Pseudo CT Estimation using Patch-based Joint Dictionary Learning.

Magnetic resonance (MR) simulators have recently gained popularity; it avoids the unnecessary radiation exposure associated with Computed Tomography (CT) when used for radiation therapy planning. We propose a method for pseudo CT estimation from MR images based on joint dictionary learning. Patient-specific anatomical features were extracted from the aligned training images and adopted as signatures for each voxel. The most relevant and informative features were identified to train the joint dictionary learning-based model. The well-trained dictionary was used to predict the pseudo CT of a new patient. This prediction technique was validated with a clinical study of 12 patients with MR and CT images of the brain. The mean absolute error (MAE), peak signal-to-noise ratio (PSNR), normalized cross correlation (NCC) indexes were used to quantify the prediction accuracy. We compared our proposed method with a state-of-the-art dictionary learning method. Overall our proposed method significantly improves the prediction accuracy over the state-of-the-art dictionary learning method. We have investigated a novel joint dictionary Iearning- based approach to predict CT images from routine MRIs and demonstrated its reliability. This CT prediction technique could be a useful tool for MRI-based radiation treatment planning or attenuation correction for quantifying PET images for PET/MR imaging.

Role of Ku70 in deubiquitination of Mcl-1 and suppression of apoptosis.

Mcl-1 is a unique antiapoptotic Bcl2 family member with a short half-life due to its rapid turnover through ubiquitination. We discovered that Ku70, a DNA double-strand break repair protein, functions as a deubiquitinase to stabilize Mcl-1. Ku70 knockout in mouse embryonic fibroblast (MEF) cells or depletion from human lung cancer H1299 cells leads to the accumulation of polyubiquitinated Mcl-1 and a reduction in its half-life and protein expression. Conversely, expression of exogenous Ku70 in Ku70(-/-) MEF cells restores Mcl-1 expression. Subcellular fractionation indicates that Ku70 extensively colocalizes with Mcl-1 in mitochondria, endoplasmic reticulum and nucleus in H1299 cells. Ku70 directly interacts with Mcl-1 via its C terminus (that is, aa 536-609), which is required and sufficient for deubiquitination and stabilization of Mcl-1, leading to suppression of apoptosis. Purified Ku70 protein directly deubiquitinates Mcl-1 by removing K48-linked polyubiquitin chains. Ku70 knockdown not only promotes Mcl-1 turnover but also enhances antitumor efficacy of the BH3-mimetic ABT-737 in human lung cancer xenografts. These findings identify Ku70 as a novel Mcl-1 deubiquitinase that could be a potential target for cancer therapy by manipulating Mcl-1 deubiquitination.

Low CHD5 expression activates the DNA damage response and predicts poor outcome in patients undergoing adjuvant therapy for resected pancreatic cancer.

The DNA damage response (DDR) promotes genome integrity and serves as a cancer barrier in precancerous lesions but paradoxically may promote cancer survival. Genes that activate the DDR when dysregulated could function as useful biomarkers for outcome in cancer patients. Using a siRNA screen in human pancreatic cancer cells, we identified the CHD5 tumor suppressor as a gene, which, when silenced, activates the DDR. We evaluated the relationship of CHD5 expression with DDR activation in human pancreatic cancer cells and the association of CHD5 expression in 80 patients with resected pancreatic adenocarcinoma (PAC) by immunohistochemical analysis with clinical outcome. CHD5 depletion and low CHD5 expression in human pancreatic cancer cells lead to increased H2AX-Ser139 and CHK2-Thr68 phosphorylation and accumulation into nuclear foci. On Kaplan-Meier log-rank survival analysis, patients with low CHD5 expression had a median recurrence-free survival (RFS) of 5.3 vs 15.4 months for patients with high CHD5 expression (P=0.03). In 59 patients receiving adjuvant chemotherapy, low CHD5 expression was associated with decreased RFS (4.5 vs 16.3 months; P=0.001) and overall survival (OS) (7.2 vs 21.6 months; P=0.003). On multivariate Cox regression analysis, low CHD5 expression remained associated with worse OS (HR: 3.187 (95% CI: 1.49-6.81); P=0.003) in patients undergoing adjuvant chemotherapy. Thus, low CHD5 expression activates the DDR and predicts for worse OS in patients with resected PAC receiving adjuvant chemotherapy. Our findings support a model in which dysregulated expression of tumor suppressor genes that induce DDR activation can be utilized as biomarkers for poor outcome.

Thromboembolic Events Associated with Thalidomide and Multimodality Therapy for Soft Tissue Sarcomas: Results of RTOG 0330.

Introduction. RTOG 0330 was developed to address the toxicity of RTOG 9514 and to add thalidomide (THAL) to MAID chemoradiation for intermediate/high grade soft tissue sarcomas (STSs) and to preoperative radiation (XRT) for low-grade STS. Methods. Primary/locally recurrent extremity/trunk STS: ≥8 cm, intermediate/high grade (cohort A): >5 cm, low grade (cohort B). Cohort A: 3 cycles of neoadjuvant MAID, 2 cycles of interdigitated THAL (200 mg/day)/concurrent 22 Gy XRT, resection, 12 months of adjuvant THAL. Cohort B: neoadjuvant THAL/concurrent 50 Gy XRT, resection, 6 months of adjuvant THAL. Planned accrual 44 patients. Results. 22 primary STS patients (cohort A/B 15/7). Cohort A/B: median age of 49/47 years; median tumor size 12.8/10 cm. 100% preoperative THAL/XRT and surgical resection. Three cycles of MAID were delivered in 93% cohort A. Positive margins: 27% cohort A/29% cohort B. Adjuvant THAL: 60% cohort A/57% cohort B. Grade 3/4 venous thromboembolic (VTE) events: 40% cohort A (1 catheter thrombus and 5 DVT or PE) versus 0% cohort B. RTOG 0330 closed early due to cohort A VTE risk and cohort B poor accrual. Conclusion. Neoadjuvant MAID with THAL/XRT was associated with increased VTE events not seen with THAL/XRT alone or in RTOG 9514 with neoadjuvant MAID/XRT.

SU-E-J-189: The Kullback-Leiber Divergence for Quantifying Changes in Radiotherapy Treatment Response.

PURPOSE: Repeated imaging is an extremely powerful tool in current radiotherapy practice since it allows advanced tumor detection and personalized treatment assessment by quantify tumor response. Change detection algorithms have been developed for remote sensing images to mathematically quantify relevant modifications occurring between datasets of the same subject acquired at different times. We propose usage of change detectors in radiotherapy for an automated quantification of clinical changes occurring in repeated imaging. METHODS: We explore usage of the Kullback-Leiber divergence as indicator of tumor change and quantification of treatment response. The Kullbach-Leiber divergence uses the likelihood theory to measures the distance between two statistical distributions and thus does not assume consistency in imaging. By it's general nature, it can accommodate the presence of noise and variations in imaging acquisition parameters that usually hinder automated identification of clinically-relevant features. RESULTS: In a comparison of simple difference maps and the Kullbach-Leiber divergence operator, the difference maps were affected by noise and did not consistently detect changes of low intensity. In contrast, the proposed operator discerned noise by considering regional statistics around each voxel, and marked both regions with low and high contrast changes. CONCLUSIONS: Statistical comparison through Kullback-Leiber divergence provides a reliable means to automatically quantify changes in repeated radiotherapy imaging.

SU-E-J-191: A Multivariate Framework for N-Tissue Classification in Treatment Assessment of Glioblastomas.

PURPOSE: Glioblastoma is the most common primary brain tumor in adults and is rapidly fatal. Treatment monitoring of these patients has increased awareness that many patients have new areas of contrast enhancement without progressive clinical signs and symptoms. Although the enhancing areas mimic tumor progression, the lesions result from treatment effects and subsequently stabilize or improve without further treatment and are not correlated with poorer outcomes. This phenomenon has been termed pseudoprogression and is hypothesized to occur secondarily to edema and vessel permeability in the tumor area as a result of the combined effects of radiation and chemotherapy. Since the new enhancing lesions of pseudoprogression are indistinguishable from true disease progression, there is a need for a predictive model to distinguish the two phenomena. METHOD: We developed a classification algorithm that combines perfusion and diffusion MRI imaging to effectively partition the cases as one exhibiting true or pseudo progression based on a vector of features containing T1, rCBV and ADC imaging. The multi-sequence classification algorithm uses an expectation maximization (EM) algorithm that learns from training cases with known clinical outcome to assigns each voxel to a type of tissue. RESULTS: A training set of 20 where the clinical outcome is known from biopsy or from long-term follow-up was used by EM algorithm to model typical imaging values within tissue of pseudo, tumor, edema, necrosis, vessels or brain anatomy to construct a database of expected values for each tissue type. When presented with a new case, the algorithm automatically classifies voxels by their geographical proximities and Mahalanobis distance to the pre-sampled values. CONCLUSION: Usage of advanced classification techniques allows automated labeling of voxels into normal, pseudoprogression or tumoral tissue types. The technique allows for early detection of pseudo progression to spare patients from unnecessary surgery or toxic chemotherapy.

Spectrophotometer and ultrasound evaluation of late toxicity following breast-cancer radiotherapy.

PURPOSE: Radiation-induced normal-tissue toxicities are common, complex, and distressing side effects that affect 90% of patients receiving breast-cancer radiotherapy and 40% of patients post radiotherapy. In this study, the authors investigated the use of spectrophotometry and ultrasound to quantitatively measure radiation-induced skin discoloration and subcutaneous-tissue fibrosis. The study's purpose is to determine whether skin discoloration correlates with the development of fibrosis in breast-cancer radiotherapy. METHODS: Eighteen breast-cancer patients were enrolled in our initial study. All patients were previously treated with a standard course of radiation, and the median follow-up time was 22 months. The treated and untreated breasts were scanned with a spectrophotometer and an ultrasound. Two spectrophotometer parameters-melanin and erythema indices-were used to quantitatively assess skin discoloration. Two ultrasound parameters-skin thickness and Pearson coefficient of the hypodermis-were used to quantitatively assess severity of fibrosis. These measurements were correlated with clinical assessments (RTOG late morbidity scores). RESULTS: Significant measurement differences between the treated and contralateral breasts were observed among all patients: 27.3% mean increase in skin thickness (p < 0.001), 34.1% mean decrease in Pearson coefficient (p < 0.001), 27.3% mean increase in melanin (p < 0.001), and 22.6% mean increase in erythema (p < 0.001). All parameters except skin thickness correlated with RTOG scores. A moderate correlation exists between melanin and erythema; however, spectrophotometer parameters do not correlate with ultrasound parameters. CONCLUSIONS: Spectrophotometry and quantitative ultrasound are objective tools that assess radiation-induced tissue injury. Spectrophotometer parameters did not correlate with those of quantitative ultrasound suggesting that skin discoloration cannot be used as a marker for subcutaneous fibrosis. These tools may prove useful for the reduction of radiation morbidities and improvement of patient quality of life.

Early toxicity predicts long-term survival in high-grade glioma.

BACKGROUND: Patients with high-grade gliomas are treated with surgery followed by chemoradiation. The risk factors and implications of neurological side effects are not known. METHODS: Acute and late ≥ grade 3 neurological toxicities (NTs) were analysed among 2761 patients from 14 RTOG trials accrued from 1983 to 2003. The association between acute and late toxicity was analysed using a stepwise logistic regression model. The association between the occurrence of acute NT and survival was analysed as an independent variable. RESULTS: There were 2610 analysable patients (86% glioblastoma, 10% anaplastic astrocytoma). All received a systemic agent during radiation (83% chemotherapy, 17% biological agents). Median radiation dose was 60 Gy. There were 182 acute and 83 late NT events. On univariate analysis, older age, poor performance status, aggressive surgery, pre-existing neurological dysfunction, poor mental status and twice-daily radiation were associated with increased acute NT. In a stepwise logistic regression model the occurrence of acute NT was significantly associated with late NT (OR=2.40; 95% CI=1.2-4.8; P=0.014). The occurrence of acute NT predicted poorer overall survival, independent of recursive partitioning analysis class (median 7.8 vs 11.8 months). INTERPRETATION: Acute NT is significantly associated with both late NT and overall survival.

The combined effects of high pressure and nisin on germination and inactivation of Bacillus spores in milk.

AIMS: The aim of this work was to investigate the germination and inactivation of spores of Bacillus species in buffer and milk subjected to high pressure (HP) and nisin. METHODS AND RESULTS: Spores of Bacillus subtilis and Bacillus cereus suspended in milk or buffer were treated at 100 or 500 MPa at 40 degrees C with or without 500 IU ml(-1) of nisin. Treatment at 500 MPa resulted in high levels of germination (4 log units) of B. subtilis spores in both milk and buffer; this increased to >6 logs by applying a second cycle of pressure. Viability of B. subtilis spores in milk and buffer was reduced by 2.5 logs by cycled HP, while the addition of nisin (500 IU ml(-1)) prior to HP treatment resulted in log reductions of 5.7 and 5.9 in phosphate buffered saline and milk, respectively. Physical damage of spores of B. subtilis following HP was apparent using scanning electron microscopy. Treating four strains of B. cereus at 500 MPa for 5 min twice at 40 degrees C in the presence of 500 IU ml(-1) nisin proved less effective at inactivating the spores of these isolates compared with B. subtilis and some strain-to-strain variability was observed. CONCLUSIONS: Although high levels of germination of Bacillus spores could be achieved by combining HP and nisin, complete inactivation was not achieved using the aforementioned treatments. SIGNIFICANCE AND IMPACT OF THE STUDY: Combinations of HP treatment and nisin may be an appealing alternative to heat pasteurization of milk.

Fractal rotation isolates mechanisms for form-dependent motion in human vision.

Here, we describe a motion stimulus in which the quality of rotation is fractal. This makes its motion unavailable to the translation-based motion analysis known to underlie much of our motion perception. In contrast, normal rotation can be extracted through the aggregation of the outputs of translational mechanisms. Neural adaptation of these translation-based motion mechanisms is thought to drive the motion after-effect, a phenomenon in which prolonged viewing of motion in one direction leads to a percept of motion in the opposite direction. We measured the motion after-effects induced in static and moving stimuli by fractal rotation. The after-effects found were an order of magnitude smaller than those elicited by normal rotation. Our findings suggest that the analysis of fractal rotation involves different neural processes than those for standard translational motion. Given that the percept of motion elicited by fractal rotation is a clear example of motion derived from form analysis, we propose that the extraction of fractal rotation may reflect the operation of a general mechanism for inferring motion from changes in form.

A comparison of intra- and inter-limb relative motion information in modelling a novel motor skill.

The importance of intra- and inter-limb relative motion in modelling a whole body coordination skill was examined. Participants were assigned to one of four groups: Full-Body point light model of a cricket bowler, INTRA-LIMB relative motion of the bowling arm, INTER-LIMB relative motions of the right and left wrists or NO-Relative motion, showing only the motions of the right wrist. During 60 acquisition trials, participants viewed the model five times before each 10-trial block. Retention was examined the following day. Although all groups improved on intra-limb coordination of the bowling arm, the INTRA-LIMB and FULL-BODY groups were more accurate than the INTER-LIMB group in acquisition, although these groups did not differ in retention. For inter-limb coordination, the three groups who received relative motion information performed more like the model than the NO-Relative motion group (even though the INTRA-LIMB group did not see the other limb). The amount of information within a display plays a constraining role on acquisition, perhaps more so than the type of information, such that the acquisition of coordination is more an emergent feature of observational learning, rather than a direct approximation of the model.

Virological and serological evidence of bovine herpesvirus type 4 in cattle in Northern Ireland.

Bovine herpesvirus type 4 (BHV-4), a member of the genus Rhadinovirus, subfamily Gammaherpesvirinae, within the family Herpesviridae, was isolated in fetal bovine lung cells from samples of vaginal discharge taken from a dairy herd in which approximately 50 per cent of the cattle developed metritis after calving. The identity of the isolate was confirmed by immunofluorescent staining with a BHV-4-specific monoclonal antibody and partial sequencing of a portion of the glycoprotein B gene. Serological testing failed to demonstrate a significant association between the exposure of the cattle to BHV-4 and the metritis, but several cattle seroconverted during the periparturient period, consistent with the recrudescence and shedding of virus associated with the stresses of parturition and the onset of lactation. Despite the previous failure to detect BHV-4 in Northern Ireland, a serological survey of 999 cattle in 49 dairy herds and 51 beef herds found widespread evidence of exposure: 29 of the dairy herds and 35 of the beef herds contained one or more seropositive cattle, and 33.3 per cent of the dairy cattle and 23.3 per cent of the beef cattle were positive.

Secondary analysis of Radiation Therapy Oncology Group study (RTOG) 9310: an intergroup phase II combined modality treatment of primary central nervous system lymphoma.

PURPOSE: To determine whether a lower dose of hyperfractionated whole brain radiation reduces central nervous system morbidity without compromising survival for primary CNS lymphoma (PCNSL) patients receiving combined modality treatment. MATERIALS AND METHODS: One hundred and two patients received a course of pre-radiation chemotherapy, followed by whole brain radiation, followed by cytosine-arabinoside. Initial radiation dose was 45 Gy/25 fractions (RT) then the study was amended to reduce this dose for complete responders to induction chemotherapy to 36 Gy/30 fractions/3 weeks (HFX). Eighty-two patients received radiotherapy and were evaluable for toxicity analysis (66 RT patients and 16 HFX patients). MMSE scores and survival for the 40 patients who received radiotherapy after complete response to chemotherapy (27 RT and 13 HFX) were compared. There were no notable differences in pre-treatment patient characteristics between the RT and HFX groups. RESULTS: Neurotoxicity: By 4 years, there were 8/82 (10%) grade 5 neurotoxicities which included 2/16 (13%) grade 5 encephalopathies and 0/27 in the RT group of complete responders to chemotherapy. Survival: There was no statistically significant difference in overall or progression-free survival (PFS) between the chemotherapy-complete responders who received RT and HFX. Cognitive function testing: MMSE scores improved at 8 months across both treatment groups. Analysis of the area under the MMSE curve at 8 months showed no statistically significant difference between RT and HFX groups (P=0.81). Leukoencephalopathy occurred later in the HFX group than in the RT patients. CONCLUSION: Although the HFX schedule represented a 25% reduction in biologically effective tumor dose in comparison, PFS and overall survival were not significantly affected. The HFX regimen delayed but did not eliminate severe neurotoxicity from chemoradiation in PCNSL patients.

Isolation of bovine adenovirus serotype 6 from a calf in the United Kingdom.

Two viruses, designated 99-8130(C) and 99-8130(I), were isolated in calf testis cells from the colon and ileum, respectively, of a suckled beef calf which had developed dysentery and died. Electron microscopy indicated that the mean (sd) size of the viral particles, 83 (2.5) nm, and their morphology were consistent with their being members of the family Adenoviridae. They were confirmed as adenoviruses by PCR when products of the expected size (608 bp) were amplified from both isolates by using a primer pair specific for members of the genus Atadenovirus. A comparison of the sequence of a 567 bp segment of the 99-8130(C) amplicon with that of other prototype bovine adenovirus (BAdV) strains of atadenoviruses identified the isolate as BAdV serotype 6 (BAdV-6), which had 99.3 per cent and 100 per cent identities at the nucleotide and amino acid levels, respectively, with the prototype BAdV-6 strain 671130. A virus neutralisation test was developed and indicated a high prevalence of antibody to BAdV-6 in Northern Irish cattle. There was no evidence of adenoviral inclusions in tissues from the affected calf and no antigen was detected when the tissues were stained by an immunoperoxidase technique, using a homologous antiserum raised in rabbits. The two viruses were the third reported isolation of BAdV-6, and the first from a clinically ill bovine animal.

First observation of herpes-like virus particles in northern pike, Esox lucius L., associated with bluespot-like disease in Ireland.

Circular whitish granular lesions, 5-12 mm in diameter, were observed on the skin and fins of a wild northern pike, Esox lucius, caught in a lake in the Republic of Ireland. Histological examination of the lesions revealed hypertrophied cells in the epidermis with deeply basophilic enlarged nuclei and dark-staining granular material in the cytoplasm. Transmission electron microscopy of these cells revealed naked hexagonal herpes-like virus nucleocapsids (97 +/- 7 nm) in their nuclei while the cytoplasm contained multiple aggregates of enveloped viral particles. This is the first report of herpes-like virus particles in northern pike originating outside North America, where esocid herpesvirus-1 (EsHV-1) has previously been reported. Shared clinical, histological, morphological and epidemiological findings suggest that the observed particles in this report may also be EsHV-1.

Comparison of three IMRT inverse planning techniques that allow for partial esophagus sparing in patients receiving thoracic radiation therapy for lung cancer.

The purpose of this study is to compare 3 intensity-modulated radiation therapy (IMRT) inverse treatment planning techniques as applied to locally-advanced lung cancer. This study evaluates whether sufficient radiotherapy (RT) dose is given for durable control of tumors while sparing a portion of the esophagus, and whether large number of segments and monitor units are required. We selected 5 cases of locally-advanced lung cancer with large central tumor, abutting the esophagus. To ensure that no more than half of the esophagus circumference at any level received the specified dose limit, it was divided into disk-like sections and dose limits were imposed on each. Two sets of dose objectives were specified for tumor and other critical structures for standard dose RT and for dose escalation RT. Plans were generated using an aperture-based inverse planning (ABIP) technique with the Cimmino algorithm for optimization. Beamlet-based inverse treatment planning was carried out with a commercial simulated annealing package (CORVUS) and with an in-house system that used the Cimmino projection algorithm (CIMM). For 3 of the 5 cases, results met all of the constraints from the 3 techniques for the 2 sets of dose objectives. The CORVUS system without delivery efficiency consideration required the most segments and monitor units. The CIMM system reduced the number while the ABIP techniques showed a further reduction, although for one of the cases, a solution was not readily obtained using the ABIP technique for dose escalation objectives.

Outcomes research in cancer clinical trial cooperative groups: the RTOG model.

BACKGROUND: The Radiation Therapy Oncology Group (RTOG), a National Cancer Institute sponsored cancer clinical trials research cooperative, has recently formed an Outcomes Committee to assess a comprehensive array of clinical trial endpoints and factors impacting the net effect of therapy. METHODS: To study outcomes in a consistent, comprehensive and coordinated manner, the RTOG Outcomes Committee developed a model to assess clinical, humanistic, and economic outcomes important in clinical trials. RESULTS: This paper reviews how the RTOG incorporates outcomes research into cancer clinical trials, and demonstrates utilization of the RTOG Outcomes Model to test hypotheses related to non-small-cell lung cancer (NSCLC). In this example, the clinical component of the model indicates that the addition of chemotherapy to radiotherapy (RT) improves survival but increases the risk of toxicity. The humanistic component indicates that esophagitis is the symptom impacting quality of life the greatest and may outweigh the benefits in elderly (> or =70 years) patients. The economic component of the model indicates that accounting for quality-adjusted survival, concurrent chemoRT for the treatment of NSCLC is within the range of economically acceptable recommendations. CONCLUSION: The RTOG Outcomes Model guides a comprehensive program of research that systematically measures a triad of endpoints considered important to clinical trials research.

Comparison of the structures of three circoviruses: chicken anemia virus, porcine circovirus type 2, and beak and feather disease virus.

Circoviruses are small, nonenveloped icosahedral animal viruses characterized by circular single-stranded DNA genomes. Their genomes are the smallest possessed by animal viruses. Infections with circoviruses, which can lead to economically important diseases, frequently result in virus-induced damage to lymphoid tissue and immunosuppression. Within the family Circoviridae, different genera are distinguished by differences in genomic organization. Thus, Chicken anemia virus is in the genus Gyrovirus, while porcine circoviruses and Beak and feather disease virus belong to the genus CIRCOVIRUS: Little is known about the structures of circoviruses. Accordingly, we investigated the structures of these three viruses with a view to determining whether they are related. Three-dimensional maps computed from electron micrographs showed that all three viruses have a T=1 organization with capsids formed from 60 subunits. Porcine circovirus type 2 and beak and feather disease virus show similar capsid structures with flat pentameric morphological units, whereas chicken anemia virus has stikingly different protruding pentagonal trumpet-shaped units. It thus appears that the structures of viruses in the same genus are related but that those of viruses in different genera are unrelated.