Multi-Model Data Query Languages and Processing Paradigms

Peer reviewe

Prospective Study of the Effect of the 21-Gene Assay on Adjuvant Clinical Decision-Making in Japanese Women With Estrogen Receptor-Positive, Node-Negative, and Node-Positive Breast Cancer

AbstractBackgroundIn this study we investigated if the 21-gene assay result affects adjuvant decision-making in Japanese women with ER+ invasive EBC.Patients and MethodsA total of 124 consecutive eligible patients with ER+, HER2-negative EBC and 0 to 3 positive lymph nodes were enrolled. Treatment recommendations, physicians' confidence and patients' decisional conflict before and after knowledge of the Recurrence Score results of the 21-gene assay were recorded.ResultsOne-hundred four patients (84%) had N0 disease, including micrometastases, and 20 (16%) had N+ disease. Overall, recommendations changed in 33% (95% CI, 24%-43%) of N0 and 65% (95% CI, 41%-85%) of N+ patients. In 27 of 48 (56%) of N0 and 13 of 15 (87%) of N+ patients an initial recommendation for chemohormonal therapy was revised to only hormonal therapy after assay results, and in 7 of 56 (13%) of N0 and 0 of 5 N+ patients from only hormonal to combined chemohormonal therapy. Decisions appeared to follow the Recurrence Score results for low and high values. For patients with intermediate Recurrence Score values, overall recommendations for chemohormonal treatment tended to decrease after assay results. Physicians' confidence increased in 106 of 124 (85.5%; 95% CI, 78%-91%) cases. Patients' decisional conflict significantly improved as indicated by changes in the total score and the 5 defined subscores (P = .014 for Informed Subscore; P < .001 for all others).ConclusionResults from this prospective study in a Japanese population confirm an effect of the 21-gene assay results on adjuvant treatment decision-making, consistent with reported experiences from the United States and Europe

Fast Iterative Reconstruction in MVCT

Statistical iterative reconstruction is expected to improve the image quality of computed tomography (CT). However, one of the challenges of iterative reconstruction is its large computational cost. The purpose of this review is to summarize a fast iterative reconstruction algorithm by optimizing reconstruction parameters. Megavolt projection data was acquired from a TomoTherapy system and reconstructed using in-house statistical iterative reconstruction algorithm. Total variation was used as the regularization term and the weight of the regularization term was determined by evaluating signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), and visual assessment of spatial resolution using Gammex and Cheese phantoms. Gradient decent with an adaptive convergence parameter, ordered subset expectation maximization (OSEM), and CPU/GPU parallelization were applied in order to accelerate the present reconstruction algorithm. The SNR and CNR of the iterative reconstruction were several times better than that of filtered back projection (FBP). The GPU parallelization code combined with the OSEM algorithm reconstructed an image several hundred times faster than a CPU calculation. With 500 iterations, which provided good convergence, our method produced a 512 × 512 pixel image within a few seconds. The image quality of the present algorithm was much better than that of FBP for patient data

Liquid-shaped microlens for scalable production of ultrahigh-resolution OCT microendoscope

Endoscopic optical coherence tomography (OCT) is a valuable tool for providing diagnostic images of internal organs and guiding interventions in real time. Miniaturized OCT endoscopes are essential for imaging small and convoluted luminal organs while minimizing invasiveness. However, current methods for fabricating miniature fiber probes have limited ability to correct optical aberrations, leading to suboptimal imaging performance. In this study, we introduce a new paradigm of liquid shaping technique for the rapid and scalable fabrication of ultrathin and high-performance OCT microendoscopes suitable for minimally invasive clinical applications. This technique enables the flexible customization of freeform microlenses with sub-nanometer optical surface roughness by regulating the minimum energy state of curable optical liquid on a wettability-modified substrate and precisely controlling the liquid volume and physical boundary on a substrate. Using this technique, we simultaneously fabricated 800-nm OCT microendoscopes with a diameter of approximately 0.6 mm and evaluated their ultrahigh-resolution imaging performance in the esophagus of rats and the aorta and brain of mice.Comment: 42 pages, 7 figures in the main tex

Structural and functional basis for RNA cleavage by Ire1

BACKGROUND: The unfolded protein response (UPR) controls the protein folding capacity of the endoplasmic reticulum (ER). Central to this signaling pathway is the ER-resident bifunctional transmembrane kinase/endoribonuclease Ire1. The endoribonuclease (RNase) domain of Ire1 initiates a non-conventional mRNA splicing reaction, leading to the production of a transcription factor that controls UPR target genes. The mRNA splicing reaction is an obligatory step of Ire1 signaling, yet its mechanism has remained poorly understood due to the absence of substrate-bound crystal structures of Ire1, the lack of structural similarity between Ire1 and other RNases, and a scarcity of quantitative enzymological data. Here, we experimentally define the active site of Ire1 RNase and quantitatively evaluate the contribution of the key active site residues to catalysis. RESULTS: This analysis and two new crystal structures suggest that Ire1 RNase uses histidine H1061 and tyrosine Y1043 as the general acid-general base pair contributing \u3e/=7.6 kcal/mol and 1.4 kcal/mol to transition state stabilization, respectively, and asparagine N1057 and arginine R1056 for coordination of the scissile phosphate. Investigation of the stem-loop recognition revealed that additionally to the stem-loops derived from the classic Ire1 substrates HAC1 and Xbp1 mRNA, Ire1 can site-specifically and rapidly cleave anticodon stem-loop (ASL) of unmodified tRNAPhe, extending known substrate specificity of Ire1 RNase. CONCLUSIONS: Our data define the catalytic center of Ire1 RNase and suggest a mechanism of RNA cleavage: each RNase monomer apparently contains a separate catalytic apparatus for RNA cleavage, whereas two RNase subunits contribute to RNA stem-loop docking. Conservation of the key residues among Ire1 homologues suggests that the mechanism elucidated here for yeast Ire1 applies to Ire1 in metazoan cells, and to the only known Ire1 homologue RNase L