SU-E-J-69: Development of an Ambiguity-Free Optical Tracking System for SBRT

PURPOSE

Commercial optical tracking system such as BrainLab ExacTrac© suffers from ambiguous markers which can cause significant delay in patient treatment. We developed an ambiguity-free optical tracking system for high precision SBRT.

METHODS

The optical tracking system consists of a pair of camera sensors, 4∼8 infra-red (IR) reflective markers affixed on patient skin and in-house developed software. We developed an effective algorithm to automatically eliminate ambiguous markers. A recursive backtracking algorithm was developed to build one-to-one correspondence between reference markers and optical markers. The algorithm was able to deal with missing, misplaced, or occluded markers by introducing 'dummy' markers. Isocenter displacements were calculated in six-degree of freedom through rigid-body registration between reference markers and optical markers. The system accuracy was evaluated with a pelvis phantom against cone beam CT (CBCT) and ExacTrac. The impact of number of markers on tracking accuracy was also evaluated. The performance of automatic ambiguity elimination was assessed with synthetic and clinic marker patterns.

RESULTS

Difference of isocenter displacement reported by our system and commercial systems (CBCT, ExacTrac) were within 0.5 mm/0.1o. Impact of number of markers on tracking accuracy in our phantom test was negligible with isocenter displacement varying within 0.2 mm/0.2o when number of markers varied from 4 to 8. The system successfully identified and eliminated ambiguous markers in both synthetic and clinic marker patterns.

CONCLUSIONS

An accurate optical tracking system free of ambiguous markers was developed for patient positioning and monitoring in high precision SBRT. The developed algorithms to eliminate ambiguous markers and to handle missing, misplaced or occluded markers were effective and efficient.

SU-D-BRCD-02: A Novel Cylindrical 3D Water Scanner for Beam Data Collection: I. Validation of the Automatic-Setup

PURPOSE

To determine the accuracy and reproducibility of the automatic- setup procedure of a 3D water scanner (3D SCANNER, Sun Nuclear Corp). The procedure automatically aligns the scanner's coordinate system to the Linac coordinate system. A unique off-center detector holder extends the scan range to 630 mm, eliminating the need for scanner shifts for large-field scans.

METHODS

The automatic-setup procedure provides means to automatically (1) level the tank; (2) zero the detector position to water surface; (3) align the scanner's coordinate system to the Linac system; and (4) correct motor hysteresis. After automatic-setup, (1) and (2) were evaluated visually by three physicists. Step (3) was tested by moving one of the jaws to the isocenter and scans were made along the jaw edge. Angular misalignment between the scanner and the Linac would Result in a noticeably tilted profile. Step (4) was tested by scanning with the chamber moving forward and then backward five times. The accuracy of the off-center detector holder was tested by comparing scans made using the regularand the off-center detector holders. All tests were repeated three times.

RESULTS

All tests of the water surface and horizontal chamber movementwere acceptable from the nine independent evaluations. Scans along the jawedge resulted in < 1% in profile tilt, corresponding to < 0.05 degree in angular misalignment. Same direction scans resulted in field edge differences < 0.05 mm, and < 0.2 mm when compared to scans in thereverse direction. There was no difference in accuracy when different scan speeds were used. Profiles obtained using the regular and the off-centerdetector holders were identical.

CONCLUSIONS

The automatic-setupprocedure resulted in accurate alignment of the 3D SCANNER to the Linac. These results were user-independent. It also provides the ability to scan large fields without the need to change tank setup. This work was partially supported by a research grant from Sun Nuclear Corp., Melbourne, FL.

NUR77 inhibits the expression of TIMP2 and increases the migration and invasion of HTR-8/SVneo cells induced by CYR61

OBJECTIVE

To investigate the function and mechanism of CYR61 on the migration and invasion of the trophoblast cell line, HTR-8/SVneo cells.

STUDY DESIGN

The mRNA and protein levels of NUR77 in the placentas of normal and preeclampsia (PE) women were evaluated using real-time PCR and Western blot, respectively. Paraffin-embedded tissues were processed for localization of NUR77 protein in placental villus by immunohistochemistry. HTR-8/SVneo cells were cultured in the presence of CYR61, Ad-NUR77 or a small interfering RNA for NUR77 (Ad-sinur77). The expression of NUR77 in the HTR-8/SVneo cells was detected and the effects of CYR61 on the migration and invasion of HTR-8/SVneo cells were assessed in wound-healing and transwell experiments, respectively. Gelatin zymography was used to measure the MMP2 release in HTR-8/SVneo cells.

RESULTS

NUR77 is significantly decreased in the placenta of women with PE compared with the levels during a normal pregnancy. CYR61 can significantly increase the expression of NUR77 in HTR-8/SVneo cells. CYR61, as well as NUR77, can promote HTR-8/SVneo cells migration and invasion, which can be blocked by Ad-sinur77. Both CYR61 and Ad-nur77 reduced the mRNA expression of TIMP2 in HTR-8/SVneo cells.

CONCLUSIONS

CYR61 may promote HTR-8/SVneo cells migration and invasion through the upregulation of NUR77, leading to the increase of MMP2 release and the downregulation of TIMP2 expression.

A prototype of an anchoring and extending intestinal micro-robot and an in vitro experiment

In order to minimize the invasiveness of intestinal disease diagnosis and surgery, we propose an anchoring and extending micro-robot. The gait of the micro-robot was designed according to the biomechanical features of the intestinal tract. The locomotion condition showed that the anchoring capability and extending ability should be balanced to enhance locomotion efficiency. The mechanical and control system was designed and fabricated under the requirements of the locomotive model. The assembled micro-robot was 90 mm in length and 13 mm in diameter. The micro-robot prototype was tested in in vitro experiments; its locomotion efficiency was approximately 100% in an ideal environment, but around 50% in a pig's small bowel (20 mm in diameter). The in vitro experiment results demonstrated that the gait is feasible for locomotion in the small bowel although the diameter of the small bowel is a limiting factor.

Detection and quantification of Pratylenchus thornei in DNA extracted from soil using real-time PCR

The root-lesion nematode Pratylenchus thornei is one of the most important pests restricting productivity of wheat in the Pacific Northwest (PNW). It is laborious and difficult to use microscopy to count and identify the nematodes in soils. A SYBR Green I-based real-time polymerase chain reaction (PCR) assay was developed to detect and quantify this species from DNA extracts of soil. A primer set, designed from the internal transcribed spacer region (ITS1) of rDNA, was highly specific to P. thornei and did not amplify DNA from 27 isolates of other Pratylenchus spp., other nematodes, and six fungal species present in PNW wheat fields. A standard curve relating threshold cycle and log values of nematode number was generated from artificially infested soils. The standard curve was supported by a high correlation between the numbers of P. thornei added to soil and the numbers quantified using real-time PCR. Examination of 15 PNW dryland field soils and 20 greenhouse samples revealed significant positive correlations between the numbers determined by real-time PCR and by the Whitehead tray and microscopic method. Real-time PCR is a rapid, sensitive alternative to time-consuming nematode extractions, microscopic identification, and counting of P. thornei from field and greenhouse soils.

MiR-135a functions as a selective killer of malignant glioma

Glioma is the most common and fatal primary brain tumor. Thus far, therapeutic strategies to efficiently and specifically antagonize glioma are limited and poorly developed. Here we report that glia-enriched miR-135a, a microRNA that is dramatically downregulated in malignant glioma and correlated with the pathological grading, is capable of inducing mitochondria-dependent apoptosis of malignant glioma by regulating various genes including STAT6, SMAD5 and BMPR2, as well as affecting the signaling pathway downstream. Moreover, this lethal effect is selectively towards malignant glioma cells, but not neurons and glial cells, through a novel mechanism. Our findings suggest an important role of miR-135a in glioma etiology and provide a potential candidate for malignant glioma therapy.

The clinical values of methylation status of P16 and APC genes in bile in diagnosis of malignant obstructive jaundice

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Background: Preoperative definitive diagnosis of malignant obstructive jaundice caused by biliary and pancreatic carcinomas still remains a major challenge. Hypermethylation of tumor suppressor genes have been implied in carcinogenesis of biliary and pancreatic malignancies. The diagnostic values of methylation status of tumor suppressor genes in bile in malignant obstructive jaundice have not been well-documented.

Methods: Bile was prospectively collected from 70 patients with obstructive jaundice treated at our hospital between November 2008 and Sepetember 2009. Forty-eight of them were proved to be malignant obstructive jaundice (biliary carcinoma in 36, pancreatic carcinoma in 8 and duodenal carcinoma in 4) by pathological examination, and 22 were benign obstructive jaundice caused by cholelithiasis. DNA was extracted from bile and modified by sodium bisulfite. Methylation-specific PCR was run to detect methylation status of P16 and APC gene promoters. Their diagnostic values in malignant obstructive jaundice were assessed.

Results: Hypermethylation of P16 promoter was presented in 72.9% (35/48) malignant obstructive jaundice, and 9% (2/22) bengin obstructive jaundice (p<0.05). Hypermethylation of APC promoter was presented in 56.2% (27/48) malignant obstructive jaundice, and 9% (2/22) bengin obstructive jaundice (p<0.05). With respect to their diagnostic values in malignant obstructive jaundice, sensitivity, specificity, positive predictivity and negative predictivity were 72.9%, 90.9%, 94.6% and 60.6%, respectively, for P16 gene; 56.2%, 90.9%, 93.1%, 48.8%, respectively, for APC gene.

Conclusions: Methylation status of P16 and APC gene promoters in bile was valuable in diagnosis of malignant obstructive jaundice, with an excellent specificity. P16 gene had a higher sensitivity than APC gene.

No significant financial relationships to disclose.

First Report of Bituminaria Witches'-Broom in Australia Caused by a 16SrII Phytoplasma

Bituminaria bituminosa (L.) Stirt. is a perennial legume known as Arabian pea that is used as a forage in arid areas and for stabilization of degraded soils. It is widely distributed in the Mediterranean Basin with wider adaptation across the Canary Islands (4). In July 2010, during a survey for phytoplasma, some Canary Island B. bituminosa plants with typical phytoplasma symptoms, including stunted growth with small leaves, shortened internodes, and bushy growth, were found in seed multiplication nurseries at Medina, Perth, Western Australia (115°48.5'E; 32°13.2'S). Two samples from plants with clear disease symptoms and two visibly healthy plants were collected and total DNA was extracted with the Illustra DNA extraction kit Phytopure (GE Healthcare) according to the manufacturer's instructions. Direct and nested PCR were used to test the presence of phytoplasma 16S rDNA in samples with universal primers P1/P7 and R16F2n/R16R2, respectively (1,3). The PCR amplifications from all diseased samples yielded an expected product of 1.8 kb by direct and 1.2 kb by nested PCR, but not from the healthy plant samples. The direct PCR product was used as a template DNA in sequencing and the DNA sequence was deposited in the NCBI GenBank (Accession No. HQ404357). Sequence homology analysis indicated there was a perfect match between the two isolates. BLAST search of the NCBI GenBank revealed that B. bituminosa phytoplasma shares >99% sequence identity with Crotalaria witches'-broom phytoplasma (Accession No. EU650181.1), pear decline phytoplasma (Accession No. EF656453.1), and Scaevola witches'-broom phytoplasma (Accession No. AB257291.1). On the basis of BLAST analyses of 16S rRNA gene sequences, B. bituminosa phytoplasma in Western Australia appears to belong to the peanut witches'-broom group (16SrII-D) of phytoplasma. Restriction fragment length polymorphism analysis was also performed on nested PCR products of two samples of B. bituminosa phytoplasma by separate digestion with HaeIII, Hind6I, HpaII, MboI, RsaI, Tru9I, and T-HB8I restriction enzymes. Samples yielded patterns similar to alfalfa witches'-broom phytoplasma (Accession No. AF438413) belonging to subgroup 16SrII-D (2). To our knowledge, this is the first report of a phytoplasma of the 16SrII-D group infecting B. bituminosa in Australia and should be referred to as "Bituminaria witches'-broom phytoplasma" (BiWB). This report also indicates that the occurrence of the phytoplasma in B. bituminosa may be widespread in the Canary Islands and other species of Bituminaria might be susceptible to infection by Bituminaria witches'-broom phytoplasma. References: (1) D. E. Gundersen and I.-M. Lee. Phytopathol. Mediterr. 35:144, 1996. (2) A. J. Khan et al. Phytopathology 92:1038, 2002. (3) I.-M. Lee et al. Int. J. Syst. Evol. Microbiol. 54:337, 2004. (4) P. Mendez et al. Grassland Sci. Eur. 11:300, 2006.

Resistance of wheat, barley and oat to Heterodera avenae in the Pacific Northwest, USA

Abstract

The cereal cyst nematode, Heterodera avenae, occurs in at least seven western states of the USA and reduces grain yield in localised regions and in selected crop management systems. Virulence phenotypes for H. avenae populations in North America have not been reported. Nine individual assays in six experiments were conducted to determine the reactions of barley, oat and wheat cultivars to five H. avenae populations in the Pacific Northwest (PNW) states of Idaho, Oregon and Washington. Three populations were evaluated for virulence to 23 entries of the 'International Test Assortment for Defining Cereal Cyst Nematode Pathotypes', plus selected local cultivars and entries representing a greater diversity of resistance genes. The virulence phenotype(s) for populations of H. avenae in the PNW did not correspond to any of the 11 pathotypes defined by the Test Assortment. Five PNW populations exhibited affinities with Group 2 but were not defined by pathotypes Ha12 and Ha22. Reproduction was prevented or greatly inhibited by barley carrying the Rha3 resistance gene and by most carriers of Rha2 resistance, and by selected oat cultivars with multigenic resistance. Wheat cultivars carrying the Cre1 resistance gene were highly effective in suppressing H. avenae reproduction. Current PNW wheat cultivars do not carry the Cre1 resistance gene. Crosses between Ouyen, an Australian bread wheat with Cre1 resistance, and several PNW wheat cultivars were resistant. The CreR gene also prevented H. avenae reproduction in the trial where it was tested. Intermediate levels of reproduction occurred on wheat cultivars carrying the Cre5, Cre7 and Cre8 resistance genes, each of which was considered useful for pyramiding into cultivars with Cre1 resistance. This research identified genetic resources of value in PNW cereal crop breeding programmes.

BP neural network classification for bleeding detection in wireless capsule endoscopy

Bleeding in the digestive tract is one of the most common gastrointestinal tract (GI) diseases, as well as the complication of some fatal diseases. Wireless capsule endoscopy (WCE) allows physicians to noninvasively examine the entire GI tract. However it is very laborious and time-consuming to inspect large numbers of WCE images, which limits the wider application of WCE. It is therefore important to develop an automatic and intelligent computer-aided bleeding detection technique. In this paper, a new method aimed at bleeding detection in WCE images is proposed. Colour texture features distinguishing the bleeding regions from non-bleeding regions are extracted in RGB and HSI colour spaces; then a neural network using the colour texture features as the feature vector inputs is designed to recognize the bleeding regions. The experiments demonstrate that the bleeding regions can be correctly recognized and clearly marked out. The sensitivity of the algorithm is 93% and the specificity is 96%.