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Sample records for accurate target delineation

  1. Understanding target delineation using simple probabilistic modelling

    NASA Astrophysics Data System (ADS)

    Willis, Chris J.

    2015-10-01

    Performance assessment is carried out for a simple target delineation process based on thresholding and shape fitting. The method uses the information contained in Receiver Operating Characteristic curves together with basic observations regarding target sizes and shapes. Performance is gauged by considering the delineations that might result from having particular arrangements of detected pixels within the vicinity of a hypothesized target. In particular, the method considers the qualities of delineations generated when having various combinations of detected pixels at a number of locations around the inner and outer boundaries of the underlying object. Three distinct types of arrangement for pixels on the inner target boundary are considered. Each has the potential to lead to a good quality delineation in a thresholding and shape fitting scheme. The deleterious effect of false alarms within the surrounding local region is also taken into account. The resulting ensembles of detected pixels are treated using familiar rules for combination to form probabilities for the delineations as a whole. Example results are produced for simple target prototypes in cluttered SAR imagery.

  2. Guidelines for delineation of lymphatic clinical target volumes for high conformal radiotherapy: head and neck region

    PubMed Central

    2011-01-01

    The success of radiotherapy depends on the accurate delineation of the clinical target volume. The delineation of the lymph node regions has most impact, especially for tumors in the head and neck region. The purpose of this article was the development an atlas for the delineation of the clinical target volume for patients, who should receive radiotherapy for a tumor of the head and neck region. Literature was reviewed for localisations of the adjacent lymph node regions and their lymph drain in dependence of the tumor entity. On this basis the lymph node regions were contoured on transversal CT slices. The probability for involvement was reviewed and a recommendation for the delineation of the CTV was generated. PMID:21854585

  3. Accurate Automatic Delineation of Heterogeneous Functional Volumes in Positron Emission Tomography for Oncology Applications

    SciTech Connect

    Hatt, Mathieu; Cheze le Rest, Catherine; Descourt, Patrice; Dekker, Andre; De Ruysscher, Dirk; Oellers, Michel; Lambin, Philippe; Pradier, Olivier; Visvikis, Dimitris

    2010-05-01

    Purpose: Accurate contouring of positron emission tomography (PET) functional volumes is now considered crucial in image-guided radiotherapy and other oncology applications because the use of functional imaging allows for biological target definition. In addition, the definition of variable uptake regions within the tumor itself may facilitate dose painting for dosimetry optimization. Methods and Materials: Current state-of-the-art algorithms for functional volume segmentation use adaptive thresholding. We developed an approach called fuzzy locally adaptive Bayesian (FLAB), validated on homogeneous objects, and then improved it by allowing the use of up to three tumor classes for the delineation of inhomogeneous tumors (3-FLAB). Simulated and real tumors with histology data containing homogeneous and heterogeneous activity distributions were used to assess the algorithm's accuracy. Results: The new 3-FLAB algorithm is able to extract the overall tumor from the background tissues and delineate variable uptake regions within the tumors, with higher accuracy and robustness compared with adaptive threshold (T{sub bckg}) and fuzzy C-means (FCM). 3-FLAB performed with a mean classification error of less than 9% +- 8% on the simulated tumors, whereas binary-only implementation led to errors of 15% +- 11%. T{sub bckg} and FCM led to mean errors of 20% +- 12% and 17% +- 14%, respectively. 3-FLAB also led to more robust estimation of the maximum diameters of tumors with histology measurements, with <6% standard deviation, whereas binary FLAB, T{sub bckg} and FCM lead to 10%, 12%, and 13%, respectively. Conclusion: These encouraging results warrant further investigation in future studies that will investigate the impact of 3-FLAB in radiotherapy treatment planning, diagnosis, and therapy response evaluation.

  4. Interobserver Variation of Clinical Target Volume Delineation in Gastric Cancer

    SciTech Connect

    Jansen, Edwin; Verheij, Marcel

    2010-07-15

    Purpose: To evaluate interobserver variability in clinical target volume (CTV) delineation in gastric cancer performed with the help of a delineation guide. Patients and Methods: Ten radiotherapy centers that participate in the CRITICS Phase III trial were provided with a delineation atlas, preoperative CT scans, a postoperative planning CT scan, and clinical information for a gastric cancer case and were asked to construct a CTV and create a dosimetric plan according to departmental policy. Results: The volumes of the CTVs and planning target volumes (PTVs) differed greatly, with a mean (SD) CTV volume of 392 (176) cm{sup 3} (range, 240-821cm{sup 3}) and PTV volume of 915 (312) cm{sup 3} (range, 634-1677cm{sup 3}). The overlapping volume was 376cm{sup 3} for the CTV and 890cm{sup 3} for the PTV. The greatest differences in the CTV were seen at the cranial and caudal parts. After planning, dose coverage of the overlapping PTV volume showed less variability than the CTV. Conclusion: In this series of 10 plans, variability of the CTV in postoperative chemoradiotherapy for gastric cancer is large. Strict and clear delineation guidelines should be provided, especially in Phase III multicenter studies. Adaptations of these guidelines should be evaluated in clinical studies.

  5. The impact of tumor motion upon CT image integrity and target delineation

    SciTech Connect

    Gagne, Isabelle M.; Robinson, Don M.

    2004-12-01

    Accurate planning target volume delineation is vital to the success of conformal radiation techniques such as standard three-dimensional conformal radiotherapy and intensity modulated radiation therapy. With the exception of breath-hold schemes, all current approaches acquire images while the tumor is nonstationary and, as such, are subject to the presence of motion artifacts. In lung cancer sites where tumor mobility can be significant, the detrimental effect of these motion-induced distortions on image quality and subsequently target volume delineation cannot be ignored in the pursuit of improved treatment outcomes. To investigate the fundamental nature and functional dependence of computed tomography (CT) artifacts associated with lung tumor motion, and the implications for tumor delineation, a filtered backprojection algorithm was developed in MATLAB to generate transverse CT simulation images. In addition, a three-dimensional phantom capable of mimicking the essential motions of lung tumors was constructed for experimental verification. Results show that the spatial extent of a mobile object is distorted from its true shape and location and does not accurately reflect the volume occupied during the extent of motion captured. The presence of motion also negatively impacts image intensity (density) integrity rendering accurate volume delineation highly problematic and calling into question the use of such data in CT-based heterogeneity correction algorithms for dosimetric calculation.

  6. Intensity-modulated radiation therapy for head and neck cancer: emphasis on the selection and delineation of the targets.

    PubMed

    Eisbruch, Avraham; Foote, Robert L; O'Sullivan, Brian; Beitler, Jonathan J; Vikram, Bhadrasain

    2002-07-01

    The head and neck contain many critical, noninvolved structures in close vicinity to the targets. The tightly conformal doses produced by intensity-modulated radiation therapy (IMRT), and the lack of internal organ motion in the head and neck, provide the potential for organ sparing and improved tumor irradiation. Many studies of treatment planning for head and neck cancer have demonstrated the dosimetric superiority of IMRT over conventional techniques in these respects. The initial results of clinical studies demonstrate reduced xerostomia. They suggest an improvement in tumor control, which needs to be verified in larger studies and longer follow-up. Critical issues for successful outcome of head and neck IMRT are accurate selection of the neck lymph nodes that require adjuvant treatment, and accurate delineation on the planning computed tomography (CT) of the lymph-node bearing areas and subclinical disease adjoining the gross tumor. This review emphasizes these topics and provides some guidelines. PMID:12118389

  7. In Vitro Characterization of a Targeted, Dye-Loaded Nanodevice for Intraoperative Tumor Delineation

    PubMed Central

    Orringer, Daniel A.; Koo, Yong-Eun L.; Chen, Thomas; Kim, Gwangseong; Hah, Hoe Jin; Xu, Hao; Wang, Shouyan; Keep, Richard; Philbert, Martin A.; Kopelman, Raoul; Sagher, Oren

    2009-01-01

    OBJECTIVE To synthesize and complete in vitro characterization of a novel, tumor-targeted nanodevice for visible intraoperative delineation of brain tumors. METHODS The ability of dye-loaded polyacrylamide nanoparticles (NPs) containing methylene blue, Coomassie blue, or indocyanine green, to cause color change in the 9L glioma cell lines was evaluated. Cells were incubated with dye-loaded NPs, photographed, and analyzed colorimetrically. Confocal microscopy was used to determine subcellular localization of NPs in treated cells. RESULTS Incubation of glioma cell lines with dye-loaded NPs resulted in clearly visible, quantifiable cell tagging in a dose- and time-dependent fashion. Dye-loaded NPs were observed to bind to the surface and become internalized by glioma cells. Coating the NP surface with F3, a peptide that binds to the tumor cell surface receptor nucleolin, significantly increased NP affinity for glioma cells. F3-targeting also significantly increased the rate of cell tagging by dye-loaded NPs. Finally, F3-targeted NPs demonstrated specificity for targeting various cancer cell lines based on their surface expression of cell surface nucleolin. CONCLUSIONS F3-targeted dye-loaded NPs efficiently cause definitive color change in glioma cells. This report represents the first use of targeted NPs to cause a visible color change in tumor cell lines. Similar nanodevices may be used in the future to enable visible intraoperative tumor delineation during tumor resection. PMID:19404156

  8. Photo-acoustic imaging of blue nanoparticle targeted brain tumor for intra-operative glioma delineation

    NASA Astrophysics Data System (ADS)

    Ray, Aniruddha; Wang, Xueding; Koo Lee, Yong-Eun; Hah, HoeJin; Kim, Gwangseong; Chen, Thomas; Orrienger, Daniel; Sagher, Oren; Kopelman, Raoul

    2011-07-01

    Distinguishing the tumor from the background neo-plastic tissue is challenging for cancer surgery such as surgical resection of glioma. Attempts have been made to use visible or fluorescent markers to delineate the tumors during surgery. However, the systemic injection of the dyes requires high dose, resulting in negative side effects. A novel method to delineate rat brain tumors intra-operatively, as well as post-operatively, using a highly sensitive photoacoustic imaging technique enhanced by tumor targeting blue nanoparticle as contrast agent is demonstrated. The nanoparticles are made of polyacrylamide (PAA) matrix with covalently linked Coomassie-Blue dye. They contain 7.0% dye and the average size is 80nm. Their surface was conjugated with F3 peptide for active tumor targeting. These nanoparticles are nontoxic, chemically inert and have long plasma circulation lifetime, making them suitable as nanodevices for imaging using photoacoustics. Experiments on phantoms and rat brains tumors ex-vivo demonstrate the high sensitivity of photoacoustic imaging in delineating the tumor, containing contrast agent at concentrations too low to be visualized by eye. The control tumors without nanoparticles did not show any enhanced signal. This study shows that photoacoustic imaging facilitated with the nanoparticle contrast agent could contribute to future surgical procedures for glioma.

  9. Evaluation of Peritumoral Edema in the Delineation of Radiotherapy Clinical Target Volumes for Glioblastoma

    SciTech Connect

    Chang, Eric L. . E-mail: echang@mdanderson.org; Akyurek, Serap; Avalos, Tedde C; Rebueno, Neal C; Spicer, Chris C; Garcia, John C; Famiglietti, Robin; Allen, Pamela K.; Chao, K.S. Clifford; Mahajan, Anita; Woo, Shiao Y.; Maor, Moshe H.

    2007-05-01

    Purpose: To evaluate the spatial relationship between peritumoral edema and recurrence pattern in patients with glioblastoma (GBM). Methods and Materials: Forty-eight primary GBM patients received three-dimensional conformal radiotherapy that did not intentionally include peritumoral edema within the clinical target volume between July 2000 and June 2001. All 48 patients have subsequently recurred, and their original treatment planning parameters were used for this study. New theoretical radiation treatment plans were created for the same 48 patients, based on Radiation Therapy Oncology Group (RTOG) target delineation guidelines that specify inclusion of peritumoral edema. Target volume and recurrent tumor coverage, as well as percent volume of normal brain irradiated, were assessed for both methods of target delineation using dose-volume histograms. Results: A comparison between the location of recurrent tumor and peritumoral edema volumes from all 48 cases failed to show correlation by linear regression modeling (r {sup 2} 0.0007; p = 0.3). For patients with edema >75 cm{sup 3}, the percent volume of brain irradiated to 46 Gy was significantly greater in treatment plans that intentionally included peritumoral edema compared with those that did not (38% vs. 31%; p = 0.003). The pattern of failure was identical between the two sets of plans (40 central, 3 in-field, 3 marginal, and 2 distant recurrence). Conclusion: Clinical target volume delineation based on a 2-cm margin rather than on peritumoral edema did not seem to alter the central pattern of failure for patients with GBM. For patients with peritumoral edema >75 cm{sup 3}, using a constant 2-cm margin resulted in a smaller median percent volume of brain being irradiated to 30 Gy, 46 Gy, and 50 Gy compared with corresponding theoretical RTOG plans that deliberately included peritumoral edema.

  10. SU-E-J-231: Comparison of 3D Angiogram and MRI in Delineating the AVM Target for Frameless Stereotactic Radiosurgery

    SciTech Connect

    Avkshtol, V; Tanny, S; Reddy, K; Chen, C; Parsai, E

    2014-06-01

    Purpose: Stereotactic radiation therapy (SRT) provides an excellent alternative to embolization and surgical excision for the management of appropriately selected cerebral arteriovenous malformations (AVMs). The currently accepted standard for delineating AVMs is planar digital subtraction angiography (DSA). DSA can be used to acquire a 3D data set that preserves osseous structures (3D-DA) at the time of the angiography for SRT planning. Magnetic resonance imaging (MRI) provides an alternative noninvasive method of visualizing the AVM nidus with comparable spatial resolution. We utilized 3D-DA and T1 post-contrast MRI data to evaluate the differences in SRT target volumes. Methods: Four patients underwent 3D-DA and high-resolution MRI. 3D T1 post-contrast images were obtained in all three reconstruction planes. A planning CT was fused with MRI and 3D-DA data sets. The AVMs were contoured utilizing one of the image sets at a time. Target volume, centroid, and maximum and minimum dimensions were analyzed for each patient. Results: Targets delineated using post-contrast MRI demonstrated a larger mean volume. AVMs >2 cc were found to have a larger difference between MRI and 3D-DA volumes. Larger AVMs also demonstrated a smaller relative uncertainty in contour centroid position (1 mm). AVM targets <2 cc had smaller absolute differences in volume, but larger differences in contour centroid position (2.5 mm). MRI targets demonstrated a more irregular shape compared to 3D-DA targets. Conclusions: Our preliminary data supports the use of MRI alone to delineate AVM targets >2 cc. The greater centroid stability for AVMs >2 cc ensures accurate target localization during image fusion. The larger MRI target volumes did not result in prohibitively greater volumes of normal brain tissue receiving the prescription dose. The larger centroid instability for AVMs <2 cc precludes the use of MRI alone for target delineation. We recommend incorporating a 3D-DA for these patients.

  11. Delineation of radiation therapy target volumes for patients with postoperative glioblastoma: a review

    PubMed Central

    Zhao, Fen; Li, Minghuan; Kong, Li; Zhang, Guoli; Yu, Jinming

    2016-01-01

    Glioblastoma is the most aggressive and lethal primary malignancy of the brain, and radiotherapy (RT) is a fundamental part of its treatment. However, the optimal radiation treatment conditions are still a matter of debate, and there is no clear consensus concerning the inclusion of peritumoral edema in the clinical target volume calculation. Target delineation calculations that use postoperative residual tumor and cavity volumes plus 2 cm margins result in smaller volumes of normal brain receiving high-dose irradiation, compared to calculations that include expanded edema. Smaller RT fields may be more appropriate than larger RT fields, possibly reducing the risk of late neurological deterioration, especially in patients with significant peritumoral edema. This review focuses on the factors influencing target delineation, such as peritumoral edema, failure patterns, and prognostic factors (clinical and pathological characteristics) of patients with glioblastoma. Based on this information, we make three suggestions for radiation oncologists to refer to in daily practice. Further study is necessary to investigate the unresolved problems related to routine clinical application of RT. PMID:27313465

  12. Postoperative radiation in esophageal squamous cell carcinoma and target volume delineation

    PubMed Central

    Zhu, Yingming; Li, Minghuan; Kong, Li; Yu, Jinming

    2016-01-01

    Esophageal cancer is the sixth leading cause of cancer death worldwide, and patients who are treated with surgery alone, without neoadjuvant therapies, experience frequent relapses. Whether postoperative therapies could reduce the recurrence or improve overall survival is still controversial for these patients. The purpose of our review is to figure out the value of postoperative adjuvant therapy and address the disputes about target volume delineation according to published data. Based on the evidence of increased morbidity and disadvantages on patient survival caused by postoperative chemotherapy or radiotherapy (RT) alone provided by studies in the early 1990s, the use of postoperative adjuvant therapies in cases of esophageal squamous cell carcinoma has diminished substantially and has been replaced gradually by neoadjuvant chemoradiation. With advances in surgery and RT, accumulating evidence has recently rekindled interest in the delivery of postoperative RT or chemoradiotherapy in patients with stage T3/T4 or N1 (lymph node positive) carcinomas after radical surgery. However, due to complications with the standard radiation field, a nonconforming modified field has been adopted in most studies. Therefore, we analyze different field applications and provide suggestions on the optimization of the radiation field based on the major sites of relapse and the surgical non-clearance area. For upper and middle thoracic esophageal carcinomas, the bilateral supraclavicular and superior mediastinal areas remain common sites of recurrence and should be encompassed within the clinical target volume. In contrast, a consensus has yet to be reached regarding lower thoracic esophageal carcinomas; the “standard” clinical target volume is still recommended. Further studies of larger sample sizes should focus on different recurrence patterns, categorized by tumor locations, refined classifications, and differing molecular biology, to provide more information on the

  13. Is internal target volume accurate for dose evaluation in lung cancer stereotactic body radiotherapy?

    PubMed Central

    Peng, Jiayuan; Zhang, Zhen; Wang, Jiazhou; Xie, Jiang; Hu, Weigang

    2016-01-01

    Purpose 4DCT delineated internal target volume (ITV) was applied to determine the tumor motion and used as planning target in treatment planning in lung cancer stereotactic body radiotherapy (SBRT). This work is to study the accuracy of using ITV to predict the real target dose in lung cancer SBRT. Materials and methods Both for phantom and patient cases, the ITV and gross tumor volumes (GTVs) were contoured on the maximum intensity projection (MIP) CT and ten CT phases, respectively. A SBRT plan was designed using ITV as the planning target on average projection (AVG) CT. This plan was copied to each CT phase and the dose distribution was recalculated. The GTV_4D dose was acquired through accumulating the GTV doses over all ten phases and regarded as the real target dose. To analyze the ITV dose error, the ITV dose was compared to the real target dose by endpoints of D99, D95, D1 (doses received by the 99%, 95% and 1% of the target volume), and dose coverage endpoint of V100(relative volume receiving at least the prescription dose). Results The phantom study shows that the ITV underestimates the real target dose by 9.47%∼19.8% in D99, 4.43%∼15.99% in D95, and underestimates the dose coverage by 5% in V100. The patient cases show that the ITV underestimates the real target dose and dose coverage by 3.8%∼10.7% in D99, 4.7%∼7.2% in D95, and 3.96%∼6.59% in V100 in motion target cases. Conclusions Cautions should be taken that ITV is not accurate enough to predict the real target dose in lung cancer SBRT with large tumor motions. Restricting the target motion or reducing the target dose heterogeneity could reduce the ITV dose underestimation effect in lung SBRT. PMID:26968812

  14. Target Volume Delineation for Partial Breast Radiotherapy Planning: Clinical Characteristics Associated with Low Interobserver Concordance

    SciTech Connect

    Petersen, Ross P.; Truong, Pauline T. Kader, Hosam A.; Berthelet, Eric; Lee, Junella C.; Hilts, Michelle L.; Kader, Adam S.; Beckham, Wayne A.; Olivotto, Ivo A.

    2007-09-01

    Purpose: To examine variability in target volume delineation for partial breast radiotherapy planning and evaluate characteristics associated with low interobserver concordance. Methods and Materials: Thirty patients who underwent planning CT for adjuvant breast radiotherapy formed the study cohort. Using a standardized scale to score seroma clarity and consensus contouring guidelines, three radiation oncologists independently graded seroma clarity and delineated seroma volumes for each case. Seroma geometric center coordinates, maximum diameters in three axes, and volumes were recorded. Conformity index (CI), the ratio of overlapping volume and encompassing delineated volume, was calculated for each case. Cases with CI {<=}0.50 were analyzed to identify features associated with low concordance. Results: The median time from surgery to CT was 42.5 days. For geometric center coordinates, variations from the mean were 0.5-1.1 mm and standard deviations (SDs) were 0.5-1.8 mm. For maximum seroma dimensions, variations from the mean and SDs were predominantly <5 mm, with the largest SDs observed in the medial-lateral axis. The mean CI was 0.61 (range, 0.27-0.84). Five cases had CI {<=}0.50. Conformity index was significantly associated with seroma clarity (p < 0.001) and seroma volume (p < 0.002). Features associated with reduced concordance included tissue stranding from the surgical cavity, proximity to muscle, dense breast parenchyma, and benign calcifications that may be mistaken for surgical clips. Conclusion: Variability in seroma contouring occurred in three dimensions, with the largest variations in the medial-lateral axis. Awareness of clinical features associated with reduced concordance may be applied toward training staff and refining contouring guidelines for partial breast radiotherapy trials.

  15. Definition and delineation of the clinical target volume for rectal cancer

    SciTech Connect

    Roels, Sarah; Duthoy, Wim; Haustermans, Karin . E-mail: Karin.Haustermans@uzleuven.be; Penninckx, Freddy; Vandecaveye, Vincent; Boterberg, Tom; Neve, Wilfried de

    2006-07-15

    Purpose: Optimization of radiation techniques to maximize local tumor control and to minimize small bowel toxicity in locally advanced rectal cancer requires proper definition and delineation guidelines for the clinical target volume (CTV). The purpose of this investigation was to analyze reported data on the predominant locations and frequency of local recurrences and lymph node involvement in rectal cancer, to propose a definition of the CTV for rectal cancer and guidelines for its delineation. Methods and Materials: Seven reports were analyzed to assess the incidence and predominant location of local recurrences in rectal cancer. The distribution of lymphatic spread was analyzed in another 10 reports to record the relative frequency and location of metastatic lymph nodes in rectal cancer, according to the stage and level of the primary tumor. Results: The mesorectal, posterior, and inferior pelvic subsites are most at risk for local recurrences, whereas lymphatic tumor spread occurs mainly in three directions: upward into the inferior mesenteric nodes; lateral into the internal iliac lymph nodes; and, in a few cases, downward into the external iliac and inguinal lymph nodes. The risk for recurrence or lymph node involvement is related to the stage and the level of the primary lesion. Conclusion: Based on a review of articles reporting on the incidence and predominant location of local recurrences and the distribution of lymphatic spread in rectal cancer, we defined guidelines for CTV delineation including the pelvic subsites and lymph node groups at risk for microscopic involvement. We propose to include the primary tumor, the mesorectal subsite, and the posterior pelvic subsite in the CTV in all patients. Moreover, the lateral lymph nodes are at high risk for microscopic involvement and should also be added in the CTV.

  16. Improving superficial target delineation in radiation therapy with endoscopic tracking and registration

    SciTech Connect

    Weersink, R. A.; Qiu, J.; Hope, A. J.; Daly, M. J.; Cho, B. C. J.; DaCosta, R. S.; Sharpe, M. B.; Breen, S. L.; Chan, H.; Jaffray, D. A.

    2011-12-15

    Purpose: Target delineation within volumetric imaging is a critical step in the planning process of intensity modulated radiation therapy. In endoluminal cancers, endoscopy often reveals superficial areas of visible disease beyond what is seen on volumetric imaging. Quantitatively relating these findings to the volumetric imaging is prone to human error during the recall and contouring of the target. We have developed a method to improve target delineation in the radiation therapy planning process by quantitatively registering endoscopic findings contours traced on endoscopic images to volumetric imaging. Methods: Using electromagnetic sensors embedded in an endoscope, 2D endoscopic images were registered to computed tomography (CT) volumetric images by tracking the position and orientation of the endoscope relative to a CT image set. Regions-of-interest (ROI) in the 2D endoscopic view were delineated. A mesh created within the boundary of the ROI was projected onto the 3D image data, registering the ROI with the volumetric image. This 3D ROI was exported to clinical radiation treatment planning software. The precision and accuracy of the procedure was tested on two solid phantoms with superficial markings visible on both endoscopy and CT images. The first phantom was T-shaped tube with X-marks etched on the interior. The second phantom was an anatomically correct skull phantom with a phantom superficial lesion placed on the pharyngeal surface. Markings were contoured on the endoscope images and compared with contours delineated in the treatment planning system based on the CT images. Clinical feasibility was tested on three patients with early stage glottic cancer. Image-based rendering using manually identified landmarks was used to improve the registration. Results: Using the T-shaped phantom with X-markings, the 2D to 3D registration accuracy was 1.5-3.5 mm, depending on the endoscope position relative to the markings. Intraobserver standard variation was 0

  17. Consensus Guidelines for Delineation of Clinical Target Volume for Intensity-Modulated Pelvic Radiotherapy for the Definitive Treatment of Cervix Cancer

    SciTech Connect

    Lim, Karen; Portelance, Lorraine; Creutzberg, Carien; Juergenliemk-Schulz, Ina M.; Mundt, Arno; Mell, Loren K.; Mayr, Nina; Viswanathan, Akila; Jhingran, Anuja; Erickson, Beth; De Los Santos, Jennifer; Gaffney, David; Yashar, Catheryn; Beriwal, Sushil; Wolfson, Aaron

    2011-02-01

    Purpose: Accurate target definition is vitally important for definitive treatment of cervix cancer with intensity-modulated radiotherapy (IMRT), yet a definition of clinical target volume (CTV) remains variable within the literature. The aim of this study was to develop a consensus CTV definition in preparation for a Phase 2 clinical trial being planned by the Radiation Therapy Oncology Group. Methods and Materials: A guidelines consensus working group meeting was convened in June 2008 for the purposes of developing target definition guidelines for IMRT for the intact cervix. A draft document of recommendations for CTV definition was created and used to aid in contouring a clinical case. The clinical case was then analyzed for consistency and clarity of target delineation using an expectation maximization algorithm for simultaneous truth and performance level estimation (STAPLE), with kappa statistics as a measure of agreement between participants. Results: Nineteen experts in gynecological radiation oncology generated contours on axial magnetic resonance images of the pelvis. Substantial STAPLE agreement sensitivity and specificity values were seen for gross tumor volume (GTV) delineation (0.84 and 0.96, respectively) with a kappa statistic of 0.68 (p < 0.0001). Agreement for delineation of cervix, uterus, vagina, and parametria was moderate. Conclusions: This report provides guidelines for CTV definition in the definitive cervix cancer setting for the purposes of IMRT, building on previously published guidelines for IMRT in the postoperative setting.

  18. A Phase I Trial of Preoperative Partial Breast Radiotherapy: Patient Selection, Target Delineation, and Dose Delivery

    PubMed Central

    Blitzblau, Rachel C.; Arya, Ritu; Yoo, Sua; Baker, Jay A.; Chang, Zheng; Palta, Manisha; Duffy, Eileen; Horton, Janet K.

    2015-01-01

    Purpose Diffusion of accelerated partial breast irradiation (APBI) into clinical practice is limited by the need for specialized equipment and training. The accessible external beam technique yields unacceptable complication rates, likely due to large post-operative target volumes. We designed a phase I trial evaluating preoperative radiotherapy to the intact tumor utilizing widely available technology. Methods Patients received 15, 18, or 21Gy in a single fraction to the breast tumor plus margin. Magnetic resonance imaging (MRI) was used in conjunction with standard computed tomography (CT)-based planning to identify contrast enhancing tumor. Skin markers and an intra-tumor biopsy marker were utilized for verification during treatment. Results MRI imaging was critical for target delineation as not all breast tumors were reliably identified on CT scan. Breast shape differences were consistently seen between CT and MRI but did not impede image registration or tumor identification. Target volumes were markedly smaller than historical post-operative volumes and normal tissue constraints were easily met. A biopsy marker within the breast proved sufficient for set up localization. Conclusions This single fraction linear-accelerator based ABPI approach can be easily incorporated at most treatment centers. In vivo targeting may improve accuracy and can reduce the dose to normal tissues. PMID:25834942

  19. Retroperitoneal Sarcoma Target Volume and Organ at Risk Contour Delineation Agreement Among NRG Sarcoma Radiation Oncologists

    SciTech Connect

    Baldini, Elizabeth H.; Abrams, Ross A.; Bosch, Walter; Roberge, David; Haas, Rick L.M.; Catton, Charles N.; Indelicato, Daniel J.; Olsen, Jeffrey R.; Deville, Curtiland; Chen, Yen-Lin; Finkelstein, Steven E.; DeLaney, Thomas F.; Wang, Dian

    2015-08-01

    Purpose: The purpose of this study was to evaluate the variability in target volume and organ at risk (OAR) contour delineation for retroperitoneal sarcoma (RPS) among 12 sarcoma radiation oncologists. Methods and Materials: Radiation planning computed tomography (CT) scans for 2 cases of RPS were distributed among 12 sarcoma radiation oncologists with instructions for contouring gross tumor volume (GTV), clinical target volume (CTV), high-risk CTV (HR CTV: area judged to be at high risk of resulting in positive margins after resection), and OARs: bowel bag, small bowel, colon, stomach, and duodenum. Analysis of contour agreement was performed using the simultaneous truth and performance level estimation (STAPLE) algorithm and kappa statistics. Results: Ten radiation oncologists contoured both RPS cases, 1 contoured only RPS1, and 1 contoured only RPS2 such that each case was contoured by 11 radiation oncologists. The first case (RPS 1) was a patient with a de-differentiated (DD) liposarcoma (LPS) with a predominant well-differentiated (WD) component, and the second case (RPS 2) was a patient with DD LPS made up almost entirely of a DD component. Contouring agreement for GTV and CTV contours was high. However, the agreement for HR CTVs was only moderate. For OARs, agreement for stomach, bowel bag, small bowel, and colon was high, but agreement for duodenum (distorted by tumor in one of these cases) was fair to moderate. Conclusions: For preoperative treatment of RPS, sarcoma radiation oncologists contoured GTV, CTV, and most OARs with a high level of agreement. HR CTV contours were more variable. Further clarification of this volume with the help of sarcoma surgical oncologists is necessary to reach consensus. More attention to delineation of the duodenum is also needed.

  20. SU-E-J-34: Clinical Evaluation of Targeting Accuracy and Tractogrphy Delineation of Radiosurgery

    SciTech Connect

    Juh, R; Suh, T; Kim, Y; Han, J; Kim, C; Oh, C; Kim, D

    2014-06-01

    Purpose: Focal radiosurgery is a common treatment modality for trigeminal neuralgia (TN), a neuropathic facial pain condition. Assessment of treatment effectiveness is primarily clinical, given the paucity of investigational tools to assess trigeminal nerve changes. The efficiency of radiosurgery is related to its highly precise targeting. We assessed clinically the targeting accuracy of radiosurgery with Gamma knife. We hypothesized that trigeminal tractography provides more information than 2D-MR imaging, allowing detection of unique, focal changes in the target area after radiosurgery. Methods: Sixteen TN patients (2 females, 4 male, average age 65.3 years) treated with Gamma Knife radiosurgery, 40 Gy/50% isodose line underwent 1.5Tesla MR trigeminal nerve . Target accuracy was assessed from deviation of the coordinates of the target compared with the center of enhancement on post MRI. Radiation dose delivered at the borders of contrast enhancement was evaluated Results: The median deviation of the coordinates between the intended target and the center of contrast enhancement was within 1mm. The radiation doses fitting within the borders of the contrast enhancement the target ranged from 37.5 to 40 Gy. Trigeminal tractography accurately detected the radiosurgical target. Radiosurgery resulted in 47% drop in FA values at the target with no significant change in FA outside the target, suggesting that radiosurgery primarily affects myelin. Tractography was more sensitive, since FA changes were detected regardless of trigeminal nerve enhancement Conclusion: The median deviation found in clinical assessment of gamma knife treatment for TN Is low and compatible with its high rate of efficiency. DTI parameters accurately detect the effects of focal radiosurgery on the trigeminal nerve, serving as an in vivo imaging tool to study TN. This study is a proof of principle for further assessment of DTI parameters to understand the pathophysiology of TN and treatment effects.

  1. Achieving target voriconazole concentrations more accurately in children and adolescents.

    PubMed

    Neely, Michael; Margol, Ashley; Fu, Xiaowei; van Guilder, Michael; Bayard, David; Schumitzky, Alan; Orbach, Regina; Liu, Siyu; Louie, Stan; Hope, William

    2015-01-01

    Despite the documented benefit of voriconazole therapeutic drug monitoring, nonlinear pharmacokinetics make the timing of steady-state trough sampling and appropriate dose adjustments unpredictable by conventional methods. We developed a nonparametric population model with data from 141 previously richly sampled children and adults. We then used it in our multiple-model Bayesian adaptive control algorithm to predict measured concentrations and doses in a separate cohort of 33 pediatric patients aged 8 months to 17 years who were receiving voriconazole and enrolled in a pharmacokinetic study. Using all available samples to estimate the individual Bayesian posterior parameter values, the median percent prediction bias relative to a measured target trough concentration in the patients was 1.1% (interquartile range, -17.1 to 10%). Compared to the actual dose that resulted in the target concentration, the percent bias of the predicted dose was -0.7% (interquartile range, -7 to 20%). Using only trough concentrations to generate the Bayesian posterior parameter values, the target bias was 6.4% (interquartile range, -1.4 to 14.7%; P = 0.16 versus the full posterior parameter value) and the dose bias was -6.7% (interquartile range, -18.7 to 2.4%; P = 0.15). Use of a sample collected at an optimal time of 4 h after a dose, in addition to the trough concentration, resulted in a nonsignificantly improved target bias of 3.8% (interquartile range, -13.1 to 18%; P = 0.32) and a dose bias of -3.5% (interquartile range, -18 to 14%; P = 0.33). With the nonparametric population model and trough concentrations, our control algorithm can accurately manage voriconazole therapy in children independently of steady-state conditions, and it is generalizable to any drug with a nonparametric pharmacokinetic model. (This study has been registered at ClinicalTrials.gov under registration no. NCT01976078.). PMID:25779580

  2. Achieving Target Voriconazole Concentrations More Accurately in Children and Adolescents

    PubMed Central

    Margol, Ashley; Fu, Xiaowei; van Guilder, Michael; Bayard, David; Schumitzky, Alan; Orbach, Regina; Liu, Siyu; Louie, Stan; Hope, William

    2015-01-01

    Despite the documented benefit of voriconazole therapeutic drug monitoring, nonlinear pharmacokinetics make the timing of steady-state trough sampling and appropriate dose adjustments unpredictable by conventional methods. We developed a nonparametric population model with data from 141 previously richly sampled children and adults. We then used it in our multiple-model Bayesian adaptive control algorithm to predict measured concentrations and doses in a separate cohort of 33 pediatric patients aged 8 months to 17 years who were receiving voriconazole and enrolled in a pharmacokinetic study. Using all available samples to estimate the individual Bayesian posterior parameter values, the median percent prediction bias relative to a measured target trough concentration in the patients was 1.1% (interquartile range, −17.1 to 10%). Compared to the actual dose that resulted in the target concentration, the percent bias of the predicted dose was −0.7% (interquartile range, −7 to 20%). Using only trough concentrations to generate the Bayesian posterior parameter values, the target bias was 6.4% (interquartile range, −1.4 to 14.7%; P = 0.16 versus the full posterior parameter value) and the dose bias was −6.7% (interquartile range, −18.7 to 2.4%; P = 0.15). Use of a sample collected at an optimal time of 4 h after a dose, in addition to the trough concentration, resulted in a nonsignificantly improved target bias of 3.8% (interquartile range, −13.1 to 18%; P = 0.32) and a dose bias of −3.5% (interquartile range, −18 to 14%; P = 0.33). With the nonparametric population model and trough concentrations, our control algorithm can accurately manage voriconazole therapy in children independently of steady-state conditions, and it is generalizable to any drug with a nonparametric pharmacokinetic model. (This study has been registered at ClinicalTrials.gov under registration no. NCT01976078.) PMID:25779580

  3. Variability of Target and Normal Structure Delineation for Breast Cancer Radiotherapy: An RTOG Multi-Institutional and Multiobserver Study

    SciTech Connect

    Li, X. Allen Tai, An; Arthur, Douglas W.; Buchholz, Thomas A.; Macdonald, Shannon; Marks, Lawrence B.; Moran, Jean M.; Pierce, Lori J.; Rabinovitch, Rachel; Taghian, Alphonse; Vicini, Frank; Woodward, Wendy; White, Julia R.

    2009-03-01

    Purpose: To quantify the multi-institutional and multiobserver variability of target and organ-at-risk (OAR) delineation for breast-cancer radiotherapy (RT) and its dosimetric impact as the first step of a Radiation Therapy Oncology Group effort to establish a breast cancer atlas. Methods and Materials: Nine radiation oncologists specializing in breast RT from eight institutions independently delineated targets (e.g., lumpectomy cavity, boost planning target volume, breast, supraclavicular, axillary and internal mammary nodes, chest wall) and OARs (e.g., heart, lung) on the same CT images of three representative breast cancer patients. Interobserver differences in structure delineation were quantified regarding volume, distance between centers of mass, percent overlap, and average surface distance. Mean, median, and standard deviation for these quantities were calculated for all possible combinations. To assess the impact of these variations on treatment planning, representative dosimetric plans based on observer-specific contours were generated. Results: Variability in contouring the targets and OARs between the institutions and observers was substantial. Structure overlaps were as low as 10%, and volume variations had standard deviations up to 60%. The large variability was related both to differences in opinion regarding target and OAR boundaries and approach to incorporation of setup uncertainty and dosimetric limitations in target delineation. These interobserver differences result in substantial variations in dosimetric planning for breast RT. Conclusions: Differences in target and OAR delineation for breast irradiation between institutions/observers appear to be clinically and dosimetrically significant. A systematic consensus is highly desirable, particularly in the era of intensity-modulated and image-guided RT.

  4. Clinical target volume delineation in glioblastomas: pre-operative versus post-operative/pre-radiotherapy MRI

    PubMed Central

    Farace, P; Giri, M G; Meliadò, G; Amelio, D; Widesott, L; Ricciardi, G K; Dall'Oglio, S; Rizzotti, A; Sbarbati, A; Beltramello, A; Maluta, S; Amichetti, M

    2011-01-01

    Objectives Delineation of clinical target volume (CTV) is still controversial in glioblastomas. In order to assess the differences in volume and shape of the radiotherapy target, the use of pre-operative vs post-operative/pre-radiotherapy T1 and T2 weighted MRI was compared. Methods 4 CTVs were delineated in 24 patients pre-operatively and post-operatively using T1 contrast-enhanced (T1PRECTV and T1POSTCTV) and T2 weighted images (T2PRECTV and T2POSTCTV). Pre-operative MRI examinations were performed the day before surgery, whereas post-operative examinations were acquired 1 month after surgery and before chemoradiation. A concordance index (CI) was defined as the ratio between the overlapping and composite volumes. Results The volumes of T1PRECTV and T1POSTCTV were not statistically different (248 ± 88 vs 254 ± 101), although volume differences >100 cm3 were observed in 6 out of 24 patients. A marked increase due to tumour progression was shown in three patients. Three patients showed a decrease because of a reduced mass effect. A significant reduction occurred between pre-operative and post-operative T2 volumes (139 ± 68 vs 78 ± 59). Lack of concordance was observed between T1PRECTV and T1POSTCTV (CI = 0.67 ± 0.09), T2PRECTV and T2POSTCTV (CI = 0.39 ± 0.20) and comparing the portion of the T1PRECTV and T1POSTCTV not covered by that defined on T2PRECTV images (CI = 0.45 ± 0.16 and 0.44 ± 0.17, respectively). Conclusion Using T2 MRI, huge variations can be observed in peritumoural oedema, which are probably due to steroid treatment. Using T1 MRI, brain shifts after surgery and possible progressive enhancing lesions produce substantial differences in CTVs. Our data support the use of post-operative/pre-radiotherapy T1 weighted MRI for planning purposes. PMID:21045069

  5. SU-D-16A-02: A Novel Methodology for Accurate, Semi-Automated Delineation of Oral Mucosa for Radiation Therapy Dose-Response Studies

    SciTech Connect

    Dean, J; Welsh, L; Gulliford, S; Harrington, K; Nutting, C

    2014-06-01

    Purpose: The significant morbidity caused by radiation-induced acute oral mucositis means that studies aiming to elucidate dose-response relationships in this tissue are a high priority. However, there is currently no standardized method for delineating the mucosal structures within the oral cavity. This report describes the development of a methodology to delineate the oral mucosa accurately on CT scans in a semi-automated manner. Methods: An oral mucosa atlas for automated segmentation was constructed using the RayStation Atlas-Based Segmentation (ABS) module. A radiation oncologist manually delineated the full surface of the oral mucosa on a planning CT scan of a patient receiving radiotherapy (RT) to the head and neck region. A 3mm fixed annulus was added to incorporate the mucosal wall thickness. This structure was saved as an atlas template. ABS followed by model-based segmentation was performed on four further patients sequentially, adding each patient to the atlas. Manual editing of the automatically segmented structure was performed. A dose comparison between these contours and previously used oral cavity volume contours was performed. Results: The new approach was successful in delineating the mucosa, as assessed by an experienced radiation oncologist, when applied to a new series of patients receiving head and neck RT. Reductions in the mean doses obtained when using the new delineation approach, compared with the previously used technique, were demonstrated for all patients (median: 36.0%, range: 25.6% – 39.6%) and were of a magnitude that might be expected to be clinically significant. Differences in the maximum dose that might reasonably be expected to be clinically significant were observed for two patients. Conclusion: The method developed provides a means of obtaining the dose distribution delivered to the oral mucosa more accurately than has previously been achieved. This will enable the acquisition of high quality dosimetric data for use in

  6. Head-and-Neck Target Delineation Among Radiation Oncology Residents After a Teaching Intervention: A Prospective, Blinded Pilot Study

    SciTech Connect

    Bekelman, Justin E. Wolden, Suzanne; Lee, Nancy

    2009-02-01

    Purpose: We conducted this study to determine the feasibility of incorporating a teaching intervention on target delineation into the educational curriculum of a radiation oncology residency program and to assess the short-term effects on resident skills. Methods and Materials: The study schema consisted of a baseline evaluation, the teaching intervention, and a follow-up evaluation. At the baseline evaluation, the participants contoured three clinical tumor volumes (CTVs) (70 Gy, 59.4 Gy, and 54 Gy) on six contrast-enhanced axial computed tomography images of a de-identified patient with Stage T2N2bM0 squamous cell carcinoma of the right base of the tongue. The participants attended a series of head-and-neck oncology and anatomy seminars. The teaching intervention consisted of a didactic lecture and an interactive hands-on practical session designed to improve the knowledge and skills for target delineation in the head and neck. At the follow-up evaluation, the residents again contoured the CTVs. Results: Of the 14 eligible residents, 11 (79%) actually participated in the study. For all participants, but especially for those who had not had previous experience with head-and-neck target delineation, the teaching intervention was associated with improvement in the delineation of the node-negative neck (CTV 54 Gy contour). Regardless of clinical experience, participants had difficulty determining what should be included in the CTV 59.4 Gy contour to ensure adequate coverage of potential microscopic disease. Conclusion: Incorporating a teaching intervention into the education curriculum of a radiation oncology residency program is feasible and was associated with short-term improvements in target delineation skills. Subsequent interventions will require content refinement, additional validation, longer term follow-up, and multi-institutional collaboration.

  7. Radiotherapy planning for glioblastoma based on a tumor growth model: improving target volume delineation.

    PubMed

    Unkelbach, Jan; Menze, Bjoern H; Konukoglu, Ender; Dittmann, Florian; Le, Matthieu; Ayache, Nicholas; Shih, Helen A

    2014-02-01

    crucial model input. We conclude that the tumor growth model provides a method to account for anisotropic growth patterns of glioma, and may therefore provide a tool to make target delineation more objective and automated. PMID:24440875

  8. Radiotherapy planning for glioblastoma based on a tumor growth model: improving target volume delineation

    NASA Astrophysics Data System (ADS)

    Unkelbach, Jan; Menze, Bjoern H.; Konukoglu, Ender; Dittmann, Florian; Le, Matthieu; Ayache, Nicholas; Shih, Helen A.

    2014-02-01

    crucial model input. We conclude that the tumor growth model provides a method to account for anisotropic growth patterns of glioma, and may therefore provide a tool to make target delineation more objective and automated.

  9. SU-E-J-136: Multimodality-Image-Based Target Delineation for Dose Painting of Pancreatic Cancer

    SciTech Connect

    Dalah, E; Paulson, E; Erickson, B; Li, X

    2014-06-01

    Purpose: Dose escalated RT may provide improved disease local-control for selected unresectable pancreatic cancer. Accurate delineation of the gross tumor volume (GTV) inside pancreatic head or body would allow safe dose escalation considering the tolerances of adjacent organs at risk (OAR). Here we explore the potential of multi-modality imaging (DCE-MRI, ADC-MRI, and FDG-PET) to define the GTV for dose painting of pancreatic cancer. Volumetric variations of DCE-MRI, ADC-MRI and FDG-PET defined GTVs were assessed in comparison to the findings on CT, and to pathology specimens for resectable and borderline reseactable cases of pancreatic cancer. Methods: A total of 19 representative patients with DCE-MRI, ADC-MRI and FDG-PET data were analyzed. Of these, 8 patients had pathological specimens. GTV, inside pancreatic head/neck, or body, were delineated on MRI (denoted GTVDCE, and GTVADC), on FDG-PET using SUV of 2.5, 40% SUVmax, and 50% SUVmax (denoted GTV2.5, GTV40%, and GTV50%). A Kruskal-Wallis test was used to determine whether significant differences existed between GTV volumes. Results: Significant statistical differences were found between the GTVs defined by DCE-MRI, ADC-MRI, and FDG-PET, with a mean and range of 4.73 (1.00–9.79), 14.52 (3.21–25.49), 22.04 (1.00–45.69), 19.10 (4.84–45.59), and 9.80 (0.32–35.21) cm3 (p<0.0001) for GTVDCE, GTVADC, GTV2.5, GTV40%, and GTV50%, respectively. The mean difference and range in the measurements of maximum dimension of GTVs based on DCE-MRI, ADC-MRI, SUV2.5, 40% SUVmax, and 50% SUVmax compared with pathologic specimens were −0.84 (−2.24 to 0.9), 0.41 (−0.15 to 2.3), 0.58 (−1.41 to 3.69), 0.66 (−0.67 to 1.32), and 0.15 (−1.53 to 2.38) cm, respectively. Conclusion: Differences exists between DCE, ADC, and PET defined target volumes for RT of pancreatic cancer. Further studies combined with pathological specimens are required to identify the optimal imaging modality and/or acquisition method to

  10. Variability of Target and Normal Structure Delineation Using Multimodality Imaging for Radiation Therapy of Pancreatic Cancer

    SciTech Connect

    Dalah, Entesar; Moraru, Ion; Paulson, Eric; Erickson, Beth; Li, X. Allen

    2014-07-01

    Purpose: To explore the potential of multimodality imaging (dynamic contrast–enhanced magnetic resonance imaging [DCE-MRI], apparent diffusion-coefficient diffusion-weighted imaging [ADC-DWI], fluorodeoxyglucose positron emission tomography [FDG-PET], and computed tomography) to define the gross tumor volume (GTV) and organs at risk in radiation therapy planning for pancreatic cancer. Delineated volumetric changes of DCE-MRI, ADC-DWI, and FDG-PET were assessed in comparison with the finding on 3-dimensional/4-dimensional CT with and without intravenous contrast, and with pathology specimens for resectable and borderline resectable cases of pancreatic cancer. Methods and Materials: We studied a total of 19 representative patients, whose DCE-MRI, ADC-DWI, and FDG-PET data were reviewed. Gross tumor volume and tumor burden/active region inside pancreatic head/neck or body were delineated on MRI (denoted GTV{sub DCE}, and GTV{sub ADC}), a standardized uptake value (SUV) of 2.5, 40%SUVmax, and 50%SUVmax on FDG-PET (GTV2.5, GTV{sub 40%}, and GTV{sub 50%}). Volumes of the pancreas, duodenum, stomach, liver, and kidneys were contoured according to CT (V{sub CT}), T1-weighted MRI (V{sub T1}), and T2-weighted MRI (V{sub T2}) for 7 patients. Results: Significant statistical differences were found between the GTVs from DCE-MRI, ADC-DW, and FDG-PET, with a mean and range of 4.73 (1.00-9.79), 14.52 (3.21-25.49), 22.04 (1.00-45.69), 19.10 (4.84-45.59), and 9.80 (0.32-35.21) cm{sup 3} for GTV{sub DCE}, GTV{sub ADC}, GTV2.5, GTV{sub 40%}, and GTV{sub 50%}, respectively. The mean difference and range in the measurements of maximum dimension of tumor on DCE-MRI, ADC-DW, SUV2.5, 40%SUVmax, and 50%SUVmax compared with pathologic specimens were −0.84 (−2.24 to 0.9), 0.41 (−0.15 to 2.3), 0.58 (−1.41 to 3.69), 0.66 (−0.67 to 1.32), and 0.15 (−1.53 to 2.38) cm, respectively. The T1- and T2-based volumes for pancreas, duodenum, stomach, and liver were generally smaller

  11. {sup 11}C-methionine PET improves the target volume delineation of meningiomas treated with stereotactic fractionated radiotherapy

    SciTech Connect

    Grosu, Anca-Ligia . E-mail: anca-ligia.grosu@lrz.tum.de; Weber, Wolfgang A.; Astner, Sabrina T.; Adam, Markus; Krause, Bernd J.; Schwaiger, Markus; Molls, Michael; Nieder, Carsten

    2006-10-01

    Purpose: To evaluate the role of {sup 11}C-methionine positron emission tomography (MET-PET) in target volume delineation for meningiomas and to determine the interobserver variability. Methods and Materials: Two independent observers performed treatment planning in 10 patients according to a prospective written protocol. In the first step, they used coregistered computed tomography (CT) and magnetic resonance imaging (MRI). In the second step, MET-PET was added to CT/MRI (image fusion based on mutual information). Results: The correlation between gross tumor volume (GTVs) delineated by the two observers based on CT/MRI was r = 0.855 (Spearman's correlation coefficient, p = 0.002) and r = 0.988 (p = 0.000) when MET-PET/CT/MRI were used. The number of patients with agreement in more then 80% of the outlined volume increased with the availability of MET-PET from 1 in 10 to 5 in 10. The median volume of intersection between the regions delineated by two observers increased significantly from 69% (from the composite volume) to 79%, by the addition of MET-PET (p = 0.005). The information of MET-PET was useful to delineate GTV in the area of cavernous sinus, orbit, and base of the skull. Conclusions: The hypothesis-generating findings of potential normal tissue sparing and reduced interobserver variability provide arguments for invasive studies of the correlation between MET-PET images and histologic tumor extension and for prospective trials of target volume delineation with CT/MRI/MET-PET image fusion.

  12. Detection and delineation of oral cancer with a PARP1 targeted optical imaging agent.

    PubMed

    Kossatz, Susanne; Brand, Christian; Gutiontov, Stanley; Liu, Jonathan T C; Lee, Nancy Y; Gönen, Mithat; Weber, Wolfgang A; Reiner, Thomas

    2016-01-01

    Earlier and more accurate detection of oral squamous cell carcinoma (OSCC) is essential to improve the prognosis of patients and to reduce the morbidity of surgical therapy. Here, we demonstrate that the nuclear enzyme Poly(ADP-ribose)Polymerase 1 (PARP1) is a promising target for optical imaging of OSCC with the fluorescent dye PARPi-FL. In patient-derived OSCC specimens, PARP1 expression was increased 7.8 ± 2.6-fold when compared to normal tissue. Intravenous injection of PARPi-FL allowed for high contrast in vivo imaging of human OSCC models in mice with a surgical fluorescence stereoscope and high-resolution imaging systems. The emitted signal was specific for PARP1 expression and, most importantly, PARPi-FL can be used as a topical imaging agent, spatially resolving the orthotopic tongue tumors in vivo. Collectively, our results suggest that PARP1 imaging with PARPi-FL can enhance the detection of oral cancer, serve as a screening tool and help to guide surgical resections. PMID:26900125

  13. Detection and delineation of oral cancer with a PARP1 targeted optical imaging agent

    PubMed Central

    Kossatz, Susanne; Brand, Christian; Gutiontov, Stanley; Liu, Jonathan T. C.; Lee, Nancy Y.; Gönen, Mithat; Weber, Wolfgang A.; Reiner, Thomas

    2016-01-01

    Earlier and more accurate detection of oral squamous cell carcinoma (OSCC) is essential to improve the prognosis of patients and to reduce the morbidity of surgical therapy. Here, we demonstrate that the nuclear enzyme Poly(ADP-ribose)Polymerase 1 (PARP1) is a promising target for optical imaging of OSCC with the fluorescent dye PARPi-FL. In patient-derived OSCC specimens, PARP1 expression was increased 7.8 ± 2.6-fold when compared to normal tissue. Intravenous injection of PARPi-FL allowed for high contrast in vivo imaging of human OSCC models in mice with a surgical fluorescence stereoscope and high-resolution imaging systems. The emitted signal was specific for PARP1 expression and, most importantly, PARPi-FL can be used as a topical imaging agent, spatially resolving the orthotopic tongue tumors in vivo. Collectively, our results suggest that PARP1 imaging with PARPi-FL can enhance the detection of oral cancer, serve as a screening tool and help to guide surgical resections. PMID:26900125

  14. Target Volume Delineation in Dynamic Positron Emission Tomography Based on Time Activity Curve Differences

    NASA Astrophysics Data System (ADS)

    Teymurazyan, Artur

    Tumor volume delineation plays a critical role in radiation treatment planning and simulation, since inaccurately defined treatment volumes may lead to the overdosing of normal surrounding structures and potentially missing the cancerous tissue. However, the imaging modality almost exclusively used to determine tumor volumes, X-ray Computed Tomography (CT), does not readily exhibit a distinction between cancerous and normal tissue. It has been shown that CT data augmented with PET can improve radiation treatment plans by providing functional information not available otherwise. Presently, static PET scans account for the majority of procedures performed in clinical practice. In the radiation therapy (RT) setting, these scans are visually inspected by a radiation oncologist for the purpose of tumor volume delineation. This approach, however, often results in significant interobserver variability when comparing contours drawn by different experts on the same PET/CT data sets. For this reason, a search for more objective contouring approaches is underway. The major drawback of conventional tumor delineation in static PET images is the fact that two neighboring voxels of the same intensity can exhibit markedly different overall dynamics. Therefore, equal intensity voxels in a static analysis of a PET image may be falsely classified as belonging to the same tissue. Dynamic PET allows the evaluation of image data in the temporal domain, which often describes specific biochemical properties of the imaged tissues. Analysis of dynamic PET data can be used to improve classification of the imaged volume into cancerous and normal tissue. In this thesis we present a novel tumor volume delineation approach (Single Seed Region Growing algorithm in 4D (dynamic) PET or SSRG/4D-PET) in dynamic PET based on TAC (Time Activity Curve) differences. A partially-supervised approach is pursued in order to allow an expert reader to utilize the information available from other imaging

  15. Accurate Optical Target Pose Determination for Applications in Aerial Photogrammetry

    NASA Astrophysics Data System (ADS)

    Cucci, D. A.

    2016-06-01

    We propose a new design for an optical coded target based on concentric circles and a position and orientation determination algorithm optimized for high distances compared to the target size. If two ellipses are fitted on the edge pixels corresponding to the outer and inner circles, quasi-analytical methods are known to obtain the coordinates of the projection of the circles center. We show the limits of these methods for quasi-frontal target orientations and in presence of noise and we propose an iterative refinement algorithm based on a geometric invariant. Next, we introduce a closed form, computationally inexpensive, solution to obtain the target position and orientation given the projected circle center and the parameters of the outer circle projection. The viability of the approach is demonstrated based on aerial pictures taken by an UAV from elevations between 10 to 100 m. We obtain a distance RMS below 0.25 % under 50 m and below 1 % under 100 m with a target size of 90 cm, part of which is a deterministic bias introduced by image exposure.

  16. Planning Evaluation of C-Arm Cone Beam CT Angiography for Target Delineation in Stereotactic Radiation Surgery of Brain Arteriovenous Malformations

    SciTech Connect

    Kang, Jun; Huang, Judy; Gailloud, Philippe; Rigamonti, Daniele; Lim, Michael; Bernard, Vincent; Ehtiati, Tina; Ford, Eric C.

    2014-10-01

    Purpose: Stereotactic radiation surgery (SRS) is one of the therapeutic modalities currently available to treat cerebral arteriovenous malformations (AVM). Conventionally, magnetic resonance imaging (MRI) and MR angiography (MRA) and digital subtraction angiography (DSA) are used in combination to identify the target volume for SRS treatment. The purpose of this study was to evaluate the use of C-arm cone beam computed tomography (CBCT) in the treatment planning of SRS for cerebral AVMs. Methods and Materials: Sixteen consecutive patients treated for brain AVMs at our institution were included in this retrospective study. Prior to treatment, all patients underwent MRA, DSA, and C-arm CBCT. All images were coregistered using the GammaPlan planning system. AVM regions were delineated independently by 2 physicians using either C-arm CBCT or MRA, resulting in 2 volumes: a CBCT volume (VCBCT) and an MRA volume (V{sub MRA}). SRS plans were generated based on the delineated regions. Results: The average volume of treatment targets delineated using C-arm CBCT and MRA were similar, 6.40 cm{sup 3} and 6.98 cm{sup 3}, respectively (P=.82). However, significant regions of nonoverlap existed. On average, the overlap of the MRA with the C-arm CBCT was only 52.8% of the total volume. In most cases, radiation plans based on V{sub MRA} did not provide adequate dose to the region identified on C-arm CBCT; the mean minimum dose to V{sub CBCT} was 29.5%, whereas the intended goal was 45% (P<.001). The mean volume of normal brain receiving 12 Gy or more in C-arm CBCT-based plans was not greater than in the MRA-based plans. Conclusions: Use of C-arm CBCT images significantly alters the delineated regions of AVMs for SRS planning, compared to that of MRA/MRI images. CT-based planning can be accomplished without increasing the dose to normal brain and may represent a more accurate definition of the nidus, increasing the chances for successful obliteration.

  17. Target Volume Delineation in Oropharyngeal Cancer: Impact of PET, MRI, and Physical Examination

    SciTech Connect

    Thiagarajan, Anuradha; Caria, Nicola; Schoeder, Heiko; Iyer, N. Gopalakrishna; Wolden, Suzanne; Wong, Richard J.; Sherman, Eric; Fury, Matthew G.; Lee, Nancy

    2012-05-01

    Introduction: Sole utilization of computed tomography (CT) scans in gross tumor volume (GTV) delineation for head-and-neck cancers is subject to inaccuracies. This study aims to evaluate contributions of magnetic resonance imaging (MRI), positron emission tomography (PET), and physical examination (PE) to GTV delineation in oropharyngeal cancer (OPC). Methods: Forty-one patients with OPC were studied. All underwent contrast-enhanced CT simulation scans (CECTs) that were registered with pretreatment PETs and MRIs. For each patient, three sets of primary and nodal GTV were contoured. First, reference GTVs (GTVref) were contoured by the treating radiation oncologist (RO) using CT, MRI, PET, and PE findings. Additional GTVs were created using fused CT/PET scans (GTVctpet) and CT/MRI scans (GTVctmr) by two other ROs blinded to GTVref. To compare GTVs, concordance indices (CI) were calculated by dividing the respective overlap volumes by overall volumes. To evaluate the contribution of PE, composite GTVs derived from CT, MRI, and PET (GTVctpetmr) were compared with GTVref. Results: For primary tumors, GTVref was significantly larger than GTVctpet and GTVctmr (p < 0.001). Although no significant difference in size was noted between GTVctpet and GTVctmr (p = 0.39), there was poor concordance between them (CI = 0.62). In addition, although CI (ctpetmr vs. ref) was low, it was significantly higher than CI (ctpet vs. ref) and CI (ctmr vs. ref) (p < 0.001), suggesting that neither modality should be used alone. Qualitative analyses to explain the low CI (ctpetmr vs. ref) revealed underestimation of mucosal disease when GTV was contoured without knowledge of PE findings. Similar trends were observed for nodal GTVs. However, CI (ctpet vs. ref), CI (ctmr vs. ref), and CI (ctpetmr vs. ref) were high (>0.75), indicating that although the modalities were complementary, the added benefit was small in the context of CECTs. In addition, PE did not aid greatly in nodal GTV delineation

  18. Cranial location of level II lymph nodes in laryngeal cancer: Implications for elective nodal target volume delineation

    SciTech Connect

    Braam, Petra M. . E-mail: P.M.Braam@umcutrecht.nl; Raaijmakers, Cornelis P.J.; Terhaard, Chris

    2007-02-01

    Purpose: To analyze the cranial distribution of level II lymph nodes in patients with laryngeal cancer to optimize the elective radiation nodal target volume delineation. Methods and Materials: The most cranially located metastatic lymph node was delineated in 67 diagnostic CT data sets. The minimum distance from the base of the skull (BOS) to the lymph node was determined. Results: A total of 98 lymph nodes were delineated including 62 ipsilateral and 36 contralateral lymph nodes. The mean ipsilateral and contralateral distance from the top of the most cranial metastatic lymph node to the BOS was 36 mm (range, -9-120; standard deviation [SD], 17.9) and 35 mm (range, 14-78; SD 15.0), respectively. Only 5% and 12% of the ipsilateral and 3% and 9% of the contralateral metastatic lymph nodes were located within 15 mm and 20 mm below the BOS, respectively. No significant differences were found between patients with only ipsilateral metastatic lymph nodes and patients with bilateral metastatic lymph nodes. Between tumors that do cross the midline and those that do not, no significant difference was found in the distance of the most cranial lymph node to the BOS and the occurrence ipsilateral or contralateral. Conclusions: Setting the cranial border of the nodal target volume 1.5 cm below the base of the skull covers 95% of the lymph nodes and should be considered in elective nodal irradiation for laryngeal cancer. Bilateral neck irradiation is mandatory, including patients with unilateral laryngeal cancer, when elective irradiation is advised.

  19. Combined {sup 18}F-FDG-PET/CT Imaging in Radiotherapy Target Delineation for Head-and-Neck Cancer

    SciTech Connect

    Guido, Alessandra; Fuccio, Lorenzo; Rombi, Barbara; Castellucci, Paolo; Cecconi, Agnese; Bunkheila, Feisal; Fuccio, Chiara; Spezi, Emiliano; Angelini, Anna Lisa; Barbieri, Enza

    2009-03-01

    Purpose: To evaluate the effect of the use of {sup 18}F-fluorodeoxyglucose (FDG)-positron emission tomography (PET)/computed tomography (CT) in radiotherapy target delineation for head-and-neck cancer compared with CT alone. Methods and Materials: A total of 38 consecutive patients with head-and-neck cancer were included in this study. The primary tumor sites were as follow: 20 oropharyngeal tumors, 4 laryngeal tumors, 2 hypopharyngeal tumors, 2 paranasal sinuses tumors, 9 nasopharyngeal tumors, and 1 parotid gland tumor. The FDG-PET and CT scans were performed with a dedicated PET/CT scanner in one session and then fused. Subsequently, patients underwent treatment planning CT with intravenous contrast enhancement. The radiation oncologist defined all gross tumor volumes (GTVs) using both the PET/CT and CT scans. Results: In 35 (92%) of 38 cases, the CT-based GTVs were larger than the PET/CT-based GTVs. The average total GTV from the CT and PET/CT scans was 34.54 cm{sup 3} (range, 3.56-109) and 29.38 cm{sup 3} (range, 2.87-95.02), respectively (p < 0.05). Separate analyses of the difference between the CT- and PET/CT-based GTVs of the primary tumor compared with the GTVs of nodal disease were not statistically significant. The comparison between the PET/CT-based and CT-based boost planning target volumes did not show a statistically significant difference. All patients were alive at the end of the follow-up period (range, 3-38 months). Conclusion: GTVs, but not planning target volumes, were significantly changed by the implementation of combined PET/CT. Large multicenter studies are needed to ascertain whether combined PET/CT in target delineation can influence the main clinical outcomes.

  20. SU-C-BRA-02: Gradient Based Method of Target Delineation On PET/MR Image of Head and Neck Cancer Patients

    SciTech Connect

    Dance, M; Chera, B; Falchook, A; Das, S; Lian, J

    2015-06-15

    Purpose: Validate the consistency of a gradient-based segmentation tool to facilitate accurate delineation of PET/CT-based GTVs in head and neck cancers by comparing against hybrid PET/MR-derived GTV contours. Materials and Methods: A total of 18 head and neck target volumes (10 primary and 8 nodal) were retrospectively contoured using a gradient-based segmentation tool by two observers. Each observer independently contoured each target five times. Inter-observer variability was evaluated via absolute percent differences. Intra-observer variability was examined by percentage uncertainty. All target volumes were also contoured using the SUV percent threshold method. The thresholds were explored case by case so its derived volume matched with the gradient-based volume. Dice similarity coefficients (DSC) were calculated to determine overlap of PET/CT GTVs and PET/MR GTVs. Results: The Levene’s test showed there was no statistically significant difference of the variances between the observer’s gradient-derived contours. However, the absolute difference between the observer’s volumes was 10.83%, with a range from 0.39% up to 42.89%. PET-avid regions with qualitatively non-uniform shapes and intensity levels had a higher absolute percent difference near 25%, while regions with uniform shapes and intensity levels had an absolute percent difference of 2% between observers. The average percentage uncertainty between observers was 4.83% and 7%. As the volume of the gradient-derived contours increased, the SUV threshold percent needed to match the volume decreased. Dice coefficients showed good agreement of the PET/CT and PET/MR GTVs with an average DSC value across all volumes at 0.69. Conclusion: Gradient-based segmentation of PET volume showed good consistency in general but can vary considerably for non-uniform target shapes and intensity levels. PET/CT-derived GTV contours stemming from the gradient-based tool show good agreement with the anatomically and

  1. Efficacy of salvage stereotactic radiotherapy for recurrent glioma: impact of tumor morphology and method of target delineation on local control

    PubMed Central

    Ogura, Kengo; Mizowaki, Takashi; Arakawa, Yoshiki; Sakanaka, Katsuyuki; Miyamoto, Susumu; Hiraoka, Masahiro

    2013-01-01

    In this study, we assessed the efficacy of salvage stereotactic radiotherapy (SRT) for recurrent glioma. From August 2008 to December 2012, 30 patients with recurrent glioma underwent salvage SRT. The initial histological diagnoses were World Health Organization (WHO) grades II, III, and IV in 6, 9, and 15 patients, respectively. Morphologically, the type of recurrence was classified as diffuse or other. Two methods of clinical target delineation were used: A, a contrast-enhancing tumor; or B, a contrast-enhancing tumor with a 3–10-mm margin and/or surrounding fluid attenuation inversion recovery (FLAIR) high-intensity areas. The prescribed dose was 22.5–35 Gy delivered in five fractions at an isocenter using a dynamic conformal arc technique. The overall survival (OS) and local control probability (LCP) after SRT were calculated using the Kaplan–Meier method. A univariate analysis was used to test the effect of clinical variables on OS/LCP. The median follow-up period was 272 days after SRT. The OS and LCP were 83% and 56% at 6 months after SRT, respectively. Morphologically, the tumor type correlated significantly with both OS and LCP (P = 0.006 and <0.001, respectively). The method of target delineation also had a significant influence on LCP (P = 0.016). Grade 3 radiation necrosis was observed in two patients according to Common Terminology Criteria for Adverse Events, version 3. Salvage SRT was safe and effective for recurrent glioma, especially non-diffuse recurrences. Improved local control might be obtained by adding a margin to contrast-enhancing tumors or including increased FLAIR high-intensity areas. PMID:24403268

  2. Integrating respiratory-gated PET-based target volume delineation in liver SBRT planning, a pilot study

    PubMed Central

    2014-01-01

    Background To assess the feasibility and benefit of integrating four-dimensional (4D) Positron Emission Tomography (PET) – computed tomography (CT) for liver stereotactic body radiation therapy (SBRT) planning. Methods 8 patients with 14 metastases were accrued in the study. They all underwent a non-gated PET and a 4D PET centered on the liver. The same CT scan was used for attenuation correction, registration, and considered the planning CT for SBRT planning. Six PET phases were reconstructed for each 4D PET. By applying an individualized threshold to the 4D PET, a Biological Internal Target Volume (BITV) was generated for each lesion. A gated Planning Target Volume (PTVg) was created by adding 3 mm to account for set-up margins. This volume was compared to a manual Planning Target Volume (PTV) delineated with the help of a semi-automatic Biological Target Volume (BTV) obtained from the non-gated exam. A 5 mm radial and a 10 mm craniocaudal margins were applied to account for tumor motion and set-up margins to create the PTV. Results One undiagnosed liver metastasis was discovered thanks to the 4D PET. The semi-automatic BTV were significantly smaller than the BITV (p = 0.0031). However, after applying adapted margins, 4D PET allowed a statistically significant decrease in the PTVg as compared to the PTV (p = 0.0052). Conclusions In comparison to non-gated PET, 4D PET may better define the respiratory movements of liver targets and improve SBRT planning for liver metastases. Furthermore, non respiratory-gated PET exams can both misdiagnose liver metastases and underestimate the real internal target volumes. PMID:24885897

  3. Validation of a 4D-PET Maximum Intensity Projection for Delineation of an Internal Target Volume

    SciTech Connect

    Callahan, Jason; Kron, Tomas; Schneider-Kolsky, Michal; Dunn, Leon; Thompson, Mick; Siva, Shankar; Aarons, Yolanda; Binns, David; Hicks, Rodney J.

    2013-07-15

    Purpose: The delineation of internal target volumes (ITVs) in radiation therapy of lung tumors is currently performed by use of either free-breathing (FB) {sup 18}F-fluorodeoxyglucose-positron emission tomography-computed tomography (FDG-PET/CT) or 4-dimensional (4D)-CT maximum intensity projection (MIP). In this report we validate the use of 4D-PET-MIP for the delineation of target volumes in both a phantom and in patients. Methods and Materials: A phantom with 3 hollow spheres was prepared surrounded by air then water. The spheres and water background were filled with a mixture of {sup 18}F and radiographic contrast medium. A 4D-PET/CT scan was performed of the phantom while moving in 4 different breathing patterns using a programmable motion device. Nine patients with an FDG-avid lung tumor who underwent FB and 4D-PET/CT and >5 mm of tumor motion were included for analysis. The 3 spheres and patient lesions were contoured by 2 contouring methods (40% of maximum and PET edge) on the FB-PET, FB-CT, 4D-PET, 4D-PET-MIP, and 4D-CT-MIP. The concordance between the different contoured volumes was calculated using a Dice coefficient (DC). The difference in lung tumor volumes between FB-PET and 4D-PET volumes was also measured. Results: The average DC in the phantom using 40% and PET edge, respectively, was lowest for FB-PET/CT (DCAir = 0.72/0.67, DCBackground 0.63/0.62) and highest for 4D-PET/CT-MIP (DCAir = 0.84/0.83, DCBackground = 0.78/0.73). The average DC in the 9 patients using 40% and PET edge, respectively, was also lowest for FB-PET/CT (DC = 0.45/0.44) and highest for 4D-PET/CT-MIP (DC = 0.72/0.73). In the 9 lesions, the target volumes of the FB-PET using 40% and PET edge, respectively, were on average 40% and 45% smaller than the 4D-PET-MIP. Conclusion: A 4D-PET-MIP produces volumes with the highest concordance with 4D-CT-MIP across multiple breathing patterns and lesion sizes in both a phantom and among patients. Freebreathing PET/CT consistently

  4. Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics

    PubMed Central

    2013-01-01

    The more than 300 currently identified post-translational modifications (PTMs) provides great scope for subtle or dramatic alteration of protein structure and function. Furthermore, the rapid and transient nature of many PTMs allows efficient signal transmission in response to internal and environmental stimuli. PTMs are predominantly added by enzymes, and the enzymes responsible (such as kinases) are thus attractive targets for therapeutic interventions. Modifications can be grouped according to their stability or transience (reversible versus irreversible): irreversible types (such as irreversible redox modifications or protein deamidation) are often associated with aging or tissue injury, whereas transient modifications are associated with signal propagation and regulation. This is particularly important in the setting of heart disease, which comprises a diverse range of acute (such as ischemia/reperfusion), chronic (such as heart failure, dilated cardiomyopathy) and genetic (such as hypertrophic cardiomyopathy) disease states, all of which have been associated with protein PTM. Recently the interplay between diverse PTMs has been suggested to also influence cellular function, with cooperation or competition for sites of modification possible. Here we discuss the utility of proteomics for examining PTMs in the context of the molecular mechanisms of heart disease. PMID:23445784

  5. SU-E-J-78: Internal Target Volume Delineation for Lung Tumors in Patients Treated with Robotic Radiosurgery

    SciTech Connect

    Descovich, M; Pinnaduwage, D; Kirby, N; Gottschalk, A; Yom, S; Pouliot, J; Braunstein, S

    2014-06-01

    Purpose: To compare different approaches for Internal Target Volume (ITV) delineation for patients treated with fiducial-free robotic radiosurgery for primary and metastatic lung tumors. Methods: Ten patients undergoing Lung-Optimized Treatment (LOT) for robotic radiosurgery were imaged with inhale and exhale breath-hold CT scans and 8-phase 4DCT scan. We evaluated the differences in internal target volume (ITV) delineated using three approaches: 1) maximum intensity projection (MIP) images reconstructed from 4DCT scan (ITV-MIP); 2) linear interpolation of Gross Tumor Volumes (GTV) segmented on inhale and exhale breath-hold scans (ITV-BH); 3) linear interpolation of GTV segmented on inhale and exhale phases of 4DCT scan (ITV-2Phase). All contours were independently generated by the same radiation oncologist using lung window settings. Patients had ITV-MIP volumes ranging from 1.5 to 146.9 cc (mean 36.8 cc) located in various parts of the lung. Volume overlap and matching index (MI) were calculated and compared. The MI between two volumes was defined as the ratio of their intersection to their union. MI of 1 indicates the volumes are identical; MI of 0 indicates that there is no overlap. Results: The three approaches generated very different results. The average (SD) MI for ITV-MIP and ITV-BH was 0.52 (0.24); for ITV-MIP and ITV-2Phase it was 0.69 (0.13); and for ITV-BH and ITV-2Phase was 0.57 (0.21), (ANOVA, p=0.16). Relative to the ITV-MIP, the percentage of volume overlap was 72% (26%) and 90% (7%) for ITV-BH and ITV-2Phase, respectively (t-test, p=0.05). Conclusion: Differences between ITV-BH and ITV-MIP are due to inconsistent lung filling at breath-hold and nonlinear tumor motion. Therefore, methods to check breath-hold scanning against regular patient breathing patterns should be developed. Whenever possible, ITV-BH generated by the LOT workflow should be verified by 4DCT data.

  6. p53 Pulses Diversify Target Gene Expression Dynamics in an mRNA Half-Life-Dependent Manner and Delineate Co-regulated Target Gene Subnetworks.

    PubMed

    Porter, Joshua R; Fisher, Brian E; Batchelor, Eric

    2016-04-27

    The transcription factor p53 responds to DNA double-strand breaks by increasing in concentration in a series of pulses of fixed amplitude, duration, and period. How p53 pulses influence the dynamics of p53 target gene expression is not understood. Here, we show that, in bulk cell populations, patterns of p53 target gene expression cluster into groups with stereotyped temporal behaviors, including pulsing and rising dynamics. These behaviors correlate statistically with the mRNA decay rates of target genes: short mRNA half-lives produce pulses of gene expression. This relationship can be recapitulated by mathematical models of p53-dependent gene expression in single cells and cell populations. Single-cell transcriptional profiling demonstrates that expression of a subset of p53 target genes is coordinated across time within single cells; p53 pulsing attenuates this coordination. These results help delineate how p53 orchestrates the complex DNA damage response and give insight into the function of pulsatile signaling pathways. PMID:27135539

  7. Reduce in Variation and Improve Efficiency of Target Volume Delineation by a Computer-Assisted System Using a Deformable Image Registration Approach

    SciTech Connect

    Chao, K.S. Clifford . E-mail: cchao@mdanderson.org; Bhide, Shreerang FRCR; Chen, Hansen; Asper, Joshua PAC; Bush, Steven; Franklin, Gregg; Kavadi, Vivek; Liengswangwong, Vichaivood; Gordon, William; Raben, Adam; Strasser, Jon; Koprowski, Christopher; Frank, Steven; Chronowski, Gregory; Ahamad, Anesa; Malyapa, Robert; Zhang Lifei; Dong Lei

    2007-08-01

    Purpose: To determine whether a computer-assisted target volume delineation (CAT) system using a deformable image registration approach can reduce the variation of target delineation among physicians with different head and neck (HN) IMRT experiences and reduce the time spent on the contouring process. Materials and Methods: We developed a deformable image registration method for mapping contours from a template case to a patient case with a similar tumor manifestation but different body configuration. Eight radiation oncologists with varying levels of clinical experience in HN IMRT performed target delineation on two HN cases, one with base-of-tongue (BOT) cancer and another with nasopharyngeal cancer (NPC), by first contouring from scratch and then by modifying the contours deformed by the CAT system. The gross target volumes were provided. Regions of interest for comparison included the clinical target volumes (CTVs) and normal organs. The volumetric and geometric variation of these regions of interest and the time spent on contouring were analyzed. Results: We found that the variation in delineating CTVs from scratch among the physicians was significant, and that using the CAT system reduced volumetric variation and improved geometric consistency in both BOT and NPC cases. The average timesaving when using the CAT system was 26% to 29% for more experienced physicians and 38% to 47% for the less experienced ones. Conclusions: A computer-assisted target volume delineation approach, using a deformable image-registration method with template contours, was able to reduce the variation among physicians with different experiences in HN IMRT while saving contouring time.

  8. A dimensionless dynamic contrast enhanced MRI parameter for intra-prostatic tumour target volume delineation: initial comparison with histology

    NASA Astrophysics Data System (ADS)

    Hrinivich, W. Thomas; Gibson, Eli; Gaed, Mena; Gomez, Jose A.; Moussa, Madeleine; McKenzie, Charles A.; Bauman, Glenn S.; Ward, Aaron D.; Fenster, Aaron; Wong, Eugene

    2014-03-01

    Purpose: T2 weighted and diffusion weighted magnetic resonance imaging (MRI) show promise in isolating prostate tumours. Dynamic contrast enhanced (DCE)-MRI has also been employed as a component in multi-parametric tumour detection schemes. Model-based parameters such as Ktrans are conventionally used to characterize DCE images and require arterial contrast agent (CR) concentration. A robust parameter map that does not depend on arterial input may be more useful for target volume delineation. We present a dimensionless parameter (Wio) that characterizes CR wash-in and washout rates without requiring arterial CR concentration. Wio is compared to Ktrans in terms of ability to discriminate cancer in the prostate, as demonstrated via comparison with histology. Methods: Three subjects underwent DCE-MRI using gadolinium contrast and 7 s imaging temporal resolution. A pathologist identified cancer on whole-mount histology specimens, and slides were deformably registered to MR images. The ability of Wio maps to discriminate cancer was determined through receiver operating characteristic curve (ROC) analysis. Results: There is a trend that Wio shows greater area under the ROC curve (AUC) than Ktrans with median AUC values of 0.74 and 0.69 respectively, but the difference was not statistically significant based on a Wilcoxon signed-rank test (p = 0.13). Conclusions: Preliminary results indicate that Wio shows potential as a tool for Ktrans QA, showing similar ability to discriminate cancer in the prostate as Ktrans without requiring arterial CR concentration.

  9. Simulation of tissue activity curves of 64Cu-ATSM for sub-target volume delineation in radiotherapy

    NASA Astrophysics Data System (ADS)

    Dalah, E.; Bradley, D.; Nisbet, A.

    2010-02-01

    There is much interest in positron emission tomography (PET) for measurements of regional tracer concentration in hypoxic tumour-bearing tissue, focusing on the need for accurate radiotherapy treatment planning. Generally, relevant data are taken over multiple time frames in the form of tissue activity curves (TACs), thus providing an indication of vasculature structure and geometry. This is a potential key in providing information on cellular perfusion and limited diffusion. A number of theoretical studies have attempted to describe tracer uptake in tissue cells in an effort to understand such complicated behaviour of cellular uptake and the mechanism of washout. More recently, a novel computerized reaction diffusion equation method was developed by Kelly and Brady (2006 A model to simulate tumour oxygenation and dynamic [18F]-FMISO PET data Phys. Med. Biol. 51 5859-73), where they managed to simulate the realistic dynamic TACs of 18F-FMISO. The model was developed over a multi-step process. Here we present a refinement to the work of Kelly and Brady, such that the model allows simulation of a realistic tissue activity curve (TAC) of any hypoxia selective PET tracer, in a single step process. In this work we show particular interest in simulating the TAC of perhaps the most promising hypoxia selective tracer, 64Cu-ATSM. In addition, we demonstrate its potential role in tumour sub-volume delineation for radiotherapy treatment planning. Simulation results have demonstrated the significant high contrast of imaging using ATSM, with a tumour to blood ratio ranging from 2.24 to 4.1.

  10. A New Brain Positron Emission Tomography Scanner With Semiconductor Detectors for Target Volume Delineation and Radiotherapy Treatment Planning in Patients With Nasopharyngeal Carcinoma

    SciTech Connect

    Katoh, Norio; Yasuda, Koichi; Shiga, Tohru; Hasegawa, Masakazu; Onimaru, Rikiya; Shimizu, Shinichi; Bengua, Gerard; Ishikawa, Masayori; Tamaki, Nagara; Shirato, Hiroki

    2012-03-15

    Purpose: We compared two treatment planning methods for stereotactic boost for treating nasopharyngeal carcinoma (NPC): the use of conventional whole-body bismuth germanate (BGO) scintillator positron emission tomography (PET{sub CONV}WB) versus the new brain (BR) PET system using semiconductor detectors (PET{sub NEW}BR). Methods and Materials: Twelve patients with NPC were enrolled in this study. [{sup 18}F]Fluorodeoxyglucose-PET images were acquired using both the PET{sub NEW}BR and the PET{sub CONV}WB system on the same day. Computed tomography (CT) and two PET data sets were transferred to a treatment planning system, and the PET{sub CONV}WB and PET{sub NEW}BR images were coregistered with the same set of CT images. Window width and level values for all PET images were fixed at 3000 and 300, respectively. The gross tumor volume (GTV) was visually delineated on PET images by using either PET{sub CONV}WB (GTV{sub CONV}) images or PET{sub NEW}BR (GTV{sub NEW}) images. Assuming a stereotactic radiotherapy boost of 7 ports, the prescribed dose delivered to 95% of the planning target volume (PTV) was set to 2000 cGy in 4 fractions. Results: The average absolute volume ({+-}standard deviation [SD]) of GTV{sub NEW} was 15.7 ml ({+-}9.9) ml, and that of GTV{sub CONV} was 34.0 ({+-}20.5) ml. The average GTV{sub NEW} was significantly smaller than that of GTV{sub CONV} (p = 0.0006). There was no statistically significant difference between the maximum dose (p = 0.0585) and the mean dose (p = 0.2748) of PTV. The radiotherapy treatment plan based on the new gross tumor volume (PLAN{sub NEW}) significantly reduced maximum doses to the cerebrum and cerebellum (p = 0.0418) and to brain stem (p = 0.0041). Conclusion: Results of the present study suggest that the new brain PET system using semiconductor detectors can provide more accurate tumor delineation than the conventional whole-body BGO PET system and may be an important tool for functional and molecular radiotherapy

  11. Preclinical evaluation of a novel CEA-targeting near-infrared fluorescent tracer delineating colorectal and pancreatic tumors.

    PubMed

    Boonstra, Martin C; Tolner, Berend; Schaafsma, Boudewijn E; Boogerd, Leonora S F; Prevoo, Hendrica A J M; Bhavsar, Guarav; Kuppen, Peter J K; Sier, Cornelis F M; Bonsing, Bert A; Frangioni, John V; van de Velde, Cornelis J H; Chester, Kerry A; Vahrmeijer, Alexander L

    2015-10-15

    Surgery is the cornerstone of oncologic therapy with curative intent. However, identification of tumor cells in the resection margins is difficult, resulting in nonradical resections, increased cancer recurrence and subsequent decreased patient survival. Novel imaging techniques that aid in demarcating tumor margins during surgery are needed. Overexpression of carcinoembryonic antigen (CEA) is found in the majority of gastrointestinal carcinomas, including colorectal and pancreas. We developed ssSM3E/800CW, a novel CEA-targeted near-infrared fluorescent (NIRF) tracer, based on a disulfide-stabilized single-chain antibody fragment (ssScFv), to visualize colorectal and pancreatic tumors in a clinically translatable setting. The applicability of the tracer was tested for cell and tissue binding characteristics and dosing using immunohistochemistry, flow cytometry, cell-based plate assays and orthotopic colorectal (HT-29, well differentiated) and pancreatic (BXPC-3, poorly differentiated) xenogeneic human-mouse models. NIRF signals were visualized using the clinically compatible FLARE™ imaging system. Calculated clinically relevant doses of ssSM3E/800CW selectively accumulated in colorectal and pancreatic tumors/cells, with highest tumor-to-background ratios of 5.1 ± 0.6 at 72 hr postinjection, which proved suitable for intraoperative detection and delineation of tumor boarders and small (residual) tumor nodules in mice, between 8 and 96 hr postinjection. Ex vivo fluorescence imaging and pathologic examination confirmed tumor specificity and the distribution of the tracer. Our results indicate that ssSM3E/800CW shows promise as a diagnostic tool to recognize colorectal and pancreatic cancers for fluorescent-guided surgery applications. If successfully translated clinically, this tracer could help improve the completeness of surgery and thus survival. PMID:25895046

  12. TU-A-12A-06: Intra-Observer Variability in Delineation of Target Volumes in Breast Radiotherapy and Its Effect On Accuracy of Deformation Measurements

    SciTech Connect

    Juneja, P; Harris, E; Bonora, M; Evans, P

    2014-06-15

    Purpose: In breast radiotherapy, the target volume may change during treatment and need adaptation of the treatment plan. This is possible for both tumour bed (TB) and whole breast (WB) target volumes. Delineation of the target (to detect changes) is also subject to uncertainty due to intra- and inter-observer variability. This work measured the uncertainty, due to intraobserver variability, in the quantification of tissue deformation. Methods: Datasets consisting of paired prone and supine CT scans of three patients were used. Significant deformation in target volumes is expected between prone and supine patient positions. The selected cases had 1) no seroma, 2) some seroma, and 3) large seroma. The TB and WB were outlined on each dataset three times by one clinician. Delineation variability was defined as the standard deviations of the distances between observer outlines. For each target volume and each case, tissue deformation between prone and supine delineations was quantified using the Dice similarity coefficient (DSC) and the average surface distance (ASD). The uncertainty in the tissue deformation (due to delineation variability) was quantified by measuring the ranges of DSC and ASD using all combinations of pairs of outlines (9 pairs). Results: For the TB, the range of delineation variability was 0.44-1.16 mm. The deformation, DSC and ASD, (and uncertainty in measurement) of the TB between prone and supine position of the cases were: 1) 0.21 (0.17-0.28) and 12.4 mm (11.8-13 mm); 2) 0.54 (0.51-0.57) and 3.3 mm (3.1-3.5 mm); 3) 0.62 (0.61-0.64) and 4.9 mm (4.6-5.2 mm). WB deformation measurements were subject to less uncertainty due to delineation variability than TB deformation measurements. Conclusion: For the first time, the uncertainty, due to observer variability, in the measurement of the deformation of breast target volumes was investigated. Deformations in these ranges would be difficult to detect. This work was supported in part by Cancer Research

  13. Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

    PubMed Central

    Singh, Ritambhara; Kuscu, Cem; Quinlan, Aaron; Qi, Yanjun; Adli, Mazhar

    2015-01-01

    The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CRISPR/Cas9 Off-target Prediction and Identification Tool (CROP-IT) that performs improved off-target binding and cleavage site predictions. Unlike existing prediction programs that solely use DNA sequence information; CROP-IT integrates whole genome level biological information from existing Cas9 binding and cleavage data sets. Utilizing whole-genome chromatin state information from 125 human cell types further enhances its computational prediction power. Comparative analyses on experimentally validated datasets show that CROP-IT outperforms existing computational algorithms in predicting both Cas9 binding as well as cleavage sites. With a user-friendly web-interface, CROP-IT outputs scored and ranked list of potential off-targets that enables improved guide RNA design and more accurate prediction of Cas9 binding or cleavage sites. PMID:26032770

  14. Optimal target VOI size for accurate 4D coregistration of DCE-MRI

    NASA Astrophysics Data System (ADS)

    Park, Brian; Mikheev, Artem; Zaim Wadghiri, Youssef; Bertrand, Anne; Novikov, Dmitry; Chandarana, Hersh; Rusinek, Henry

    2016-03-01

    Dynamic contrast enhanced (DCE) MRI has emerged as a reliable and diagnostically useful functional imaging technique. DCE protocol typically lasts 3-15 minutes and results in a time series of N volumes. For automated analysis, it is important that volumes acquired at different times be spatially coregistered. We have recently introduced a novel 4D, or volume time series, coregistration tool based on a user-specified target volume of interest (VOI). However, the relationship between coregistration accuracy and target VOI size has not been investigated. In this study, coregistration accuracy was quantitatively measured using various sized target VOIs. Coregistration of 10 DCE-MRI mouse head image sets were performed with various sized VOIs targeting the mouse brain. Accuracy was quantified by measures based on the union and standard deviation of the coregistered volume time series. Coregistration accuracy was determined to improve rapidly as the size of the VOI increased and approached the approximate volume of the target (mouse brain). Further inflation of the VOI beyond the volume of the target (mouse brain) only marginally improved coregistration accuracy. The CPU time needed to accomplish coregistration is a linear function of N that varied gradually with VOI size. From the results of this study, we recommend the optimal size of the VOI to be slightly overinclusive, approximately by 5 voxels, of the target for computationally efficient and accurate coregistration.

  15. SU-E-J-221: A Novel Expansion Method for MRI Based Target Delineation in Prostate Radiotherapy

    SciTech Connect

    Ruiz, B; Feng, Y; Shores, R; Fung, C

    2015-06-15

    Purpose: To compare a novel bladder/rectum carveout expansion method on MRI delineated prostate to standard CT and expansion based methods for maintaining prostate coverage while providing superior bladder and rectal sparing. Methods: Ten prostate cases were planned to include four trials: MRI vs CT delineated prostate/proximal seminal vesicles, and each image modality compared to both standard expansions (8mm 3D expansion and 5mm posterior, i.e. ∼8mm) and carveout method expansions (5mm 3D expansion, 4mm posterior for GTV-CTV excluding expansion into bladder/rectum followed by additional 5mm 3D expansion to PTV, i.e. ∼1cm). All trials were planned to total dose 7920 cGy via IMRT. Evaluation and comparison was made using the following criteria: QUANTEC constraints for bladder/rectum including analysis of low dose regions, changes in PTV volume, total control points, and maximum hot spot. Results: ∼8mm MRI expansion consistently produced the most optimal plan with lowest total control points and best bladder/rectum sparing. However, this scheme had the smallest prostate (average 22.9% reduction) and subsequent PTV volume, consistent with prior literature. ∼1cm MRI had an average PTV volume comparable to ∼8mm CT at 3.79% difference. Bladder QUANTEC constraints were on average less for the ∼1cm MRI as compared to the ∼8mm CT and observed as statistically significant with 2.64% reduction in V65. Rectal constraints appeared to follow the same trend. Case-by-case analysis showed variation in rectal V30 with MRI delineated prostate being most favorable regardless of expansion type. ∼1cm MRI and ∼8mm CT had comparable plan quality. Conclusion: MRI delineated prostate with standard expansions had the smallest PTV leading to margins that may be too tight. Bladder/rectum carveout expansion method on MRI delineated prostate was found to be superior to standard CT based methods in terms of bladder and rectal sparing while maintaining prostate coverage

  16. Consequences of anorectal cancer atlas implementation in the cooperative group setting: Radiobiologic analysis of a prospective randomized in silico target delineation study

    PubMed Central

    Mavroidis, Panayiotis; Giantsoudis, Drosoula; Awan, Musaddiq J.; Nijkamp, Jasper; Rasch, Coen R. N.; Duppen, Joop C.; Thomas, Charles R.; Okunieff, Paul; Jones, William E.; Kachnicc, Lisa A.; Papanikolaou, Niko; Fuller, Clifton D.

    2014-01-01

    Purpose The aim of this study is to ascertain the subsequent radiobiological impact of using a consensus guideline target volume delineation atlas. Materials and methods Using a representative case and target volume delineation instructions derived from a proposed IMRT rectal cancer clinical trial, gross tumor volume (GTV) and clinical/planning target volumes (CTV/PTV) were contoured by 13 physician observers (Phase 1). The observers were then randomly assigned to follow (atlas) or not-follow (control) a consensus guideline/atlas for anorectal cancers, and instructed to re-contour the same case (Phase 2). Results The atlas group was found to have increased tumor control probability (TCP) after the atlas intervention for both the CTV (p < 0.0001) and PTV1 (p = 0.0011) with decreasing normal tissue complication probability (NTCP) for small intestine, while the control group did not. Additionally, the atlas group had reduced variance in TCP for all target volumes and reduced variance in NTCP for the bowel. In Phase 2, the atlas group had increased TCP relative to the control for CTV (p = 0.03). Conclusions Visual atlas and consensus treatment guidelines usage in the development of rectal cancer IMRT treatment plans reduced the inter-observer radiobiological variation, with clinically relevant TCP alteration for CTV and PTV volumes. PMID:24996454

  17. Application of the Geo-Anomaly Unit Concept in Quantitative Delineation and Assessment of Gold Ore Targets in Western Shandong Uplift Terrain, Eastern China

    SciTech Connect

    Chen Yongqing Zhao Pengda; Chen Jianguo; Liu Jiping

    2001-03-15

    A number of large and giant ore deposits have been discovered within the relatively small areas of lithospheric structure anomalies, including various boundary zones of tectonic plates. The regions have become the well-known intercontinental ore-forming belts, such as the circum-Pacific gold-copper, copper-molybdenum, and tungsten-tin metallogenic belts. These belts are typical geological anomalous areas. An investigation into the hydrothermal ore deposits in different regions in the former Soviet Union illustrated that the geologic structures of ore fields of almost all major commercial deposits have distinct features compared with the neighboring areas. These areas with distinct features are defined as geo-anomalies. A geo-anomaly refers to such a geologic body or a combination of bodies that their composition, texture-structure, and genesis are significantly different from those of their surroundings. A geo-anomaly unit (GU) is an area containing distinct features that can be delineated with integrated ore-forming information using computer techniques on the basis of the geo-anomaly concept. Herein, the GU concept is illustrated by a case study of delineating the gold ore targets in the western Shandong uplift terrain, eastern China. It includes: (1) analyses of gold ore-forming factors; (2) compilation of normalized regional geochemical map and extraction of geochemical anomalies; (3) compilation of gravitational and aeromagnetic tectonic skeleton map and extraction of gravitational and aeromagnetic anomalies; (4) extraction of circular and linear anomalies from remote-sensing Landsat TM images; (5) establishment of a geo-anomaly conceptual model associated with known gold mineralization; (6) establishment of gold ore-forming favorability by computing techniques; and (7) delineation and assessment of ore-forming units. The units with high favorability are suggested as ore targets.

  18. Prospective Randomized Double-Blind Pilot Study of Site-Specific Consensus Atlas Implementation for Rectal Cancer Target Volume Delineation in the Cooperative Group Setting

    SciTech Connect

    Fuller, Clifton D.; Nijkamp, Jasper; Duppen, Joop C.; Rasch, Coen R.N.; Thomas, Charles R.; Wang, Samuel J.; Okunieff, Paul; Jones, William E.; Baseman, Daniel; Patel, Shilpen; Demandante, Carlo G.N.; Harris, Anna M.; Smith, Benjamin D.; Katz, Alan W.; McGann, Camille

    2011-02-01

    Purpose: Variations in target volume delineation represent a significant hurdle in clinical trials involving conformal radiotherapy. We sought to determine the effect of a consensus guideline-based visual atlas on contouring the target volumes. Methods and Materials: A representative case was contoured (Scan 1) by 14 physician observers and a reference expert with and without target volume delineation instructions derived from a proposed rectal cancer clinical trial involving conformal radiotherapy. The gross tumor volume (GTV), and two clinical target volumes (CTVA, including the internal iliac, presacral, and perirectal nodes, and CTVB, which included the external iliac nodes) were contoured. The observers were randomly assigned to receipt (Group A) or nonreceipt (Group B) of a consensus guideline and atlas for anorectal cancers and then instructed to recontour the same case/images (Scan 2). Observer variation was analyzed volumetrically using the conformation number (CN, where CN = 1 equals total agreement). Results: Of 14 evaluable contour sets (1 expert and 7 Group A and 6 Group B observers), greater agreement was found for the GTV (mean CN, 0.75) than for the CTVs (mean CN, 0.46-0.65). Atlas exposure for Group A led to significantly increased interobserver agreement for CTVA (mean initial CN, 0.68, after atlas use, 0.76; p = .03) and increased agreement with the expert reference (initial mean CN, 0.58; after atlas use, 0.69; p = .02). For the GTV and CTVB, neither the interobserver nor the expert agreement was altered after atlas exposure. Conclusion: Consensus guideline atlas implementation resulted in a detectable difference in interobserver agreement and a greater approximation of expert volumes for the CTVA but not for the GTV or CTVB in the specified case. Visual atlas inclusion should be considered as a feature in future clinical trials incorporating conformal RT.

  19. Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory.

    PubMed

    Clune, Jeff; Goldsby, Heather J; Ofria, Charles; Pennock, Robert T

    2011-03-01

    Inclusive fitness theory predicts that natural selection will favour altruist genes that are more accurate in targeting altruism only to copies of themselves. In this paper, we provide evidence from digital evolution in support of this prediction by competing multiple altruist-targeting mechanisms that vary in their accuracy in determining whether a potential target for altruism carries a copy of the altruist gene. We compete altruism-targeting mechanisms based on (i) kinship (kin targeting), (ii) genetic similarity at a level greater than that expected of kin (similarity targeting), and (iii) perfect knowledge of the presence of an altruist gene (green beard targeting). Natural selection always favoured the most accurate targeting mechanism available. Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker. The green beard altruism levels stably increased only when mutations that changed the altruism level also changed the marker (e.g. beard colour), such that beard colour reliably indicated the altruism level. For kin- and similarity-targeting mechanisms, we found that evolution was able to stably adjust altruism levels. Our results confirm that natural selection favours altruist genes that are increasingly accurate in targeting altruism to only their copies. Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces. PMID:20843843

  20. Selective pressures for accurate altruism targeting: evidence from digital evolution for difficult-to-test aspects of inclusive fitness theory

    PubMed Central

    Clune, Jeff; Goldsby, Heather J.; Ofria, Charles; Pennock, Robert T.

    2011-01-01

    Inclusive fitness theory predicts that natural selection will favour altruist genes that are more accurate in targeting altruism only to copies of themselves. In this paper, we provide evidence from digital evolution in support of this prediction by competing multiple altruist-targeting mechanisms that vary in their accuracy in determining whether a potential target for altruism carries a copy of the altruist gene. We compete altruism-targeting mechanisms based on (i) kinship (kin targeting), (ii) genetic similarity at a level greater than that expected of kin (similarity targeting), and (iii) perfect knowledge of the presence of an altruist gene (green beard targeting). Natural selection always favoured the most accurate targeting mechanism available. Our investigations also revealed that evolution did not increase the altruism level when all green beard altruists used the same phenotypic marker. The green beard altruism levels stably increased only when mutations that changed the altruism level also changed the marker (e.g. beard colour), such that beard colour reliably indicated the altruism level. For kin- and similarity-targeting mechanisms, we found that evolution was able to stably adjust altruism levels. Our results confirm that natural selection favours altruist genes that are increasingly accurate in targeting altruism to only their copies. Our work also emphasizes that the concept of targeting accuracy must include both the presence of an altruist gene and the level of altruism it produces. PMID:20843843

  1. Systematic evaluation of MRI findings in different stages of treatment of cervical cancer: Potential of MRI on delineation of target, pathoanatomic structures, and organs at risk

    SciTech Connect

    Dimopoulos, Johannes . E-mail: johannes.dimopoulos@akhwien.at; Schard, Gerdi; Berger, Daniel; Lang, Stefan; Goldner, Gregor; Helbich, Thomas; Poetter, Richard

    2006-04-01

    Purpose: To compare magnetic resonance imaging (MRI) findings at different stages of cervix cancer treatment and to define the potential of MRI to delineate the gross tumor volume (GTV), clinical target volume (CTV), pathoanatomic structures, and organs at risk (OAR) in brachytherapy. Methods and Materials: Forty-nine patients underwent MRI at diagnosis and at brachytherapy. The ability to discriminate anatomic structures on MRI was assessed (quality factor: 0 = inability to discriminate; 1 = fair discrimination; 2 = good discrimination; 3 = excellent discrimination). The overall ability to visualize (percentage of patients with quality factors greater than 0) and the overall discrimination quality score (mean quality factors of all patients) were estimated for the applicator, GTV at diagnosis (GTV{sub D}), GTV at brachytherapy (GTV{sub BT})/'gray zones,' cervix rim/uterine corpus, OAR, vaginal wall, and parametria. Results: The overall ability to visualize the applicator on MRI at brachytherapy was 100%; for the GTV{sub BT}/'gray zones,' cervix rim/uterine corpus, OAR, and vaginal wall, visualization was 98% (overall discrimination quality factors: 1.2, 2.9, 2.1, 1.9, 1.7, and 2.6). Three of 4 borders of parametrial space were defined in more than 98% (discrimination quality factors: 2.9, 2.1, and 1.2). Conclusion: Magnetic resonance imaging provides appropriate information for definition of the applicator, GTV, CTV, pathoanatomic structures, and OAR that enables precise delineation for cervix cancer brachytherapy.

  2. Radiation Therapy Oncology Group Consensus Panel Guidelines for the Delineation of the Clinical Target Volume in the Postoperative Treatment of Pancreatic Head Cancer

    SciTech Connect

    Goodman, Karyn A.; Regine, William F.; Dawson, Laura A.; Ben-Josef, Edgar; Haustermans, Karin; Bosch, Walter R.; Turian, Julius; Abrams, Ross A.

    2012-07-01

    Purpose: To develop contouring guidelines to be used in the Radiation Therapy Oncology Group protocol 0848, a Phase III randomized trial evaluating the benefit of adjuvant chemoradiation in patients with resected head of pancreas cancer. Methods and Materials: A consensus committee of six radiation oncologists with expertise in gastrointestinal radiotherapy developed stepwise contouring guidelines and an atlas for the delineation of the clinical target volume (CTV) in the postoperative treatment of pancreas cancer, based on identifiable regions of interest and margin expansions. Areas at risk for subclinical disease to be included in the CTV were defined, including nodal regions, anastomoses, and the preoperative primary tumor location. Regions of interest that could be reproducibly contoured on postoperative imaging after a pancreaticoduodenectomy were identified. Standardized expansion margins to encompass areas at risk were developed after multiple iterations to determine the optimal margin expansions. Results: New contouring recommendations based on CT anatomy were established. Written guidelines for the delineation of the postoperative CTV and normal tissues, as well as a Web-based atlas, were developed. Conclusions: The postoperative abdomen has been a difficult area for effective radiotherapy. These new guidelines will help physicians create fields that better encompass areas at risk and minimize dose to normal tissues.

  3. Postoperative Intensity-Modulated Radiotherapy for Squamous Cell Carcinoma of the External Auditory Canal and Middle Ear: Treatment Outcomes, Marginal Misses, and Perspective on Target Delineation

    SciTech Connect

    Chen, Wan-Yu; Kuo, Sung-Hsin; Chen, Yu-Hsuan; Lu, Szu-Huai; Tsai, Chiao-Ling; Chia-Hsien Cheng, Jason; Hong, Ruey-Long; Chen, Ya-Fang; Hsu, Chuan-Jen; Lin, Kai-Nan; Ko, Jenq-Yuh; Lou, Pei-Jen; Wang, Cheng-Ping; Chong, Fok-Ching; Wang, Chun-Wei

    2012-03-15

    Purpose: To report outcomes of the rare disease of squamous cell carcinoma (SCC) of the external auditory canal (EAC) and middle ear treated with surgery and postoperative intensity-modulated radiotherapy (IMRT). Failure patterns related to spatial dose distribution were also analyzed to provide insight into target delineation. Methods and Materials: A retrospective review was conducted of the records of 11 consecutive patients with SCC of the EAC and middle ear who were treated with curative surgery and postoperative IMRT at one institution between January 2007 and February 2010. The prescribed IMRT dose was 60 to 66 Gy at 2 Gy per fraction. Three patients also received concurrent cisplatin-based chemotherapy, and 1 patient received concurrent oral tegafur/uracil. The median follow-up time was 19 months (range, 6-33 months). Results: Four patients had locoregional recurrence, yielding an estimated 2-year locoregional control rate of 70.7%. Among them, 1 patient had persistent disease after treatment, and 3 had marginal recurrence. Distant metastasis occurred in 1 patient after extensive locoregional recurrence, yielding an estimated 2-year distant control rate of 85.7%. The estimated 2-year overall survival was 67.5%. The three cases of marginal recurrence were near the preauricular space and glenoid fossa of the temporomandibular joint, adjacent to the apex of the ear canal and glenoid fossa of the temporomandibular joint, and in the postauricular subcutaneous area and ipsilateral parotid nodes, respectively. Conclusions: Marginal misses should be recognized to improve target delineation. When treating SCC of the EAC and middle ear, care should be taken to cover the glenoid fossa of the temporomandibular joint and periauricular soft tissue. Elective ipsilateral parotid irradiation should be considered. The treatment planning procedure should also be refined to balance subcutaneous soft-tissue dosimetry and toxicity.

  4. Treatment Optimization Using Computed Tomography-Delineated Targets Should be Used for Supraclavicular Irradiation for Breast Cancer

    SciTech Connect

    Liengsawangwong, Raweewan; Yu, T.-K.; Sun, T.-L.; Erasmus, Jeremy J.; Perkins, George H.; Tereffe, Welela; Oh, Julia L.; Woodward, Wendy A.; Strom, Eric A.; Salephour, Mohammad; Buchholz, Thomas A.

    2007-11-01

    Background: The purpose of this study was to determine whether the use of optimized CT treatment planning offered better coverage of axillary level III (LIII)/supraclavicular (SC) targets than the empirically derived dose prescription that are commonly used. Materials/Methods: Thirty-two consecutive breast cancer patients who underwent CT treatment planning of a SC field were evaluated. Each patient was categorized according to body mass index (BMI) classes: normal, overweight, or obese. The SC and LIII nodal beds were contoured, and four treatment plans for each patient were generated. Three of the plans used empiric dose prescriptions, and these were compared with a CT-optimized plan. Each plan was evaluated by two criteria: whether 98% of target volume receive >90% of prescribed dose and whether < 5% of the irradiated volume received 105% of prescribed dose. Results: The mean depth of SC and LIII were 3.2 cm (range, 1.4-6.7 cm) and 3.1 (range, 1.7-5.8 cm). The depth of these targets varied according across BMI classes (p = 0.01). Among the four sets of plans, the CT-optimized plans were the most successful at achieving both of the dosimetry objectives for every BMI class (normal BMI, p = .003; overweight BMI, p < .0001; obese BMI, p < .001). Conclusions: Across all BMI classes, routine radiation prescriptions did not optimally cover intended targets for every patient. Optimized CT-based treatment planning generated the most successful plans; therefore, we recommend the use of routine CT simulation and treatment planning of SC fields in breast cancer.

  5. L-[METHYL-{sup 11}C] Methionine Positron Emission Tomography for Target Delineation in Malignant Gliomas: Impact on Results of Carbon Ion Radiotherapy

    SciTech Connect

    Mahasittiwat, Pawinee; Mizoe, Jun-etsu Hasegawa, Azusa; Ishikawa, Hiroyuki; Yoshikawa, Kyosan; Mizuno, Hideyuki; Yanagi, Takeshi; Takagi, Ryou D.D.S.; Pattaranutaporn, Pittayapoom; Tsujii, Hirohiko

    2008-02-01

    Purpose: To assess the importance of {sup 11}C-methionine (MET)-positron emission tomography (PET) for clinical target volume (CTV) delineation. Methods and Materials: This retrospective study analyzed 16 patients with malignant glioma (4 patients, anaplastic astrocytoma; 12 patients, glioblastoma multiforme) treated with surgery and carbon ion radiotherapy from April 2002 to Nov 2005. The MET-PET target volume was compared with gross tumor volume and CTV, defined by using computed tomography/magnetic resonance imaging (MRI). Correlations with treatment results were evaluated between positive and negative extended volumes (EVs) of the MET-PET target for CTV. Results: Mean volumes of the MET-PET targets, CTV1 (defined by means of high-intensity volume on T2-weighted MRI), and CTV2 (defined by means of contrast-enhancement volume on T1-weighted MRI) were 6.35, 264.7, and 117.7 cm{sup 3}, respectively. Mean EVs of MET-PET targets for CTV1 and CTV2 were 0.6 and 2.2 cm{sup 3}, respectively. The MET-PET target volumes were included in CTV1 and CTV2 in 13 (81.3%) and 11 patients (68.8%), respectively. Patients with a negative EV for CTV1 had significantly greater survival rate (p = 0.0069), regional control (p = 0.0047), and distant control time (p = 0.0267) than those with a positive EV. Distant control time also was better in patients with a negative EV for CTV2 than those with a positive EV (p = 0.0401). Conclusions: For patients with malignant gliomas, MET-PET has a possibility to be a predictor of outcome in carbon ion radiotherapy. Direct use of MET-PET fused to planning computed tomography will be useful and yield favorable results for the therapy.

  6. Gene network inference and biochemical assessment delineates GPCR pathways and CREB targets in small intestinal neuroendocrine neoplasia.

    PubMed

    Drozdov, Ignat; Svejda, Bernhard; Gustafsson, Bjorn I; Mane, Shrikant; Pfragner, Roswitha; Kidd, Mark; Modlin, Irvin M

    2011-01-01

    Small intestinal (SI) neuroendocrine tumors (NET) are increasing in incidence, however little is known about their biology. High throughput techniques such as inference of gene regulatory networks from microarray experiments can objectively define signaling machinery in this disease. Genome-wide co-expression analysis was used to infer gene relevance network in SI-NETs. The network was confirmed to be non-random, scale-free, and highly modular. Functional analysis of gene co-expression modules revealed processes including 'Nervous system development', 'Immune response', and 'Cell-cycle'. Importantly, gene network topology and differential expression analysis identified over-expression of the GPCR signaling regulators, the cAMP synthetase, ADCY2, and the protein kinase A, PRKAR1A. Seven CREB response element (CRE) transcripts associated with proliferation and secretion: BEX1, BICD1, CHGB, CPE, GABRB3, SCG2 and SCG3 as well as ADCY2 and PRKAR1A were measured in an independent SI dataset (n = 10 NETs; n = 8 normal preparations). All were up-regulated (p<0.035) with the exception of SCG3 which was not differently expressed. Forskolin (a direct cAMP activator, 10(-5) M) significantly stimulated transcription of pCREB and 3/7 CREB targets, isoproterenol (a selective ß-adrenergic receptor agonist and cAMP activator, 10(-5) M) stimulated pCREB and 4/7 targets while BIM-53061 (a dopamine D(2) and Serotonin [5-HT(2)] receptor agonist, 10(-6) M) stimulated 100% of targets as well as pCREB; CRE transcription correlated with the levels of cAMP accumulation and PKA activity; BIM-53061 stimulated the highest levels of cAMP and PKA (2.8-fold and 2.5-fold vs. 1.8-2-fold for isoproterenol and forskolin). Gene network inference and graph topology analysis in SI NETs suggests that SI NETs express neural GPCRs that activate different CRE targets associated with proliferation and secretion. In vitro studies, in a model NET cell system, confirmed that transcriptional effects are

  7. Contribution of {sup 68}Ga-DOTATOC PET/CT to Target Volume Delineation of Skull Base Meningiomas Treated With Stereotactic Radiation Therapy

    SciTech Connect

    Graf, Reinhold; Nyuyki, Fonyuy; Steffen, Ingo G.; Michel, Roger; Fahdt, Daniel; Wust, Peter; Brenner, Winfried; Budach, Volker; Wurm, Reinhard; Plotkin, Michail

    2013-01-01

    Purpose: To investigate the potential impact of {sup 68}Ga-DOTATOC positron emission tomography ({sup 68}Ga-DOTATOC-PET) in addition to magnetic resonance imaging (MRI) and computed tomography (CT) for retrospectively assessing the gross tumor volume (GTV) delineation of meningiomas of the skull base in patients treated with fractionated stereotactic radiation therapy (FSRT). Methods and Materials: The study population consisted of 48 patients with 54 skull base meningiomas, previously treated with FSRT. After scans were coregistered, the GTVs were first delineated with MRI and CT data (GTV{sub MRI/CT}) and then by PET (GTV{sub PET}) data. The overlapping regions of both datasets resulted in the GTV{sub common}, which was enlarged to the GTV{sub final} by adding volumes defined by only one of the complementary modalities (GTV{sub MRI/CT-added} or GTV{sub PET-added}). We then evaluated the contribution of conventional imaging modalities (MRI, CT) and {sup 68}Ga-DOTATOC-PET to the GTV{sub final}, which was used for planning purposes. Results: Forty-eight of the 54 skull base lesions in 45 patients showed increased {sup 68}Ga-DOTATOC uptake and were further analyzed. The mean GTV{sub MRI/CT} and GTV{sub PET} were approximately 21 cm{sup 3} and 25 cm{sup 3}, with a common volume of approximately 15 cm{sup 3}. PET contributed a mean additional GTV of approximately 1.5 cm{sup 3} to the common volume (16% {+-} 34% of the GTV{sub common}). Approximately 4.5 cm{sup 3} of the GTV{sub MRI/CT} was excluded from the contribution to the common volume. The resulting mean GTV{sub final} was significantly smaller than both the GTV{sub MRI/CT} and the GTV{sub PET}. Compared with the initial GTV{sub MRI/CT}, the addition of {sup 68}Ga-DOTATOC-PET resulted in more than 10% modification of the size of the GTV{sub final} in 32 (67%) meningiomas Conclusions: {sup 68}Ga-DOTATOC-PET/CT seems to improve the target volume delineation in skull base meningiomas, often leading to a reduction of

  8. Delineation of clinical target volume for postoperative radiotherapy in stage IIIA-pN2 non-small-cell lung cancer

    PubMed Central

    Jing, Xuquan; Meng, Xue; Sun, Xindong; Yu, Jinming

    2016-01-01

    With the high locoregional relapse rate and the improvement of radiation technology, postoperative radiotherapy (PORT) has been widely used in the treatment of completely resected stage IIIA-pN2 non-small-cell lung cancer (NSCLC). However, there is still no definitive consensus on clinical target volume for the pN2 subgroup. This review will discuss how to delineate the clinical target volume (CTV) for pN2 subgroups of IIIA-N2 NSCLC based on the published literature and to investigate the optimal PORT CTV in this cohort of patients. Besides overall survival (OS), locoregional recurrence (LR), and radiotherapy-related toxicity of this subset of the population in the modern PORT era, selection of proper patients will also be considered in this review. In summary, it is appropriate to include involved lymph node stations and uninvolved stations at high risk in PORT CTV for patients with pN2 disease when PORT is administered. PORT can reduce LR and has the potential to improve OS. In the current era of modern radiation technology, PORT can be administered safely with well-tolerated toxicity. Clinicopathological characteristics may be helpful in selecting proper candidates for PORT. PMID:26929651

  9. Magnetic Resonance Imaging-Based Target Volume Delineation in Radiation Therapy Treatment Planning for Brain Tumors Using Localized Region-Based Active Contour

    SciTech Connect

    Aslian, Hossein; Sadeghi, Mahdi; Mahdavi, Seied Rabie; Babapour Mofrad, Farshid; Astarakee, Mahdi; Khaledi, Navid; Fadavi, Pedram

    2013-09-01

    Purpose: To evaluate the clinical application of a robust semiautomatic image segmentation method to determine the brain target volumes in radiation therapy treatment planning. Methods and Materials: A local robust region-based algorithm was used on MRI brain images to study the clinical target volume (CTV) of several patients. First, 3 oncologists delineated CTVs of 10 patients manually, and the process time for each patient was calculated. The averages of the oncologists’ contours were evaluated and considered as reference contours. Then, to determine the CTV through the semiautomatic method, a fourth oncologist who was blind to all manual contours selected 4-8 points around the edema and defined the initial contour. The time to obtain the final contour was calculated again for each patient. Manual and semiautomatic segmentation were compared using 3 different metric criteria: Dice coefficient, Hausdorff distance, and mean absolute distance. A comparison also was performed between volumes obtained from semiautomatic and manual methods. Results: Manual delineation processing time of tumors for each patient was dependent on its size and complexity and had a mean (±SD) of 12.33 ± 2.47 minutes, whereas it was 3.254 ± 1.7507 minutes for the semiautomatic method. Means of Dice coefficient, Hausdorff distance, and mean absolute distance between manual contours were 0.84 ± 0.02, 2.05 ± 0.66 cm, and 0.78 ± 0.15 cm, and they were 0.82 ± 0.03, 1.91 ± 0.65 cm, and 0.7 ± 0.22 cm between manual and semiautomatic contours, respectively. Moreover, the mean volume ratio (=semiautomatic/manual) calculated for all samples was 0.87. Conclusions: Given the deformability of this method, the results showed reasonable accuracy and similarity to the results of manual contouring by the oncologists. This study shows that the localized region-based algorithms can have great ability in determining the CTV and can be appropriate alternatives for manual approaches in brain cancer.

  10. Quantitative comparison of delineated structure shape in radiotherapy

    NASA Astrophysics Data System (ADS)

    Price, G. J.; Moore, C. J.

    2006-03-01

    There has been an influx of imaging and treatment technologies into cancer radiotherapy over the past fifteen years. The result is that radiation fields can now be accurately shaped to target disease delineated on pre-treatment planning scans whilst sparing critical healthy structures. Two well known problems remain causes for concern. The first is inter- and intra-observer variability in planning scan delineations, the second is the motion and deformation of a tumour and interacting adjacent organs during the course of radiotherapy which compromise the planned targeting regime. To be able to properly address these problems, and hence accurately shape the margins of error used to account for them, an intuitive and quantitative system of describing this variability must be used. This paper discusses a method of automatically creating correspondence points over similar non-polar delineation volumes, via spherical parameterisation, so that their shape variability can be analysed as a set of independent one dimensional statistical problems. The importance of 'pole' selection to initial parameterisation and hence ease of optimisation is highlighted, the use of sparse anatomical landmarks rather than spherical harmonic expansion for establishing point correspondence discussed, and point variability mapping introduced. A case study is presented to illustrate the method. A group of observers were asked to delineate a rectum on a series of time-of-treatment Cone Beam CT scans over a patient's fractionation schedule. The overall observer variability was calculated using the above method and the significance of the organ motion over time evaluated.

  11. Accurate State Estimation and Tracking of a Non-Cooperative Target Vehicle

    NASA Technical Reports Server (NTRS)

    Thienel, Julie K.; Sanner, Robert M.

    2006-01-01

    Autonomous space rendezvous scenarios require knowledge of the target vehicle state in order to safely dock with the chaser vehicle. Ideally, the target vehicle state information is derived from telemetered data, or with the use of known tracking points on the target vehicle. However, if the target vehicle is non-cooperative and does not have the ability to maintain attitude control, or transmit attitude knowledge, the docking becomes more challenging. This work presents a nonlinear approach for estimating the body rates of a non-cooperative target vehicle, and coupling this estimation to a tracking control scheme. The approach is tested with the robotic servicing mission concept for the Hubble Space Telescope (HST). Such a mission would not only require estimates of the HST attitude and rates, but also precision control to achieve the desired rate and maintain the orientation to successfully dock with HST.

  12. Watch the target! Effects in the affective misattribution procedure become weaker (but not eliminated) when participants are motivated to provide accurate responses to the target

    PubMed Central

    Eder, Andreas B.; Deutsch, Roland

    2015-01-01

    Previous research showed that priming effects in the affective misattribution procedure (AMP) are unaffected by direct warnings to avoid an influence of the primes. The present research examined whether a priming influence is diminished by task procedures that encourage accurate judgments of the targets. Participants were motivated to categorize the affective meaning of nonsense targets accurately by being made to believe that a true word was presented in each trial and by providing feedback on (allegedly) incorrect responses. This condition produced robust priming effects. Priming was however reduced and less reliable relative to more typical AMP conditions in which participants guessed the meaning of openly presented nonsense targets. Affective judgments of nonsense targets were not affected by advance knowledge of the response mapping during the priming phase, which argues against a response-priming explanation of AMP effects. These findings show that affective primes influence evaluative judgments even in conditions in which the motivation to provide accurate responses is high and a priming of motor responses is not possible. Priming effects were however weaker with high accuracy motivation, suggesting that a focus on accurate judgments is an effective strategy to control for an unwanted priming influence in the AMP. PMID:26441807

  13. Watch the target! Effects in the affective misattribution procedure become weaker (but not eliminated) when participants are motivated to provide accurate responses to the target.

    PubMed

    Eder, Andreas B; Deutsch, Roland

    2015-01-01

    Previous research showed that priming effects in the affective misattribution procedure (AMP) are unaffected by direct warnings to avoid an influence of the primes. The present research examined whether a priming influence is diminished by task procedures that encourage accurate judgments of the targets. Participants were motivated to categorize the affective meaning of nonsense targets accurately by being made to believe that a true word was presented in each trial and by providing feedback on (allegedly) incorrect responses. This condition produced robust priming effects. Priming was however reduced and less reliable relative to more typical AMP conditions in which participants guessed the meaning of openly presented nonsense targets. Affective judgments of nonsense targets were not affected by advance knowledge of the response mapping during the priming phase, which argues against a response-priming explanation of AMP effects. These findings show that affective primes influence evaluative judgments even in conditions in which the motivation to provide accurate responses is high and a priming of motor responses is not possible. Priming effects were however weaker with high accuracy motivation, suggesting that a focus on accurate judgments is an effective strategy to control for an unwanted priming influence in the AMP. PMID:26441807

  14. Accurate microRNA target prediction correlates with protein repression levels

    PubMed Central

    Maragkakis, Manolis; Alexiou, Panagiotis; Papadopoulos, Giorgio L; Reczko, Martin; Dalamagas, Theodore; Giannopoulos, George; Goumas, George; Koukis, Evangelos; Kourtis, Kornilios; Simossis, Victor A; Sethupathy, Praveen; Vergoulis, Thanasis; Koziris, Nectarios; Sellis, Timos; Tsanakas, Panagiotis; Hatzigeorgiou, Artemis G

    2009-01-01

    Background MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pairing of the microRNA to sites in the messenger RNA of protein coding genes. Since experimental identification of miRNA target genes poses difficulties, computational microRNA target prediction is one of the key means in deciphering the role of microRNAs in development and disease. Results DIANA-microT 3.0 is an algorithm for microRNA target prediction which is based on several parameters calculated individually for each microRNA and combines conserved and non-conserved microRNA recognition elements into a final prediction score, which correlates with protein production fold change. Specifically, for each predicted interaction the program reports a signal to noise ratio and a precision score which can be used as an indication of the false positive rate of the prediction. Conclusion Recently, several computational target prediction programs were benchmarked based on a set of microRNA target genes identified by the pSILAC method. In this assessment DIANA-microT 3.0 was found to achieve the highest precision among the most widely used microRNA target prediction programs reaching approximately 66%. The DIANA-microT 3.0 prediction results are available online in a user friendly web server at PMID:19765283

  15. Precision Pointing Control to and Accurate Target Estimation of a Non-Cooperative Vehicle

    NASA Technical Reports Server (NTRS)

    VanEepoel, John; Thienel, Julie; Sanner, Robert M.

    2006-01-01

    In 2004, NASA began investigating a robotic servicing mission for the Hubble Space Telescope (HST). Such a mission would not only require estimates of the HST attitude and rates in order to achieve capture by the proposed Hubble Robotic Vehicle (HRV), but also precision control to achieve the desired rate and maintain the orientation to successfully dock with HST. To generalize the situation, HST is the target vehicle and HRV is the chaser. This work presents a nonlinear approach for estimating the body rates of a non-cooperative target vehicle, and coupling this estimation to a control scheme. Non-cooperative in this context relates to the target vehicle no longer having the ability to maintain attitude control or transmit attitude knowledge.

  16. Non-targeted screening of house dust samples using accurate mass TOFMS

    EPA Science Inventory

    House dust exists as an environmental repository of chemicals to which we are exposed in our homes. A growing number of studies have targeted select persistent organic and inorganic pollutants found in house dust. Many have concluded that dust exists as an important human expos...

  17. Automated Crater Delineation

    NASA Astrophysics Data System (ADS)

    Marques, J. S.; Pina, P.

    2015-05-01

    An algorithm to delineate impact craters based on Edge Maps and Dynamic Programming is presented. The global performance obtained on 1045 craters from Mars (5 m to about 200 km in diameter), achieved 96% of correct contour delineations.

  18. Improved targeting device and computer navigation for accurate placement of brachytherapy needles

    SciTech Connect

    Pappas, Ion P.I.; Ryan, Paul; Cossmann, Peter; Kowal, Jens; Borgeson, Blake; Caversaccio, Marco

    2005-06-15

    Successful treatment of skull base tumors with interstitial brachytherapy requires high targeting accuracy for the brachytherapy needles to avoid harming vital anatomical structures. To enable safe placement of the needles in this area, we developed an image-based planning and navigation system for brachytherapy, which includes a custom-made mechanical positioning arm that allows rough and fine adjustment of the needle position. The fine-adjustment mechanism consists of an XYZ microstage at the base of the arm and a needle holder with two fine-adjustable inclinations. The rotation axes of the inclinations cross at the tip of the needle so that the inclinational adjustments do not interfere with the translational adjustments. A vacuum cushion and a noninvasive fixation frame are used for the head immobilization. To avoid mechanical bending of the needles due to the weight of attached tracking markers, which would be detrimental for targeting accuracy, only a single LED marker on the tail of the needle is used. An experimental phantom-based targeting study with this setup demonstrated that a positioning accuracy of 1.4 mm (rms) can be achieved. The study showed that the proposed setup allows brachytherapy needles to be easily aligned and inserted with high targeting accuracy according to a preliminary plan. The achievable accuracy is higher than if the needles are inserted manually. The proposed system can be linked to a standard afterloader and standard dosimetry planning module. The associated additional effort is reasonable for the clinical practice and therefore the proposed procedure provides a promising tool for the safe treatment of tumors in the skull base area.

  19. Integrated-boost IMRT or 3-D-CRT using FET-PET based auto-contoured target volume delineation for glioblastoma multiforme - a dosimetric comparison

    PubMed Central

    2009-01-01

    Background Biological brain tumor imaging using O-(2-[18F]fluoroethyl)-L-tyrosine (FET)-PET combined with inverse treatment planning for locally restricted dose escalation in patients with glioblastoma multiforme seems to be a promising approach. The aim of this study was to compare inverse with forward treatment planning for an integrated boost dose application in patients suffering from a glioblastoma multiforme, while biological target volumes are based on FET-PET and MRI data sets. Methods In 16 glioblastoma patients an intensity-modulated radiotherapy technique comprising an integrated boost (IB-IMRT) and a 3-dimensional conventional radiotherapy (3D-CRT) technique were generated for dosimetric comparison. FET-PET, MRI and treatment planning CT (P-CT) were co-registrated. The integrated boost volume (PTV1) was auto-contoured using a cut-off tumor-to-brain ratio (TBR) of ≥ 1.6 from FET-PET. PTV2 delineation was MRI-based. The total dose was prescribed to 72 and 60 Gy for PTV1 and PTV2, using daily fractions of 2.4 and 2 Gy. Results After auto-contouring of PTV1 a marked target shape complexity had an impact on the dosimetric outcome. Patients with 3-4 PTV1 subvolumes vs. a single volume revealed a significant decrease in mean dose (67.7 vs. 70.6 Gy). From convex to complex shaped PTV1 mean doses decreased from 71.3 Gy to 67.7 Gy. The homogeneity and conformity for PTV1 and PTV2 was significantly improved with IB-IMRT. With the use of IB-IMRT the minimum dose within PTV1 (61.1 vs. 57.4 Gy) and PTV2 (51.4 vs. 40.9 Gy) increased significantly, and the mean EUD for PTV2 was improved (59.9 vs. 55.3 Gy, p < 0.01). The EUD for PTV1 was only slightly improved (68.3 vs. 67.3 Gy). The EUD for the brain was equal with both planning techniques. Conclusion In the presented planning study the integrated boost concept based on inversely planned IB-IMRT is feasible. The FET-PET-based automatically contoured PTV1 can lead to very complex geometric configurations, limiting the

  20. Comparison and Consensus Guidelines for Delineation of Clinical Target Volume for CT- and MR-Based Brachytherapy in Locally Advanced Cervical Cancer

    SciTech Connect

    Viswanathan, Akila N.; Gaffney, David K.; Beriwal, Sushil; Bhatia, Sudershan K.; Lee Burnett, Omer; D'Souza, David P.; Patil, Nikhilesh; Haddock, Michael G.; Jhingran, Anuja; Jones, Ellen L.; Kunos, Charles A.; Lee, Larissa J.; Mayr, Nina A.; Petersen, Ivy; Petric, Primoz; Portelance, Lorraine; Small, William; Strauss, Jonathan B.; and others

    2014-10-01

    Objective: To create and compare consensus clinical target volume (CTV) contours for computed tomography (CT) and 3-Tesla (3-T) magnetic resonance (MR) image-based cervical-cancer brachytherapy. Methods and Materials: Twenty-three experts in gynecologic radiation oncology contoured the same 3 cervical cancer brachytherapy cases: 1 stage IIB near-complete response (CR) case with a tandem and ovoid, 1 stage IIB partial response (PR) case with tandem and ovoid with needles, and 1 stage IB2 CR case with a tandem and ring applicator. The CT contours were completed before the MRI contours. These were analyzed for consistency and clarity of target delineation using an expectation maximization algorithm for simultaneous truth and performance level estimation (STAPLE), with κ statistics as a measure of agreement between participants. The conformity index was calculated for each of the 6 data sets. Dice coefficients were generated to compare the CT and MR contours of the same case. Results: For all 3 cases, the mean tumor volume was smaller on MR than on CT (P<.001). The κ and conformity index estimates were slightly higher for CT, indicating a higher level of agreement on CT. The Dice coefficients were 89% for the stage IB2 case with a CR, 74% for the stage IIB case with a PR, and 57% for the stage IIB case with a CR. Conclusion: In a comparison of MR-contoured with CT-contoured CTV volumes, the higher level of agreement on CT may be due to the more distinct contrast medium visible on the images at the time of brachytherapy. MR at the time of brachytherapy may be of greatest benefit in patients with large tumors with parametrial extension that have a partial or complete response to external beam. On the basis of these results, a 95% consensus volume was generated for CT and for MR. Online contouring atlases are available for instruction at (http://www.nrgoncology.org/Resources/ContouringAtlases/GYNCervicalBrachytherapy.aspx)

  1. A Pilot Prospective Feasibility Study of Organ-at-Risk Definition using Target Contour Testing/Instructional Computer Software (TaCTICS), a Training and Evaluation Platform for Radiotherapy Target Delineation.

    PubMed Central

    Kalpathy-Cramer, Jayashree; Bedrick, Steven D.; Boccia, Kelly; Fuller, Clifton D.

    2011-01-01

    Target volume delineation is a critical, but time-consuming step in the creation of radiation therapy plans used in the treatment of many types of cancer. However, variability in target volume definitions can introduce substantial differences in resulting doses to tumors and critical structures. We developed TaCTICS, a web-based educational training software application targeted towards non-expert users. We report on a small, prospective study to evaluate the utility of this online tool in improving conformance of regions-of-interest (ROIs) with a reference set. Eight residents contoured a set of structures for a head-and-neck cancer case. Subsequently, they were provided access to TaCTICS as well as contouring atlases to allow evaluation of their contours in reference to other users as well as reference ROIs. The residents then contoured a second case using these resources. Volume overlap metrics between the users showed a substantial improvement following the intervention. Additionally, 66% of users reported that they found TaCTICS to be a useful educational tool and all participants reported they would like to use TaCTICS to track their contouring skills over the course of their residency. PMID:22195121

  2. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing.

    PubMed

    Guo, Xiaoge; Lehner, Kevin; O'Connell, Karen; Zhang, Jenny; Dave, Sandeep S; Jinks-Robertson, Sue

    2015-12-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  3. SMRT Sequencing for Parallel Analysis of Multiple Targets and Accurate SNP Phasing

    PubMed Central

    Guo, Xiaoge; Lehner, Kevin; O’Connell, Karen; Zhang, Jenny; Dave, Sandeep S.; Jinks-Robertson, Sue

    2015-01-01

    Single-molecule real-time (SMRT) sequencing generates much longer reads than other widely used next-generation (next-gen) sequencing methods, but its application to whole genome/exome analysis has been limited. Here, we describe the use of SMRT sequencing coupled with barcoding to simultaneously analyze one or a small number of genomic targets derived from multiple sources. In the budding yeast system, SMRT sequencing was used to analyze strand-exchange intermediates generated during mitotic recombination and to analyze genetic changes in a forward mutation assay. The general barcoding-SMRT approach was then extended to diffuse large B-cell lymphoma primary tumors and cell lines, where detected changes agreed with prior Illumina exome sequencing. A distinct advantage afforded by SMRT sequencing over other next-gen methods is that it immediately provides the linkage relationships between SNPs in the target segment sequenced. The strength of our approach for mutation/recombination studies (as well as linkage identification) derives from its inherent computational simplicity coupled with a lack of reliance on sophisticated statistical analyses. PMID:26497143

  4. DCP-collected absolute target reflectance signatures assist accurate interpretation of ERTS-1 imagery

    NASA Technical Reports Server (NTRS)

    Weber, F. P.

    1973-01-01

    Data collection platforms (DCP's) are being used at a Black Hills, South Dakota, test site (MMC 226A) to record radiometric measurements needed to determine solar and atmospheric parameters that affect ERTS-1 multispectral scanner radiance measurements. A total of 72 channels of analog data transmitted from an unattended ground truth site via three DCP's at least six times a day. The system has operated with only minor problems since September, sending forth daily measurements of biophysical responses and atmospheric conditions. Comparisons of scene radiance data calculated from ERTS images with that measured on the ground show the image-measured values to be 35 percent higher for the green channel and 20 percent higher for the red channel for the same scene targets. Radiance values for channels 6 and 7 are nearly the same from the ground data and from the imagery.

  5. Noninvasive, accurate assessment of the behavior of representative populations of motor units in targeted reinnervated muscles.

    PubMed

    Farina, Dario; Rehbaum, Hubertus; Holobar, Aleš; Vujaklija, Ivan; Jiang, Ning; Hofer, Christian; Salminger, Stefan; van Vliet, Hans-Willem; Aszmann, Oskar C

    2014-07-01

    Targeted muscle reinnervation (TMR) redirects nerves that have lost their target, due to amputation, to remaining muscles in the region of the stump with the intent of establishing intuitive myosignals to control a complex prosthetic device. In order to directly recover the neural code underlying an attempted limb movement, in this paper, we present the decomposition of high-density surface electromyographic (EMG) signals detected from three TMR patients into the individual motor unit spike trains. The aim was to prove, for the first time, the feasibility of decoding the neural drive that would reach muscles of the missing limb in TMR patients, to show the accuracy of the decoding, and to demonstrate the representativeness of the pool of extracted motor units. Six to seven flexible EMG electrode grids of 64 electrodes each were mounted over the reinnervated muscles of each patient, resulting in up to 448 EMG signals. The subjects were asked to attempt elbow extension and flexion, hand open and close, wrist extension and flexion, wrist pronation and supination, of their missing limb. The EMG signals were decomposed using the Convolution Kernel Compensation technique and the decomposition accuracy was evaluated with a signal-based index of accuracy, called pulse-to-noise ratio (PNR). The results showed that the spike trains of 3 to 27 motor units could be identified for each task, with a sensitivity of the decomposition > 90%, as revealed by PNR. The motor unit discharge rates were within physiological values of normally innervated muscles. Moreover, the detected motor units showed a high degree of common drive so that the set of extracted units per task was representative of the behavior of the population of active units. The results open a path for a new generation of human-machine interfaces in which the control signals are extracted from noninvasive recordings and the obtained neural information is based directly on the spike trains of motor neurons. PMID

  6. Rapid and accurate tumor-target bio-imaging through specific in vivo biosynthesis of a fluorescent europium complex.

    PubMed

    Ye, Jing; Wang, Jianling; Li, Qiwei; Dong, Xiawei; Ge, Wei; Chen, Yun; Jiang, Xuerui; Liu, Hongde; Jiang, Hui; Wang, Xuemei

    2016-04-22

    A new and facile method for rapidly and accurately achieving tumor targeting fluorescent images has been explored using a specifically biosynthesized europium (Eu) complex in vivo and in vitro. It demonstrated that a fluorescent Eu complex could be bio-synthesized through a spontaneous molecular process in cancerous cells and tumors, but not prepared in normal cells and tissues. In addition, the proteomics analyses show that some biological pathways of metabolism, especially for NADPH production and glutamine metabolism, are remarkably affected during the relevant biosynthesis process, where molecular precursors of europium ions are reduced to fluorescent europium complexes inside cancerous cells or tumor tissues. These results proved that the specific self-biosynthesis of a fluorescent Eu complex by cancer cells or tumor tissues can provide a new strategy for accurate diagnosis and treatment strategies in the early stages of cancers and thus is beneficial for realizing precise surgical intervention based on the relevant cheap and readily available agents. PMID:26810592

  7. Failure of target heart rate to accurately monitor intensity during aerobic dance.

    PubMed

    Parker, S B; Hurley, B F; Hanlon, D P; Vaccaro, P

    1989-04-01

    Fourteen untrained females (age 19 +/- 1, range 18-21) were studied to examine the heart rate-VO2 relationship during a single aerobic dance training session. These findings were used to help explain the changes in VO2max resulting from an aerobic dance training program. VO2max and body composition were determined before and after an 8 wk training period. In addition, the heart rate-VO2 responses to an aerobic dance training session were monitored and compared to the heart rate responses of treadmill jogging performed at the same VO2. The aerobic dance session elicited a significantly lower oxygen pulse than did treadmill exercise (7.2 +/- 0.3 vs 8.1 +/- 0.8 ml.beat-1; P less than 0.01). There were no significant changes in percent body fat, whereas VO2max increased by 11% (34.4 +/- 0.9 vs 38.1 +/- 0.8 ml.kg-1.min-1; P less than 0.05). No significant changes in any of the parameters tested were observed in 10 untrained controls. These findings indicate that the heart rate elicited from aerobic dance represents a lower relative exercise intensity (VO2) than that of running. Therefore, the assumption that aerobic dance training produces the same cardiovascular adaptations as running training when performed at the same target rate may be unwarranted. PMID:2709986

  8. SU-E-J-76: Incorporation of Ultrasound Elastography in Target Volume Delineation for Partial Breast Radiotherapy Planning: A Comparative Study

    SciTech Connect

    Juneja, P; Harris, E; Bamber, J

    2014-06-01

    Purpose: There is substantial observer variability in the delineation of target volumes for post-surgical partial breast radiotherapy because the tumour bed has poor x-ray contrast. This variability may result in substantial variations in planned dose distribution. Ultrasound elastography (USE) has an ability to detect mechanical discontinuities and therefore, the potential to image the scar and distortion in breast tissue architecture. The goal of this study was to compare USE techniques: strain elastography (SE), shear wave elastography (SWE) and acoustic radiation force impulse (ARFI) imaging using phantoms that simulate features of the tumour bed, for the purpose of incorporating USE in breast radiotherapy planning. Methods: Three gelatine-based phantoms (10% w/v) containing: a stiff inclusion (gelatine 16% w/v) with adhered boundaries, a stiff inclusion (gelatine 16% w/v) with mobile boundaries and fluid cavity inclusion (to mimic seroma), were constructed and used to investigate the USE techniques. The accuracy of the elastography techniques was quantified by comparing the imaged inclusion with the modelled ground-truth using the Dice similarity coefficient (DSC). For two regions of interest (ROI), the DSC measures their spatial overlap. Ground-truth ROIs were modelled using geometrical measurements from B-mode images. Results: The phantoms simulating stiff scar tissue with adhered and mobile boundaries and seroma were successfully developed and imaged using SE and SWE. The edges of the stiff inclusions were more clearly visible in SE than in SWE. Subsequently, for all these phantoms the measured DSCs were found to be higher for SE (DSCs: 0.91–0.97) than SWE (DSCs: 0.68–0.79) with an average relative difference of 23%. In the case of seroma phantom, DSC values for SE and SWE were similar. Conclusion: This study presents a first attempt to identify the most suitable elastography technique for use in breast radiotherapy planning. Further analysis will

  9. Accurate guidance for percutaneous access to a specific target in soft tissues: preclinical study of computer-assisted pericardiocentesis.

    PubMed

    Chavanon, O; Barbe, C; Troccaz, J; Carrat, L; Ribuot, C; Noirclerc, M; Maitrasse, B; Blin, D

    1999-06-01

    In the field of percutaneous access to soft tissues, our project was to improve classical pericardiocentesis by performing accurate guidance to a selected target, according to a model of the pericardial effusion acquired through three-dimensional (3D) data recording. Required hardware is an echocardiographic device and a needle, both linked to a 3D localizer, and a computer. After acquiring echographic data, a modeling procedure allows definition of the optimal puncture strategy, taking into consideration the mobility of the heart, by determining a stable region, whatever the period of the cardiac cycle. A passive guidance system is then used to reach the planned target accurately, generally a site in the middle of the stable region. After validation on a dynamic phantom and a feasibility study in dogs, an accuracy and reliability analysis protocol was realized on pigs with experimental pericardial effusion. Ten consecutive successful punctures using various trajectories were performed on eight pigs. Nonbloody liquid was collected from pericardial effusions in the stable region (5 to 9 mm wide) within 10 to 15 minutes from echographic acquisition to drainage. Accuracy of at least 2.5 mm was demonstrated. This study demonstrates the feasibility of computer-assisted pericardiocentesis. Beyond the simple improvement of the current technique, this method could be a new way to reach the heart or a new tool for percutaneous access and image-guided puncture of soft tissues. Further investigation will be necessary before routine human application. PMID:10414543

  10. Automated individual tree crown delineation from LIDAR data using morphological techniques

    NASA Astrophysics Data System (ADS)

    Jing, L.; Hu, B.; Li, H.; Li, J.; Noland, T.

    2014-03-01

    In current tree crown delineation from LiDAR data, treetops and 3D geometric shapes of tree crowns are frequently extracted from LiDAR-derived Crown Height Model (CHM) and used as references to localize and delineate crowns. However, it is difficult to detect deciduous treetops and delineate deciduous tree crowns. The 3D shape of a crown, which can be derived from CHM, may be taken as a half ellipsoid, and any horizontal slice of the ellipsoid contains the treetop and indicates not only the location but also the spatial extent of the crown. Based on such slices, a novel multi-scale method for individual tree crown delineation from CHM was proposed in this study. This method consists mainly of two steps: (1) morphologically open the CHM over the scale range of target tree crowns; and (2) take local maxima within each resulting opened CHM as the horizontal slices of target crowns at the corresponding scale level and integrate all the slices within the scale range together to represent the spatial distribution of target crowns. In an experiment on CHMs over two natural closed canopy forests in Ontario, Canada, the proposed method accurately delineated the majority of the tree crowns from closed canopy forests.

  11. {sup 18}F-Fluorodeoxyglucose Positron Emission Tomography/Computed Tomography-Based Radiotherapy Target Volume Definition in Non-Small-Cell Lung Cancer: Delineation by Radiation Oncologists vs. Joint Outlining With a PET Radiologist?

    SciTech Connect

    Hanna, Gerard G.; Carson, Kathryn J.; Lynch, Tom; McAleese, Jonathan; Cosgrove, Vivian P.; Eakin, Ruth L.; Stewart, David P.; Zatari, Ashraf; O'Sullivan, Joe M.; Hounsell, Alan R.

    2010-11-15

    Purpose: {sup 18}F-Fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) has benefits in target volume (TV) definition in radiotherapy treatment planning (RTP) for non-small-cell lung cancer (NSCLC); however, an optimal protocol for TV delineation has not been determined. We investigate volumetric and positional variation in gross tumor volume (GTV) delineation using a planning PET/CT among three radiation oncologists and a PET radiologist. Methods and Materials: RTP PET/CT scans were performed on 28 NSCLC patients (Stage IA-IIIB) of which 14 patients received prior induction chemotherapy. Three radiation oncologists and one PET radiologist working with a fourth radiation oncologist independently delineated the GTV on CT alone (GTV{sub CT}) and on fused PET/CT images (GTV{sub PETCT}). The mean percentage volume change (PVC) between GTV{sub CT} and GTV{sub PETCT} for the radiation oncologists and the PVC between GTV{sub CT} and GTV{sub PETCT} for the PET radiologist were compared using the Wilcoxon signed-rank test. Concordance index (CI) was used to assess both positional and volume change between GTV{sub CT} and GTV{sub PETCT} in a single measurement. Results: For all patients, a significant difference in PVC from GTV{sub CT} to GTV{sub PETCT} exists between the radiation oncologist (median, 5.9%), and the PET radiologist (median, -0.4%, p = 0.001). However, no significant difference in median concordance index (comparing GTV{sub CT} and GTV{sub FUSED} for individual cases) was observed (PET radiologist = 0.73; radiation oncologists = 0.66; p = 0.088). Conclusions: Percentage volume changes from GTV{sub CT} to GTV{sub PETCT} were lower for the PET radiologist than for the radiation oncologists, suggesting a lower impact of PET/CT in TV delineation for the PET radiologist than for the oncologists. Guidelines are needed to standardize the use of PET/CT for TV delineation in RTP.

  12. Delineation of ecosystem regions

    NASA Astrophysics Data System (ADS)

    Bailey, Robert G.

    1983-07-01

    As a means of developing reliable estimates of ecosystem productivity, ecosystem classification needs to be placed within a geographical framework of regions or zones. This paper explains the basis for the regions delineated on the 1976 map Ecoregions of the United States. Four ecological levels are discussed—domain, division, province, and section—based on climatic and vegetational criteria. Statistical tests are needed to verify and refine map units.

  13. SPARSE: Seed Point Auto-Generation for Random Walks Segmentation Enhancement in medical inhomogeneous targets delineation of morphological MR and CT images.

    PubMed

    Chen, Haibin; Zhen, Xin; Gu, Xuejun; Yan, Hao; Cervino, Laura; Xiao, Yang; Zhou, Linghong

    2015-01-01

    In medical image processing, robust segmentation of inhomogeneous targets is a challenging problem. Because of the complexity and diversity in medical images, the commonly used semiautomatic segmentation algorithms usually fail in the segmentation of inhomogeneous objects. In this study, we propose a novel algorithm imbedded with a seed point autogeneration for random walks segmentation enhancement, namely SPARSE, for better segmentation of inhomogeneous objects. With a few user-labeled points, SPARSE is able to generate extended seed points by estimating the probability of each voxel with respect to the labels. The random walks algorithm is then applied upon the extended seed points to achieve improved segmentation result. SPARSE is implemented under the compute unified device architecture (CUDA) programming environment on graphic processing unit (GPU) hardware platform. Quantitative evaluations are performed using clinical homogeneous and inhomogeneous cases. It is found that the SPARSE can greatly decrease the sensitiveness to initial seed points in terms of location and quantity, as well as the freedom of selecting parameters in edge weighting function. The evaluation results of SPARSE also demonstrate substantial improvements in accuracy and robustness to inhomogeneous target segmentation over the original random walks algorithm. PMID:26103201

  14. RepurposeVS: A Drug Repurposing-Focused Computational Method for Accurate Drug-Target Signature Predictions.

    PubMed

    Issa, Naiem T; Peters, Oakland J; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2015-01-01

    We describe here RepurposeVS for the reliable prediction of drug-target signatures using X-ray protein crystal structures. RepurposeVS is a virtual screening method that incorporates docking, drug-centric and protein-centric 2D/3D fingerprints with a rigorous mathematical normalization procedure to account for the variability in units and provide high-resolution contextual information for drug-target binding. Validity was confirmed by the following: (1) providing the greatest enrichment of known drug binders for multiple protein targets in virtual screening experiments, (2) determining that similarly shaped protein target pockets are predicted to bind drugs of similar 3D shapes when RepurposeVS is applied to 2,335 human protein targets, and (3) determining true biological associations in vitro for mebendazole (MBZ) across many predicted kinase targets for potential cancer repurposing. Since RepurposeVS is a drug repurposing-focused method, benchmarking was conducted on a set of 3,671 FDA approved and experimental drugs rather than the Database of Useful Decoys (DUDE) so as to streamline downstream repurposing experiments. We further apply RepurposeVS to explore the overall potential drug repurposing space for currently approved drugs. RepurposeVS is not computationally intensive and increases performance accuracy, thus serving as an efficient and powerful in silico tool to predict drug-target associations in drug repurposing. PMID:26234515

  15. Consensus Guidelines for Delineation of Clinical Target Volume for Intensity-Modulated Pelvic Radiotherapy in Postoperative Treatment of Endometrial and Cervical Cancer

    SciTech Connect

    Small, William Mell, Loren K.; Anderson, Penny; Creutzberg, Carien; De Los Santos, Jennifer; Gaffney, David; Jhingran, Anuja; Portelance, Lorraine; Schefter, Tracey; Iyer, Revathy; Varia, Mahesh; Winter, Kathryn M.S.; Mundt, Arno J.

    2008-06-01

    Purpose: To develop an atlas of the clinical target volume (CTV) definitions for postoperative radiotherapy of endometrial and cervical cancer to be used for planning pelvic intensity-modulated radiotherapy. Methods and Materials: The Radiation Therapy Oncology Group led an international collaberation of cooperative groups in the development of the atlas. The groups included the Radiation Therapy Oncology Group, Gynecologic Oncology Group, National Cancer Institute of Canada, European Society of Therapeutic Radiology and Oncology, and American College of Radiology Imaging Network. The members of the group were asked by questionnaire to define the areas that were to be included in the CTV and to outline theses areas on individual computed tomography images. The initial formulation of the group began in late 2004 and culminated with a formal consensus conference in June 2005. Results: The committee achieved a consensus CTV definition for postoperative therapy for endometrial and cervical cancer. The CTV should include the common, external, and internal iliac lymph node regions. The upper 3.0 cm of the vagina and paravaginal soft tissue lateral to the vagina should also be included. For patients with cervical cancer, or endometrial cancer with cervical stromal invasion, it is also recommended that the CTV include the presacral lymph node region. Conclusion: This report serves as an international template for the definition of the CTV for postoperative intensity-modulated radiotherapy for endometrial and cervical cancer.

  16. Polyallelic structural variants can provide accurate, highly informative genetic markers focused on diagnosis and therapeutic targets: Accuracy vs. Precision.

    PubMed

    Roses, A D

    2016-02-01

    Structural variants (SVs) include all insertions, deletions, and rearrangements in the genome, with several common types of nucleotide repeats including single sequence repeats, short tandem repeats, and insertion-deletion length variants. Polyallelic SVs provide highly informative markers for association studies with well-phenotyped cohorts. SVs can influence gene regulation by affecting epigenetics, transcription, splicing, and/or translation. Accurate assays of polyallelic SV loci are required to define the range and allele frequency of variable length alleles. PMID:26517180

  17. Audio-Visual Biofeedback Does Not Improve the Reliability of Target Delineation Using Maximum Intensity Projection in 4-Dimensional Computed Tomography Radiation Therapy Planning

    SciTech Connect

    Lu, Wei; Neuner, Geoffrey A.; George, Rohini; Wang, Zhendong; Sasor, Sarah; Huang, Xuan; Regine, William F.; Feigenberg, Steven J.; D'Souza, Warren D.

    2014-01-01

    Purpose: To investigate whether coaching patients' breathing would improve the match between ITV{sub MIP} (internal target volume generated by contouring in the maximum intensity projection scan) and ITV{sub 10} (generated by combining the gross tumor volumes contoured in 10 phases of a 4-dimensional CT [4DCT] scan). Methods and Materials: Eight patients with a thoracic tumor and 5 patients with an abdominal tumor were included in an institutional review board-approved prospective study. Patients underwent 3 4DCT scans with: (1) free breathing (FB); (2) coaching using audio-visual (AV) biofeedback via the Real-Time Position Management system; and (3) coaching via a spirometer system (Active Breathing Coordinator or ABC). One physician contoured all scans to generate the ITV{sub 10} and ITV{sub MIP}. The match between ITV{sub MIP} and ITV{sub 10} was quantitatively assessed with volume ratio, centroid distance, root mean squared distance, and overlap/Dice coefficient. We investigated whether coaching (AV or ABC) or uniform expansions (1, 2, 3, or 5 mm) of ITV{sub MIP} improved the match. Results: Although both AV and ABC coaching techniques improved frequency reproducibility and ABC improved displacement regularity, neither improved the match between ITV{sub MIP} and ITV{sub 10} over FB. On average, ITV{sub MIP} underestimated ITV{sub 10} by 19%, 19%, and 21%, with centroid distance of 1.9, 2.3, and 1.7 mm and Dice coefficient of 0.87, 0.86, and 0.88 for FB, AV, and ABC, respectively. Separate analyses indicated a better match for lung cancers or tumors not adjacent to high-intensity tissues. Uniform expansions of ITV{sub MIP} did not correct for the mismatch between ITV{sub MIP} and ITV{sub 10}. Conclusions: In this pilot study, audio-visual biofeedback did not improve the match between ITV{sub MIP} and ITV{sub 10}. In general, ITV{sub MIP} should be limited to lung cancers, and modification of ITV{sub MIP} in each phase of the 4DCT data set is recommended.

  18. A Tumor-specific MicroRNA Recognition System Facilitates the Accurate Targeting to Tumor Cells by Magnetic Nanoparticles.

    PubMed

    Yu, Yingting; Yao, Yi; Yan, Hao; Wang, Rui; Zhang, Zhenming; Sun, Xiaodan; Zhao, Lingyun; Ao, Xiang; Xie, Zhen; Wu, Qiong

    2016-01-01

    Targeted therapy for cancer is a research area of great interest, and magnetic nanoparticles (MNPs) show great potential as targeted carriers for therapeutics. One important class of cancer biomarkers is microRNAs (miRNAs), which play a significant role in tumor initiation and progression. In this study, a cascade recognition system containing multiple plasmids, including a Tet activator, a lacI repressor gene driven by the TetOn promoter, and a reporter gene repressed by the lacI repressor and influenced by multiple endogenous miRNAs, was used to recognize cells that display miRNA signals that are characteristic of cancer. For this purpose, three types of signal miRNAs with high proliferation and metastasis abilities were chosen (miR-21, miR-145, and miR-9). The response of this system to the human breast cancer MCF-7 cell line was 3.2-fold higher than that to the human breast epithelial HBL100 cell line and almost 7.5-fold higher than that to human embryonic kidney HEK293T cells. In combination with polyethyleneimine-modified MNPs, this recognition system targeted the tumor location in situ in an animal model, and an ~42% repression of tumor growth was achieved. Our study provides a new combination of magnetic nanocarrier and gene therapy based on miRNAs that are active in vivo, which has potential for use in future cancer therapies. PMID:27138178

  19. An N-targeting real-time PCR strategy for the accurate detection of spring viremia of carp virus.

    PubMed

    Shao, Ling; Xiao, Yu; He, Zhengkan; Gao, Longying

    2016-03-01

    Spring viremia of carp virus (SVCV) is a highly pathogenic agent of several economically important Cyprinidae fish species. Currently, there are no effective vaccines or drugs for this virus, and prevention of the disease mostly relies on prompt diagnosis. Previously, nested RT-PCR and RT-qPCR detection methods based on the glycoprotein gene G have been developed. However, the high genetic diversity of the G gene seriously limits the reliability of those methods. Compared with the G gene, phylogenetic analyses indicate that the nucleoprotein gene N is more conserved. Furthermore, studies in other members of the Rhabdoviridae family reveals that their gene transcription level follows the order N>P>M>G>L, indicating that an N gene based RT-PCR should have higher sensitivity. Therefore, two pairs of primers and two corresponding probes targeting the conserved regions of the N gene were designed. RT-qPCR assays demonstrated all primers and probes could detect phylogenetically distant isolates specifically and efficiently. Moreover, in artificially infected fish, the detected copy numbers of the N gene were much higher than those of the G gene in all tissues, and both the N and G gene copy numbers were highest in the kidney and spleen. Testing in 1100 farm-raised fish also showed that the N-targeting strategy was more reliable than the G-targeting methods. The method developed in this study provides a reliable tool for the rapid diagnosis of SVCV. PMID:26717888

  20. A robust MRI-compatible system to facilitate highly accurate stereotactic administration of therapeutic agents to targets within the brain of a large animal model

    PubMed Central

    White, E.; Woolley, M.; Bienemann, A.; Johnson, D.E.; Wyatt, M.; Murray, G.; Taylor, H.; Gill, S.S.

    2011-01-01

    Achieving accurate intracranial electrode or catheter placement is critical in clinical practice in order to maximise the efficacy of deep brain stimulation and drug delivery respectively as well as to minimise side-effects. We have developed a highly accurate and robust method for MRI-guided, stereotactic delivery of catheters and electrodes to deep target structures in the brain of pigs. This study outlines the development of this equipment and animal model. Specifically this system enables reliable head immobilisation, acquisition of high-resolution MR images, precise co-registration of MRI and stereotactic spaces and overall rigidity to facilitate accurate burr hole-generation and catheter implantation. To demonstrate the utility of this system, in this study a total of twelve catheters were implanted into the putamen of six Large White Landrace pigs. All implants were accurately placed into the putamen. Target accuracy had a mean Euclidean distance of 0.623 mm (standard deviation of 0.33 mm). This method has allowed us to accurately insert fine cannulae, suitable for the administration of therapeutic agents by convection-enhanced delivery (CED), into the brain of pigs. This study provides summary evidence of a robust system for catheter implantation into the brain of a large animal model. We are currently using this stereotactic system, implantation procedure and animal model to develop catheter-based drug delivery systems that will be translated into human clinical trials, as well as to model the distribution of therapeutic agents administered by CED over large volumes of brain. PMID:21074564

  1. High-Grade Glioma Radiation Therapy Target Volumes and Patterns of Failure Obtained From Magnetic Resonance Imaging and {sup 18}F-FDOPA Positron Emission Tomography Delineations From Multiple Observers

    SciTech Connect

    Kosztyla, Robert; Chan, Elisa K.; Hsu, Fred; Wilson, Don; Ma, Roy; Cheung, Arthur; Zhang, Susan; Moiseenko, Vitali; Benard, Francois; Nichol, Alan

    2013-12-01

    Purpose: The objective of this study was to compare recurrent tumor locations after radiation therapy with pretreatment delineations of high-grade gliomas from magnetic resonance imaging (MRI) and 3,4-dihydroxy-6-[{sup 18}F]fluoro-L-phenylalanine ({sup 18}F-FDOPA) positron emission tomography (PET) using contours delineated by multiple observers. Methods and Materials: Nineteen patients with newly diagnosed high-grade gliomas underwent computed tomography (CT), gadolinium contrast-enhanced MRI, and {sup 18}F-FDOPA PET/CT. The image sets (CT, MRI, and PET/CT) were registered, and 5 observers contoured gross tumor volumes (GTVs) using MRI and PET. Consensus contours were obtained by simultaneous truth and performance level estimation (STAPLE). Interobserver variability was quantified by the percentage of volume overlap. Recurrent tumor locations after radiation therapy were contoured by each observer using CT or MRI. Consensus recurrence contours were obtained with STAPLE. Results: The mean interobserver volume overlap for PET GTVs (42% ± 22%) and MRI GTVs (41% ± 22%) was not significantly different (P=.67). The mean consensus volume was significantly larger for PET GTVs (58.6 ± 52.4 cm{sup 3}) than for MRI GTVs (30.8 ± 26.0 cm{sup 3}, P=.003). More than 95% of the consensus recurrence volume was within the 95% isodose surface for 11 of 12 (92%) cases with recurrent tumor imaging. Ten (91%) of these cases extended beyond the PET GTV, and 9 (82%) were contained within a 2-cm margin on the MRI GTV. One recurrence (8%) was located outside the 95% isodose surface. Conclusions: High-grade glioma contours obtained with {sup 18}F-FDOPA PET had similar interobserver agreement to volumes obtained with MRI. Although PET-based consensus target volumes were larger than MRI-based volumes, treatment planning using PET-based volumes may not have yielded better treatment outcomes, given that all but 1 recurrence extended beyond the PET GTV and most were contained by a 2-cm

  2. Accurate 3D rigid-body target motion and structure estimation by using GMTI/HRR with template information

    NASA Astrophysics Data System (ADS)

    Wu, Shunguang; Hong, Lang

    2008-04-01

    A framework of simultaneously estimating the motion and structure parameters of a 3D object by using high range resolution (HRR) and ground moving target indicator (GMTI) measurements with template information is given. By decoupling the motion and structure information and employing rigid-body constraints, we have developed the kinematic and measurement equations of the problem. Since the kinematic system is unobservable by using only one scan HRR and GMTI measurements, we designed an architecture to run the motion and structure filters in parallel by using multi-scan measurements. Moreover, to improve the estimation accuracy in large noise and/or false alarm environments, an interacting multi-template joint tracking (IMTJT) algorithm is proposed. Simulation results have shown that the averaged root mean square errors for both motion and structure state vectors have been significantly reduced by using the template information.

  3. A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data

    PubMed Central

    Zhang, Yuan; Sun, Yanni; Cole, James R.

    2014-01-01

    Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material. PMID:25122209

  4. A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.

    PubMed

    Zhang, Yuan; Sun, Yanni; Cole, James R

    2014-08-01

    Gene assembly, which recovers gene segments from short reads, is an important step in functional analysis of next-generation sequencing data. Lacking quality reference genomes, de novo assembly is commonly used for RNA-Seq data of non-model organisms and metagenomic data. However, heterogeneous sequence coverage caused by heterogeneous expression or species abundance, similarity between isoforms or homologous genes, and large data size all pose challenges to de novo assembly. As a result, existing assembly tools tend to output fragmented contigs or chimeric contigs, or have high memory footprint. In this work, we introduce a targeted gene assembly program SAT-Assembler, which aims to recover gene families of particular interest to biologists. It addresses the above challenges by conducting family-specific homology search, homology-guided overlap graph construction, and careful graph traversal. It can be applied to both RNA-Seq and metagenomic data. Our experimental results on an Arabidopsis RNA-Seq data set and two metagenomic data sets show that SAT-Assembler has smaller memory usage, comparable or better gene coverage, and lower chimera rate for assembling a set of genes from one or multiple pathways compared with other assembly tools. Moreover, the family-specific design and rapid homology search allow SAT-Assembler to be naturally compatible with parallel computing platforms. The source code of SAT-Assembler is available at https://sourceforge.net/projects/sat-assembler/. The data sets and experimental settings can be found in supplementary material. PMID:25122209

  5. 2D/3D Image fusion for accurate target localization and evaluation of a mask based stereotactic system in fractionated stereotactic radiotherapy of cranial lesions

    SciTech Connect

    Jin, J.-Y.; Ryu, Samuel; Faber, Kathleen; Mikkelsen, Tom; Chen Qing; Li Shidong; Movsas, Benjamin

    2006-12-15

    The purpose of this study was to evaluate the accuracy of a two-dimensional (2D) to three-dimensional (3D) image-fusion-guided target localization system and a mask based stereotactic system for fractionated stereotactic radiotherapy (FSRT) of cranial lesions. A commercial x-ray image guidance system originally developed for extracranial radiosurgery was used for FSRT of cranial lesions. The localization accuracy was quantitatively evaluated with an anthropomorphic head phantom implanted with eight small radiopaque markers (BBs) in different locations. The accuracy and its clinical reliability were also qualitatively evaluated for a total of 127 fractions in 12 patients with both kV x-ray images and MV portal films. The image-guided system was then used as a standard to evaluate the overall uncertainty and reproducibility of the head mask based stereotactic system in these patients. The phantom study demonstrated that the maximal random error of the image-guided target localization was {+-}0.6 mm in each direction in terms of the 95% confidence interval (CI). The systematic error varied with measurement methods. It was approximately 0.4 mm, mainly in the longitudinal direction, for the kV x-ray method. There was a 0.5 mm systematic difference, primarily in the lateral direction, between the kV x-ray and the MV portal methods. The patient study suggested that the accuracy of the image-guided system in patients was comparable to that in the phantom. The overall uncertainty of the mask system was {+-}4 mm, and the reproducibility was {+-}2.9 mm in terms of 95% CI. The study demonstrated that the image guidance system provides accurate and precise target positioning.

  6. Inter-modality variation in gross tumor volume delineation in 18FDG-PET guided IMRT treatment planning for lung cancer.

    PubMed

    Song, Yulin; Chan, Maria; Burman, Chandra; Cann, Donald

    2006-01-01

    Rapid advances in 18FDG-PET/CT technology and novel co-registration algorithms have created a strong interest in 18FDG-PET/CT's application in intensity modulated radiation therapy (IMRT) and image-guided radiation therapy (IGRT). Accurate target volume delineation, particularly identification of pathologically positive lymph nodes, could translate into favorable treatment outcome. However, gross tumor volume (GTV) delineation on both CT and 18FDG-PET is very sensitive to observer variation. The objectives of the study were to investigate the inter-modality variation in gross tumor volume delineation defined by two imaging modalities for lung cancer: CT and 18FDG-PET/CT and its dosimetric implications in intensity modulated radiation therapy (IMRT). PMID:17946204

  7. 30 CFR 282.22 - Delineation Plan.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 30 Mineral Resources 2 2010-07-01 2010-07-01 false Delineation Plan. 282.22 Section 282.22 Mineral... § 282.22 Delineation Plan. All exploration activities shall be conducted in accordance with a Delineation Plan submitted by the lessee and approved by the Director. The Delineation Plan shall describe...

  8. REFERENCE SITE WATERSHED DELINEATION PROJECT

    EPA Science Inventory

    The use of geographic information systems for the delineation of watersheds and analysis of land use / land cover associated with 250 reference sites on wadeable streams as identified by the Central Plains Bioassessment workgroup and located in the States of Kansas, Iowa, Missour...

  9. Rapid and Accurate Species-Level Identification of Coagulase-Negative Staphylococci by Using the sodA Gene as a Target

    PubMed Central

    Poyart, Claire; Quesne, Gilles; Boumaila, Claire; Trieu-Cuot, Patrick

    2001-01-01

    Simple PCR and sequencing assays that utilize a single pair of degenerate primers were used to characterize a 429-bp-long DNA fragment internal (sodAint) to the sodA gene encoding the manganese-dependent superoxide dismutase in 40 coagulase-negative staphylococcal (CNS) type strains. The topology of the phylogenetic tree obtained was in general agreement with that which was inferred from an analysis of their 16S rRNA or hsp60 gene sequences. Sequence analysis revealed that the staphylococcal sodA genes exhibit a higher divergence than does the corresponding 16S ribosomal DNA. These results confirm that the sodA gene constitutes a highly discriminative target sequence for differentiating closely related bacterial species. Clinical isolates that could not be identified at the species level by phenotypical tests were identified by use of this database. These results demonstrate the usefulness of this method for rapid and accurate species identification of CNS isolates, although it does not allow discrimination of subspecies. The sodA sequence polymorphisms observed with staphylococcal species offer good opportunities for the development of assays based on DNA chip technologies. PMID:11724835

  10. Non-targeted screening for contaminants in paper and board food-contact materials using effect-directed analysis and accurate mass spectrometry.

    PubMed

    Bengtström, Linda; Rosenmai, Anna Kjerstine; Trier, Xenia; Jensen, Lisbeth Krüger; Granby, Kit; Vinggaard, Anne Marie; Driffield, Malcolm; Højslev Petersen, Jens

    2016-06-01

    Due to large knowledge gaps in chemical composition and toxicological data for substances involved, paper and board food-contact materials (P&B FCM) have been emerging as a FCM type of particular concern for consumer safety. This study describes the development of a step-by-step strategy, including extraction, high-performance liquid chromatography (HPLC) fractionation, tentative identification of relevant substances and in vitro testing of selected tentatively identified substances. As a case study, we used two fractions from a recycled pizza box sample which exhibited aryl hydrocarbon receptor (AhR) activity. These fractions were analysed by gas chromatography (GC) and ultra-HPLC (UHPLC) coupled to quadrupole time-of-flight mass spectrometers (QTOF MS) in order tentatively to identify substances. The elemental composition was determined for peaks above a threshold, and compared with entries in a commercial mass spectral library for GC-MS (GC-EI-QTOF MS) analysis and an in-house built library of accurate masses for substances known to be used in P&B packaging for UHPLC-QTOF analysis. Of 75 tentatively identified substances, 15 were initially selected for further testing in vitro; however, only seven were commercially available and subsequently tested in vitro and quantified. Of these seven, the identities of three pigments found in printing inks were confirmed by UHPLC tandem mass spectrometry (QqQ MS/MS). Two pigments had entries in the database, meaning that a material relevant accurate mass database can provide a fast tentative identification. Pure standards of the seven tentatively identified substances were tested in vitro but could not explain a significant proportion of the AhR-response in the extract. Targeted analyses of dioxins and PCBs, both well-known AhR agonists, was performed. However, the dioxins could explain approximately 3% of the activity observed in the pizza box extract indicating that some very AhR active substance(s) still remain to be

  11. Detection and delineation of buildings from airborne ladar measurements

    NASA Astrophysics Data System (ADS)

    Swirski, Yoram; Wolowelsky, Karni; Adar, Renen; Figov, Zvi

    2004-11-01

    Automatic delineation of buildings is very attractive for both civilian and military applications. Such applications include general mapping, detection of unauthorized constructions, change detection, etc. For military applications, high demand exists for accurate building change updates, covering large areas, and over short time periods. We present two algorithms coupled together. The height image algorithm is a fast coarse algorithm operating on large areas. This algorithm is capable of defining blocks of buildings and regions of interest. The point-cloud algorithm is a fine, 3D-based, accurate algorithm for building delineation. Since buildings may be separated by alleys, whose width is similar or narrower than the LADAR resolution, the height image algorithm marks those crowded buildings as a single object. The point-cloud algorithm separates and accurately delineates individual building boundaries and building sub-sections utilizing roof shape analysis in 3D. Our focus is on the ability to cover large areas with accuracy and high rejection of non-building objects, like trees. We report a very good detection performance with only few misses and false alarms. It is believed that LADAR measurements, coupled with good segmentation algorithms, may replace older systems and methods that require considerable manual work for such applications.

  12. Automated delineation of stroke lesions using brain CT images

    PubMed Central

    Gillebert, Céline R.; Humphreys, Glyn W.; Mantini, Dante

    2014-01-01

    Computed tomographic (CT) images are widely used for the identification of abnormal brain tissue following infarct and hemorrhage in stroke. Manual lesion delineation is currently the standard approach, but is both time-consuming and operator-dependent. To address these issues, we present a method that can automatically delineate infarct and hemorrhage in stroke CT images. The key elements of this method are the accurate normalization of CT images from stroke patients into template space and the subsequent voxelwise comparison with a group of control CT images for defining areas with hypo- or hyper-intense signals. Our validation, using simulated and actual lesions, shows that our approach is effective in reconstructing lesions resulting from both infarct and hemorrhage and yields lesion maps spatially consistent with those produced manually by expert operators. A limitation is that, relative to manual delineation, there is reduced sensitivity of the automated method in regions close to the ventricles and the brain contours. However, the automated method presents a number of benefits in terms of offering significant time savings and the elimination of the inter-operator differences inherent to manual tracing approaches. These factors are relevant for the creation of large-scale lesion databases for neuropsychological research. The automated delineation of stroke lesions from CT scans may also enable longitudinal studies to quantify changes in damaged tissue in an objective and reproducible manner. PMID:24818079

  13. Automated delineation of radiotherapy volumes: are we going in the right direction?

    PubMed Central

    Whitfield, G A; Price, P; Price, G J; Moore, C J

    2013-01-01

    ABSTRACT. Rapid and accurate delineation of target volumes and multiple organs at risk, within the enduring International Commission on Radiation Units and Measurement framework, is now hugely important in radiotherapy, owing to the rapid proliferation of intensity-modulated radiotherapy and the advent of four-dimensional image-guided adaption. Nevertheless, delineation is still generally clinically performed with little if any machine assistance, even though it is both time-consuming and prone to interobserver variation. Currently available segmentation tools include those based on image greyscale interrogation, statistical shape modelling and body atlas-based methods. However, all too often these are not able to match the accuracy of the expert clinician, which remains the universally acknowledged gold standard. In this article we suggest that current methods are fundamentally limited by their lack of ability to incorporate essential human clinical decision-making into the underlying models. Hybrid techniques that utilise prior knowledge, make sophisticated use of greyscale information and allow clinical expertise to be integrated are needed. This may require a change in focus from automated segmentation to machine-assisted delineation. Similarly, new metrics of image quality reflecting fitness for purpose would be extremely valuable. We conclude that methods need to be developed to take account of the clinician's expertise and honed visual processing capabilities as much as the underlying, clinically meaningful information content of the image data being interrogated. We illustrate our observations and suggestions through our own experiences with two software tools developed as part of research council-funded projects. PMID:23239689

  14. MRI to delineate the gross tumor volume of nasopharyngeal cancers: which sequences and planes should be used?

    PubMed Central

    Popovtzer, Aron; Ibrahim, Mohannad; Tatro, Daniel; Feng, Felix Y.; Ten Haken, Randall K.; Eisbruch, Avraham

    2014-01-01

    Background Magnetic resonance imaging (MRI) has been found to be better than computed tomography for defining the extent of primary gross tumor volume (GTV) in advanced nasopharyngeal cancer. It is routinely applied for target delineation in planning radiotherapy. However, the specific MRI sequences/planes that should be used are unknown. Methods Twelve patients with nasopharyngeal cancer underwent primary GTV evaluation with gadolinium-enhanced axial T1 weighted image (T1) and T2 weighted image (T2), coronal T1, and sagittal T1 sequences. Each sequence was registered with the planning computed tomography scans. Planning target volumes (PTVs) were derived by uniform expansions of the GTVs. The volumes encompassed by the various sequences/planes, and the volumes common to all sequences/planes, were compared quantitatively and anatomically to the volume delineated by the commonly used axial T1-based dataset. Results Addition of the axial T2 sequence increased the axial T1-based GTV by 12% on average (p = 0.004), and composite evaluations that included the coronal T1 and sagittal T1 planes increased the axial T1-based GTVs by 30% on average (p = 0.003). The axial T1-based PTVs were increased by 20% by the additional sequences (p = 0.04). Each sequence/plane added unique volume extensions. The GTVs common to all the T1 planes accounted for 38% of the total volumes of all the T1 planes. Anatomically, addition of the coronal and sagittal-based GTVs extended the axial T1-based GTV caudally and cranially, notably to the base of the skull. Conclusions Adding MRI planes and sequences to the traditional axial T1 sequence yields significant quantitative and anatomically important extensions of the GTVs and PTVs. For accurate target delineation in nasopharyngeal cancer, we recommend that GTVs be outlined in all MRI sequences/planes and registered with the planning computed tomography scans. PMID:25177248

  15. An Accurate and Fault-Tolerant Target Positioning System for Buildings Using Laser Rangefinders and Low-Cost MEMS-Based MARG Sensors.

    PubMed

    Zhao, Lin; Guan, Dongxue; Landry, René; Cheng, Jianhua; Sydorenko, Kostyantyn

    2015-01-01

    Target positioning systems based on MEMS gyros and laser rangefinders (LRs) have extensive prospects due to their advantages of low cost, small size and easy realization. The target positioning accuracy is mainly determined by the LR's attitude derived by the gyros. However, the attitude error is large due to the inherent noises from isolated MEMS gyros. In this paper, both accelerometer/magnetometer and LR attitude aiding systems are introduced to aid MEMS gyros. A no-reset Federated Kalman Filter (FKF) is employed, which consists of two local Kalman Filters (KF) and a Master Filter (MF). The local KFs are designed by using the Direction Cosine Matrix (DCM)-based dynamic equations and the measurements from the two aiding systems. The KFs can estimate the attitude simultaneously to limit the attitude errors resulting from the gyros. Then, the MF fuses the redundant attitude estimates to yield globally optimal estimates. Simulation and experimental results demonstrate that the FKF-based system can improve the target positioning accuracy effectively and allow for good fault-tolerant capability. PMID:26512672

  16. An Accurate and Fault-Tolerant Target Positioning System for Buildings Using Laser Rangefinders and Low-Cost MEMS-Based MARG Sensors

    PubMed Central

    Zhao, Lin; Guan, Dongxue; Landry, René Jr.; Cheng, Jianhua; Sydorenko, Kostyantyn

    2015-01-01

    Target positioning systems based on MEMS gyros and laser rangefinders (LRs) have extensive prospects due to their advantages of low cost, small size and easy realization. The target positioning accuracy is mainly determined by the LR’s attitude derived by the gyros. However, the attitude error is large due to the inherent noises from isolated MEMS gyros. In this paper, both accelerometer/magnetometer and LR attitude aiding systems are introduced to aid MEMS gyros. A no-reset Federated Kalman Filter (FKF) is employed, which consists of two local Kalman Filters (KF) and a Master Filter (MF). The local KFs are designed by using the Direction Cosine Matrix (DCM)-based dynamic equations and the measurements from the two aiding systems. The KFs can estimate the attitude simultaneously to limit the attitude errors resulting from the gyros. Then, the MF fuses the redundant attitude estimates to yield globally optimal estimates. Simulation and experimental results demonstrate that the FKF-based system can improve the target positioning accuracy effectively and allow for good fault-tolerant capability. PMID:26512672

  17. Sequencer-Based Capillary Gel Electrophoresis (SCGE) Targeting the rDNA Internal Transcribed Spacer (ITS) Regions for Accurate Identification of Clinically Important Yeast Species

    PubMed Central

    Chen, Sharon C.-A.; Wang, He; Zhang, Li; Fan, Xin; Xu, Zhi-Peng; Cheng, Jing-Wei; Kong, Fanrong; Zhao, Yu-Pei; Xu, Ying-Chun

    2016-01-01

    Accurate species identification of Candida, Cryptococcus, Trichosporon and other yeast pathogens is important for clinical management. In the present study, we developed and evaluated a yeast species identification scheme by determining the rDNA internal transcribed spacer (ITS) region length types (LTs) using a sequencer-based capillary gel electrophoresis (SCGE) approach. A total of 156 yeast isolates encompassing 32 species were first used to establish a reference SCGE ITS LT database. Evaluation of the ITS LT database was then performed on (i) a separate set of (n = 97) clinical isolates by SCGE, and (ii) 41 isolates of 41 additional yeast species from GenBank by in silico analysis. Of 156 isolates used to build the reference database, 41 ITS LTs were identified, which correctly identified 29 of the 32 (90.6%) species, with the exception of Trichosporon asahii, Trichosporon japonicum and Trichosporon asteroides. In addition, eight of the 32 species revealed different electropherograms and were subtyped into 2–3 different ITS LTs each. Of the 97 test isolates used to evaluate the ITS LT scheme, 96 (99.0%) were correctly identified to species level, with the remaining isolate having a novel ITS LT. Of the additional 41 isolates for in silico analysis, none was misidentified by the ITS LT database except for Trichosporon mucoides whose ITS LT profile was identical to that of Trichosporon dermatis. In conclusion, yeast identification by the present SCGE ITS LT assay is a fast, reproducible and accurate alternative for the identification of clinically important yeasts with the exception of Trichosporon species. PMID:27105313

  18. Magnetic nanoparticles-cooperated fluorescence sensor for sensitive and accurate detection of DNA methyltransferase activity coupled with exonuclease III-assisted target recycling.

    PubMed

    Xue, Qingwang; Zhang, Youna; Xu, Shuling; Li, Haibo; Wang, Lei; Li, Rui; Zhang, Yuanfu; Yue, Qiaoli; Gu, Xiaohong; Zhang, Shuqiu; Liu, Jifeng; Wang, Huaisheng

    2015-11-21

    A fluorescence magnetic biosensor for the DNA methyltransferase activity was developed based on the cooperative amplification by combining the magnetic nanoparticles synergistic exonuclease III (Exo III)-assisted circular exponential amplification and a supramolecular structure ZnPPIX/G-quadruplex. First, a duplex DNA probe, which was constructed by the hybridization of a quadruplex-forming oligomer with a molecular beacon, was assembled on the magnetic nanoparticles (MNPs) as a reporter. A hairpin probe (HP)-containing sequence of GATC was used as the methylation substrate of DNA adenine methyltransferase (DAM). Once HP was methylated by DAM, it could be recognized and cleaved by Dpn I, which allows the release of a single-stranded DNA. The DNA (tDNA1) then hybridizes to the MNP probe, which then triggers the exonuclease III-mediated target exponential recycling reaction. Simultaneously, numerous quadruplex forming oligomers are liberated and folded into the G-quadruplex-ZnPPIX complexes with the help of zinc(ii)-protoporphyrin IX(ZnPPIX) on the MNP surface to give a remarkable fluorescence response. In the developed sensor, a small amount of target DAM can be converted to a large number of stable DNA triggers, leading to remarkable amplification of the target. Moreover, using MNPs as a vector of the sensor may reduce the interference from the real samples, which increases the anti-interference of the sensing system. Based on this unique amplification strategy, a very low detection limit down to 2.0 × 10(-4) U mL(-1) was obtained. Furthermore, the sensor could be used to evaluate the DAM activity in different growth stages of E. coli cells and screen Dam MTase inhibitors. Therefore, the strategy proposed here provides a promising platform for monitoring the activity and inhibition of DNA MTases and has great potential to be applied further in early clinical diagnostics and medical research. PMID:26421322

  19. Use of dose-dependent absorption into target tissues to more accurately predict cancer risk at low oral doses of hexavalent chromium.

    PubMed

    Haney, J

    2015-02-01

    The mouse dose at the lowest water concentration used in the National Toxicology Program hexavalent chromium (CrVI) drinking water study (NTP, 2008) is about 74,500 times higher than the approximate human dose corresponding to the 35-city geometric mean reported in EWG (2010) and over 1000 times higher than that based on the highest reported tap water concentration. With experimental and environmental doses differing greatly, it is a regulatory challenge to extrapolate high-dose results to environmental doses orders of magnitude lower in a meaningful and toxicologically predictive manner. This seems particularly true for the low-dose extrapolation of results for oral CrVI-induced carcinogenesis since dose-dependent differences in the dose fraction absorbed by mouse target tissues are apparent (Kirman et al., 2012). These data can be used for a straightforward adjustment of the USEPA (2010) draft oral slope factor (SFo) to be more predictive of risk at environmentally-relevant doses. More specifically, the evaluation of observed and modeled differences in the fraction of dose absorbed by target tissues at the point-of-departure for the draft SFo calculation versus lower doses suggests that the draft SFo be divided by a dose-specific adjustment factor of at least an order of magnitude to be less over-predictive of risk at more environmentally-relevant doses. PMID:25445295

  20. MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets

    PubMed Central

    Incarnato, Danny; Neri, Francesco; Diamanti, Daniela; Oliviero, Salvatore

    2013-01-01

    The prediction of pairing between microRNAs (miRNAs) and the miRNA recognition elements (MREs) on mRNAs is expected to be an important tool for understanding gene regulation. Here, we show that mRNAs that contain Pumilio recognition elements (PRE) in the proximity of predicted miRNA-binding sites are more likely to form stable secondary structures within their 3′-UTR, and we demonstrated using a PUM1 and PUM2 double knockdown that Pumilio proteins are general regulators of miRNA accessibility. On the basis of these findings, we developed a computational method for predicting miRNA targets that accounts for the presence of PRE in the proximity of seed-match sequences within poorly accessible structures. Moreover, we implement the miRNA-MRE duplex pairing as a two-step model, which better fits the available structural data. This algorithm, called MREdictor, allows for the identification of miRNA targets in poorly accessible regions and is not restricted to a perfect seed-match; these features are not present in other computational prediction methods. PMID:23863844

  1. Accurate fundamental parameters of CoRoT asteroseismic targets. The solar-like stars HD 49933, HD 175726, HD 181420, and HD 181906

    NASA Astrophysics Data System (ADS)

    Bruntt, H.

    2009-10-01

    Context: The CoRoT satellite has provided high-quality light curves of several solar-like stars. Analysis of these light curves provides oscillation frequencies that make it possible to probe the interior of the stars. However, additional constraints on the fundamental parameters of the stars are important for the theoretical modelling to be successful. Aims: We estimate the fundamental parameters (mass, radius, and luminosity) of the first four solar-like targets to be observed in the asteroseismic field. In addition, we determine their effective temperature, metallicity, and detailed abundance patterns. Methods: To constrain the stellar mass, radius and age we used the shotgun software, which compares the location of the stars in the Hertzsprung-Russell diagram with theoretical evolution models. This method takes the uncertainties of the observed parameters into account, including the large separation determined from the solar-like oscillations. We determined the effective temperatures and abundance patterns in the stars from the analysis of high-resolution spectra obtained with the HARPS, NARVAL, ELODIE and FEROS spectrographs. Results: We determined the mass, radius, and luminosity of the four CoRoT targets to within 5{-}10%, 2{-}4% and 5{-}13%, respectively. The quality of the stellar spectra determines how well we can constrain the effective temperature. For the two best spectra we get 1-σ uncertainties below 60 K and 100{-}150 K for the other two. The uncertainty on the surface gravity is less than 0.08 dex for three stars, while it is 0.15 dex for HD 181906. The reason for the larger uncertainty is that the spectrum has two components with a luminosity ratio of L_p/Ls = 0.50±0.15. While Hipparcos astrometric data strongly suggest it is a binary star, we find evidence that the fainter star may be a background star, since it is less luminous but hotter.

  2. Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification.

    PubMed

    Wright, Erik S; Yilmaz, L Safak; Corcoran, Andrew M; Ökten, Hatice E; Noguera, Daniel R

    2014-08-01

    Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu). PMID:24928876

  3. Variability Among Breast Radiation Oncologists in Delineation of the Postsurgical Lumpectomy Cavity

    SciTech Connect

    Landis, Daniel M. . E-mail: Daniel.Landis@swedish.org; Luo Weixiu; Song Jun; Harris, Jay R.

    2007-04-01

    Purpose: Partial breast irradiation (PBI) is becoming more widely used. Accurate determination of the surgical lumpectomy cavity volume is more critical with PBI than with whole breast radiation therapy. We examined the interobserver variability in delineation of the lumpectomy cavity among four academic radiation oncologists who specialize in the treatment of breast cancer. Methods and Materials: Thirty-four lumpectomy cavities in 33 consecutive patients were evaluated. Each physician contoured the cavity and a 1.5-cm margin was added to define the planning target volume (PTV). A cavity visualization score (CVS) was assigned (1-5). To eliminate bias, the physician of record was eliminated from the analysis in all cases. Three measures of variability of the PTV were developed: average shift of the center of mass (COM), average percent overlap between the PTV of two physicians (PVO), and standard deviation of the PTV. Results: Of variables examined, pathologic resection volume was significantly correlated with CVS, with larger volumes more easily visualized. Shift of the COM decreased and PVO increased significantly as CVS increased. For CVS 4 and 5 cases, the average COM shift was 3 mm and 2 mm, respectively, and PVO was 77% and 87%, respectively. In multiple linear regression, pathologic diameter >4 cm and CVS {>=}3 were significantly associated with smaller COM shift. When CVS was omitted from analysis, PVO was significantly larger with pathologic diameter {>=}5 cm, days to planning <36, and older age. Conclusions: Even among radiation oncologists who specialize in breast radiotherapy, there can be substantial differences in delineation of the postsurgical radiotherapy target volume. Large treatment margins may be prudent if the cavity is not clearly defined.

  4. Stratiform/convective rain delineation for TRMM microwave imager

    NASA Astrophysics Data System (ADS)

    Islam, Tanvir; Srivastava, Prashant K.; Dai, Qiang; Gupta, Manika; Wan Jaafar, Wan Zurina

    2015-10-01

    This article investigates the potential for using machine learning algorithms to delineate stratiform/convective (S/C) rain regimes for passive microwave imager taking calibrated brightness temperatures as only spectral parameters. The algorithms have been implemented for the Tropical Rainfall Measuring Mission (TRMM) microwave imager (TMI), and calibrated as well as validated taking the Precipitation Radar (PR) S/C information as the target class variables. Two different algorithms are particularly explored for the delineation. The first one is metaheuristic adaptive boosting algorithm that includes the real, gentle, and modest versions of the AdaBoost. The second one is the classical linear discriminant analysis that includes the Fisher's and penalized versions of the linear discriminant analysis. Furthermore, prior to the development of the delineation algorithms, a feature selection analysis has been conducted for a total of 85 features, which contains the combinations of brightness temperatures from 10 GHz to 85 GHz and some derived indexes, such as scattering index, polarization corrected temperature, and polarization difference with the help of mutual information aided minimal redundancy maximal relevance criterion (mRMR). It has been found that the polarization corrected temperature at 85 GHz and the features derived from the "addition" operator associated with the 85 GHz channels have good statistical dependency to the S/C target class variables. Further, it has been shown how the mRMR feature selection technique helps to reduce the number of features without deteriorating the results when applying through the machine learning algorithms. The proposed scheme is able to delineate the S/C rain regimes with reasonable accuracy. Based on the statistical validation experience from the validation period, the Matthews correlation coefficients are in the range of ~0.60-0.70. Since, the proposed method does not rely on any a priori information, this makes it very

  5. Are Lateral Electronic Portal Images Adequate for Accurate On-Line Daily Targeting of the Prostate? Results of a Prospective Study

    SciTech Connect

    Lometti, Michael W. Thurston, Damon; Aubin, Michele; Bock, Andrea; Verhey, Lynn; Lockhart, James M.; Bland, Roger; Pouliot, Jean; Roach, Mack

    2008-04-01

    The purpose of this report was to evaluate the magnitude of the error that would be introduced if only a lateral (LAT) portal image, as opposed to a pair of orthogonal images, was used to verify and correct daily setup errors and organ motion in external beam radiation therapy (EBRT) of prostate cancer. The 3-dimensional (3D) coordinates of gold markers from 12 consecutive prostate patients were reconstructed using a pair of orthogonal images. The data were re-analyzed using only the LAT images. Couch moves from the 2-dimensional (2D)-only data were compared with the complete 3D data set. The 2D-only data provided couch moves that differed on average from the 3D data by 2.3 {+-} 3.0, 0.0 {+-} 0.0, and 0.8 {+-} 1.0 mm in the Lat, AP, and SI directions, respectively. Along AP and SI axes, the LAT image provided positional information similar to the orthogonal pair. The error along the LAT axis may be acceptable provided lateral margins are large enough. A LAT-only setup protocol reduces patient treatment times and increases patient throughput. In most circumstances, with exceptions such as morbidly obese patients, acquisition of only a LAT image for daily targeting of the prostate will provide adequate positional precision.

  6. Delineation of geological facies from poorly differentiated data

    SciTech Connect

    Wohlberg, Brendt; Tartakovsky, Daniel

    2008-01-01

    The ability to delineate geologic facies and to estima.te their properties from sparse data is essential for modeling physical and biochemical processes occurring in the 'ubsurface. If such data are poorly differentiated, this challcnrring task is complicated further by the absence of a clear distinction between different hydrofacies even at locations where data. are available. vVe consider three alt mative approaches for analysis of poorly differentiated data: a k-means clU!:iterinrr algorithm, an expectation-maximization algorithm, and a minimum-variance algorithm. Two distinct synthetically generated geological settings are used to r:tnalyze the ability of these algorithmti to as ign accurately the membership of such data in a given geologic facies. On average, the minimum-variance algorithm provides a more robust p rformance than its two counterparts and when combined with a nearest-neighbor algorithm, it also yields the most accurate reconstruction of the boundaries between the facies.

  7. Efficiency of Integrated Geophysical techniques in delineating the extension of Bauxites ore in north Riyadh, Saudi Arabia

    NASA Astrophysics Data System (ADS)

    Almutairi, Yasir; Alanazi, Abdulrahman; Almutairi, Muteb; Alsama, Ali; Alhenaki, Bander; Almalki, Awadh

    2014-05-01

    We exploit the integration of Ground Penetrating Radar (GPR) techniques, magnetic gradiometry, resistivity measurements and seismic tomography for the high-resolution non-invasive study for delineating the subsurface Bauxite layer in Zabira locality, north of Riyadh. Integrated GPR, magnetic gradiometry resistivity and seismic refraction are used in the case of high contrast targets and provide an accurate subsurface reconstruction of foundations in sediments. Resistivity pseudo-sections are in particular useful for the areal identification of contacts between soils and foundations while GPR and magnetic gradiometry provide detailed information about location and depth of the structures. Results obtained by GPR, Magnetics and resistivity shows a very good agreement in mapping the bauxite layer depth at range of 5 m to 10 m while the depth obtained by seismic refraction was 10 m to 15 m due to lack of velocity information.

  8. Development and evaluation of multilead wavelet-based ECG delineation algorithms for embedded wireless sensor nodes.

    PubMed

    Rincón, Francisco; Recas, Joaquin; Khaled, Nadia; Atienza, David

    2011-11-01

    This work is devoted to the evaluation of multilead digital wavelet transform (DWT)-based electrocardiogram (ECG) wave delineation algorithms, which were optimized and ported to a commercial wearable sensor platform. More specifically, we investigate the use of root-mean squared (RMS)-based multilead followed by a single-lead online delineation algorithm, which is based on a state-of-the-art offline single-lead delineator. The algorithmic transformations and software optimizations necessary to enable embedded ECG delineation notwithstanding the limited processing and storage resources of the target platform are described, and the performance of the resulting implementations are analyzed in terms of delineation accuracy, execution time, and memory usage. Interestingly, RMS-based multilead delineation is shown to perform equivalently to the best single-lead delineation for the 2-lead QT database (QTDB), within a fraction of a sample duration of the Common Standards for Electrocardiography (CSE) committee tolerances. Finally, a comprehensive evaluation of the energy consumption entailed by the considered algorithms is proposed, which allows very relevant insights into the dominant energy-draining functionalities and which suggests suitable design guidelines for long-lasting wearable ECG monitoring systems. PMID:21827976

  9. Delineation of Supraclavicular Target Volumes in Breast Cancer Radiation Therapy

    SciTech Connect

    Brown, Lindsay C.; Diehn, Felix E.; Boughey, Judy C.; Childs, Stephanie K.; Park, Sean S.; Yan, Elizabeth S.; Petersen, Ivy A.; Mutter, Robert W.

    2015-07-01

    Purpose: To map the location of gross supraclavicular metastases in patients with breast cancer, in order to determine areas at highest risk of harboring subclinical disease. Methods and Materials: Patients with axial imaging of gross supraclavicular disease were identified from an institutional breast cancer registry. Locations of the metastatic lymph nodes were transferred onto representative axial computed tomography images of the supraclavicular region and compared with the Radiation Therapy Oncology Group (RTOG) breast cancer atlas for radiation therapy planning. Results: Sixty-two patients with 161 supraclavicular nodal metastases were eligible for study inclusion. At the time of diagnosis, 117 nodal metastases were present in 44 patients. Forty-four nodal metastases in 18 patients were detected at disease recurrence, 4 of whom had received prior radiation to the supraclavicular fossa. Of the 161 nodal metastases, 95 (59%) were within the RTOG consensus volume, 4 nodal metastases (2%) in 3 patients were marginally within the volume, and 62 nodal metastases (39%) in 30 patients were outside the volume. Supraclavicular disease outside the RTOG consensus volume was located in 3 regions: at the level of the cricoid and thyroid cartilage (superior to the RTOG volume), in the posterolateral supraclavicular fossa (posterolateral to the RTOG volume), and in the lateral low supraclavicular fossa (lateral to the RTOG volume). Only women with multiple supraclavicular metastases had nodal disease that extended superiorly to the level of the thyroid cartilage. Conclusions: For women with risk of harboring subclinical supraclavicular disease warranting the addition of supraclavicular radiation, coverage of the posterior triangle and the lateral low supraclavicular region should be considered. For women with known supraclavicular disease, extension of neck coverage superior to the cricoid cartilage may be warranted.

  10. Plastic and Glass Greenhouses Detection and Delineation from WORLDVIEW-2 Satellite Imagery

    NASA Astrophysics Data System (ADS)

    Koc-San, D.; Sonmez, N. K.

    2016-06-01

    Greenhouse detection using remote sensing technologies is an important research area for yield estimation, sustainable development, urban and rural planning and management. An approach was developed in this study for the detection and delineation of greenhouse areas from high resolution satellite imagery. Initially, the candidate greenhouse patches were detected using supervised classification techniques. For this purpose, Maximum Likelihood (ML), Random Forest (RF), and Support Vector Machines (SVM) classification techniques were applied and compared. Then, sieve filter and morphological operations were performed for improving the classification results. Finally, the obtained candidate plastic and glass greenhouse areas were delineated using boundary tracing and Douglas Peucker line simplification algorithms. The proposed approach was implemented in the Kumluca district of Antalya, Turkey utilizing pan-sharpened WorldView-2 satellite imageries. Kumluca is the prominent district of Antalya with greenhouse cultivation and includes both plastic and glass greenhouses intensively. When the greenhouse classification results were analysed, it can be stated that the SVM classification provides most accurate results and RF classification follows this. The SVM classification overall accuracy was obtained as 90.28%. When the greenhouse boundary delineation results were considered, the plastic greenhouses were delineated with 92.11% accuracy, while glass greenhouses were delineated with 80.67% accuracy. The obtained results indicate that, generally plastic and glass greenhouses can be detected and delineated successfully from WorldView-2 satellite imagery.

  11. pyLIDEM: A Python-Based Tool to Delineate Coastal Watersheds Using LIDAR Data

    NASA Astrophysics Data System (ADS)

    O'Banion, R.; Alameddine, I.; Gronewold, A.; Reckhow, K.

    2008-12-01

    Accurately identifying the boundary of a watershed is one of the most fundamental and important steps in any hydrological assessment. Representative applications include defining a study area, predicting overland flow, estimating groundwater infiltration, modeling pollutant accumulation and wash-off rates, and evaluating effectiveness of pollutant mitigation measures. The United States Environmental Protection Agency (USEPA) Total Maximum Daily Load (TMDL) program, the most comprehensive water quality management program in the United States (US), is just one example of an application in which accurate and efficient watershed delineation tools play a critical role. For example, many impaired water bodies currently being addressed through the TMDL program drain small coastal watersheds with relatively flat terrain, making watershed delineation particularly challenging. Most of these TMDL studies use 30-meter digital elevation models (DEMs) that rarely capture all of the small elevation changes in coastal watersheds, leading to errors not only in watershed boundary delineation, but in subsequent model predictions (such as watershed runoff flow and pollutant deposition rate predictions) for which watershed attributes are key inputs. Manually delineating these low-relief coastal watersheds through the use of expert knowledge of local water flow patterns, often produces relatively accurate (and often more accurate) watershed boundaries as compared to the boundaries generated by the 30-meter DEMs. Yet, manual delineation is a costly and time consuming procedure that is often not opted for. There is a growing need, therefore, particularly to address the ongoing needs of the TMDL program (and similar environmental management programs), for software tools which can utilize high resolution topography data to more accurately delineate coastal watersheds. Here, we address this need by developing pyLIDEM (python LIdar DEM), a python-based tool which processes bare earth high

  12. Semi-automated method for delineation of landmarks on models of the cerebral cortex

    PubMed Central

    Shattuck, David W.; Joshi, Anand A.; Pantazis, Dimitrios; Kan, Eric; Dutton, Rebecca A.; Sowell, Elizabeth R.; Thompson, Paul M.; Toga, Arthur W.; Leahy, Richard M.

    2009-01-01

    Sulcal and gyral landmarks on the human cerebral cortex are required for various studies of the human brain. Whether used directly to examine sulcal geometry, or indirectly to drive cortical surface registration methods, the accuracy of these landmarks is essential. While several methods have been developed to automatically identify sulci and gyri, their accuracy may be insufficient for certain neuroanatomical studies. We describe a semi-automated procedure that delineates a sulcus or gyrus given a limited number of user-selected points. The method uses a graph theory approach to identify the lowest-cost path between the points, where the cost is a combination of local curvature features and the distance between vertices on the surface representation. We implemented the algorithm in an interface that guides the user through a cortical surface delineation protocol, and we incorporated this tool into our BrainSuite software. We performed a study to compare the results produced using our method with results produced using Display, a popular tool that has been used extensively for manual delineation of sulcal landmarks. Six raters were trained on the delineation protocol. They performed delineations on 12 brains using both software packages. We performed a statistical analysis of 3 aspects of the delineation task: time required to delineate the surface, registration accuracy achieved compared to an expert-delineated gold-standard, and variation among raters. Our new method was shown to be faster to use, to provide reduced inter-rater variability, and to provide results that were at least as accurate as those produced using Display. PMID:19162074

  13. 30 CFR 282.22 - Delineation Plan.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 30 Mineral Resources 2 2011-07-01 2011-07-01 false Delineation Plan. 282.22 Section 282.22 Mineral Resources BUREAU OF OCEAN ENERGY MANAGEMENT, REGULATION, AND ENFORCEMENT, DEPARTMENT OF THE INTERIOR... that the seafloor is left free of obstructions or structures that may present a hazard to other uses...

  14. 43 CFR 3922.40 - Tract delineation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Tract delineation. 3922.40 Section 3922.40 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR RANGE MANAGEMENT (4000) OIL SHALE LEASING Application Processing § 3922.40...

  15. 43 CFR 3922.40 - Tract delineation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 43 Public Lands: Interior 2 2013-10-01 2013-10-01 false Tract delineation. 3922.40 Section 3922.40 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) OIL SHALE LEASING Application Processing §...

  16. Delineation of recharge areas for selected wells in the St. Peter-Prairie du Chien-Jordan Aquifer, Rochester, Minnesota

    USGS Publications Warehouse

    Delin, G.N.; Almendinger, James Edward

    1991-01-01

    Hydrogeologic mapping and numerical modeling were used to delineate zones of contribution to wells, defined as all parts of a ground-water-flow system that could supply water to a well. The zones of contribution delineated by use of numerical modeling have similar orientation (parallel to regional flow directions) but significantly different areas than the zones of contribution delineated by use of hydrogeologic mapping. Differences in computed areas of recharge are attributed to the capability of the numerical model to more accurately represent (1) the three-dimensional flow system, (2) hydrologic boundaries like streams, (3) variable recharge, and (4) the influence of nearby pumped wells, compared to the analytical models.

  17. Delineation of recharge areas for selected wells in the St. Peter-Prairie du Chien-Jordan aquifer, Rochester, Minnesota

    USGS Publications Warehouse

    Delin, G.N.; Almendinger, James Edward

    1993-01-01

    Hydrogeologic mapping and numerical modeling were used to delineate zones of contribution to wells, defined as all parts of a ground-water-flow system that could supply water to a well. The zones of contribution delineated by use of numerical modeling have similar orientation (parallel to regional flow directions) but significantly different areas than the zones of contribution delineated by use of hydrogeologic mapping. Differences in computed areas of recharge are attributed to the capability of the numerical model to more accurately represent (1) the three-dimensional flow system, (2) hydrologic boundaries such as streams, (3) variable recharge, and (4) the influence of nearby pumped wells, compared to the analytical models.

  18. Simple diagrammatic approach to delineate duodenum on a radiotherapy planning CT scan.

    PubMed

    Kataria, Tejinder; Gupta, Deepak; Basu, Trinanjan; Gupta, Shivani; Goyal, Shikha; Banerjee, Susovan; Abhishek, Ashu; Bisht, Shyam S; Narang, Kushal

    2016-01-01

    In recent years, there has been increasing application of intensity-modulated radiotherapy and stereotactic body radiotherapy for the treatment of abdominal malignancies (stomach, pancreas, liver, spinal metastases). This warrants accurate delineation of organs at risk, especially the duodenum. The tortuous and curvy anatomy of duodenum often indistinguishable from adjoining organs is a practical challenge. Radiation Therapy Oncology Group (RTOG) has already published upper abdominal normal structure contouring guidelines to ease the delineation process. This pictorial essay following the RTOG guideline elaborates the step-by-step identification of the different parts of duodenum in relation to the adjoining important structures. PMID:26647654

  19. Application of higher order spectra for accurate delineation of atrial arrhythmia.

    PubMed

    Prasad, Hari; Martis, Roshan Joy; Acharya, U Rajendra; Min, Lim Choo; Suri, Jasjit S

    2013-01-01

    The electrocardiogram (ECG) is being commonly used as a diagnostic tool to distinguish different types of atrial tachyarrhythmias. The inherent complexity and mechanistic and clinical inter-relationships often brings about diagnostic difficulties to treating physicians and primary health care professionals creating frequent misdiagnoses and cross classifications using visual criteria. The current paper presents a methodology for ECG based pattern analysis for detection of atrial flutter, atrial fibrillation and normal sinus rhythm beats. ECG is an inherently non-linear and non-stationary signal; its variation may contain indicators of current disease, or warnings about impending cardiac diseases. Routinely used time domain and frequency domain methods will not be able to capture the hidden information present in the ECG beats. In the present study, we have used non-linear features of higher order spectra (HOS) to differentiate the normal, atrial fibrillation and atrial flutter ECG beats. The bispectrum features were subjected to independent component analysis (ICA) for data reduction. The ICA coefficients were subsequently subjected to K-nearest-neighbor (KNN), classification and regression tree (CART) and neural network (NN) classifiers to evaluate the best automated classifier. We have obtained an average accuracy of 97.65%, sensitivity and specificity of 98.75% and 99.53% respectively using ten-fold cross validation. Overall, the results show that application of higher order spectra statistics is useful for the classification of atrial tachyarrhythmias with reasonably high accuracies. Further validation of the proposed technique will yield acceptable results for clinical implementation. PMID:24109623

  20. Automated, reproducible delineation of zones at risk from inundation by large volcanic debris flows

    USGS Publications Warehouse

    Schilling, Steve P.; Iverson, Richard M.

    1997-01-01

    Large debris flows can pose hazards to people and property downstream from volcanoes. We have developed a rapid, reproducible, objective, and inexpensive method to delineate distal debris-flow hazard zones. Our method employs the results of scaling and statistical analyses of the geometry of volcanic debris flows (lahars) to predict inundated valley cross-sectional areas (A) and planimetric areas (B) as functions of lahar volume. We use a range of specified lahar volumes to evaluate A and B. In a Geographic Information System (GIS) we employ the resulting range of predicted A and B to delineate gradations in inundation hazard, which is highest near the volcano and along valley thalwegs and diminishes as distances from the volcano and elevations above valley floors increase. Comparison of our computer-generated hazard maps with those constructed using traditional, field-based methods indicates that our method can provide an accurate means of delineating lahar hazard zones.

  1. Delineation, characterization, and classification of topographic eminences

    NASA Astrophysics Data System (ADS)

    Sinha, Gaurav

    Topographic eminences are defined as upwardly rising, convex shaped topographic landforms that are noticeably distinct in their immediate surroundings. As opposed to everyday objects, the properties of a topographic eminence are dependent not only on how it is conceptualized, but is also intrinsically related to its spatial extent and its relative location in the landscape. In this thesis, a system for automated detection, delineation and characterization of topographic eminences based on an analysis of digital elevation models is proposed. Research has shown that conceptualization of eminences (and other landforms) is linked to the cultural and linguistic backgrounds of people. However, the perception of stimuli from our physical environment is not subject to cultural or linguistic bias. Hence, perceptually salient morphological and spatial properties of the natural landscape can form the basis for generically applicable detection and delineation of topographic eminences. Six principles of cognitive eminence modeling are introduced to develop the philosophical foundation of this research regarding eminence delineation and characterization. The first step in delineating eminences is to automatically detect their presence within digital elevation models. This is achieved by the use of quantitative geomorphometric parameters (e.g., elevation, slope and curvature) and qualitative geomorphometric features (e.g., peaks, passes, pits, ridgelines, and valley lines). The process of eminence delineation follows that of eminence detection. It is posited that eminences may be perceived either as monolithic terrain objects, or as composites of morphological parts (e.g., top, bottom, slope). Individual eminences may also simultaneously be conceived as comprising larger, higher order eminence complexes (e.g., mountain ranges). Multiple algorithms are presented for the delineation of simple and complex eminences, and the morphological parts of eminences. The proposed eminence

  2. Delineation of fault zones using imaging radar

    NASA Technical Reports Server (NTRS)

    Toksoz, M. N.; Gulen, L.; Prange, M.; Matarese, J.; Pettengill, G. H.; Ford, P. G.

    1986-01-01

    The assessment of earthquake hazards and mineral and oil potential of a given region requires a detailed knowledge of geological structure, including the configuration of faults. Delineation of faults is traditionally based on three types of data: (1) seismicity data, which shows the location and magnitude of earthquake activity; (2) field mapping, which in remote areas is typically incomplete and of insufficient accuracy; and (3) remote sensing, including LANDSAT images and high altitude photography. Recently, high resolution radar images of tectonically active regions have been obtained by SEASAT and Shuttle Imaging Radar (SIR-A and SIR-B) systems. These radar images are sensitive to terrain slope variations and emphasize the topographic signatures of fault zones. Techniques were developed for using the radar data in conjunction with the traditional types of data to delineate major faults in well-known test sites, and to extend interpretation techniques to remote areas.

  3. Computer Aids Delineation Of Boundaries In Farmlands

    NASA Technical Reports Server (NTRS)

    Slyle, R.; Cheng, T.; Ma, M.; Angelici, G.

    1992-01-01

    Computer-aided stratification (CAS) procedure developmental procedure of image-processing computer equipment and programs partly automating delineation of boundaries between areas. These areas, "primary sampling units", are images of primarily agricultural lands composed by melding digital Landsat Thematic Mapper data and Digital Line Graph data from United States Geological Survey. CAS output data used as inputs for subsequent sampling procedures from which statistics on uses of agricultural lands developed.

  4. Multimodality Tumor Delineation and Predictive Modelling via Fuzzy-Fusion Deformable Models and Biological Potential Functions

    NASA Astrophysics Data System (ADS)

    Wasserman, Richard Marc

    The radiation therapy treatment planning (RTTP) process may be subdivided into three planning stages: gross tumor delineation, clinical target delineation, and modality dependent target definition. The research presented will focus on the first two planning tasks. A gross tumor target delineation methodology is proposed which focuses on the integration of MRI, CT, and PET imaging data towards the generation of a mathematically optimal tumor boundary. The solution to this problem is formulated within a framework integrating concepts from the fields of deformable modelling, region growing, fuzzy logic, and data fusion. The resulting fuzzy fusion algorithm can integrate both edge and region information from multiple medical modalities to delineate optimal regions of pathological tissue content. The subclinical boundaries of an infiltrating neoplasm cannot be determined explicitly via traditional imaging methods and are often defined to extend a fixed distance from the gross tumor boundary. In order to improve the clinical target definition process an estimation technique is proposed via which tumor growth may be modelled and subclinical growth predicted. An in vivo, macroscopic primary brain tumor growth model is presented, which may be fit to each patient undergoing treatment, allowing for the prediction of future growth and consequently the ability to estimate subclinical local invasion. Additionally, the patient specific in vivo tumor model will be of significant utility in multiple diagnostic clinical applications.

  5. More Accurate Definition of Clinical Target Volume Based on the Measurement of Microscopic Extensions of the Primary Tumor Toward the Uterus Body in International Federation of Gynecology and Obstetrics Ib-IIa Squamous Cell Carcinoma of the Cervix

    SciTech Connect

    Xie, Wen-Jia; Wu, Xiao; Xue, Ren-Liang; Lin, Xiang-Ying; Kidd, Elizabeth A.; Yan, Shu-Mei; Zhang, Yao-Hong; Zhai, Tian-Tian; Lu, Jia-Yang; Wu, Li-Li; Zhang, Hao; Huang, Hai-Hua; Chen, Zhi-Jian; Li, De-Rui; Xie, Liang-Xi

    2015-01-01

    Purpose: To more accurately define clinical target volume for cervical cancer radiation treatment planning by evaluating tumor microscopic extension toward the uterus body (METU) in International Federation of Gynecology and Obstetrics stage Ib-IIa squamous cell carcinoma of the cervix (SCCC). Patients and Methods: In this multicenter study, surgical resection specimens from 318 cases of stage Ib-IIa SCCC that underwent radical hysterectomy were included. Patients who had undergone preoperative chemotherapy, radiation, or both were excluded from this study. Microscopic extension of primary tumor toward the uterus body was measured. The association between other pathologic factors and METU was analyzed. Results: Microscopic extension toward the uterus body was not common, with only 12.3% of patients (39 of 318) demonstrating METU. The mean (±SD) distance of METU was 0.32 ± 1.079 mm (range, 0-10 mm). Lymphovascular space invasion was associated with METU distance and occurrence rate. A margin of 5 mm added to gross tumor would adequately cover 99.4% and 99% of the METU in the whole group and in patients with lymphovascular space invasion, respectively. Conclusion: According to our analysis of 318 SCCC specimens for METU, using a 5-mm gross tumor volume to clinical target volume margin in the direction of the uterus should be adequate for International Federation of Gynecology and Obstetrics stage Ib-IIa SCCC. Considering the discrepancy between imaging and pathologic methods in determining gross tumor volume extent, we recommend a safer 10-mm margin in the uterine direction as the standard for clinical practice when using MRI for contouring tumor volume.

  6. An automatic, stagnation point based algorithm for the delineation of Wellhead Protection Areas

    NASA Astrophysics Data System (ADS)

    Tosco, Tiziana; Sethi, Rajandrea; di Molfetta, Antonio

    2008-07-01

    Time-related capture areas are usually delineated using the backward particle tracking method, releasing circles of equally spaced particles around each well. In this way, an accurate delineation often requires both a very high number of particles and a manual capture zone encirclement. The aim of this work was to propose an Automatic Protection Area (APA) delineation algorithm, which can be coupled with any model of flow and particle tracking. The computational time is here reduced, thanks to the use of a limited number of nonequally spaced particles. The particle starting positions are determined coupling forward particle tracking from the stagnation point, and backward particle tracking from the pumping well. The pathlines are postprocessed for a completely automatic delineation of closed perimeters of time-related capture zones. The APA algorithm was tested for a two-dimensional geometry, in homogeneous and nonhomogeneous aquifers, steady state flow conditions, single and multiple wells. Results show that the APA algorithm is robust and able to automatically and accurately reconstruct protection areas with a very small number of particles, also in complex scenarios.

  7. Development of a software for quantitative evaluation radiotherapy target and organ-at-risk segmentation comparison.

    PubMed

    Kalpathy-Cramer, Jayashree; Awan, Musaddiq; Bedrick, Steven; Rasch, Coen R N; Rosenthal, David I; Fuller, Clifton D

    2014-02-01

    Modern radiotherapy requires accurate region of interest (ROI) inputs for plan optimization and delivery. Target delineation, however, remains operator-dependent and potentially serves as a major source of treatment delivery error. In order to optimize this critical, yet observer-driven process, a flexible web-based platform for individual and cooperative target delineation analysis and instruction was developed in order to meet the following unmet needs: (1) an open-source/open-access platform for automated/semiautomated quantitative interobserver and intraobserver ROI analysis and comparison, (2) a real-time interface for radiation oncology trainee online self-education in ROI definition, and (3) a source for pilot data to develop and validate quality metrics for institutional and cooperative group quality assurance efforts. The resultant software, Target Contour Testing/Instructional Computer Software (TaCTICS), developed using Ruby on Rails, has since been implemented and proven flexible, feasible, and useful in several distinct analytical and research applications. PMID:24043593

  8. A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population.

    PubMed

    Pelleymounter, Linda L; Moon, Irene; Johnson, Julie A; Laederach, Alain; Halvorsen, Matt; Eckloff, Bruce; Abo, Ryan; Rossetti, Sandro

    2011-12-01

    The detection of single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) with precision from high-throughput data remains a significant bioinformatics challenge. Accurate detection is necessary before next-generation sequencing can routinely be used in the clinic. In research, scientific advances are inhibited by gaps in data, exemplified by the underrepresented discovery of rare variants, variants in non-coding regions and indels. The continued presence of false positives and false negatives prevents full automation and requires additional manual verification steps. Our methodology presents applications of both pattern recognition and sensitivity analysis to eliminate false positives and aid in the detection of SNP/indel loci and genotypes from high-throughput data. We chose FK506-binding protein 51(FKBP5) (6p21.31) for our clinical target because of its role in modulating pharmacological responses to physiological and synthetic glucocorticoids and because of the complexity of the genomic region. We detected genetic variation across a 160 kb region encompassing FKBP5. 613 SNPs and 57 indels, including a 3.3 kb deletion were discovered. We validated our method using three independent data sets and, with Sanger sequencing and Affymetrix and Illumina microarrays, achieved 99% concordance. Furthermore we were able to detect 267 novel rare variants and assess linkage disequilibrium. Our results showed both a sensitivity and specificity of 98%, indicating near perfect classification between true and false variants. The process is scalable and amenable to automation, with the downstream filters taking only 1.5h to analyze 96 individuals simultaneously. We provide examples of how our level of precision uncovered the interactions of multiple loci, their predicted influences on mRNA stability, perturbations of the hsp90 binding site, and individual variation in FKBP5 expression. Finally we show how our discovery of rare variants may change current

  9. Tree Crown Delineation using Watershed Techniques and Forest Metrics from NEON LiDAR Data

    NASA Astrophysics Data System (ADS)

    Luong, K. Y.

    2014-12-01

    LiDAR is a powerful remote sensing tool allowing for forest metrics to be taken on varying scales, which ultimately provide important forestry variables used to calculate factors such as total biomass or leaf area index. These variables are most useful when calculated for individual trees throughout a stand, but in very dense forests, identifying single trees becomes more difficult by traditional means. Full forests can be quantified uniquely for the best understanding of ecological contributions as opposed to purely in situ tree inventories which are time consuming and extremely localized. Canopy height models (CHM) can be used to understand the forest as a whole. By inverting the CHM, the tree data becomes sinks in the ground, mimicking ponds; by applying watershed-related spatial analyst tools in ArcGIS and GrassGIS, the trees are delineated by makeshift "flooding." Within this algorithm, the crown peaks are also extracted as an intermediate step to delineation, but this is a reliable means to obtain an accurate number of trees, as well as their individual heights with high reliability (R2 = 0.87). Delineated tree polygons can be directly overlaid onto different rasters to get many forest variables. In tightly clustered and very sparse stands, this method of delineation has a high level of accuracy. Following the workflow studies conducted on NEON LiDAR data on the Soaproot Saddle site, a ground-truth comparison was made with the Teakettle Experimental Forest site due to the availability of tree inventory data.

  10. Delineating future megathrust rupture in southern Cascadia with episodic tremor and slip

    NASA Astrophysics Data System (ADS)

    Szeliga, W. M.; Melbourne, T. I.; Brudzinski, M. R.

    2012-12-01

    Recent work using a suite of 15 ETS events imaged with GPS and seismic data between 1997-2008 beneath the Olympic Peninsula region of the northern Cascadia subduction zone has shown that the fault is accumulating stress to at least 25 km depth, well inland of the Pacific coast. Although delineated by using ETS, this plate coupling profile also accurately predicts current, GPS-measured interseismic deformation of the overlying North America plate, as constrained by nearly 100 new continuous GPS receivers. Moreover, when extrapolated over the 550-year average recurrence interval of great Cascadia megathrust earthquakes, the ETS-delineated coupling profile also replicates both the pattern and amplitude of coseismic coastal subsidence inferred for previous great earthquakes. GPS-determined slip and seismic tremor thus offers a new means of mapping current fault locking, future rupture magnitude, and associated hazards of future earthquakes on the Cascadia megathrust fault. Since the installation of the plate boundary observatory, along-strike variations in interplate coupling along the southern Cascadia arc are now constrained by more than 200 cGPS and 300 seismic stations. We have utilized this recently expanded network to extend the ETS-delineation of interplate coupling to the southern Cascadia subduction zone. We present estimates of the along-strike variation of seismogenic plate coupling along the southern Cascadia megathrust fault using Episodic Tremor and Slip (ETS). Importantly, this ETS-delineation of seismogenic locking refines previous estimates of megathrust hazards along the Oregon and northern California coastal regions.

  11. DNA Probe Pooling for Rapid Delineation of Chromosomal Breakpoints

    SciTech Connect

    Lu, Chun-Mei; Kwan, Johnson; Baumgartner, Adolf; Weier, Jingly F.; Wang, Mei; Escudero, Tomas; Munne', Santiago; Zitzelsberger, Horst F.; Weier, Heinz-Ulrich

    2009-01-30

    Structural chromosome aberrations are hallmarks of many human genetic diseases. The precise mapping of translocation breakpoints in tumors is important for identification of genes with altered levels of expression, prediction of tumor progression, therapy response, or length of disease-free survival as well as the preparation of probes for detection of tumor cells in peripheral blood. Similarly, in vitro fertilization (IVF) and preimplantation genetic diagnosis (PGD) for carriers of balanced, reciprocal translocations benefit from accurate breakpoint maps in the preparation of patient-specific DNA probes followed by a selection of normal or balanced oocytes or embryos. We expedited the process of breakpoint mapping and preparation of case-specific probes by utilizing physically mapped bacterial artificial chromosome (BAC) clones. Historically, breakpoint mapping is based on the definition of the smallest interval between proximal and distal probes. Thus, many of the DNA probes prepared for multi-clone and multi-color mapping experiments do not generate additional information. Our pooling protocol described here with examples from thyroid cancer research and PGD accelerates the delineation of translocation breakpoints without sacrificing resolution. The turnaround time from clone selection to mapping results using tumor or IVF patient samples can be as short as three to four days.

  12. A tree canopy height delineation method based on Morphological Reconstruction—Open Crown Decomposition

    NASA Astrophysics Data System (ADS)

    Liu, Q.; Jing, L.; Li, Y.; Tang, Y.; Li, H.; Lin, Q.

    2016-04-01

    For the purpose of forest management, high resolution LIDAR and optical remote sensing imageries are used for treetop detection, tree crown delineation, and classification. The purpose of this study is to develop a self-adjusted dominant scales calculation method and a new crown horizontal cutting method of tree canopy height model (CHM) to detect and delineate tree crowns from LIDAR, under the hypothesis that a treetop is radiometric or altitudinal maximum and tree crowns consist of multi-scale branches. The major concept of the method is to develop an automatic selecting strategy of feature scale on CHM, and a multi-scale morphological reconstruction–open crown decomposition (MRCD) to get morphological multi-scale features of CHM by: cutting CHM from treetop to the ground; analysing and refining the dominant multiple scales with differential horizontal profiles to get treetops; segmenting LiDAR CHM using watershed a segmentation approach marked with MRCD treetops. This method has solved the problems of false detection of CHM side-surface extracted by the traditional morphological opening canopy segment (MOCS) method. The novel MRCD delineates more accurate and quantitative multi-scale features of CHM, and enables more accurate detection and segmentation of treetops and crown. Besides, the MRCD method can also be extended to high optical remote sensing tree crown extraction. In an experiment on aerial LiDAR CHM of a forest of multi-scale tree crowns, the proposed method yielded high-quality tree crown maps.

  13. Grading More Accurately

    ERIC Educational Resources Information Center

    Rom, Mark Carl

    2011-01-01

    Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…

  14. Hydrocone groundwater study delineates petroleum contamination

    SciTech Connect

    Prochaska, K.; Hartness, J.; Christenson, K.

    1994-12-31

    Law Environmental, Inc., (LAW), conducted a groundwater survey at Myrtle Beach Air Force Base, South Carolina, to delineate the horizontal and vertical extent of petroleum contamination at the BX Service station. The survey was performed using the In-Situ Technology Hydrocone in conjunction with a field gas chromatograph. The Hydrocone proved to be a reliable, cost-effective method of extracting multi-depth groundwater samples without incurring the expenses associated with the installation and maintenance of monitoring wells. The process generates virtually no investigation-derived waste. The Hydrocone system consists of an elongated cylindrical steel sampler attached to drill rods on a direct push trailer mounted rig. A gas/electronic cable connects to the sampler, and a computer installed on the rig displays pressure on the tool, sampling time, and groundwater volume collected. A total of 18 groundwater samples were collected from 12 locations around the site at sampling depths of approximately 10, 20, and 30 feet below the ground surface. The Hydrocone/gas chromatograph method produced a large volume of groundwater quality data within a relatively short time interval.

  15. Delineating groundwater and subsurface structures by

    NASA Astrophysics Data System (ADS)

    Araffa, Sultan Awad Sultan; Helaly, Ahmed S.; Khozium, Ashraf; Lala, Amir M. S.; Soliman, Shokry A.; Hassan, Noha M.

    2015-06-01

    Geophysical tools such as magnetic, gravity and electric resistivity have been used to delineate subsurface structures, groundwater aquifer around Cairo-Belbies Desert road. A dipole-dipole section was measured at the central part of the study area with 2100 m length and electrode spacing 50 m for greater penetration depth. The results of the inverse resistivity data indicate that the study area includes two groundwater aquifers at different depths. The shallow aquifer water is near the surface and the deep aquifer lies at depth of about 115 m and exhibits low resistivity values ranging from 20 to 100 ohm m. One hundred and fifty-two gravity stations were measured using Autograv gravimeter (CG3), different gravity corrections (drift, elevation and latitude corrections) were applied. The corrected data represented by Bouguer anomaly map were filtered into regional and residual gravity anomaly maps. The residual gravity map indicates that the area is dissected by many faults with NW-SE, N-S, E-W and NE-SW trends. One hundred and fifty-three ground magnetic measurements are collected using two Proton magnetometers (Envimag). The corrected magnetic data are represented by total magnetic intensity map that was reduced to the magnetic pole. 3D magnetic modeling was applied to detect the depth of basaltic sheet and basement complex. The results indicated that the elevation of upper surface of basalt is ranging from 148 to -153 m and the elevation of lower surface of basalt is ranging from 148 to 269 m.

  16. Adaptive technique for P and T wave delineation in electrocardiogram signals.

    PubMed

    Bayasi, Nourhan; Tekeste, Temesghen; Saleh, Hani; Khandoker, Ahsan; Mohammad, Baker; Ismail, Mohammed

    2014-01-01

    The T and P waves of electrocardiogram signals are excellent indicators in the analysis and interpretation of cardiac arrhythmia. As such, the need to address and develop an accurate delineation technique for the detection of these waves is necessary. In this paper, we present a novel robust and adaptive T and P wave delineation method for real-time analysis and nonstandard ECG morphologies. The proposed method is based on ECG signal filtering, value estimation of different fiducial points, applying backward and forward search windows as well as adaptive thresholds. Simulations and evaluations prove the accuracy of the proposed technique in comparison to those proposed techniques in the literature. The mean error for the T peak, T offset, P peak and P offset values are found to be 9.8, 2.3, 7.3 and 3.5 milliseconds, respectively, based on the Physionet QT database, rendering our algorithm as an excellent candidate for ECG signal analysis. PMID:25569904

  17. Accurate monotone cubic interpolation

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1991-01-01

    Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.

  18. Accurate Finite Difference Algorithms

    NASA Technical Reports Server (NTRS)

    Goodrich, John W.

    1996-01-01

    Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.

  19. 18 CFR 415.43 - Mapped and unmapped delineations.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Mapped and unmapped delineations. 415.43 Section 415.43 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Administration § 415.43 Mapped and unmapped delineations. (a) Whenever...

  20. 18 CFR 415.43 - Mapped and unmapped delineations.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Administration § 415.43 Mapped and unmapped delineations. (a) Whenever an official flood plain map providing the pertinent information is available with respect to a given project, the map shall be used for the delineation of the flood hazard area,...

  1. 18 CFR 415.43 - Mapped and unmapped delineations.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Administration § 415.43 Mapped and unmapped delineations. (a) Whenever an official flood plain map providing the pertinent information is available with respect to a given project, the map shall be used for the delineation of the flood hazard area,...

  2. 18 CFR 415.43 - Mapped and unmapped delineations.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Administration § 415.43 Mapped and unmapped delineations. (a) Whenever an official flood plain map providing the pertinent information is available with respect to a given project, the map shall be used for the delineation of the flood hazard area,...

  3. Eye Choice for Acquisition of Targets in Alternating Strabismus

    PubMed Central

    Economides, John R.; Adams, Daniel L.

    2014-01-01

    In strabismus, potentially either eye can inform the brain about the location of a target so that an accurate saccade can be made. Sixteen human subjects with alternating exotropia were tested dichoptically while viewing stimuli on a tangent screen. Each trial began with a fixation cross visible to only one eye. After the subject fixated the cross, a peripheral target visible to only one eye flashed briefly. The subject's task was to look at it. As a rule, the eye to which the target was presented was the eye that acquired the target. However, when stimuli were presented in the far nasal visual field, subjects occasionally performed a “crossover” saccade by placing the other eye on the target. This strategy avoided the need to make a large adducting saccade. In such cases, information about target location was obtained by one eye and used to program a saccade for the other eye, with a corresponding latency increase. In 10/16 subjects, targets were presented on some trials to both eyes. Binocular sensory maps were also compiled to delineate the portions of the visual scene perceived with each eye. These maps were compared with subjects' pattern of eye choice for target acquisition. There was a correspondence between suppression scotoma maps and the eye used to acquire peripheral targets. In other words, targets were fixated by the eye used to perceive them. These studies reveal how patients with alternating strabismus, despite eye misalignment, manage to localize and capture visual targets in their environment. PMID:25355212

  4. Delineation of the movement disorders associated with FOXG1 mutations

    PubMed Central

    Papandreou, Apostolos; Schneider, Ruth B.; Augustine, Erika F.; Ng, Joanne; Mankad, Kshitij; Meyer, Esther; McTague, Amy; Ngoh, Adeline; Hemingway, Cheryl; Robinson, Robert; Varadkar, Sophia M.; Kinali, Maria; Salpietro, Vincenzo; O'Driscoll, Margaret C.; Basheer, S. Nigel; Webster, Richard I.; Mohammad, Shekeeb S.; Pula, Shpresa; McGowan, Marian; Trump, Natalie; Jenkins, Lucy; Elmslie, Frances; Scott, Richard H.; Hurst, Jane A.; Perez-Duenas, Belen; Paciorkowski, Alexander R.

    2016-01-01

    Objective: The primary objective of this research was to characterize the movement disorders associated with FOXG1 mutations. Methods: We identified patients with FOXG1 mutations who were referred to either a tertiary movement disorder clinic or tertiary epilepsy service and retrospectively reviewed medical records, clinical investigations, neuroimaging, and available video footage. We administered a telephone-based questionnaire regarding the functional impact of the movement disorders and perceived efficacy of treatment to the caregivers of one cohort of participants. Results: We identified 28 patients with FOXG1 mutations, of whom 6 had previously unreported mutations. A wide variety of movement disorders were identified, with dystonia, choreoathetosis, and orolingual/facial dyskinesias most commonly present. Ninety-three percent of patients had a mixed movement disorder phenotype. In contrast to the phenotype classically described with FOXG1 mutations, 4 patients with missense mutations had a milder phenotype, with independent ambulation, spoken language, and normocephaly. Hyperkinetic involuntary movements were a major clinical feature in these patients. Of the symptomatic treatments targeted to control abnormal involuntary movements, most did not emerge as clearly beneficial, although 4 patients had a caregiver-reported response to levodopa. Conclusions: Abnormal involuntary movements are a major feature of FOXG1 mutations. Our study delineates the spectrum of movement disorders and confirms an expanding clinical phenotype. Symptomatic treatment may be considered for severe or disabling cases, although further research regarding potential treatment strategies is necessary. PMID:27029630

  5. Optimising delineation accuracy of tumours in PET for radiotherapy planning using blind deconvolution

    PubMed Central

    Guvenis, A.; Koc, A.

    2015-01-01

    Positron emission tomography (PET) imaging has been proven to be useful in radiotherapy planning for the determination of the metabolically active regions of tumours. Delineation of tumours, however, is a difficult task in part due to high noise levels and the partial volume effects originating mainly from the low camera resolution. The goal of this work is to study the effect of blind deconvolution on tumour volume estimation accuracy for different computer-aided contouring methods. The blind deconvolution estimates the point spread function (PSF) of the imaging system in an iterative manner in a way that the likelihood of the given image being the convolution output is maximised. In this way, the PSF of the imaging system does not need to be known. Data were obtained from a NEMA NU-2 IQ-based phantom with a GE DSTE-16 PET/CT scanner. The artificial tumour diameters were 13, 17, 22, 28 and 37 mm with a target/background ratio of 4:1. The tumours were delineated before and after blind deconvolution. Student's two-tailed paired t-test showed a significant decrease in volume estimation error (p < 0.001) when blind deconvolution was used in conjunction with computer-aided delineation methods. A manual delineation confirmation demonstrated an improvement from 26 to 16 % for the artificial tumour of size 37 mm while an improvement from 57 to 15 % was noted for the small tumour of 13 mm. Therefore, it can be concluded that blind deconvolution of reconstructed PET images may be used to increase tumour delineation accuracy. PMID:25836686

  6. Automatic delineation of geomorphological slope units

    NASA Astrophysics Data System (ADS)

    Alvioli, Massimiliano; Marchesini, Ivan; Fiorucci, Federica; Ardizzone, Francesca; Rossi, Mauro; Reichenbach, Paola; Guzzetti, Fausto

    2014-05-01

    Slope units are portions of land surface, defined by the general requirement of maximizing homogeneity within a single unit and heterogeneity between different units, but whose formal characterization and practical delineation has been done in different ways. This is often justified by the statement that the slope unit partitioning of a territory can be used to describe a variety of landforms and processes, and for the assessment of natural hazards. As a result, they need to be tailored according to the specific model in use. This may result in an ambiguous definition of such objects, while an objective definition is highly desirable, which would also allow their reproducibility. We have developed a publicly accessible Web Processing Service (WPS) with the aim of incrementally achieve a satisfactory definition of slope unit. The service allows any user to connect to a CNR-IRPI (Perugia) server, upload his own Digital Elevation Model (DEM) and optional additional data, specify parameters constraining the size and aspect of slope units, and quickly obtain the result in a layer in vector format. The calculation is performed using a parallel algorithm, resulting in a processing time short enough to allow the user to tune the input parameters, repeating the process for a sufficient number of times in order to obtain a satisfactory result. We use quantitative criteria to define and draw the slope units, depending on the input parameters. The algorithm starts from a hydrologically consistent partition of the study area into half-basins with a large number of contributing DEM cells. Each of the half-basins is then checked against a few requirements: maximum area required by the user and maximum standard deviation of the aspect on two orthogonal directions. Those specific half-basin that do not meet the requirements are partitioned further, requiring a lower number of contributing cells. The process is iterated until no half-basin exceeds the user-specified thresholds. Our

  7. A detailed study on Catchment delineation for Urban areas

    NASA Astrophysics Data System (ADS)

    Sharma, B.; B M, A.; Lohani, B.; Jain, A.

    2015-12-01

    Urban flood modelling is carried out for predicting, analysing and planning of floods in urban areas. Catchment information is an important input for urban flood modelling. Automatic catchment delineation at gully gratings for urban areas using appropriate software packages/methods along with an appropriate set of input data and parameters is still a research challenge. Considering the above, the aim of this study is to (i) identify the best suitable software for automatic catchment delineation by considering gully grating as outlet (ii) understand the effect of resolution of DEM on catchments delineated (iii) understand whether to consider DEM or DSM for catchment delineation (iv) study the effect of grid based and TIN based DEM. In this study catchment delineation has been investigated considering IIT Kanpur as a study site. LiDAR data are used to generate DEM/DSM of the study area. A comparative study of catchment delineation has been carried out between ArcHydro 10.1, BASINS 4.1, ArcSWAT, WMS 7.1, and HEC-GeoHMS approaches. Catchments have been delineated for different drainage threshold areas using gully grating points as outlets and their effects have been compared for the aforementioned software. In order to understand the effect of resolution of data, DEMs of 1m and 5m resolution have been generated and compared against each other. Effects of building ridge lines and their contribution to catchment delineation has been studied by generating a DSM of 1m resolution, and comparing the results with catchments delineated using 1m DEM. In order to assess the effects of the types of DEM over catchment delineation, a grid based DEM and TIN based DEM are compared against each other using WMS 7.1 software. The results for the catchment delineation using various software illustrate that ArcHydro 10.1 performs better than any other aforementioned software. Also, it is noted that varied drainage threshold area parameters, resolutions of DEM, selection of DEM

  8. Accurate measurement of time

    NASA Astrophysics Data System (ADS)

    Itano, Wayne M.; Ramsey, Norman F.

    1993-07-01

    The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.

  9. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  10. Computerized Delineation of Nuclei in Liquid-Based Pap Smears stained with immunohistochemical biomarkers

    PubMed Central

    Qin, Yi; Walts, Ann E.; Knudsen, Beatrice S.; Gertych, Arkadiusz

    2014-01-01

    Background Infection with high-risk human papillomaviruses (hrHPV) is a frequent cause of cervical intraepithelial neoplasias and carcinomas. The recently developed p16/Ki67 dual-stain of cytologic preparations possesses superior specificity over current HPV testing for detecting moderate and high-grade dysplasias and can potentially be applied in routine cytology screening. Image analysis can possibly improve the efficiency of evaluating Pap smears, if dual stained nuclei are accurately localized and reliably distinguished from the background of other cells. Methods Here we describe a technique comprising color deconvolution, radial symmetry detector and a superpixel-based segmentation for computerized delineation of nuclei in Pap smears stained with p16/Ki67. Results The performance of the method was determined by the precision and recall in 99 images (n=19323 cells) and reached 0.952 and 0.958, respectively. The accuracy of delineation, assessed by the Jaccard index (n=1080 cells), was 0.794. In single cells the precision and recall was higher than in clumps (p = 0.005). Conclusions In summary, the new technique delineates large and small nuclei irrespectively of coloration with a significantly better performance than a method solely involving the radial symmetry detector. Therefore, it is suited to automatically define nuclear areas for quantification of nuclear biomarkers in smears. PMID:25280117

  11. SU-E-J-07: A Functional MR Protocol for the Pancreatic Tumor Delineation

    SciTech Connect

    Andreychenko, A; Heerkens, H; Meijer, G; Vulpen, M van; Lagendijk, J; Berg, C van den

    2014-06-01

    Purpose: Pancreatic cancer is one of the cancers with the poorest survival prognosis. At the time of diagnosis most of pancreatic cancers are unresectable and those patients can be treated by radiotherapy. Radiotherapy for pancreatic cancer is limited due to uncertainties in CT-based delineations. MRI provides an excellent soft tissue contrast. Here, an MR protocol is developed to improve delineations for radiotherapy treatment of pancreatic cancer. In a later stage this protocol can also be used for on-line visualization of the pancreas during MRI guided treatments. Methods: Nine pancreatic cancer patients were included. The MR protocol included T2 weighted(T2w), T1 weighted(T1w), diffusion weighted(DWI) and dynamic contrast enhanced(DCE) techniques. The tumor was delineated on T2w and T1w MRI by an experienced radiation oncologist. Healthy pancreas or pancreatitis (assigned by the oncologist based on T2w) areas were also delineated. Apparent diffusion coefficient(ADC), and area under the curve(AUC)/time to peak(TTP) maps were obtained from DWI and DCE scans, respectively. Results: A clear demarcation of tumor area was visible on b800 DWI images in 5 patients. ADC maps of those patients characterized tumor as an area with restricted water diffusion. Tumor delineations based on solely DCE were possible in 7 patients. In 6 of those patients AUC maps demonstrated tumor heterogeneity: a hypointense area with a hyperintense ring. TTP values clearly discriminated the tumor and the healthy pancreas but could not distinguish tumor and the pancreatitis accurately. Conclusion: MR imaging results in a more pronounced tumor contrast than contrast enhanced CT. The addition of quantitative, functional MRI provides valuable, additional information to the radiation oncologist on the spatial tumor extent by discriminating tumor from the healthy pancreas(TTP, DWI) and characterizing the tumor(ADC). Our findings indicate that tumor delineation in pancreatic cancer can greatly

  12. How large is the Upper Indus Basin? The pitfalls of auto-delineation using DEMs

    NASA Astrophysics Data System (ADS)

    Khan, Asif; Richards, Keith S.; Parker, Geoffrey T.; McRobie, Allan; Mukhopadhyay, Biswajit

    2014-02-01

    Extraction of watershed areas from Digital Elevation Models (DEMs) is increasingly required in a variety of environmental analyses. It is facilitated by the availability of DEMs based on remotely sensed data, and by Geographical Information System (GIS) software. However, accurate delineation depends on the quality of the DEM and the methodology adopted. This paper considers automated and supervised delineation in a case study of the Upper Indus Basin (UIB), Pakistan, for which published estimates of the basin area show significant disagreement, ranging from 166,000 to 266,000 km2. Automated delineation used ArcGIS Archydro and hydrology tools applied to three good quality DEMs (two from SRTM data with 90m resolution, and one from 30m resolution ASTER data). Automatic delineation defined a basin area of c.440,000 km2 for the UIB, but included a large area of internal drainage in the western Tibetan Plateau. It is shown that discrepancies between different estimates reflect differences in the initial extent of the DEM used for watershed delineation, and the unchecked effect of iterative pit-filling of the DEM (going beyond the filling of erroneous pixels to filling entire closed basins). For the UIB we have identified critical points where spurious addition of catchment area has arisen, and use Google Earth to examine the geomorphology adjacent to these points, and also examine the basin boundary data provided by the HydroSHEDS database. We show that the Pangong Tso watershed and some other areas in the western Tibetan plateau are not part of the UIB, but are areas of internal drainage. Our best estimate of the area of the Upper Indus Basin (at Besham Qila) is 164,867 km2 based on the SRTM DEM, and 164,853 km2 using the ASTER DEM). This matches the catchment area measured by WAPDA SWHP. An important lesson from this investigation is that one should not rely on automated delineation, as iterative pit-filling can produce spurious drainage networks and basins, when

  13. Delinating Thermohaline Double-Diffusive Rayleigh Regimes

    NASA Astrophysics Data System (ADS)

    Graf, T.; Walther, M.; Kolditz, O.; Liedl, R.

    2013-12-01

    In natural systems, convective flow induced from density differences may occur in near-coastal aquifers, atmospheric boundary layers, oceanic streams or within the earth crust. Whether an initially stable, diffusive regime evolves into a convective (stable or chaotic) regime, or vice versa, depends on the system's framing boundary conditions. A conventional parameter to express the relation between diffusive and convective forces of such a density-driven regime is Rayleigh number (Ra). While most systems are mainly dominated by only a single significant driving force (i.e. only temperature or salinity), some systems need to consider two boundary processes (e.g. deep, thus warm, haline flow in porous media). In that case, a two-dimensional, 'double-diffusive' Rayleigh system can be defined. Nield (1998) postulated a boundary between diffusive and convective regime at RaT + RaC = 4pi^2 in the first quadrant (Q1), with Rayleigh numbers for temperature and concentration respectively. The boundary in the forth quadrant (Q4) could not exactly be determined, yet the approximate position estimated. Simulations with HydroGeoSphere (Therrien, 2010) using a vertical, quadratic, homogeneous, isotropic setup confirmed the existence of the 4pi^2-boundary and revealed additional regimes (diffusive, single-roll, double-roll, chaotic) in Q1. Also, non-chaotic, oscillating patterns could be identified in Q4. More detailed investigations with OpenGeoSys (Kolditz, 2012) confirmed the preceding HGS results, and, using a 1:10-scaled domain (height:length), uncovered even more distinctive regimes (diffusive, minimum ten roles, supposely up to 25 roles, and chaotic?) in Q1, while again, oscillating patterns were found in the transition zone between diffusive and chaotic regimes in Q4. Output of numerical simulations from Q1 and Q4 show the mentioned regimes (diffusive, stable-convective, stable-oscillatory, chaotic) while results are displayed in context of a possible delination between

  14. 1. PHOTOCOPY OF HISTORIC DRAWING OF SHIP SECTION, UNKNOWN DELINEATOR ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. PHOTOCOPY OF HISTORIC DRAWING OF SHIP SECTION, UNKNOWN DELINEATOR AND DATE, SOURCE: BISHOP MUSEUM, HONOLULU, HI. - Ship "Falls of Clyde", Hawaii Maritime Center,Pier 7, Honolulu, Honolulu County, HI

  15. Photocopy of site plan, Dene Hendrick, delineator, 1977, for the ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Photocopy of site plan, Dene Hendrick, delineator, 1977, for the City of San Jose in cooperative agreement with the California Department of Transportation (from the San Jose Historical Museum) - Stevens Ranch Complex, State Route 101, Coyote, Santa Clara County, CA

  16. 356. Delineator Unknown March 1946 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    356. Delineator Unknown March 1946 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; GENERAL DATA; PLAT III - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  17. Polymer delineation system. [Patent application: traffic lane lines

    DOEpatents

    Woolman, S.; Steinberg, M.

    1975-06-24

    A delineation system (traffic lane lines) for highways is described in which polymerizable substances are applied to existing or newly prepared highway pavements. The substances would contain a suitable pigment and may incorporate reflective elements.

  18. 10. Photocopy of map (from Benicia Historical Society) Delineator unknown ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. Photocopy of map (from Benicia Historical Society) Delineator unknown May 1, 1894, revised to Mar. 27, 1918 'MAP OF BENICIA ARSENAL RESERVATION' - Benicia Arsenal, Benicia Industrial Park, Benicia, Solano County, CA

  19. 22. Photocopy of drawing Delineator unknown, ca. 1931 Wright Studio, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    22. Photocopy of drawing Delineator unknown, ca. 1931 Wright Studio, photographer View from Kellogg Blvd. - St. Paul City Hall & Ramsey County Courthouse, 15 West Kellogg Boulevard, Saint Paul, Ramsey County, MN

  20. Description and application of capture zone delineation for a wellfield at Hilton Head Island, South Carolina

    USGS Publications Warehouse

    Landmeyer, J.E.

    1994-01-01

    Ground-water capture zone boundaries for individual pumped wells in a confined aquffer were delineated by using groundwater models. Both analytical and numerical (semi-analytical) models that more accurately represent the $round-water-flow system were used. All models delineated 2-dimensional boundaries (capture zones) that represent the areal extent of groundwater contribution to a pumped well. The resultant capture zones were evaluated on the basis of the ability of each model to realistically rapresent the part of the ground-water-flow system that contributed water to the pumped wells. Analytical models used were based on a fixed radius approach, and induded; an arbitrary radius model, a calculated fixed radius model based on the volumetric-flow equation with a time-of-travel criterion, and a calculated fixed radius model derived from modification of the Theis model with a drawdown criterion. Numerical models used induded the 2-dimensional, finite-difference models RESSQC and MWCAP. The arbitrary radius and Theis analytical models delineated capture zone boundaries that compared least favorably with capture zones delineated using the volumetric-flow analytical model and both numerical models. The numerical models produced more hydrologically reasonable capture zones (that were oriented parallel to the regional flow direction) than the volumetric-flow equation. The RESSQC numerical model computed more hydrologically realistic capture zones than the MWCAP numerical model by accounting for changes in the shape of capture zones caused by multiple-well interference. The capture zone boundaries generated by using both analytical and numerical models indicated that the curnmtly used 100-foot radius of protection around a wellhead in South Carolina is an underestimate of the extent of ground-water capture for pumped wetis in this particular wellfield in the Upper Floridan aquifer. The arbitrary fixed radius of 100 feet was shown to underestimate the upgradient

  1. Coverage-based treatment planning to accommodate delineation uncertainties in prostate cancer treatment

    PubMed Central

    Xu, Huijun; Gordon, J. James; Siebers, Jeffrey V.

    2015-01-01

    Purpose: To compare two coverage-based planning (CP) techniques with fixed margin-based (FM) planning for high-risk prostate cancer treatments, with the exclusive consideration of the dosimetric impact of delineation uncertainties of target structures and normal tissues. Methods: In this work, 19-patient data sets were involved. To estimate structure dose for each delineated contour under the influence of interobserver contour variability and CT image quality limitations, 1000 alternative structures were simulated by an average-surface-of-standard-deviation model, which utilized the patient-specific information of delineated structure and CT image contrast. An IMRT plan with zero planning-target-volume (PTV) margin on the delineated prostate and seminal vesicles [clinical-target-volume (CTVprostate) and CTVSV] was created and dose degradation due to contour variability was quantified by the dosimetric consequences of 1000 alternative structures. When D98 failed to achieve a 95% coverage probability objective D98,95 ≥ 78 Gy (CTVprostate) or D98,95 ≥ 66 Gy (CTVSV), replanning was performed using three planning techniques: (1) FM (PTVprostate margin = 4,5,6 mm and PTVSV margin = 4,5,7 mm for RL, PA, and SI directions, respectively), (2) CPOM which optimized uniform PTV margins for CTVprostate and CTVSV to meet the D98,95 objectives, and (3) CPCOP which directly optimized coverage-based objectives for all the structures. These plans were intercompared by computing percentile dose-volume histograms and tumor-control probability/normal tissue complication probability (TCP/NTCP) distributions. Results: Inherent contour variability resulted in unacceptable CTV coverage for the zero-PTV-margin plans for all patients. For plans designed to accommodate contour variability, 18/19 CP plans were most favored by achieving desirable D98,95 and TCP/NTCP values. The average improvement of probability of complication free control was 9.3% for CPCOP plans and 3.4% for CPOM plans

  2. Microbial species delineation using whole genome sequences

    PubMed Central

    Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Kostas; Kyrpides, Nikos C.; Pati, Amrita

    2015-01-01

    Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. PMID:26150420

  3. Delineate subsurface structures with ground penetrating radar

    SciTech Connect

    Wyatt, D.E.; Hu, L.Z.; Ramaswamy, M.; Sexton, B.G.

    1992-10-01

    High resolution ground penetrating radar (GPR) surveys were conducted at the Savannah River Site in South Carolina in late 1991 to demonstrate the radar techniques in imaging shallow utility and soil structures. Targets of interest at two selected sites, designated as H- and D-areas, were a buried backfilled trench, buried drums, geologic stratas, and water table. Multiple offset 2-D and single offset 3-D survey methods were used to acquire high resolution radar data. This digital data was processed using standard seismic processing software to enhance signal quality and improve resolution. Finally, using a graphics workstation, the 3D data was interpreted. In addition, a small 3D survey was acquired in The Woodlands, Texas, with very dense spatial sampling. This data set adequately demonstrated the potential of this technology in imaging subsurface features.

  4. Delineate subsurface structures with ground penetrating radar

    SciTech Connect

    Wyatt, D.E. ); Hu, L.Z. ); Ramaswamy, M. ); Sexton, B.G. )

    1992-01-01

    High resolution ground penetrating radar (GPR) surveys were conducted at the Savannah River Site in South Carolina in late 1991 to demonstrate the radar techniques in imaging shallow utility and soil structures. Targets of interest at two selected sites, designated as H- and D-areas, were a buried backfilled trench, buried drums, geologic stratas, and water table. Multiple offset 2-D and single offset 3-D survey methods were used to acquire high resolution radar data. This digital data was processed using standard seismic processing software to enhance signal quality and improve resolution. Finally, using a graphics workstation, the 3D data was interpreted. In addition, a small 3D survey was acquired in The Woodlands, Texas, with very dense spatial sampling. This data set adequately demonstrated the potential of this technology in imaging subsurface features.

  5. Delineating small karst watersheds based on digital elevation model and eco-hydrogeological principles

    NASA Astrophysics Data System (ADS)

    Jie Luo, Guang; Jie Wang, Shi; Bai, Xiao Yong; Liu, Xiu Ming; Cheng, An Yun

    2016-03-01

    Dominated by specific eco-hydrogeological backgrounds, a small watershed delineated by using the traditional method is always inauthentic in karst regions because it cannot accurately reflect the eco-hydrological process of the dual structure of the surface and subsurface. This study proposes a new method for the delineation of small watersheds based on digital elevation models (DEMs) and eco-hydrogeological principles in karst regions. This method is applied to one section of the tributary area (Sancha River) of the Yangtze River in China. By comparing the quantity, shape, superimposition, and characteristics of the internal hydrological process of a small watershed extracted by using the digital elevation model with that extracted by using the proposed method of this study, we conclude that the small karst watersheds extracted by the new method accurately reflect the hydrological process of the river basin. Furthermore, we propose that the minimum unit of the river basin in karst regions should be the watershed, whose exit is the corrosion and corrasion baselevel and a further division of watershed may cause a significant inconsistency with the true eco-hydrological process.

  6. Improvement in Interobserver Accuracy in Delineation of the Lumpectomy Cavity Using Fiducial Markers

    SciTech Connect

    Shaikh, Talha; Chen Ting; Khan, Atif; Yue, Ning J.

    2010-11-15

    Purpose: To determine, whether the presence of gold fiducial markers would improve the inter- and intraphysician accuracy in the delineation of the surgical cavity compared with a matched group of patients who did not receive gold fiducial markers in the setting of accelerated partial-breast irradiation (APBI). Methods and Materials: Planning CT images of 22 lumpectomy cavities were reviewed in a cohort of 22 patients; 11 patients received four to six gold fiducial markers placed at the time of surgery. Three physicians categorized the seroma cavity according to cavity visualization score criteria and delineated each of the 22 seroma cavities and the clinical target volume. Distance between centers of mass, percentage overlap, and average surface distance for all patients were assessed. Results: The mean seroma volume was 36.9 cm{sup 3} and 34.2 cm{sup 3} for fiducial patients and non-fiducial patients, respectively (p = ns). Fiducial markers improved the mean cavity visualization score, to 3.6 {+-} 1.0 from 2.5 {+-} 1.3 (p < 0.05). The mean distance between centers of mass, average surface distance, and percentage overlap for the seroma and clinical target volume were significantly improved in the fiducial marker patients as compared with the non-fiducial marker patients (p < 0.001). Conclusions: The placement of gold fiducial markers placed at the time of lumpectomy improves interphysician identification and delineation of the seroma cavity and clinical target volume. This has implications in radiotherapy treatment planning for accelerated partial-breast irradiation and for boost after whole-breast irradiation.

  7. Delineating parton distributions and the strong coupling

    DOE PAGESBeta

    Jimenez-Delgado, P.; Reya, E.

    2014-04-29

    In this study, global fits for precision determinations of parton distributions, together with the highly correlated strong coupling αs, are presented up to next-to-next-to- leading order (NNLO) of QCD utilizing most world data (charm and jet production data are used where theoretically possible), except Tevatron gauge boson production data and LHC data which are left for genuine predictions. This is done within the 'dynamical' (valencelike input at Q02 = 0.8 GeV2 ) and 'standard' (input at Q02 = 2 GeV2) approach. The stability and reliability of the results are ensured by including nonperturbative higher-twist terms, nuclear corrections as well asmore » target mass corrections, and by applying various (Q2, W2) cuts on available data. In addition, the Q02 dependence of the results is studied in detail. Predictions are given, in particular for LHC, on gauge and Higgs boson as well as for top-quark pair production. At NNLO the dynamical approach results in αs(MZ2) = 0.1136 ± 0.0004, whereas the somewhat less constrained standard fit gives αs(MZ2) = 0.1162 ± 0.0006.« less

  8. Respiration effect on single and multi lead ECG delineation strategies.

    PubMed

    Noriega, M; Martinez, J P; Laguna, P; Romero, D; Bailon, R; Almeida, R

    2010-01-01

    The main purpose of this work is to study the influence of the mechanical effect of the respiration over T wave end delineation. The performance of automatic delineation systems based in Wavelet Transform (WT) was compared, considering single lead (SL), post processing selection rules (SLR) and multi lead (ML) approaches. The T wave locations obtained over real and simulated ECG signals were analyzed together with the respective respiratory signal (ECG-derived or simulated). The linear relation between the variations on obtained marks and the mechanical effect of the respiration was measured using spectral coherence. With respect to the ML strategy we also explored the evolution of the vectorcardiographic spatial loop using the direction of maximum projection of the WT in the region close to the T wave end (T(e)). The relation between this direction and the respiration is also explored. The marks obtained from the SLR and ML delineation strategies show advantage over the SL strategy based marks. The coherence around the respiratory frequency between the respiratory signal and the error in T end marks was found to be higher using SLR (a minimum of 0.92) than using ML (a maximum of 0.80). According to obtained results, the multi lead delineation presents a lower sensibility to the mechanical effect of the respiration for the T wave end delineation, particularly the obtained with ML. PMID:21096831

  9. From anatomical to biological target volumes: the role of PET in radiation treatment planning

    PubMed Central

    Schinagl, D A X; Kaanders, J H A M; Oyen, W J G

    2006-01-01

    Progress in radiation oncology requires a re-evaluation of the methods of target volume delineation beyond anatomical localization. New molecular imaging techniques for tumour visualisation such as positron emission tomography (PET) provide insight into tumour characteristics and can be complementary to the anatomical data of computed tomography or magnetic resonance imaging. In this review, three issues are discussed: First, can PET identify a tumour more accurately? Second, can biological tumour characteristics be visualised? Third, can intratumoural heterogeneity of these characteristics be identified? PMID:17114062

  10. Comparison of Eh and H2 measurements for delineating redox processes in a contaminated aquifer

    USGS Publications Warehouse

    Chapelle, Francis H.; Haack, Sheridan K.; Adriaens, Peter; Henry, Mark A.; Bradley, Paul M.

    1996-01-01

    Measurements of oxidation−reduction potential (Eh) and concentrations of dissolved hydrogen (H2) were made in a shallow groundwater system contaminated with solvents and jet fuel to delineate the zonation of redox processes. Eh measurements ranged from +69 to −158 mV in a cross section of the contaminated plume and accurately delineated oxic from anoxic groundwater. Plotting measured Eh and pH values on an equilibrium stability diagram indicated that Fe(III) reduction was the predominant redox process in the anoxic zone and did not indicate the presence of methanogenesis and sulfate reduction. In contrast, measurements of H2concentrations indicated that methanogenesis predominated in heavily contaminated sediments near the water table surface (H2 ∼ 7.0 nM) and that the methanogenic zone was surrounded by distinct sulfate-reducing (H2 ∼ 1−4 nM) and Fe(III)-reducing (H2 ∼ 0.1−0.8 nM) zones. The presence of methanogenesis, sulfate reduction, and Fe(III) reduction was confirmed by the distribution of dissolved oxygen, sulfate, Fe(II), and methane in groundwater. These results show that H2 concentrations were more useful for identifying anoxic redox processes than Ehmeasurements in this groundwater system. However, H2-based redox zone delineations are more reliable when H2 concentrations are interpreted in the context of electron-acceptor (oxygen, nitrate, sulfate) availability and the presence of final products [Fe(II), sulfide, methane] of microbial metabolism.

  11. 362. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    362. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SAN FRANCISCO ANCHORAGE; EYE BAR ANCHOR CHAIN; CONTRACT NO. 3; SUP. DRAWING NO. 11-A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  12. 374. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    374. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; YERBA BUENA CROSSING; EYE BAR CHAIN; CONTRACT NO. 5; SUP. DRAWING NO. 12A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  13. 359. Delineator Unknown April 1935 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    359. Delineator Unknown April 1935 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; BRIDGE RAILWAY SAN FRANCISCO LOOP; DETAILS OF VIADUCT; FINAL REPORT; DRG. NO. 92 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  14. 385. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    385. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - WEST BAY CROSSING; ROCKER POSTS AND BEARING; CONTRACT NO. 6; DRAWINGS NO. 42 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  15. 390. Delineator Unknown October 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    390. Delineator Unknown October 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - EAST BAY CROSSING; SPANS YBI TO El - E9 TO El ; TYPICAL CROSSSECTION; CONTRACT NO. 7; SUP. DRAWING NO. 82 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  16. 379. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    379. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CABLES AND ATTACHMENTS - WEST BAY CROSSING; SPLAY CASTINGS; CONTRACT NO. 6A; DRAWING NO. 4 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  17. 375. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    375. Delineator Unknown June 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; YERBA BUENA CROSSING; ANCHORAGE TUNNELS; CONTRACT NO. 5; DRAWING NO. 10A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  18. 380. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    380. Delineator Unknown December 1932 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CABLES & ATTACHMENTS WEST BAY CROSSING; CABLE BANDS; CONTRACT NO. 6A; DRAWING NO. 3 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  19. 1. Photocopy of site plan, Dene Hendrick, delineator, 1977, for ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Photocopy of site plan, Dene Hendrick, delineator, 1977, for the City of San Jose in cooperative agreement with the California Department of Transportation (from the San Jose Historical Museum). - Twin Oaks Dairy, Northwest of Metcalfe Road, off State Route 101 (Monterey Road), Coyote, Santa Clara County, CA

  20. Delineation of nuclear structures in 3D multicellular systems

    2013-09-13

    A pipeline, implemented within the Insight Segmentation and Registration Toolkit (ITK) and The Visualization Toolkit (VTK) framework, to delineate each nucleus and to profile morphometric and colony organization. At an abstract level, our approach is an extension of a previously developed method for monolayer call structure models.

  1. The Regionalization of Africa: Delineating Africa's Subregions Using Airline Data

    ERIC Educational Resources Information Center

    Good, Pieter R.; Derudder, Ben; Witlox, Frank J.

    2011-01-01

    Current regionalizations of Africa have limitations in that they are attribute-based and regions are delineated according to national boundaries. Taking the world city network approach as starting point, it is possible to use relational data (i.e., information about the relationships between cities) rather than attribute data, and moreover, it…

  2. 43 CFR 3420.3-3 - Preliminary tract delineation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 43 Public Lands: Interior 2 2011-10-01 2011-10-01 false Preliminary tract delineation. 3420.3-3 Section 3420.3-3 Public Lands: Interior Regulations Relating to Public Lands (Continued) BUREAU OF LAND MANAGEMENT, DEPARTMENT OF THE INTERIOR MINERALS MANAGEMENT (3000) COMPETITIVE LEASING Competitive Leasing § 3420.3-3 Preliminary tract...

  3. 18 CFR 415.43 - Mapped and unmapped delineations.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Mapped and unmapped... ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Administration § 415.43 Mapped and unmapped delineations. (a) Whenever an official flood plain map providing the pertinent information is available...

  4. 406. Delineator Unknown April 19, 1933 ELEVATION STUDY FOR SAN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    406. Delineator Unknown April 19, 1933 ELEVATION STUDY FOR SAN FRANCISCO ANCHORAGE; SAN FRANCISCO - OAKLAND BAY BRIDGE; BOARD OF CONSULTING ARCHITECTS; TIMOTHY L. PFLUEGER, ARTHUR BROWN JR., JOHN J. DONOVAN; SHEET 23 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  5. Dynamic Stereochemistry: A Simple Approach to Delineating Relative Configuration

    ERIC Educational Resources Information Center

    Mandal, Dipak K.

    2007-01-01

    A simple approach for delineating the stereochemistry of the products relative to that of the reactants in reactions involving stereogenic centers is addressed. The reaction at the tetrahedral center involves the cleavage of a bond to one of the ligands in the reactant and the resulting new ligand in the product is labeled by affixing prime to the…

  6. 1. Photocopy of delineation circa 1910 from The Bells Ringing ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. Photocopy of delineation circa 1910 from The Bells Ringing the Message of Progress in Monroe County, Pa. 1915, pp. 96-7 GENERAL VIEW OF FARM - John Turn Farm, River Road (Middle Smithfield Township), Shawnee on Delaware, Monroe County, PA

  7. Automated Radiation Targeting in Head-and-Neck Cancer Using Region-Based Texture Analysis of PET and CT Images

    SciTech Connect

    Yu Huan; Caldwell, Curtis Mah, Katherine; Poon, Ian; Balogh, Judith; MacKenzie, Robert; Khaouam, Nader; Tirona, Romeo

    2009-10-01

    Purpose: A co-registered multimodality pattern analysis segmentation system (COMPASS) was developed to automatically delineate the radiation targets in head-and-neck cancer (HNC) using both {sup 18}F-fluoro-deoxy glucose-positron emission tomography (PET) and computed tomography (CT) images. The performance of the COMPASS was compared with the results of existing threshold-based methods and radiation oncologist-drawn contours. Methods and Materials: The COMPASS extracted texture features from corresponding PET and CT voxels. Using these texture features, a decision-tree-based K-nearest-neighbor classifier labeled each voxel as either 'normal' or 'abnormal.' The COMPASS was applied to the PET/CT images of 10 HNC patients. Automated segmentation results were validated against the manual segmentations of three radiation oncologists using the volume, sensitivity, and specificity. The performance of the COMPASS was compared with three PET-based threshold methods: standard uptake value of 2.5, 50% maximal intensity, and signal/background ratio. Results: The tumor delineations of the COMPASS were both quantitatively and qualitatively more similar to those of the radiation oncologists than the delineations from the other methods. The specificity was 95% {+-} 2%, 84% {+-} 9%, 98% {+-} 3%, and 96% {+-} 4%, and the sensitivity was 90% {+-} 12%, 93% {+-} 10%, 48% {+-} 20%, and 68% {+-} 25% for the COMPASS, for a standard uptake value of 2.5, 50% maximal intensity, and signal/background ratio, respectively. The COMPASS distinguished HNC from adjacent normal tissues with high physiologic uptake and consistently defined tumors with large variability in {sup 18}F-fluoro-deoxy glucose uptake, which are often problematic with the threshold-based methods. Conclusion: Automated segmentation using texture analysis of PET/CT images has the potential to provide accurate delineation of HNC. This could lead to reduced interobserver variability, reduced uncertainty in target delineation

  8. Dynamic Puddle Delineation and Threshold-Driven Hydrotopographic Processes

    NASA Astrophysics Data System (ADS)

    Chu, X.; Yang, J.; Habtezion, N.

    2012-12-01

    DEM-based watershed delineation is a common practice and an essential step for watershed hydrologic and environmental modeling. Generally, this is a one-time work. That is, such a delineated watershed with invariant overland flow properties (e.g., flow directions, flow accumulations, and contributing areas) and a "fixed" drainage system is then used for modeling under any hydrologic conditions, including rainfall, surface ponding, soil moisture, and other conditions. This method herein is referred to as "static delineation." Additionally, it is assumed in many existing watershed models that the entire watershed contributes surface runoff to the outlet. In reality, however, a watershed surface is not a uniformly inclined plane surface and overland flow may not be sheet flow. Threshold behaviors associated with surface topography can be critical. Flow directions and accumulations for any grids may change over time, depending upon the surface depression filling-merging-spilling dynamics. Particularly, contributing areas vary, not only in relation to the watershed properties, but also the inputs of the system, such as rainfall characteristics. In the current study, we developed a new "dynamic" delineation method to precisely characterize depressions/puddles, their hydrotopographic properties and hierarchical relationships, and the threshold-controlled dynamics. Efforts also were made to deal with complex topographic conditions (e.g., flats). Testing of the new method and program was performed by using a set of topographic surfaces. In addition, an object-oriented approach was developed for image-based topographic analysis and extraction of topographic features, which were compared with the delineation results.

  9. Comparison of three nonparametric kriging methods for delineating heavy-metal contaminated soils

    SciTech Connect

    Juang, K.W.; Lee, D.Y

    2000-02-01

    The probability of pollutant concentrations greater than a cutoff value is useful for delineating hazardous areas in contaminated soils. It is essential for risk assessment and reclamation. In this study, three nonparametric kriging methods [indicator kriging, probability kriging, and kriging with the cumulative distribution function (CDF) of order statistics (CDF kriging)] were used to estimate the probability of heavy-metal concentrations lower than a cutoff value. In terms of methodology, the probability kriging estimator and CDF kriging estimator take into account the information of the order relation, which is not considered in indicator kriging. Since probability kriging has been shown to be better than indicator kriging for delineating contaminated soils, the performance of CDF kriging, which the authors propose, was compared with that of probability kriging in this study. A data set of soil Cd and Pb concentrations obtained from a 10-ha heavy-metal contaminated site in Taoyuan, Taiwan, was used. The results demonstrated that the probability kriging and CDF kriging estimations were more accurate than the indicator kriging estimation. On the other hand, because the probability kriging was based on the cokriging estimator, some unreliable estimates occurred in the probability kriging estimation. This indicated that probability kriging was not as robust as CDF kriging. Therefore, CDF kriging is more suitable than probability kriging for estimating the probability of heavy-metal concentrations lower than a cutoff value.

  10. Kriging with cumulative distribution function of order statistics for delineation of heavy-metal contaminated soils

    SciTech Connect

    Juang, K.W.; Lee, D.Y.; Hsiao, C.K.

    1998-10-01

    Accurate delineation of contaminated soils is essential for risk assessment and remediation. The probability of pollutant concentrations lower than a cutoff value is more important than the best estimate of pollutant concentrations for unsampled locations in delineating contaminated soils. In this study, a new method, kriging with the cumulative distribution function (CDF) of order statistics (CDF kriging), is introduced and compared with indicator kriging. It is used to predict the probability that extractable concentrations of Zn will be less than a cut-off value for soils to be declared hazardous. The 0.1 M HCl-extractable Zn concentrations of topsoil of a paddy field having an area of about 2000 ha located in Taiwan are used. A comparison of the CDF of order statistics and indicator function transformation shows that the variance and the coefficient of variation (CV) of the CDF of order statistics transformed data are smaller than those of the indicator function transformed data. This suggests that the CDF of order statistics transformation possesses less variability than does the indicator function transformation. In addition, based on cross-validation, CDF kriging is found to reduce the mean squared errors of estimations by about 30% and to reduce the mean kriging variances by about 26% compared with indicator kriging.

  11. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  12. Techniques of Fluorescence Cholangiography During Laparoscopic Cholecystectomy for Better Delineation of the Bile Duct Anatomy

    PubMed Central

    Kono, Yoshiharu; Ishizawa, Takeaki; Tani, Keigo; Harada, Nobuhiro; Kaneko, Junichi; Saiura, Akio; Bandai, Yasutsugu; Kokudo, Norihiro

    2015-01-01

    Abstract To evaluate the clinical and technical factors affecting the ability of fluorescence cholangiography (FC) using indocyanine green (ICG) to delineate the bile duct anatomy during laparoscopic cholecystectomy (LC). Application of FC during LC began after laparoscopic fluorescence imaging systems became commercially available. In 108 patients undergoing LC, FC was performed by preoperative intravenous injection of ICG (2.5 mg) during dissection of Calot's triangle, and clinical factors affecting the ability of FC to delineate the extrahepatic bile ducts were evaluated. Equipment-related factors associated with bile duct detectability were also assessed among 5 laparoscopic systems and 1 open fluorescence imaging system in ex vivo studies. FC delineated the confluence between the cystic duct and common hepatic duct (CyD–CHD) before and after dissection of Calot's triangle in 80 patients (74%) and 99 patients (92%), respectively. The interval between ICG injection and FC before dissection of Calot's triangle was significantly longer in the 80 patients in whom the CyD–CHD confluence was detected by fluorescence imaging before dissection (median, 90 min; range, 15–165 min) than in the remaining 28 patients in whom the confluence was undetectable (median, 47 min; range, 21–205 min; P < 0.01). The signal contrast on the fluorescence images of the bile duct samples was significantly different among the laparoscopic imaging systems and tended to decrease more steeply than those of the open imaging system as the target-laparoscope distance increased and porcine tissues covering the samples became thicker. FC is a simple navigation tool for obtaining a biliary roadmap to reach the “critical view of safety” during LC. Key factors for better bile duct identification by FC are administration of ICG as far in advance as possible before surgery, sufficient extension of connective tissues around the bile ducts, and placement of the tip of

  13. How to accurately bypass damage

    PubMed Central

    Broyde, Suse; Patel, Dinshaw J.

    2016-01-01

    Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203

  14. Accurate Evaluation of Quantum Integrals

    NASA Technical Reports Server (NTRS)

    Galant, David C.; Goorvitch, D.

    1994-01-01

    Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.

  15. Insight on automated lesion delineation methods for PET data

    PubMed Central

    2014-01-01

    Background Defining tumour volume for treatment response and radiotherapy planning is challenging and prone to inter- and intra-observer variability. Various automated tumour delineation methods have been proposed in the literature, each having abilities and limitations. Therefore, there is a need to provide clinicians with practical information on delineation method selection. Methods Six different automated positron emission tomography (PET) delineation methods were evaluated and compared using National Electrical Manufacturer Association image quality (NEMA IQ) phantom data and three in-house synthetic phantoms with clinically relevant lesion shapes including spheres with necrotic core and irregular shapes. The impact of different contrast ratios, emission counts, realisations and reconstruction algorithms on delineation performance was also studied using similarity index (SI) and percentage volume error (%VE) as performance measures. Results With the NEMA IQ phantom, contrast thresholding (CT) performed best on average for all sphere sizes and parameter settings (SI = 0.83; %VE = 5.65% ± 24.34%). Adaptive thresholding at 40% (AT40) was the next best method and required no prior parameter tuning (SI = 0.78; %VE = 23.22% ± 70.83%). When using SUV harmonisation filtering prior to delineation (EQ.PET), AT40 remains the best method without prior parameter tuning (SI = 0.81; %VE = 11.39% ± 85.28%). For necrotic core spheres and irregular shapes of the synthetic phantoms, CT remained the best performing method (SI = 0.83; %VE = 26.31% ± 38.26% and SI = 0.62; %VE = 24.52% ± 46.89%, respectively). The second best method was fuzzy locally adaptive Bayesian (FLAB) (SI = 0.83; %VE = 29.51% ± 81.79%) for necrotic core sphere and AT40 (SI = 0.58; %VE = 25.11% ± 32.41%) for irregular shapes. When using EQ.PET prior to delineation, AT40 was the best performing method without prior

  16. Delineation of LASIK Flaps with Prednisolone Acetate Eyedrops

    PubMed Central

    Fahd, Daoud C; Fahed, Sharbel D

    2014-01-01

    We describe the use and safety of prednisolone acetate eyedrops at the end of laser in situ keratomileusis (LASIK) to aid proper positioning of the corneal flap. The LASIK flap is created using the preferred technique. Following laser ablation and flap repositioning, one drop of prednisolone acetate is instilled on the eye. This delineates the flap “gutters” and allows perfect flap positioning and centration. We used this technique in 425 eyes undergoing LASIK for correction of spherocylindrical refractive errors. Flap margins were adequately delineated intraoperatively. The only complication related to the use of the steroid suspension was crystal deposition under the flap in one case which resolved completely in 48 hours. PMID:24982743

  17. A Comparative Review of North American Tundra Delineations

    NASA Technical Reports Server (NTRS)

    Silver, Kirk C.; Carroll, Mark

    2013-01-01

    Recent profound changes have been observed in the Arctic environment, including record low sea ice extents and high latitude greening. Studying the Arctic and how it is changing is an important element of climate change science. The Tundra, an ecoregion of the Arctic, is directly related to climate change due to its effects on the snow ice feedback mechanism and greenhouse gas cycling. Like all ecoregions, the Tundra border is shifting, yet studies and policies require clear delineation of boundaries. There are many options for ecoregion classification systems, as well as resources for creating custom maps. To help decision makers identify the best classification system possible, we present a review of North American Tundra ecoregion delineations and further explore the methodologies, purposes, limitations, and physical properties of five common ecoregion classification systems. We quantitatively compare the corresponding maps by area using a geographic information system.

  18. Population delineation of polar bears using satellite collar data

    USGS Publications Warehouse

    Bethke, R.; Taylor, M.; Amstrup, S.; Messler, F.

    1996-01-01

    To produce reliable estimates of the size or vital rates of a given population, it is important that the boundaries of the population under study are clearly defined. This is particularly critical for large, migratory animals where levels of sustainable harvest are based on these estimates, and where small errors may have serious long-term consequences for the population. Once populations are delineated, rates of exchange between adjacent populations can be determined and accounted/corrected for when calculating abundance (e.g., based on mark-recapture data). Using satellite radio-collar locations for polar bears in the western Canadian Arctic, we illustrate one approach to delineating wildlife populations that integrates cluster analysis methods for determining group membership with home range plotting procedures to define spatial utilization. This approach is flexible with respect to the specific procedures used and provides an objective and quantitative basis for defining population boundaries.

  19. Interactive boundary delineation of agricultural lands using graphics workstations

    NASA Technical Reports Server (NTRS)

    Cheng, Thomas D.; Angelici, Gary L.; Slye, Robert E.; Ma, Matt

    1992-01-01

    A review is presented of the computer-assisted stratification and sampling (CASS) system developed to delineate the boundaries of sample units for survey procedures. CASS stratifies the sampling units by land-cover and land-use type, employing image-processing software and hardware. This procedure generates coverage areas and the boundaries of stratified sampling units that are utilized for subsequent sampling procedures from which agricultural statistics are developed.

  20. Enhanced delineation of degradation in aortic walls through OCT

    NASA Astrophysics Data System (ADS)

    Real, Eusebio; Val-Bernal, José Fernando; Revuelta, José M.; Pontón, Alejandro; Calvo Díez, Marta; Mayorga, Marta; López-Higuera, José M.; Conde, Olga M.

    2015-03-01

    Degradation of the wall of human ascending thoracic aorta has been assessed through Optical Coherence Tomography (OCT). OCT images of the media layer of the aortic wall exhibit micro-structure degradation in case of diseased aortas from aneurysmal vessels or in aortas prone to aortic dissections. The degeneration in vessel walls appears as low-reflectivity areas due to the invasive appearance of acidic polysaccharides and mucopolysaccharides within a typical ordered microstructure of parallel lamellae of smooth muscle cells, elastin and collagen fibers. An OCT indicator of wall degradation can be generated upon the spatial quantification of the extension of degraded areas in a similar way as conventional histopathology. This proposed OCT marker offers a real-time clinical insight of the vessel status to help cardiovascular surgeons in vessel repair interventions. However, the delineation of degraded areas on the B-scan image from OCT is sometimes difficult due to presence of speckle noise, variable SNR conditions on the measurement process, etc. Degraded areas could be outlined by basic thresholding techniques taking advantage of disorders evidences in B-scan images, but this delineation is not always optimum and requires complex additional processing stages. This work proposes an optimized delineation of degraded spots in vessel walls, robust to noisy environments, based on the analysis of the second order variation of image intensity of backreflection to determine the type of local structure. Results improve the delineation of wall anomalies providing a deeper physiological perception of the vessel wall conditions. Achievements could be also transferred to other clinical scenarios: carotid arteries, aorto-iliac or ilio-femoral sections, intracranial, etc.

  1. Delineation of major soil associations using ERTS-1 imagery

    NASA Technical Reports Server (NTRS)

    Parks, W. L.; Bodenheimer, R. E.

    1973-01-01

    The delineation of a major soil association in the loess region of Obion County has been accomplished using ERTS-1 imagery. Channel 7 provides the clearest differentiation. The separation of other smaller soil associations in an intensive row crop agricultural area is somewhat more difficult. Soil differentiation has been accomplished visually as well as electronically using a scanning microdensitometer. Lower altitude aircraft imagery permits a more refined soil association identification and where imagery is of sufficient scale, even individual soils may be identified.

  2. Delineation of a clinical syndrome caused by mosaic trisomy 15

    SciTech Connect

    Buehler, E.M.; Bienz, G.; Straumann, E.; Bosceh, N.

    1996-03-15

    We report on a boy with mosaic trisomy 15. The clinical manifestations are compared with those of the few cases reported up to now. A clinical syndrome is delineated consisting of a characteristic shape of the nose and other minor craniofacial anomalies, as well as typical deformities of the hands and feet. Different degrees of mosaicism may explain the more or less severe manifestations in individual patients. 10 refs., 4 figs., 1 tab.

  3. A locally adaptive kernel regression method for facies delineation

    NASA Astrophysics Data System (ADS)

    Fernàndez-Garcia, D.; Barahona-Palomo, M.; Henri, C. V.; Sanchez-Vila, X.

    2015-12-01

    Facies delineation is defined as the separation of geological units with distinct intrinsic characteristics (grain size, hydraulic conductivity, mineralogical composition). A major challenge in this area stems from the fact that only a few scattered pieces of hydrogeological information are available to delineate geological facies. Several methods to delineate facies are available in the literature, ranging from those based only on existing hard data, to those including secondary data or external knowledge about sedimentological patterns. This paper describes a methodology to use kernel regression methods as an effective tool for facies delineation. The method uses both the spatial and the actual sampled values to produce, for each individual hard data point, a locally adaptive steering kernel function, self-adjusting the principal directions of the local anisotropic kernels to the direction of highest local spatial correlation. The method is shown to outperform the nearest neighbor classification method in a number of synthetic aquifers whenever the available number of hard data is small and randomly distributed in space. In the case of exhaustive sampling, the steering kernel regression method converges to the true solution. Simulations ran in a suite of synthetic examples are used to explore the selection of kernel parameters in typical field settings. It is shown that, in practice, a rule of thumb can be used to obtain suboptimal results. The performance of the method is demonstrated to significantly improve when external information regarding facies proportions is incorporated. Remarkably, the method allows for a reasonable reconstruction of the facies connectivity patterns, shown in terms of breakthrough curves performance.

  4. Methods for Data-based Delineation of Spatial Regions

    SciTech Connect

    Wilson, John E.

    2012-10-01

    In data analysis, it is often useful to delineate or segregate areas of interest from the general population of data in order to concentrate further analysis efforts on smaller areas. Three methods are presented here for automatically generating polygons around spatial data of interest. Each method addresses a distinct data type. These methods were developed for and implemented in the sample planning tool called Visual Sample Plan (VSP). Method A is used to delineate areas of elevated values in a rectangular grid of data (raster). The data used for this method are spatially related. Although VSP uses data from a kriging process for this method, it will work for any type of data that is spatially coherent and appears on a regular grid. Method B is used to surround areas of interest characterized by individual data points that are congregated within a certain distance of each other. Areas where data are “clumped” together spatially will be delineated. Method C is used to recreate the original boundary in a raster of data that separated data values from non-values. This is useful when a rectangular raster of data contains non-values (missing data) that indicate they were outside of some original boundary. If the original boundary is not delivered with the raster, this method will approximate the original boundary.

  5. Harmonization of the Volume of Interest Delineation among All Eleven Radiotherapy Centers in the North of France

    PubMed Central

    Pasquier, David; Boutaud de la Combe-Chossiere, Laurence; Carlier, Damien; Darloy, Franck; Degrendel-Courtecuisse, Anne Catherine; Dufour, Chantal; Fares, Mustapha; Gilbeau, Laurent; Liem, Xavier; Martin, Philippe; Meyer, Pascal; Minne, Jean François; Olszyk, Olimpia; Rhliouch, Hassan; Tokarski, Marc; Viot, Chloé; Castelain, Bernard; Lartigau, Eric

    2016-01-01

    Background Inter-observer delineation variation has been detailed for many years in almost every tumor location. Inadequate delineation can impair the chance of cure and/or increase toxicity. The aim of our original work was to prospectively improve the homogeneity of delineation among all of the senior radiation oncologists in the Nord-Pas de Calais region, irrespective of the conditions of practice. Methods All 11 centers were involved. The first studied cancer was prostate cancer. Three clinical cases were studied: a low-risk prostate cancer case (case 1), a high-risk prostate cancer case (pelvic nodes, case 2) and a case of post-operative biochemical elevated PSA (case 3). All of the involved physicians delineated characteristically the clinical target volume (CTV) and organs at risk. The volumes were compared using validated indexes: the volume ratio (VR), common and additional volumes (CV and AV), volume overlap (VO) and Dice similarity coefficient (DSC). A second delineation of the same three cases was performed after discussion of the slice results and the choice of shared guidelines to evaluate homogenization. A comparative analysis of the indexes before and after discussion was conducted using the Wilcoxon test for paired samples. A p-value less than 0.05 was considered to indicate statistical significance. Results The indexes were not improved in case 1, for which the inter-observer agreement was considered good after the first comparison (DSC = 0.83±0.06). In case 2, the second comparison showed homogenization of the CTV delineation with a significant improvement in CV (81.4±11.7 vs. 88.6±10.26, respectively, p = 0.048), VO (0.41±0.09 vs. 0.47±0.07, respectively; p = 0.009) and DSC (0.58±0.09 vs. 0.63±0.07, respectively; p = 0.0098). In case 3, VR and AV were significantly improved: VR: 1.71(±0.6) vs. 1.34(±0.46), respectively, p = 0.0034; AV: 46.58(±14.50) vs. 38.08(±15.10), respectively, p = 0.0024. DSC was not improved, but it was already

  6. Impact of FDG-PET/CT on Radiotherapy Volume Delineation in Non-Small-Cell Lung Cancer and Correlation of Imaging Stage With Pathologic Findings

    SciTech Connect

    Faria, Sergio L. Menard, Sonia; Devic, Slobodan; Sirois, Christian; Souhami, Luis; Lisbona, Robert; Freeman, Carolyn R.

    2008-03-15

    Purpose: Fluorodeoxyglucose-positron emission tomography (FDG-PET)/computed tomography (CT) is more accurate than CT in determining the extent of non-small-cell lung cancer. We performed a study to evaluate the impact of FDG-PET/CT on the radiotherapy volume delineation compared with CT without using any mathematical algorithm and to correlate the findings with the pathologic examination findings. Methods and Materials: A total of 32 patients with proven non-small-cell lung cancer, pathologic specimens from the mediastinum and lung primary, and pretreatment chest CT and FDG-PET/CT scans were studied. For each patient, two data sets of theoretical gross tumor volumes were contoured. One set was determined using the chest CT only, and the second, done separately, was based on the co-registered FDG-PET/CT data. The disease stage of each patient was determined using the TNM staging system for three data sets: the CT scan only, FDG-PET/CT scan, and pathologic findings. Results: Pathologic examination altered the CT-determined stage in 22 (69%) of 32 patients and the PET-determined stage in 16 (50%) of 32 patients. The most significant alterations were related to the N stage. PET altered the TNM stage in 15 (44%) of 32 patients compared with CT alone, but only 7 of these 15 alterations were confirmed by the pathologic findings. With respect to contouring the tumor volume for radiotherapy, PET altered the contour in 18 (56%) of 32 cases compared with CT alone. Conclusion: The contour of the tumor volume of non-small-cell lung cancer patients with co-registered FDG-PET/CT resulted in >50% alterations compared with CT targeting, findings similar to those of other publications. However, the significance of this change is unknown. Furthermore, pathologic examination showed that PET is not always accurate and histologic examination should be obtained to confirm the findings of PET whenever possible.

  7. Newer Imaging Modalities to Assist With Target Localization in the Radiation Treatment of Prostate Cancer and Possible Lymph Node Metastases

    SciTech Connect

    John, Subhash S. Zietman, Anthony L.; Shipley, William U.; Harisinghani, Mukesh G.

    2008-05-01

    Precise localization of prostate cancer and the drainage lymph nodes is mandatory to define an accurate clinical target volume for conformal radiotherapy. Better target definition and delineation on a daily basis is surely important in quality assurance for fractionated radiation therapy. This article reviews the evidence for major emerging techniques that show promise in better identifying the clinical target volume. Partial prostate boost by brachytherapy, intensity-modulated radiation therapy, or protons has become possible not only with standard imaging techniques but also with the availability of metabolic images obtained by magnetic resonance spectroscopy. Even though fluorine-18 fluorodeoxyglucose ({sup 18}F-FDG) positron emission tomography has not been found to be useful, novel radiolabeled tracers may eventually prove of value in the diagnosis and treatment planning of prostate cancer. For the metastatic lymph nodes, lymphotropic nanoparticle-enhanced magnetic resonance imaging using ultra-small superparamagnetic iron oxide particles has greater accuracy as compared with conventional techniques and has been instrumental in delineating the lymphatic drainage of the prostate gland. These novel investigational techniques could further help in optimizing conformal radiotherapy for patients with prostate cancer. The concepts of biologic target volume, real target volume, and multidimensional conformal radiotherapy are being explored.

  8. Hessian analysis for the delineation of amorphous anomalies in optical coherence tomography images of the aortic wall

    PubMed Central

    Real, Eusebio; Val-Bernal, José Fernando; Revuelta, José M.; Pontón, Alejandro; Díez, Marta Calvo; Mayorga, Marta; López-Higuera, José M.; Conde, Olga M.

    2016-01-01

    The aortic aneurysm is a disease originated mainly in the media layer of the aortic wall due to the occurrence of degraded areas of altered biological composition. These anomalous regions affect the structure and strength of the aorta artery, being their occurrence and extension proportional to the arterial vessel health. Optical Coherence Tomography (OCT) is applied to obtain cross-sectional images of the artery wall. The backscattering mechanisms in tissue make aorta images difficult to analyze due to noise and strong attenuation with penetration. The morphology of anomalies in pathological specimens is also diverse with amorphous shapes and varied dimensions, being these factors strongly related with tissue degradation and the aorta physiological condition. Hessian analysis of OCT images from aortic walls is used to assess the accurate delineation of these anomalous regions. A specific metric of the Hessian determinant is used to delineate degraded regions under blurry conditions and noise. A multiscale approach, based on an anisotropic Gaussian kernel filter, is applied to highlight and aggregate all the heterogeneity present in the aortic wall. An accuracy estimator metric has been implemented to evaluate and optimize the delineation process avoiding subjectivity. Finally, a degradation quantification score has been developed to assess aorta wall condition by OCT with validation against common histology. PMID:27446665

  9. Evaluation of terrain datasets for LiDAR data thinning and DEM generation for watershed delineation applications

    NASA Astrophysics Data System (ADS)

    Olivera, F.; Ferreira, C.; Djokic, D.

    2010-12-01

    Watershed delineation based on Digital Elevation Models (DEM) is currently a standard practice in hydrologic studies. Efforts to develop DEMs of high resolution continues to take place, although the advantages of increasing the accuracy of the results are partially offset by the increased file size, difficulty to handle them, slow screen rendering and increase computational effort. Among these efforts, those based on the use of Light Detection and Ranging (LiDAR) pose the problem that interpolation techniques in commercially available GIS software packages (e.g., IDW, Spline, Kriging and TOPORASTER, among others) for developing DEMs from point elevations have difficulty processing large amounts of data. Terrain Dataset is an alternative format for storing topographic data that intelligently decimates data points and creates simplified, yet equally accurate for practical purposes, DEMs or Triangular Irregular Networks (TIN). This study uses terrain datasets to evaluate the impact that the thinning method (i.e., window size and z-value), pyramid level and the interpolation technique (linear or natural neighbor) used to create the DEMs have on the watersheds delineated from them. Two case studies were considered for assessing the effect of the different methods and techniques. One of them consisted of dendritic topography in Williamson Creek, Austin, Texas, and the other of deranged topography in Hillsborough County, Florida. The results were compared using three standardized error metrics that measure the accuracy of the watershed boundaries, and computational effort. For the Williamson creek (steeper terrain), point thinning during the terrain creation process or the interpolation method choice did not affect the watershed delineation; while, in the Hillsborough (flat terrain), the method for point thinning and interpolation techniques highly influenced the resulting watershed delineation.

  10. Delineating Rearrangements in Single Yeast Artificial Chromosomes by Quantitative DNA Fiber Mapping

    SciTech Connect

    Weier, Heinz-Ulrich G.; Greulich-Bode, Karin M.; Wu, Jenny; Duell, Thomas

    2009-09-18

    Cloning of large chunks of human genomic DNA in recombinant systems such as yeast or bacterial artificial chromosomes has greatly facilitated the construction of physical maps, the positional cloning of disease genes or the preparation of patient-specific DNA probes for diagnostic purposes. For this process to work efficiently, the DNA cloning process and subsequent clone propagation need to maintain stable inserts that are neither deleted nor otherwise rearranged. Some regions of the human genome; however, appear to have a higher propensity than others to rearrange in any host system. Thus, techniques to detect and accurately characterize such rearrangements need to be developed. We developed a technique termed 'Quantitative DNA Fiber Mapping (QDFM)' that allows accurate tagging of sequence elements of interest with near kilobase accuracy and optimized it for delineation of rearrangements in recombinant DNA clones. This paper demonstrates the power of this microscopic approach by investigating YAC rearrangements. In our examples, high-resolution physical maps for regions within the immunoglobulin lambda variant gene cluster were constructed for three different YAC clones carrying deletions of 95 kb and more. Rearrangements within YACs could be demonstrated unambiguously by pairwise mapping of cosmids along YAC DNA molecules. When coverage by YAC clones was not available, distances between cosmid clones were estimated by hybridization of cosmids onto DNA fibers prepared from human genomic DNA. In addition, the QDFM technology provides essential information about clone stability facilitating closure of the maps of the human genome as well as those of model organisms.

  11. 12. J. Fuss, delineator (from Folder 5) 'PLAN ETC. OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    12. J. Fuss, delineator (from Folder 5) 'PLAN ETC. OF NEW ARSENAL FOR BENICIA DEPOT CAL.' PLAN, ELEVATIONS, SECTIONS, DETAILS (right half of CA-1828-13) 13. (From Folder 5) PLAN, ELEVATION, SECTION (left half of CA-1828-12) 14. (From Folder 2) PLAN, ELEVATION, AND DETAILS OF STONES TO BE CUT 15. (From Folder 4) PLAN AND ELEVATION OF MAIN DOORWAY 16. (From Folder 5) DETAILS OF CANNON EMBRASURES - Benicia Arsenal, Storehouse, Comandant's Lane, Benicia Industrial Park, Benicia, Solano County, CA

  12. Validation of holistic nursing competencies: role-delineation study, 2012.

    PubMed

    Erickson, Helen Lorraine; Erickson, Margaret Elizabeth; Campbell, Joan A; Brekke, Mary E; Sandor, M Kay

    2013-12-01

    The American Holistic Nurses Credentialing Corporation (AHNCC), certifying body for nurses practicing within the precepts of holistic nursing, uses a systematic process to guide program development. A previous publication described their early work that distinguished basic and advanced holistic nursing and development of related examinations. A more recent publication described the work of AHNCC from 2004 to 2012, including a role-delineation study (RDS) that was undertaken to identify and validate competencies currently used by holistic nurses. A final report describes the RDS design, methods, and raw data information. This article discusses AHNCC's goals for undertaking the 2012 Holistic Nursing RDS and the implications for the certification programs. PMID:23783664

  13. Plume Delineation in the BC Cribs and Trenches Area

    SciTech Connect

    Rucker, Dale F.; Sweeney, Mark D.

    2004-11-30

    HydroGEOPHYSICS, Inc. and Pacific Northwest National Laboratory (PNNL) were contracted by Fluor Hanford Group, Inc. to conduct a geophysical investigation in the area of the BC Cribs and Trenches (subject site) at the Hanford Site in Richland, Washington. The BC Cribs and Trenches are located south of the 200 East Area. This document provides the details of the investigation to identify existing infrastructure from legacy disposal activities and to delineate the edges of a groundwater plume that contains radiological and heavy metal constituents beneath the 216-B-26 and 216-B-52 Trenches, and the 216-B-14 through 216-B-19 Cribs.

  14. Delineating forested river habitats and riparian floodplain hydrology with LiDAR

    NASA Astrophysics Data System (ADS)

    Vondrasek, Chris

    Rivers and the riparian forest corridor comprise a valuable freshwater ecosystem that has been altered by human activities including timber management, road building, and other land conversions. The habitats of river dependent species in the Pacific Northwest, in particular salmon have often been degraded by these activities. Many salmon runs have become threatened with extinction and have been Endangered Species Act listed. New conservation planning and policies have developed around protecting freshwater habitats and restoring more natural river processes. In WA State, timber landowners, officials from State and Federal agencies, Native tribes, and other stakeholders developed Forest Practice rules and codified a Habitat Conservation Plan with dual goals of providing regulatory surety for timber land owners and helping to recover the threatened salmon runs in forested watersheds. Conserving critical stream ecological functions and potential fish habitats throughout watersheds while managing and regulating timber harvest across the State requires accurate and up-to-date delineation and mapping of channels, tributaries, and off-channel wetlands. Monitoring the effectiveness of protection efforts is necessary but can also be difficult. Agency staff and resources are limited for both day-to-day implementation of Forest Practice rules and adaptive management. The goal of this research has been to develop efficient and accessible methods to delineate wetlands, side-channels, tributaries, and pools and backwaters created by large log jams in forested watersheds. It was also essential to use publicly available LiDAR data and to model these waters at ecologically meaningful flows. I tested a hydraulic model at a 2-year and 50-year flows, and a relative height above river surface model and compared them. I completed two additional remote sensing investigations to correlate channel movement and the locations of off-channel wetlands: an analysis of historical aerial imagery

  15. An Automated Method for Delineating Braided River Water Surface Area from RGB Imagery

    NASA Astrophysics Data System (ADS)

    Gleason, C. J.; Smith, L. C.; Finnegan, D. C.; LeWinter, A. L.; Pitcher, L. H.; Balog, J. D.

    2012-12-01

    Hydrologic research is increasingly conducted from remote sensing platforms, allowing for efficient, non-contact sampling of hydraulic parameters. In this study, a new method is presented for fully automated delineation of braided river water surfaces from Extreme Ice Survey (EIS) oblique-view RGB camera imagery, enabling rapid calculation of hydraulic parameters such as effective width (inundation area divided by reach length Smith et al., 1995; 1996) and braiding index. The test dataset is 200 high-resolution camera images obtained for the proglacial Isortoq River, southwestern Greenland, in July 2011. First, images are segmented via automated histogram thresholding, a process that also determines which images to reject for poor quality. These quality-screened images then initialize an active contouring (AC) image delineation process using the method of Li et al. (2010). This method seeks to minimize changes in contrast gradients as an initial contour determined by the automated thresholding evolves toward a final, stable solution. Comparison of this coupled thresholding/AC method with traditional supervised classification suggests that supervised classification is superior for low quality images and marginally superior for high quality images. However, this method is time consuming and impractical for long term hydrologic studies with large data volumes. Coupled AC and traditional unsupervised classifications present automated solutions for extracting hydraulic parameters, and AC proved more effective at water surface classification for the river images in this study. Results indicate that an automated solution for image selection and hydraulic parameter calculation for large data volumes can be both accurate and practical. Such a methodology will be useful in numerous hydrologic studies that monitor complex river systems using large data volumes of camera, video, or remotely sensed imagery.

  16. A System for Continual Quality Improvement of Normal Tissue Delineation for Radiation Therapy Treatment Planning

    SciTech Connect

    Breunig, Jennifer; Hernandez, Sophy; Lin, Jeffrey; Alsager, Stacy; Dumstorf, Christine; Price, Jennifer; Steber, Jennifer; Garza, Richard; Nagda, Suneel; Melian, Edward; Emami, Bahman; Roeske, John C.

    2012-08-01

    Purpose: To implement the 'plan-do-check-act' (PDCA) cycle for the continual quality improvement of normal tissue contours used for radiation therapy treatment planning. Methods and Materials: The CT scans of patients treated for tumors of the brain, head and neck, thorax, pancreas and prostate were selected for this study. For each scan, a radiation oncologist and a diagnostic radiologist, outlined the normal tissues ('gold' contours) using Radiation Therapy Oncology Group (RTOG) guidelines. A total of 30 organs were delineated. Independently, 5 board-certified dosimetrists and 1 trainee then outlined the same organs. Metrics used to compare the agreement between the dosimetrists' contours and the gold contours included the Dice Similarity Coefficient (DSC), and a penalty function using distance to agreement. Based on these scores, dosimetrists were re-trained on those organs in which they did not receive a passing score, and they were subsequently re-tested. Results: Passing scores were achieved on 19 of 30 organs evaluated. These scores were correlated to organ volume. For organ volumes <8 cc, the average DSC was 0.61 vs organ volumes {>=}8 cc, for which the average DSC was 0.91 (P=.005). Normal tissues that had the lowest scores included the lenses, optic nerves, chiasm, cochlea, and esophagus. Of the 11 organs that were considered for re-testing, 10 showed improvement in the average score, and statistically significant improvement was noted in more than half of these organs after education and re-assessment. Conclusions: The results of this study indicate the feasibility of applying the PDCA cycle to assess competence in the delineation of individual organs, and to identify areas for improvement. With testing, guidance, and re-evaluation, contouring consistency can be obtained across multiple dosimetrists. Our expectation is that continual quality improvement using the PDCA approach will ensure more accurate treatments and dose assessment in radiotherapy

  17. Medical staff appointment and delineation of pediatric privileges in hospitals.

    PubMed

    Rauch, Daniel A

    2012-04-01

    The review and verification of credentials and the granting of clinical privileges are required of every hospital to ensure that members of the medical staff are competent and qualified to provide specified levels of patient care. The credentialing process involves the following: (1) assessment of the professional and personal background of each practitioner seeking privileges; (2) assignment of privileges appropriate for the clinician's training and experience; (3) ongoing monitoring of the professional activities of each staff member; and (4) periodic reappointment to the medical staff on the basis of objectively measured performance. We examine the essential elements of a credentials review for initial and renewed medical staff appointments along with suggested criteria for the delineation of clinical privileges. Sample forms for the delineation of privileges can be found on the American Academy of Pediatrics Committee on Hospital Care Web site (http://www.aap.org/visit/cmte19.htm). Because of differences among individual hospitals, no 1 method for credentialing is universally applicable. The medical staff of each hospital must, therefore, establish its own process based on the general principles reviewed in this report. The issues of medical staff membership and credentialing have become very complex, and institutions and medical staffs are vulnerable to legal action. Consequently, it is advisable for hospitals and medical staffs to obtain expert legal advice when medical staff bylaws are constructed or revised. PMID:22451705

  18. Ocean-outfall mixing zone delineation using Doppler radar

    SciTech Connect

    Chin, D.A.; Ding, L.; Huang, H.

    1997-12-01

    A methodology has been developed to use data collected by ocean surface current radar (OSCR) systems to predict the fate and transport of pollutants released from ocean outfalls. The proposed OSCR-based transport model was validated at the Miami Central-District (MCD) outfall using data collected during the Southeast Florida Outfall Experiment 2 (SEFLOE 2). A comparison between the measured dye concentration versus distance from the outfall and the predictions of the OSCR-based transport model showed good agreement. A second validation test of the OSCR-based transport model compared the growth of variance versus time and diffusion coefficients versus length scale with the conventional Okubo diagrams for instantaneous tracer releases. This comparison indicated that the mixing characteristics simulated explicitly by the OSCR-based transport model are in good agreement with field measurements in the coastal ocean. Mixing zones based on worst-case and probabilistic criteria were delineated using the OSCR-based model. The results indicate that an OSCR-based transport model is a significant improvement over conventional models that are used to delineate mixing zones surrounding ocean outfalls with surfacing plumes. This claim is strongly supported by the field data collected during the SEFLOE 2 study in south Florida.

  19. Delineating Biophysical Environments of the Sunda Banda Seascape, Indonesia

    PubMed Central

    Wang, Mingshu; Ahmadia, Gabby N.; Chollett, Iliana; Huang, Charles; Fox, Helen; Wijonarno, Anton; Madden, Marguerite

    2015-01-01

    The Sunda Banda Seascape (SBS), located in the center of the Coral Triangle, is a global center of marine biodiversity and a conservation priority. We proposed the first biophysical environmental delineation of the SBS using globally available satellite remote sensing and model-assimilated data to categorize this area into unique and meaningful biophysical classes. Specifically, the SBS was partitioned into eight biophysical classes characterized by similar sea surface temperature, chlorophyll a concentration, currents, and salinity patterns. Areas within each class were expected to have similar habitat types and ecosystem functions. Our work supplemented prevailing global marine management schemes by focusing in on a regional scale with finer spatial resolution. It also provided a baseline for academic research, ecological assessments and will facilitate marine spatial planning and conservation activities in the area. In addition, the framework and methods of delineating biophysical environments we presented can be expanded throughout the whole Coral Triangle to support research and conservation activities in this important region. PMID:25648170

  20. A circumscribing active contour model for delineation of nuclei and membranes of megakaryocytes in bone marrow trephine biopsy images

    NASA Astrophysics Data System (ADS)

    Song, Tzu-Hsi; Sanchez, Victor; EIDaly, Hesham; Rajpoot, Nasir M.

    2015-03-01

    The assessment of megakaryocytes (MKs) in bone marrow trephine images is an important step in the classification of different subtypes of myeloproliferative neoplasms (MPNs). In general, bone marrow trephine images include several types of cells mixed together, which make it quite difficult to visually identify MKs. In order to aid hematopathologists in the identification and study of MKs, we develop an image processing framework with supervised machine learning approaches and a novel circumscribing active contour model to identify potential MKs and then to accurately delineate the corresponding nucleus and membrane. Specifically, a number of color and texture features are used in a nave Bayesian classifier and an Adaboost classifier to locate the regions with a high probability of depicting MKs. A region-based active contour is used on the candidate MKs to accurately delineate the boundaries of nucleus and membrane. The proposed circumscribing active contour model employs external forces not only based on pixel intensities, but also on the probabilities of depicting MKs as computed by the classifiers. Experimental results suggest that the machine learning approach can detect potential MKs with an accuracy of more than 75%. When our circumscribing active contour model is employed on the candidate MKs, the nucleus and membrane boundaries are segmented with an accuracy of more than 80% as measured by the Dice similarity coefficient. Compared to traditional region-based active contours, the use of additional external forces based on the probability of depicting MKs improves segmentation performance and computational time by an average 5%.

  1. Patterns of epidural progression following postoperative spine stereotactic body radiotherapy: implications for clinical target volume delineation.

    PubMed

    Chan, Michael W; Thibault, Isabelle; Atenafu, Eshetu G; Yu, Eugene; John Cho, B C; Letourneau, Daniel; Lee, Young; Yee, Albert; Fehlings, Michael G; Sahgal, Arjun

    2016-04-01

    OBJECT The authors performed a pattern-of-failure analysis, with a focus on epidural disease progression, in patients treated with postoperative spine stereotactic body radiotherapy (SBRT). METHODS Of the 70 patients with 75 spinal metastases (cases) treated with postoperative spine SBRT, there were 26 cases of local disease recurrence and 25 cases with a component of epidural disease progression. Twenty-four of the 25 cases had preoperative epidural disease with subsequent epidural disease progression, and this cohort was the focus of this epidural-specific pattern-of-failure investigation. Preoperative, postoperative, and follow-up MRI scans were reviewed, and epidural disease was characterized based on location according to a system in which the vertebral anatomy is divided into 6 sectors, with the anterior compartment comprising Sectors 1, 2, and 6, and the posterior compartment comprising Sectors 3, 4, and 5. RESULTS Patterns of epidural progression are reported specifically for the 24 cases with preoperative epidural disease and subsequent epidural progression. Epidural disease progression within the posterior compartment was observed to be significantly lower in those with preoperative epidural disease confined to the anterior compartment than in those with preoperative epidural disease involving both anterior and posterior compartments (56% vs 93%, respectively; p = 0.047). In a high proportion of patients with epidural disease progression, treatment failure was found in the anterior compartment, including both those with preoperative epidural disease confined to the anterior compartment and those with preoperative epidural disease involving both anterior and posterior compartments (100% vs. 73%, respectively). When epidural disease was confined to the anterior compartment on the preoperative and postoperative MRIs, no epidural disease progression was observed in Sector 4, which is the most posterior sector. Postoperative epidural disease characteristics alone were not predictive of the pattern of epidural treatment failure. CONCLUSIONS Reviewing the extent of epidural disease on preoperative MRI is imperative when planning postoperative SBRT. When epidural disease is confined to the anterior epidural sectors pre- and postoperatively, covering the entire epidural space circumferentially with a prophylactic "donut" distribution may not be needed. PMID:26682603

  2. Evaluation of catchment delineation methods for the medium-resolution National Hydrography Dataset

    USGS Publications Warehouse

    Johnston, Craig M.; Dewald, Thomas G.; Bondelid, Timothy R.; Worstell, Bruce B.; McKay, Lucinda D.; Rea, Alan; Moore, Richard B.; Goodall, Jonathan L.

    2009-01-01

    Different methods for determining catchments (incremental drainage areas) for stream segments of the medium-resolution (1:100,000-scale) National Hydrography Dataset (NHD) were evaluated by the U.S. Geological Survey (USGS), in cooperation with the U.S. Environmental Protection Agency (USEPA). The NHD is a comprehensive set of digital spatial data that contains information about surface-water features (such as lakes, ponds, streams, and rivers) of the United States. The need for NHD catchments was driven primarily by the goal to estimate NHD streamflow and velocity to support water-quality modeling. The application of catchments for this purpose also demonstrates the broader value of NHD catchments for supporting landscape characterization and analysis. Five catchment delineation methods were evaluated. Four of the methods use topographic information for the delineation of the NHD catchments. These methods include the Raster Seeding Method; two variants of a method first used in a USGS New England study-one used the Watershed Boundary Dataset (WBD) and the other did not-termed the 'New England Methods'; and the Outlet Matching Method. For these topographically based methods, the elevation data source was the 30-meter (m) resolution National Elevation Dataset (NED), as this was the highest resolution available for the conterminous United States and Hawaii. The fifth method evaluated, the Thiessen Polygon Method, uses distance to the nearest NHD stream segments to determine catchment boundaries. Catchments were generated using each method for NHD stream segments within six hydrologically and geographically distinct Subbasins to evaluate the applicability of the method across the United States. The five methods were evaluated by comparing the resulting catchments with the boundaries and the computed area measurements available from several verification datasets that were developed independently using manual methods. The results of the evaluation indicated that the two

  3. Computer-aided boundary delineation of agricultural lands

    NASA Technical Reports Server (NTRS)

    Cheng, Thomas D.; Angelici, Gary L.; Slye, Robert E.; Ma, Matt

    1989-01-01

    The National Agricultural Statistics Service of the United States Department of Agriculture (USDA) presently uses labor-intensive aerial photographic interpretation techniques to divide large geographical areas into manageable-sized units for estimating domestic crop and livestock production. Prototype software, the computer-aided stratification (CAS) system, was developed to automate the procedure, and currently runs on a Sun-based image processing system. With a background display of LANDSAT Thematic Mapper and United States Geological Survey Digital Line Graph data, the operator uses a cursor to delineate agricultural areas, called sampling units, which are assigned to strata of land-use and land-cover types. The resultant stratified sampling units are used as input into subsequent USDA sampling procedures. As a test, three counties in Missouri were chosen for application of the CAS procedures. Subsequent analysis indicates that CAS was five times faster in creating sampling units than the manual techniques were.

  4. Electrocardiogram ST-Segment Morphology Delineation Method Using Orthogonal Transformations

    PubMed Central

    2016-01-01

    Differentiation between ischaemic and non-ischaemic transient ST segment events of long term ambulatory electrocardiograms is a persisting weakness in present ischaemia detection systems. Traditional ST segment level measuring is not a sufficiently precise technique due to the single point of measurement and severe noise which is often present. We developed a robust noise resistant orthogonal-transformation based delineation method, which allows tracing the shape of transient ST segment morphology changes from the entire ST segment in terms of diagnostic and morphologic feature-vector time series, and also allows further analysis. For these purposes, we developed a new Legendre Polynomials based Transformation (LPT) of ST segment. Its basis functions have similar shapes to typical transient changes of ST segment morphology categories during myocardial ischaemia (level, slope and scooping), thus providing direct insight into the types of time domain morphology changes through the LPT feature-vector space. We also generated new Karhunen and Lo ève Transformation (KLT) ST segment basis functions using a robust covariance matrix constructed from the ST segment pattern vectors derived from the Long Term ST Database (LTST DB). As for the delineation of significant transient ischaemic and non-ischaemic ST segment episodes, we present a study on the representation of transient ST segment morphology categories, and an evaluation study on the classification power of the KLT- and LPT-based feature vectors to classify between ischaemic and non-ischaemic ST segment episodes of the LTST DB. Classification accuracy using the KLT and LPT feature vectors was 90% and 82%, respectively, when using the k-Nearest Neighbors (k = 3) classifier and 10-fold cross-validation. New sets of feature-vector time series for both transformations were derived for the records of the LTST DB which is freely available on the PhysioNet website and were contributed to the LTST DB. The KLT and LPT

  5. Electrocardiogram ST-Segment Morphology Delineation Method Using Orthogonal Transformations.

    PubMed

    Amon, Miha; Jager, Franc

    2016-01-01

    Differentiation between ischaemic and non-ischaemic transient ST segment events of long term ambulatory electrocardiograms is a persisting weakness in present ischaemia detection systems. Traditional ST segment level measuring is not a sufficiently precise technique due to the single point of measurement and severe noise which is often present. We developed a robust noise resistant orthogonal-transformation based delineation method, which allows tracing the shape of transient ST segment morphology changes from the entire ST segment in terms of diagnostic and morphologic feature-vector time series, and also allows further analysis. For these purposes, we developed a new Legendre Polynomials based Transformation (LPT) of ST segment. Its basis functions have similar shapes to typical transient changes of ST segment morphology categories during myocardial ischaemia (level, slope and scooping), thus providing direct insight into the types of time domain morphology changes through the LPT feature-vector space. We also generated new Karhunen and Lo ève Transformation (KLT) ST segment basis functions using a robust covariance matrix constructed from the ST segment pattern vectors derived from the Long Term ST Database (LTST DB). As for the delineation of significant transient ischaemic and non-ischaemic ST segment episodes, we present a study on the representation of transient ST segment morphology categories, and an evaluation study on the classification power of the KLT- and LPT-based feature vectors to classify between ischaemic and non-ischaemic ST segment episodes of the LTST DB. Classification accuracy using the KLT and LPT feature vectors was 90% and 82%, respectively, when using the k-Nearest Neighbors (k = 3) classifier and 10-fold cross-validation. New sets of feature-vector time series for both transformations were derived for the records of the LTST DB which is freely available on the PhysioNet website and were contributed to the LTST DB. The KLT and LPT

  6. Predict amine solution properties accurately

    SciTech Connect

    Cheng, S.; Meisen, A.; Chakma, A.

    1996-02-01

    Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.

  7. Accurate thickness measurement of graphene

    NASA Astrophysics Data System (ADS)

    Shearer, Cameron J.; Slattery, Ashley D.; Stapleton, Andrew J.; Shapter, Joseph G.; Gibson, Christopher T.

    2016-03-01

    Graphene has emerged as a material with a vast variety of applications. The electronic, optical and mechanical properties of graphene are strongly influenced by the number of layers present in a sample. As a result, the dimensional characterization of graphene films is crucial, especially with the continued development of new synthesis methods and applications. A number of techniques exist to determine the thickness of graphene films including optical contrast, Raman scattering and scanning probe microscopy techniques. Atomic force microscopy (AFM), in particular, is used extensively since it provides three-dimensional images that enable the measurement of the lateral dimensions of graphene films as well as the thickness, and by extension the number of layers present. However, in the literature AFM has proven to be inaccurate with a wide range of measured values for single layer graphene thickness reported (between 0.4 and 1.7 nm). This discrepancy has been attributed to tip-surface interactions, image feedback settings and surface chemistry. In this work, we use standard and carbon nanotube modified AFM probes and a relatively new AFM imaging mode known as PeakForce tapping mode to establish a protocol that will allow users to accurately determine the thickness of graphene films. In particular, the error in measuring the first layer is reduced from 0.1-1.3 nm to 0.1-0.3 nm. Furthermore, in the process we establish that the graphene-substrate adsorbate layer and imaging force, in particular the pressure the tip exerts on the surface, are crucial components in the accurate measurement of graphene using AFM. These findings can be applied to other 2D materials.

  8. Semi-automatic delineation using weighted CT-MRI registered images for radiotherapy of nasopharyngeal cancer

    SciTech Connect

    Fitton, I.; Cornelissen, S. A. P.; Duppen, J. C.; Rasch, C. R. N.; Herk, M. van; Steenbakkers, R. J. H. M.; Peeters, S. T. H.; Hoebers, F. J. P.; Kaanders, J. H. A. M.; Nowak, P. J. C. M.

    2011-08-15

    Purpose: To develop a delineation tool that refines physician-drawn contours of the gross tumor volume (GTV) in nasopharynx cancer, using combined pixel value information from x-ray computed tomography (CT) and magnetic resonance imaging (MRI) during delineation. Methods: Operator-guided delineation assisted by a so-called ''snake'' algorithm was applied on weighted CT-MRI registered images. The physician delineates a rough tumor contour that is continuously adjusted by the snake algorithm using the underlying image characteristics. The algorithm was evaluated on five nasopharyngeal cancer patients. Different linear weightings CT and MRI were tested as input for the snake algorithm and compared according to contrast and tumor to noise ratio (TNR). The semi-automatic delineation was compared with manual contouring by seven experienced radiation oncologists. Results: A good compromise for TNR and contrast was obtained by weighing CT twice as strong as MRI. The new algorithm did not notably reduce interobserver variability, it did however, reduce the average delineation time by 6 min per case. Conclusions: The authors developed a user-driven tool for delineation and correction based a snake algorithm and registered weighted CT image and MRI. The algorithm adds morphological information from CT during the delineation on MRI and accelerates the delineation task.

  9. Digital panoramic radiography versus cone beam computed tomography in the delineation of maxillomandibular tumors.

    PubMed

    Almeida-Barros, Renata Quirino de; Abilio, Vanessa Maria Freire; Yamamoto, Angela Toshie Araki; Melo, Daniela Pita de; Godoy, Gustavo Pina; Bento, Patricia Meira

    2015-01-01

    This research aimed to compare the efficacy of digital panoramic radiography (DPR) with that of cone beam computed tomography (CBCT) for delineation of odontogenic and nonodontogenic tumors. From November 2009 through March 2011, 23 tumors in the maxillomandibular complex were diagnosed by histopathological examination. All DPRs and CBCTs were obtained and analyzed by a single previously calibrated radiologist, who considered the following radiographic aspects: clarity of the lesion edges, relation with dental elements, involvement of adjacent anatomical structures, cortical bone expansion and disruption, and, if present, type of involved anatomical structures and site of bone expansion and disruption. Of 23 patients, 15 (65.2%) were male and 8 (34.8%) were female. The tumor was classified as odontogenic in 73.9% of patients and nonodontogenic in 26.1% of patients. Analysis revealed that 56.5% of the tumors were located in the mandible, 34.8% in the maxilla, and 8.7% in both arches. For all analyzed variables, CBCTs offered more accurate details than did DPRs. Panoramic radiography should not be the examination of choice to visualize lesions in the maxillomandibular complex. PMID:26545285

  10. A screening tool for delineating subregions of steady recharge within groundwater models

    USGS Publications Warehouse

    Dickinson, Jesse E.; Ferré, T. P. A.; Bakker, Mark; Crompton, Becky

    2014-01-01

    We have developed a screening method for simplifying groundwater models by delineating areas within the domain that can be represented using steady-state groundwater recharge. The screening method is based on an analytical solution for the damping of sinusoidal infiltration variations in homogeneous soils in the vadose zone. The damping depth is defined as the depth at which the flux variation damps to 5% of the variation at the land surface. Groundwater recharge may be considered steady where the damping depth is above the depth of the water table. The analytical solution approximates the vadose zone diffusivity as constant, and we evaluated when this approximation is reasonable. We evaluated the analytical solution through comparison of the damping depth computed by the analytic solution with the damping depth simulated by a numerical model that allows variable diffusivity. This comparison showed that the screening method conservatively identifies areas of steady recharge and is more accurate when water content and diffusivity are nearly constant. Nomograms of the damping factor (the ratio of the flux amplitude at any depth to the amplitude at the land surface) and the damping depth were constructed for clay and sand for periodic variations between 1 and 365 d and flux means and amplitudes from nearly 0 to 1 × 10−3 m d−1. We applied the screening tool to Central Valley, California, to identify areas of steady recharge. A MATLAB script was developed to compute the damping factor for any soil and any sinusoidal flux variation.

  11. A Compressive Sensing Approach for Glioma Margin Delineation Using Mass Spectrometry

    PubMed Central

    Gholami, Behnood; Agar, Nathalie Y. R.; Jolesz, Ferenc A.; Haddad, Wassim M.; Tannenbaum, Allen R.

    2013-01-01

    Surgery, and specifically, tumor resection, is the primary treatment for most patients suffering from brain tumors. Medical imaging techniques, and in particular, magnetic resonance imaging are currently used in diagnosis as well as image-guided surgery procedures. However, studies show that computed tomography and magnetic resonance imaging fail to accurately identify the full extent of malignant brain tumors and their microscopic infiltration. Mass spectrometry is a well-known analytical technique used to identify molecules in a given sample based on their mass. In a recent study, it is proposed to use mass spectrometry as an intraoperative tool for discriminating tumor and non-tumor tissue. Integration of mass spectrometry with the resection module allows for tumor resection and immediate molecular analysis. In this paper, we propose a framework for tumor margin delineation using compressive sensing. Specifically, we show that the spatial distribution of tumor cell concentration can be efficiently reconstructed and updated using mass spectrometry information from the resected tissue. In addition, our proposed framework is model-free, and hence, requires no prior information of spatial distribution of the tumor cell concentration. PMID:22255629

  12. ModBack - simplified contaminant source zone delineation using backtracking

    NASA Astrophysics Data System (ADS)

    Thielsch, K.; Herold, M.; Ptak, T.

    2012-12-01

    Contaminated groundwater poses a serious threat to drinking water resources all over the world. Even though contaminated water might be detected in observation wells, a proper clean up is often only successful if the source of the contamination is detected and subsequently removed, contained or remediated. The high costs of groundwater remediation could be possibly significantly reduced if, from the outset, a focus is placed on source zone detection. ModBack combines several existing modelling tools in one easy to use GIS-based interface helping to delineate potential contaminant source zones in the subsurface. The software is written in Visual Basic 3.5 and uses the ArcObjects library to implement all required GIS applications. It can run without modification on any Microsoft Windows based PC with sufficient RAM and at least Microsoft .NET Framework 3.5. Using ModBack requires additional installation of the following software: Processing Modflow Pro 7.0, ModPath, CSTREAM (Bayer-Raich et al., 2003), Golden Software Surfer and Microsoft Excel. The graphical user interface of ModBack is separated into four blocks of procedures dealing with: data input, groundwater modelling, backtracking and analyses. Geographical data input includes all georeferenced information pertaining to the study site. Information on subsurface contamination is gathered either by conventional sampling of monitoring wells or by conducting integral pumping tests at control planes with a specific sampling scheme. Hydraulic data from these pumping tests together with all other available information are then used to set up a groundwater flow model of the study site, which provides the flow field for transport simulations within the subsequent contamination backtracking procedures, starting from the defined control planes. The backtracking results are then analysed within ModBack. The potential areas of contamination source presence or absence are determined based on the procedure used by Jarsjö et

  13. Delineation of colluvial soils in different soil regions

    NASA Astrophysics Data System (ADS)

    Zádorová, Tereza; Penížek, Vít; Vašát, Radim

    2015-04-01

    Colluvial soils are considered to be the direct result of accelerated soil erosion in agricultural landscape, resulting in accumulation of humus-rich soil material in terrain depressions and toe slopes. They represent an important soil cover element in landscapes influenced by soil erosion and form an important soil organic carbon (SOC) pool. Delineation of colluvial soils can identify areas with high sediment input and potential deep organic carbon storage and thus improve our knowledge on soil mass and SOC stock redistribution in dissected landscapes. Different prediction methods (ordinary kriging, multiple linear regression, supervised fuzzy classification, artificial neural network, support vector machines) for colluvial soils delineation have been tested in three different soil regions (Cambisol, Luvisol and Chernozem) at two scales (plot and watershed) in the Czech Republic. The approach is based on exploitation of relationship between soil and terrain units and assumes that colluvial soil can be defined by particular range of terrain attributes values. Terrain attributes derived from precise DEMs were used as predictors in applied models. The soil-terrain relationship was assessed using a large dataset of field investigations (300 cores at each plot and 100 cores at each watershed). Models were trained at plot scale (15-33 ha) and the best performing model was then calibrated and validated at watershed scale (25-55 km2). The study proved high potential of terrain variables as predictors in colluvial soil delineation. Support vector machines method was the best performing method for colluvial soil occurrence prediction at all the three sites. However, significant differences in performance have been identified among the studied plots. The best results were obtained in Luvisol region where both determination coefficient and prediction accuracy reached the highest values. The model performance was satisfactory also in Chernozem region. The model showed its

  14. SPEQTACLE: An automated generalized fuzzy C-means algorithm for tumor delineation in PET

    SciTech Connect

    Lapuyade-Lahorgue, Jérôme; Visvikis, Dimitris; Hatt, Mathieu; Pradier, Olivier; Cheze Le Rest, Catherine

    2015-10-15

    Purpose: Accurate tumor delineation in positron emission tomography (PET) images is crucial in oncology. Although recent methods achieved good results, there is still room for improvement regarding tumors with complex shapes, low signal-to-noise ratio, and high levels of uptake heterogeneity. Methods: The authors developed and evaluated an original clustering-based method called spatial positron emission quantification of tumor—Automatic Lp-norm estimation (SPEQTACLE), based on the fuzzy C-means (FCM) algorithm with a generalization exploiting a Hilbertian norm to more accurately account for the fuzzy and non-Gaussian distributions of PET images. An automatic and reproducible estimation scheme of the norm on an image-by-image basis was developed. Robustness was assessed by studying the consistency of results obtained on multiple acquisitions of the NEMA phantom on three different scanners with varying acquisition parameters. Accuracy was evaluated using classification errors (CEs) on simulated and clinical images. SPEQTACLE was compared to another FCM implementation, fuzzy local information C-means (FLICM) and fuzzy locally adaptive Bayesian (FLAB). Results: SPEQTACLE demonstrated a level of robustness similar to FLAB (variability of 14% ± 9% vs 14% ± 7%, p = 0.15) and higher than FLICM (45% ± 18%, p < 0.0001), and improved accuracy with lower CE (14% ± 11%) over both FLICM (29% ± 29%) and FLAB (22% ± 20%) on simulated images. Improvement was significant for the more challenging cases with CE of 17% ± 11% for SPEQTACLE vs 28% ± 22% for FLAB (p = 0.009) and 40% ± 35% for FLICM (p < 0.0001). For the clinical cases, SPEQTACLE outperformed FLAB and FLICM (15% ± 6% vs 37% ± 14% and 30% ± 17%, p < 0.004). Conclusions: SPEQTACLE benefitted from the fully automatic estimation of the norm on a case-by-case basis. This promising approach will be extended to multimodal images and multiclass estimation in future developments.

  15. Delineating optimal settlement areas of juvenile reef fish in Ngederrak Reef, Koror state, Republic of Palau.

    PubMed

    Ticzon, Victor S; Foster, Greg; David, Laura T; Mumby, Peter J; Samaniego, Badi R; Madrid, Val Randolf

    2015-01-01

    Establishing the effectiveness of habitat features to act as surrogate measures of diversity and abundance of juvenile reef fish provides information that is critical to coral reef management. When accurately set on a broader spatial context, microhabitat information becomes more meaningful and its management application becomes more explicit. The goal of the study is to identify coral reef areas potentially important to juvenile fishes in Ngederrak Reef, Republic of Palau, across different spatial scales. To achieve this, the study requires the accomplishment of the following tasks: (1) structurally differentiate the general microhabitat types using acoustics; (2) quantify microhabitat association with juvenile reef fish community structure; and (3) conduct spatial analysis of the reef-wide data and locate areas optimal for juvenile reef fish settlement. The results strongly suggest the importance of branching structures in determining species count and abundance of juvenile reef fish at the outer reef slope of Ngederrak Reef. In the acoustic map, the accurate delineation of these features allowed us to identify reef areas with the highest potential to harbor a rich aggregation of juvenile reef fish. Using a developed spatial analysis tool that ranks pixel groups based on user-defined parameters, the reef area near the Western channel of Ngederrak is predicted to have the most robust aggregation of juvenile reef fish. The results have important implications not only in management, but also in modeling the impacts of habitat loss on reef fish community. At least for Ngederrak Reef, the results advanced the utility of acoustic systems in predicting spatial distribution of juvenile fish. PMID:25394769

  16. Using kernels and ecological niche modeling to delineate conservation areas in an endangered patch-breeding phenotype.

    PubMed

    Denoël, Mathieu; Ficetola, Gentile Francesco

    2015-10-01

    Efficient delineation of conservation areas is a great challenge in maintaining biodiversity. Kernel density estimators (KDEs) are a powerful tool in this perspective, but they have not been applied at the population level on patch-distributed organisms. This would be particularly worthy for species that need broad habitats beyond those where they can be sampled; such as terrestrial lands for pond-breeding amphibians. The aim of this study was to compare different approaches for the identification of suitable areas for conservation: KDE, ecological niche modelling, and a combination of KDE and niche models. Paedomorphosis was chosen as a model system because this is an important form of intraspecific variation that is present in numerous taxa, but geographically localized within species and globally endangered. 277 ponds were sampled in one of the hotspots of paedomorphosis to determine the abundance and distribution of paedomorphs (i.e., individuals retaining gills at the adult stage) of the palmate newt (Lissotriton helveticus), with emphasis on the connections between the most valuable populations. KDEs gave insights into the surface areas required to balance the maintenance of certain number of connected ponds and the respective number of disjoint areas in which the whole population is divided. The inclusion of barriers in the models helped in accurately designing the limits of the areas to protect. Alone, habitat models were not able to successfully delineate the area to protect, but the integration between terrestrial suitable areas or barriers and KDE allowed an objective identification of areas required for conservation. Overall, the best performance was observed by the KDE integrating ecological barriers, and by the combination between KDE and niche modelling. In a broader perspective, KDEs are thus a pertinent tool in providing quantitative spatial measurements to delineate conservation areas based on patch-abundance data with a specific focus to

  17. Quality metric for accurate overlay control in <20nm nodes

    NASA Astrophysics Data System (ADS)

    Klein, Dana; Amit, Eran; Cohen, Guy; Amir, Nuriel; Har-Zvi, Michael; Huang, Chin-Chou Kevin; Karur-Shanmugam, Ramkumar; Pierson, Bill; Kato, Cindy; Kurita, Hiroyuki

    2013-04-01

    The semiconductor industry is moving toward 20nm nodes and below. As the Overlay (OVL) budget is getting tighter at these advanced nodes, the importance in the accuracy in each nanometer of OVL error is critical. When process owners select OVL targets and methods for their process, they must do it wisely; otherwise the reported OVL could be inaccurate, resulting in yield loss. The same problem can occur when the target sampling map is chosen incorrectly, consisting of asymmetric targets that will cause biased correctable terms and a corrupted wafer. Total measurement uncertainty (TMU) is the main parameter that process owners use when choosing an OVL target per layer. Going towards the 20nm nodes and below, TMU will not be enough for accurate OVL control. KLA-Tencor has introduced a quality score named `Qmerit' for its imaging based OVL (IBO) targets, which is obtained on the-fly for each OVL measurement point in X & Y. This Qmerit score will enable the process owners to select compatible targets which provide accurate OVL values for their process and thereby improve their yield. Together with K-T Analyzer's ability to detect the symmetric targets across the wafer and within the field, the Archer tools will continue to provide an independent, reliable measurement of OVL error into the next advanced nodes, enabling fabs to manufacture devices that meet their tight OVL error budgets.

  18. Accurate ab Initio Spin Densities

    PubMed Central

    2012-01-01

    We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921

  19. Anatomical Brain Images Alone Can Accurately Diagnose Chronic Neuropsychiatric Illnesses

    PubMed Central

    Bansal, Ravi; Staib, Lawrence H.; Laine, Andrew F.; Hao, Xuejun; Xu, Dongrong; Liu, Jun; Weissman, Myrna; Peterson, Bradley S.

    2012-01-01

    Objective Diagnoses using imaging-based measures alone offer the hope of improving the accuracy of clinical diagnosis, thereby reducing the costs associated with incorrect treatments. Previous attempts to use brain imaging for diagnosis, however, have had only limited success in diagnosing patients who are independent of the samples used to derive the diagnostic algorithms. We aimed to develop a classification algorithm that can accurately diagnose chronic, well-characterized neuropsychiatric illness in single individuals, given the availability of sufficiently precise delineations of brain regions across several neural systems in anatomical MR images of the brain. Methods We have developed an automated method to diagnose individuals as having one of various neuropsychiatric illnesses using only anatomical MRI scans. The method employs a semi-supervised learning algorithm that discovers natural groupings of brains based on the spatial patterns of variation in the morphology of the cerebral cortex and other brain regions. We used split-half and leave-one-out cross-validation analyses in large MRI datasets to assess the reproducibility and diagnostic accuracy of those groupings. Results In MRI datasets from persons with Attention-Deficit/Hyperactivity Disorder, Schizophrenia, Tourette Syndrome, Bipolar Disorder, or persons at high or low familial risk for Major Depressive Disorder, our method discriminated with high specificity and nearly perfect sensitivity the brains of persons who had one specific neuropsychiatric disorder from the brains of healthy participants and the brains of persons who had a different neuropsychiatric disorder. Conclusions Although the classification algorithm presupposes the availability of precisely delineated brain regions, our findings suggest that patterns of morphological variation across brain surfaces, extracted from MRI scans alone, can successfully diagnose the presence of chronic neuropsychiatric disorders. Extensions of these

  20. Optical Delineation of Benthic Habitat Using an Autonomous Underwater Vehicle

    SciTech Connect

    Moline, Mark A.; Woodruff, Dana L.; Evans, Nathan R.

    2007-06-01

    To improve understanding and characterization of coastal regions, there has been an increasing emphasis on autonomous systems that can sample the ocean on relevant scales. Autonomous underwater vehicles (AUVs) with active propulsion are especially well suited for studies of the coastal ocean because they are able to provide systematic and near-synoptic spatial observations. With this capability, science users are beginning to integrate sensor suits for a broad range of specific and often novel applications. Here, the relatively mature Remote Environmental Monitoring Units (REMUS) AUV system is configured with multi-spectral radiometers to delineate benthic habitat in Sequim Bay, WA. The vehicle was deployed in a grid pattern along 5 km of coastline in depths from 30 to less than 2 meters. Similar to satellite and/or aerial remote sensing, the bandwidth ratios from the downward looking radiance sensor and upward looking irradiance sensor were used to identify beds of eelgrass on sub-meter scales. Strong correlations were found between the optical reflectance signals and the geo-referenced in situ data collected with underwater video within the grid. Results demonstrate the ability of AUVs to map littoral habitats at high resolution and highlight the overall utility of the REMUS vehicle for nearshore oceanography.

  1. Automatic segmentation of chromatographic images for region of interest delineation

    NASA Astrophysics Data System (ADS)

    Mendonça, Ana M.; Sousa, António V.; Sá-Miranda, M. Clara; Campilho, Aurélio C.

    2011-03-01

    This paper describes a segmentation method for automating the region of interest (ROI) delineation in chromatographic images, thus allowing the definition of the image area that contains the fundamental information for further processing while excluding the frame of the chromatographic plate that does not contain relevant data for disease identification. This is the first component of a screening tool for Fabry disease, which will be based on the automatic analysis of the chromatographic patterns extracted from the image ROI. Image segmentation is performed in two phases, where each individual pixel is finally considered as frame or ROI. In the first phase, an unsupervised learning method is used for classifying image pixels into three classes: frame, ROI or unknown. In the second phase, distance features are used for deciding which class the unknown pixels belong to. The segmentation result is post-processed using a sequence of morphological operators in order to obtain the final ROI rectangular area. The proposed methodology was successfully evaluated in a dataset of 41 chromatographic images.

  2. Delineation of individual tree crowns for mobile laser scanning data

    NASA Astrophysics Data System (ADS)

    Wu, Rosen; Chen, Yiping; Wen, Chenglu; Wang, Cheng; Li, Jonathan

    2016-03-01

    The information of individual trees plays an important role in urban surveying and mapping. With the development of Light Detection and Ranging (LiDAR) technology, 3-Dimenisonal (3D) structure of trees can be generated in point clouds with high spatial resolution and accuracy. Individual tree segmentations are used to derive tree structural attributes such as tree height, crown diameter, stem position etc. In this study, a framework is proposed to take advantage of the detailed structures of tree crowns which are represented in the mobile laser scanning (MLS) data. This framework consists of five steps: (1) Automatically detect and remove ground points using RANSAC; (2) Compress all the above ground points to image grid with 3D knowledge reserved; (3) Simplify and remove unqualified grids; (4) Find tree peaks using a heuristic searching method; (5) Delineate the individual tree crowns by applying a modified watershed method. In an experiment on the point clouds on Xiamen Island, China, individual tree crowns from MLS point cloud data are successfully extracted.

  3. Hornblendite delineates zones of mass transfer through the lower crust

    PubMed Central

    Daczko, Nathan R.; Piazolo, Sandra; Meek, Uvana; Stuart, Catherine A.; Elliott, Victoria

    2016-01-01

    Geochemical signatures throughout the layered Earth require significant mass transfer through the lower crust, yet geological pathways are under-recognized. Elongate bodies of basic to ultrabasic rocks are ubiquitous in exposures of the lower crust. Ultrabasic hornblendite bodies hosted within granulite facies gabbroic gneiss of the Pembroke Valley, Fiordland, New Zealand, are typical occurrences usually reported as igneous cumulate hornblendite. Their igneous features contrast with the metamorphic character of their host gabbroic gneiss. Both rock types have a common parent; field relationships are consistent with modification of host gabbroic gneiss into hornblendite. This precludes any interpretation involving cumulate processes in forming the hornblendite; these bodies are imposter cumulates. Instead, replacement of the host gabbroic gneiss formed hornblendite as a result of channeled high melt flux through the lower crust. High melt/rock ratios and disequilibrium between the migrating magma (granodiorite) and its host gabbroic gneiss induced dissolution (grain-scale magmatic assimilation) of gneiss and crystallization of mainly hornblende from the migrating magma. The extent of this reaction-replacement mechanism indicates that such hornblendite bodies delineate significant melt conduits. Accordingly, many of the ubiquitous basic to ultrabasic elongate bodies of the lower crust likely map the ‘missing’ mass transfer zones. PMID:27546342

  4. Hornblendite delineates zones of mass transfer through the lower crust.

    PubMed

    Daczko, Nathan R; Piazolo, Sandra; Meek, Uvana; Stuart, Catherine A; Elliott, Victoria

    2016-01-01

    Geochemical signatures throughout the layered Earth require significant mass transfer through the lower crust, yet geological pathways are under-recognized. Elongate bodies of basic to ultrabasic rocks are ubiquitous in exposures of the lower crust. Ultrabasic hornblendite bodies hosted within granulite facies gabbroic gneiss of the Pembroke Valley, Fiordland, New Zealand, are typical occurrences usually reported as igneous cumulate hornblendite. Their igneous features contrast with the metamorphic character of their host gabbroic gneiss. Both rock types have a common parent; field relationships are consistent with modification of host gabbroic gneiss into hornblendite. This precludes any interpretation involving cumulate processes in forming the hornblendite; these bodies are imposter cumulates. Instead, replacement of the host gabbroic gneiss formed hornblendite as a result of channeled high melt flux through the lower crust. High melt/rock ratios and disequilibrium between the migrating magma (granodiorite) and its host gabbroic gneiss induced dissolution (grain-scale magmatic assimilation) of gneiss and crystallization of mainly hornblende from the migrating magma. The extent of this reaction-replacement mechanism indicates that such hornblendite bodies delineate significant melt conduits. Accordingly, many of the ubiquitous basic to ultrabasic elongate bodies of the lower crust likely map the 'missing' mass transfer zones. PMID:27546342

  5. Challenge in Flow Path Delineation and Modification: SECUREarth Initiative

    NASA Astrophysics Data System (ADS)

    Bodvarsson, G. S.; Majer, E. L.; Wang, J. S.; Colwell, F.; Redden, G.

    2005-12-01

    After decades of studies, our knowledge about subsurface flow paths has large uncertainty and our capability to enhance or reduce formation permeability is inefficient and rudimentary. This is the case for fossil energy production, in environment remediation, in greenhouse gas sequestration, in nuclear waste disposal, in geothermal heat extraction, and in groundwater management. Fluid imaging, in addition to rock structure imaging, is needed to enhance petroleum extraction, to isolate contaminant plumes, and to prevent leakage from storage reservoirs. Flow focusing from surface to depth must be quantified to determine the flow path magnitude and spacing in order to determine the degrees of dissolution and transport of emplaced wastes. These diverse problems have common goals: either to isolate or to enhance subsurface fluid movement. It is crucial to identify the common features from different problems and refocus our efforts to delineate and then to manipulate flow paths. Geochemical engineering and geomicrobiological engineering need to combine laboratory studies, field experiments, and modeling approaches to verify and validate our understanding and to design solutions. An initiative SECUREarth is being developed to rally the scientists and engineers from national laboratories, universities, and industry to address key critical bottlenecks that prevent significant progress in solving common subsurface issues. SECUREarth is aimed to develop cross-cutting, multi-disciplinary approaches for solving urgent energy and environment problems in the earth, in order to achieve quantum leaps and breakthroughs in earth science and technology.

  6. Multivariate Analysis of the Ecoregion Delineation for Aquatic Systems

    NASA Astrophysics Data System (ADS)

    Jenerette, G. Darrel; Lee, Jay; Waller, David W.; Carlson, Robert E.

    2002-01-01

    The ecoregion concept is a popular method of understanding the spatial distribution of the environment', however, it has yet to be adequately demonstrated that the environment is distributed in accordance with these bounded units. In this paper, we generated a testable hypothesis based on the current usage of ecoregions: the ecoregion classification will allow for discrimination between lakes of different water quality. The ecoregion classification should also be more effective better than a comparably scaled classification based on political boundaries, land-use class, or random grouping. To test this hypothesis we used the Environmental Monitoring and Assessment Program (EMAP) lake water chemistry data from the northeast United States. The water chemistry data were reduced to four components using principal component analysis. For comparison to an optimal grouping of these data we used K-means cluster analysis to define the extent at which these lakes could be segregated into distinct classes. Jackknifed discriminant analysis was used to determine the classification rate of ecoregions, the three alternative spatial classification methods, and the clustering algorithm. The classification based on ecoregions was successful for 35% of the lakes included in this study, in comparison to the clustered groups accuracy of 98%. These results suggest that the large scale spatial distribution of ecosystem types is more complicated than that suggested by the present ecoregion boundaries. Further tests of ecoregion delineations are needed and alternative large-scale management strategies should be investigated.

  7. Delineation of Steroid-Degrading Microorganisms through Comparative Genomic Analysis

    PubMed Central

    Bergstrand, Lee H.; Cardenas, Erick; Holert, Johannes; Van Hamme, Jonathan D.

    2016-01-01

    ABSTRACT Steroids are ubiquitous in natural environments and are a significant growth substrate for microorganisms. Microbial steroid metabolism is also important for some pathogens and for biotechnical applications. This study delineated the distribution of aerobic steroid catabolism pathways among over 8,000 microorganisms whose genomes are available in the NCBI RefSeq database. Combined analysis of bacterial, archaeal, and fungal genomes with both hidden Markov models and reciprocal BLAST identified 265 putative steroid degraders within only Actinobacteria and Proteobacteria, which mainly originated from soil, eukaryotic host, and aquatic environments. These bacteria include members of 17 genera not previously known to contain steroid degraders. A pathway for cholesterol degradation was conserved in many actinobacterial genera, particularly in members of the Corynebacterineae, and a pathway for cholate degradation was conserved in members of the genus Rhodococcus. A pathway for testosterone and, sometimes, cholate degradation had a patchy distribution among Proteobacteria. The steroid degradation genes tended to occur within large gene clusters. Growth experiments confirmed bioinformatic predictions of steroid metabolism capacity in nine bacterial strains. The results indicate there was a single ancestral 9,10-seco-steroid degradation pathway. Gene duplication, likely in a progenitor of Rhodococcus, later gave rise to a cholate degradation pathway. Proteobacteria and additional Actinobacteria subsequently obtained a cholate degradation pathway via horizontal gene transfer, in some cases facilitated by plasmids. Catabolism of steroids appears to be an important component of the ecological niches of broad groups of Actinobacteria and individual species of Proteobacteria. PMID:26956583

  8. Catchment delineation and morphometric analysis using geographical information system.

    PubMed

    Kumar, Manoj; Kumar, Rohitashw; Singh, P K; Singh, Manjeet; Yadav, K K; Mittal, H K

    2015-01-01

    The geographical information system (GIS) has emerged as an efficient tool in delineation of drainage patterns of watershed planning and management. The morphometric parameters of basins can address linear, areal and relief aspects. The study deals with the integrated watershed management of Baliya micro-watersheds, located in the Udaipur district of Rajasthan, India. Morphometric analysis in hydrological investigation is an important aspect and it is inevitable in the development and management of drainage basins. The determination of linear, areal and relief parameters indicate fairly good significance. The low value of the bifurcation ratio of 4.19 revealed that the drainage pattern has not been distorted by structural disturbance. The high value of the elongation ratio (0.68) compared to the circulatory ratio (0.27) indicates an elongated shape of the watershed. The high value of drainage density (5.39 km/km(2)) and stream frequency (12.32) shows that the region has impermeable subsoil material under poor vegetative cover with a low relief factor. The morphometric parameters of relief ratio (0.041) and relative relief (0.99%) show that the watershed can be treated using GIS techniques to determine the morphometric presence of dendritic drainage pattern, with a view to selecting the soil and water conservation measures and water harvesting. PMID:26398032

  9. The delineation and interpretation of the Earth's gravity field

    NASA Technical Reports Server (NTRS)

    Marsh, Bruce D.

    1987-01-01

    The geoid and topographic fields of the central Pacific were delineated and shown to correlate closely at intermediate wavelengths (500 to 2500 km). The associated admittance shows that anomalies having wavelengths less than about 1000 km are probably supported by the elastic strength of the lithosphere. Larger wavelength anomalies are due to dynamic effects in the sublithosphere. Direct modeling of small scale convection in the asthenosphere shows that the amplitudes of observed geoid and topographic anomalies can be independently matched, but that the observed admittance cannot. Only by imposing an initial regional variation in the thermal regime is it possible to match the admittance. It is proposed that this variation may be due to differences in the onset time of convection beneath the lithosphere of different ages. That is, convection beneath thickening lithosphere is strongly dependent on the rate of thickening (V) relative to the rise time for convection. The critical Rayleigh number contains the length scale K/V, where K is thermal diffusivity. Young, fast growing lithosphere stabilizes the underlying asthenosphere unless it has an unusually low viscosity. Lithosphere of different age, separated by fracture zones, will go unstable at different times, producing regional horizontal temperature gradient that may strongly influence convection. Laboratory and numerical experiments are proposed to study this form of convection and its influence on the geoid.

  10. Boundary delineation in transrectal ultrasound image for prostate cancer.

    PubMed

    Zhang, Ying; Sankar, Ravi; Qian, Wei

    2007-11-01

    This paper presents a new advanced automatic edge delineation model for the detection and diagnosis of prostate cancer on transrectal ultrasound (TRUS) images. The proposed model is to improve prostate boundary detection system by modifying a set of preprocessing algorithms including tree-structured nonlinear filter (TSF), directional wavelet transforms (DWT) and tree-structured wavelet transform (TSWT). The model consists of a preprocessing module and a segmentation module. The preprocessing module is implemented for noise suppression, image smoothing and boundary enhancement. The active contours model is used in the segmentation module for prostate boundary detection in two-dimensional (2D) TRUS images. Experimental results show that the addition of the preprocessing module improves the accuracy and sensitivity of the segmentation module, compared to the implementation of the segmentation module alone. It is believed that the proposed automatic boundary detection module for the TRUS images is a promising approach, which provides an efficient and robust detection and diagnosis strategy and acts as "second opinion" for the physician's interpretation of prostate cancer. PMID:17466966

  11. Delineating the glycoproteome of elongating cotton fiber cells

    PubMed Central

    Kumar, Saravanan; Pandey, Pankaj; Kumar, Krishan; Rajamani, Vijayalakshmi; Padmalatha, Kethireddy Venkata; Dhandapani, Gurusamy; Kanakachari, Mogilicherla; Leelavathi, Sadhu; Kumar, Polumetla Ananda; Reddy, Vanga Siva

    2015-01-01

    The data presented here delineates the glycoproteome component in the elongating cotton fiber cells attained using complementary proteomic approaches followed by protein and N-linked glycosylation site identification (Kumar et al., 2013) [1]. Utilizing species specific protein sequence databases in proteomic approaches often leads to additional information that may not be obtained using cross-species databases. In this context we have reanalyzed our glycoproteome dataset with the Gossypium arboreum, Gossypium raimondii (version 2.0) and Gossypium hirsutum protein databases that has led to the identification of 21 N-linked glycosylation sites and 18 unique glycoproteins that were not reported in our previous study. The 1D PAGE and solution based glycoprotein identification data is publicly available at the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaíno et al., 2013) [2] using the dataset identifier PXD000178 and the 2D PAGE based protein identification and glycopeptide approach based N-linked glycosylation site identification data is available at the ProteomeXchange Consortium via the PRIDE partner repository (Vizcaíno et al., 2013) [2] using the dataset identifier PXD002849. PMID:26693171

  12. Volcanic calderas delineate biogeographic provinces among Yellowstone thermophiles.

    PubMed

    Takacs-Vesbach, Cristina; Mitchell, Kendra; Jackson-Weaver, Olan; Reysenbach, Anna-Louise

    2008-07-01

    It has been suggested that the distribution of microorganisms should be cosmopolitan because of their enormous capacity for dispersal. However, recent studies have revealed that geographically isolated microbial populations do exist. Geographic distance as a barrier to dispersal is most often invoked to explain these distributions. Here we show that unique and diverse sequences of the bacterial genus Sulfurihydrogenibium exist in Yellowstone thermal springs, indicating that these sites are geographically isolated. Although there was no correlation with geographic distance or the associated geochemistry of the springs, there was a strong historical signal. We found that the Yellowstone calderas, remnants of prehistoric volcanic eruptions, delineate biogeographical provinces for the Sulfurihydrogenibium within Yellowstone (chi(2): 9.7, P = 0.002). The pattern of distribution that we have detected suggests that major geological events in the past 2 million years explain more of the variation in sequence diversity in this system than do contemporary factors such as habitat or geographic distance. These findings highlight the importance of historical legacies in determining contemporary microbial distributions and suggest that the same factors that determine the biogeography of macroorganisms are also evident among bacteria. PMID:18363714

  13. Fully Automated Gis-Based Individual Tree Crown Delineation Based on Curvature Values from a LIDAR Derived Canopy Height Model in a Coniferous Plantation

    NASA Astrophysics Data System (ADS)

    Argamosa, R. J. L.; Paringit, E. C.; Quinton, K. R.; Tandoc, F. A. M.; Faelga, R. A. G.; Ibañez, C. A. G.; Posilero, M. A. V.; Zaragosa, G. P.

    2016-06-01

    The generation of high resolution canopy height model (CHM) from LiDAR makes it possible to delineate individual tree crown by means of a fully-automated method using the CHM's curvature through its slope. The local maxima are obtained by taking the maximum raster value in a 3 m x 3 m cell. These values are assumed as tree tops and therefore considered as individual trees. Based on the assumptions, thiessen polygons were generated to serve as buffers for the canopy extent. The negative profile curvature is then measured from the slope of the CHM. The results show that the aggregated points from a negative profile curvature raster provide the most realistic crown shape. The absence of field data regarding tree crown dimensions require accurate visual assessment after the appended delineated tree crown polygon was superimposed to the hill shaded CHM.

  14. Feasibility study for image guided kidney surgery: assessment of required intraoperative surface for accurate image to physical space registrations

    NASA Astrophysics Data System (ADS)

    Benincasa, Anne B.; Clements, Logan W.; Herrell, S. Duke; Chang, Sam S.; Cookson, Michael S.; Galloway, Robert L.

    2006-03-01

    Currently, the removal of kidney tumor masses uses only direct or laparoscopic visualizations, resulting in prolonged procedure and recovery times and reduced clear margin. Applying current image guided surgery (IGS) techniques, as those used in liver cases, to kidney resections (nephrectomies) presents a number of complications. Most notably is the limited field of view of the intraoperative kidney surface, which constrains the ability to obtain a surface delineation that is geometrically descriptive enough to drive a surface-based registration. Two different phantom orientations were used to model the laparoscopic and traditional partial nephrectomy views. For the laparoscopic view, fiducial point sets were compiled from a CT image volume using anatomical features such as the renal artery and vein. For the traditional view, markers attached to the phantom set-up were used for fiducials and targets. The fiducial points were used to perform a point-based registration, which then served as a guide for the surface-based registration. Laser range scanner (LRS) obtained surfaces were registered to each phantom surface using a rigid iterative closest point algorithm. Subsets of each phantom's LRS surface were used in a robustness test to determine the predictability of their registrations to transform the entire surface. Results from both orientations suggest that about half of the kidney's surface needs to be obtained intraoperatively for accurate registrations between the image surface and the LRS surface, suggesting the obtained kidney surfaces were geometrically descriptive enough to perform accurate registrations. This preliminary work paves the way for further development of kidney IGS systems.

  15. Feasibility of geometric-intensity based semi-automated delineation of the tentorium cerebelli from MRI scans

    PubMed Central

    Penumetcha, Neeraja; Kabadi, Suraj; Jedynak, Bruno; Walcutt, Charles; Gado, Mokhtar H.; Wang, Lei; Ratnanather, J. Tilak

    2009-01-01

    This paper describes a feasibility study of a method for delineating the tentorium cerebelli in MRI brain scans. The tentorium cerebelli is a thin sheet of dura matter covering the cerebellum and separating it from the posterior part of the temporal lobe and the occipital lobe of the cerebral hemispheres. Cortical structures such as the parahippocampal gyrus can be indistinguishable from tentorium in MPRAGE and T1 weighted magnetic resonance image scans. Similar intensities in these neighboring regions make it difficult to perform accurate cortical analysis in neuroimaging studies of schizophrenia and Alzheimer's disease. A semi-automated, geometric, intensity-based procedure for delineating the tentorium from a whole brain scan is described. Initial and final curves are traced within the tentorium. A cost function, based on intensity and Euclidean distance, is computed between the two curves using the Fast Marching method. The initial curve is then evolved to the final curve based on the gradient of the computed costs, generating a series of intermediate curves. These curves are then used to generate a triangulated surface of the tentorium. For three scans, surfaces were found to be within 2 voxels from hand-segmentations. PMID:19659568

  16. A vocabulary for the identification and delineation of teratoma tissue components in hematoxylin and eosin-stained samples

    PubMed Central

    Bhagavatula, Ramamurthy; McCann, Michael T.; Fickus, Matthew; Castro, Carlos A.; Ozolek, John A.; Kovacevic, Jelena

    2014-01-01

    We propose a methodology for the design of features mimicking the visual cues used by pathologists when identifying tissues in hematoxylin and eosin (H&E)-stained samples. Background: H&E staining is the gold standard in clinical histology; it is cheap and universally used, producing a vast number of histopathological samples. While pathologists accurately and consistently identify tissues and their pathologies, it is a time-consuming and expensive task, establishing the need for automated algorithms for improved throughput and robustness. Methods: We use an iterative feedback process to design a histopathology vocabulary (HV), a concise set of features that mimic the visual cues used by pathologists, e.g. “cytoplasm color” or “nucleus density”. These features are based in histology and understood by both pathologists and engineers. We compare our HV to several generic texture-feature sets in a pixel-level classification algorithm. Results: Results on delineating and identifying tissues in teratoma tumor samples validate our expert knowledge-based approach. Conclusions: The HV can be an effective tool for identifying and delineating teratoma components from images of H&E-stained tissue samples. PMID:25191619

  17. Metabolic approach for tumor delineation in glioma surgery: 3D MR spectroscopy image-guided resection.

    PubMed

    Zhang, Jie; Zhuang, Dong-Xiao; Yao, Cheng-Jun; Lin, Ching-Po; Wang, Tian-Liang; Qin, Zhi-Yong; Wu, Jin-Song

    2016-06-01

    OBJECT The extent of resection is one of the most essential factors that influence the outcomes of glioma resection. However, conventional structural imaging has failed to accurately delineate glioma margins because of tumor cell infiltration. Three-dimensional proton MR spectroscopy ((1)H-MRS) can provide metabolic information and has been used in preoperative tumor differentiation, grading, and radiotherapy planning. Resection based on glioma metabolism information may provide for a more extensive resection and yield better outcomes for glioma patients. In this study, the authors attempt to integrate 3D (1)H-MRS into neuronavigation and assess the feasibility and validity of metabolically based glioma resection. METHODS Choline (Cho)-N-acetylaspartate (NAA) index (CNI) maps were calculated and integrated into neuronavigation. The CNI thresholds were quantitatively analyzed and compared with structural MRI studies. Glioma resections were performed under 3D (1)H-MRS guidance. Volumetric analyses were performed for metabolic and structural images from a low-grade glioma (LGG) group and high-grade glioma (HGG) group. Magnetic resonance imaging and neurological assessments were performed immediately after surgery and 1 year after tumor resection. RESULTS Fifteen eligible patients with primary cerebral gliomas were included in this study. Three-dimensional (1)H-MRS maps were successfully coregistered with structural images and integrated into navigational system. Volumetric analyses showed that the differences between the metabolic volumes with different CNI thresholds were statistically significant (p < 0.05). For the LGG group, the differences between the structural and the metabolic volumes with CNI thresholds of 0.5 and 1.5 were statistically significant (p = 0.0005 and 0.0129, respectively). For the HGG group, the differences between the structural and metabolic volumes with CNI thresholds of 0.5 and 1.0 were statistically significant (p = 0.0027 and 0

  18. Objective Delineation of River Bed Surface Patches from High-Resolution Spatial Grain Size Data

    NASA Astrophysics Data System (ADS)

    Nelson, P. A.; Bellugi, D.; Dietrich, W. E.

    2010-12-01

    Gravel-bed rivers commonly display distinct sorting patterns on their beds. Visually, this heterogeneity often appears to form an organization of distinct textural patches or facies. The local bed surface grain size, and therefore bed surface patchiness, exerts considerable influence on local bed mobility, bedload transport rates, hydrodynamic roughness, and benthic microhabitats. Despite the ecological and morphodynamic importance of bed surface patchiness, we lack accurate and objective methods to delineate bed patches. However, recent advances in photographic measurement of bed surface grain size distributions are capable of providing data at a spatial resolution high enough to allow us an opportunity to answer the question: what is a patch? Here, we explore a variety of techniques that can be applied to high-resolution spatial grain size data to automatically generate maps of grain size patches. We apply a state-of-the-art image processing and machine learning procedure to a photographic survey of the bed surface of a near-field scale flume to extract grain size data and to generate a spatial grid of bed surface grain size distributions. The flume bed was composed of gravel 2-45 mm in diameter and it featured clearly identifiable sorting features. Using this dataset, we investigate several possible methods of patch delineation. The grid of grain size distributions can be represented by a graph of nodes (grain size distributions) connected by edges whose weight is a function of the similarity between two nodes. Spectral graph theory is then used to optimally cut the edges in order to produce a spatial structure of patches that minimizes the association between patches and maximizes the association of nodes within a patch. In a different approach, agglomerative clustering of spatially adjacent grain size distributions is used to produce a hierarchical dendrogram that can be thresholded to partition the bed into patches. We also explore using the k-means algorithm

  19. Towards a High-Resolution Global Inundation Delineation Dataset

    NASA Astrophysics Data System (ADS)

    Fluet-Chouinard, E.; Lehner, B.

    2011-12-01

    Although their importance for biodiversity, flow regulation and ecosystem service provision is widely recognized, wetlands and temporarily inundated landscapes remain poorly mapped globally because of their inherent elusive nature. Inventorying of wetland resources has been identified in international agreements as an essential component of appropriate conservation efforts and management initiatives of these threatened ecosystems. However, despite recent advances in remote sensing surface water monitoring, current inventories of surface water variations remain incomplete at the regional-to-global scale due to methodological limitations restricting truly global application. Remote sensing wetland applications such as SAR L-band are particularly constrained by image availability and heterogeneity of acquisition dates, while coarse resolution passive microwave and multi-sensor methods cannot discriminate distinct surface water bodies. As a result, the most popular global wetland dataset remains to this day the Global Lake & Wetland Database (Lehner and Doll, 2004) a spatially inconsistent database assembled from various existing data sources. The approach taken in this project circumvents the limitations of current global wetland monitoring methods by combining globally available topographic and hydrographic data to downscale coarse resolution global inundation data (Prigent et al., 2007) and thus create a superior inundation delineation map product. The developed procedure downscales inundation data from the coarse resolution (~27km) of current passive microwave sensors to the finer spatial resolution (~500m) of the topographic and hydrographic layers of HydroSHEDS' data suite (Lehner et al., 2006), while retaining the high temporal resolution of the multi-sensor inundation dataset. From the downscaling process emerges new information on the specific location of inundation, but also on its frequency and duration. The downscaling algorithm employs a decision tree

  20. Sensitivity of Soil Moisture and Runoff Dynamics to Hydrologic Response Unit Delineations in SMART

    NASA Astrophysics Data System (ADS)

    Ajami, H.; Khan, U.; Tuteja, N. K.; Sharma, A.

    2015-12-01

    A new approach of semi-distributed hydrologic modelling has been developed to reduce the computational time and effort in distributed hydrologic modelling at large catchment scales. The GIS-based semi-distributed hydrological modelling framework, SMART, delineates contiguous and topologically connected Hydrologic Response Units (HRUs) and simulates soil moisture and runoff dynamics using a 2-dimensional model based on Richards' equation at the scale of cross sections or equivalent cross sections (ECS). Simulated fluxes from every cross section or ECS are weighted by the respective area from which the cross sections or ECSs were formulated in a first-order sub-basin. These are then aggregated to obtain catchment scale fluxes. Herewith, we investigate the impact of HRU delineation methodology in simulating hydrologic fluxes at the catchment scale using SMART. The HRU delineation methodology consists of delineating first order sub-basins and landforms. Landforms which transfer fluxes from the upper part of a hillslope to the lower regions are delineated using topographic and geomorphologic descriptors of the catchment. However, obtaining the appropriate thresholds for landform delineation is impacted by the metric and landform delineation approach chosen by the modeller. We use variation in a number of topographic and geomorphologic descriptors of the entire catchment or groups of sub-catchments in relation to distance from the stream to assess the impact of landform delineation approach on simulated hydrologic fluxes. In addition to the spatial resolution of a digital elevation model, , three landform delineation approaches of SMART are examined. In the next step, we extend this approach to catchments with different topographic and geomorphic characteristics to find appropriate metrics for landform delineation in different settings.

  1. A Parametric Study Delineating Irreversible Electroporation from Thermal Damage Based on a Minimally Invasive Intracranial Procedure

    PubMed Central

    2011-01-01

    Background Irreversible electroporation (IRE) is a new minimally invasive technique to kill undesirable tissue in a non-thermal manner. In order to maximize the benefits from an IRE procedure, the pulse parameters and electrode configuration must be optimized to achieve complete coverage of the targeted tissue while preventing thermal damage due to excessive Joule heating. Methods We developed numerical simulations of typical protocols based on a previously published computed tomographic (CT) guided in vivo procedure. These models were adapted to assess the effects of temperature, electroporation, pulse duration, and repetition rate on the volumes of tissue undergoing IRE alone or in superposition with thermal damage. Results Nine different combinations of voltage and pulse frequency were investigated, five of which resulted in IRE alone while four produced IRE in superposition with thermal damage. Conclusions The parametric study evaluated the influence of pulse frequency and applied voltage on treatment volumes, and refined a proposed method to delineate IRE from thermal damage. We confirm that determining an IRE treatment protocol requires incorporating all the physical effects of electroporation, and that these effects may have significant implications in treatment planning and outcome assessment. The goal of the manuscript is to provide the reader with the numerical methods to assess multiple-pulse electroporation treatment protocols in order to isolate IRE from thermal damage and capitalize on the benefits of a non-thermal mode of tissue ablation. PMID:21529373

  2. Accurate Fission Data for Nuclear Safety

    NASA Astrophysics Data System (ADS)

    Solders, A.; Gorelov, D.; Jokinen, A.; Kolhinen, V. S.; Lantz, M.; Mattera, A.; Penttilä, H.; Pomp, S.; Rakopoulos, V.; Rinta-Antila, S.

    2014-05-01

    The Accurate fission data for nuclear safety (AlFONS) project aims at high precision measurements of fission yields, using the renewed IGISOL mass separator facility in combination with a new high current light ion cyclotron at the University of Jyväskylä. The 30 MeV proton beam will be used to create fast and thermal neutron spectra for the study of neutron induced fission yields. Thanks to a series of mass separating elements, culminating with the JYFLTRAP Penning trap, it is possible to achieve a mass resolving power in the order of a few hundred thousands. In this paper we present the experimental setup and the design of a neutron converter target for IGISOL. The goal is to have a flexible design. For studies of exotic nuclei far from stability a high neutron flux (1012 neutrons/s) at energies 1 - 30 MeV is desired while for reactor applications neutron spectra that resembles those of thermal and fast nuclear reactors are preferred. It is also desirable to be able to produce (semi-)monoenergetic neutrons for benchmarking and to study the energy dependence of fission yields. The scientific program is extensive and is planed to start in 2013 with a measurement of isomeric yield ratios of proton induced fission in uranium. This will be followed by studies of independent yields of thermal and fast neutron induced fission of various actinides.

  3. Fast and Provably Accurate Bilateral Filtering

    NASA Astrophysics Data System (ADS)

    Chaudhury, Kunal N.; Dabhade, Swapnil D.

    2016-06-01

    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires $O(S)$ operations per pixel, where $S$ is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to $O(1)$ per pixel for any arbitrary $S$. The algorithm has a simple implementation involving $N+1$ spatial filterings, where $N$ is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to to estimate the order $N$ required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with state-of-the-art methods in terms of speed and accuracy.

  4. Fast and Provably Accurate Bilateral Filtering.

    PubMed

    Chaudhury, Kunal N; Dabhade, Swapnil D

    2016-06-01

    The bilateral filter is a non-linear filter that uses a range filter along with a spatial filter to perform edge-preserving smoothing of images. A direct computation of the bilateral filter requires O(S) operations per pixel, where S is the size of the support of the spatial filter. In this paper, we present a fast and provably accurate algorithm for approximating the bilateral filter when the range kernel is Gaussian. In particular, for box and Gaussian spatial filters, the proposed algorithm can cut down the complexity to O(1) per pixel for any arbitrary S . The algorithm has a simple implementation involving N+1 spatial filterings, where N is the approximation order. We give a detailed analysis of the filtering accuracy that can be achieved by the proposed approximation in relation to the target bilateral filter. This allows us to estimate the order N required to obtain a given accuracy. We also present comprehensive numerical results to demonstrate that the proposed algorithm is competitive with the state-of-the-art methods in terms of speed and accuracy. PMID:27093722

  5. Fast, Accurate and Precise Mid-Sagittal Plane Location in 3D MR Images of the Brain

    NASA Astrophysics Data System (ADS)

    Bergo, Felipe P. G.; Falcão, Alexandre X.; Yasuda, Clarissa L.; Ruppert, Guilherme C. S.

    Extraction of the mid-sagittal plane (MSP) is a key step for brain image registration and asymmetry analysis. We present a fast MSP extraction method for 3D MR images, based on automatic segmentation of the brain and on heuristic maximization of the cerebro-spinal fluid within the MSP. The method is robust to severe anatomical asymmetries between the hemispheres, caused by surgical procedures and lesions. The method is also accurate with respect to MSP delineations done by a specialist. The method was evaluated on 64 MR images (36 pathological, 20 healthy, 8 synthetic), and it found a precise and accurate approximation of the MSP in all of them with a mean time of 60.0 seconds per image, mean angular variation within a same image (precision) of 1.26o and mean angular difference from specialist delineations (accuracy) of 1.64o.

  6. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2013-07-01 2013-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  7. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2010-07-01 2010-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  8. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2011-07-01 2011-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  9. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2014-07-01 2014-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  10. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 1 2012-07-01 2012-07-01 false Accurate measurement. 4... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate measurement of the length of stumps, excursion of joints, dimensions and location of scars with respect...

  11. Bombing Target Identification from Limited Transect Data

    SciTech Connect

    Roberts, Barry L.; Hathaway, John E.; Pulsipher, Brent A.; McKenna, Sean A.

    2006-08-07

    A series of sensor data combined with geostatistical techniques were used to determine likely target areas for a historic military aerial bombing range. Primary data consisted of magnetic anomaly information from limited magnetometer transects across the site. Secondary data included airborne LIDAR, orthophotography, and other general site characterization information. Identification of likely target areas relied primarily upon kriging estimates of magnetic anomaly densities across the site. Secondary information, such as impact crater locations, was used to refine the boundary delineations.

  12. Targeted anti-inflammatory therapeutics in asthma and chronic obstructive lung disease

    PubMed Central

    Durham, Andrew L.; Caramori, Gaetano; Chung, Kian F.; Adcock, Ian M.

    2016-01-01

    Asthma and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the airway, although the drivers and site of the inflammation differ between diseases. Asthmatics with a neutrophilic airway inflammation are associated with a poor response to corticosteroids, whereas asthmatics with eosinophilic inflammation respond better to corticosteroids. Biologicals targeting the Th2-eosinophil nexus such as anti–interleukin (IL)-4, anti–IL-5, and anti–IL-13 are ineffective in asthma as a whole but are more effective if patients are selected using cellular (eg, eosinophils) or molecular (eg, periostin) biomarkers. This highlights the key role of individual inflammatory mediators in driving the inflammatory response and for accurate disease phenotyping to allow greater understanding of disease and development of patient-oriented antiasthma therapies. In contrast to asthmatic patients, corticosteroids are relatively ineffective in COPD patients. Despite stratification of COPD patients, the results of targeted therapy have proved disappointing with the exception of recent studies using CXC chemokine receptor (CXCR)2 antagonists. Currently, several other novel mediator-targeted drugs are undergoing clinical trials. As with asthma specifically targeted treatments may be of most benefit in specific COPD patient endotypes. The use of novel inflammatory mediator-targeted therapeutic agents in selected patients with asthma or COPD and the detection of markers of responsiveness or nonresponsiveness will allow a link between clinical phenotypes and pathophysiological mechanisms to be delineated reaching the goal of endotyping patients. PMID:26334389

  13. Targeted anti-inflammatory therapeutics in asthma and chronic obstructive lung disease.

    PubMed

    Durham, Andrew L; Caramori, Gaetano; Chung, Kian F; Adcock, Ian M

    2016-01-01

    Asthma and chronic obstructive pulmonary disease (COPD) are chronic inflammatory diseases of the airway, although the drivers and site of the inflammation differ between diseases. Asthmatics with a neutrophilic airway inflammation are associated with a poor response to corticosteroids, whereas asthmatics with eosinophilic inflammation respond better to corticosteroids. Biologicals targeting the Th2-eosinophil nexus such as anti-interleukin (IL)-4, anti-IL-5, and anti-IL-13 are ineffective in asthma as a whole but are more effective if patients are selected using cellular (eg, eosinophils) or molecular (eg, periostin) biomarkers. This highlights the key role of individual inflammatory mediators in driving the inflammatory response and for accurate disease phenotyping to allow greater understanding of disease and development of patient-oriented antiasthma therapies. In contrast to asthmatic patients, corticosteroids are relatively ineffective in COPD patients. Despite stratification of COPD patients, the results of targeted therapy have proved disappointing with the exception of recent studies using CXC chemokine receptor (CXCR)2 antagonists. Currently, several other novel mediator-targeted drugs are undergoing clinical trials. As with asthma specifically targeted treatments may be of most benefit in specific COPD patient endotypes. The use of novel inflammatory mediator-targeted therapeutic agents in selected patients with asthma or COPD and the detection of markers of responsiveness or nonresponsiveness will allow a link between clinical phenotypes and pathophysiological mechanisms to be delineated reaching the goal of endotyping patients. PMID:26334389

  14. Delineation of pipeline river crossing using cable and pipe locator with real-time differential GPS

    SciTech Connect

    Waddington, B.S.; Maxwell, M.

    1996-11-01

    The location and depth of cover over pipeline river crossings must be checked periodically to ascertain that the pipeline remains undisturbed and adequately covered. We have developed a technique to determine pipeline plan location and depth of cover utilizing a combination of electromagnetic detection and echosounding with real-time navigation, in this case differential GPS. The technique offers an alternative to acoustic location methods where small pipe size or the presence of acoustically opaque sediments prevent pipe detection. In addition, the technique can be used in fast-flowing rivers or in heavy marine traffic where anchoring is an unlikely option. We have successfully applied the method to locate and profile a 168 mm steel pipeline crossing under the Fraser River, near Vancouver, Canada. Site conditions consisted of a 250 m wide river with 3-5 knot current. The 168 mm steel pipeline was buried in silts from 2-6 m thick below water up to 9 m deep. In addition, approximately 80 m of the river surface was permanently covered by log booms and hence inaccessible by boat. Initial attempts to locate the pipe using an acoustic sub-bottom profiler were unsuccessful. The 3.5 kHz system used did not provide sufficient penetration to delineate the pipe, probably due to the presence of biogenic gas in the river-bottom sediments. A Radiodetection{reg_sign} cable and pipe locator system was used to establish shoreline and shallow water locations. Unfortunately river currents and marine traffic prevented accurate location and depth determination using standard location techniques. The development of digital pipe locators with RS-232 interfacing permitted us to develop a technique utilizing simultaneous recording of digital magnetic field strength and real-time differential GPS location data. The Radiodetection{reg_sign} transmitter was connected to a riverside pipe valve.

  15. Delineating Discontinuous Permafrost on the Seward Peninsula, Alaska, With Two-Dimensional Resistivity and Electromagnetic Techniques

    NASA Astrophysics Data System (ADS)

    Astley, B. N.; Delaney, A. J.; Douglas, T. A.; Engel, C.

    2005-12-01

    Soils at the Stewart River Training Area near Nome, Alaska were investigated in July 2005 to determine suitability for trail relocation. The area contains classic cryogenic features including thermokarst ponds, ice wedge polygons, sorted circles, cobble pavement, and solifluction lobes. The soils range from silty gravel to clayey silt, typical of a glacial depositional environment. Discontinuous permafrost is present in the region. We collected 2D resistivity and EM31 on a study grid 525 m long by 300 m wide that was bisected north to south by a stream valley. We used Wenner, Schlumberger, and Dipole-Dipole arrays with a 5-m electrode spacing and array length of 275 m. Soil pits were excavated to determine the depth to the top of permafrost, to measure soil horizon thicknesses and to collect soil samples for water content measurements. Frost probes were also used to determine permafrost depth. Soil moisture content ranged from 47% by weight in frozen silt to 11% in thawed poorly-sorted silty gravel. The depth to permafrost ranged from 15 to120 cm below the surface. Soil type appeared to be the dominant control on the presence of permafrost in the study area with all permafrost found in silt and no permafrost found in gravels. The presence of willow thickets corresponded with thawed areas. Willows were absent in areas containing massive permafrost, but were present in low numbers where permafrost was degrading. High resistivity anomalies correlated with frozen soil on the east side of the stream. On the west side of the stream, high resistivity associated with a cobble pavement and large gravel clasts had similar resistivity values as permafrost. The EM31 data correlated well with permafrost, and determined the location of a highly conductive area in the schistose bedrock. Our results suggest that a combination of geophysical tools and shallow ground truth explorations using probes and shovels can provide an accurate delineation of horizontal and vertical permafrost

  16. P13.21ORGANS AT RISK IN THE BRAIN AND THEIR DOSE-CONSTRAINTS IN THE ADULTS AND IN THE CHILDREN: A RADIATION ONCOLOGIST'S GUIDE FOR DELINEATION

    PubMed Central

    Scoccianti, S.; Detti, B.; Greto, D.; Gadda, D.; Furfaro, I.F.; Di Brina, L.; Meacci, F.; Cassani, S.; Giacomelli, I.; Livi, L.

    2014-01-01

    The aim of this study is to provide a stepwise contouring guide to delineate the organs at risk in the brain as it would be done in the everyday practice of planning radiotherapy for brain cancer treatment. Acute and late toxicity with risk of visual and hearing deficits, hormonal impairment and neurocognitive alterations, is a critical point in radiation treatment of patients affected by brain tumors. Moreover, accurate delineation of organ at risks is essential for the inverse-planning process of intensity modulated radiation treatment (IMRT). However, anatomic cerebral normal structures are not always easily recognizable either on simulation CT scan and on coregistered MRI scan used for radiotherapy planning. We have developed a detailed anatomy atlas on Computed tomography (CT) imaging and magnetic resonance (MR) imaging of brain. The following regions of interest were defined: optic chiasm, cochlea, pituitary gland, temporal lobe and hippocampus. Some main notions of anatomy of the organs at risk are provided together with some landmarks easily to be found on the imaging scans. Detailed contouring recommendations are provided in order to significantly improve the contour accuracy and concordance. This report also provides for all the above-mentioned organs at risk a systematic review for the recommended dose constraints both for adult and pediatric patients. This guide is a useful tool for improving daily practice and decreasing the differences in organs at risk delineation between radiation oncologists.

  17. Targeting of deep-brain structures in nonhuman primates using MR and CT Images

    NASA Astrophysics Data System (ADS)

    Chen, Antong; Hines, Catherine; Dogdas, Belma; Bone, Ashleigh; Lodge, Kenneth; O'Malley, Stacey; Connolly, Brett; Winkelmann, Christopher T.; Bagchi, Ansuman; Lubbers, Laura S.; Uslaner, Jason M.; Johnson, Colena; Renger, John; Zariwala, Hatim A.

    2015-03-01

    In vivo gene delivery in central nervous systems of nonhuman primates (NHP) is an important approach for gene therapy and animal model development of human disease. To achieve a more accurate delivery of genetic probes, precise stereotactic targeting of brain structures is required. However, even with assistance from multi-modality 3D imaging techniques (e.g. MR and CT), the precision of targeting is often challenging due to difficulties in identification of deep brain structures, e.g. the striatum which consists of multiple substructures, and the nucleus basalis of meynert (NBM), which often lack clear boundaries to supporting anatomical landmarks. Here we demonstrate a 3D-image-based intracranial stereotactic approach applied toward reproducible intracranial targeting of bilateral NBM and striatum of rhesus. For the targeting we discuss the feasibility of an atlas-based automatic approach. Delineated originally on a high resolution 3D histology-MR atlas set, the NBM and the striatum could be located on the MR image of a rhesus subject through affine and nonrigid registrations. The atlas-based targeting of NBM was compared with the targeting conducted manually by an experienced neuroscientist. Based on the targeting, the trajectories and entry points for delivering the genetic probes to the targets could be established on the CT images of the subject after rigid registration. The accuracy of the targeting was assessed quantitatively by comparison between NBM locations obtained automatically and manually, and finally demonstrated qualitatively via post mortem analysis of slices that had been labelled via Evan Blue infusion and immunohistochemistry.

  18. Anatomic Boundaries of the Clinical Target Volume (Prostate Bed) After Radical Prostatectomy

    SciTech Connect

    Wiltshire, Kirsty L.; Brock, Kristy K.; Haider, Masoom A.; Zwahlen, Daniel; Kong, Vickie; Chan, Elisa; Moseley, Joanne; Bayley, Andrew; Catton, Charles; Chung, Peter W.M.; Gospodarowicz, Mary; Milosevic, Michael; Kneebone, Andrew; Warde, Padraig; Menard, Cynthia

    2007-11-15

    Purpose: We sought to derive and validate an interdisciplinary consensus definition for the anatomic boundaries of the postoperative clinical target volume (CTV, prostate bed). Methods and Materials: Thirty one patients who had planned for radiotherapy after radical prostatectomy were enrolled and underwent computed tomography and magnetic resonance imaging (MRI) simulation prior to radiotherapy. Through an iterative process of consultation and discussion, an interdisciplinary consensus definition was derived based on a review of published data, patterns of local failure, surgical practice, and radiologic anatomy. In validation, we analyzed the distribution of surgical clips in reference to the consensus CTV and measured spatial uncertainties in delineating the CTV and vesicourethral anastomosis. Clinical radiotherapy plans were retrospectively evaluated against the consensus CTV (prostate bed). Results: Anatomic boundaries of the consensus CTV (prostate bed) are described. Surgical clips (n = 339) were well distributed throughout the CTV. The vesicourethral anastomosis was accurately localized using central sagittal computed tomography reconstruction, with a mean {+-} standard deviation uncertainty of 1.8 {+-} 2.5 mm. Delineation uncertainties were small for both MRI and computed tomography (mean reproducibility, 0-3.8 mm; standard deviation, 1.0-2.3); they were most pronounced in the anteroposterior and superoinferior dimensions and at the superior/posterior-most aspect of the CTV. Retrospectively, the mean {+-} standard deviation CTV (prostate bed) percentage of volume receiving 100% of prescribed dose was only 77% {+-} 26%. Conclusions: We propose anatomic boundaries for the CTV (prostate bed) and present evidence supporting its validity. In the absence of gross recurrence, the role of MRI in delineating the CTV remains to be confirmed. The CTV is larger than historically practiced at our institution and should be encompassed by a microscopic tumoricidal dose.

  19. Protein deacetylation by sirtuins: delineating a post-translational regulatory program responsive to nutrient and redox stressors

    PubMed Central

    Bao, Jianjun

    2012-01-01

    Lysine acetylation/deacetylation is increasingly being recognized as common post-translational modification that appears to be broadly operational throughout the cell. The functional roles of these modifications, outside of the nucleus, have not been extensively studied. Moreover, as acetyl-CoA donates the acetyl group for acetylation, nutrient availability and energetic status may be pivotal in this modification. Similarly, nutrient limitation is associated with the deacetylation reaction. This modification is orchestrated by a novel family of sirtuin deacetylases that function in a nutrient and redox dependent manner and targets non-histone protein deacetylation. In compartment-specific locations, candidate target proteins undergoing lysine-residue deacetylation are being identified. Through these investigations, the functional role of this post-translational modification is being delineated. We review the sirtuin family proteins, discuss their functional effects on target proteins, and postulate on potential biological programs and disease processes that may be modified by sirtuin-mediated deacetylation of target proteins. PMID:20680393

  20. Endothelial and Epithelial Cell Transition to a Mesenchymal Phenotype Was Delineated by Nestin Expression.

    PubMed

    Chabot, Andréanne; Hertig, Vanessa; Boscher, Elena; Nguyen, Quang Trinh; Boivin, Benoît; Chebli, Jasmine; Bissonnette, Lyse; Villeneuve, Louis; Brochiero, Emmanuelle; Dupuis, Jocelyn; Calderone, Angelino

    2016-07-01

    Cover: The cover image, by Angelino Calderone et al., is based on the Original Research Article Endothelial and Epithelial Cell Transition to a Mesenchymal Phenotype Was Delineated by Nestin Expression, DOI: 10.1002/jcp.25257. PMID:26995059

  1. Delineation of a cellular hierarchy in lung cancer reveals an oncofetal antigen expressed on tumor-initiating cells.

    PubMed

    Damelin, Marc; Geles, Kenneth G; Follettie, Maximillian T; Yuan, Ping; Baxter, Michelle; Golas, Jonathon; DiJoseph, John F; Karnoub, Maha; Huang, Shuguang; Diesl, Veronica; Behrens, Carmen; Choe, Sung E; Rios, Carol; Gruzas, Janet; Sridharan, Latha; Dougher, Maureen; Kunz, Arthur; Hamann, Philip R; Evans, Deborah; Armellino, Douglas; Khandke, Kiran; Marquette, Kimberly; Tchistiakova, Lioudmila; Boghaert, Erwin R; Abraham, Robert T; Wistuba, Ignacio I; Zhou, Bin-Bing S

    2011-06-15

    Poorly differentiated tumors in non-small cell lung cancer (NSCLC) have been associated with shorter patient survival and shorter time to recurrence following treatment. Here, we integrate multiple experimental models with clinicopathologic analysis of patient tumors to delineate a cellular hierarchy in NSCLC. We show that the oncofetal protein 5T4 is expressed on tumor-initiating cells and associated with worse clinical outcome in NSCLC. Coexpression of 5T4 and factors involved in the epithelial-to-mesenchymal transition were observed in undifferentiated but not in differentiated tumor cells. Despite heterogeneous expression of 5T4 in NSCLC patient-derived xenografts, treatment with an anti-5T4 antibody-drug conjugate resulted in complete and sustained tumor regression. Thus, the aggressive growth of heterogeneous solid tumors can be blocked by therapeutic agents that target a subpopulation of cells near the top of the cellular hierarchy. PMID:21540235

  2. P wave detection and delineation in the ECG based on the phase free stationary wavelet transform and using intracardiac atrial electrograms as reference.

    PubMed

    Lenis, Gustavo; Pilia, Nicolas; Oesterlein, Tobias; Luik, Armin; Schmitt, Claus; Dössel, Olaf

    2016-02-01

    Robust and exact automatic P wave detection and delineation in the electrocardiogram (ECG) is still an interesting but challenging research topic. The early prognosis of cardiac afflictions such as atrial fibrillation and the response of a patient to a given treatment is believed to improve if the P wave is carefully analyzed during sinus rhythm. Manual annotation of the signals is a tedious and subjective task. Its correctness depends on the experience of the annotator, quality of the signal, and ECG lead. In this work, we present a wavelet-based algorithm to detect and delineate P waves in individual ECG leads. We evaluated a large group of commonly used wavelets and frequency bands (wavelet levels) and introduced a special phase free wavelet transformation. The local extrema of the transformed signals are directly related to the delineating points of the P wave. First, the algorithm was studied using synthetic signals. Then, the optimal parameter configuration was found using intracardiac electrograms and surface ECGs measured simultaneously. The reverse biorthogonal wavelet 3.3 was found to be optimal for this application. In the end, the method was validated using the QT database from PhysioNet. We showed that the algorithm works more accurately and more robustly than other methods presented in literature. The validation study delivered an average delineation error of the P wave onset of -0.32±12.41 ms when compared to manual annotations. In conclusion, the algorithm is suitable for handling varying P wave shapes and low signal-to-noise ratios. PMID:26136298

  3. Comparison of [{sup 11}C]choline Positron Emission Tomography With T2- and Diffusion-Weighted Magnetic Resonance Imaging for Delineating Malignant Intraprostatic Lesions

    SciTech Connect

    Chang, Joe H.; Lim Joon, Daryl; Davis, Ian D.; Lee, Sze Ting; Hiew, Chee-Yan; Esler, Stephen; Gong, Sylvia J.; Wada, Morikatsu; Clouston, David; O'Sullivan, Richard; Goh, Yin P.; Bolton, Damien; Scott, Andrew M.; Khoo, Vincent

    2015-06-01

    Purpose: The purpose of this study was to compare the accuracy of [{sup 11}C]choline positron emission tomography (CHOL-PET) with that of the combination of T2-weighted and diffusion-weighted (T2W/DW) magnetic resonance imaging (MRI) for delineating malignant intraprostatic lesions (IPLs) for guiding focal therapies and to investigate factors predicting the accuracy of CHOL-PET. Methods and Materials: This study included 21 patients who underwent CHOL-PET and T2W/DW MRI prior to radical prostatectomy. Two observers manually delineated IPL contours for each scan, and automatic IPL contours were generated on CHOL-PET based on varying proportions of the maximum standardized uptake value (SUV). IPLs identified on prostatectomy specimens defined reference standard contours. The imaging-based contours were compared with the reference standard contours using Dice similarity coefficient (DSC), and sensitivity and specificity values. Factors that could potentially predict the DSC of the best contouring method were analyzed using linear models. Results: The best automatic contouring method, 60% of the maximum SUV (SUV{sub 60}) , had similar correlations (DSC: 0.59) with the manual PET contours (DSC: 0.52, P=.127) and significantly better correlations than the manual MRI contours (DSC: 0.37, P<.001). The sensitivity and specificity values were 72% and 71% for SUV{sub 60}; 53% and 86% for PET manual contouring; and 28% and 92% for MRI manual contouring. The tumor volume and transition zone pattern could independently predict the accuracy of CHOL-PET. Conclusions: CHOL-PET is superior to the combination of T2W/DW MRI for delineating IPLs. The accuracy of CHOL-PET is insufficient for gland-sparing focal therapies but may be accurate enough for focal boost therapies. The transition zone pattern is a new classification that may predict how well CHOL-PET delineates IPLs.

  4. DEM-based Watershed Delineation - Comparison of Different Methods and applications

    NASA Astrophysics Data System (ADS)

    Chu, X.; Zhang, J.; Tahmasebi Nasab, M.

    2015-12-01

    Digital elevation models (DEMs) are commonly used for large-scale watershed hydrologic and water quality modeling. With aid of the latest LiDAR technology, submeter scale DEM data are often available for many areas in the United States. Precise characterization of the detailed variations in surface microtopography using such high-resolution DEMs is crucial to the related watershed modeling. Various methods have been developed to delineate a watershed, including determination of flow directions and accumulations, identification of subbasin boundaries, and calculation of the relevant topographic parameters. The objective of this study is to examine different DEM-based watershed delineation methods by comparing their unique features and the discrepancies in their results. Not only does this study cover the traditional watershed delineation methods, but also a new puddle-based unit (PBU) delineation method. The specific topics and issues to be presented involve flow directions (D8 single flow direction vs. multi-direction methods), segmentation of stream channels, drainage systems (single "depressionless" drainage network vs. hierarchical depression-dominated drainage system), and hydrologic connectivity (static structural connectivity vs. dynamic functional connectivity). A variety of real topographic surfaces are selected and delineated by using the selected methods. Comparisons of their delineation results emphasize the importance of selection of the methods and highlight their applicability and potential impacts on watershed modeling.

  5. A method of dose reconstruction for moving targets compatible with dynamic treatments

    PubMed Central

    Poulsen, Per Rugaard; Schmidt, Mai Lykkegaard; Keall, Paul; Worm, Esben Schjødt; Fledelius, Walther; Hoffmann, Lone

    2012-01-01

    Purpose: To develop a method that allows a commercial treatment planning system (TPS) to perform accurate dose reconstruction for rigidly moving targets and to validate the method in phantom measurements for a range of treatments including intensity modulated radiation therapy (IMRT), volumetric arc therapy (VMAT), and dynamic multileaf collimator (DMLC) tracking. Methods: An in-house computer program was developed to manipulate Dicom treatment plans exported from a TPS (Eclipse, Varian Medical Systems) such that target motion during treatment delivery was incorporated into the plans. For each treatment, a motion including plan was generated by dividing the intratreatment target motion into 1 mm position bins and construct sub-beams that represented the parts of the treatment that were delivered, while the target was located within each position bin. For each sub-beam, the target shift was modeled by a corresponding isocenter shift. The motion incorporating Dicom plans were reimported into the TPS, where dose calculation resulted in motion including target dose distributions. For experimental validation of the dose reconstruction a thorax phantom with a moveable lung equivalent rod with a tumor insert of solid water was first CT scanned. The tumor insert was delineated as a gross tumor volume (GTV), and a planning target volume (PTV) was formed by adding margins. A conformal plan, two IMRT plans (step-and-shoot and sliding windows), and a VMAT plan were generated giving minimum target doses of 95% (GTV) and 67% (PTV) of the prescription dose (3 Gy). Two conformal fields with MLC leaves perpendicular and parallel to the tumor motion, respectively, were generated for DMLC tracking. All treatment plans were delivered to the thorax phantom without tumor motion and with a sinusoidal tumor motion. The two conformal fields were delivered with and without portal image guided DMLC tracking based on an embedded gold marker. The target dose distribution was measured with a

  6. USGS aerial resolution targets.

    USGS Publications Warehouse

    Salamonowicz, P.H.

    1982-01-01

    It is necessary to measure the achievable resolution of any airborne sensor that is to be used for metric purposes. Laboratory calibration facilities may be inadequate or inappropriate for determining the resolution of non-photographic sensors such as optical-mechanical scanners, television imaging tubes, and linear arrays. However, large target arrays imaged in the field can be used in testing such systems. The USGS has constructed an array of resolution targets in order to permit field testing of a variety of airborne sensing systems. The target array permits any interested organization with an airborne sensing system to accurately determine the operational resolution of its system. -from Author

  7. Delineating subsurface zones of natural bioreduction using the complex resistivity method

    NASA Astrophysics Data System (ADS)

    Flores-Orozco, A.; Williams, K. H.; Kemna, A.; Campbell, K. M.; Kukkadapu, R. K.; Peacock, A.; Long, P. E.

    2009-12-01

    Measurements of complex resistivity (CR) were made in order to spatially delineate zones of natural bioreduction (NBZ’s) within an aquifer underlying a former uranium mill tailings site near Rifle, Colorado. Previous studies at the site have demonstrated the ability to remove aqueous uranium from groundwater by stimulating iron and sulfate reducing bacteria through injection of acetate. Time-lapse CR measurements have proven to be a useful technique for assessing changes in sediment redox status accompanying biostimulation, with laboratory and field CR phase anomalies strongly correlated with the accumulation of metal sulfides and electroactive ions, such as Fe(II). In the present study, we show that CR measurements can also be used to identify zones where natural bioreduction processes have occurred or are ongoing in the absence of exogenous organic carbon. These zones are a critical component of the natural attenuation process and enable the slow but sustained removal of uranium from groundwater. As such, identifying the presence and distribution of NBZ’s is an important aspect of assessing the potential for natural attenuation at a site of interest. Measurements were obtained in both the time and frequency domain along surface transects oriented parallel and perpendicular to groundwater flow direction using an electrode separation of either 1 or 2 m. A modified dipole-dipole configuration was used to improve the signal-to-noise ratio and the depth of investigation; reciprocal measurements were performed in order to estimate the error in resistance and phase. Well-defined phase anomalies along several of the CR transects were used to define drilling targets, and recovery of aquifer materials from these locations revealed sediments enriched in refractory organic carbon, reduced inorganic sulfur, framboidal pyrites, and uranium. Based on these results, the CR method appears to be an exploration technique well suited for characterizing the spatial distribution

  8. An Integrated Genomic Strategy Delineates Candidate Mediator Genes Regulating Grain Size and Weight in Rice

    PubMed Central

    Malik, Naveen; Dwivedi, Nidhi; Singh, Ashok K.; Parida, Swarup K.; Agarwal, Pinky; Thakur, Jitendra K.; Tyagi, Akhilesh K.

    2016-01-01

    The present study deployed a Mediator (MED) genes-mediated integrated genomic strategy for understanding the complex genetic architecture of grain size/weight quantitative trait in rice. The targeted multiplex amplicon resequencing of 55 MED genes annotated from whole rice genome in 384 accessions discovered 3971 SNPs, which were structurally and functionally annotated in diverse coding and non-coding sequence-components of genes. Association analysis, using the genotyping information of 3971 SNPs in a structured population of 384 accessions (with 50–100 kb linkage disequilibrium decay), detected 10 MED gene-derived SNPs significantly associated (46% combined phenotypic variation explained) with grain length, width and weight in rice. Of these, one strong grain weight-associated non-synonymous SNP (G/A)-carrying OsMED4_2 gene was validated successfully in low- and high-grain weight parental accessions and homozygous individuals of a rice mapping population. The seed-specific expression, including differential up/down-regulation of three grain size/weight-associated MED genes (including OsMED4_2) in six low and high-grain weight rice accessions was evident. Altogether, combinatorial genomic approach involving haplotype-based association analysis delineated diverse functionally relevant natural SNP-allelic variants in 10 MED genes, including three potential novel SNP haplotypes in an OsMED4_2 gene governing grain size/weight differentiation in rice. These molecular tags have potential to accelerate genomics-assisted crop improvement in rice. PMID:27000976

  9. Single-cell analysis delineates a trajectory toward the human early otic lineage.

    PubMed

    Ealy, Megan; Ellwanger, Daniel C; Kosaric, Nina; Stapper, Andres P; Heller, Stefan

    2016-07-26

    Efficient pluripotent stem cell guidance protocols for the production of human posterior cranial placodes such as the otic placode that gives rise to the inner ear do not exist. Here we use a systematic approach including defined monolayer culture, signaling modulation, and single-cell gene expression analysis to delineate a developmental trajectory for human otic lineage specification in vitro. We found that modulation of bone morphogenetic protein (BMP) and WNT signaling combined with FGF and retinoic acid treatments over the course of 18 days generates cell populations that develop chronological expression of marker genes of non-neural ectoderm, preplacodal ectoderm, and early otic lineage. Gene expression along this differentiation path is distinct from other lineages such as endoderm, mesendoderm, and neural ectoderm. Single-cell analysis exposed the heterogeneity of differentiating cells and allowed discrimination of non-neural ectoderm and otic lineage cells from off-target populations. Pseudotemporal ordering of human embryonic stem cell and induced pluripotent stem cell-derived single-cell gene expression profiles revealed an initially synchronous guidance toward non-neural ectoderm, followed by comparatively asynchronous occurrences of preplacodal and otic marker genes. Positive correlation of marker gene expression between both cell lines and resemblance to mouse embryonic day 10.5 otocyst cells implied reasonable robustness of the guidance protocol. Single-cell trajectory analysis further revealed that otic progenitor cell types are induced in monolayer cultures, but further development appears impeded, likely because of lack of a lineage-stabilizing microenvironment. Our results provide a framework for future exploration of stabilizing microenvironments for efficient differentiation of stem cell-generated human otic cell types. PMID:27402757

  10. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

    PubMed

    Yang, Mingjun; Angles d'Ortoli, Thibault; Säwén, Elin; Jana, Madhurima; Widmalm, Göran; MacKerell, Alexander D

    2016-07-28

    The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence. PMID:27346493

  11. Implications of different digital elevation models and preprocessing techniques to delineate debris flow inundation hazard zones in El Salvador

    NASA Astrophysics Data System (ADS)

    Anderson, E. R.; Griffin, R.; Irwin, D.

    2013-12-01

    Heavy rains and steep, volcanic slopes in El Salvador cause numerous landslides every year, posing a persistent threat to the population, economy and environment. Although potential debris inundation hazard zones have been delineated using digital elevation models (DEMs), some disparities exist between the simulated zones and actual affected areas. Moreover, these hazard zones have only been identified for volcanic lahars and not the shallow landslides that occur nearly every year. This is despite the availability of tools to delineate a variety of landslide types (e.g., the USGS-developed LAHARZ software). Limitations in DEM spatial resolution, age of the data, and hydrological preprocessing techniques can contribute to inaccurate hazard zone definitions. This study investigates the impacts of using different elevation models and pit filling techniques in the final debris hazard zone delineations, in an effort to determine which combination of methods most closely agrees with observed landslide events. In particular, a national DEM digitized from topographic sheets from the 1970s and 1980s provide an elevation product at a 10 meter resolution. Both natural and anthropogenic modifications of the terrain limit the accuracy of current landslide hazard assessments derived from this source. Global products from the Shuttle Radar Topography Mission (SRTM) and the Advanced Spaceborne Thermal Emission and Reflection Radiometer Global DEM (ASTER GDEM) offer more recent data but at the cost of spatial resolution. New data derived from the NASA Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) in 2013 provides the opportunity to update hazard zones at a higher spatial resolution (approximately 6 meters). Hydrological filling of sinks or pits for current hazard zone simulation has previously been achieved through ArcInfo spatial analyst. Such hydrological processing typically only fills pits and can lead to drastic modifications of original elevation values

  12. A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery using a Probabilistic Learning Framework

    NASA Astrophysics Data System (ADS)

    Basu, S.; Ganguly, S.; Michaelis, A.; Votava, P.; Roy, A.; Mukhopadhyay, S.; Nemani, R. R.

    2015-12-01

    Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

  13. A High Performance Computing Approach to Tree Cover Delineation in 1-m NAIP Imagery Using a Probabilistic Learning Framework

    NASA Technical Reports Server (NTRS)

    Basu, Saikat; Ganguly, Sangram; Michaelis, Andrew; Votava, Petr; Roy, Anshuman; Mukhopadhyay, Supratik; Nemani, Ramakrishna

    2015-01-01

    Tree cover delineation is a useful instrument in deriving Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) airborne imagery data. Numerous algorithms have been designed to address this problem, but most of them do not scale to these datasets, which are of the order of terabytes. In this paper, we present a semi-automated probabilistic framework for the segmentation and classification of 1-m National Agriculture Imagery Program (NAIP) for tree-cover delineation for the whole of Continental United States, using a High Performance Computing Architecture. Classification is performed using a multi-layer Feedforward Backpropagation Neural Network and segmentation is performed using a Statistical Region Merging algorithm. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field, which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by relabeling misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the whole state of California, spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles. The framework produced true positive rates of around 88% for fragmented forests and 74% for urban tree cover areas, with false positive rates lower than 2% for both landscapes. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR canopy height model (CHM) showed the effectiveness of our framework for generating accurate high-resolution tree-cover maps.

  14. Delineating Spatial Patterns in the Yellowstone Hydrothermal System using Geothermometry

    NASA Astrophysics Data System (ADS)

    King, J.; Hurwitz, S.; Lowenstern, J. B.

    2015-12-01

    Yellowstone National Park is unmatched with regard to its quantity of active hydrothermal features. Origins of thermal waters in its geyser basins have been traced to mixing of a deep parent water with meteoric waters in shallow local reservoirs (Fournier, 1989). A mineral-solution equilibrium model was developed to calculate water-rock chemical re-equilibration temperatures in these shallow reservoirs. We use the GeoT program, which uses water composition data as input to calculate saturation indices of selected minerals; the "best-clustering" minerals are then statistically determined to infer reservoir temperatures (Spycher et al., 2013). We develop the method using water composition data from Heart Lake Geyser Basin (HLGB), for which both chemical and isotopic geothermometers predict a reservoir water temperature of 205°C ± 10°C (Lowenstern et al., 2012), and minerals found in drill cores in Yellowstone's geyser basins. We test the model for sensitivity to major element composition, pH, Total Inorganic Carbon (TIC) and selected minerals to optimize model parameters. Calculated temperatures are most accurate at pH values below 9.0, and closely match the equilibrium saturation indices of quartz, stilbite, microcline, and albite. The model is optimized with a TIC concentration that is consistent with the mass of diffuse CO2 flux in HLGB (Lowenstern et al., 2012). We then use water compositions from other thermal basins in Yellowstone in search of spatial variations in reservoir temperatures. We then compare the calculated temperatures with various SiO2 and cation geothermometers.

  15. Simple indicator kriging for estimating the probability of incorrectly delineating hazardous areas in a contaminated site

    SciTech Connect

    Juang, K.W.; Lee, D.Y.

    1998-09-01

    The probability of incorrectly delineating hazardous areas in a contaminated site is very important for decision-makers because it indicates the magnitude of confidence that decision-makers have in determining areas in need of remediation. In this study, simple indicator kriging (SIK) was used to estimate the probability of incorrectly delineating hazardous areas in a heavy metal-contaminated site, which is located at Taoyuan, Taiwan, and is about 10 ha in area. In the procedure, the values 0 and 1 were assigned to be the stationary means of the indicator codes in the SIK model to represent two hypotheses, hazardous and safe, respectively. The spatial distribution of the conditional probability of heavy metal concentrations lower than a threshold, given each hypothesis, was estimated using SIK. Then, the probabilities of false positives ({alpha}) (i.e., the probability of declaring a location hazardous when it is not) and false negatives ({beta}) (i.e., the probability of declaring a location safe when it is not) in delineating hazardous areas for the heavy metal-contaminated site could be obtained. The spatial distribution of the probabilities of false positives and false negatives could help in delineating hazardous areas based on a tolerable probability level of incorrect delineation. In addition, delineation complicated by the cost of remediation, hazards in the environment, and hazards to human health could be made based on the minimum values of {alpha} and {beta}. The results suggest that the proposed SIK procedure is useful for decision-makers who need to delineate hazardous areas in a heavy metal-contaminated site.

  16. Prostate contours delineation using interactive directional active contours model and parametric shape prior model.

    PubMed

    Derraz, Foued; Forzy, Gérard; Delebarre, Arnaud; Taleb-Ahmed, Abdelmalik; Oussalah, Mourad; Peyrodie, Laurent; Verclytte, Sebastien

    2015-11-01

    Prostate contours delineation on Magnetic Resonance (MR) images is a challenging and important task in medical imaging with applications of guiding biopsy, surgery and therapy. While a fully automated method is highly desired for this application, it can be a very difficult task due to the structure and surrounding tissues of the prostate gland. Traditional active contours-based delineation algorithms are typically quite successful for piecewise constant images. Nevertheless, when MR images have diffuse edges or multiple similar objects (e.g. bladder close to prostate) within close proximity, such approaches have proven to be unsuccessful. In order to mitigate these problems, we proposed a new framework for bi-stage contours delineation algorithm based on directional active contours (DAC) incorporating prior knowledge of the prostate shape. We first explicitly addressed the prostate contour delineation problem based on fast globally DAC that incorporates both statistical and parametric shape prior model. In doing so, we were able to exploit the global aspects of contour delineation problem by incorporating a user feedback in contours delineation process where it is shown that only a small amount of user input can sometimes resolve ambiguous scenarios raised by DAC. In addition, once the prostate contours have been delineated, a cost functional is designed to incorporate both user feedback interaction and the parametric shape prior model. Using data from publicly available prostate MR datasets, which includes several challenging clinical datasets, we highlighted the effectiveness and the capability of the proposed algorithm. Besides, the algorithm has been compared with several state-of-the-art methods. PMID:26009857

  17. A hierarchical network-based algorithm for multi-scale watershed delineation

    NASA Astrophysics Data System (ADS)

    Castronova, Anthony M.; Goodall, Jonathan L.

    2014-11-01

    Watershed delineation is a process for defining a land area that contributes surface water flow to a single outlet point. It is a commonly used in water resources analysis to define the domain in which hydrologic process calculations are applied. There has been a growing effort over the past decade to improve surface elevation measurements in the U.S., which has had a significant impact on the accuracy of hydrologic calculations. Traditional watershed processing on these elevation rasters, however, becomes more burdensome as data resolution increases. As a result, processing of these datasets can be troublesome on standard desktop computers. This challenge has resulted in numerous works that aim to provide high performance computing solutions to large data, high resolution data, or both. This work proposes an efficient watershed delineation algorithm for use in desktop computing environments that leverages existing data, U.S. Geological Survey (USGS) National Hydrography Dataset Plus (NHD+), and open source software tools to construct watershed boundaries. This approach makes use of U.S. national-level hydrography data that has been precomputed using raster processing algorithms coupled with quality control routines. Our approach uses carefully arranged data and mathematical graph theory to traverse river networks and identify catchment boundaries. We demonstrate this new watershed delineation technique, compare its accuracy with traditional algorithms that derive watershed solely from digital elevation models, and then extend our approach to address subwatershed delineation. Our findings suggest that the open-source hierarchical network-based delineation procedure presented in the work is a promising approach to watershed delineation that can be used summarize publicly available datasets for hydrologic model input pre-processing. Through our analysis, we explore the benefits of reusing the NHD+ datasets for watershed delineation, and find that the our technique

  18. Auto-basin delineation in the Himalayas: how much is enough?

    NASA Astrophysics Data System (ADS)

    Khan, A.

    2015-12-01

    Digital Elevation Models (DEMs) are increasingly used for basin boundaries delineation in a variety of hydro-climatic studies. However, accuracy of basin areas depends on quality of DEMs and adopted methods. This study presents auto and supervised delineation in a case study of the Indus Basin (IB), which originates in the Himalayan Mountains and ends in the Arabian Sea. The published estimates of the IB area show significant variability, ranging from 866,000 to 1,230,000 km2. Auto-delineation has been carried out using three DEMs: 1. GTOPO 30 (1km resolution), 2. GTOPO 30 Hydro1K (1km resolution), and 3. SRTM DEM (90m resolution). It is shown that discrepancies between different estimates reflect differences in the initial extent of the DEMs used for basin delineation, and are due to reiterating auto pit-filling process. Four critical points (where overestimates were suspected) have been selected, based on auto-delineated streams together with overlay of the minimum and maximum available basin boundaries, and were evaluated based on Google Earth and flow data. This study shows that the Pangong basin (in western Tibet), Gaggar-Hakra basin (starts from Himachal Pradesh and ends in the western part of the Thar desert) concomitant with downstream part of the Sukkur Barrage are not part of the IB, but are areas of either internal drainage basins or downstream command areas of the Indus River. Our best estimate of the IB area is ~833,000 km2, and is in good agreement with the basin area by HydroSHEDS. This study recommends a revisit of earlier hydro-climatic studies, which are based on overestimated basin boundaries, and recommends to use the current study's results for future improvements. The important cautionary message of current study is to adopt supervised delineation, and to evaluate accuracy of auto-delineated areas based on geomorphology and flow data, particularly when there are endorheic lake basins or deserts in the vicinity.

  19. Colorectal Cancer Genetic Heterogeneity Delineated by Multi-Region Sequencing

    PubMed Central

    Liang, Rui; Xie, Zhen-Rong; Luo, Hua-You; Zeng, Yu-Jian; Xu, Yu; Wang, La-Mei; Kong, Xiang-Yang; Wang, Kun-Hua

    2016-01-01

    Intratumor heterogeneity (ITH) leads to an underestimation of the mutational landscape portrayed by a single needle biopsy and consequently affects treatment precision. The extent of colorectal cancer (CRC) genetic ITH is not well understood in Chinese patients. Thus, we conducted deep sequencing by using the OncoGxOne™ Plus panel, targeting 333 cancer-specific genes in multi-region biopsies of primary and liver metastatic tumors from three Chinese CRC patients. We determined that the extent of ITH varied among the three cases. On average, 65% of all the mutations detected were common within individual tumors. KMT2C aberrations and the NCOR1 mutation were the only ubiquitous events. Subsequent phylogenetic analysis showed that the tumors evolved in a branched manner. Comparison of the primary and metastatic tumors revealed that PPP2R1A (E370X), SETD2 (I1608V), SMAD4 (G382T), and AR splicing site mutations may be specific to liver metastatic cancer. These mutations might contribute to the initiation and progression of distant metastasis. Collectively, our analysis identified a substantial level of genetic ITH in CRC, which should be considered for personalized therapeutic strategies. PMID:27023146

  20. Accurate and robust estimation of camera parameters using RANSAC

    NASA Astrophysics Data System (ADS)

    Zhou, Fuqiang; Cui, Yi; Wang, Yexin; Liu, Liu; Gao, He

    2013-03-01

    Camera calibration plays an important role in the field of machine vision applications. The popularly used calibration approach based on 2D planar target sometimes fails to give reliable and accurate results due to the inaccurate or incorrect localization of feature points. To solve this problem, an accurate and robust estimation method for camera parameters based on RANSAC algorithm is proposed to detect the unreliability and provide the corresponding solutions. Through this method, most of the outliers are removed and the calibration errors that are the main factors influencing measurement accuracy are reduced. Both simulative and real experiments have been carried out to evaluate the performance of the proposed method and the results show that the proposed method is robust under large noise condition and quite efficient to improve the calibration accuracy compared with the original state.

  1. Groundtruth approach to accurate quantitation of fluorescence microarrays

    SciTech Connect

    Mascio-Kegelmeyer, L; Tomascik-Cheeseman, L; Burnett, M S; van Hummelen, P; Wyrobek, A J

    2000-12-01

    To more accurately measure fluorescent signals from microarrays, we calibrated our acquisition and analysis systems by using groundtruth samples comprised of known quantities of red and green gene-specific DNA probes hybridized to cDNA targets. We imaged the slides with a full-field, white light CCD imager and analyzed them with our custom analysis software. Here we compare, for multiple genes, results obtained with and without preprocessing (alignment, color crosstalk compensation, dark field subtraction, and integration time). We also evaluate the accuracy of various image processing and analysis techniques (background subtraction, segmentation, quantitation and normalization). This methodology calibrates and validates our system for accurate quantitative measurement of microarrays. Specifically, we show that preprocessing the images produces results significantly closer to the known ground-truth for these samples.

  2. Mill profiler machines soft materials accurately

    NASA Technical Reports Server (NTRS)

    Rauschl, J. A.

    1966-01-01

    Mill profiler machines bevels, slots, and grooves in soft materials, such as styrofoam phenolic-filled cores, to any desired thickness. A single operator can accurately control cutting depths in contour or straight line work.

  3. Remote balance weighs accurately amid high radiation

    NASA Technical Reports Server (NTRS)

    Eggenberger, D. N.; Shuck, A. B.

    1969-01-01

    Commercial beam-type balance, modified and outfitted with electronic controls and digital readout, can be remotely controlled for use in high radiation environments. This allows accurate weighing of breeder-reactor fuel pieces when they are radioactively hot.

  4. A Trial of the Delineation of Gas Hydrate Bearing Zones using Seismic Methods Offshore Tokai Japan

    NASA Astrophysics Data System (ADS)

    Inamori, T.; Hato, M.

    2002-12-01

    MITI Research Well 'Nankai Trough' was drilled at offshore Tokai Japan in 1999/2000 and the existence of gas hydrate was confirmed by various proofs through borehole measurement or coring. It gave so big impact to the view of Japan_fs future energy resources and other scientific interests.The METI, Ministry of Economy, Trade and Industry, has started the national project "Methane Hydrate Exploration study" in Japan since the fall 2001. Bottom Simulating Reflectors (BSRs) were widely found on the marine seismic data acquired offshore Japan especially in the shelf-slope near Nankai Trough. BSRs are thought to be the bottom of gas hydrate stability zones, we cannot, however, get the information of gas hydrate bearing zones, such as the height of those, the porosity, the gas hydrate saturation etc, only from BSRs. In order to estimate the amount of gas hydrate accurately, we have to get those reservoir parameters of gas hydrate bearing zones from marine seismic data. The velocity of these zones is greater than that of the surrounding sediment, because pure gas hydrate has high velocity that is more than 3,000 m/s. This means the interval velocity is the key for exploration of gas hydrate. First, we have tried to image the gas hydrate bearing zones from seismic stacking velocity analysis. After the conversion to interval velocity from NMO velocity by Dix's equation, we imaged the P-wave velocity section through 2D seismic line. We successfully imaged high velocity zones above BSRs and low velocity zones beneath BSRs on P-wave velocity section. But the resolution of the section from the velocity analysis is not so high. Although we have only two adjacent well log data on the seismic line, in order to make more detailed map, we tried to execute the seismic impedance inversion with MITI Nankai Trough Well data. We made a simple initial model and inverted to seismic impedance value. We got the good impedance section and delineated the gas hydrate bearing zones through it

  5. Understanding the Code: keeping accurate records.

    PubMed

    Griffith, Richard

    2015-10-01

    In his continuing series looking at the legal and professional implications of the Nursing and Midwifery Council's revised Code of Conduct, Richard Griffith discusses the elements of accurate record keeping under Standard 10 of the Code. This article considers the importance of accurate record keeping for the safety of patients and protection of district nurses. The legal implications of records are explained along with how district nurses should write records to ensure these legal requirements are met. PMID:26418404

  6. Delineating ecotypes of marine photosynthetic picoeukaryotes in the wild

    NASA Astrophysics Data System (ADS)

    Limardo, A. J.; Sudek, S.; Rii, Y. M.; Church, M. J.; Wei, C. L.; Armbrust, E. V.; Worden, A. Z.

    2015-12-01

    Extremely small eukaryotic green algae are abundant primary producers found in diverse marine habitats. Over the last decade several studies have revealed extensive diversity within the "pico-prasinophytes" (≤2 µm diameter) that was previously unrecognized due to a lack of distinguishing morphological features. Using whole genome and marker gene analyses, distinct species have since been recognized within the Micromonas and Ostreococcus genera. Relatively little is known about environmental factors driving distributions of these species, but for Ostreococcus, laboratory studies suggested that differentiation reflects high- and low-light adapted ecotypes. Subsequent field studies indicated that Ostreococcus Clade OI and Clade OII rarely co-occur but partition according to distinct habitats - representing 'mesotrophic' and 'oligotrophic' ecotypes, respectively. Unlike Micromonas and Ostreococcus, Bathycoccus was presumed to be a single cosmopolitan species because identical 18S rRNA gene sequences are observed in cultured isolates and in environmental surveys. However, analysis of a targeted metagenome from a Bathycoccus population in the tropical Atlantic led to the hypothesis that Bathycoccus also harbors distinct ecotypes. Here, we have developed qPCR assays to enumerate the two Bathycoccus types which can be discriminated based on the internal transcribed spacer (ITS). Statistical analysis of qPCR and environmental data from >200 North Pacific Ocean samples shows that the two Bathycoccus clades are only somewhat analogous to oligotrophic and mesotrophic Ostreococcus clades. The two Bathycoccus clades co-occurred more than twice as often as the Ostreococcus clades. Additionally, while Bathycoccus BII and oligotrophic Ostreococcus OII were found at warm temperatures up to 26°C, BII extended into colder waters than OII. Similarly, Bathycoccus BI extended into warmer waters than mesotrophic Ostreococcus OI. Currently, we are analyzing metatranscriptomes to

  7. Delineation of Tsunami Risk Zones for Sri Lanka

    NASA Astrophysics Data System (ADS)

    Wijetunge, J. J.

    2008-12-01

    The coastal belts of several Indian Ocean countries including Indonesia, Sri Lanka, India and Thailand suffered massive loss of life and damage to property due to the tsunami unleashed by the great earthquake of moment magnitude 9.1-9.3 in the Andaman-Sunda subduction zone on December 26, 2004. In Sri Lanka, 13 of the 14 administrative districts lying along the coastal belt were affected: the death toll was over 35,000 with 20,000 injured and about 100,000 dwellings and other buildings either completely or partially damaged leaving half a million people homeless and causing massive disruption to livelihoods. However, it was clear in the immediate aftermath of the tsunami that the degree of damage along the coastal belt of Sri Lanka was not uniform: some areas suffered more damage, some less, and in certain other areas, often not far away, there was no damage at all. This suggests that the level of risk for coastal communities from future events of tsunami exhibits considerable variation even along a short stretch of the shoreline. The high cost and the scarcity of coastal lands in many areas demand an accurate assessment of the tsunami risk rather than arbitrary conservative zonation. Moreover, information relating to the spatial distribution of tsunami risk is essential in formulating post-tsunami coastal land use plans as well as in planning of evacuation of people during tsunami warnings. However, neither comprehensive probabilistic assessments of the tsunami hazard nor detailed information pertaining to the vulnerability of coastal communities are available at present for the coastal zone of Sri Lanka. Consequently, the methodology adopted in the present paper is to use field observations and numerical simulations of the December 2004 tsunami, which may be considered a worst-case scenario, in order to obtain the variation along the coastline of three parameters that quantify the tsunami impact. These three parameters are the tsunami height, the horizontal

  8. Flood-plain delineation for Cub Run basin, Fairfax County, Virginia

    USGS Publications Warehouse

    Soule, Pat LeRoy

    1978-01-01

    Flood-plain delineation for Cub Run basin water-surface profiles of the 25-, 50-, and 100-year recurrence interval discharges have been computed for all streams and reaches of channels in Fairfax County, Virginia having a drainage area greater than 1 square mile except for Dogue Creek, Little Hunting Creek, and that part of the Cameron Run above Lake Barcroft. Maps having a 2-foot contour interval and a horizontal scale of 1 inch equals 100 feet have been used for base on which flood boundaries were delineated for 25-, 50-, and 100-year floods to be expected in each basin under ultimate development conditions. This report is one of a series and presents a discussion of techniques employed in computing discharges and profiles as well as the flood profiles and maps on which flood boundaries have been delineated for the Cub Run basin in Fairfax County. (Woodard-USGS)

  9. Flood-plain delineation for Cameron Run Basin, Fairfax County-Alexandria City, Virginia

    USGS Publications Warehouse

    Soule, Pat L.

    1976-01-01

    Flood-Plain Delineation for Cameron Run Basin Water-surface profiles of the 25-, 50-, and 100-year recurrence interval discharges have been computed for all streams and reaches of channels in Fairfax County, Virginia, having a drainage area greater than 1 square mile except for Dogue Creek, Little Hunting Creek, and that part of Cameron Run above Lake Barcroft. Maps having a 2-foot contour interval and a horizontal scale of 1 inch equals 100 feet have been used for a base on which flood boundaries were delineated for 25-, 50-, and 100-year floods to be expected in each basin under ultimate development conditions. Included are techniques employed in computing discharges and profiles as well as the flood profiles and maps on which flood boundaries have been delineated for that part of Cameron Run basin below Lake Barcroft in both Fairfax County and the city of Alexandria.

  10. Oncology nurse navigator role delineation study: an oncology nursing society report.

    PubMed

    Brown, Carlton G; Cantril, Cynthia; McMullen, Lori; Barkley, Dana L; Dietz, Michele; Murphy, Cynthia Miller; Fabrey, Lawrence J

    2012-12-01

    The purpose of the Oncology Nursing Society (ONS) Oncology Nurse Navigator Role Delineation Study was to examine the job-function activities of the oncology nurse navigator, thus providing an understanding of this unique role. The Role Delineation Advisory Committee consisting mainly of oncology nurse navigators was formed to provide content expertise to Applied Measurement Professionals, which conducted the role delineation study. Three hundred and thirty nurses completed the survey. The study clearly defined tasks, knowledge areas, and skills that are very specific to the nurse navigator role; however, the overlap in knowledge with the general oncology nurse role needs to be explored. The ONS Board of Directors and the Oncology Nursing Certification Corporation Board of Directors currently are exploring the need for additional initiatives to help define the role and competencies of the oncology nurse navigator. PMID:23178350

  11. Enhancements to TauDEM to support Rapid Watershed Delineation Services

    NASA Astrophysics Data System (ADS)

    Sazib, N. S.; Tarboton, D. G.

    2015-12-01

    Watersheds are widely recognized as the basic functional unit for water resources management studies and are important for a variety of problems in hydrology, ecology, and geomorphology. Nevertheless, delineating a watershed spread across a large region is still cumbersome due to the processing burden of working with large Digital Elevation Model. Terrain Analysis Using Digital Elevation Models (TauDEM) software supports the delineation of watersheds and stream networks from within desktop Geographic Information Systems. A rich set of watershed and stream network attributes are computed. However limitations of the TauDEM desktop tools are (1) it supports only one type of raster (tiff format) data (2) requires installation of software for parallel processing, and (3) data have to be in projected coordinate system. This paper presents enhancements to TauDEM that have been developed to extend its generality and support web based watershed delineation services. The enhancements of TauDEM include (1) reading and writing raster data with the open-source geospatial data abstraction library (GDAL) not limited to the tiff data format and (2) support for both geographic and projected coordinates. To support web services for rapid watershed delineation a procedure has been developed for sub setting the domain based on sub-catchments, with preprocessed data prepared for each catchment stored. This allows the watershed delineation to function locally, while extending to the full extent of watersheds using preprocessed information. Additional capabilities of this program includes computation of average watershed properties and geomorphic and channel network variables such as drainage density, shape factor, relief ratio and stream ordering. The updated version of TauDEM increases the practical applicability of it in terms of raster data type, size and coordinate system. The watershed delineation web service functionality is useful for web based software as service deployments

  12. Breast ultrasound lesions classification: a performance evaluation between manual delineation and computer segmentation

    NASA Astrophysics Data System (ADS)

    Yap, Moi Hoon; Yap, Chuin Hong

    2016-03-01

    Breast cancer is a threat to women worldwide. Manual delineation on breast ultrasound lesions is time-consuming and operator dependent. Computer segmentation of ultrasound breast lesions can be a challenging task due to the ill-defined lesions boundaries and issues related to the speckle noise in ultrasound images. The main contribution of this paper is to compare the performance of the computer classifier on the manual delineation and computer segmentation in malignant and benign lesions classification. This paper we implement computer segmentation using multifractal approach on a database consists of 120 images (50 malignant lesions and 70 benign lesions). The computer segmentation result is compared with the manual delineation using Jaccard Similarity Index (JSI). The result shows that the average JSI of 0.5010 (+/-0.2088) for malignant lesions and the average JSI of 0.6787 (+/-0.1290) for benign lesions. These results indicate lower agreement in malignant lesions due to the irregular shape while the higher agreement in benign lesions with regular shape. Further, we extract the shape descriptors for the lesions. By using logistic regression with 10 fold cross validation, the classification rates of manual delineation and computer segmentation are computed. The computer segmentation produced results with sensitivity 0.780 and specificity 0.871. However, the manual delineation produced sensitivity of 0.520 and specificity of 0.800. The results show that there are no clear differences between the delineation in MD and CS in benign lesions but the computer segmentation on malignant lesions shows better accuracy for computer classifier.

  13. Applicability of VI in arid vegetation delineation using shadow-affected SPOT imagery.

    PubMed

    Gunasekara, N K; Al-Wardy, M M; Al-Rawas, G A; Charabi, Y

    2015-07-01

    GDVI(3), GDVI(2), NDVI, MSAVI and SAVI were evaluated for their dynamic ranges, the class accuracy of the Vegetation Index (VI) classifications, the effects of shadow delineation on the other land use classes and their applicability in vegetation delineation in Al-Qara Mountains, Oman. Supervised classifications of a SPOT scene by Support Vector Machines (SVM) algorithm were employed. GDVI(3) showed the widest dynamic range in all land use types, while GDVI(2) also exhibited evidently wider dynamic ranges for arid to semi-arid Al-Qara than NDVI, MSAVI and SAVI. GDVI(3) reported the highest accuracies in delineating natural vegetation (dense - 74.80%, medium-dense- 43.19%), except for low-dense vegetation (40.51%). It also performs the best in delineating bare soil and dry grass with over 80% and 60% accuracies. The attenuated reflectance created by the shadows results in VI signals in the range of dry grass to bare soil, enabling us to neglect the shadow effect on natural vegetation delineation due to below 9.50% omissions from the shadows class. GDVI(3) also limits shadow delineation better than the other indices, which will enable us to analyze spectral information recovery by the VI with the help of ground truth information under the shadows. For applications such as land degradation assessments, GDVI(3) has better prospects over the other indices explored. Saturation at high-vigor vegetation is an issue in GDVI(3), GDVI(2) and NDVI. Our study also points to a dependency of a VI's capability to weaken shadows on the number of training data pixels to be utilized in a supervised classification. PMID:26093893

  14. Digital soil mapping for the support of delineation of Areas Facing Natural Constraints defined by common European biophysical criteria

    NASA Astrophysics Data System (ADS)

    Pásztor, László; Bakacsi, Zsófia; Laborczi, Annamária; Takács, Katalin; Szatmári, Gábor; Tóth, Tibor; Szabó, József

    2016-04-01

    One of the main objectives of the EU's Common Agricultural Policy is to encourage maintaining agricultural production in Areas Facing Natural Constraints (ANC) in order to sustain agricultural production and use natural resources, in such a way to secure both stable production and income to farmers and to protect the environment. ANC assignment has both ecological and severe economical aspects. Recently the delimitation of ANCs is suggested to be carried out by using common biophysical diagnostic criteria on low soil productivity and poor climate conditions all over Europe. The criterion system was elaborated and has been repeatedly upgraded by JRC. The operational implementation is under member state competence. This process requires application of available soil databases and proper thematic and spatial inference methods. In our paper we present the inferences applied for the latest identification and delineation of areas with low soil productivity in Hungary according to JRC biophysical criteria related to soil: limited soil drainage, texture and stoniness (coarse texture, heavy clay, vertic properties), shallow rooting depth, chemical properties (salinity, sodicity, low pH). The compilation of target specific maps were based on the available legacy and recently collected data. In the present work three different data sources were used. The most relevant available data were queried from the datasets for each mapped criterion for either direct application or for the compilation a suitable, synthetic (non-measured) parameter. In some cases the values of the target variable originated from only one, in other cases from more databases. The reference dataset used in the mapping process was set up after substantial statistical analysis and filtering. It consisted of the values of the target variable attributed to the finally selected georeferenced locations. For spatial inference regression kriging was applied. Accuracy assessment was carried out by Leave One Out

  15. The use of remote sensing and natural indicators to delineate floodplains - Preliminary findings

    NASA Technical Reports Server (NTRS)

    Sollers, S. C.; Petersen, G. W.; Henninger, D. L.; Borden, F. Y.

    1974-01-01

    Feasibility studies to delineate floodplains using aerial photography have been conducted by the Army Corps of Engineers. The objective of this project is to establish floodplain boundaries using natural indicators such as vegetation types, soil types, moisture differences, and geologic variations. Using aircraft multispectral data, an automated mapping routine should enable the Corps of Engineers to reduce costly field surveys and improve the accuracy of floodplain delineation in pristine areas. The purpose of this paper is to document the methodology utilized in this investigation while using one of a series of available data sets and test sites and to report preliminary findings.

  16. Methods for delineating flood-prone areas in the Great Basin of Nevada and adjacent states

    USGS Publications Warehouse

    Burkham, D.E.

    1988-01-01

    The Great Basin is a region of about 210,000 square miles having no surface drainage to the ocean; it includes most of Nevada and parts of Utah, California, Oregon, Idaho, and Wyoming. The area is characterized by many parallel mountain ranges and valleys trending north-south. Stream channels usually are well defined and steep within the mountains, but on reaching the alluvial fan at the canyon mouth, they may diverge into numerous distributary channels, be discontinuous near the apex of the fan, or be deeply entrenched in the alluvial deposits. Larger rivers normally have well-defined channels to or across the valley floors, but all terminate at lakes or playas. Major floods occur in most parts of the Great Basin and result from snowmelt, frontal-storm rainfall, and localized convective rainfall. Snowmelt floods typically occur during April-June. Floods resulting from frontal rain and frontal rain on snow generally occur during November-March. Floods resulting from convective-type rainfall during localized thunderstorms occur most commonly during the summer months. Methods for delineating flood-prone areas are grouped into five general categories: Detailed, historical, analytical, physiographic, and reconnaissance. The detailed and historical methods are comprehensive methods; the analytical and physiographic are intermediate; and the reconnaissance method is only approximate. Other than the reconnaissance method, each method requires determination of a T-year discharge (the peak rate of flow during a flood with long-term average recurrence interval of T years) and T-year profile and the development of a flood-boundary map. The procedure is different, however, for each method. Appraisal of the applicability of each method included consideration of its technical soundness, limitations and uncertainties, ease of use, and costs in time and money. Of the five methods, the detailed method is probably the most accurate, though most expensive. It is applicable to

  17. Profiling human protein degradome delineates cellular responses to proteasomal inhibition and reveals a feedback mechanism in regulating proteasome homeostasis.

    PubMed

    Yu, Tao; Tao, Yonghui; Yang, Meiqiang; Chen, Peng; Gao, Xiaobo; Zhang, Yanbo; Zhang, Tao; Chen, Zi; Hou, Jian; Zhang, Yan; Ruan, Kangcheng; Wang, Hongyan; Hu, Ronggui

    2014-10-01

    Global change in protein turnover (protein degradome) constitutes a central part of cellular responses to intrinsic or extrinsic stimuli. However, profiling protein degradome remains technically challenging. Recently, inhibition of the proteasome, e.g., by using bortezomib (BTZ), has emerged as a major chemotherapeutic strategy for treating multiple myeloma and other human malignancies, but systematic understanding of the mechanisms for BTZ drug action and tumor drug resistance is yet to be achieved. Here we developed and applied a dual-fluorescence-based Protein Turnover Assay (ProTA) to quantitatively profile global changes in human protein degradome upon BTZ-induced proteasomal inhibition. ProTA and subsequent network analyses delineate potential molecular basis for BTZ action and tumor drug resistance in BTZ chemotherapy. Finally, combined use of BTZ with drugs targeting the ProTA-identified key genes or pathways in BTZ action reduced BTZ resistance in multiple myeloma cells. Remarkably, BTZ stabilizes proteasome subunit PSMC1 and proteasome assembly factor PSMD10, suggesting a previously under-appreciated mechanism for regulating proteasome homeostasis. Therefore, ProTA is a novel tool for profiling human protein degradome to elucidate potential mechanisms of drug action and resistance, which might facilitate therapeutic development targeting proteostasis to treat human disorders. PMID:25223703

  18. Tumor Bed Delineation for Partial Breast and Breast Boost Radiotherapy Planned in the Prone Position: What Does MRI Add to X-ray CT Localization of Titanium Clips Placed in the Excision Cavity Wall?

    SciTech Connect

    Kirby, Anna M. Yarnold, John R.; Evans, Philip M.; Morgan, Veronica A.; Schmidt, Maria A.; Scurr, Erica D.; Souza, Nandita de

    2009-07-15

    Purpose: To compare tumor bed (TB) volumes delineated using magnetic resonance imaging plus computed tomography and clips (MRCT) with those delineated using CT and clips (CT/clips) alone in postlumpectomy breast cancer patients positioned prone and to determine the value of MRCT for planning partial breast irradiation (PBI). Methods and Materials: Thirty women with breast cancer each had 6 to 12 titanium clips secured in the excision cavity walls at lumpectomy. Patients underwent CT imaging in the prone position, followed by MRI (T{sub 1}-weighted [standard and fat-suppressed] and T{sub 2}-weighted sequences) in the prone position. TB volumes were delineated separately on CT and on fused MRCT datasets. Clinical target volumes (CTV) (where CTV = TB + 15 mm) and planning target volumes (PTV) (where PTV = CTV + 10 mm) were generated. Conformity indices between CT- and MRCT-defined target volumes were calculated (ratio of the volume of agreement to total delineated volume). Discordance was expressed as a geographical miss index (GMI) (where the GMI = the fraction of total delineated volume not defined by CT) and a normal tissue index (the fraction of total delineated volume designated as normal tissue on MRCT). PBI dose distributions were generated to cover CT-defined CTV (CTV{sub CT}) with {>=}95% of the reference dose. The percentage of MRCT-defined CTV (CTV{sub MRCT}) receiving {>=}95% of the reference dose was measured. Results: Mean conformity indices were 0.54 (TB), 0.84 (CTV), and 0.89 (PTV). For TB volumes, the GMI was 0.37, and the NTI was 0.09. Median percentage volume coverage of CTV{sub CT} was 97.1% (range, 95.3%-100.0%) and of CTV{sub MRCT} was 96.5% (range, 89.0%-100.0%). Conclusions: Addition of MR to CT/clip data generated TB volumes that were discordant with those based on CT/clips alone. However, clinically satisfactory coverage of CTV{sub MRCT} by CTV{sub CT}-based tangential PBI fields provides support for CT/clip-based TB delineation remaining the

  19. A highly accurate interatomic potential for argon

    NASA Astrophysics Data System (ADS)

    Aziz, Ronald A.

    1993-09-01

    A modified potential based on the individually damped model of Douketis, Scoles, Marchetti, Zen, and Thakkar [J. Chem. Phys. 76, 3057 (1982)] is presented which fits, within experimental error, the accurate ultraviolet (UV) vibration-rotation spectrum of argon determined by UV laser absorption spectroscopy by Herman, LaRocque, and Stoicheff [J. Chem. Phys. 89, 4535 (1988)]. Other literature potentials fail to do so. The potential also is shown to predict a large number of other properties and is probably the most accurate characterization of the argon interaction constructed to date.

  20. Automatic Delineation of On-Line Head-And-Neck Computed Tomography Images: Toward On-Line Adaptive Radiotherapy

    SciTech Connect

    Zhang Tiezhi . E-mail: tiezhi.zhang@beaumont.edu; Chi Yuwei; Meldolesi, Elisa; Yan Di

    2007-06-01

    Purpose: To develop and validate a fully automatic region-of-interest (ROI) delineation method for on-line adaptive radiotherapy. Methods and Materials: On-line adaptive radiotherapy requires a robust and automatic image segmentation method to delineate ROIs in on-line volumetric images. We have implemented an atlas-based image segmentation method to automatically delineate ROIs of head-and-neck helical computed tomography images. A total of 32 daily computed tomography images from 7 head-and-neck patients were delineated using this automatic image segmentation method. Manually drawn contours on the daily images were used as references in the evaluation of automatically delineated ROIs. Two methods were used in quantitative validation: (1) the dice similarity coefficient index, which indicates the overlapping ratio between the manually and automatically delineated ROIs; and (2) the distance transformation, which yields the distances between the manually and automatically delineated ROI surfaces. Results: Automatic segmentation showed agreement with manual contouring. For most ROIs, the dice similarity coefficient indexes were approximately 0.8. Similarly, the distance transformation evaluation results showed that the distances between the manually and automatically delineated ROI surfaces were mostly within 3 mm. The distances between two surfaces had a mean of 1 mm and standard deviation of <2 mm in most ROIs. Conclusion: With atlas-based image segmentation, it is feasible to automatically delineate ROIs on the head-and-neck helical computed tomography images in on-line adaptive treatments.

  1. Novel Approaches for Delineating and Studying "Hotspots" and "Hot Moments" in Fluvial Environments

    NASA Astrophysics Data System (ADS)

    Williams, K. H.; Bücker, M.; Flores Orozco, A.; Hobson, C.; Robbins, M.

    2014-12-01

    Experiments at the Department of Energy's Rifle, CO (USA) field site have long focused on stimulated biogeochemical pathways arising from organic carbon injection. While reductive pathways and their relation to uranium immobilization have been a focus since 2002, ongoing studies are exploring oxidative pathways and their role in mediating fluxes of C, N, S, and aqueous metals. Insights gained from 'stimulation' experiments are providing insight into analogous natural biogeochemical pathways that mediate elemental cycling in the absence of exogenous carbon. Such reactions are instead mediated by endogenous pools of natural organic matter (NOM) deposited during aggradation of aquifer sediments associated with fluvial processes within the Colorado River floodplain. Discrete lenses of fine-grained, organic-rich sediments enriched in reduced species, such as Fe(II) and iron sulfides have been identified along the active margin of the floodplain. Referred to as "naturally reduced zones" (NRZs), these localities constitute a distinct facies type within an otherwise gravel-dominated, largely NOM-deficient matrix. NRZs represent 'hotspots' of seasonally intense C, N, S, and U cycling during excursions in groundwater elevation. Air bubble imbibition within the capillary fringe is inferred to contribute to seasonally oxic groundwater, with its puntuated, 'hot moment' like impact on redox-mediated reactions exhibiting close correspondence to those induced through the intentional introduction of oxidants. Reactions induce sharp gradients in nitrate and sulfate resulting from elevated rates of nitrification and oxidation of reduced sulfur as dissolved oxygen becomes non-limiting. Given their outsized role in constraining the location and timing of critcal element cycling pathways, delineating the distribution of NRZs across scales of relevance to natural field systems is of great importance. Novel mapping approaches borrowed from the field of exploration geophysics provide one

  2. Delineation of inundated area and vegetation along the Amazon floodplain with the SIR-C synthetic aperture radar

    SciTech Connect

    Hess, L.L.; Melack, J.M.; Filoso, S.; Wang, Y. |

    1995-07-01

    Floodplain inundation and vegetation along the Negro and Amazon rivers near Manaus, Brazil were accurately delineated using multi-frequency, polarimetric synthetic aperture radar (SAR) data from the April and October 1994 SIR-C missions. A decision-tree model was used to formulate rules for a supervised classification into five categories: water, clearing (pasture), aquatic macrophyte (floating meadow), nonflooded forest, and flooded forest. Classified images were produced and tested within three days of SIR-C data acquisition. Both C-band (5.7 cm) and L-band (24 cm) wavelengths were necessary to distinguish the cover types. HH polarization was most useful for distinguishing flooded from nonflooded vegetation (C-HH for macrophyte versus pasture, and L-HH for flooded versus nonflooded forest), and cross-polarized L-band data provided the best separation between woody and nonwoody vegetation. Between the April and October missions, the Amazon River level fell about 3.6 m and the portion of the study area covered by flooded forest decreased from 23% to 12%. This study demonstrates the ability of multifrequency SAR to quantify in near realtime the extent of inundation on forested floodplains, and its potential application for timely monitoring of flood events.

  3. Semi-automated extraction and delineation of 3D roads of street scene from mobile laser scanning point clouds

    NASA Astrophysics Data System (ADS)

    Yang, Bisheng; Fang, Lina; Li, Jonathan

    2013-05-01

    Accurate 3D road information is important for applications such as road maintenance and virtual 3D modeling. Mobile laser scanning (MLS) is an efficient technique for capturing dense point clouds that can be used to construct detailed road models for large areas. This paper presents a method for extracting and delineating roads from large-scale MLS point clouds. The proposed method partitions MLS point clouds into a set of consecutive "scanning lines", which each consists of a road cross section. A moving window operator is used to filter out non-ground points line by line, and curb points are detected based on curb patterns. The detected curb points are tracked and refined so that they are both globally consistent and locally similar. To evaluate the validity of the proposed method, experiments were conducted using two types of street-scene point clouds captured by Optech's Lynx Mobile Mapper System. The completeness, correctness, and quality of the extracted roads are over 94.42%, 91.13%, and 91.3%, respectively, which proves the proposed method is a promising solution for extracting 3D roads from MLS point clouds.

  4. An object-based approach to delineate wetlands across landscapes of varied disturbance with high spatial resolution satellite imagery

    NASA Astrophysics Data System (ADS)

    Mui, Amy; He, Yuhong; Weng, Qihao

    2015-11-01

    Mapping wetlands across both natural and human-altered landscapes is important for the management of these ecosystems. Though they are considered important landscape elements providing both ecological and socioeconomic benefits, accurate wetland inventories do not exist in many areas. In this study, a multi-scale geographic object-based image analysis (GEOBIA) approach was employed to segment three high spatial resolution images acquired over landscapes of varying heterogeneity due to human-disturbance to determine the robustness of this method to changing scene variability. Multispectral layers, a digital elevation layer, normalized-difference vegetation index (NDVI) layer, and a first-order texture layer were used to segment images across three segmentation scales with a focus on accurate delineation of wetland boundaries and wetland components. Each ancillary input layer contributed to improving segmentation at different scales. Wetlands were classified using a nearest neighbor approach across a relatively undisturbed park site and an agricultural site using GeoEye1 imagery, and an urban site using WorldView2 data. Successful wetland classification was achieved across all study sites with an accuracy above 80%, though results suggest that overall a higher degree of landscape heterogeneity may negatively affect both segmentation and classification. The agricultural site suffered from the greatest amount of over and under segmentation, and lowest map accuracy (kappa: 0.78) which was partially attributed to confusion among a greater proportion of mixed vegetated classes from both wetlands and uplands. Accuracy of individual wetland classes based on the Canadian Wetland Classification system varied between each site, with kappa values ranging from 0.64 for the swamp class and 0.89 for the marsh class. This research developed a unique approach to mapping wetlands of various degrees of disturbance using GEOBIA, which can be applied to study other wetlands of similar

  5. Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients.

    PubMed

    Lanigan, Fiona; Brien, Gerard L; Fan, Yue; Madden, Stephen F; Jerman, Emilia; Maratha, Ashwini; Aloraifi, Fatima; Hokamp, Karsten; Dunne, Eiseart J; Lohan, Amanda J; Flanagan, Louise; Garbe, James C; Stampfer, Martha R; Fridberg, Marie; Jirstrom, Karin; Quinn, Cecily M; Loftus, Brendan; Gallagher, William M; Geraghty, James; Bracken, Adrian P

    2015-09-01

    The majority of women diagnosed with lymph node-negative breast cancer are unnecessarily treated with damaging chemotherapeutics after surgical resection. This highlights the importance of understanding and more accurately predicting patient prognosis. In the present study, we define the transcriptional networks regulating well-established prognostic gene expression signatures. We find that the same set of transcriptional regulators consistently lie upstream of both 'prognosis' and 'proliferation' gene signatures, suggesting that a central transcriptional network underpins a shared phenotype within these signatures. Strikingly, the master transcriptional regulators within this network predict recurrence risk for lymph node-negative breast cancer better than currently used multigene prognostic assays, particularly in estrogen receptor-positive patients. Simultaneous examination of p16(INK4A) expression, which predicts tumours that have bypassed cellular senescence, revealed that intermediate levels of p16(INK4A) correlate with an intact pRB pathway and improved survival. A combination of these master transcriptional regulators and p16(INK4A), termed the OncoMasTR score, stratifies tumours based on their proliferative and senescence capacity, facilitating a clearer delineation of lymph node-negative breast cancer patients at high risk of recurrence, and thus requiring chemotherapy. Furthermore, OncoMasTR accurately classifies over 60% of patients as 'low risk', an improvement on existing prognostic assays, which has the potential to reduce overtreatment in early-stage patients. Taken together, the present study provides new insights into the transcriptional regulation of cellular proliferation in breast cancer and provides an opportunity to enhance and streamline methods of predicting breast cancer prognosis. PMID:26094870

  6. Post-lumpectomy CT-guided tumor bed delineation for breast boost and partial breast irradiation: Can additional pre- and postoperative imaging reduce interobserver variability?

    PubMed Central

    DEN HARTOGH, MARISKA D.; PHILIPPENS, MARIELLE E.P.; VAN DAM, IRIS E.; KLEYNEN, CATHARINA E.; TERSTEEG, ROBBERT J.H.A.; KOTTE, ALEXIS N.T.J.; VAN VULPEN, MARCO; VAN ASSELEN, BRAM; VAN DEN BONGARD, DESIRÉE H.J.G.

    2015-01-01

    -guided TB delineation, while target volumes marginally increased. The value of additional imaging may be dependent on CVS. PMID:26722244

  7. {sup 18}F-FDG PET Definition of Gross Tumor Volume for Radiotherapy of Lung Cancer: Is the Tumor Uptake Value-Based Approach Appropriate for Lymph Node Delineation?

    SciTech Connect

    Rodriguez, Nuria; Sanz, Xavier; Trampal, Carlos; Foro, Palmira; Reig, Anna; Lacruz, Marti; Membrive, Ismael; Lozano, Joan; Quera, Jaime; Algara, Manuel

    2010-11-01

    Purpose: Positron emission tomography (PET) with the glucose analogue [18F] fluoro-2-deoxy-D-glucose ({sup 18}F-FDG-PET) has been used in radiation treatment planning for non-small-cell carcinoma. To date, lymph nodes have been contoured according to the uptake of the tumor. This prospective study was performed to evaluate if nodal volume delineates according to FDG uptake within the primary tumor (PET-GTVnt) is suitable for nodal target volume delineation or if individualized nodal FDG uptake measure (PET-GTVnn) is necessary to better nodal target definition. Methods and Materials: Forty cases, who underwent a diagnostic {sup 18}F-FDG PET/computed tomography (CT) scan, were included. Two PET-based GTVs for each lymph node were contoured and compared. First, we used an isocontour of 40% of the maximum tumor uptake (PET-GTVnt). Second, an isocontour of 40% of the maximum uptake of each node (PET-GTVnn) was employed. To avoid interobserver variability, this was carried out by the same radiation oncologist. Afterwards, the difference between both lymph node volumes was plotted against the ratio of the maximum uptakes (I{sub n}/I{sub t}) in a linear regression analysis. Results: Compared with CT-based lymph node volume (CT-GTVn), the intraclass correlation coefficient of PET-GTVnn was higher than the coefficient of PET-GTVnt (p < 0.001). All cases could be divided into four groups: undetected (17.5%), detected but overestimated (10%), detected but underestimated (35%), and correctly detected (37.5%). Conclusions: If a method of automatic delineation shall be applied, this method must be applied to every lesion separately. However, to facilitate the delineation in daily practice, when I{sub n}/I{sub t} is {<=}25%, lymph nodes could be delineated in accordance with tumor uptake, keeping an absolute difference in radii <5 mm.

  8. Instructor Strategic Ambiguity: Delineation of the Construct and Development of a Measure

    ERIC Educational Resources Information Center

    Klyukovski, Andrei A.; Medlock-Klyukovski, Amanda L.

    2016-01-01

    This article presents research to delineate the construct of instructor strategic ambiguity (ISA) and develop a measure. The first study analyzed instructor uses of ambiguity, identified 18 strategies, and classified them into four categories. The second study developed an Instructor Strategic Ambiguity Measure (ISAM) for the college classroom.…

  9. Nursing Delineation Pilot Study, 1981-1982. Volume 1: Methods Report. Kentucky Nursing Education Project.

    ERIC Educational Resources Information Center

    Kentucky State Council on Higher Education, Frankfort.

    A methodology was developed for the systematic analysis of the nursing profession, as part of the Kentucky Nursing Education Project's Nursing Delineation Study. The methodology defined and ranked nursing tasks according to the degree of complexity in order to promote articulation in nursing practice and education and to better utilize the…

  10. Factors Interfering with Delineation on MRCP of Pancreaticobiliary Maljunction in Paediatric Patients

    PubMed Central

    Huang, Shun-gen; Guo, Wan-liang; Wang, Jian; Sheng, Mao; Lan, Xing-hao; Fang, Lin

    2016-01-01

    Background The aim of this study was to assess factors for delineating the pancreaticobiliary junction in the presence of pediatric congenital choledochal cysts (CCC) using Magnetic resonance cholangiopancreatography (MRCP). Methods Retrospective review of medical records for 48 patients with CCC was conducted, including demographics, biliary amylase and MRCP findings if available. With univariate and multivariate logistic regression, we measured significant factors affecting pancreaticobiliary maljunction(PBM) diagnoses by MRCP. Results Of the subjects enrolled with CCC. Twenty-eight cases had PBM according to MRCP. Univariate analysis confirmed that age, cyst diameter > 30 mm and cysts that descended to the introitus pelvis affected junctional delineation and detection of PBM (P<0.05). Stepwise logistic regression analysis confirmed large cysts in the introitus pelvis predicted pancreaticobiliary junctional delineation in MRCP and these data agreed with the literature. A correlation between cyst diameter and the length of the common channel was found as was cyst diameter and biliary amylase although there were no significant differences between them. Conclusions Age, cyst diameter >30 mm and descending cysts into the introitus pelvis affected junctional delineation of the pancreatic and bile duct in PBM with MRCP. Large cyst descension into the introitus pelvis was an independent factors affecting PBM detection. PMID:27104956

  11. 388. D.E.M., Delineator December 1932 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    388. D.E.M., Delineator December 1932 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - WEST BAY CROSSING; SUSPENDED STRUCTURE; SIDE SPAN TRUSSES AT ANCHORAGES; CONTRACT NO. 6; DRAWING NO. 40 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  12. 365. J.W., Delineator February 1934 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    365. J.W., Delineator February 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SAN FRANCISCO ANCHORAGE; PIER NO. 1 - DETAILS; CONTRACT NO. 3; SUP. DRAWING NO. 22A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  13. 367. J.W.G., Delineator August 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    367. J.W.G., Delineator August 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - WEST BAY CROSSING; PIER NO. 5; GENERAL PLAN & ELEVATION; CONTRACT NO. 2; SUP. DRAWING NO. 10A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  14. 392. J.R.L., Delineator August 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    392. J.R.L., Delineator August 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - EAST BAY CROSSING; PIER El; ANCHORAGE STEEL WORK; CONTRACT NO. 7; SUP. DRAWING NO. 72A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  15. 371. A.J.M. and D.L.S., Delineators April 1934. STATE OF CALIFORNIA; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    371. A.J.M. and D.L.S., Delineators April 1934. STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - WEST BAY CROSSING; PIER NO. 4; VERTICAL SECTIONS; CONTRACT NO. 2; SUP. DRAWING NO. 17A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  16. 358. E.S.T., Delineator April 1935 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    358. E.S.T., Delineator April 1935 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SAN FRANCISCO SECTION AND APPROACHES; GIRDER AND FLOOR BEAM DETAILS; SPANS 5 TO 32; CONTRACT NO. 15 & 15A; SUP. DRAWING NO. 8A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  17. 376. A.J.M. and D.L.S., Delineators February 1934 STATE OF CALIFORNIA; ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    376. A.J.M. and D.L.S., Delineators February 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; YERBA BUENA CROSSING; CROSS-SECTIONS OF CABLE ANCHORAGE; CONTRACT NO. 5; SUP. DRAWING NO. 4A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  18. 357. E.S.T., Delineator April 1935 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    357. E.S.T., Delineator April 1935 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SAN FRANCISCO SECTION AND APPROACHES; GENERAL PLAN AND ELEVATION; CONTRACT NO. 15 AND 15A; SUP. DRAWINGS NO. 1-A - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  19. 387. D.E.M., Delineator December 1932 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    387. D.E.M., Delineator December 1932 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; SUPERSTRUCTURE - WEST BAY CROSSING; TOWERS 2, 3, 5 & 6; BRACING DETAILS - LOWER DECK; CONTRACT NO. 6; DRAWING NO. 27 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  20. Delineating recharge areas for Onondaga and Cathedral Caves using groundwater tracing techniques

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Onondaga Cave and Cathedral Cave are two large, significant cave systems with active streams located along the Meramec River in the Ozarks ecoregion of Missouri. Groundwater dye tracing has delineated recharge areas for both caves in order to aid in the management of the cave systems by Onondaga Cav...

  1. Is it enough to have one ECa map for the site-specific management delineation?

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The soil apparent electrical conductivity (ECa) has been used to map soil spatial variability and to relate it to the variability of various soil properties thus delineating zones of site-specific management. Most often, a single ECa survey is done and the generated ECa map is considered to infer t...

  2. 363. A.C.S., Delineator March 1934 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    363. A.C.S., Delineator March 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6A; SUPERSTRUCTURE - WEST BAY CROSSING; SAN FRANCISCO ANCHORAGE; AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G4866; SHEET NO E3 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  3. 364. J.G.M., Delineator February 1934 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    364. J.G.M., Delineator February 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6; SUPERSTRUCTURE - WEST BAY CROSSING; SAN FRANCISCO ANCHORAGE CABLE BENT CASTING; AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G 4852 C; SHEET NO. 100 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  4. 378. A.C.S., Delineator March 1933 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    378. A.C.S., Delineator March 1933 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6A; SUPERSTRUCTURE - WEST BAY CROSSING; YERBA BUENA ANCHORAGE & CABLE BENT. AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G 4866; SHEET NO. E4 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  5. Delineation of Roles and Functions of Respiratory Therapy Personnel. Final Report.

    ERIC Educational Resources Information Center

    American Association for Respiratory Therapy, Dallas, TX.

    Frequently assigned tasks performed by qualified respiratory therapy personnel are delineated in the document in such a manner that proficiency examinations within the profession can be prepared from them. Four distinct proficiency levels are identified and defined. Due to the fact that proficiency examinations will be assigned for them,…

  6. INVESTIGATION OF HYDROGEOLOGIC MAPPING TO DELINEATE PROTECTION ZONES AROUND SPRINGS: REPORT OF TWO CASE STUDIES

    EPA Science Inventory

    Methods commonly used to delineate protection zones for water-supply wells are often not directly applicable for springs. This investigation focuses on the use of hydrogeologic mapping methods to identify physical and hydrologic features that control ground-water flow to springs...

  7. MANAGEMENT ZONE ANALYST (MZA): SOFTWARE FOR SUB-FIELD MANAGEMENT ZONE DELINEATION

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Producers using site-specific crop management (SSCM) have a need for strategies to delineate areas within fields that management can be tailored for. These areas are often referred to as "management zones." Quick and automated procedures are desirable for creating management zones and for testing ...

  8. Resource Documentation and Recharge Area Delineation of a Large Fluvial Karst System: Carroll Cave, Missouri

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Located along Wet Glaize Creek in the central Missouri Ozarks, Toronto Spring is a distributary spring system where surface stream flow mixes with flow from the Carroll Cave system. Following recharge area delineations for Thunder River and Confusion Creek in Carroll Cave, flow from these rivers wa...

  9. Differential assessment of designations of wetland status using two delineation methods.

    PubMed

    Wu, Meiyin; Kalma, Dennis; Treadwell-Steitz, Carol

    2014-07-01

    Two different methods are commonly used to delineate and characterize wetlands. The U.S. Army Corps of Engineers (ACOE) delineation method uses field observation of hydrology, soils, and vegetation. The U.S. Fish and Wildlife Service's National Wetland Inventory Program (NWI) relies on remote sensing and photointerpretation. This study compared designations of wetland status at selected study sites using both methods. Twenty wetlands from the Wetland Boundaries Map of the Ausable-Boquet River Basin (created using the revised NWI method) in the Ausable River watershed in Essex and Clinton Counties, NY, were selected for this study. Sampling sites within and beyond the NWI wetland boundaries were selected. During the summers of 2008 and 2009, wetland hydrology, soils, and vegetation were examined for wetland indicators following the methods described in the ACOE delineation manual. The study shows that the two methods agree at 78 % of the sampling sites and disagree at 22 % of the sites. Ninety percent of the sampling locations within the wetland boundaries on the NWI maps were categorized as ACOE wetlands with all three ACOE wetland indicators present. A binary linear logistic regression model analyzed the relationship between the designations of the two methods. The outcome of the model indicates that 83 % of the time, the two wetland designation methods agree. When discrepancies are found, it is the presence or absence of wetland hydrology and vegetation that causes the differences in delineation. PMID:24748237

  10. 75 FR 39052 - 2010 Standards for Delineating Metropolitan and Micropolitan Statistical Areas

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-07

    ... BUDGET 2010 Standards for Delineating Metropolitan and Micropolitan Statistical Areas Correction In... Statistical Areas and New England City and Town Areas, in the last line of paragraph (a), ``75'' should read... column, in paragraph (f), in the first and second lines, ``Metropolitan and Metropolitan Statistical...

  11. What Community College Students Value: Delineating a Normative Structure for Community College Students

    ERIC Educational Resources Information Center

    Akin, Renea; Park, Toby J.

    2016-01-01

    This manuscript delineates a normative structure for community college students, outlines how this structure varies by student characteristics, and compares this structure to that of a previously established normative structure identified at a 4-year institution. A total of 512 student survey responses on the College Student Behaviors Inventory…

  12. 370. F.A.N., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    370. F.A.N., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; WEST BAY CROSSING; PIER W-4; PLANS AND ELEVATIONS; DRG. NO. 17 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  13. 382. J.R.L., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    382. J.R.L., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; WEST BAY CROSSING; TOWERS; GENERAL ELEVATIONS & SECTIONS; DRG. NO. 28 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  14. Automatic delineation of tumor volumes by co-segmentation of combined PET/MR data

    NASA Astrophysics Data System (ADS)

    Leibfarth, S.; Eckert, F.; Welz, S.; Siegel, C.; Schmidt, H.; Schwenzer, N.; Zips, D.; Thorwarth, D.

    2015-07-01

    Combined PET/MRI may be highly beneficial for radiotherapy treatment planning in terms of tumor delineation and characterization. To standardize tumor volume delineation, an automatic algorithm for the co-segmentation of head and neck (HN) tumors based on PET/MR data was developed. Ten HN patient datasets acquired in a combined PET/MR system were available for this study. The proposed algorithm uses both the anatomical T2-weighted MR and FDG-PET data. For both imaging modalities tumor probability maps were derived, assigning each voxel a probability of being cancerous based on its signal intensity. A combination of these maps was subsequently segmented using a threshold level set algorithm. To validate the method, tumor delineations from three radiation oncologists were available. Inter-observer variabilities and variabilities between the algorithm and each observer were quantified by means of the Dice similarity index and a distance measure. Inter-observer variabilities and variabilities between observers and algorithm were found to be comparable, suggesting that the proposed algorithm is adequate for PET/MR co-segmentation. Moreover, taking into account combined PET/MR data resulted in more consistent tumor delineations compared to MR information only.

  15. Electrochemical method for defect delineation in silicon-on-insulator wafers

    DOEpatents

    Guilinger, Terry R.; Jones, Howland D. T.; Kelly, Michael J.; Medernach, John W.; Stevenson, Joel O.; Tsao, Sylvia S.

    1991-01-01

    An electrochemical method for defect delineation in thin-film SOI or SOS wafers in which a surface of a silicon wafer is electrically connected so as to control the voltage of the surface within a specified range, the silicon wafer is then contacted with an electrolyte, and, after removing the electrolyte, defects and metal contamination in the silicon wafer are identified.

  16. 368. J.R.L., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    368. J.R.L., Delineator Date Unknown STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; TYPICAL CAISSON DETAILS; PIER W-3, W-4, W-5 & W-6; DRG. NO. 21 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  17. Models of Racial and Ethnic Identity Development: Delineation of Practice Implications.

    ERIC Educational Resources Information Center

    Kwan, Kwong-Liem Karl

    2001-01-01

    Summarizes common themes that emerged from the articles in this special issue of "Journal of Mental Health Counseling" on the counseling of racially diverse clients. Discusses variables that need to be addressed when working with members of visible racial and ethnic groups, and delineates some assessment questions for counselors. (Contains 22…

  18. Accurate pointing of tungsten welding electrodes

    NASA Technical Reports Server (NTRS)

    Ziegelmeier, P.

    1971-01-01

    Thoriated-tungsten is pointed accurately and quickly by using sodium nitrite. Point produced is smooth and no effort is necessary to hold the tungsten rod concentric. The chemically produced point can be used several times longer than ground points. This method reduces time and cost of preparing tungsten electrodes.

  19. Retroperitoneal Sarcoma (RPS) High Risk Gross Tumor Volume Boost (HR GTV Boost) Contour Delineation Agreement Among NRG Sarcoma Radiation and Surgical Oncologists

    PubMed Central

    Baldini, Elizabeth H.; Bosch, Walter; Kane, John M.; Abrams, Ross A.; Salerno, Kilian E.; Deville, Curtiland; Raut, Chandrajit P.; Petersen, Ivy A.; Chen, Yen-Lin; Mullen, John T.; Millikan, Keith W.; Karakousis, Giorgos; Kendrick, Michael L.; DeLaney, Thomas F.; Wang, Dian

    2015-01-01

    Purpose Curative intent management of retroperitoneal sarcoma (RPS) requires gross total resection. Preoperative radiotherapy (RT) often is used as an adjuvant to surgery, but recurrence rates remain high. To enhance RT efficacy with acceptable tolerance, there is interest in delivering “boost doses” of RT to high-risk areas of gross tumor volume (HR GTV) judged to be at risk for positive resection margins. We sought to evaluate variability in HR GTV boost target volume delineation among collaborating sarcoma radiation and surgical oncologist teams. Methods Radiation planning CT scans for three cases of RPS were distributed to seven paired radiation and surgical oncologist teams at six institutions. Teams contoured HR GTV boost volumes for each case. Analysis of contour agreement was performed using the simultaneous truth and performance level estimation (STAPLE) algorithm and kappa statistics. Results HRGTV boost volume contour agreement between the seven teams was “substantial” or “moderate” for all cases. Agreement was best on the torso wall posteriorly (abutting posterior chest abdominal wall) and medially (abutting ipsilateral para-vertebral space and great vessels). Contours varied more significantly abutting visceral organs due to differing surgical opinions regarding planned partial organ resection. Conclusions Agreement of RPS HRGTV boost volumes between sarcoma radiation and surgical oncologist teams was substantial to moderate. Differences were most striking in regions abutting visceral organs, highlighting the importance of collaboration between the radiation and surgical oncologist for “individualized” target delineation on the basis of areas deemed at risk and planned resection. PMID:26018727

  20. Global biogeography of reef fishes: a hierarchical quantitative delineation of regions.

    PubMed

    Kulbicki, Michel; Parravicini, Valeriano; Bellwood, David R; Arias-Gonzàlez, Ernesto; Chabanet, Pascale; Floeter, Sergio R; Friedlander, Alan; McPherson, Jana; Myers, Robert E; Vigliola, Laurent; Mouillot, David

    2013-01-01

    Delineating regions is an important first step in understanding the evolution and biogeography of faunas. However, quantitative approaches are often limited at a global scale, particularly in the marine realm. Reef fishes are the most diversified group of marine fishes, and compared to most other phyla, their taxonomy and geographical distributions are relatively well known. Based on 169 checklists spread across all tropical oceans, the present work aims to quantitatively delineate biogeographical entities for reef fishes at a global scale. Four different classifications were used to account for uncertainty related to species identification and the quality of checklists. The four classifications delivered converging results, with biogeographical entities that can be hierarchically delineated into realms, regions and provinces. All classifications indicated that the Indo-Pacific has a weak internal structure, with a high similarity from east to west. In contrast, the Atlantic and the Eastern Tropical Pacific were more strongly structured, which may be related to the higher levels of endemism in these two realms. The "Coral Triangle", an area of the Indo-Pacific which contains the highest species diversity for reef fishes, was not clearly delineated by its species composition. Our results show a global concordance with recent works based upon endemism, environmental factors, expert knowledge, or their combination. Our quantitative delineation of biogeographical entities, however, tests the robustness of the results and yields easily replicated patterns. The similarity between our results and those from other phyla, such as corals, suggests that our approach may be of broad utility in describing and understanding global marine biodiversity patterns. PMID:24386083

  1. Global Biogeography of Reef Fishes: A Hierarchical Quantitative Delineation of Regions

    PubMed Central

    Kulbicki, Michel; Parravicini, Valeriano; Bellwood, David R.; Arias-Gonzàlez, Ernesto; Chabanet, Pascale; Floeter, Sergio R.; Friedlander, Alan; McPherson, Jana; Myers, Robert E.; Vigliola, Laurent; Mouillot, David

    2013-01-01

    Delineating regions is an important first step in understanding the evolution and biogeography of faunas. However, quantitative approaches are often limited at a global scale, particularly in the marine realm. Reef fishes are the most diversified group of marine fishes, and compared to most other phyla, their taxonomy and geographical distributions are relatively well known. Based on 169 checklists spread across all tropical oceans, the present work aims to quantitatively delineate biogeographical entities for reef fishes at a global scale. Four different classifications were used to account for uncertainty related to species identification and the quality of checklists. The four classifications delivered converging results, with biogeographical entities that can be hierarchically delineated into realms, regions and provinces. All classifications indicated that the Indo-Pacific has a weak internal structure, with a high similarity from east to west. In contrast, the Atlantic and the Eastern Tropical Pacific were more strongly structured, which may be related to the higher levels of endemism in these two realms. The “Coral Triangle”, an area of the Indo-Pacific which contains the highest species diversity for reef fishes, was not clearly delineated by its species composition. Our results show a global concordance with recent works based upon endemism, environmental factors, expert knowledge, or their combination. Our quantitative delineation of biogeographical entities, however, tests the robustness of the results and yields easily replicated patterns. The similarity between our results and those from other phyla, such as corals, suggests that our approach may be of broad utility in describing and understanding global marine biodiversity patterns. PMID:24386083

  2. Sputter target

    DOEpatents

    Gates, Willard G.; Hale, Gerald J.

    1980-01-01

    The disclosure relates to an improved sputter target for use in the deposition of hard coatings. An exemplary target is given wherein titanium diboride is brazed to a tantalum backing plate using a gold-palladium-nickel braze alloy.

  3. Improving the delineation of hydrocarbon-impacted soils and water through induced polarization (IP) tomographies: a field study at an industrial waste land.

    PubMed

    Deceuster, John; Kaufmann, Olivier

    2012-08-01

    Without a good estimation of samples representativeness, the delineation of the contaminated plume extent and the evaluation of volumes of hydrocarbon-impacted soils may remain difficult. To contribute to this question, a time domain induced polarization (IP) field experiment was conducted on an industrial waste land. Boreholes were drilled to specify the local geological context. Cross-hole seismic tomographies were performed to extend borehole logs and to draw an interpreted geological cross-section. Soil samples taken during drillings were analysed in laboratory. A preliminary survey was conducted to locate the IP profile. The polarization signatures linked to the presence of clayey sediments were filtered out from the data set. Chargeability and resistivity depth soundings were computed and compared to mean concentrations of total organic products to overcome the data support issue between the geophysical models and the spot samples of soils. A logarithmic relation between chargeabilities and smoothed hydrocarbon concentrations in soils was found. Taking into account contaminant's concentration thresholds defined in local codes and regulations allows defining chargeability classes to delineate hotspots on this site. This showed that IP tomography can be an accurate screening methodology. A statistical methodology is proposed to assess the efficiency of the investigation strategy. PMID:22659399

  4. Toward Semi-automated Assessment of Target Volume Delineation in Radiotherapy Trials: The SCOPE 1 Pretrial Test Case

    SciTech Connect

    Gwynne, Sarah; Spezi, Emiliano; Wills, Lucy; Nixon, Lisette; Hurt, Chris; Joseph, George; Evans, Mererid; Griffiths, Gareth; Crosby, Tom; Staffurth, John

    2012-11-15

    Purpose: To evaluate different conformity indices (CIs) for use in the analysis of outlining consistency within the pretrial quality assurance (Radiotherapy Trials Quality Assurance [RTTQA]) program of a multicenter chemoradiation trial of esophageal cancer and to make recommendations for their use in future trials. Methods and Materials: The National Cancer Research Institute SCOPE 1 trial is an ongoing Cancer Research UK-funded phase II/III randomized controlled trial of chemoradiation with capecitabine and cisplatin with or without cetuximab for esophageal cancer. The pretrial RTTQA program included a detailed radiotherapy protocol, an educational package, and a single mid-esophageal tumor test case that were sent to each investigator to outline. Investigator gross tumor volumes (GTVs) were received from 50 investigators in 34 UK centers, and CERR (Computational Environment for Radiotherapy Research) was used to perform an assessment of each investigator GTV against a predefined gold-standard GTV using different CIs. A new metric, the local conformity index (l-CI), that can localize areas of maximal discordance was developed. Results: The median Jaccard conformity index (JCI) was 0.69 (interquartile range, 0.62-0.70), with 14 of 50 investigators (28%) achieving a JCI of 0.7 or greater. The median geographical miss index was 0.09 (interquartile range, 0.06-0.16), and the mean discordance index was 0.27 (95% confidence interval, 0.25-0.30). The l-CI was highest in the middle section of the volume, where the tumor was bulky and more easily definable, and identified 4 slices where fewer than 20% of investigators achieved an l-CI of 0.7 or greater. Conclusions: The available CIs analyze different aspects of a gold standard-observer variation, with JCI being the most useful as a single metric. Additional information is provided by the l-CI and can focus the efforts of the RTTQA team in these areas, possibly leading to semi-automated outlining assessment.

  5. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  6. Feedback about more accurate versus less accurate trials: differential effects on self-confidence and activation.

    PubMed

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-06-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected byfeedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On day 1, participants performed a golf putting task under one of two conditions: one group received feedback on the most accurate trials, whereas another group received feedback on the least accurate trials. On day 2, participants completed an anxiety questionnaire and performed a retention test. Shin conductance level, as a measure of arousal, was determined. The results indicated that feedback about more accurate trials resulted in more effective learning as well as increased self-confidence. Also, activation was a predictor of performance. PMID:22808705

  7. New model accurately predicts reformate composition

    SciTech Connect

    Ancheyta-Juarez, J.; Aguilar-Rodriguez, E. )

    1994-01-31

    Although naphtha reforming is a well-known process, the evolution of catalyst formulation, as well as new trends in gasoline specifications, have led to rapid evolution of the process, including: reactor design, regeneration mode, and operating conditions. Mathematical modeling of the reforming process is an increasingly important tool. It is fundamental to the proper design of new reactors and revamp of existing ones. Modeling can be used to optimize operating conditions, analyze the effects of process variables, and enhance unit performance. Instituto Mexicano del Petroleo has developed a model of the catalytic reforming process that accurately predicts reformate composition at the higher-severity conditions at which new reformers are being designed. The new AA model is more accurate than previous proposals because it takes into account the effects of temperature and pressure on the rate constants of each chemical reaction.

  8. Accurate colorimetric feedback for RGB LED clusters

    NASA Astrophysics Data System (ADS)

    Man, Kwong; Ashdown, Ian

    2006-08-01

    We present an empirical model of LED emission spectra that is applicable to both InGaN and AlInGaP high-flux LEDs, and which accurately predicts their relative spectral power distributions over a wide range of LED junction temperatures. We further demonstrate with laboratory measurements that changes in LED spectral power distribution with temperature can be accurately predicted with first- or second-order equations. This provides the basis for a real-time colorimetric feedback system for RGB LED clusters that can maintain the chromaticity of white light at constant intensity to within +/-0.003 Δuv over a range of 45 degrees Celsius, and to within 0.01 Δuv when dimmed over an intensity range of 10:1.

  9. Accurate mask model for advanced nodes

    NASA Astrophysics Data System (ADS)

    Zine El Abidine, Nacer; Sundermann, Frank; Yesilada, Emek; Ndiaye, El Hadji Omar; Mishra, Kushlendra; Paninjath, Sankaranarayanan; Bork, Ingo; Buck, Peter; Toublan, Olivier; Schanen, Isabelle

    2014-07-01

    Standard OPC models consist of a physical optical model and an empirical resist model. The resist model compensates the optical model imprecision on top of modeling resist development. The optical model imprecision may result from mask topography effects and real mask information including mask ebeam writing and mask process contributions. For advanced technology nodes, significant progress has been made to model mask topography to improve optical model accuracy. However, mask information is difficult to decorrelate from standard OPC model. Our goal is to establish an accurate mask model through a dedicated calibration exercise. In this paper, we present a flow to calibrate an accurate mask enabling its implementation. The study covers the different effects that should be embedded in the mask model as well as the experiment required to model them.

  10. Accurate guitar tuning by cochlear implant musicians.

    PubMed

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼ 30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  11. Two highly accurate methods for pitch calibration

    NASA Astrophysics Data System (ADS)

    Kniel, K.; Härtig, F.; Osawa, S.; Sato, O.

    2009-11-01

    Among profiles, helix and tooth thickness pitch is one of the most important parameters of an involute gear measurement evaluation. In principle, coordinate measuring machines (CMM) and CNC-controlled gear measuring machines as a variant of a CMM are suited for these kinds of gear measurements. Now the Japan National Institute of Advanced Industrial Science and Technology (NMIJ/AIST) and the German national metrology institute the Physikalisch-Technische Bundesanstalt (PTB) have each developed independently highly accurate pitch calibration methods applicable to CMM or gear measuring machines. Both calibration methods are based on the so-called closure technique which allows the separation of the systematic errors of the measurement device and the errors of the gear. For the verification of both calibration methods, NMIJ/AIST and PTB performed measurements on a specially designed pitch artifact. The comparison of the results shows that both methods can be used for highly accurate calibrations of pitch standards.

  12. Accurate modeling of parallel scientific computations

    NASA Technical Reports Server (NTRS)

    Nicol, David M.; Townsend, James C.

    1988-01-01

    Scientific codes are usually parallelized by partitioning a grid among processors. To achieve top performance it is necessary to partition the grid so as to balance workload and minimize communication/synchronization costs. This problem is particularly acute when the grid is irregular, changes over the course of the computation, and is not known until load time. Critical mapping and remapping decisions rest on the ability to accurately predict performance, given a description of a grid and its partition. This paper discusses one approach to this problem, and illustrates its use on a one-dimensional fluids code. The models constructed are shown to be accurate, and are used to find optimal remapping schedules.

  13. Accurate Guitar Tuning by Cochlear Implant Musicians

    PubMed Central

    Lu, Thomas; Huang, Juan; Zeng, Fan-Gang

    2014-01-01

    Modern cochlear implant (CI) users understand speech but find difficulty in music appreciation due to poor pitch perception. Still, some deaf musicians continue to perform with their CI. Here we show unexpected results that CI musicians can reliably tune a guitar by CI alone and, under controlled conditions, match simultaneously presented tones to <0.5 Hz. One subject had normal contralateral hearing and produced more accurate tuning with CI than his normal ear. To understand these counterintuitive findings, we presented tones sequentially and found that tuning error was larger at ∼30 Hz for both subjects. A third subject, a non-musician CI user with normal contralateral hearing, showed similar trends in performance between CI and normal hearing ears but with less precision. This difference, along with electric analysis, showed that accurate tuning was achieved by listening to beats rather than discriminating pitch, effectively turning a spectral task into a temporal discrimination task. PMID:24651081

  14. An accurate registration technique for distorted images

    NASA Technical Reports Server (NTRS)

    Delapena, Michele; Shaw, Richard A.; Linde, Peter; Dravins, Dainis

    1990-01-01

    Accurate registration of International Ultraviolet Explorer (IUE) images is crucial because the variability of the geometrical distortions that are introduced by the SEC-Vidicon cameras ensures that raw science images are never perfectly aligned with the Intensity Transfer Functions (ITFs) (i.e., graded floodlamp exposures that are used to linearize and normalize the camera response). A technique for precisely registering IUE images which uses a cross correlation of the fixed pattern that exists in all raw IUE images is described.

  15. Accurate maser positions for MALT-45

    NASA Astrophysics Data System (ADS)

    Jordan, Christopher; Bains, Indra; Voronkov, Maxim; Lo, Nadia; Jones, Paul; Muller, Erik; Cunningham, Maria; Burton, Michael; Brooks, Kate; Green, James; Fuller, Gary; Barnes, Peter; Ellingsen, Simon; Urquhart, James; Morgan, Larry; Rowell, Gavin; Walsh, Andrew; Loenen, Edo; Baan, Willem; Hill, Tracey; Purcell, Cormac; Breen, Shari; Peretto, Nicolas; Jackson, James; Lowe, Vicki; Longmore, Steven

    2013-10-01

    MALT-45 is an untargeted survey, mapping the Galactic plane in CS (1-0), Class I methanol masers, SiO masers and thermal emission, and high frequency continuum emission. After obtaining images from the survey, a number of masers were detected, but without accurate positions. This project seeks to resolve each maser and its environment, with the ultimate goal of placing the Class I methanol maser into a timeline of high mass star formation.

  16. Accurate phase-shift velocimetry in rock.

    PubMed

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139

  17. Accurate Molecular Polarizabilities Based on Continuum Electrostatics

    PubMed Central

    Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.

    2013-01-01

    A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034

  18. Accurate phase-shift velocimetry in rock

    NASA Astrophysics Data System (ADS)

    Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.

    2016-06-01

    Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.

  19. Delineating Reactive Natural Attenuation Zones: Multi-level Sampling in an Ammonium Plume

    NASA Astrophysics Data System (ADS)

    Hüttmann, A.; Wilson, R. D.; Thornton, S. F.; Lerner, D. N.

    2003-12-01

    Current natural attenuation monitoring involves observing concentrations along some transect parallel to flow, often in long--screened observation wells. Vertically integrated geochemical signals essentially compresses 3D-problems into 2D ones and the loss of process resolution does not allow for robust plume transport prediction. On the other hand, a monitoring approach that is based on process quantification will yield field data necessary for current natural attenuation assessment and allow more accurate prediction to plume behaviour. To quantify these spatially discrete processes, the resolution of sampling points must be higher to delineate reactive zones, that account for the bulk of natural attenuation. These reactive zones are dependent on aquifer properties, contaminant type, redox zonation and other factors. In many cases, the plume fringe will be the most active zone, because influx of certain nutrients necessary to support bacteria will be greatest in these zones. Most importantly, consortia of degrading bacteria are dependent on supply of electron--acceptors such as dissolved {O2} and nitrate from background ground water and recharge; electron--acceptors are rapidly consumed at the fringes and concentrations decrease significantly towards the centre of the plume. Thus, if a process--based approach is to be achieved, one has to focus not only on the overall extent and mass of a contaminant plume, but, more importantly, on a sound analysis of the most reactive zones. The site of a former coal processing plant in the UK was chosen as a field site where the afore--mentioned hypothesis is currently being investigated by means of two recently installed multi--level samplers. Previous investigations have located an ammonium plume at the site with outwash from the thick unsaturated zone as ongoing source since the demolition of the actual plant in 1970. The conceptual model drawn from the analysis of these data shows that certain zones exhibit higher rates of

  20. High Frequency QRS ECG Accurately Detects Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    Schlegel, Todd T.; Arenare, Brian; Poulin, Gregory; Moser, Daniel R.; Delgado, Reynolds

    2005-01-01

    High frequency (HF, 150-250 Hz) analysis over the entire QRS interval of the ECG is more sensitive than conventional ECG for detecting myocardial ischemia. However, the accuracy of HF QRS ECG for detecting cardiomyopathy is unknown. We obtained simultaneous resting conventional and HF QRS 12-lead ECGs in 66 patients with cardiomyopathy (EF = 23.2 plus or minus 6.l%, mean plus or minus SD) and in 66 age- and gender-matched healthy controls using PC-based ECG software recently developed at NASA. The single most accurate ECG parameter for detecting cardiomyopathy was an HF QRS morphological score that takes into consideration the total number and severity of reduced amplitude zones (RAZs) present plus the clustering of RAZs together in contiguous leads. This RAZ score had an area under the receiver operator curve (ROC) of 0.91, and was 88% sensitive, 82% specific and 85% accurate for identifying cardiomyopathy at optimum score cut-off of 140 points. Although conventional ECG parameters such as the QRS and QTc intervals were also significantly longer in patients than controls (P less than 0.001, BBBs excluded), these conventional parameters were less accurate (area under the ROC = 0.77 and 0.77, respectively) than HF QRS morphological parameters for identifying underlying cardiomyopathy. The total amplitude of the HF QRS complexes, as measured by summed root mean square voltages (RMSVs), also differed between patients and controls (33.8 plus or minus 11.5 vs. 41.5 plus or minus 13.6 mV, respectively, P less than 0.003), but this parameter was even less accurate in distinguishing the two groups (area under ROC = 0.67) than the HF QRS morphologic and conventional ECG parameters. Diagnostic accuracy was optimal (86%) when the RAZ score from the HF QRS ECG and the QTc interval from the conventional ECG were used simultaneously with cut-offs of greater than or equal to 40 points and greater than or equal to 445 ms, respectively. In conclusion 12-lead HF QRS ECG employing

  1. Residual Tumor After Neoadjuvant Chemoradiation Outside the Radiation Therapy Target Volume: A New Prognostic Factor for Survival in Esophageal Cancer

    SciTech Connect

    Muijs, Christina; Smit, Justin; Karrenbeld, Arend; Beukema, Jannet; Mul, Veronique; Dam, Go van; Hospers, Geke; Kluin, Phillip; Langendijk, Johannes; Plukker, John

    2014-03-15

    Purpose/Objective(s): The aim of this study was to analyze the accuracy of gross tumor volume (GTV) delineation and clinical target volume (CTV) margins for neoadjuvant chemoradiation therapy (neo-CRT) in esophageal carcinoma at pathologic examination and to determine the impact on survival. Methods and Materials: The study population consisted of 63 esophageal cancer patients treated with neo-CRT. GTV and CTV borders were demarcated in situ during surgery on the esophagus, using anatomical reference points to provide accurate information regarding tumor location at pathologic evaluation. To identify prognostic factors for disease-free survival (DFS) and overall survival (OS), a Cox regression analysis was performed. Results: After resection, macroscopic residual tumor was found outside the GTV in 7 patients (11%). Microscopic residual tumor was located outside the CTV in 9 patients (14%). The median follow-up was 15.6 months. With multivariate analysis, only microscopic tumor outside the CTV (hazard ratio [HR], 4.96; 95% confidence interval [CI], 1.03-15.36), and perineural growth (HR, 5.77; 95% CI, 1.27-26.13) were identified as independent prognostic factors for OS. The 1-year OS was 20% for patients with tumor outside the CTV and 86% for those without (P<.01). For DFS, microscopic tumor outside the CTV (HR, 5.92; 95% CI, 1.89-18.54) and ypN+ (HR, 3.36; 95% CI, 1.33-8.48) were identified as independent adverse prognostic factors. The 1-year DFS was 23% versus 77% for patients with or without tumor outside the CTV (P<.01). Conclusions: Microscopic tumor outside the CTV is associated with markedly worse OS after neo-CRT. This may either stress the importance of accurate tumor delineation or reflect aggressive tumor behavior requiring new adjuvant treatment modalities.

  2. Muon-catalyzed fusion experiment target and detector system. Preliminary design report

    SciTech Connect

    Jones, S.E.; Watts, K.D.; Caffrey, A.J.; Walter, J.B.

    1982-03-01

    We present detailed plans for the target and particle detector systems for the muon-catalyzed fusion experiment. Requirements imposed on the target vessel by experimental conditions and safety considerations are delineated. Preliminary designs for the target vessel capsule and secondary containment vessel have been developed which meet these requirements. In addition, the particle detection system is outlined, including associated fast electronics and on-line data acquisition. Computer programs developed to study the target and detector system designs are described.

  3. Auto-segmentation of normal and target structures in head and neck CT images: A feature-driven model-based approach

    SciTech Connect

    Qazi, Arish A.; Pekar, Vladimir; Kim, John; Xie, Jason; Breen, Stephen L.; Jaffray, David A.

    2011-11-15

    Purpose: Intensity modulated radiation therapy (IMRT) allows greater control over dose distribution, which leads to a decrease in radiation related toxicity. IMRT, however, requires precise and accurate delineation of the organs at risk and target volumes. Manual delineation is tedious and suffers from both interobserver and intraobserver variability. State of the art auto-segmentation methods are either atlas-based, model-based or hybrid however, robust fully automated segmentation is often difficult due to the insufficient discriminative information provided by standard medical imaging modalities for certain tissue types. In this paper, the authors present a fully automated hybrid approach which combines deformable registration with the model-based approach to accurately segment normal and target tissues from head and neck CT images. Methods: The segmentation process starts by using an average atlas to reliably identify salient landmarks in the patient image. The relationship between these landmarks and the reference dataset serves to guide a deformable registration algorithm, which allows for a close initialization of a set of organ-specific deformable models in the patient image, ensuring their robust adaptation to the boundaries of the structures. Finally, the models are automatically fine adjusted by our boundary refinement approach which attempts to model the uncertainty in model adaptation using a probabilistic mask. This uncertainty is subsequently resolved by voxel classification based on local low-level organ-specific features. Results: To quantitatively evaluate the method, they auto-segment several organs at risk and target tissues from 10 head and neck CT images. They compare the segmentations to the manual delineations outlined by the expert. The evaluation is carried out by estimating two common quantitative measures on 10 datasets: volume overlap fraction or the Dice similarity coefficient (DSC), and a geometrical metric, the median symmetric

  4. Target capture and target ghosts

    NASA Astrophysics Data System (ADS)

    Auerbach, Steven P.

    1996-05-01

    Optimal detection methods for small targets rely on whitened matched filters, which convolve the measured data with the signal model, and whiten the result with the noise covariance. In real-world implementations of such filters, the noise covariance must be estimated from the data, and the resulting covariance estimate may be corrupted by presence of the target. The resulting loss in SNR is called 'target capture'. Target capture is often thought to be a problem only for bright targets. This presentation shows that target capture also arises for dim targets, leading to an SNR loss which is independent of target strength and depends on the averaging method used to estimate the noise covariance. This loss is due to a 'coherent beat' between the true noise and that portion of the estimated noise covariance due to the target. This beat leads to 'ghost targets', which diminish the target SNR by producing a negative target ghost at the target's position. A quantitative estimate of this effect will be given, and shown to agree with numerical results. The effect of averaging on SNR is also discussed for data scenes with synthetic injected targets, in cases where the noise covariance is estimated using 'no target' data. For these cases, it is shown that the so-called 'optimal' filter, which uses the true noise covariance, is actually worse than a 'sub-optimal' filter which estimates the noise from scene. This apparent contradiction is resolved by showing that the optimal filter is best if the same filter is used for many scenes, but is outperformed by a filter adapted to a specific scene.

  5. A Semi-Automated Machine Learning Algorithm for Tree Cover Delineation from 1-m Naip Imagery Using a High Performance Computing Architecture

    NASA Astrophysics Data System (ADS)

    Basu, S.; Ganguly, S.; Nemani, R. R.; Mukhopadhyay, S.; Milesi, C.; Votava, P.; Michaelis, A.; Zhang, G.; Cook, B. D.; Saatchi, S. S.; Boyda, E.

    2014-12-01

    Accurate tree cover delineation is a useful instrument in the derivation of Above Ground Biomass (AGB) density estimates from Very High Resolution (VHR) satellite imagery data. Numerous algorithms have been designed to perform tree cover delineation in high to coarse resolution satellite imagery, but most of them do not scale to terabytes of data, typical in these VHR datasets. In this paper, we present an automated probabilistic framework for the segmentation and classification of 1-m VHR data as obtained from the National Agriculture Imagery Program (NAIP) for deriving tree cover estimates for the whole of Continental United States, using a High Performance Computing Architecture. The results from the classification and segmentation algorithms are then consolidated into a structured prediction framework using a discriminative undirected probabilistic graphical model based on Conditional Random Field (CRF), which helps in capturing the higher order contextual dependencies between neighboring pixels. Once the final probability maps are generated, the framework is updated and re-trained by incorporating expert knowledge through the relabeling of misclassified image patches. This leads to a significant improvement in the true positive rates and reduction in false positive rates. The tree cover maps were generated for the state of California, which covers a total of 11,095 NAIP tiles and spans a total geographical area of 163,696 sq. miles. Our framework produced correct detection rates of around 85% for fragmented forests and 70% for urban tree cover areas, with false positive rates lower than 3% for both regions. Comparative studies with the National Land Cover Data (NLCD) algorithm and the LiDAR high-resolution canopy height model shows the effectiveness of our algorithm in generating accurate high-resolution tree cover maps.

  6. Targeted Nanotechnology for Cancer Imaging

    PubMed Central

    Toy, Randall; Bauer, Lisa; Hoimes, Christopher; Ghaghada, Ketan B.; Karathanasis, Efstathios

    2014-01-01

    Targeted nanoparticle imaging agents provide many benefits and new opportunities to facilitate accurate diagnosis of cancer and significantly impact patient outcome. Due to the highly engineerable nature of nanotechnology, targeted nanoparticles exhibit significant advantages including increased contrast sensitivity, binding avidity and targeting specificity. Considering the various nanoparticle designs and their adjustable ability to target a specific site and generate detectable signals, nanoparticles can be optimally designed in terms of biophysical interactions (i.e., intravascular and interstitial transport) and biochemical interactions (i.e., targeting avidity towards cancer-related biomarkers) for site-specific detection of very distinct microenvironments. This review seeks to illustrate that the design of a nanoparticle dictates its in vivo journey and targeting of hard-to-reach cancer sites, facilitating early and accurate diagnosis and interrogation of the most aggressive forms of cancer. We will report various targeted nanoparticles for cancer imaging using X-ray computed tomography, ultrasound, magnetic resonance imaging, nuclear imaging and optical imaging. Finally, to realize the full potential of targeted nanotechnology for cancer imaging, we will describe the challenges and opportunities for the clinical translation and widespread adaptation of targeted nanoparticles imaging agents. PMID:25116445

  7. Pathologic Validation of a Model Based on Diffusion-Weighted Imaging and Dynamic Contrast-Enhanced Magnetic Resonance Imaging for Tumor Delineation in the Prostate Peripheral Zone

    SciTech Connect

    Groenendaal, Greetje; Borren, Alie; Moman, Maaike R.; Monninkhof, Evelyn; Diest, Paul J. van; Philippens, Marielle E.P.; Vulpen, Marco van; Heide, Uulke A. van der

    2012-03-01

    Purpose: For focal boost strategies in the prostate, the robustness of magnetic resonance imaging-based tumor delineations needs to be improved. To this end we developed a statistical model that predicts tumor presence on a voxel level (2.5 Multiplication-Sign 2.5 Multiplication-Sign 2.5 mm3) inside the peripheral zone. Furthermore, we show how this model can be used to derive a valuable input for radiotherapy treatment planning. Methods and Materials: The model was created on 87 radiotherapy patients. For the validation of the voxelwise performance of the model, an independent group of 12 prostatectomy patients was used. After model validation, the model was stratified to create three different risk levels for tumor presence: gross tumor volume (GTV), high-risk clinical target volume (CTV), and low-risk CTV. Results: The model gave an area under the receiver operating characteristic curve of 0.70 for the prediction of tumor presence in the prostatectomy group. When the registration error between magnetic resonance images and pathologic delineation was taken into account, the area under the curve further improved to 0.89. We propose that model outcome values with a high positive predictive value can be used to define the GTV. Model outcome values with a high negative predictive value can be used to define low-risk CTV regions. The intermediate outcome values can be used to define a high-risk CTV. Conclusions: We developed a logistic regression with a high diagnostic performance for voxelwise prediction of tumor presence. The model output can be used to define different risk levels for tumor presence, which in turn could serve as an input for dose planning. In this way the robustness of tumor delineations for focal boost therapy can be greatly improved.

  8. Geospatial datasets for watershed delineation and characterization used in the Hawaii StreamStats web application

    USGS Publications Warehouse

    Rea, Alan; Skinner, Kenneth D.

    2012-01-01

    The U.S. Geological Survey Hawaii StreamStats application uses an integrated suite of raster and vector geospatial datasets to delineate and characterize watersheds. The geospatial datasets used to delineate and characterize watersheds on the StreamStats website, and the methods used to develop the datasets are described in this report. The datasets for Hawaii were derived primarily from 10 meter resolution National Elevation Dataset (NED) elevation models, and the National Hydrography Dataset (NHD), using a set of procedures designed to enforce the drainage pattern from the NHD into the NED, resulting in an integrated suite of elevation-derived datasets. Additional sources of data used for computing basin characteristics include precipitation, land cover, soil permeability, and elevation-derivative datasets. The report also includes links for metadata and downloads of the geospatial datasets.

  9. Delineation of Waters of the United States for Lawrence Livermore National Laboratory, Site 300

    SciTech Connect

    Preston, R E

    2006-09-25

    This report presents the results of a delineation of waters of the United States, including wetlands, for Lawrence Livermore National Laboratory's Site 300 in Alameda and San Joaquin Counties, California. Jones & Stokes mapped vegetation at Site 300 in August, 2001, using Global Positioning System (GPS) data recorders to collect point locations and to record linear features and map unit polygons. We identified wetlands boundaries in the field on the basis of the plant community present. We returned to collect additional information on wetland soils on July 3, 2002. Forty-six wetlands were identified, with a total area of 3.482 hectares (8.605 acres). The wetlands include vernal pools, freshwater seeps, and seasonal ponds. Wetlands appearing to meet the criteria for federal jurisdictional total 1.776 hectares (4.388 acres). A delineation map is presented and a table is provided with information on the type, size, characteristic plant species of each wetland, and a preliminary jurisdictional assessment.

  10. Body-Wide Hierarchical Fuzzy Modeling, Recognition, and Delineation of Anatomy in Medical Images

    PubMed Central

    Udupa, Jayaram K.; Odhner, Dewey; Zhao, Liming; Tong, Yubing; Matsumoto, Monica M.S.; Ciesielski, Krzysztof C.; Falcao, Alexandre X.; Vaideeswaran, Pavithra; Ciesielski, Victoria; Saboury, Babak; Mohammadianrasanani, Syedmehrdad; Sin, Sanghun; Arens, Raanan; Torigian, Drew A.

    2014-01-01

    To make Quantitative Radiology (QR) a reality in radiological practice, computerized body-wide automatic anatomy recognition (AAR) becomes essential. With the goal of building a general AAR system that is not tied to any specific organ system, body region, or image modality, this paper presents an AAR methodology for localizing and delineating all major organs in different body regions based on fuzzy modeling ideas and a tight integration of fuzzy models with an Iterative Relative Fuzzy Connectedness (IRFC) delineation algorithm. The methodology consists of five main steps: (a) gathering image data for both building models and testing the AAR algorithms from patient image sets existing in our health system; (b) formulating precise definitions of each body region and organ and delineating them following these definitions; (c) building hierarchical fuzzy anatomy models of organs for each body region; (d) recognizing and locating organs in given images by employing the hierarchical models; and (e) delineating the organs following the hierarchy. In Step (c), we explicitly encode object size and positional relationships into the hierarchy and subsequently exploit this information in object recognition in Step (d) and delineation in Step (e). Modality-independent and dependent aspects are carefully separated in model encoding. At the model building stage, a learning process is carried out for rehearsing an optimal threshold-based object recognition method. The recognition process in Step (d) starts from large, well-defined objects and proceeds down the hierarchy in a global to local manner. A fuzzy model-based version of the IRFC algorithm is created by naturally integrating the fuzzy model constraints into the delineation algorithm. The AAR system is tested on three body regions – thorax (on CT), abdomen (on CT and MRI), and neck (on MRI and CT) – involving a total of over 35 organs and 130 data sets (the total used for model building and testing). The training and

  11. Accurately Mapping M31's Microlensing Population

    NASA Astrophysics Data System (ADS)

    Crotts, Arlin

    2004-07-01

    We propose to augment an existing microlensing survey of M31 with source identifications provided by a modest amount of ACS {and WFPC2 parallel} observations to yield an accurate measurement of the masses responsible for microlensing in M31, and presumably much of its dark matter. The main benefit of these data is the determination of the physical {or "einstein"} timescale of each microlensing event, rather than an effective {"FWHM"} timescale, allowing masses to be determined more than twice as accurately as without HST data. The einstein timescale is the ratio of the lensing cross-sectional radius and relative velocities. Velocities are known from kinematics, and the cross-section is directly proportional to the {unknown} lensing mass. We cannot easily measure these quantities without knowing the amplification, hence the baseline magnitude, which requires the resolution of HST to find the source star. This makes a crucial difference because M31 lens m ass determinations can be more accurate than those towards the Magellanic Clouds through our Galaxy's halo {for the same number of microlensing events} due to the better constrained geometry in the M31 microlensing situation. Furthermore, our larger survey, just completed, should yield at least 100 M31 microlensing events, more than any Magellanic survey. A small amount of ACS+WFPC2 imaging will deliver the potential of this large database {about 350 nights}. For the whole survey {and a delta-function mass distribution} the mass error should approach only about 15%, or about 6% error in slope for a power-law distribution. These results will better allow us to pinpoint the lens halo fraction, and the shape of the halo lens spatial distribution, and allow generalization/comparison of the nature of halo dark matter in spiral galaxies. In addition, we will be able to establish the baseline magnitude for about 50, 000 variable stars, as well as measure an unprecedentedly deta iled color-magnitude diagram and luminosity

  12. Accurate measurement of unsteady state fluid temperature

    NASA Astrophysics Data System (ADS)

    Jaremkiewicz, Magdalena

    2016-07-01

    In this paper, two accurate methods for determining the transient fluid temperature were presented. Measurements were conducted for boiling water since its temperature is known. At the beginning the thermometers are at the ambient temperature and next they are immediately immersed into saturated water. The measurements were carried out with two thermometers of different construction but with the same housing outer diameter equal to 15 mm. One of them is a K-type industrial thermometer widely available commercially. The temperature indicated by the thermometer was corrected considering the thermometers as the first or second order inertia devices. The new design of a thermometer was proposed and also used to measure the temperature of boiling water. Its characteristic feature is a cylinder-shaped housing with the sheath thermocouple located in its center. The temperature of the fluid was determined based on measurements taken in the axis of the solid cylindrical element (housing) using the inverse space marching method. Measurements of the transient temperature of the air flowing through the wind tunnel using the same thermometers were also carried out. The proposed measurement technique provides more accurate results compared with measurements using industrial thermometers in conjunction with simple temperature correction using the inertial thermometer model of the first or second order. By comparing the results, it was demonstrated that the new thermometer allows obtaining the fluid temperature much faster and with higher accuracy in comparison to the industrial thermometer. Accurate measurements of the fast changing fluid temperature are possible due to the low inertia thermometer and fast space marching method applied for solving the inverse heat conduction problem.

  13. Accurate upwind methods for the Euler equations

    NASA Technical Reports Server (NTRS)

    Huynh, Hung T.

    1993-01-01

    A new class of piecewise linear methods for the numerical solution of the one-dimensional Euler equations of gas dynamics is presented. These methods are uniformly second-order accurate, and can be considered as extensions of Godunov's scheme. With an appropriate definition of monotonicity preservation for the case of linear convection, it can be shown that they preserve monotonicity. Similar to Van Leer's MUSCL scheme, they consist of two key steps: a reconstruction step followed by an upwind step. For the reconstruction step, a monotonicity constraint that preserves uniform second-order accuracy is introduced. Computational efficiency is enhanced by devising a criterion that detects the 'smooth' part of the data where the constraint is redundant. The concept and coding of the constraint are simplified by the use of the median function. A slope steepening technique, which has no effect at smooth regions and can resolve a contact discontinuity in four cells, is described. As for the upwind step, existing and new methods are applied in a manner slightly different from those in the literature. These methods are derived by approximating the Euler equations via linearization and diagonalization. At a 'smooth' interface, Harten, Lax, and Van Leer's one intermediate state model is employed. A modification for this model that can resolve contact discontinuities is presented. Near a discontinuity, either this modified model or a more accurate one, namely, Roe's flux-difference splitting. is used. The current presentation of Roe's method, via the conceptually simple flux-vector splitting, not only establishes a connection between the two splittings, but also leads to an admissibility correction with no conditional statement, and an efficient approximation to Osher's approximate Riemann solver. These reconstruction and upwind steps result in schemes that are uniformly second-order accurate and economical at smooth regions, and yield high resolution at discontinuities.

  14. The first accurate description of an aurora

    NASA Astrophysics Data System (ADS)

    Schröder, Wilfried

    2006-12-01

    As technology has advanced, the scientific study of auroral phenomena has increased by leaps and bounds. A look back at the earliest descriptions of aurorae offers an interesting look into how medieval scholars viewed the subjects that we study.Although there are earlier fragmentary references in the literature, the first accurate description of the aurora borealis appears to be that published by the German Catholic scholar Konrad von Megenberg (1309-1374) in his book Das Buch der Natur (The Book of Nature). The book was written between 1349 and 1350.

  15. Are Kohn-Sham conductances accurate?

    PubMed

    Mera, H; Niquet, Y M

    2010-11-19

    We use Fermi-liquid relations to address the accuracy of conductances calculated from the single-particle states of exact Kohn-Sham (KS) density functional theory. We demonstrate a systematic failure of this procedure for the calculation of the conductance, and show how it originates from the lack of renormalization in the KS spectral function. In certain limits this failure can lead to a large overestimation of the true conductance. We also show, however, that the KS conductances can be accurate for single-channel molecular junctions and systems where direct Coulomb interactions are strongly dominant. PMID:21231333

  16. Accurate density functional thermochemistry for larger molecules.

    SciTech Connect

    Raghavachari, K.; Stefanov, B. B.; Curtiss, L. A.; Lucent Tech.

    1997-06-20

    Density functional methods are combined with isodesmic bond separation reaction energies to yield accurate thermochemistry for larger molecules. Seven different density functionals are assessed for the evaluation of heats of formation, Delta H 0 (298 K), for a test set of 40 molecules composed of H, C, O and N. The use of bond separation energies results in a dramatic improvement in the accuracy of all the density functionals. The B3-LYP functional has the smallest mean absolute deviation from experiment (1.5 kcal mol/f).

  17. New law requires 'medically accurate' lesson plans.

    PubMed

    1999-09-17

    The California Legislature has passed a bill requiring all textbooks and materials used to teach about AIDS be medically accurate and objective. Statements made within the curriculum must be supported by research conducted in compliance with scientific methods, and published in peer-reviewed journals. Some of the current lesson plans were found to contain scientifically unsupported and biased information. In addition, the bill requires material to be "free of racial, ethnic, or gender biases." The legislation is supported by a wide range of interests, but opposed by the California Right to Life Education Fund, because they believe it discredits abstinence-only material. PMID:11366835

  18. Use of an inertial navigation system for accurate track recovery and coastal oceanographic measurements

    NASA Technical Reports Server (NTRS)

    Oliver, B. M.; Gower, J. F. R.

    1977-01-01

    A data acquisition system using a Litton LTN-51 inertial navigation unit (INU) was tested and used for aircraft track recovery and for location and tracking from the air of targets at sea. The characteristic position drift of the INU is compensated for by sighting landmarks of accurately known position at discrete time intervals using a visual sighting system in the transparent nose of the Beechcraft 18 aircraft used. For an aircraft altitude of about 300 m, theoretical and experimental tests indicate that calculated aircraft and/or target positions obtained from the interpolated INU drift curve will be accurate to within 10 m for landmarks spaced approximately every 15 minutes in time. For applications in coastal oceanography, such as surface current mapping by tracking artificial targets, the system allows a broad area to be covered without use of high altitude photography and its attendant needs for large targets and clear weather.

  19. Delineation of Early and Later Adult Onset Depression by Diffusion Tensor Imaging

    PubMed Central

    Yu, Hongjun; Nie, Binbin; Li, Na; Luo, Chunrong; Li, Haijun; Liu, Fang; Bai, Yan; Shan, Baoci; Xu, Lin; Xu, Xiufeng

    2014-01-01

    Background Due to a lack of evidence, there is no consistent age of onset to define early onset (EO) versus later onset (LO) major depressive disorder (MDD). Fractional anisotropy (FA), derived from diffusion tensor imaging (DTI), has been widely used to study neuropsychiatric disorders by providing information about the brain circuitry, abnormalities of which might facilitate the delineation of EO versus LO MDD. Method In this study, 61 pairs of untreated, non-elderly, first-episode MDD patients and healthy controls (HCs) aged 18–45 years old received DTI scans. The voxel-based analysis method (VBM), classification analysis, using the Statistical Package for the Social Sciences (SPSS), and regression analyses were used to determine abnormal FA clusters and their correlations with age of onset and clinical symptoms. Results Classification analysis suggested in the best model that there were two subgroups of MDD patients, delineated by an age of onset of 30 years old, by which MDD patients could be divided into EO (18–29 years old) and LO (30–45 years old) groups. LO MDD was characterized by decreased FA, especially in the white matter (WM) of the fronto-occipital fasciculus and posterior limb of internal capsule, with a negative correlation with the severity of depressive symptoms; in marked contrast, EO MDD showed increased FA, especially in the WM of the corpus callosum, corticospinal midbrain and inferior fronto-occipital fasciculus, while FA of the WM near the midbrain had a positive correlation with the severity of depressive symptoms. Conclusion Specific abnormalities of the brain circuitry in EO vs. LO MDD were delineated by an age of onset of 30 years old, as demonstrated by distinct abnormal FA clusters with opposite correlations with clinical symptoms. This DTI study supported the evidence of an exact age for the delineation of MDD, which could have broad multidisciplinary importance. Trial Registration ClinicalTrials.gov NCT00703742 PMID:25393297

  20. 372. J.W.M., Delineator August 1934 STATE OF CALIFORNIA; DEPARTMENT OF ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    372. J.W.M., Delineator August 1934 STATE OF CALIFORNIA; DEPARTMENT OF PUBLIC WORKS; SAN FRANCISCO - OAKLAND BAY BRIDGE; CONTRACT NO. 6; SUPERSTRUCTURE - WEST BAY CROSSING; OUTSIDE ELEVATION OF HOUSING; CENTER ANCHORAGE - PIER NO. 4; AMERICAN BRIDGE CO.; AMBRIDGE PLANT; ORDER NO. G 4854-XI; SHEET NO. E8 - San Francisco Oakland Bay Bridge, Spanning San Francisco Bay, San Francisco, San Francisco County, CA

  1. Using SAR Interferograms and Coherence Images for Object-Based Delineation of Unstable Slopes

    NASA Astrophysics Data System (ADS)

    Friedl, Barbara; Holbling, Daniel

    2015-05-01

    This study uses synthetic aperture radar (SAR) interferometric products for the semi-automated identification and delineation of unstable slopes and active landslides. Single-pair interferograms and coherence images are therefore segmented and classified in an object-based image analysis (OBIA) framework. The rule-based classification approach has been applied to landslide-prone areas located in Taiwan and Southern Germany. The semi-automatically obtained results were validated against landslide polygons derived from manual interpretation.

  2. Iterative Otsu's method for OCT improved delineation in the aorta wall

    NASA Astrophysics Data System (ADS)

    Alonso, Daniel; Real, Eusebio; Val-Bernal, José F.; Revuelta, José M.; Pontón, Alejandro; Calvo Díez, Marta; Mayorga, Marta; López-Higuera, José M.; Conde, Olga M.

    2015-07-01

    Degradation of human ascending thoracic aorta has been visualized with Optical Coherence Tomography (OCT). OCT images of the vessel wall exhibit structural degradation in the media layer of the artery, being this disorder the final trigger of the pathology. The degeneration in the vessel wall appears as low-reflectivity areas due to different optical properties of acidic polysaccharides and mucopolysaccharides in contrast with typical ordered structure of smooth muscle cells, elastin and collagen fibers. An OCT dimension indicator of wall degradation can be generated upon the spatial quantification of the extension of degraded areas in a similar way as conventional histopathology. This proposed OCT marker can offer in the future a real-time clinical perception of the vessel status to help cardiovascular surgeons in vessel repair interventions. However, the delineation of degraded areas on the B-scan image from OCT is sometimes difficult due to presence of speckle noise, variable signal to noise ratio (SNR) conditions on the measurement process, etc. Degraded areas can be delimited by basic thresholding techniques taking advantage of disorders evidences in B-scan images, but this delineation is not optimum in the aorta samples and requires complex additional processing stages. This work proposes an optimized delineation of degraded areas within the aorta wall, robust to noisy environments, based on the iterative application of Otsu's thresholding method. Results improve the delineation of wall anomalies compared with the simple application of the algorithm. Achievements could be also transferred to other clinical scenarios: carotid arteries, aorto-iliac or ilio-femoral sections, intracranial, etc.

  3. Delineating Floodplain in North Korea using Remote Sensing and Geographic Information System

    NASA Astrophysics Data System (ADS)

    Lim, J.; Lee, K. S.

    2015-12-01

    Korea has been divided into two countries after World War II. So environmental studies about North Korean are not easy and very limited. There were several flood damages every summer in North Korea since 1995, which induces lots of economic loss and agricultural production decrease. Delineating floodplain is indispensable to estimate the magnitude of flood damage and restore the flooded paddy field after unification. Remote Sensing (RS) can provide opportunity to study inaccessible area. In addition, flooding detection is possible. Several research groups study about flooding disaster using RS. Optical images and microwave images have been used in that field. Also, Digital topographic data have been used for flooding detection. Therefore, the purpose of this study is to investigate the land characteristics of floodplain by delineating floodplain in inaccessible North Korea using Landsat and digital topographic data. Landsat TM 5 images were used in this study. North Korea had severe flooding disaster since 1995. Among them 1995, 2007 and 2012 flooding are known for serious damages. Two Landsat images before and after flooding of each year were used to delineate floodplain. Study areas are Pyongyang City, Nampo City, North and South Hwanghae Province and South Pyongan Province. Floodplain are derived from overlaid classification image and flood-depth map. 1:25,000 scale digital topographic data were used to make flood-depth map. For land cover classification image enhancement and supervised classification with maximum likelihood classifier were used. Training areas were selected by visual interpretation using Daum-map which provides high resolution image of whole North Korea. The spatial characteristics of the floodplain were discussed based on floodplain map delineated in this study.

  4. Accurate localization of needle entry point in interventional MRI.

    PubMed

    Daanen, V; Coste, E; Sergent, G; Godart, F; Vasseur, C; Rousseau, J

    2000-10-01

    In interventional magnetic resonance imaging (MRI), the systems designed to help the surgeon during biopsy must provide accurate knowledge of the positions of the target and also the entry point of the needle on the skin of the patient. In some cases, this needle entry point can be outside the B(0) homogeneity area, where the distortions may be larger than a few millimeters. In that case, major correction for geometric deformation must be performed. Moreover, the use of markers to highlight the needle entry point is inaccurate. The aim of this study was to establish a three-dimensional coordinate correction according to the position of the entry point of the needle. We also describe a 2-degree of freedom electromechanical device that is used to determine the needle entry point on the patient's skin with a laser spot. PMID:11042649

  5. A Wavelet-Based ECG Delineation Method: Adaptation to an Experimental Electrograms with Manifested Global Ischemia.

    PubMed

    Hejč, Jakub; Vítek, Martin; Ronzhina, Marina; Nováková, Marie; Kolářová, Jana

    2015-09-01

    We present a novel wavelet-based ECG delineation method with robust classification of P wave and T wave. The work is aimed on an adaptation of the method to long-term experimental electrograms (EGs) measured on isolated rabbit heart and to evaluate the effect of global ischemia in experimental EGs on delineation performance. The algorithm was tested on a set of 263 rabbit EGs with established reference points and on human signals using standard Common Standards for Quantitative Electrocardiography Standard Database (CSEDB). On CSEDB, standard deviation (SD) of measured errors satisfies given criterions in each point and the results are comparable to other published works. In rabbit signals, our QRS detector reached sensitivity of 99.87% and positive predictivity of 99.89% despite an overlay of spectral components of QRS complex, P wave and power line noise. The algorithm shows great performance in suppressing J-point elevation and reached low overall error in both, QRS onset (SD = 2.8 ms) and QRS offset (SD = 4.3 ms) delineation. T wave offset is detected with acceptable error (SD = 12.9 ms) and sensitivity nearly 99%. Variance of the errors during global ischemia remains relatively stable, however more failures in detection of T wave and P wave occur. Due to differences in spectral and timing characteristics parameters of rabbit based algorithm have to be highly adaptable and set more precisely than in human ECG signals to reach acceptable performance. PMID:26577367

  6. Delineating native and invasive plant functional groups in shrub-steppe vegetation using bidirectional reflectance

    NASA Astrophysics Data System (ADS)

    Naupari, Javier A.; Vierling, Lee A.; Eitel, Jan U. H.

    2013-01-01

    Delineating invasive and native plant types using remote sensing is important for managing rangelands. Remote characterization of rangeland vegetation often utilizes only the nadir view, which can be complicated by background soil reflectance. We therefore collected bidirectional radiometric measurements on a shrub-steppe vegetated landscape throughout the mid- to late-growing season to: (1) quantify the BRFs of four rangeland vegetation functional groups (native shrub, native grasses, invasive annual grasses, and forbs), and (2) examine ways in which bidirectional reflectance values may help delineate native and invasive vegetation types. We found that the invasive grass medusahead rye (Taeniatherum caput-medusae [L.] Nevski) could be discriminated from other vegetation types at nadir and across four forward-viewing zenith angles because this species exhibited structural changes when leaf orientation changed from erectophile to planophile during and after the filling of seedheads. We also confirmed that native shrubs exhibited the highest anisotropy in all wavebands, as the relatively complex structure of the shrub canopy and concomitant shadowing greatly affected values of normalized difference vegetation index across all view angles. In order to delineate rangeland vegetation types at coarser scales, further study is needed to quantify the spectral angular signatures of these plant groups using satellite-based images.

  7. Delineating Species with DNA Barcodes: A Case of Taxon Dependent Method Performance in Moths

    PubMed Central

    Kekkonen, Mari; Mutanen, Marko; Kaila, Lauri; Nieminen, Marko; Hebert, Paul D. N.

    2015-01-01

    The accelerating loss of biodiversity has created a need for more effective ways to discover species. Novel algorithmic approaches for analyzing sequence data combined with rapidly expanding DNA barcode libraries provide a potential solution. While several analytical methods are available for the delineation of operational taxonomic units (OTUs), few studies have compared their performance. This study compares the performance of one morphology-based and four DNA-based (BIN, parsimony networks, ABGD, GMYC) methods on two groups of gelechioid moths. It examines 92 species of Finnish Gelechiinae and 103 species of Australian Elachistinae which were delineated by traditional taxonomy. The results reveal a striking difference in performance between the two taxa with all four DNA-based methods. OTU counts in the Elachistinae showed a wider range and a relatively low (ca. 65%) OTU match with reference species while OTU counts were more congruent and performance was higher (ca. 90%) in the Gelechiinae. Performance rose when only monophyletic species were compared, but the taxon-dependence remained. None of the DNA-based methods produced a correct match with non-monophyletic species, but singletons were handled well. A simulated test of morphospecies-grouping performed very poorly in revealing taxon diversity in these small, dull-colored moths. Despite the strong performance of analyses based on DNA barcodes, species delineated using single-locus mtDNA data are best viewed as OTUs that require validation by subsequent integrative taxonomic work. PMID:25849083

  8. Fast automatic delineation of cardiac volume of interest in MSCT images

    NASA Astrophysics Data System (ADS)

    Lorenz, Cristian; Lessick, Jonathan; Lavi, Guy; Bulow, Thomas; Renisch, Steffen

    2004-05-01

    Computed Tomography Angiography (CTA) is an emerging modality for assessing cardiac anatomy. The delineation of the cardiac volume of interest (VOI) is a pre-processing step for subsequent visualization or image processing. It serves the suppression of anatomic structures being not in the primary focus of the cardiac application, such as sternum, ribs, spinal column, descending aorta and pulmonary vasculature. These structures obliterate standard visualizations such as direct volume renderings or maximum intensity projections. In addition, outcome and performance of post-processing steps such as ventricle suppression, coronary artery segmentation or the detection of short and long axes of the heart can be improved. The structures being part of the cardiac VOI (coronary arteries and veins, myocardium, ventricles and atria) differ tremendously in appearance. In addition, there is no clear image feature associated with the contour (or better cut-surface) distinguishing between cardiac VOI and surrounding tissue making the automatic delineation of the cardiac VOI a difficult task. The presented approach locates in a first step chest wall and descending aorta in all image slices giving a rough estimate of the location of the heart. In a second step, a Fourier based active contour approach delineates slice-wise the border of the cardiac VOI. The algorithm has been evaluated on 41 multi-slice CT data-sets including cases with coronary stents and venous and arterial bypasses. The typical processing time amounts to 5-10s on a 1GHz P3 PC.

  9. Modeling Fire Susceptibility to Delineate Wildland-Urban Interface for Municipal-Scale Fire Risk Management

    NASA Astrophysics Data System (ADS)

    Whitman, Ellen; Rapaport, Eric; Sherren, Kate

    2013-12-01

    The wildland-urban interface (WUI) is the region where development meets and intermingles with wildlands. The WUI has an elevated fire risk due to the proximity of development and residents to wildlands with natural wildfire regimes. Existing methods of delineating WUI are typically applied over a large region, use proxies for risk, and do not consider site-specific fire hazard drivers. While these models are appropriate for federal and provincial risk management, municipal managers require models intended for smaller regions. The model developed here uses the Burn-P3 fire behavior model to model WUI from local fire susceptibility (FS) in two study communities. Forest fuel code (FFC) maps for the study communities were modified using remote sensing data to produce detailed forest edges, including ladder fuels, update data currency, and add buildings and roads. The modified FFC maps used in Burn-P3 produced bimodal FS distributions for each community. The WUI in these communities was delineated as areas within community bounds where FS was greater than or equal to -1 SD from the mean FS value (), which fell in the trough of the bimodal distribution. The WUI so delineated conformed to the definition of WUI. This model extends WUI modeling for broader risk management initiatives for municipal management of risk, as it (a) considers site-specific drivers of fire behavior; (b) models risk, represented by WUI, specific to a community; and, (c) does not use proxies for risk.

  10. Modeling fire susceptibility to delineate wildland-urban interface for municipal-scale fire risk management.

    PubMed

    Whitman, Ellen; Rapaport, Eric; Sherren, Kate

    2013-12-01

    The wildland-urban interface (WUI) is the region where development meets and intermingles with wildlands. The WUI has an elevated fire risk due to the proximity of development and residents to wildlands with natural wildfire regimes. Existing methods of delineating WUI are typically applied over a large region, use proxies for risk, and do not consider site-specific fire hazard drivers. While these models are appropriate for federal and provincial risk management, municipal managers require models intended for smaller regions. The model developed here uses the Burn-P3 fire behavior model to model WUI from local fire susceptibility (FS) in two study communities. Forest fuel code (FFC) maps for the study communities were modified using remote sensing data to produce detailed forest edges, including ladder fuels, update data currency, and add buildings and roads. The modified FFC maps used in Burn-P3 produced bimodal FS distributions for each community. The WUI in these communities was delineated as areas within community bounds where FS was greater than or equal to -1 SD from the mean FS value ([Formula: see text]), which fell in the trough of the bimodal distribution. The WUI so delineated conformed to the definition of WUI. This model extends WUI modeling for broader risk management initiatives for municipal management of risk, as it (a) considers site-specific drivers of fire behavior; (b) models risk, represented by WUI, specific to a community; and, (c) does not use proxies for risk. PMID:24036629

  11. An efficient approach to 3D single tree-crown delineation in LiDAR data

    NASA Astrophysics Data System (ADS)

    Mongus, Domen; Žalik, Borut

    2015-10-01

    This paper proposes a new method for 3D delineation of single tree-crowns in LiDAR data by exploiting the complementaries of treetop and tree trunk detections. A unified mathematical framework is provided based on the graph theory, allowing for all the segmentations to be achieved using marker-controlled watersheds. Treetops are defined by detecting concave neighbourhoods within the canopy height model using locally fitted surfaces. These serve as markers for watershed segmentation of the canopy layer where possible oversegmentation is reduced by merging the regions based on their heights, areas, and shapes. Additional tree crowns are delineated from mid- and under-storey layers based on tree trunk detection. A new approach for estimating the verticalities of the points' distributions is proposed for this purpose. The watershed segmentation is then applied on a density function within the voxel space, while boundaries of delineated trees from the canopy layer are used to prevent the overspreading of regions. The experiments show an approximately 6% increase in the efficiency of the proposed treetop definition based on locally fitted surfaces in comparison with the traditionally used local maxima of the smoothed canopy height model. In addition, 4% increase in the efficiency is achieved by the proposed tree trunk detection. Although the tree trunk detection alone is dependent on the data density, supplementing it with the treetop detection the proposed approach is efficient even when dealing with low density point-clouds.

  12. A pilot study for delineation of areas contributing water to wellfields at Jackson, Tennessee

    USGS Publications Warehouse

    Broshears, R.E.; Connell, J.F.; Short, N.C.

    1991-01-01

    The U.S. Geological Survey, in cooperation with the Tennessee Department of Health and Environment, Division of Groundwater Protection, and the Jackson Utility Division, conducted a pilot study to determine data needs and the applicability of four methods for the delineation of wellhead protection areas. Jackson Utility Division in Jackson, Madison County, Tennessee, pumps about 9 million gallons of ground water daily from two municipal wellfields that tap an unconfined sand aquifer. Under natural hydraulic gradients, ground waterflows southward toward the South Wellfield at approximately 2 to 3 feet per day; natural flow toward the North Wellfield from the east at 1 to 2 feet per day. Water quality generally is suitable for most uses. Concentrations of dissolved solids are low, and excessive iron is the only significant naturally occurring water-quality problem. However, trace concentrations of volatile organic compounds have been detected in water pumps from the South Wellfield; the highest concentration of a single compound has been 23 micrograms per liter of tetrachloroethylene. Potential sources of ground-water contamination in the Jackson area include a hazardous-waste site, municipal and industrial landfill, and underground-storage tanks. Some of the four method for delineating wellhead protection areas did not adequately describe zones contributing flow to the wellfields. Calculations based on a uniform flow equation provided a preliminary delineation of zones of contribution for the wellfields and ground-water time-of-travel contours. Limitations of the applied methods motivated the design of a more rigorous hydrogeologic investigation.

  13. Delineating incised stream sediment sources within a San Francisco Bay tributary basin

    NASA Astrophysics Data System (ADS)

    Bigelow, Paul; Benda, Lee; Pearce, Sarah

    2016-07-01

    Erosion and sedimentation pose ubiquitous problems for land and watershed managers, requiring delineation of sediment sources and sinks across landscapes. However, the technical complexity of many spatially explicit erosion models precludes their use by practitioners. To address this critical gap, we demonstrate a contemporary use of applied geomorphometry through a straightforward GIS analysis of sediment sources in the San Francisco Bay Area in California, USA, designed to support erosion reduction strategies. Using 2 m lidar digital elevation models, we delineated the entire river network in the Arroyo Mocho watershed (573 km2) at the scale of ˜ 30 m segments and identified incised landforms using a combination of hillslope gradient and planform curvature. Chronic erosion to the channel network was estimated based on these topographic attributes and the size of vegetation, and calibrated to sediment gage data, providing a spatially explicit estimate of sediment yield from incised channels across the basin. Rates of erosion were summarized downstream through the channel network, revealing patterns of sediment supply at the reach scale. Erosion and sediment supply were also aggregated to subbasins, allowing comparative analyses at the scale of tributaries. The erosion patterns delineated using this approach provide land use planners with a robust framework to design erosion reduction strategies. More broadly, the study demonstrates a modern analysis of important geomorphic processes affected by land use that is easily applied by agencies to solve common problems in watersheds, improving the integration between science and environmental management.

  14. Delineating spring recharge areas in a fractured sandstone aquifer (Luxembourg) based on pesticide mass balance

    NASA Astrophysics Data System (ADS)

    Farlin, J.; Drouet, L.; Gallé, T.; Pittois, D.; Bayerle, M.; Braun, C.; Maloszewski, P.; Vanderborght, J.; Elsner, M.; Kies, A.

    2013-06-01

    A simple method to delineate the recharge areas of a series of springs draining a fractured aquifer is presented. Instead of solving the flow and transport equations, the delineation is reformulated as a mass balance problem assigning arable land in proportion to the pesticide mass discharged annually in a spring at minimum total transport cost. The approach was applied to the Luxembourg Sandstone, a fractured-rock aquifer supplying half of the drinking water for Luxembourg, using the herbicide atrazine. Predictions of the recharge areas were most robust in situations of strong competition by neighbouring springs while the catchment boundaries for isolated springs were extremely sensitive to the parameter controlling flow direction. Validation using a different pesticide showed the best agreement with the simplest model used, whereas using historical crop-rotation data and spatially distributed soil-leaching data did not improve predictions. The whole approach presents the advantage of integrating objectively information on land use and pesticide concentration in spring water into the delineation of groundwater recharge zones in a fractured-rock aquifer.

  15. Strategy for accurate liver intervention by an optical tracking system

    PubMed Central

    Lin, Qinyong; Yang, Rongqian; Cai, Ken; Guan, Peifeng; Xiao, Weihu; Wu, Xiaoming

    2015-01-01

    Image-guided navigation for radiofrequency ablation of liver tumors requires the accurate guidance of needle insertion into a tumor target. The main challenge of image-guided navigation for radiofrequency ablation of liver tumors is the occurrence of liver deformations caused by respiratory motion. This study reports a strategy of real-time automatic registration to track custom fiducial markers glued onto the surface of a patient’s abdomen to find the respiratory phase, in which the static preoperative CT is performed. Custom fiducial markers are designed. Real-time automatic registration method consists of the automatic localization of custom fiducial markers in the patient and image spaces. The fiducial registration error is calculated in real time and indicates if the current respiratory phase corresponds to the phase of the static preoperative CT. To demonstrate the feasibility of the proposed strategy, a liver simulator is constructed and two volunteers are involved in the preliminary experiments. An ex-vivo porcine liver model is employed to further verify the strategy for liver intervention. Experimental results demonstrate that real-time automatic registration method is rapid, accurate, and feasible for capturing the respiratory phase from which the static preoperative CT anatomical model is generated by tracking the movement of the skin-adhered custom fiducial markers. PMID:26417501

  16. A spectrally accurate algorithm for electromagnetic scattering in three dimensions

    NASA Astrophysics Data System (ADS)

    Ganesh, M.; Hawkins, S.

    2006-09-01

    In this work we develop, implement and analyze a high-order spectrally accurate algorithm for computation of the echo area, and monostatic and bistatic radar cross-section (RCS) of a three dimensional perfectly conducting obstacle through simulation of the time-harmonic electromagnetic waves scattered by the conductor. Our scheme is based on a modified boundary integral formulation (of the Maxwell equations) that is tolerant to basis functions that are not tangential on the conductor surface. We test our algorithm with extensive computational experiments using a variety of three dimensional perfect conductors described in spherical coordinates, including benchmark radar targets such as the metallic NASA almond and ogive. The monostatic RCS measurements for non-convex conductors require hundreds of incident waves (boundary conditions). We demonstrate that the monostatic RCS of small (to medium) sized conductors can be computed using over one thousand incident waves within a few minutes (to a few hours) of CPU time. We compare our results with those obtained using method of moments based industrial standard three dimensional electromagnetic codes CARLOS, CICERO, FE-IE, FERM, and FISC. Finally, we prove the spectrally accurate convergence of our algorithm for computing the surface current, far-field, and RCS values of a class of conductors described globally in spherical coordinates.

  17. Exploring the Process of Energy Generation in Pathophysiology by Targeted Metabolomics: Performance of a Simple and Quantitative Method

    NASA Astrophysics Data System (ADS)

    Riera-Borrull, Marta; Rodríguez-Gallego, Esther; Hernández-Aguilera, Anna; Luciano, Fedra; Ras, Rosa; Cuyàs, Elisabet; Camps, Jordi; Segura-Carretero, Antonio; Menendez, Javier A.; Joven, Jorge; Fernández-Arroyo, Salvador

    2016-01-01

    Abnormalities in mitochondrial metabolism and regulation of energy balance contribute to human diseases. The consequences of high fat and other nutrient intake, and the resulting acquired mitochondrial dysfunction, are essential to fully understand common disorders, including obesity, cancer, and atherosclerosis. To simultaneously and noninvasively measure and quantify indirect markers of mitochondrial function, we have developed a method based on gas chromatography coupled to quadrupole-time of flight mass spectrometry and an electron ionization interface, and validated the system using plasma from patients with peripheral artery disease, human cancer cells, and mouse tissues. This approach was used to increase sensibility in the measurement of a wide dynamic range and chemical diversity of multiple intermediate metabolites used in energy metabolism. We demonstrate that our targeted metabolomics method allows for quick and accurate identification and quantification of molecules, including the measurement of small yet significant biological changes in experimental samples. The apparently low process variability required for its performance in plasma, cell lysates, and tissues allowed a rapid identification of correlations between interconnected pathways. Our results suggest that delineating the process of energy generation by targeted metabolomics can be a valid surrogate for predicting mitochondrial dysfunction in biological samples. Importantly, when used in plasma, targeted metabolomics should be viewed as a robust and noninvasive source of biomarkers in specific pathophysiological scenarios.

  18. Accurate basis set truncation for wavefunction embedding

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.

    2013-07-01

    Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.

  19. Accurate radiative transfer calculations for layered media.

    PubMed

    Selden, Adrian C

    2016-07-01

    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700

  20. Fast and accurate propagation of coherent light

    PubMed Central

    Lewis, R. D.; Beylkin, G.; Monzón, L.

    2013-01-01

    We describe a fast algorithm to propagate, for any user-specified accuracy, a time-harmonic electromagnetic field between two parallel planes separated by a linear, isotropic and homogeneous medium. The analytical formulation of this problem (ca 1897) requires the evaluation of the so-called Rayleigh–Sommerfeld integral. If the distance between the planes is small, this integral can be accurately evaluated in the Fourier domain; if the distance is very large, it can be accurately approximated by asymptotic methods. In the large intermediate region of practical interest, where the oscillatory Rayleigh–Sommerfeld kernel must be applied directly, current numerical methods can be highly inaccurate without indicating this fact to the user. In our approach, for any user-specified accuracy ϵ>0, we approximate the kernel by a short sum of Gaussians with complex-valued exponents, and then efficiently apply the result to the input data using the unequally spaced fast Fourier transform. The resulting algorithm has computational complexity , where we evaluate the solution on an N×N grid of output points given an M×M grid of input samples. Our algorithm maintains its accuracy throughout the computational domain. PMID:24204184

  1. How Accurately can we Calculate Thermal Systems?

    SciTech Connect

    Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A

    2004-04-20

    I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.

  2. Accurate shear measurement with faint sources

    SciTech Connect

    Zhang, Jun; Foucaud, Sebastien; Luo, Wentao E-mail: walt@shao.ac.cn

    2015-01-01

    For cosmic shear to become an accurate cosmological probe, systematic errors in the shear measurement method must be unambiguously identified and corrected for. Previous work of this series has demonstrated that cosmic shears can be measured accurately in Fourier space in the presence of background noise and finite pixel size, without assumptions on the morphologies of galaxy and PSF. The remaining major source of error is source Poisson noise, due to the finiteness of source photon number. This problem is particularly important for faint galaxies in space-based weak lensing measurements, and for ground-based images of short exposure times. In this work, we propose a simple and rigorous way of removing the shear bias from the source Poisson noise. Our noise treatment can be generalized for images made of multiple exposures through MultiDrizzle. This is demonstrated with the SDSS and COSMOS/ACS data. With a large ensemble of mock galaxy images of unrestricted morphologies, we show that our shear measurement method can achieve sub-percent level accuracy even for images of signal-to-noise ratio less than 5 in general, making it the most promising technique for cosmic shear measurement in the ongoing and upcoming large scale galaxy surveys.

  3. Accurate pose estimation for forensic identification

    NASA Astrophysics Data System (ADS)

    Merckx, Gert; Hermans, Jeroen; Vandermeulen, Dirk

    2010-04-01

    In forensic authentication, one aims to identify the perpetrator among a series of suspects or distractors. A fundamental problem in any recognition system that aims for identification of subjects in a natural scene is the lack of constrains on viewing and imaging conditions. In forensic applications, identification proves even more challenging, since most surveillance footage is of abysmal quality. In this context, robust methods for pose estimation are paramount. In this paper we will therefore present a new pose estimation strategy for very low quality footage. Our approach uses 3D-2D registration of a textured 3D face model with the surveillance image to obtain accurate far field pose alignment. Starting from an inaccurate initial estimate, the technique uses novel similarity measures based on the monogenic signal to guide a pose optimization process. We will illustrate the descriptive strength of the introduced similarity measures by using them directly as a recognition metric. Through validation, using both real and synthetic surveillance footage, our pose estimation method is shown to be accurate, and robust to lighting changes and image degradation.

  4. Accurate determination of characteristic relative permeability curves

    NASA Astrophysics Data System (ADS)

    Krause, Michael H.; Benson, Sally M.

    2015-09-01

    A recently developed technique to accurately characterize sub-core scale heterogeneity is applied to investigate the factors responsible for flowrate-dependent effective relative permeability curves measured on core samples in the laboratory. The dependency of laboratory measured relative permeability on flowrate has long been both supported and challenged by a number of investigators. Studies have shown that this apparent flowrate dependency is a result of both sub-core scale heterogeneity and outlet boundary effects. However this has only been demonstrated numerically for highly simplified models of porous media. In this paper, flowrate dependency of effective relative permeability is demonstrated using two rock cores, a Berea Sandstone and a heterogeneous sandstone from the Otway Basin Pilot Project in Australia. Numerical simulations of steady-state coreflooding experiments are conducted at a number of injection rates using a single set of input characteristic relative permeability curves. Effective relative permeability is then calculated from the simulation data using standard interpretation methods for calculating relative permeability from steady-state tests. Results show that simplified approaches may be used to determine flowrate-independent characteristic relative permeability provided flow rate is sufficiently high, and the core heterogeneity is relatively low. It is also shown that characteristic relative permeability can be determined at any typical flowrate, and even for geologically complex models, when using accurate three-dimensional models.

  5. Using aquatic invertebrates to delineate seasonal and temporary wetlands in the Prairie Pothole Region of North America

    USGS Publications Warehouse

    Euliss, N.H., Jr.; Mushet, D.M.; Johnson, D.H.

    2002-01-01

    Tillage can destroy or greatly disturb indicators of hydric soils and hydrophytic vegetation, making delineation of tilled wetlands difficult. The remains of aquatic invertebrates (e.g., shells, drought-resistant eggs, and trichopteran cases) are easily identifiable and persist in wetland substrates even when wetlands are dry. Additionally, these remains are not easily destroyed by mechanical tillage. To test the feasibility of using invertebrate remains to delineate wetlands, we used two methods to identify the wetland edge of ten seasonal and ten temporary wetlands, evenly divided between grassland and cropland landscapes. First, we identified the wetland edge using hydric soil and vegetation indicators along six evenly spaced transects in each wetland (our standard delineation). We then identified the wetland edge along the same transects using aquatic invertebrate remains as our indicator. In grassland landscapes, delineations of the wetland edge made using invertebrate remains were consistently at the same location or closer to the wetland center as the standard delineations for both seasonal and temporary wetlands. In cropland landscapes, however, many of our invertebrate delineations of seasonal and temporary wetlands were on the upland side of our standard delineations. We attribute the differences to movement of remains during tillage, increased maximum pool levels in cropland wetlands, and disturbance of hydric soils and plants. We found that the elevations of the wetland edge indicated by invertebrate remains were more consistent within a wetland than elevations determined by standard delineations. Aquatic invertebrate remains can be useful in delineating wetlands when other indicators have been destroyed or severely disturbed by tillage.

  6. LIQUID TARGET

    DOEpatents

    Martin, M.D.; Salsig, W.W. Jr.

    1959-01-13

    A liquid handling apparatus is presented for a liquid material which is to be irradiated. The apparatus consists essentially of a reservoir for the liquid, a target element, a drain tank and a drain lock chamber. The target is in the form of a looped tube, the upper end of which is adapted to be disposed in a beam of atomic particles. The lower end of the target tube is in communication with the liquid in the reservoir and a means is provided to continuously circulate the liquid material to be irradiated through the target tube. Means to heat the reservoir tank is provided in the event that a metal is to be used as the target material. The apparatus is provided with suitable valves and shielding to provide maximum safety in operation.

  7. Landsat TM image segmentation for delineating geological zone correlated vegetation stratification in the Kruger National Park, South Africa

    NASA Astrophysics Data System (ADS)

    Munyati, Christopher; Ratshibvumo, Thihanedzwi; Ogola, Jason

    Image classification approaches are widely used in mapping vegetation on remotely sensed images. Vegetation assemblages are equivalent to habitats. Whereas sub-pixel classification approaches potentially can produce more realistic, homogenous habitat maps, pixel-based hard classifier approaches often result in non-homogenous habitat zones. This salt-and-pepper habitat mapping is particularly a challenge on images of savannas, given the characteristic patchy texture of scattered trees and grass. Image segmentation techniques offer possibilities for homogenous habitat classification. This study aimed at establishing the extent to which established, field surveyed and geology-related vegetation types in South Africa’s Kruger National Park (KNP) can be reproduced using image segmentation. Rain season Landsat TM images were used, selected to coincide with the peak in vegetation productivity, which was deemed the time of year when discrimination between key habitats in KNP is most likely to be successful. The multiresolution segmentation mode in eCognition 5.0 was employed, object classification accomplished using the nearest neighbour (NN) classifier, using object texture and training area mean values in the NN feature space. Compared to delineations of the vegetation types of KNP on a digital map of the vegetation zones that was tested, image segmentation successfully mapped the zones (overall accuracy 85.3%, K^ = 82.7%) despite slight shifts in the location of vegetation zone boundaries. Maximum likelihood classification (MLC) of the same images was only 37% accurate (K^ = 24.2%). Whereas the vegetation zones resulting from MLC were non-homogenous, with considerable spectral confusion among the vegetation zones, image segmentation produced more homogenous vegetation zones, comparably more useful for conservation management, because realistic and meaningful habitat maps are important in biodiversity conservation as input data upon which to base management decisions

  8. Delineating the subsidence drivers in the Po River delta (Italy) by combining L- and X-band SAR Interferometry

    NASA Astrophysics Data System (ADS)

    Teatini, Pietro; Tosi, Luigi; Da Lio, Cristina; Strozzi, Tazio

    2016-04-01

    From leveling to SAR-based interferometry, the monitoring of land subsidence has improved significantly. However, the accurate assessment of the ground movements by SAR in deltaic regions, where marshlands, coastal infrastructures, river embankments, farmlands, and urbanized areas coexist, is still a challenge. Usually, relatively small built-up zones and infrastructures are scattered within large natural and rural lands. In this contribution we present a multi-band SAR methodology to integrate COSMO-SkyMed and ALOS-PALSAR images. The method consists in a proper combination of the very high-resolution X-band Persistent Scatterer Interferometry (PSI), which achieves high-density and precise measurements on single structures and constructed areas, with the L-band Short-Baseline SAR Interferometry (SBAS), properly implemented to rise its effectiveness in retrieving information in vegetated and wet zones. The combined methodology is applied on the Po River Delta, northern Italy, using 16 ALOS-PALSAR and 31 COSMO-SkyMed images covering the period between 2007 and 2011. After a proper calibration of the single PSI and SBAS solution using available GPS records, the dataset have been combined at both the regional and local scales. The measured displacements range from ~0 mm/yr to -35 mm/yr. The results reveal the variable pattern of the subsidence characterizing the more natural and rural environments without losing the accuracy in quantifying the sinking of urban areas and infrastructures. Moreover, they allow improving the interpretation of the natural and anthropogenic processes responsible for the ongoing subsidence, helping to delineate the relative importance of the various drivers contributing to the cumulative subsidence.

  9. Combined reflectance confocal microscopy-optical coherence tomography for delineation of basal cell carcinoma margins: an ex vivo study

    NASA Astrophysics Data System (ADS)

    Iftimia, Nicusor; Peterson, Gary; Chang, Ernest W.; Maguluri, Gopi; Fox, William; Rajadhyaksha, Milind

    2016-01-01

    We present a combined reflectance confocal microscopy (RCM) and optical coherence tomography (OCT) approach, integrated within a single optical layout, for diagnosis of basal cell carcinomas (BCCs) and delineation of margins. While RCM imaging detects BCC presence (diagnoses) and its lateral spreading (margins) with measured resolution of ˜1 μm, OCT imaging delineates BCC depth spreading (margins) with resolution of ˜7 μm. When delineating margins in 20 specimens of superficial and nodular BCCs, depth could be reliably determined down to ˜600 μm, and agreement with histology was within about ±50 μm.

  10. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2003-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  11. Accurate Thermal Stresses for Beams: Normal Stress

    NASA Technical Reports Server (NTRS)

    Johnson, Theodore F.; Pilkey, Walter D.

    2002-01-01

    Formulations for a general theory of thermoelasticity to generate accurate thermal stresses for structural members of aeronautical vehicles were developed in 1954 by Boley. The formulation also provides three normal stresses and a shear stress along the entire length of the beam. The Poisson effect of the lateral and transverse normal stresses on a thermally loaded beam is taken into account in this theory by employing an Airy stress function. The Airy stress function enables the reduction of the three-dimensional thermal stress problem to a two-dimensional one. Numerical results from the general theory of thermoelasticity are compared to those obtained from strength of materials. It is concluded that the theory of thermoelasticity for prismatic beams proposed in this paper can be used instead of strength of materials when precise stress results are desired.

  12. Highly accurate articulated coordinate measuring machine

    DOEpatents

    Bieg, Lothar F.; Jokiel, Jr., Bernhard; Ensz, Mark T.; Watson, Robert D.

    2003-12-30

    Disclosed is a highly accurate articulated coordinate measuring machine, comprising a revolute joint, comprising a circular encoder wheel, having an axis of rotation; a plurality of marks disposed around at least a portion of the circumference of the encoder wheel; bearing means for supporting the encoder wheel, while permitting free rotation of the encoder wheel about the wheel's axis of rotation; and a sensor, rigidly attached to the bearing means, for detecting the motion of at least some of the marks as the encoder wheel rotates; a probe arm, having a proximal end rigidly attached to the encoder wheel, and having a distal end with a probe tip attached thereto; and coordinate processing means, operatively connected to the sensor, for converting the output of the sensor into a set of cylindrical coordinates representing the position of the probe tip relative to a reference cylindrical coordinate system.

  13. Practical aspects of spatially high accurate methods

    NASA Technical Reports Server (NTRS)

    Godfrey, Andrew G.; Mitchell, Curtis R.; Walters, Robert W.

    1992-01-01

    The computational qualities of high order spatially accurate methods for the finite volume solution of the Euler equations are presented. Two dimensional essentially non-oscillatory (ENO), k-exact, and 'dimension by dimension' ENO reconstruction operators are discussed and compared in terms of reconstruction and solution accuracy, computational cost and oscillatory behavior in supersonic flows with shocks. Inherent steady state convergence difficulties are demonstrated for adaptive stencil algorithms. An exact solution to the heat equation is used to determine reconstruction error, and the computational intensity is reflected in operation counts. Standard MUSCL differencing is included for comparison. Numerical experiments presented include the Ringleb flow for numerical accuracy and a shock reflection problem. A vortex-shock interaction demonstrates the ability of the ENO scheme to excel in simulating unsteady high-frequency flow physics.

  14. The thermodynamic cost of accurate sensory adaptation

    NASA Astrophysics Data System (ADS)

    Tu, Yuhai

    2015-03-01

    Living organisms need to obtain and process environment information accurately in order to make decisions critical for their survival. Much progress have been made in identifying key components responsible for various biological functions, however, major challenges remain to understand system-level behaviors from the molecular-level knowledge of biology and to unravel possible physical principles for the underlying biochemical circuits. In this talk, we will present some recent works in understanding the chemical sensory system of E. coli by combining theoretical approaches with quantitative experiments. We focus on addressing the questions on how cells process chemical information and adapt to varying environment, and what are the thermodynamic limits of key regulatory functions, such as adaptation.

  15. Accurate numerical solutions of conservative nonlinear oscillators

    NASA Astrophysics Data System (ADS)

    Khan, Najeeb Alam; Nasir Uddin, Khan; Nadeem Alam, Khan

    2014-12-01

    The objective of this paper is to present an investigation to analyze the vibration of a conservative nonlinear oscillator in the form u" + lambda u + u^(2n-1) + (1 + epsilon^2 u^(4m))^(1/2) = 0 for any arbitrary power of n and m. This method converts the differential equation to sets of algebraic equations and solve numerically. We have presented for three different cases: a higher order Duffing equation, an equation with irrational restoring force and a plasma physics equation. It is also found that the method is valid for any arbitrary order of n and m. Comparisons have been made with the results found in the literature the method gives accurate results.

  16. Accurate Telescope Mount Positioning with MEMS Accelerometers

    NASA Astrophysics Data System (ADS)

    Mészáros, L.; Jaskó, A.; Pál, A.; Csépány, G.

    2014-08-01

    This paper describes the advantages and challenges of applying microelectromechanical accelerometer systems (MEMS accelerometers) in order to attain precise, accurate, and stateless positioning of telescope mounts. This provides a completely independent method from other forms of electronic, optical, mechanical or magnetic feedback or real-time astrometry. Our goal is to reach the subarcminute range which is considerably smaller than the field-of-view of conventional imaging telescope systems. Here we present how this subarcminute accuracy can be achieved with very cheap MEMS sensors and we also detail how our procedures can be extended in order to attain even finer measurements. In addition, our paper discusses how can a complete system design be implemented in order to be a part of a telescope control system.

  17. Accurate metacognition for visual sensory memory representations.

    PubMed

    Vandenbroucke, Annelinde R E; Sligte, Ilja G; Barrett, Adam B; Seth, Anil K; Fahrenfort, Johannes J; Lamme, Victor A F

    2014-04-01

    The capacity to attend to multiple objects in the visual field is limited. However, introspectively, people feel that they see the whole visual world at once. Some scholars suggest that this introspective feeling is based on short-lived sensory memory representations, whereas others argue that the feeling of seeing more than can be attended to is illusory. Here, we investigated this phenomenon by combining objective memory performance with subjective confidence ratings during a change-detection task. This allowed us to compute a measure of metacognition--the degree of knowledge that subjects have about the correctness of their decisions--for different stages of memory. We show that subjects store more objects in sensory memory than they can attend to but, at the same time, have similar metacognition for sensory memory and working memory representations. This suggests that these subjective impressions are not an illusion but accurate reflections of the richness of visual perception. PMID:24549293

  18. Apparatus for accurately measuring high temperatures

    DOEpatents

    Smith, Douglas D.

    1985-01-01

    The present invention is a thermometer used for measuring furnace temperaes in the range of about 1800.degree. to 2700.degree. C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  19. Apparatus for accurately measuring high temperatures

    DOEpatents

    Smith, D.D.

    The present invention is a thermometer used for measuring furnace temperatures in the range of about 1800/sup 0/ to 2700/sup 0/C. The thermometer comprises a broadband multicolor thermal radiation sensor positioned to be in optical alignment with the end of a blackbody sight tube extending into the furnace. A valve-shutter arrangement is positioned between the radiation sensor and the sight tube and a chamber for containing a charge of high pressure gas is positioned between the valve-shutter arrangement and the radiation sensor. A momentary opening of the valve shutter arrangement allows a pulse of the high gas to purge the sight tube of air-borne thermal radiation contaminants which permits the radiation sensor to accurately measure the thermal radiation emanating from the end of the sight tube.

  20. Toward Accurate and Quantitative Comparative Metagenomics.

    PubMed

    Nayfach, Stephen; Pollard, Katherine S

    2016-08-25

    Shotgun metagenomics and computational analysis are used to compare the taxonomic and functional profiles of microbial communities. Leveraging this approach to understand roles of microbes in human biology and other environments requires quantitative data summaries whose values are comparable across samples and studies. Comparability is currently hampered by the use of abundance statistics that do not estimate a meaningful parameter of the microbial community and biases introduced by experimental protocols and data-cleaning approaches. Addressing these challenges, along with improving study design, data access, metadata standardization, and analysis tools, will enable accurate comparative metagenomics. We envision a future in which microbiome studies are replicable and new metagenomes are easily and rapidly integrated with existing data. Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. PMID:27565341

  1. The importance of accurate atmospheric modeling

    NASA Astrophysics Data System (ADS)

    Payne, Dylan; Schroeder, John; Liang, Pang

    2014-11-01

    This paper will focus on the effect of atmospheric conditions on EO sensor performance using computer models. We have shown the importance of accurately modeling atmospheric effects for predicting the performance of an EO sensor. A simple example will demonstrated how real conditions for several sites in China will significantly impact on image correction, hyperspectral imaging, and remote sensing. The current state-of-the-art model for computing atmospheric transmission and radiance is, MODTRAN® 5, developed by the US Air Force Research Laboratory and Spectral Science, Inc. Research by the US Air Force, Navy and Army resulted in the public release of LOWTRAN 2 in the early 1970's. Subsequent releases of LOWTRAN and MODTRAN® have continued until the present. Please verify that (1) all pages are present, (2) all figures are correct, (3) all fonts and special characters are correct, and (4) all text and figures fit within the red margin lines shown on this review document. Complete formatting information is available at http://SPIE.org/manuscripts Return to the Manage Active Submissions page at http://spie.org/submissions/tasks.aspx and approve or disapprove this submission. Your manuscript will not be published without this approval. Please contact author_help@spie.org with any questions or concerns. The paper will demonstrate the importance of using validated models and local measured meteorological, atmospheric and aerosol conditions to accurately simulate the atmospheric transmission and radiance. Frequently default conditions are used which can produce errors of as much as 75% in these values. This can have significant impact on remote sensing applications.

  2. The high cost of accurate knowledge.

    PubMed

    Sutcliffe, Kathleen M; Weber, Klaus

    2003-05-01

    Many business thinkers believe it's the role of senior managers to scan the external environment to monitor contingencies and constraints, and to use that precise knowledge to modify the company's strategy and design. As these thinkers see it, managers need accurate and abundant information to carry out that role. According to that logic, it makes sense to invest heavily in systems for collecting and organizing competitive information. Another school of pundits contends that, since today's complex information often isn't precise anyway, it's not worth going overboard with such investments. In other words, it's not the accuracy and abundance of information that should matter most to top executives--rather, it's how that information is interpreted. After all, the role of senior managers isn't just to make decisions; it's to set direction and motivate others in the face of ambiguities and conflicting demands. Top executives must interpret information and communicate those interpretations--they must manage meaning more than they must manage information. So which of these competing views is the right one? Research conducted by academics Sutcliffe and Weber found that how accurate senior executives are about their competitive environments is indeed less important for strategy and corresponding organizational changes than the way in which they interpret information about their environments. Investments in shaping those interpretations, therefore, may create a more durable competitive advantage than investments in obtaining and organizing more information. And what kinds of interpretations are most closely linked with high performance? Their research suggests that high performers respond positively to opportunities, yet they aren't overconfident in their abilities to take advantage of those opportunities. PMID:12747164

  3. Accurate Weather Forecasting for Radio Astronomy

    NASA Astrophysics Data System (ADS)

    Maddalena, Ronald J.

    2010-01-01

    The NRAO Green Bank Telescope routinely observes at wavelengths from 3 mm to 1 m. As with all mm-wave telescopes, observing conditions depend upon the variable atmospheric water content. The site provides over 100 days/yr when opacities are low enough for good observing at 3 mm, but winds on the open-air structure reduce the time suitable for 3-mm observing where pointing is critical. Thus, to maximum productivity the observing wavelength needs to match weather conditions. For 6 years the telescope has used a dynamic scheduling system (recently upgraded; www.gb.nrao.edu/DSS) that requires accurate multi-day forecasts for winds and opacities. Since opacity forecasts are not provided by the National Weather Services (NWS), I have developed an automated system that takes available forecasts, derives forecasted opacities, and deploys the results on the web in user-friendly graphical overviews (www.gb.nrao.edu/ rmaddale/Weather). The system relies on the "North American Mesoscale" models, which are updated by the NWS every 6 hrs, have a 12 km horizontal resolution, 1 hr temporal resolution, run to 84 hrs, and have 60 vertical layers that extend to 20 km. Each forecast consists of a time series of ground conditions, cloud coverage, etc, and, most importantly, temperature, pressure, humidity as a function of height. I use the Liebe's MWP model (Radio Science, 20, 1069, 1985) to determine the absorption in each layer for each hour for 30 observing wavelengths. Radiative transfer provides, for each hour and wavelength, the total opacity and the radio brightness of the atmosphere, which contributes substantially at some wavelengths to Tsys and the observational noise. Comparisons of measured and forecasted Tsys at 22.2 and 44 GHz imply that the forecasted opacities are good to about 0.01 Nepers, which is sufficient for forecasting and accurate calibration. Reliability is high out to 2 days and degrades slowly for longer-range forecasts.

  4. Approaching system equilibrium with accurate or not accurate feedback information in a two-route system

    NASA Astrophysics Data System (ADS)

    Zhao, Xiao-mei; Xie, Dong-fan; Li, Qi

    2015-02-01

    With the development of intelligent transport system, advanced information feedback strategies have been developed to reduce traffic congestion and enhance the capacity. However, previous strategies provide accurate information to travelers and our simulation results show that accurate information brings negative effects, especially in delay case. Because travelers prefer to the best condition route with accurate information, and delayed information cannot reflect current traffic condition but past. Then travelers make wrong routing decisions, causing the decrease of the capacity and the increase of oscillations and the system deviating from the equilibrium. To avoid the negative effect, bounded rationality is taken into account by introducing a boundedly rational threshold BR. When difference between two routes is less than the BR, routes have equal probability to be chosen. The bounded rationality is helpful to improve the efficiency in terms of capacity, oscillation and the gap deviating from the system equilibrium.

  5. A variable optical target simulator

    NASA Technical Reports Server (NTRS)

    Kulas, C. E.; Crosswhite, E. D.

    1979-01-01

    A crucial experiment, relative to determining the ability of an imaging seeker to track a target and generate accurate terminal guidance, requires an optical device which can provide imagery that grows in size as a real-time estimate of true missile flight conditions. The basic components of an Optical Contrast TV Imaging Seeker are reviewed to establish the need for an optical target simulator. An optomechanical device called a Variable Optical Target Simulator (VOTS) which generates end game scene situations is discussed. The organization of optical components and their control for providing an image which grows in size as a linear estimate of real world situations is presented.

  6. Higher order accurate partial implicitization: An unconditionally stable fourth-order-accurate explicit numerical technique

    NASA Technical Reports Server (NTRS)

    Graves, R. A., Jr.

    1975-01-01

    The previously obtained second-order-accurate partial implicitization numerical technique used in the solution of fluid dynamic problems was modified with little complication to achieve fourth-order accuracy. The Von Neumann stability analysis demonstrated the unconditional linear stability of the technique. The order of the truncation error was deduced from the Taylor series expansions of the linearized difference equations and was verified by numerical solutions to Burger's equation. For comparison, results were also obtained for Burger's equation using a second-order-accurate partial-implicitization scheme, as well as the fourth-order scheme of Kreiss.

  7. 49 CFR Appendix A to Part 195 - Delineation Between Federal and State Jurisdiction-Statement of Agency Policy and Interpretation

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ..., App. A Appendix A to Part 195—Delineation Between Federal and State Jurisdiction—Statement of Agency... complaint filed with FERC would be successful or in which blind reliance on a FERC filing would result in...

  8. The effect of different delineator post configurations on driver speed in night-time traffic: a driving simulator study.

    PubMed

    Nygårdhs, Sara; Lundkvist, Sven-Olof; Andersson, Jan; Dahlbäck, Nils

    2014-11-01

    The aim of the study was to investigate how different delineator post configurations affect driver speed in night-time traffic. In addition, the potential speed effect of introducing a secondary task was investigated. The study was carried out in a car simulator on a road stretch including straight road sections as well as curves with different radii. Fourteen drivers participated in the study and the results show that absence of delineator posts leads to reduced speed. However, provided that there are delineator posts continuously present along the road, the overall driver speed is basically the same, regardless of the spacing between the delineator posts. The results also imply that to reduce driver speed in curves with small radius, using more compact spacing of posts in these curves as compared to in curves with a larger radius, could be a potential strategy. Additionally, the speed reducing effect of a secondary task was only prevailing where the task was initiated. PMID:25118126

  9. Canonical Decomposition of Ictal Scalp EEG and Accurate Source Localisation: Principles and Simulation Study

    PubMed Central

    De Vos, Maarten; De Lathauwer, Lieven; Vanrumste, Bart; Van Huffel, Sabine; Van Paesschen, W.

    2007-01-01

    Long-term electroencephalographic (EEG) recordings are important in the presurgical evaluation of refractory partial epilepsy for the delineation of the ictal onset zones. In this paper, we introduce a new concept for an automatic, fast, and objective localisation of the ictal onset zone in ictal EEG recordings. Canonical decomposition of ictal EEG decomposes the EEG in atoms. One or more atoms are related to the seizure activity. A single dipole was then fitted to model the potential distribution of each epileptic atom. In this study, we performed a simulation study in order to estimate the dipole localisation error. Ictal dipole localisation was very accurate, even at low signal-to-noise ratios, was not affected by seizure activity frequency or frequency changes, and was minimally affected by the waveform and depth of the ictal onset zone location. Ictal dipole localisation error using 21 electrodes was around 10.0 mm and improved more than tenfold in the range of 0.5–1.0 mm using 148 channels. In conclusion, our simulation study of canonical decomposition of ictal scalp EEG allowed a robust and accurate localisation of the ictal onset zone. PMID:18301715

  10. Consensus Guidelines and Contouring Atlas for Pelvic Node Delineation in Prostate and Pelvic Node Intensity Modulated Radiation Therapy

    SciTech Connect

    Harris, Victoria A.; Staffurth, John; Naismith, Olivia; Esmail, Alikhan; Gulliford, Sarah; Khoo, Vincent; Lewis, Rebecca; Littler, John; McNair, Helen; Sadoyze, Azmat; Scrase, Christopher; Sohaib, Aslam; Syndikus, Isabel; Zarkar, Anjali; Hall, Emma; Dearnaley, David

    2015-07-15

    Purpose: The purpose of this study was to establish reproducible guidelines for delineating the clinical target volume (CTV) of the pelvic lymph nodes (LN) by combining the freehand Royal Marsden Hospital (RMH) and Radiation Therapy Oncology Group (RTOG) vascular expansion techniques. Methods and Materials: Seven patients with prostate cancer underwent standard planning computed tomography scanning. Four different CTVs (RMH, RTOG, modified RTOG, and Prostate and pelvIs Versus prOsTate Alone treatment for Locally advanced prostate cancer [PIVOTAL] trial) were created for each patient, and 6 different bowel expansion margins (BEM) were created to assess bowel avoidance by the CTV. The resulting CTVs were compared visually and by using Jaccard conformity indices. The volume of overlap between bowel and planning target volume (PTV) was measured to aid selection of an appropriate BEM to enable maximal LN yet minimal normal tissue coverage. Results: In total, 84 nodal contours were evaluated. LN coverage was similar in all groups, with all of the vascular-expansion techniques (RTOG, modified RTOG, and PIVOTAL), resulting in larger CTVs than that of the RMH technique (mean volumes: 287.3 cm{sup 3}, 326.7 cm{sup 3}, 310.3 cm{sup 3}, and 256.7 cm{sup 3}, respectively). Mean volumes of bowel within the modified RTOG PTV were 19.5 cm{sup 3} (with 0 mm BEM), 17.4 cm{sup 3} (1-mm BEM), 10.8 cm{sup 3} (2-mm BEM), 6.9 cm{sup 3} (3-mm BEM), 5.0 cm{sup 3} (4-mm BEM), and 1.4 cm{sup 3} (5-mm BEM) in comparison with an overlap of 9.2 cm{sup 3} seen using the RMH technique. Evaluation of conformity between LN-CTVs from each technique revealed similar volumes and coverage. Conclusions: Vascular expansion techniques result in larger LN-CTVs than the freehand RMH technique. Because the RMH technique is supported by phase 1 and 2 trial safety data, we proposed modifications to the RTOG technique, including the addition of a 3-mm BEM, which resulted in LN-CTV coverage similar

  11. Microsatellite allele sizes alone are insufficient to delineate species boundaries in Symbiodinium.

    PubMed

    Howells, E J; Willis, B L; Bay, L K; van Oppen, M J H

    2016-06-01

    Symbiodinium are a diverse group of unicellular dinoflagellates that are important nutritional symbionts of reef-building corals. Symbiodinium putative species ('types') are commonly identified with genetic markers, mostly nuclear and chloroplast encoded ribosomal DNA regions. Population genetic analyses using microsatellite loci have provided insights into Symbiodinium biogeography, connectivity and phenotypic plasticity, but are complicated by: (i) a lack of consensus criteria used to delineate inter- vs. intragenomic variation within species; and (ii) the high density of Symbiodinium in host tissues, which results in single samples comprising thousands of individuals. To address this problem, Wham & LaJeunesse (2016) present a method for identifying cryptic Symbiodinium species from microsatellite data based on correlations between allele size distributions and nongeographic genetic structure. Multilocus genotypes that potentially do not recombine in sympatry are interpreted as secondary 'species' to be discarded from downstream population genetic analyses. However, Symbiodinium species delineations should ideally incorporate multiple physiological, ecological and molecular criteria. This is because recombination tests may be a poor indicator of species boundaries in Symbiodinium due to their predominantly asexual mode of reproduction. Furthermore, discontinuous microsatellite allele sizes in sympatry may be explained by secondary contact between previously isolated populations and by mutations that occur in a nonstepwise manner. Limitations of using microsatellites alone to delineate species are highlighted in earlier studies that demonstrate occasional bimodal distributions of allele sizes within Symbiodinium species and considerable allele size sharing among Symbiodinium species. We outline these issues and discuss the validity of reinterpretations of our previously published microsatellite data from Symbiodinium populations on the Great Barrier Reef

  12. Inter- and intra-observer variations in the delineation of lesions in mammograms

    NASA Astrophysics Data System (ADS)

    Buelow, Thomas; Heese, Harald S.; Grewer, Ruediger; Kutra, Dominik; Wiemker, Rafael

    2015-03-01

    Many clinical and research tasks require the delineation of lesions in radiological images. There is a variety of methods available for deriving such delineations, ranging from free hand manual contouring and manual positioning of lowparameter graphical objects, to (semi-)automatic computerized segmentation methods. In this paper we investigate the impact of the chosen segmentation method on the inter-observer variability of the resulting contour. Three different methods are compared in this paper, namely (1) manual positioning of an ellipse, (2) an automatic segmentation method, coined live-segmentation, which depends on the current mouse pointer position as input information and is updated in real-time as the user hovers with the mouse over the image and (3) free form segmentation which is realized by allowing the user to pull the result of method (2) to image positions that the contour is required to pass. Each of the three methods was used by three experienced radiologists to delineate a set of 215 round breast lesion images in digital mammograms. Agreement between contours was assessed by computing the Dice coefficient. The median Dice coefficient for the ellipses placed by different readers was 0.85. The intra-reader Dice coefficient comparing ellipses and livesegmentations was 0.84, thus showing that the live-segmentation results agree with ellipse segmentations to the same extent as readers agree on the ellipse placement. Inter-observer agreement when using the live-segmentation was higher than for the ellipses (median Dice = 0.91 vs. 0.85) showing that the live-segmentation is a more reproducible alternative to the ellipse placement.

  13. LNAPL source zone delineation using soil gases in a heterogeneous silty-sand aquifer

    NASA Astrophysics Data System (ADS)

    Cohen, Grégory J. V.; Jousse, Florie; Luze, Nicolas; Höhener, Patrick; Atteia, Olivier

    2016-09-01

    Source delineation of hydrocarbon contaminated sites is of high importance for remediation work. However, traditional methods like soil core extraction and analysis or recent Membrane Interface Probe methods are time consuming and costly. Therefore, the development of an in situ method based on soil gas analysis can be interesting. This includes the direct measurement of volatile organic compounds (VOCs) in soil gas taken from gas probes using a PID (Photo Ionization Detector) and the analysis of other soil gases related to VOC degradation distribution (CH4, O2, CO2) or related to presence of Light Non-Aqueous Phase Liquid (LNAPL) as 222Rn. However, in widespread heterogeneous formations, delineation by gas measurements becomes more challenging. The objective of this study is twofold: (i) to analyse the potential of several in situ gas measurement techniques in comparison to soil coring for LNAPL source delineation at a heterogeneous contaminated site where the techniques might be limited by a low diffusion potential linked to the presence of fine sands and silts, and (ii) to analyse the effect of vertical sediment heterogeneities on the performance of these gas measurement methods. Thus, five types of gases were analysed: VOCs, their three related degradation products O2, CO2 and CH4 and 222Rn. Gas measurements were compared to independent LNAPL analysis by coring. This work was conducted at an old industrial site frequently contaminated by a Diesel-Fuel mixture located in a heterogeneous fine-grained aquifer. Results show that in such heterogeneous media migration of reactive gases like VOCs occurs only across small distances and the VOC concentrations sampled with gas probes are mainly related to local conditions rather than the presence of LNAPL below the gas probe. 222Rn is not well correlated with LNAPL because of sediment heterogeneity. Oxygen, CO2, and especially CH4, have larger lengths of diffusion and give the clearest picture for LNAPL presence at this

  14. Delineation of the Pahute Mesa–Oasis Valley groundwater basin, Nevada

    USGS Publications Warehouse

    Fenelon, Joseph M.; Halford, Keith J.; Moreo, Michael T.

    2016-01-01

    This report delineates the Pahute Mesa–Oasis Valley (PMOV) groundwater basin, where recharge occurs, moves downgradient, and discharges to Oasis Valley, Nevada. About 5,900 acre-feet of water discharges annually from Oasis Valley, an area of springs and seeps near the town of Beatty in southern Nevada. Radionuclides in groundwater beneath Pahute Mesa, an area of historical underground nuclear testing at the Nevada National Security Site, are believed to be migrating toward Oasis Valley. Delineating the boundary of the PMOV groundwater basin is necessary to adequately assess the potential for transport of radionuclides from Pahute Mesa to Oasis Valley.The PMOV contributing area is defined based on regional water-level contours, geologic controls, and knowledge of adjacent flow systems. The viability of this area as the contributing area to Oasis Valley and the absence of significant interbasin flow between the PMOV groundwater basin and adjacent basins are shown regionally and locally. Regional constraints on the location of the contributing area boundary and on the absence of interbasin groundwater flow are shown by balancing groundwater discharges in the PMOV groundwater basin and adjacent basins against available water from precipitation. Internal consistency for the delineated contributing area is shown by matching measured water levels, groundwater discharges, and transmissivities with simulated results from a single-layer, steady-state, groundwater-flow model. An alternative basin boundary extending farther north than the final boundary was rejected based on a poor chloride mass balance and a large imbalance in the northern area between preferred and simulated recharge.

  15. Use of aerial photographs for assessment of soil organic carbon and delineation of agricultural management zones.

    NASA Astrophysics Data System (ADS)

    Bartholomeus, H.; Kooistra, L.

    2012-04-01

    For quantitative estimation of soil properties by means of remote sensing, often hyperspectral data are used. But these data are scarce and expensive, which prohibits wider implementation of the developed techniques in agricultural management. For precision agriculture, observations at a high spatial resolution are required. Colour aerial photographs at this scale are widely available, and can be acquired at no of very low costs. Therefore, we investigated whether publically available aerial photographs can be used to a) automatically delineate management zones and b) estimate levels of organic carbon spatially. We selected three study areas within the Netherlands that cover a large variance in soil type (peat, sand, and clay). For the fields of interest, RGB aerial photographs with a spatial resolution of 50 cm were extracted from a publically available data provider. Further pre-processing exists of geo-referencing only. Since the images originate from different sources and are potentially acquired under unknown illumination conditions, the exact radiometric properties of the data are unknown. Therefore, we used spectral indices to emphasize the differences in reflectance and normalize for differences in radiometry. To delineate management zones we used image segmentation techniques, using the derived indices as input. Comparison with management zone maps as used by the farmers shows that there is good correspondence. Regression analysis between a number of soil properties and the derived indices shows that organic carbon is the major explanatory variable for differences in index values within the fields. However, relations do not hold for large regions, indicating that local models will have to be used, which is a problem that is also still relevant for hyperspectral remote sensing data. With this research, we show that low-cost aerial photographs can be a valuable tool for quantitative analysis of organic carbon and automatic delineation of management zones

  16. Spatial and thematic assessment of object-based forest stand delineation using an OFA-matrix

    NASA Astrophysics Data System (ADS)

    Hernando, A.; Tiede, D.; Albrecht, F.; Lang, S.

    2012-10-01

    The delineation and classification of forest stands is a crucial aspect of forest management. Object-based image analysis (OBIA) can be used to produce detailed maps of forest stands from either orthophotos or very high resolution satellite imagery. However, measures are then required for evaluating and quantifying both the spatial and thematic accuracy of the OBIA output. In this paper we present an approach for delineating forest stands and a new Object Fate Analysis (OFA) matrix for accuracy assessment. A two-level object-based orthophoto analysis was first carried out to delineate stands on the Dehesa Boyal public land in central Spain (Avila Province). Two structural features were first created for use in class modelling, enabling good differentiation between stands: a relational tree cover cluster feature, and an arithmetic ratio shadow/tree feature. We then extended the OFA comparison approach with an OFA-matrix to enable concurrent validation of thematic and spatial accuracies. Its diagonal shows the proportion of spatial and thematic coincidence between a reference data and the corresponding classification. New parameters for Spatial Thematic Loyalty (STL), Spatial Thematic Loyalty Overall (STLOVERALL) and Maximal Interfering Object (MIO) are introduced to summarise the OFA-matrix accuracy assessment. A stands map generated by OBIA (classification data) was compared with a map of the same area produced from photo interpretation and field data (reference data). In our example the OFA-matrix results indicate good spatial and thematic accuracies (>65%) for all stand classes except for the shrub stands (31.8%), and a good STLOVERALL (69.8%). The OFA-matrix has therefore been shown to be a valid tool for OBIA accuracy assessment.

  17. Accuracy Assessment of Crown Delineation Methods for the Individual Trees Using LIDAR Data

    NASA Astrophysics Data System (ADS)

    Chang, K. T.; Lin, C.; Lin, Y. C.; Liu, J. K.

    2016-06-01

    Forest canopy density and height are used as variables in a number of environmental applications, including the estimation of biomass, forest extent and condition, and biodiversity. The airborne Light Detection and Ranging (LiDAR) is very useful to estimate forest canopy parameters according to the generated canopy height models (CHMs). The purpose of this work is to introduce an algorithm to delineate crown parameters, e.g. tree height and crown radii based on the generated rasterized CHMs. And accuracy assessment for the extraction of volumetric parameters of a single tree is also performed via manual measurement using corresponding aerial photo pairs. A LiDAR dataset of a golf course acquired by Leica ALS70-HP is used in this study. Two algorithms, i.e. a traditional one with the subtraction of a digital elevation model (DEM) from a digital surface model (DSM), and a pit-free approach are conducted to generate the CHMs firstly. Then two algorithms, a multilevel morphological active-contour (MMAC) and a variable window filter (VWF), are implemented and used in this study for individual tree delineation. Finally, experimental results of two automatic estimation methods for individual trees can be evaluated with manually measured stand-level parameters, i.e. tree height and crown diameter. The resulting CHM generated by a simple subtraction is full of empty pixels (called "pits") that will give vital impact on subsequent analysis for individual tree delineation. The experimental results indicated that if more individual trees can be extracted, tree crown shape will became more completely in the CHM data after the pit-free process.

  18. LNAPL source zone delineation using soil gases in a heterogeneous silty-sand aquifer.

    PubMed

    Cohen, Grégory J V; Jousse, Florie; Luze, Nicolas; Höhener, Patrick; Atteia, Olivier

    2016-09-01

    Source delineation of hydrocarbon contaminated sites is of high importance for remediation work. However, traditional methods like soil core extraction and analysis or recent Membrane Interface Probe methods are time consuming and costly. Therefore, the development of an in situ method based on soil gas analysis can be interesting. This includes the direct measurement of volatile organic compounds (VOCs) in soil gas taken from gas probes using a PID (Photo Ionization Detector) and the analysis of other soil gases related to VOC degradation distribution (CH4, O2, CO2) or related to presence of Light Non-Aqueous Phase Liquid (LNAPL) as (222)Rn. However, in widespread heterogeneous formations, delineation by gas measurements becomes more challenging. The objective of this study is twofold: (i) to analyse the potential of several in situ gas measurement techniques in comparison to soil coring for LNAPL source delineation at a heterogeneous contaminated site where the techniques might be limited by a low diffusion potential linked to the presence of fine sands and silts, and (ii) to analyse the effect of vertical sediment heterogeneities on the performance of these gas measurement methods. Thus, five types of gases were analysed: VOCs, their three related degradation products O2, CO2 and CH4 and (222)Rn. Gas measurements were compared to independent LNAPL analysis by coring. This work was conducted at an old industrial site frequently contaminated by a Diesel-Fuel mixture located in a heterogeneous fine-grained aquifer. Results show that in such heterogeneous media migration of reactive gases like VOCs occurs only across small distances and the VOC concentrations sampled with gas probes are mainly related to local conditions rather than the presence of LNAPL below the gas probe. (222)Rn is not well correlated with LNAPL because of sediment heterogeneity. Oxygen, CO2, and especially CH4, have larger lengths of diffusion and give the clearest picture for LNAPL presence at

  19. Reservoir delineation using high resolution seismic data in the South China Sea

    SciTech Connect

    Tsay, D.L.J.

    1996-12-31

    Conventional seismic data with the frequency bandwidth of 10-80 hz has been playing an invaluable role in mapping favorable subsurface structure for initial exploratory drilling. However, in order to characterize the reservoir properties over the discovered field for reservoir delineation, the seismic data must have the frequency components higher than 80 hz. This is particularly true when the desirable reservoir properties to be delineated are the thickness and porosity of several thin layers within the Miocene carbonate reservoir in the South China Sea. In this paper, two methods of enhancing seismic resolution will be discussed and illustrated with the examples of real data taken from the South China Sea. The first method of enhancing seismic resolution is to apply the technique of spectral whitening to the original seismic data. The resulted data shows that the frequency bandwidth is almost doubled from the original 10-80 hz to 10-140 hz. As a result, the thickness of each thin layer within Miocene carbonate reservoir can be resolved at 7m instead of 12m from the original data. The second method is to designed a new field parameter by using a shallower towed depth of seismic energy source at 4m instead of 6m used previously. Because of shallower towed depth, the first notch of source ghost becomes higher and leads to higher resolution of acquired field data with the frequency range of 10-140 hz. Consequently, a thin bed of 7m within carbonate reservoir can be resolved. The success of enhancing seismic resolution has led to better reservoir delineation, drilling operation design and development plan.

  20. Accurate Prediction of Docked Protein Structure Similarity.

    PubMed

    Akbal-Delibas, Bahar; Pomplun, Marc; Haspel, Nurit

    2015-09-01

    One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin. PMID:26335807

  1. Accurate lineshape spectroscopy and the Boltzmann constant

    PubMed Central

    Truong, G.-W.; Anstie, J. D.; May, E. F.; Stace, T. M.; Luiten, A. N.

    2015-01-01

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m. PMID:26465085

  2. How Accurate are SuperCOSMOS Positions?

    NASA Astrophysics Data System (ADS)

    Schaefer, Adam; Hunstead, Richard; Johnston, Helen

    2014-02-01

    Optical positions from the SuperCOSMOS Sky Survey have been compared in detail with accurate radio positions that define the second realisation of the International Celestial Reference Frame (ICRF2). The comparison was limited to the IIIaJ plates from the UK/AAO and Oschin (Palomar) Schmidt telescopes. A total of 1 373 ICRF2 sources was used, with the sample restricted to stellar objects brighter than BJ = 20 and Galactic latitudes |b| > 10°. Position differences showed an rms scatter of 0.16 arcsec in right ascension and declination. While overall systematic offsets were < 0.1 arcsec in each hemisphere, both the systematics and scatter were greater in the north.

  3. Accurate adiabatic correction in the hydrogen molecule

    SciTech Connect

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-14

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  4. Accurate adiabatic correction in the hydrogen molecule

    NASA Astrophysics Data System (ADS)

    Pachucki, Krzysztof; Komasa, Jacek

    2014-12-01

    A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.

  5. MEMS accelerometers in accurate mount positioning systems

    NASA Astrophysics Data System (ADS)

    Mészáros, László; Pál, András.; Jaskó, Attila

    2014-07-01

    In order to attain precise, accurate and stateless positioning of telescope mounts we apply microelectromechanical accelerometer systems (also known as MEMS accelerometers). In common practice, feedback from the mount position is provided by electronic, optical or magneto-mechanical systems or via real-time astrometric solution based on the acquired images. Hence, MEMS-based systems are completely independent from these mechanisms. Our goal is to investigate the advantages and challenges of applying such devices and to reach the sub-arcminute range { that is well smaller than the field-of-view of conventional imaging telescope systems. We present how this sub-arcminute accuracy can be achieved with very cheap MEMS sensors. Basically, these sensors yield raw output within an accuracy of a few degrees. We show what kind of calibration procedures could exploit spherical and cylindrical constraints between accelerometer output channels in order to achieve the previously mentioned accuracy level. We also demonstrate how can our implementation be inserted in a telescope control system. Although this attainable precision is less than both the resolution of telescope mount drive mechanics and the accuracy of astrometric solutions, the independent nature of attitude determination could significantly increase the reliability of autonomous or remotely operated astronomical observations.

  6. Accurate, reliable prototype earth horizon sensor head

    NASA Technical Reports Server (NTRS)

    Schwarz, F.; Cohen, H.

    1973-01-01

    The design and performance is described of an accurate and reliable prototype earth sensor head (ARPESH). The ARPESH employs a detection logic 'locator' concept and horizon sensor mechanization which should lead to high accuracy horizon sensing that is minimally degraded by spatial or temporal variations in sensing attitude from a satellite in orbit around the earth at altitudes in the 500 km environ 1,2. An accuracy of horizon location to within 0.7 km has been predicted, independent of meteorological conditions. This corresponds to an error of 0.015 deg-at 500 km altitude. Laboratory evaluation of the sensor indicates that this accuracy is achieved. First, the basic operating principles of ARPESH are described; next, detailed design and construction data is presented and then performance of the sensor under laboratory conditions in which the sensor is installed in a simulator that permits it to scan over a blackbody source against background representing the earth space interface for various equivalent plant temperatures.

  7. Accurate lineshape spectroscopy and the Boltzmann constant.

    PubMed

    Truong, G-W; Anstie, J D; May, E F; Stace, T M; Luiten, A N

    2015-01-01

    Spectroscopy has an illustrious history delivering serendipitous discoveries and providing a stringent testbed for new physical predictions, including applications from trace materials detection, to understanding the atmospheres of stars and planets, and even constraining cosmological models. Reaching fundamental-noise limits permits optimal extraction of spectroscopic information from an absorption measurement. Here, we demonstrate a quantum-limited spectrometer that delivers high-precision measurements of the absorption lineshape. These measurements yield a very accurate measurement of the excited-state (6P1/2) hyperfine splitting in Cs, and reveals a breakdown in the well-known Voigt spectral profile. We develop a theoretical model that accounts for this breakdown, explaining the observations to within the shot-noise limit. Our model enables us to infer the thermal velocity dispersion of the Cs vapour with an uncertainty of 35 p.p.m. within an hour. This allows us to determine a value for Boltzmann's constant with a precision of 6 p.p.m., and an uncertainty of 71 p.p.m. PMID:26465085

  8. Fast and Accurate Exhaled Breath Ammonia Measurement

    PubMed Central

    Solga, Steven F.; Mudalel, Matthew L.; Spacek, Lisa A.; Risby, Terence H.

    2014-01-01

    This exhaled breath ammonia method uses a fast and highly sensitive spectroscopic method known as quartz enhanced photoacoustic spectroscopy (QEPAS) that uses a quantum cascade based laser. The monitor is coupled to a sampler that measures mouth pressure and carbon dioxide. The system is temperature controlled and specifically designed to address the reactivity of this compound. The sampler provides immediate feedback to the subject and the technician on the quality of the breath effort. Together with the quick response time of the monitor, this system is capable of accurately measuring exhaled breath ammonia representative of deep lung systemic levels. Because the system is easy to use and produces real time results, it has enabled experiments to identify factors that influence measurements. For example, mouth rinse and oral pH reproducibly and significantly affect results and therefore must be controlled. Temperature and mode of breathing are other examples. As our understanding of these factors evolves, error is reduced, and clinical studies become more meaningful. This system is very reliable and individual measurements are inexpensive. The sampler is relatively inexpensive and quite portable, but the monitor is neither. This limits options for some clinical studies and provides rational for future innovations. PMID:24962141

  9. Moving window analysis and riparian boundary delineation on the Northern Plains of Kruger National Park, South Africa

    NASA Astrophysics Data System (ADS)

    Kröger, Robert; Khomo, Lesego M.; Levick, Shaun; Rogers, Kevin H.

    2009-09-01

    Landscapes commonly comprise of mosaics, patches and boundaries. Riparian boundaries are complex to delineate and characterize, with a multitude of variables available for delineation. Multiple methods exist for boundary delineation such as two-dimensional wombling, constrained classification techniques and discontinuity detection. One method that has proven to be reliable in boundary delineation with one-dimensional transect data is the moving split window (MSW) analysis. This study demonstrates the efficacy of MSW to delineate grass species turnover and environmental boundaries across two geologically dissimilar riparian zones in the Kruger National Park, South Africa. There are few studies that have delineated riparian boundaries of Kruger National Park, and none that have used the MSW analysis. MSW detects significant changes in dissimilarity indices of variables along gradients. Significant shifts in dissimilarity designate boundaries at various spatial scales dictated by window sizes. Significant boundaries emerge by altering window sizes, increasing quadrat width and removing infrequent herbaceous species. By utilizing these three methods, MSW background variance was reduced and riparian and wetland/upland boundaries were sharper and more easily defined.

  10. Dosimetric Consequences of Interobserver Variability in Delineating the Organs at Risk in Gynecologic Interstitial Brachytherapy

    SciTech Connect

    Damato, Antonio L.; Bair, Ryan J.; Cormack, Robert A.; Kovacs, Arpad; Lee, Larissa J.; Lewis, John H.; Viswanathan, Akila N.

    2014-07-01

    Purpose: To investigate the dosimetric variability associated with interobserver organ-at-risk delineation differences on computed tomography in patients undergoing gynecologic interstitial brachytherapy. Methods and Materials: The rectum, bladder, and sigmoid of 14 patients treated with gynecologic interstitial brachytherapy were retrospectively contoured by 13 physicians. Geometric variability was calculated using κ statistics, conformity index (CI{sub gen}), and coefficient of variation (CV) of volumes contoured across physicians. Dosimetric variability of the single-fraction D{sub 0.1cc} and D{sub 2cc} was assessed through CV across physicians, and the standard deviation of the total EQD2 (equivalent dose in 2 Gy per fraction) brachytherapy dose (SD{sup TOT}) was calculated. Results: The population mean ± 1 standard deviation of κ, CI{sub gen}, and volume CV were, respectively: 0.77 ± 0.06, 0.70 ± 0.08, and 20% ± 6% for bladder; 0.74 ± 06, 0.67 ± 0.08, and 20% ± 5% for rectum; and 0.33 ± 0.20, 0.26 ± 0.17, and 82% ± 42% for sigmoid. Dosimetric variability was as follows: for bladder, CV = 31% ± 19% (SD{sup TOT} = 72 ± 64 Gy) for D{sub 0.1cc} and CV = 16% ± 10% (SD{sup TOT} = 9 ± 6 Gy) for D{sub 2cc}; for rectum, CV = 11% ± 5% (SD{sup TOT} = 16 ± 17 Gy) for D{sub 0.1cc} and CV = 7% ± 2% (SD{sup TOT} = 4 ± 3 Gy) for D{sub 2cc}; for sigmoid, CV = 39% ± 28% (SD{sup TOT} = 12 ± 18 Gy) for D{sub 0.1cc} and CV = 34% ± 19% (SD{sup TOT} = 4 ± 4 Gy) for D{sub 2cc.} Conclusions: Delineation of bladder and rectum by 13 physicians demonstrated substantial geometric agreement and resulted in good dosimetric agreement for all dose-volume histogram parameters except bladder D{sub 0.1cc.} Small delineation differences in high-dose regions by the posterior bladder wall may explain these results. The delineation of sigmoid showed fair geometric agreement. The higher dosimetric variability for sigmoid compared with rectum and bladder did not correlate with

  11. Delineation of Flood Prone Areas using Digital Elevation Models: Scale Dependence

    NASA Astrophysics Data System (ADS)

    di Leo, M.; Manfreda, S.; Sole, A.; Fiorentino, M.

    2009-04-01

    The delineation of the areas subject to flood inundations raises complex problems regarding the definition of hydrological forcing and the parametrization of models for flood wave propagation (e.g., Horritt & Bates, 2000, 2002). The increasing availability of new technologies for the measurement of surface elevation (eg GPS, SAR interferometry, radar and laser altimetry) led to an increase in the attraction of DEM-based procedures for the delineation of floodplains. In recent years, much effort has gone into the identification of flood prone areas through the use of hydrological and hydraulic studies carried out by River Basin Authorities (public institutions dedicated to river basins management). These studies are generally based on topographic surveys and numerical modelling for the flood wave propagation providing an enormous database rarely used for post processing. Manfreda et al. (2006) have recently used the technical documentation, produced during the definition of Hydrogeological Management Plan by the River Basin Authorities, to define a synthetic procedure for the delineation of flood inundation exposure. The relevance of such techniques lies in the ability to characterize, at least at first approximation, portions of the territory where is not possible to run expensive hydrological-hydraulic simulations. The development of simplified methodologies is taken further in the present study to investigate the relationship between areas exposed to flood inundation and the geomorphologic characteristics of the terrain (contributing area, local slope of the surface, curvature, TOPMODEL topographic index) showing a strong correlation with the TOPMODEL topographic index. Manfreda et al. (2006) also defined a new expression of the topographical index more suited to the task of delineating flood exposure directly from a DEM analysis. This permitted the definition of a fast procedure for the calculation of flood inundation areas using a threshold level (ITms) to

  12. 2D NMR Methods for Structural Delineation of Copper(II) Complexes of Penicillin and Pilocarpine

    PubMed Central

    Gaggelli, Elena; Gaggelli, Nicola

    1994-01-01

    A method was developed for delineating the structure of paramagnetic metal complexes. The selective disappearance of cross-peaks in proton-carbon shift correlated 2D NMR maps was shown to uniquely depend upon the scalar and/or dipolar interaction between ligand nuclei and the unpaired electron(s), thus providing a means of identifying binding sites. Copper(II) was shown to form metal complexes with both Penicillin (PNC) and Pilocarpine (PLC) and the structure of the two 1:2 complexes in water solution at physiological pH were determined. PMID:18476239

  13. Wetland indicators. A guide to wetland identification, delineation, classification, and mapping

    SciTech Connect

    Tiner, R.W.

    1999-07-01

    Understand the current concept of wetland and methods for identifying, describing, classifying, and delineating wetlands with ``Wetland Indicators'' capturing the current state of science's role in wetland recognition and mapping. Environmental scientists and others involved with wetland regulations can strengthen their knowledge about wetlands, and the use of various indicators, to support their decisions on difficult wetland determinations. professor Tiner primarily focuses on plants, soils, and other signs of wetland hydrology in the soil, or on the surface of wetlands in his discussion of the book.

  14. Automated volume of interest delineation and rendering of cone beam CT images in interventional cardiology

    NASA Astrophysics Data System (ADS)

    Lorenz, Cristian; Schäfer, Dirk; Eshuis, Peter; Carroll, John; Grass, Michael

    2012-02-01

    Interventional C-arm systems allow the efficient acquisition of 3D cone beam CT images. They can be used for intervention planning, navigation, and outcome assessment. We present a fast and completely automated volume of interest (VOI) delineation for cardiac interventions, covering the whole visceral cavity including mediastinum and lungs but leaving out rib-cage and spine. The problem is addressed in a model based approach. The procedure has been evaluated on 22 patient cases and achieves an average surface error below 2mm. The method is able to cope with varying image intensities, varying truncations due to the limited reconstruction volume, and partially with heavy metal and motion artifacts.

  15. Delineation of major geologic structures in Turkey using SIR-B data

    NASA Technical Reports Server (NTRS)

    Toksoz, M. N.; Pettengill, G. H.; Ford, P.; Gulen, L.

    1984-01-01

    Shuttle Imaging Radar-B (SIR-B) images of well mapped segments of major faults, such as the North Anatolian Fault (NAF) and East Anatolian Fault (EAF) will be studied to identify the prominent signatures that characterize the fault zones for those specific regions. The information will be used to delineate the unmapped fault zones in areas with similar geological and geomorphological properties. The data obtained from SIR-B images will be compared and correlated with the LANDSAT thematic mapper and seismicity alignments based on well constrained earthquake epicenters.

  16. Magnifying endoscopy with narrow-band imaging is more accurate for determination of horizontal extent of early gastric cancers than chromoendoscopy

    PubMed Central

    Asada-Hirayama, Itsuko; Kodashima, Shinya; Sakaguchi, Yoshiki; Ono, Satoshi; Niimi, Keiko; Mochizuki, Satoshi; Tsuji, Yosuke; Minatsuki, Chihiro; Shichijo, Satoki; Matsuzaka, Keisuke; Ushiku, Tetsuo; Fukayama, Masashi; Yamamichi, Nobutake; Fujishiro, Mitsuhiro; Koike, Kazuhiko

    2016-01-01

    Background and study aims: Although magnifying endoscopy with narrow-band imaging (ME-NBI) is reported to be useful for delineating the horizontal extent of early gastric cancers (EGCs), there are few reports which have objectively demonstrated the superiority of ME-NBI over chromoendoscopy with indigo carmine for this purpose. We conducted an exploratory comparison of the diagnostic accuracy of both modalities for the delineation of EGCs using prospectively collected data, and clarified the clinicopathological features related to inaccurate evaluation of the horizontal extent of EGCs. Patients and methods: EGCs were assigned to the oral narrow-band imaging (O-NBI) group or the oral chromoendoscopy (O-CE) group before endoscopic submucosal dissection (ESD). The oral border was observed according to assignment, and the anal border with the other modality. The horizontal extent of the tumor was evaluated by each modality and a marking dot was placed on the visible delineation line. After ESD, the marking dots were identified pathologically and defined as “accurate evaluation” if they were located within 1 mm of the pathological tumor border. We compared the rate of accurate evaluation of ME-NBI and chromoendoscopy, and analyzed the clinicopathological features related to inaccurate evaluation. Results: A total of 113 marking dots evaluated by ME-NBI and 116 evaluated by chromoendoscopy were analyzed. The rate of accurate evaluation by ME-NBI was significantly higher than that by chromoendoscopy (89.4 % vs 75.9 %, P = 0.0071). The EGCs with flat borders and large EGCs were significantly related to inaccurate evaluation using ME-NBI. There were no significant factors related to inaccurate evaluation with chromoendoscopy. Conclusions: The accurate evaluation rate of the horizontal extent of EGCs by ME-NBI is significantly higher than that by chromoendoscopy. Study registration: UMIN000007641 PMID:27556080

  17. Motor equivalence during multi-finger accurate force production

    PubMed Central

    Mattos, Daniela; Schöner, Gregor; Zatsiorsky, Vladimir M.; Latash, Mark L.

    2014-01-01

    We explored stability of multi-finger cyclical accurate force production action by analysis of responses to small perturbations applied to one of the fingers and inter-cycle analysis of variance. Healthy subjects performed two versions of the cyclical task, with and without an explicit target. The “inverse piano” apparatus was use