Fully automated pipeline for measurement of the thoracic aorta using joint segmentation and localization neural network.

Purpose: Diagnosis and surveillance of thoracic aortic aneurysm (TAA) involves measuring the aortic diameter at various locations along the length of the aorta, often using computed tomography angiography (CTA). Currently, measurements are performed by human raters using specialized software for three-dimensional analysis, a time-consuming process, requiring 15 to 45 min of focused effort. Thus, we aimed to develop a convolutional neural network (CNN)-based algorithm for fully automated and accurate aortic measurements. Approach: Using 212 CTA scans, we trained a CNN to perform segmentation and localization of key landmarks jointly. Segmentation mask and landmarks are subsequently used to obtain the centerline and cross-sectional diameters of the aorta. Subsequently, a cubic spline is fit to the aortic boundary at the sinuses of Valsalva to avoid errors related inclusions of coronary artery origins. Performance was evaluated on a test set of 60 scans with automated measurements compared against expert manual raters. Result: Compared to training separate networks for each task, joint training yielded higher accuracy for segmentation, especially at the boundary (p<0.001), but a marginally worse (0.2 to 0.5 mm) accuracy for landmark localization (p<0.001). Mean absolute error between human and automated was ≤1 mm at six of nine standard clinical measurement locations. However, higher errors were noted in the aortic root and arch regions, ranging between 1.4 and 2.2 mm, although agreement of manual raters was also lower in these regions. Conclusion: Fully automated aortic diameter measurements in TAA are feasible using a CNN-based algorithm. Automated measurements demonstrated low errors that are comparable in magnitude to those with manual raters; however, measurement error was highest in the aortic root and arch.

Nucleofugality in oxygen and nitrogen derived pseudohalides in Menshutkin reactions: the importance of the intrinsic barrier.

In order to study the nucleofugality of polyatomic anionic leaving groups derived from oxygen and nitrogen, a contingent of 19 methylating agents consisting of amines or alcohols activated with carbonyl or sulfonyl substituents has been examined via ab initio calculations. We have calculated gas phase activation energies for alkylation of ammonia, and methyl cation affinities. We find that polyatomic anionic leaving groups derived from nitrogen will have higher activation energies for Menshutkin (SN2) alkylation even when they have similar methyl cation affinities. This inherent deficit in the nucleofugality of nitrogen-derived leaving groups appears to be a result of the way bond cleavage is synchronized with bond formation to the incoming ammonia nucleophile. The nitrogen leaving groups showed greater dissociation from the methyl fragment than oxygen leaving groups relative to the length of the forming carbon-nitrogen bond. Additionally the second sulfonyl group present in a sulfonimide appears to be less effective at activating nitrogen due to a preference for tetrahedral geometries at the departing nitrogen in the transition states involving leaving sulfonamide groups. Optimal delocalization of electron density is therefore frustrated due to the geometry of the leaving group.

DR6 as a diagnostic and predictive biomarker in adult sarcoma.

BACKGROUND: The Death Receptor 6 (DR6) protein is elevated in the serum of ovarian cancer patients. We tested DR6 serum protein levels as a diagnostic/predictive biomarker in several epithelial tumors and sarcomas. METHODS: DR6 gene expression profiles were screened in publically available arrays of solid tumors. A quantitative immunofluorescent western blot analysis was developed to test the serum of healthy controls and patients with sarcoma, uterine carcinosarcoma, bladder, liver, and pancreatic carcinomas. Change in DR6 serum levels was used to assay the ability of DR6 to predict the response to therapy of sarcoma patients. RESULTS: DR6 mRNA is highly expressed in all tumor types assayed. Western blot analysis of serum DR6 protein demonstrated high reproducibility (r = 0.97). Compared to healthy donor controls, DR6 serum levels were not elevated in patients with uterine carcinosarcoma, bladder, liver, or pancreatic cancers. Serum DR6 protein levels from adult sarcoma patients were significantly elevated (p<0.001). This was most evident for patients with synovial sarcoma. Change in serum DR6 levels during therapy correlated with clinical benefit from therapy (sensitivity 75%, and positive predictive value 87%). CONCLUSION: DR6 may be a clinically useful diagnostic and predictive serum biomarker for some adult sarcoma subtypes. IMPACT: Diagnosis of sarcoma can be difficult and can lead to improper management of these cancers. DR6 serum protein may be a tool to aid in the diagnosis of some sarcomatous tumors to improve treatment planning. For patients with advanced disease, rising DR6 levels predict non-response to therapy and may expedite therapeutic decision making and reduce reliance on radiologic imaging.

F3-targeted cisplatin-hydrogel nanoparticles as an effective therapeutic that targets both murine and human ovarian tumor endothelial cells in vivo.

Recent studies indicate that ovarian cancer may be highly responsive to antivascular therapeutics. We have developed an antivascular tumor therapeutic using the F3 peptide to target cisplatin-loaded nanoparticles (F3-Cis-Np) to tumor vessels. We show that although F3-Cis-Np bind with high specificity to both human ovarian tumor cells and tumor endothelial cells in vitro, they only show cytotoxic activity against the tumor endothelial cells. In vivo these nanoparticles bind primarily to tumor endothelial cells. Therapeutic studies in both flank and orthotopic i.p. murine ovarian tumor models, as well as human tumor xenograft models, show rapid tumor regression with treatment. Treatment was associated with significant vascular necrosis consistent with an antivascular effect. Furthermore, treatment was active in both platinum-sensitive and platinum-resistant cell lines. Importantly, we show that F3-Cis-Np bind to human tumor endothelial cells in vitro and to human tumor vessels in vivo. Therapy targeting human vasculature in vivo with F3-Cis-Np led to near complete loss of all human tumor vessels in a murine model of human tumor vasculature. Our studies indicate that F3-targeted vascular therapeutics may be an effective treatment modality in human ovarian cancer.

Modification of serine 360 by a reactive intermediate of 17-alpha-ethynylestradiol results in mechanism-based inactivation of cytochrome P450s 2B1 and 2B6.

17-alpha-Ethynylestradiol (17EE) is a mechanism-based inactivator of P450 2B1 and P450 2B6 in the reconstituted monooxygenase system. The loss in enzymatic activity was due to the binding of a reactive intermediate of 17EE to the apoprotein. P450 2B1 and P450 2B6 were inactivated by 17EE and digested with trypsin. The peptides obtained following digestion with trypsin of 17EE-inactivated P450 2B1 and P450 2B6 were separated by liquid chromatography and analyzed by ESI-MS. Adducted peptides exhibiting an increase in mass consistent with the addition of the mass of the reactive intermediate of 17EE were identified for each enzyme. Analysis of these modified peptides by ESI-MS/MS and precursor ion scanning facilitated the identification of the Ser360 in both enzymes as a site that had been adducted by a reactive intermediate of 17EE. A P450 2B1 mutant where Ser360 was replaced by alanine was constructed, expressed, and purified. Activity and inactivation studies indicated that mutation of the Ser360 residue to alanine did not prevent inactivation of the mutant enzyme by 17EE. These observations suggest that Ser360 is not critical for the catalytic function of these P450s. Spectral binding studies of the 17EE-inactivated P450 2B1 and P450 2B6 indicated that modification of the enzymes by the reactive intermediate of 17EE resulted in an enzyme that was no longer capable of binding substrates. These results suggest that the inactivation by 17EE may be due to modification of an amino acid residue in the substrate access channel near the point of entry into the active site.