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PubMed | Sloan Kettering Cancer Center, Shandong Communication and Media College, Saint Vincent Medical Center and North Shore Long Island Jewish health System
Type: Journal Article | Journal: Medical physics | Year: 2017

Segmentation of prostate CBCT images is an essential step towards real-time adaptive radiotherapy. It is challenging For Calypso patients, as more artifacts are generated by the beacon transponders. We herein propose a novel wavelet-based segmentation algorithm for rectum, bladder, and prostate of CBCT images with implanted Calypso transponders.Five hypofractionated prostate patients with daily CBCT were studied. Each patient had 3 Calypso transponder beacons implanted, and the patients were setup and treated with Calypso tracking system. Two sets of CBCT images from each patient were studied. The structures (i.e. rectum, bladder, and prostate) were contoured by a trained expert, and these served as ground truth. For a given CBCT, the moving window-based Double Haar transformation is applied first to obtain the wavelet coefficients. Based on a user defined point in the object of interest, a cluster algorithm based adaptive thresholding is applied to the low frequency components of the wavelet coefficients, and a Lee filter theory based adaptive thresholding is applied to the high frequency components. For the next step, the wavelet reconstruction is applied to the thresholded wavelet coefficients. A binary/segmented image of the object of interest is therefore obtained. DICE, sensitivity, inclusiveness and V were used to evaluate the segmentation result.Considering all patients, the bladder has the DICE, sensitivity, inclusiveness, and V ranges of [0.81-0.95], [0.76-0.99], [0.83-0.94], [0.02-0.21]. For prostate, the ranges are [0.77-0.93], [0.84-0.97], [0.68-0.92], [0.1-0.46]. For rectum, the ranges are [0.72-0.93], [0.57-0.99], [0.73-0.98], [0.03-0.42].The proposed algorithm appeared effective segmenting prostate CBCT images with the present of the Calypso artifacts. However, it is not robust in two scenarios: 1) rectum with significant amount of gas; 2) prostate with very low contrast. Model based algorithm might improve the segmentation in these two scenarios.


Sampaio M.S.,Mendez National Institute of Transplantation | Cho Y.W.,Mendez National Institute of Transplantation | Shah T.,Mendez National Institute of Transplantation | Shah T.,Saint Vincent Medical Center | And 3 more authors.
Nephrology Dialysis Transplantation | Year: 2012

Background Post-transplant lymphoproliferative disorder (PTLD) is a serious complication of transplantation. Methods Using the OPTN/UNOS database, primary kidney recipients (20002009) were stratified according to transplant type (deceased donor, DD or living donor, LD), donor (D) and recipient (R) EpsteinBarr virus (EBV) serostatus (R+; D/R-and D-/R-) and recipient age. Incidence and adjusted risk of PTLD and death were compared. Results Of the 137 939 primary kidney recipients transplanted between 2000 and 2009, 913 subsequently developed PTLD. In 90 208 recipients with known EBV serostatus, we found a trend toward a decrease in PTLD incidence in years 20072009 when compared to 20002003. This was due to a significant decrease in PTLD incidence in EBV-recipients. Of those, 61 273 had a known donor serostatus and were further examined. In adults, PTLD incidence (in 1000 person-years) in DD and LD was 7.0 and 7.0 in D +R-; 3.0 and 2.5 in D-/R-and 1.2 and 1.0 in R+, respectively. The hazard ratio (HR) for PTLD (R+ as reference) in D +R-(6.2 in DD and 7.2 in LD) was double to thrice than for D-/R-transplants (2.4 in both DD and LD). In pediatric recipients, PTLD incidence in DD and LD was 15.9 and 17.3 in D +R-; 12 and 18 in D-/R-and 1.2 and 2.2 in R+, respectively. The HR for PTLD was 17.4 and 6.9 in D +R-and 15.9 and 7.6 in D-/R-in DD and LD, respectively. Conclusion A D/R-, compared with a D-/R-transplant, may contribute to an increase in PTLD incidence of 35 and 42% in adult DD and LD transplants, respectively. © 2012 The Author.


Sampaio M.S.,Mendez National Institute of Transplantation | Cho Y.W.,Mendez National Institute of Transplantation | Shah T.,Mendez National Institute of Transplantation | Shah T.,Saint Vincent Medical Center | And 3 more authors.
Transplantation | Year: 2012

BACKGROUND.: The association of immunosuppressive regimens (ISRs) with posttransplant lymphoproliferative disorder (PTLD) may be related with the Epstein-Barr virus (EBV) recipient serostatus. METHODS.: We selected primary kidney transplant recipients from Organ Procurement Transplant Network/United Network for Organ Sharing database (2000-2009) who were discharged with a functioning graft and were receiving an ISR including an antiproliferative drug and a calcineurin inhibitor as follows: mycophenolate mofetil (MMF)/mycophenolate sodium+tacrolimus (TAC), MMF+cyclosporine A (CsA); mammalian target of rapamycin inhibitor (mTORi)+TAC; and mTORi+CsA. Adjusted risks of PTLD, rejection, death, and graft failure were examined in all recipients and compared between EBV+ and EBV- recipients. RESULTS.: Of 114,025 recipients, 754 developed PTLD (5-year incidence of 0.84%). Adjusted hazard ratio for PTLD was 4.39 (95% CI: 3.60-5.37) for EBV- versus EBV+ recipients; and 1.40 (95% CI: 1.03-1.90) for mTORi+TAC, 0.80 (95% CI: 0.65-0.99) for MMF+CsA, and 0.90 (95% CI: 0.57-1.42) for mTORi+CsA, versus MMF+TAC users. In EBV- recipients, hazard ratio for PTLD was 1.98 (95% CI: 1.28-3.07) for mTORi+TAC, 0.45 (95% CI: 0.28-0.72) for MMF+CsA, and 0.84 (95% CI: 0.39-1.80) for mTORi+CsA users versus MMF+TAC. No difference was seen in EBV+ recipient groups. Rejection rates were higher among MMF+CsA recipients in both EBV groups. Death and graft failure risk were increased in all EBV+ISR groups, while in EBV- these risks were only increased in mTORi+TAC group versus MMF+TAC. CONCLUSIONS.: In EBV- recipients, immunosuppression with mTORi+TAC was associated with increased risk of PTLD, death, and graft failure, while MMF+CsA use was associated with a trend to increased risk of rejection, lower PTLD risk, and similar risk for graft failure when compared with MMF+TAC.


Majid A.,Beth Israel Deaconess Medical Center | Gaurav K.,Beth Israel Deaconess Medical Center | Gaurav K.,Thomas Jefferson University | Sanchez J.M.,Beth Israel Deaconess Medical Center | And 6 more authors.
Annals of the American Thoracic Society | Year: 2014

Objectives: Dynamic flexible bronchoscopy is the "gold standard" for assessing changes in airway luminal size associated with tracheobronchomalacia, but the procedure has not been adequately validated. The present study was designed to test th e validity of diagnosing tracheobronchomalacia by dynamic flexible bronchoscopy through assessing inter- and intraobserver agreements in estimating degree of central airway collapse associated with tracheobronchomalacia. Methods: This prospective observational pilot study enrolledconsecutive patients with suspected tracheobronchomalacia scheduled for dynamic flexible bronchoscopy. Images of the airway lumen were obtained at five different sites in the tracheobronchial tree during forced inspiration and expiration and were evaluated by 23 pulmonologists (not involved in the care of study patients) with different levels of training and experience at baseline (interobserver agreement) and 8 days later (intraobserver agreement). The degree of airway collapse was visually estimated by each examiner and expressed as a percentage of narrowing. A multirater generalized kappa-type statistical method was used to calculate the correlation coefficients and to assess reliability of the measurements obtained during dynamic flexible bronchoscopy. Measurements and Main Results: Between September 1 and 30, 2009, 10 patients (median age, 65 yr) underwent dynamic flexible bronchoscopy. The correlation coef ficients for inter- and intraobserver agreement were favorable and ranged for the five airway sites from 0.68 to 0.92 and from 0.80 to 0.96, respectively. Conclusions: The favorable inter- and intraobserver agreements among 23 pulmonologists using dynamic flexible bronchoscopy to estimate the degree of dynamic central airway collapse provide additional evidence that dynamic fl exible bronchoscopy is a reliable diagnostic tool for tracheobronchomalacia. Copyright © 2014 by the American Thoracic Society


PubMed | Sloan Kettering Cancer Center, University Hospitals Leuven, Saint Vincent Medical Center and Rensselaer Polytechnic Institute
Type: Journal Article | Journal: Medical physics | Year: 2017

There are clinical decision challenges to select optimal treatment positions for left-sided breast cancer patients-supine free breathing (FB), supine Deep Inspiration Breath Hold (DIBH) and prone free breathing (prone). Physicians often make the decision based on experiences and trials, which might not always result optimal OAR doses. We herein propose a mathematical model to predict the lowest OAR doses among these three positions, providing a quantitative tool for corresponding clinical decision.Patients were scanned in FB, DIBH, and prone positions under an IRB approved protocol. Tangential beam plans were generated for each position, and OAR doses were calculated. The position with least OAR doses is defined as the optimal position. The following features were extracted from each scan to build the model: heart, ipsilateral lung, breast volume, in-field heart, ipsilateral lung volume, distance between heart and target, laterality of heart, and dose to heart and ipsilateral lung. Principal Components Analysis (PCA) was applied to remove the co-linearity of the input data and also to lower the data dimensionality. Feature selection, another method to reduce dimensionality, was applied as a comparison. Support Vector Machine (SVM) was then used for classification. Thirtyseven patient data were acquired; up to now, five patient plans were available. K-fold cross validation was used to validate the accuracy of the classifier model with small training size.The classification results and K-fold cross validation demonstrated the model is capable of predicting the optimal position for patients. The accuracy of K-fold cross validations has reached 80%. Compared to PCA, feature selection allows causal features of dose to be determined. This provides more clinical insights.The proposed classification system appeared to be feasible. We are generating plans for the rest of the 37 patient images, and more statistically significant results are to be presented.


Vu D.,Mendez National Institute of Transplantation | Vu D.,Saint Vincent Medical Center | Vu D.,Western University of Health Sciences | Tellez-Corrales E.,Nova Southeastern University | And 8 more authors.
Human Immunology | Year: 2013

Cyclooxygenase-2 (COX-2) alleles have been associated with allograft outcomes in kidney transplant recipients; however, these alleles may be in linkage with other genes. Human allograft inflammatory factor-1 (AIF-1) is a cytoplasmic protein and is produced by macrophages. Its synthesis is regulated by several cytokines, including interferon gamma. We investigated whether polymorphisms of gene encoding COX-2 and AIF-1 were associated with allograft outcomes among Hispanic renal transplant recipients (RTRs).A total of 527 de novo RTRs of Hispanic ethnicity were included in this study transplanted at St. Vincent Medical Center (SVMC) during 2000-2009. Patients were genotyped for the following: COX-2 (-1195C. >. T rs689466, intron 6 rs2066826) and AlF1 (rs2269475).Analysis of the results showed that COX-2-1195 CC genotype (OR. = 1.92, CI%. = 1.00-3.67, p= 0.04) were more frequent, but COX-2-1195 CT genotype was less frequent in kidney allograft acute rejection in comparison with control group (OR. = 0.59, CI%. = 0.38-0.91, p= 0.017). The genetic variant TT/CT of the AIF-1 gene was associated with a lower risk of rejection (OR. = 0.63, CI%. = 0.41-0.98, p= 0.038). No association of COX-2 (rs2066826) was observed with allograft rejection. We are unable to find statistically significant association between COX-2 and AIF-1 gene polymorphisms and allograft survival.The -1195C. >. T in the COX-2 promoter and AIF-1 gene polymorphisms could be a potential predictor of allograft rejection in our Hispanic kidney transplant recipients. © 2013 .


PubMed | Sloan Kettering Cancer Center, Saint Vincent Medical Center, Rensselaer Polytechnic Institute, University of Wisconsin - Madison and University of Baltimore
Type: Journal Article | Journal: Medical physics | Year: 2017

(1) To perform phase space (PS) based source modeling for Tomotherapy and Varian TrueBeam 6 MV Linacs, (2) to examine the accuracy and performance of the ARCHER Monte Carlo code on a heterogeneous computing platform with Many Integrated Core coprocessors (MIC, aka Xeon Phi) and GPUs, and (3) to explore the software micro-optimization methods.The patient-specific source of Tomotherapy and Varian TrueBeam Linacs was modeled using the PS approach. For the helical Tomotherapy case, the PS data were calculated in our previous study (Su et al. 2014 41(7) Medical Physics). For the single-view Varian TrueBeam case, we analytically derived them from the raw patient-independent PS data in IAEAs database, partial geometry information of the jaw and MLC as well as the fluence map. The phantom was generated from DICOM images. The Monte Carlo simulation was performed by ARCHER-MIC and GPU codes, which were benchmarked against a modified parallel DPM code. Software micro-optimization was systematically conducted, and was focused on SIMD vectorization of tight for-loops and data prefetch, with the ultimate goal of increasing 512-bit register utilization and reducing memory access latency.Dose calculation was performed for two clinical cases, a Tomotherapy-based prostate cancer treatment and a TrueBeam-based left breast treatment. ARCHER was verified against the DPM code. The statistical uncertainty of the dose to the PTV was less than 1%. Using double-precision, the total wall time of the multithreaded CPU code on a X5650 CPU was 339 seconds for the Tomotherapy case and 131 seconds for the TrueBeam, while on 3 5110P MICs it was reduced to 79 and 59 seconds, respectively. The single-precision GPU code on a K40 GPU took 45 seconds for the Tomotherapy dose calculation.We have extended ARCHER, the MIC and GPU-based Monte Carlo dose engine to Tomotherapy and Truebeam dose calculations.


PubMed | Anhui Medical University, Saint Vincent Medical Center and Anhui University of Science and Technology
Type: Journal Article | Journal: Medical physics | Year: 2017

To evaluate the ROI contours and accumulated dose difference using different deformable image registration (DIR) algorithms for head and neck (H&N) adaptive radiotherapy.Eight H&N cancer patients were randomly selected from the affiliated hospital. During the treatment, patients were rescanned every week with ROIs well delineated by radiation oncologist on each weekly CT. New weekly treatment plans were also re-designed with consistent dose prescription on the rescanned CT and executed for one week on Siemens CT-on-rails accelerator. At the end, we got six weekly CT scans from CT1 to CT6 including six weekly treatment plans for each patient. The primary CT1 was set as the reference CT for DIR proceeding with the left five weekly CTs using ANACONDA and MORFEUS algorithms separately in RayStation and the external skin ROI was set to be the controlling ROI both. The entire calculated weekly dose were deformed and accumulated on corresponding reference CT1 according to the deformation vector field (DVFs) generated by the two different DIR algorithms respectively. Thus we got both the ANACONDA-based and MORFEUS-based accumulated total dose on CT1 for each patient. At the same time, we mapped the ROIs on CT1 to generate the corresponding ROIs on CT6 using ANACONDA and MORFEUS DIR algorithms. DICE coefficients between the DIR deformed and radiation oncologist delineated ROIs on CT6 were calculated.For DIR accumulated dose, PTV D95 and Left-Eyeball Dmax show significant differences with 67.13 cGy and 109.29 cGy respectively (Table1). For DIR mapped ROIs, PTV, Spinal cord and Left-Optic nerve show difference with -0.025, -0.127 and -0.124 (Table2).Even two excellent DIR algorithms can give divergent results for ROI deformation and dose accumulation. As more and more TPS get DIR module integrated, there is an urgent need to realize the potential risk using DIR in clinical.


Jarry J.,Military Hospital Desgenettes | Shekher M.,Saint Vincent Medical Center | Imperato M.,Military Hospital Desgenettes | Michel P.,Military Hospital Desgenettes
Clinics and Research in Hepatology and Gastroenterology | Year: 2011

Acute appendicitis is the most frequent emergency in gastrointestinal surgery. Obstruction of the appendiceal lumen appears to be one of the most common physiologic mechanisms for the development of acute appendicitis. Once obstructed, the dilatation of the lumen causes ischemia and necrosis of the wall. The most common organisms involved in appendicitis are Escherichia coli, Peptostreptococcus, Bacillus fragilis and Pseudomonas. Rarely, Actinomyces is involved in this process. In this case report, we report a case of actinomycosis of the appendix vermiformis occurring in a 19-year-old male with no predisposing factors. Along with a review of the literature, we will define the risk factors, clinical characteristics, diagnostic methods, and treatment of actinomycosis. © 2011 Elsevier Masson SAS.


Elemam A.,Saint Vincent Medical Center | Rahimian J.,Saint Vincent Medical Center | Doymaz M.,Saint Vincent Medical Center
Journal of Clinical Microbiology | Year: 2010

Since carbapenemase-producing Klebsiella pneumoniae strains were first reported in North Carolina, these highly resistant organisms have been isolated with increasing frequency, especially in the New York City area. Polymyxin B is one of the few antimicrobials that retain reliable activity against these organisms. However, polymyxin B MICs are elevated against K. pneumoniae isolates with increasing frequency, leaving clinicians with few therapeutic options. We investigated several antimicrobial agents for potential synergy with polymyxin B against 12 clinical strains of carbapenemase-producing K. pneumoniae. A broth microdilution assay using a 96-well plate was developed in which graded dilutions of polymyxin B and the study drug were incubated with resistant isolates in a checkerboard pattern. Polymyxin B was studied in combination with cefazolin, ceftriaxone, cefepime, imipenem, gentamicin, tigecycline, doxycycline, and rifampin. All K. pneumoniae strains tested positive for K. pneumoniae carbapenemase (KPC) genes by real-time PCR and had elevated polymyxin B MIC values ranging from 16 to 128 μg/ml. Synergy was observed with the combination of polymyxin B and rifampin as well as with polymyxin B and doxycycline, resulting in at least a 4-fold decrease in the polymyxin B MIC. For both combinations, this effect occurred at physiologically achievable concentrations. Less pronounced synergy was noted with tigecycline and polymyxin B. No synergy was observed at physiologic concentrations with the other antimicrobials studied. These results suggest that rifampin, doxycycline, and tigecycline may be useful additions to polymyxin B in the treatment of infections caused by highly resistant carbapenemase-producing K. pneumoniae. Further studies are warranted to determine if these in vitro findings translate into clinical efficacy. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

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