The shells of pearl oysters, Pinctada fucata, are composed of calcite and aragonite and possess remarkable mechanical properties. These shells are formed under the regulation of macromolecules, especially shell matrix proteins (SMPs). Identification of diverse SMPs will lay a foundation for understanding biomineralization process. Here, we identified 72 unique SMPs using liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of proteins extracted from the shells of P. fucata combined with a draft genome. Of 72 SMPs, 17 SMPs are related to both the prismatic and nacreous layers. Moreover, according to the diverse domains found in the SMPs, we hypothesize that in addition to controlling CaCO3 crystallization and crystal organization, these proteins may potentially regulate the extracellular microenvironment and communicate between cells and the extracellular matrix (ECM). Immunohistological localization techniques identify the SMPs in the mantle, shells and synthetic calcite. Together, these proteomic data increase the repertoires of the shell matrix proteins in P. fucata and suggest that shell formation in P. fucata may involve tight regulation of cellular activities and the extracellular microenvironment.

The Brassicaceae Database (BRAD version 3.0, BRAD V3.0; http://brassicadb.cn) has evolved from the former Brassica Database (BRAD V2.0), and represents an important community portal hosting genome information for multiple Brassica and related Brassicaceae plant species. Since the last update in 2015, the complex genomes of numerous Brassicaceae species have been decoded, accompanied by many omics datasets. To provide an up-to-date service, we report here a major upgrade of the portal. The Model-View-ViewModel (MVVM) framework of BRAD has been re-engineered to enable easy and sustainable maintenance of the database. The collection of genomes has been increased to 26 species, along with optimization of the user interface. Features of the previous version have been retained, with additional new tools for exploring syntenic genes, gene expression and variation data. In the ‘Syntenic Gene @ Subgenome’ module, we added features to view the sequence alignment and phylogenetic relationships of syntenic genes. New modules include ‘MicroSynteny’ for viewing synteny of selected fragment pairs, and ‘Polymorph’ for retrieval of variation data. The updated BRAD provides a substantial expansion of genomic data and a comprehensive improvement of the service available to the Brassicaceae research community.

Mammography is the only technique currently used for detecting microcalcification (MC) clusters, an early indicator of breast cancer. However, mammographic images superimpose a three-dimensional compressed breast image onto two-dimensional projection views, resulting in overlapped anatomical breast structures that may obscure the detection and visualization of MCs. One possible solution to this problem is the use of cone beam computed tomography (CBCT) with a flat-panel (FP) digital detector. Although feasibility studies of CBCT techniques for breast imaging have yielded promising results, they have not shown how radiation dose and x-ray tube voltage affect the accuracy with which MCs are detected by CBCT experimentally. We therefore conducted a phantom study using a FP-based CBCT system with various mean glandular doses and kVp values. An experimental CBCT scanner was constructed with a data acquisition rate of 7.5 frames/s. 10.5 and 14.5 cm diameter breast phantoms made of gelatin were used to simulate uncompressed breasts consisting of 100% glandular tissue. Eight different MC sizes of calcium carbonate grains, ranging from 180-200 microm to 355-425 microm, were used to simulate MCs. MCs of the same size were arranged to form a 5 x 5 MC cluster and embedded in the breast phantoms. These MC clusters were positioned at 2.8 cm away from the center of the breast phantoms. The phantoms were imaged at 60, 80, and 100 kVp. With a single scan (360 degrees), 300 projection images were acquired with 0.5 x, 1x, and 2x mean glandular dose limit for 10.5 cm phantom and with 1x, 2x, and 4x for 14.5 cm phantom. A Feldkamp algorithm with a pure ramp filter was used for image reconstruction. The normalized noise level was calculated for each x-ray tube voltage and dose level. The image quality of the CBCT images was evaluated by counting the number of visible MCs for each MC cluster for various conditions. The average percentage of the visible MCs was computed and plotted as a function of the MGD, the kVp, and the average MC size. The results showed that the MC visibility increased with the MGD significantly but decreased with the breast size. The results also showed that the x-ray tube voltage affects the detection of MCs under different circumstances. With a 50% threshold, the minimum detectable MC sizes for the 10.5 cm phantom were 348(+/-2), 288(+/-7), 257(+/-2) microm at 3, 6, and 12 mGy, respectively. Those for the 14.5 cm phantom were 355 (+/-1), 307 (+/-7), 275 (+/-5) microm at 6, 12, and 24 mGy, respectively. With a 75% threshold, the minimum detectable MC sizes for the 10.5 cm phantom were 367 (+/-1), 316 (+/-7), 265 (+/-3) microm at 3, 6, and 12 mGy, respectively. Those for the 14.5 cm phantom were 377 (+/-3), 334 (+/-5), 300 (+/-2) microm at 6, 12, and 24 mGy, respectively.

This work is to demonstrate that high quality cone beam CT images can be generated for a volume of interest (VOI) and to investigate the exposure reduction effect, dose saving, and scatter reduction with the VOI scanning technique. The VOI scanning technique involves inserting a filtering mask between the x-ray source and the breast during image acquisition. The mask has an opening to allow full x-ray exposure to be delivered to a preselected VOI and a lower, filtered exposure to the region outside the VOI. To investigate the effects of increased noise due to reduced exposure outside the VOI on the reconstructed VOI image, we directly extracted the projection data inside the VOI from the full-field projection data and added additional data to the projection outside the VOI to simulate the relative noise increase due to reduced exposure. The nonuniform reference images were simulated in an identical manner to normalize the projection images and measure the x-ray attenuation factor for the object. Regular Feldkamp-Davis-Kress filtered backprojection algorithm was used to reconstruct the 3D images. The noise level inside the VOI was evaluated and compared with that of the full-field higher exposure image. Calcifications phantom and low contrast phantom were imaged. Dose reduction was investigated by estimating the dose distribution in a cylindrical water phantom using Monte Carlo simulation based Geant4 package. Scatter reduction at the detector input was also studied. Our results show that with the exposure level reduced by the VOI mask, the dose levels were significantly reduced both inside and outside the VOI without compromising the accuracy of image reconstruction, allowing for the VOI to be imaged with more clarity and helping to reduce the breast dose. The contrast-to-noise ratio inside the VOI was improved. The VOI images were not adversely affected by noisier projection data outside the VOI. Scatter intensities at the detector input were also shown to decrease significantly both inside and outside the VOI in the projection images, indicating potential improvement of image quality inside the VOI and contribution to dose reduction both inside and outside the VOI.