Phantom-Based Feasibility Studies on Phase-Contrast Mammography at Indian Synchrotron Facility Indus-2.

INTRODUCTION: Use of synchrotron radiation (SR) X-ray source in medical imaging has shown great potential for improving soft-tissue image contrast such as the breast. The present study demonstrates quantitative X-ray phase-contrast imaging (XPCI) technique derived from propagation-dependent phase change observed in the breast tissue-equivalent test materials. MATERIALS AND METHODS: Indian synchrotron facility (Indus-2, Raja Ramanna Centre of Advanced Technology [RRCAT]) was used to carry out phantom feasibility study on phase-contrast mammography. Different phantoms and samples, including locally fabricated breast tissue-equivalent phantoms were used to perform absorption and phase mode imaging using 12 and 16 keV SR X-ray beam. Edge-enhancement index (EEI) and edge enhancement to noise ratio (EE/N) were measured for all the images. Absorbed dose to air values were calculated for 12 and 16 keV SR X-ray beam using the measured SR X-ray photon flux at the object plane and by applying the standard radiation dosimetry formalism. RESULTS AND CONCLUSION: It was observed in case of all the phantoms and test samples that EEI and EE/N values are relatively higher for images taken in the phase mode. The absorbed dose to air at imaging plane was found to be 75.59 mGy and 28.9 mGy for 12 and 16 keV SR energies, respectively. However, these dose values can be optimized by reducing the image acquisition time without compromising the image quality when clinical samples are imaged. This work demonstrates the feasibility of XPCI in mammography using 12 and 16 keV SR X-ray beams.

3D spatial distribution of ore mineral phases using high resolution synchrotron micro-computed tomography (µCT) combined with optical microscopy.

Ore minerals in dolomites and Graphite Mica Schist (GMS) were studied by synchrotron radiation micro-computed tomography (SR-µCT) and optical microscopy. High resolution µCT images of ore minerals were obtained at Imaging Beamline (BL-4), Indus-2 synchrotron radiation source for the comprehensive volume characterization of minerals. Optical microscopy was used for mineral identification, mineral/rock characterization and quantification of ore mineral assemblages was also confirmed by XRD. 3D images from SR-µCT have shown spatial distribution of major minerals and crystals of different minerals in the volume of samples. The results obtained shows that the GMS and dolomitic hosted rocks mined from region near Udaipur, Rajasthan contains sulfide mineral phases. SR-µCT facilitates visualization of the association of the various metallic minerals with the host rock. The presence of economically important metallic minerals galena, sphalerite and pyrite found in the samples through SR-µCT has implications on exploration and processing of ores.

Imaging and Dosimetric Study on Direct Flat-Panel Detector-Based Digital Mammography System.

INTRODUCTION: Image quality of digital mammography system is generally defined by three primary physical parameters, namely, contrast, resolution, and noise. Quantification of these metrics can be done by measuring objective image quality parameters defined as contrast-to-noise ratio (CNR), modulation transfer function (MTF), and noise power spectra (NPS). MATERIALS AND METHODS: In the present study, various imaging metrics such as CNR, contrast detail resolution, MTF, and NPS were evaluated for a direct flat-panel detector-based digital mammography system following the European Guidelines. Furthermore, system performance relating to both image quality and doses were evaluated using figure of merit (FOM) in terms of CNR2/mean glandular dose (MGD) under automatic exposure control (AEC) and clinically used OPDOSE operating mode. RESULTS AND CONCLUSION: Under AEC mode, FOM values for the 4.5 cm thick BARC polymethyl methacrylate (PMMA) phantom were found to be 15.02, 15.88, and 19.82 at Mo/Mo, Mo/Rh, and W/Rh target/filter (T/F), respectively. Under OPDOSE mode, FOM values were found to 65.32, 11.80, and 1.14 for the BARC PMMA phantom thickness of 2, 4.5, and 8 cm, respectively. Under OPDOSE mode, the calculated MGD values for three Computerized Imaging Reference Systems slab phantoms having total thickness of 7 cm were observed to be 3.03, 2.32, and 1.75 mGy with glandular/adipose tissue compositions of 70/30, 50/50, and 30/70, respectively, whereas for the 2-8-cm thick BARC PMMA phantom, the calculated MGDs were found to be in the range of 0.57-3.32 mGy. All the calculated MGDs values were found to be lower than the acceptable level of dose limits provided in European Guidelines.

Organic-Inorganic Composite Films Based on Gd3Ga3Al2O12:Ce Scintillator Nanoparticles for X-ray Imaging Applications.

Organic-inorganic nanocomposite self-standing films of Gd3Ga3Al2O12 (GGAG) uniformly dispersed in poly(methyl methacrylate) (PMMA) and polystyrene polymer are prepared for radiography application. GGAG:Ce nanoscintillator has been chosen because of its high light output and fast decay time. The nanopowder of GGAG is synthesized by coprecipitation method and dispersed in the polymer matrix by a simple blending technique. The nanocomposite films of thickness in the range of 150-450 µm with a very high inorganic content is achieved by this technique. These films are characterized by their uniformity, optical absorption, photoluminescence, and radioluminescence. These films are further tested for their application in radiography by recording X-ray images using a commercially available charge-coupled device camera. A resolution of 10 lp/mm is obtained using GGAG:PMMA composite film with 50% loading, confirming their application in imaging devices.

Synchrotron-based phase-sensitive imaging of leaves grown from magneto-primed seeds of soybean.

Experiments were conducted to study the effects of static magnetic fields (SMFs) on the venation network of soybean leaves using the synchrotron-based X-ray micro-imaging technique. The seeds of soybean (Glycine max, variety JS-335) were pretreated with different SMFs from 50 to 300 mT in steps of 50 mT for 1 h. The phase-contrast images obtained showed that, as the strength of the SMF increased, the area, width of the midrib, area of the midrib and minor vein of the middle leaflets of third trifoliate leaves also increased up to the SMF strength of 200 mT (1 h) and decreased thereafter. Quantification of the major conducting vein also showed the differences in the major and minor vein structures of the soybean leaves as compared with control leaves. Further, the phase-retrieval technique has been applied to make the segmentation process easy and to quantify the major and minor veins in the venation network. The width and area of midrib enhancement by pre-treatment with SMF implies an enhancement in the uptake of water, which in turn causes an increased rate of photosynthesis and stomatal conductance.

Synchrotron X-ray phase contrast imaging of leaf venation in soybean (Glycine max) after exclusion of solar UV (280-400†nm) radiation.

The hydraulic efficiency of a leaf depends on its vascular structure as this is responsible for transport activities. To investigate the effect of exclusion of UVAB and UVB radiation from the solar spectrum on the micro-structure of leaves of soybean (Glycine max, variety JS-335), a field experiment was conducted using synchrotron-based phase contrast imaging (PCI). Plants were grown in specially designed UV exclusion chambers, and wrapped with filters that excluded UVB (280-315 nm) or UVAB (280-400 nm), or transmitted all the ambient solar UV (280-400 nm) radiation (filter control). Qualitative observation of high-resolution X-ray PCI images obtained at 10 keV has shown the differences in major and minor vein structures of the leaves. The mid-rib width of the middle leaflet of third trifoliate leaves, for all treatments, were obtained using quantitative image analysis. The width of the mid-rib of the middle leaflet of third trifoliate leaves of UVB excluded plants was found to be more compared to leaves of filter control plants, which are exposed to ambient UV. The mid-rib or the main conducting vein transports water and sugars to the whole plant; therefore, mid-rib enhancement by the exclusion of solar UV radiation possibly implies enhancement in the leaf area which in turn causes an increased rate of photosynthesis.

Non-destructive evaluation of teeth restored with different composite resins using synchrotron based micro-imaging.

BACKGROUND: Application of high resolution synchrotron micro-imaging in microdefects studies of restored dental samples. OBJECTIVE: The purpose of this study was to identify and compare the defects in restorations done by two different resin systems on teeth samples using synchrotron based micro-imaging techniques namely Phase Contrast Imaging (PCI) and micro-computed tomography (MCT). With this aim acquired image quality was also compared with routinely used RVG (Radiovisiograph). METHODS: Crowns of human teeth samples were fractured mechanically involving only enamel and dentin, without exposure of pulp chamber and were divided into two groups depending on the restorative composite materials used. Group A samples were restored using a submicron Hybrid composite material and Group B samples were restored using a Nano-Hybrid restorative composite material. Synchrotron based PCI and MCT was performed with the aim of visualization of tooth structure, composite resin and their interface. RESULTS: The quantitative and qualitative comparison of phase contrast and absorption contrast images along with MCT on the restored teeth samples shows comparatively large number of voids in Group A samples. CONCLUSIONS: Quality assessment of dental restorations using synchrotron based micro-imaging suggests Nano-Hybrid resin restorations (Group B) are better than Group A.

Application of X-ray micro-CT for micro-structural characterization of APCVD deposited SiC coatings on graphite conduit.

SiC coatings are commonly used as oxidation protective materials in high-temperature applications. The operational performance of the coating depends on its microstructure and uniformity. This study explores the feasibility of applying tabletop X-ray micro-CT for the micro-structural characterization of SiC coating. The coating is deposited over the internal surface of pipe structured graphite fuel tube, which is a prototype of potential components of compact high-temperature reactor (CHTR). The coating is deposited using atmospheric pressure chemical vapor deposition (APCVD) and properties such as morphology, porosity, thickness variation are evaluated. Micro-structural differences in the coating caused by substrate distance from precursor inlet in a CVD reactor are also studied. The study finds micro-CT a potential tool for characterization of SiC coating during its future course of engineering. We show that depletion of reactants at larger distances causes development of larger pores in the coating, which affects its morphology, density and thickness.

Design, development and first experiments on the X-ray imaging beamline at Indus-2 synchrotron source RRCAT, India.

A full-field hard X-ray imaging beamline (BL-4) was designed, developed, installed and commissioned recently at the Indus-2 synchrotron radiation source at RRCAT, Indore, India. The bending-magnet beamline is operated in monochromatic and white beam mode. A variety of imaging techniques are implemented such as high-resolution radiography, propagation- and analyzer-based phase contrast imaging, real-time imaging, absorption and phase contrast tomography etc. First experiments on propagation-based phase contrast imaging and micro-tomography are reported.

Neutron phase contrast imaging beamline at CIRUS, reactor, India.

This paper presents the development of neutron phase contrast imaging facility at medium flux research reactor, CIRUS, India. The approach adopted for this study is innovative in the sense that both conventional and phase contrast imaging can be performed within same experiment hutch without any major modification in the experimental hutch or collimator.

A variable-wavelength-based approach of phase retrieval for contrast transfer function based methods.

X-ray phase-contrast imaging has emerged as an important method for improving contrast and sensitivity in the field of X-ray imaging. This increase in the sensitivity is attributed to the fact that, in the hard X-ray regime, the phase shift is more prominent as compared with the attenuation for materials having a low X-ray absorption coefficient. Among all the methods using the X-ray phase-contrast technique, in-line phase-contrast imaging scores over the other methods in terms of ease of implementation and efficient use of available X-ray flux. In order to retrieve the projected phase map of the object from the recorded intensity pattern, a large number of algorithms have been proposed. These algorithms generally use either the transport of intensity or contrast transfer function based approach for phase retrieval. In this paper it is proposed to use multiple wavelengths for phase retrieval using the contrast transfer function based formalism.

Laboratory-based X-ray phase-contrast imaging technique for material and medical science applications.

In-line X-ray phase-contrast imaging technique is an emerging method for the study of materials such as carbon fibers, carbon composite materials, polymers, etc. Similarly this technique is also well suited for the imaging of soft materials such as tissues, distinguishing between tumor and normal tissue. These represent the class of materials for which X-ray attenuation cross-section is very small. Thus this method promises a far better contrast for low X-ray absorbing substances than the conventional radiography method. We have set up an experimental facility using a combination of X-ray CCD detector and a microfocus X-ray source. This facility is dedicated to micro-imaging experiments such as microtomography and high-resolution phase-contrast experiments. In this paper, the results of X-ray phase-contrast imaging experiments are described.

Quantitative studies of pyrocarbon-coated materials using synchrotron radiation.

Phase-contrast imaging provides enhanced image contrast and is important for non-destructive evaluation of structural materials. In this paper, experimental results on in-line phase-contrast imaging using a synchrotron source (ELETTRA, Italy) for objects required in material science applications are discussed. Experiments have been carried out on two types of samples, pyrocarbon-coated zirconia and pyrocarbon-coated alumina microspheres. These have applications in both reactor and industrial fields. The phase-contrast imaging technique is found to be very useful in visualizing and determining the coating thickness of pyrocarbon on zirconia and alumina microspheres. The experiments were carried out at X-ray energies of 16, 18 and 20 keV and different object-to-detector distances. The results describe the contrast values and signal-to-noise ratio for both samples. A comprehensive study was carried out to determine the thickness of the pyrocarbon coating on zirconia and alumina microspheres of diameter 500 microm. The advantages of phase-contrast images are discussed in terms of contrast and resolution, and a comparison is made with absorption images. The results show considerable improvement in contrast with phase-contrast imaging as compared with absorption radiography.

Characterization of pyrocarbon coated materials using laboratory based x-ray phase contrast imaging technique.

In-line x-ray phase contrast is an emerging x-ray imaging technique that promises to improve the contrast in x-ray imaging process. This technique is most suited for x-ray imaging of soft materials, low atomic number elements such as carbon composite fibers, very thin coatings, etc. We have used this new emerging technique for visualization and characterization of the pyrocarbon coated materials using a combination of microfocus x-ray source and x-ray charge coupled device detector. These studies are important for characterization of coating and optimization of various process parameters during deposition. These experiments will help us to exploit the potential of this technique for studies in other areas of material science such as characterization of carbon fibered structures and detection of cracks and flaws in materials. The characterization of the imaging system and optimization of some process parameters for carbon deposition are also described in detail.

The role of ataxin 10 in the pathogenesis of spinocerebellar ataxia type 10.

BACKGROUND: Spinocerebellar ataxia type 10 (SCA10) is an autosomal dominant disorder characterized by cerebellar ataxia and seizures. SCA10 is caused by an expansion of an ATTCT pentanucleotide repeat in intron 9 of the ataxin 10 (ATXN10) gene encoding an approximately 55-kd protein of unknown function. However, how this mutation leads to SCA10 is unknown. METHODS: In an effort to understand the pathogenic mechanism of SCA10, the authors conducted a series of experiments to address the effect of repeat expansion on the transcription and RNA processing of the ATXN10 gene. In addition, we generated Sca10 (mouse ataxin 10 homolog)-null mice and addressed the role of Sca10 gene dosage on the cerebellum. RESULTS: Mutant ATXN10 allele is transcribed at the normal level, and the pre-mRNA containing an expanded repeat is processed normally in patient-derived cells. Sca10-null mice exhibited embryonic lethality. Heterozygous mutants were overtly normal and did not develop SCA10 phenotype CONCLUSION: A simple gain of function or loss of function of ATXN10 is unlikely to be the major pathogenic mechanism contributing to the spinocerebellar ataxia type 10 phenotype.

Heterozygous loss of Six5 in mice is sufficient to cause ocular cataracts.

Myotonic dystrophy (DM) is an autosomal dominant disorder characterized by skeletal muscle wasting, myotonia, cardiac arrhythmia, hyperinsulinaemia, mental retardation and ocular cataracts. The genetic defect in DM is a CTG repeat expansion located in the 3' untranslated region of DMPK and 5' of a homeodomain-encoding gene, SIX5 (formerly DMAHP; refs 2-5). There are three mechanisms by which CTG expansion can result in DM. First, repeat expansion may alter the processing or transport of the mutant DMPK mRNA and consequently reduce DMPK levels. Second, CTG expansion may establish a region of heterochromatin 3' of the repeat sequence and decrease SIX5 transcription. Third, toxic effects of the repeat expansion may be intrinsic to the repeated elements at the level of DNA or RNA (refs 10,11). Previous studies have demonstrated that a dose-dependent loss of Dm15 (the mouse DMPK homologue) in mice produces a partial DM phenotype characterized by decreased development of skeletal muscle force and cardiac conduction disorders. To test the role of Six5 loss in DM, we have analysed a strain of mice in which Six5 was deleted. Our results demonstrate that the rate and severity of cataract formation is inversely related to Six5 dosage and is temporally progressive. Six5+/- and Six5-/- mice show increased steady-state levels of the Na+/K+-ATPase alpha-1 subunit and decreased Dm15 mRNA levels. Thus, altered ion homeostasis within the lens may contribute to cataract formation. As ocular cataracts are a characteristic feature of DM, these results demonstrate that decreased SIX5 transcription is important in the aetiology of DM. Our data support the hypothesis that DM is a contiguous gene syndrome associated with the partial loss of both DMPK and SIX5.

CTG repeats show bimodal amplification in E. coli.

Trinucleotide repeats in human genetic disorders showing anticipation follow two inheritance patterns as a function of length. Inheritance of 35-50 repeats show incremental changes, while tracts greater than 80 repeats show large saltatory expansions. We describe a bacterial system that recapitulates this striking bimodal pattern of CTG amplification. Incremental expansions predominate in CTG tracts < Okazaki fragment size, while saltatory expansions increase in repeat tracts > or = Okazaki fragment size. CTG amplification requires loss of SbcC, a protein that modulates cleavage of single-stranded DNA and degradation of duplex DNA from double-strand breaks. These results suggest that noncanonical single strand-containing secondary structures in Okazaki fragments and/or double-strand breaks in repeat tracts are intermediates in CTG amplification.

Correlation of clinical profile of myotonic dystrophy with CTG repeats in the myotonin protein kinase gene.

The molecular genetic analyses (PCR and Southern hybridization) of Indian patients with myotonic dystrophy (DM) were carried out to determine the degree of repeat expansion and an attempt was made to correlate the repeat number with disease severity. A scoring system based on the salient clinical features was devised to objectively assess the disease severity. The repeat expansion was seen in 11 of 12 patients examined and showed an inverse correlation with the age of onset confirming the phenomenon of anticipation. This was further established in the two pedigrees studied, clearly demonstrating both clinical and genetic anticipation. The clinical severity score, however, did not correlate well with the repeat number. Nonetheless, such molecular genetic analyses may have immense value as a screening procedure to identify premutations as well as in prenatal diagnoses.

Polypurine/polypyrimidine sequences as cis-acting transcriptional regulators.

Genome sequence information has generated increasing evidence for the claim that repetitive DNA sequences present within and around genes could play a important role in the regulation of gene expression. Polypurine/polypyrimidine sequences [poly(Pu/Py)] have been observed in the vicinity of promoters and within the transcribed regions of many genes. To understand whether such sequences influence the level of gene expression, we constructed several prokaryotic and eukaryotic expression vectors incorporating poly(Pu/Py) repeats both within and upstream of a reporter gene, lacZ (encoding beta-galactosidase), and studied its expression in vivo. We find that, in contrast to the situation in Escherichia coli, the presence of poly(Pu/Py) sequences within the gene does not significantly inhibit gene expression in mammalian cells. On the other hand, the presence of such sequences upstream of lacZ leads to a several-fold reduction of gene expression in mammalian cells. Similar down-regulation was observed when a structural cassette containing poly(Pu/Py) sequences upstream of lacZ was integrated into yeast chromosome V. Sequence analysis of the nine totally sequenced yeast chromosomes shows that a large number of such sequences occur upstream of ORFs. On the basis of our experimental results and DNA sequence analysis, we propose that these sequences can function as cis-acting transcriptional regulators.

Simple repetitive sequences in the genome: structure and functional significance.

The current explosion of DNA sequence information has generated increasing evidence for the claim that noncoding repetitive DNA sequences present within and around different genes could play an important role in genetic control processes, although the precise role and mechanism by which these sequences function are poorly understood. Several of the simple repetitive sequences which occur in a large number of loci throughout the human and other eukaryotic genomes satisfy the sequence criteria for forming non-B DNA structures in vitro. We have summarized some of the features of three different types of simple repeats that highlight the importance of repetitive DNA in the control of gene expression and chromatin organization. (i) (TG/CA)n repeats are widespread and conserved in many loci. These sequences are associated with nucleosomes of varying linker length and may play a role in chromatin organization. These Z-potential sequences can help absorb superhelical stress during transcription and aid in recombination. (ii) Human telomeric repeat (TTAGGG)n adopts a novel quadruplex structure and exhibits unusual chromatin organization. This unusual structural motif could explain chromosome pairing and stability. (iii) Intragenic amplification of (CTG)n/(CAG)n trinucleotide repeat, which is now known to be associated with several genetic disorders, could down-regulate gene expression in vivo. The overall implications of these findings vis-à-vis repetitive sequences in the genome are summarized.