell feasibility: the phase transformations of layered titanium phosphates in boiling aqueous solutions of phosphoric acid, and the reaction of copper carbonate and l ‐isoleucine amino acid powders in boiling aqueous solution. In this last case the shrinking of the solid reactants and the formation of Cu(isoleucine)₂ is observed. The crystallization processes and several phase transitions have been observed during the experiments, as well as an unexpected reaction pathway.     

Counting‐loss correction for X‐ray spectroscopy using unit impulse pulse shaping

High‐precision measurement of X‐ray spectra is affected by the statistical fluctuation of the X‐ray beam under low‐counting‐rate conditions. It is also limited by counting loss resulting from the dead‐time of the system and pile‐up pulse effects, especially in a high‐counting‐rate environment. In this paper a detection system based on a FAST‐SDD detector and a new kind of unit impulse pulse‐shaping method is presented, for counting‐loss correction in X‐ray spectroscopy. The unit impulse pulse‐shaping method is evolved by inverse deviation of the pulse from a reset‐type preamplifier and a C‐R shaper. It is applied to obtain the true incoming rate of the system based on a general fast–slow channel processing model. The pulses in the fast channel are shaped to unit impulse pulse shape which possesses small width and no undershoot. The counting rate in the fast channel is corrected by evaluating the dead‐time of the fast channel before it is used to correct the counting loss in the slow channel.     

Application of a pnCCD in X‐ray diffraction: a three‐dimensional X‐ray detector

The first application of a pnCCD detector for X‐ray scattering experiments using white synchrotron radiation at BESSY II is presented. A Cd arachidate multilayer was investigated in reflection geometry within the energy range 7 keV < E < 35 keV. At fixed angle of incidence the two‐dimensional diffraction pattern containing several multilayer Bragg peaks and respective diffuse‐resonant Bragg sheets were observed. Since every pixel of the detector is able to determine the energy of every incoming photon with a resolution ΔE/E? 10^?2, a three‐dimensional dataset is finally obtained. In order to achieve this energy resolution the detector was operated in the so‐called single‐photon‐counting mode. A full dataset was evaluated taking into account all photons recorded within 10⁵ detector frames at a readout rate of 200 Hz. By representing the data in reciprocal‐space coordinates, it becomes obvious that this experiment with the pnCCD detector provides the same information as that obtained by combining a large number of monochromatic scattering experiments using conventional area detectors.     

HAXPES beamline PES‐BL14 at the Indus‐2 synchrotron radiation source

The Hard X‐ray Photo‐Electron Spectroscopy (HAXPES) beamline (PES‐BL14), installed at the 1.5 T bending‐magnet port at the Indian synchrotron (Indus‐2), is now available to users. The beamline can be used for X‐ray photo‐emission electron spectroscopy measurements on solid samples. The PES beamline has an excitation energy range from 3 keV to 15 keV for increased bulk sensitivity. An in‐house‐developed double‐crystal monochromator [Si (111)] and a platinum‐coated X‐ray mirror are used for the beam monochromatization and manipulation, respectively. This beamline is equipped with a high‐energy (up to 15 keV) high‐resolution (meV) hemispherical analyzer with a microchannel plate and CCD detector system with SpecsLab Prodigy and CasaXPS software. Additional user facilities include a thin‐film laboratory for sample preparation and a workstation for on‐site data processing. In this article, the design details of the beamline, other facilities and some recent scientific results are described.     

A new small‐angle X‐ray scattering set‐up on the crystallography beamline I711 at MAX‐lab

A small‐angle X‐ray scattering (SAXS) set‐up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009–0.3 Å^?1 for the standard set‐up but depends on the sample‐to‐detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm × 0.37 mm (full width at half‐maximum) at the sample position, with a flux of 4 × 10¹⁰ photons s^?1 and λ = 1.1 Å. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead‐throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro‐fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost‐effective SAXS station can be constructed on a multipurpose beamline.     

Quick X‐ray reflectivity using monochromatic synchrotron radiation for time‐resolved applications

A new technique for the parallel collection of X‐ray reflectivity (XRR) data, compatible with monochromatic synchrotron radiation and flat substrates, is described and applied to the in situ observation of thin‐film growth. The method employs a polycapillary X‐ray optic to produce a converging fan of radiation, incident onto a sample surface, and an area detector to simultaneously collect the XRR signal over an angular range matching that of the incident fan. Factors determining the range and instrumental resolution of the technique in reciprocal space, in addition to the signal‐to‐background ratio, are described in detail. This particular implementation records ～5° in 2gθ and resolves Kiessig fringes from samples with layer thicknesses ranging from 3 to 76 nm. The value of this approach is illustrated by showing in situ XRR data obtained with 100 ms time resolution during the growth of epitaxial La_0.7Sr_0.3MnO₃ on SrTiO₃ by pulsed laser deposition at the Cornell High Energy Synchrotron Source (CHESS). Compared with prior methods for parallel XRR data collection, this is the first method that is both sample‐independent and compatible with the highly collimated, monochromatic radiation typical of third‐generation synchrotron sources. Further, this technique can be readily adapted for use with laboratory‐based sources.     

Periodic density functional theory study of the high‐pressure behavior of crystalline 7,2′‐anhydro‐β‐d‐arabinosylorotidine

In this work, a detailed study of the structural, electronic, and absorption properties of crystalline 7,2′‐anhydro‐β‐d ‐arabinosylorotidine (Cyclo ara‐O) in the pressure range of 0–350 GPa is performed by density functional theory calculations. The detail analysis of the crystal with increasing pressure shows that complex transformations occur in Cyclo ara‐O under compression. In addition, the b‐direction is much stiffer than the a‐ and c‐axis at 0–330 GPa, suggesting that the Cyclo ara‐O crystal is anisotropic in the certain pressure region. In the pressure range of 110–290 GPa, repeated formations and disconnections of covalent bonds in O7–O6* and C3–C6* occur several times, resulting in a new six‐atom ring that forms at 220, 270, and 290 GPa, while a five‐atom ring and seven‐atom ring form between two adjacent molecules at 300 and 340 GPa, respectively. Then, the analysis of the band gap and DOS (PDOS) of Cyclo ara‐O indicates that its electronic character has changed at 300 GPa into an excellent insulator, but the electron transition is much easier at 350 GPa. Moreover, the relatively high optical activity with the pressure increases of Cyclo ara‐O is seen from the absorption spectra, and two obvious structural transformations are also observed at 180 and 230 GPa, respectively. Copyright © 2016 John Wiley & Sons, Ltd.     

Characterization of an in‐vacuum PILATUS 1M detector

A dedicated in‐vacuum X‐ray detector based on the hybrid pixel PILATUS 1M detector has been installed at the four‐crystal monochromator beamline of the PTB at the electron storage ring BESSY II in Berlin, Germany. Owing to its windowless operation, the detector can be used in the entire photon energy range of the beamline from 10 keV down to 1.75 keV for small‐angle X‐ray scattering (SAXS) experiments and anomalous SAXS at absorption edges of light elements. The radiometric and geometric properties of the detector such as quantum efficiency, pixel pitch and module alignment have been determined with low uncertainties. The first grazing‐incidence SAXS results demonstrate the superior resolution in momentum transfer achievable at low photon energies.