Discriminative structural approaches for enzyme active-site prediction.

PubMed

Kato, Tsuyoshi; Nagano, Nozomi

2011-02-15

Predicting enzyme active-sites in proteins is an important issue not only for protein sciences but also for a variety of practical applications such as drug design. Because enzyme reaction mechanisms are based on the local structures of enzyme active-sites, various template-based methods that compare local structures in proteins have been developed to date. In comparing such local sites, a simple measurement, RMSD, has been used so far. This paper introduces new machine learning algorithms that refine the similarity/deviation for comparison of local structures. The similarity/deviation is applied to two types of applications, single template analysis and multiple template analysis. In the single template analysis, a single template is used as a query to search proteins for active sites, whereas a protein structure is examined as a query to discover the possible active-sites using a set of templates in the multiple template analysis. This paper experimentally illustrates that the machine learning algorithms effectively improve the similarity/deviation measurements for both the analyses.

Robust patella motion tracking using intensity-based 2D-3D registration on dynamic bi-plane fluoroscopy: towards quantitative assessment in MPFL reconstruction surgery

NASA Astrophysics Data System (ADS)

Otake, Yoshito; Esnault, Matthieu; Grupp, Robert; Kosugi, Shinichi; Sato, Yoshinobu

2016-03-01

The determination of in vivo motion of multiple-bones using dynamic fluoroscopic images and computed tomography (CT) is useful for post-operative assessment of orthopaedic surgeries such as medial patellofemoral ligament reconstruction. We propose a robust method to measure the 3D motion of multiple rigid objects with high accuracy using a series of bi-plane fluoroscopic images and a multi-resolution, intensity-based, 2D-3D registration. A Covariance Matrix Adaptation Evolution Strategy (CMA-ES) optimizer was used with a gradient correlation similarity metric. Four approaches to register three rigid objects (femur, tibia-fibula and patella) were implemented: 1) an individual bone approach registering one bone at a time, each with optimization of a six degrees of freedom (6DOF) parameter, 2) a sequential approach registering one bone at a time but using the previous bone results as the background in DRR generation, 3) a simultaneous approach registering all the bones together (18DOF) and 4) a combination of the sequential and the simultaneous approaches. These approaches were compared in experiments using simulated images generated from the CT of a healthy volunteer and measured fluoroscopic images. Over the 120 simulated frames of motion, the simultaneous approach showed improved registration accuracy compared to the individual approach: with less than 0.68mm root-mean-square error (RMSE) for translation and less than 1.12° RMSE for rotation. A robustness evaluation was conducted with 45 trials of a randomly perturbed initialization showed that the sequential approach improved robustness significantly (74% success rate) compared to the individual bone approach (34% success) for patella registration (femur and tibia-fibula registration had a 100% success rate with each approach).

Intraoperative fluoroscopic evaluation of screw placement during pelvic and acetabular surgery.

PubMed

Yi, Chengla; Burns, Sean; Hak, David J

2014-01-01

The surgical treatment of pelvic and acetabular fractures can be technically challenging. Various techniques are available for the reconstruction of pelvic and acetabular fractures. Less invasive percutaneous fracture stabilization techniques, with closed reduction or limited open reduction, have been developed and are gaining popularity in the management of pelvic and acetabular fractures. These techniques require knowledge and interpretation of various fluoroscopic images to ensure appropriate and safe screw placement. Given the anatomic complexity of the intrapelvic structures and the 2-dimensional nature of standard fluoroscopy, multiple images oriented in different planes are needed to assess the accuracy of guide wire and screw placement. This article reviews the fluoroscopic imaging of common screw orientations during pelvic and acetabular surgery.

3D fluoroscopic image estimation using patient-specific 4DCBCT-based motion models

PubMed Central

Dhou, Salam; Hurwitz, Martina; Mishra, Pankaj; Cai, Weixing; Rottmann, Joerg; Li, Ruijiang; Williams, Christopher; Wagar, Matthew; Berbeco, Ross; Ionascu, Dan; Lewis, John H.

2015-01-01

3D fluoroscopic images represent volumetric patient anatomy during treatment with high spatial and temporal resolution. 3D fluoroscopic images estimated using motion models built using 4DCT images, taken days or weeks prior to treatment, do not reliably represent patient anatomy during treatment. In this study we develop and perform initial evaluation of techniques to develop patient-specific motion models from 4D cone-beam CT (4DCBCT) images, taken immediately before treatment, and use these models to estimate 3D fluoroscopic images based on 2D kV projections captured during treatment. We evaluate the accuracy of 3D fluoroscopic images by comparing to ground truth digital and physical phantom images. The performance of 4DCBCT- and 4DCT- based motion models are compared in simulated clinical situations representing tumor baseline shift or initial patient positioning errors. The results of this study demonstrate the ability for 4DCBCT imaging to generate motion models that can account for changes that cannot be accounted for with 4DCT-based motion models. When simulating tumor baseline shift and patient positioning errors of up to 5 mm, the average tumor localization error and the 95th percentile error in six datasets were 1.20 and 2.2 mm, respectively, for 4DCBCT-based motion models. 4DCT-based motion models applied to the same six datasets resulted in average tumor localization error and the 95th percentile error of 4.18 and 5.4 mm, respectively. Analysis of voxel-wise intensity differences was also conducted for all experiments. In summary, this study demonstrates the feasibility of 4DCBCT-based 3D fluoroscopic image generation in digital and physical phantoms, and shows the potential advantage of 4DCBCT-based 3D fluoroscopic image estimation when there are changes in anatomy between the time of 4DCT imaging and the time of treatment delivery. PMID:25905722

Designing Templates for Interactive Tasks in CALL Tutorials.

ERIC Educational Resources Information Center

Ruhlmann, Felicitas

The development of templates for computer-assisted language learning (CALL) is discussed, based on experiences with primarily linear multimedia tutorial programs. Design of templates for multiple-choice questions and interactive tasks in a prototype module is described. Possibilities of enhancing interactivity by introducing problem-oriented…

Development of a High Angular Resolution Diffusion Imaging Human Brain Template

PubMed Central

Varentsova, Anna; Zhang, Shengwei; Arfanakis, Konstantinos

2014-01-01

Brain diffusion templates contain rich information about the microstructure of the brain, and are used as references in spatial normalization or in the development of brain atlases. The accuracy of diffusion templates constructed based on the diffusion tensor (DT) model is limited in regions with complex neuronal micro-architecture. High angular resolution diffusion imaging (HARDI) overcomes limitations of the DT model and is capable of resolving intravoxel heterogeneity. However, when HARDI is combined with multiple-shot sequences to minimize image artifacts, the scan time becomes inappropriate for human brain imaging. In this work, an artifact-free HARDI template of the human brain was developed from low angular resolution multiple-shot diffusion data. The resulting HARDI template was produced in ICBM-152 space based on Turboprop diffusion data, was shown to resolve complex neuronal micro-architecture in regions with intravoxel heterogeneity, and contained fiber orientation information consistent with known human brain anatomy. PMID:24440528

Fluoroscopically Guided Diagnostic and Therapeutic Intra-Articular Sacroiliac Joint Injections: A Systematic Review.

PubMed

Kennedy, David J; Engel, Andrew; Kreiner, D Scott; Nampiaparampil, Devi; Duszynski, Belinda; MacVicar, John

2015-08-01

To assess the validity of fluoroscopically guided diagnostic intra-articular injections of local anesthetic and effectiveness of intra-articular steroid injections in treating sacroiliac joint (SIJ) pain. Systematic review. Ten reviewers independently assessed 45 publications on diagnostic validity or effectiveness of fluoroscopically guided intra-articular SIJ injections. For diagnostic injections, the primary outcome was validity; for therapeutic injections, analgesia. Secondary outcomes were also described. Of 45 articles reviewed, 39 yielded diagnostic data on physical exam findings, provocation tests, and SIJ injections for diagnosing SIJ pain, and 15 addressed therapeutic effectiveness. When confirmed by comparative local anesthetic blocks with a high degree of pain relief, no single physical exam maneuver predicts response to diagnostic injections. When at least three physical exam findings are present, sensitivity, and specificity increases significantly. The prevalence of SIJ pain is likely 20-30% among patients that have suspected SIJ pain based on history and physical examination. This estimate may be higher in certain subgroups such as the elderly and fusion patients. Two randomized controlled trials and multiple observational studies supported the effectiveness of therapeutic sacroiliac joint injections. Based on this literature, it is unclear whether image-guided intra-articular diagnostic injections of local anesthetic predict positive responses to therapeutic agents. The overall quality of evidence is moderate for the effectiveness of therapeutic SIJ injections. Wiley Periodicals, Inc.

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling.

PubMed

Meier, Armin; Söding, Johannes

2015-10-01

Homology modeling predicts the 3D structure of a query protein based on the sequence alignment with one or more template proteins of known structure. Its great importance for biological research is owed to its speed, simplicity, reliability and wide applicability, covering more than half of the residues in protein sequence space. Although multiple templates have been shown to generally increase model quality over single templates, the information from multiple templates has so far been combined using empirically motivated, heuristic approaches. We present here a rigorous statistical framework for multi-template homology modeling. First, we find that the query proteins' atomic distance restraints can be accurately described by two-component Gaussian mixtures. This insight allowed us to apply the standard laws of probability theory to combine restraints from multiple templates. Second, we derive theoretically optimal weights to correct for the redundancy among related templates. Third, a heuristic template selection strategy is proposed. We improve the average GDT-ha model quality score by 11% over single template modeling and by 6.5% over a conventional multi-template approach on a set of 1000 query proteins. Robustness with respect to wrong constraints is likewise improved. We have integrated our multi-template modeling approach with the popular MODELLER homology modeling software in our free HHpred server http://toolkit.tuebingen.mpg.de/hhpred and also offer open source software for running MODELLER with the new restraints at https://bitbucket.org/soedinglab/hh-suite.

SU-E-J-108: Template Matching Based On Multiple Templates Can Improve the Tumor Tracking Performance When There Is Large Tumor Deformation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, X; Lin, J; Diwanji, T

2014-06-01

Purpose: Recently, template matching has been shown to be able to track tumor motion on cine-MRI images. However, artifacts such as deformation, rotation, and/or out-of-plane movement could seriously degrade the performance of this technique. In this work, we demonstrate the utility of multiple templates derived from different phases of tumor motion in reducing the negative effects of artifacts and improving the accuracy of template matching methods. Methods: Data from 2 patients with large tumors and significant tumor deformation were analyzed from a group of 12 patients from an earlier study. Cine-MRI (200 frames) imaging was performed while the patients weremore » instructed to breathe normally. Ground truth tumor position was established on each frame manually by a radiation oncologist. Tumor positions were also automatically determined using template matching with either single or multiple (5) templates. The tracking errors, defined as the absolute differences in tumor positions determined by the manual and automated methods, when using either single or multiple templates were compared in both the AP and SI directions, respectively. Results: Using multiple templates reduced the tracking error of template matching. In the SI direction where the tumor movement and deformation were significant, the mean tracking error decreased from 1.94 mm to 0.91 mm (Patient 1) and from 6.61 mm to 2.06 mm (Patient 2). In the AP direction where the tumor movement was small, the reduction of the mean tracking error was significant in Patient 1 (from 3.36 mm to 1.04 mm), but not in Patient 2 ( from 3.86 mm to 3.80 mm). Conclusion: This study shows the effectiveness of using multiple templates in improving the performance of template matching when artifacts like large tumor deformation or out-of-plane motion exists. Accurate tumor tracking capabilities can be integrated with MRI guided radiation therapy systems. This work was supported in part by grants from NIH/NCI CA 124766 and Varian Medical Systems, Palo Alto, CA.« less

Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

PubMed

Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan

2011-07-01

We present a comparative account on 3D-structures of human type-1 receptor (AT1) for angiotensin II (AngII), modeled using three different methodologies. AngII activates a wide spectrum of signaling responses via the AT1 receptor that mediates physiological control of blood pressure and diverse pathological actions in cardiovascular, renal, and other cell types. Availability of 3D-model of AT1 receptor would significantly enhance the development of new drugs for cardiovascular diseases. However, templates of AT1 receptor with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies in order to use the models for sensitive applications such as rational drug design. Three models were generated for AT1 receptor by, (1) homology modeling with bovine rhodopsin as template, (2) homology modeling with multiple templates and (3) threading using I-TASSER web server. Molecular dynamics (MD) simulation (15 ns) of models in explicit membrane-water system, Ramachandran plot analysis and molecular docking with antagonists led to the conclusion that multiple template-based homology modeling outweighs other methodologies for AT1 modeling.

Fan fault diagnosis based on symmetrized dot pattern analysis and image matching

NASA Astrophysics Data System (ADS)

Xu, Xiaogang; Liu, Haixiao; Zhu, Hao; Wang, Songling

2016-07-01

To detect the mechanical failure of fans, a new diagnostic method based on the symmetrized dot pattern (SDP) analysis and image matching is proposed. Vibration signals of 13 kinds of running states are acquired on a centrifugal fan test bed and reconstructed by the SDP technique. The SDP pattern templates of each running state are established. An image matching method is performed to diagnose the fault. In order to improve the diagnostic accuracy, the single template, multiple templates and clustering fault templates are used to perform the image matching.

Development of a high angular resolution diffusion imaging human brain template.

PubMed

Varentsova, Anna; Zhang, Shengwei; Arfanakis, Konstantinos

2014-05-01

Brain diffusion templates contain rich information about the microstructure of the brain, and are used as references in spatial normalization or in the development of brain atlases. The accuracy of diffusion templates constructed based on the diffusion tensor (DT) model is limited in regions with complex neuronal micro-architecture. High angular resolution diffusion imaging (HARDI) overcomes limitations of the DT model and is capable of resolving intravoxel heterogeneity. However, when HARDI is combined with multiple-shot sequences to minimize image artifacts, the scan time becomes inappropriate for human brain imaging. In this work, an artifact-free HARDI template of the human brain was developed from low angular resolution multiple-shot diffusion data. The resulting HARDI template was produced in ICBM-152 space based on Turboprop diffusion data, was shown to resolve complex neuronal micro-architecture in regions with intravoxel heterogeneity, and contained fiber orientation information consistent with known human brain anatomy. Copyright © 2014 Elsevier Inc. All rights reserved.

First experience with zero-fluoroscopic ablation for supraventricular tachycardias using a novel impedance and magnetic-field-based mapping system.

PubMed

Walsh, Katie A; Galvin, Joseph; Keaney, John; Keelan, Edward; Szeplaki, Gabor

2018-02-23

Zero- and near-zero-fluoroscopic ablation techniques reduce the harmful effects of ionizing radiation during invasive electrophysiology procedures. We aimed to test the feasibility and safety of a zero-fluoroscopic strategy using a novel integrated magnetic and impedance-based electroanatomical mapping system for radiofrequency ablation (RFA) of supraventricular tachycardias (SVTs). We retrospectively studied 92 consecutive patients undergoing electrophysiology studies with/without RFA for supraventricular tachycardia (SVT) performed by a single operator at a single center. The first 42 (Group 1) underwent a conventional fluoroscopic-guided approach and the second 50 (Group 2) underwent a zero-fluoroscopic approach using the Ensite Precision ™ 3-D magnetic and impedance-based mapping system (Abbott Inc). Group 1 comprised 14 AV-nodal re-entrant tachycardia (AVNRT), 12 typical atrial flutter, 4 accessory pathway (AP), 2 atrial tachycardia (AT), and 9 diagnostic EP studies (EPS). Group 2 comprised 16 AVNRT, 17 atrial flutter, 6 AP, 3 AT, 2 AV-nodal ablations, and 7 EPS. A complete zero-fluoroscopic approach was achieved in 94% of Group 2 patients. All procedures were acutely successful, and no complications occurred. There was a significant reduction in fluoroscopy dose, dose area product, and time (p < 0.0001, for all), with no difference in procedure times. Ablation time for typical atrial flutter was shorter in Group 2 (p = 0.006). A zero-fluoroscopic strategy for diagnosis and treatment of SVTs using this novel 3D-electroanatomical mapping system is feasible in majority of patients, is safe, reduces ionizing radiation exposure, and does not compromise procedural times, success rates, or complication rates.

The role of the geophysical template and environmental regimes in controlling stream-living trout populations

Treesearch

Brooke E. Penaluna; Steve F. Railsback; Jason B. Dunham; Sherri Johnson; Robert E. Bilby; Arne E. Skaugset; Michael Bradford

2015-01-01

The importance of multiple processes and instream factors to aquatic biota has been explored extensively, but questions remain about how local spatiotemporal variability of aquatic biota is tied to environmental regimes and the geophysical template of streams. We used an individual-based trout model to explore the relative role of the geophysical template versus...

Memory-Based Attention Capture when Multiple Items Are Maintained in Visual Working Memory

PubMed Central

Hollingworth, Andrew; Beck, Valerie M.

2016-01-01

Efficient visual search requires that attention is guided strategically to relevant objects, and most theories of visual search implement this function by means of a target template maintained in visual working memory (VWM). However, there is currently debate over the architecture of VWM-based attentional guidance. We contrasted a single-item-template hypothesis with a multiple-item-template hypothesis, which differ in their claims about structural limits on the interaction between VWM representations and perceptual selection. Recent evidence from van Moorselaar, Theeuwes, and Olivers (2014) indicated that memory-based capture during search—an index of VWM guidance—is not observed when memory set size is increased beyond a single item, suggesting that multiple items in VWM do not guide attention. In the present study, we maximized the overlap between multiple colors held in VWM and the colors of distractors in a search array. Reliable capture was observed when two colors were held in VWM and both colors were present as distractors, using both the original van Moorselaar et al. singleton-shape search task and a search task that required focal attention to array elements (gap location in outline square stimuli). In the latter task, memory-based capture was consistent with the simultaneous guidance of attention by multiple VWM representations. PMID:27123681

SU-C-209-02: 3D Fluoroscopic Image Generation From Patient-Specific 4DCBCT-Based Motion Models Derived From Clinical Patient Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhou, S; Cai, W; Hurwitz, M

Purpose: We develop a method to generate time varying volumetric images (3D fluoroscopic images) using patient-specific motion models derived from four-dimensional cone-beam CT (4DCBCT). Methods: Motion models are derived by selecting one 4DCBCT phase as a reference image, and registering the remaining images to it. Principal component analysis (PCA) is performed on the resultant displacement vector fields (DVFs) to create a reduced set of PCA eigenvectors that capture the majority of respiratory motion. 3D fluoroscopic images are generated by optimizing the weights of the PCA eigenvectors iteratively through comparison of measured cone-beam projections and simulated projections generated from the motionmore » model. This method was applied to images from five lung-cancer patients. The spatial accuracy of this method is evaluated by comparing landmark positions in the 3D fluoroscopic images to manually defined ground truth positions in the patient cone-beam projections. Results: 4DCBCT motion models were shown to accurately generate 3D fluoroscopic images when the patient cone-beam projections contained clearly visible structures moving with respiration (e.g., the diaphragm). When no moving anatomical structure was clearly visible in the projections, the 3D fluoroscopic images generated did not capture breathing deformations, and reverted to the reference image. For the subset of 3D fluoroscopic images generated from projections with visibly moving anatomy, the average tumor localization error and the 95th percentile were 1.6 mm and 3.1 mm respectively. Conclusion: This study showed that 4DCBCT-based 3D fluoroscopic images can accurately capture respiratory deformations in a patient dataset, so long as the cone-beam projections used contain visible structures that move with respiration. For clinical implementation of 3D fluoroscopic imaging for treatment verification, an imaging field of view (FOV) that contains visible structures moving with respiration should be selected. If no other appropriate structures are visible, the images should include the diaphragm. This project was supported, in part, through a Master Research Agreement with Varian Medical Systems, Inc, Palo Alto, CA.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pettersson, N; Murphy, J; Simpson, D

Purpose: The use of respiratory gating for management of breathing motion during stereotactic body radiation therapy (SBRT) relies on a consistent relationship between the breathing signal and the actual position of the internal target. This relationship was investigated in patients treated for pancreatic cancer. Methods: Four patients with pancreatic cancer undergoing SBRT that had implanted fiducials in the tumor were included in this study. Treatment plans were generated based on the exhale phases (30–70%) from the pre-treatment 4DCT. The margin between the internal target volume (ITV) and the planning target volume was three mm. After patient setup using cone-beam CT,more » simultaneous fluoroscopic imaging and breathing motion monitoring were used during at least three breathing cycles to verify the fiducial position and to optimize the gating window. After treatment, fluoroscopic images were acquired for verification purposes and exported for retrospective analyses. Fiducial positions were determined using a template-matching algorithm. For each dataset, we established a linear relationship between the fiducial position and the anterior-posterior (AP) breathing signal. The relationships before and after treatment were compared and the dose distribution impact evaluated. Results: Seven pre- and post-treatment fluoroscopic pairs were available for fiducial position analyses in the superior-inferior (SI) and left-right (LR) directions, and five in the AP direction. Time between image acquisitions was typically six to eight minutes. An average absolute change of 1.2±0.7 mm (range: 0.1–1.7) of the SI fiducial position relative to the external signal was found. Corresponding numbers for the LR and AP fiducial positions were 0.9±1.0 mm (range: 0.2–3.0) and 0.5±0.4 mm (range: 0.2–1.2), respectively. The dose distribution impact was small in both the ITV and organs-at-risk. Conclusion: The relationship change between fiducial position and external breathing signal has been observed to be about 1 mm in four pancreas SBRT patients, leading to small dose distribution impact. Pettersson and Cervino are funded by a Varian Medical Systems grant.« less

TU-D-209-03: Alignment of the Patient Graphic Model Using Fluoroscopic Images for Skin Dose Mapping

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oines, A; Oines, A; Kilian-Meneghin, J

2016-06-15

Purpose: The Dose Tracking System (DTS) was developed to provide realtime feedback of skin dose and dose rate during interventional fluoroscopic procedures. A color map on a 3D graphic of the patient represents the cumulative dose distribution on the skin. Automated image correlation algorithms are described which use the fluoroscopic procedure images to align and scale the patient graphic for more accurate dose mapping. Methods: Currently, the DTS employs manual patient graphic selection and alignment. To improve the accuracy of dose mapping and automate the software, various methods are explored to extract information about the beam location and patient morphologymore » from the procedure images. To match patient anatomy with a reference projection image, preprocessing is first used, including edge enhancement, edge detection, and contour detection. Template matching algorithms from OpenCV are then employed to find the location of the beam. Once a match is found, the reference graphic is scaled and rotated to fit the patient, using image registration correlation functions in Matlab. The algorithm runs correlation functions for all points and maps all correlation confidences to a surface map. The highest point of correlation is used for alignment and scaling. The transformation data is saved for later model scaling. Results: Anatomic recognition is used to find matching features between model and image and image registration correlation provides for alignment and scaling at any rotation angle with less than onesecond runtime, and at noise levels in excess of 150% of those found in normal procedures. Conclusion: The algorithm provides the necessary scaling and alignment tools to improve the accuracy of dose distribution mapping on the patient graphic with the DTS. Partial support from NIH Grant R01-EB002873 and Toshiba Medical Systems Corp.« less

Memory-based attention capture when multiple items are maintained in visual working memory.

PubMed

Hollingworth, Andrew; Beck, Valerie M

2016-07-01

Efficient visual search requires that attention is guided strategically to relevant objects, and most theories of visual search implement this function by means of a target template maintained in visual working memory (VWM). However, there is currently debate over the architecture of VWM-based attentional guidance. We contrasted a single-item-template hypothesis with a multiple-item-template hypothesis, which differ in their claims about structural limits on the interaction between VWM representations and perceptual selection. Recent evidence from van Moorselaar, Theeuwes, and Olivers (2014) indicated that memory-based capture during search, an index of VWM guidance, is not observed when memory set size is increased beyond a single item, suggesting that multiple items in VWM do not guide attention. In the present study, we maximized the overlap between multiple colors held in VWM and the colors of distractors in a search array. Reliable capture was observed when 2 colors were held in VWM and both colors were present as distractors, using both the original van Moorselaar et al. singleton-shape search task and a search task that required focal attention to array elements (gap location in outline square stimuli). In the latter task, memory-based capture was consistent with the simultaneous guidance of attention by multiple VWM representations. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Single and Multiple Object Tracking Using a Multi-Feature Joint Sparse Representation.

PubMed

Hu, Weiming; Li, Wei; Zhang, Xiaoqin; Maybank, Stephen

2015-04-01

In this paper, we propose a tracking algorithm based on a multi-feature joint sparse representation. The templates for the sparse representation can include pixel values, textures, and edges. In the multi-feature joint optimization, noise or occlusion is dealt with using a set of trivial templates. A sparse weight constraint is introduced to dynamically select the relevant templates from the full set of templates. A variance ratio measure is adopted to adaptively adjust the weights of different features. The multi-feature template set is updated adaptively. We further propose an algorithm for tracking multi-objects with occlusion handling based on the multi-feature joint sparse reconstruction. The observation model based on sparse reconstruction automatically focuses on the visible parts of an occluded object by using the information in the trivial templates. The multi-object tracking is simplified into a joint Bayesian inference. The experimental results show the superiority of our algorithm over several state-of-the-art tracking algorithms.

SU-F-I-75: Half-Value Layer Thicknesses and Homogeneity Coefficients for Fluoroscopic X-Ray Beam Spectra Incorporating Spectral Filtration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wunderle, K; Wayne State University School of Medicine, Detroit, MI; Godley, A

Purpose: The purpose of this investigation is to quantify various first half-value-layers (HVLs), second HVLs and homogeneity coefficients (HCs) for a state-of-the-art fluoroscope utilizing spectral (copper) filtration. Methods: A Radcal (Monrovia, Ca) AccuPro dosimeter with a 10×6-6 calibrated ionization chamber was used to measure air kerma for radiographic x-ray exposures made on a Siemens (Erlangen, Germany) Artis ZeeGo fluoroscope operated in the service mode. The ionization chamber was centered in the x-ray beam at 72 cm from the focal spot with a source-to-image-distance of 120 cm. The collimators were introduced to limit the x-ray field to approximately 5 cm ×more » 5 cm at the ionization chamber plane. Type-1100 aluminum filters, in 0.5 mm increments, were used to determine the HVL. Two HVL calculation methods were used, log-linear interpolation and Lambert-W interpolation as described by Mathieu [Med Phys, 38(8), 4546 (2011)]. Multiple measurements were made at 60, 80, 100, 120 kVp at spectral filtration thicknesses of 0, 0.1, 0.3, 0.6 and 0.9 mm. Results: First HVL, second HVL, and HCs are presented for the fluoroscopic x-ray beam spectra indicated above, with nearly identical results from the two interpolation methods. Accuracy of the set kVp was also determined and deviated less than 2%. First HVLs for fluoroscopic x-ray beam spectra without spectral filtration determined in our study were 7%–16% greater than previously published data by Fetterly et al. [Med Phys, 28, 205 (2001)]. However, the FDA minimum HVL requirements changed since that publication, requiring larger HVLs as of 2006. Additionally, x-ray tube and generator architecture have substantially changed over the last 15 years providing different beam spectra. Conclusion: X-ray beam quality characteristics for state-of-the-art fluoroscopes with spectral filtration have not been published. This study provides reference data which will be useful for defining beam qualities encountered on fluoroscopes using spectral filtration.« less

The VALiDATe29 MRI Based Multi-Channel Atlas of the Squirrel Monkey Brain.

PubMed

Schilling, Kurt G; Gao, Yurui; Stepniewska, Iwona; Wu, Tung-Lin; Wang, Feng; Landman, Bennett A; Gore, John C; Chen, Li Min; Anderson, Adam W

2017-10-01

We describe the development of the first digital atlas of the normal squirrel monkey brain and present the resulting product, VALiDATe29. The VALiDATe29 atlas is based on multiple types of magnetic resonance imaging (MRI) contrast acquired on 29 squirrel monkeys, and is created using unbiased, nonlinear registration techniques, resulting in a population-averaged stereotaxic coordinate system. The atlas consists of multiple anatomical templates (proton density, T1, and T2* weighted), diffusion MRI templates (fractional anisotropy and mean diffusivity), and ex vivo templates (fractional anisotropy and a structural MRI). In addition, the templates are combined with histologically defined cortical labels, and diffusion tractography defined white matter labels. The combination of intensity templates and image segmentations make this atlas suitable for the fundamental atlas applications of spatial normalization and label propagation. Together, this atlas facilitates 3D anatomical localization and region of interest delineation, and enables comparisons of experimental data across different subjects or across different experimental conditions. This article describes the atlas creation and its contents, and demonstrates the use of the VALiDATe29 atlas in typical applications. The atlas is freely available to the scientific community.

Protein structure modeling for CASP10 by multiple layers of global optimization.

PubMed

Joo, Keehyoung; Lee, Juyong; Sim, Sangjin; Lee, Sun Young; Lee, Kiho; Heo, Seungryong; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2014-02-01

In the template-based modeling (TBM) category of CASP10 experiment, we introduced a new protocol called protein modeling system (PMS) to generate accurate protein structures in terms of side-chains as well as backbone trace. In the new protocol, a global optimization algorithm, called conformational space annealing (CSA), is applied to the three layers of TBM procedure: multiple sequence-structure alignment, 3D chain building, and side-chain re-modeling. For 3D chain building, we developed a new energy function which includes new distance restraint terms of Lorentzian type (derived from multiple templates), and new energy terms that combine (physical) energy terms such as dynamic fragment assembly (DFA) energy, DFIRE statistical potential energy, hydrogen bonding term, etc. These physical energy terms are expected to guide the structure modeling especially for loop regions where no template structures are available. In addition, we developed a new quality assessment method based on random forest machine learning algorithm to screen templates, multiple alignments, and final models. For TBM targets of CASP10, we find that, due to the combination of three stages of CSA global optimizations and quality assessment, the modeling accuracy of PMS improves at each additional stage of the protocol. It is especially noteworthy that the side-chains of the final PMS models are far more accurate than the models in the intermediate steps. Copyright © 2013 Wiley Periodicals, Inc.

The Affordance Template ROS Package for Robot Task Programming

NASA Technical Reports Server (NTRS)

Hart, Stephen; Dinh, Paul; Hambuchen, Kimberly

2015-01-01

This paper introduces the Affordance Template ROS package for quickly programming, adjusting, and executing robot applications in the ROS RViz environment. This package extends the capabilities of RViz interactive markers by allowing an operator to specify multiple end-effector waypoint locations and grasp poses in object-centric coordinate frames and to adjust these waypoints in order to meet the run-time demands of the task (specifically, object scale and location). The Affordance Template package stores task specifications in a robot-agnostic XML description format such that it is trivial to apply a template to a new robot. As such, the Affordance Template package provides a robot-generic ROS tool appropriate for building semi-autonomous, manipulation-based applications. Affordance Templates were developed by the NASA-JSC DARPA Robotics Challenge (DRC) team and have since successfully been deployed on multiple platforms including the NASA Valkyrie and Robonaut 2 humanoids, the University of Texas Dreamer robot and the Willow Garage PR2. In this paper, the specification and implementation of the affordance template package is introduced and demonstrated through examples for wheel (valve) turning, pick-and-place, and drill grasping, evincing its utility and flexibility for a wide variety of robot applications.

Tracking the hyoid bone in videofluoroscopic swallowing studies

NASA Astrophysics Data System (ADS)

Kellen, Patrick M.; Becker, Darci; Reinhardt, Joseph M.; van Daele, Douglas

2008-03-01

Difficulty swallowing, or dysphagia, has become a growing problem. Swallowing complications can lead to malnutrition, dehydration, respiratory infection, and even death. The current gold standard for analyzing and diagnosing dysphagia is the videofluoroscopic barium swallow study. In these studies, a fluoroscope is used to image the patient ingesting barium solutions of different volumes and viscosities. The hyoid bone anchors many key muscles involved in swallowing and plays a key role in the process. Abnormal hyoid bone motion during a swallow can indicate swallowing dysfunction. Currently in clinical settings, hyoid bone motion is assessed qualitatively, which can be subject to intra-rater and inter-rater bias. This paper presents a semi-automatic method for tracking the hyoid bone that makes quantitative analysis feasible. The user defines a template of the hyoid on one frame, and this template is tracked across subsequent frames. The matching phase is optimized by predicting the position of the template based on kinematics. An expert speech pathologist marked the position of the hyoid on each frame of ten studies to serve as the gold standard. Results from performing Bland-Altman analysis at a 95% confidence interval showed a bias of 0.0+/-0.08 pixels in x and -0.08+/-0.09 pixels in y between the manually-defined gold standard and the proposed method. The average Pearson's correlation between the gold standard and the proposed method was 0.987 in x and 0.980 in y. This paper also presents a method for automatically establishing a patient-centric coordinate system for the interpretation of hyoid motion. This coordinate system corrects for upper body patient motion during the study and identifies superior-inferior and anterior-posterior motion components. These tools make the use of quantitative hyoid motion analysis feasible in clinical and research settings.

Moving template analysis of crack growth. 1: Procedure development

NASA Astrophysics Data System (ADS)

Padovan, Joe; Guo, Y. H.

1994-06-01

Based on a moving template procedure, this two part series will develop a method to follow the crack tip physics in a self-adaptive manner which provides a uniformly accurate prediction of crack growth. For multiple crack environments, this is achieved by attaching a moving template to each crack tip. The templates are each individually oriented to follow the associated growth orientation and rate. In this part, the essentials of the procedure are derived for application to fatigue crack environments. Overall the scheme derived possesses several hierarchical levels, i.e. the global model, the interpolatively tied moving template, and a multilevel element death option to simulate the crack wake. To speed up computation, the hierarchical polytree scheme is used to reorganize the global stiffness inversion process. In addition to developing the various features of the scheme, the accuracy of predictions for various crack lengths is also benchmarked. Part 2 extends the scheme to multiple crack problems. Extensive benchmarking is also presented to verify the scheme.

A study of the x-ray image quality improvement in the examination of the respiratory system based on the new image processing technique

NASA Astrophysics Data System (ADS)

Nagai, Yuichi; Kitagawa, Mayumi; Torii, Jun; Iwase, Takumi; Aso, Tomohiko; Ihara, Kanyu; Fujikawa, Mari; Takeuchi, Yumiko; Suzuki, Katsumi; Ishiguro, Takashi; Hara, Akio

2014-03-01

Recently, the double contrast technique in a gastrointestinal examination and the transbronchial lung biopsy in an examination for the respiratory system [1-3] have made a remarkable progress. Especially in the transbronchial lung biopsy, better quality of x-ray fluoroscopic images is requested because this examination is performed under a guidance of x-ray fluoroscopic images. On the other hand, various image processing methods [4] for x-ray fluoroscopic images have been developed as an x-ray system with a flat panel detector [5-7] is widely used. A recursive filtering is an effective method to reduce a random noise in x-ray fluoroscopic images. However it has a limitation for its effectiveness of a noise reduction in case of a moving object exists in x-ray fluoroscopic images because the recursive filtering is a noise reduction method by adding last few images. After recursive filtering a residual signal was produced if a moving object existed in x-ray images, and this residual signal disturbed a smooth procedure of the examinations. To improve this situation, new noise reduction method has been developed. The Adaptive Noise Reduction [ANR] is the brand-new noise reduction technique which can be reduced only a noise regardless of the moving object in x-ray fluoroscopic images. Therefore the ANR is a very suitable noise reduction method for the transbronchial lung biopsy under a guidance of x-ray fluoroscopic images because the residual signal caused of the moving object in x-ray fluoroscopic images is never produced after the ANR. In this paper, we will explain an advantage of the ANR by comparing of a performance between the ANR images and the conventional recursive filtering images.

Templated Oligosaccharide Synthesis: The Linker Effect on the Stereoselectivity of Glycosylation

PubMed Central

Pornsuriyasak, Papapida; Jia, Xiao G.; Kaeothip, Sophon; Demchenko, Alexei V.

2016-01-01

A new method for intramolecular oligosaccharide synthesis that is conceptually related to the general molecular clamp approach is introduced. Exceptional α-selectivity has been achieved in a majority of applications. Unlike other related concepts, this approach is based on the bisphenol A template, which allows one to connect multiple building blocks to perform templated oligosaccharide synthesis with complete stereoselectivity. This principle was demonstrated by the synthesis of an α,α-linked trisaccharide. PMID:27115718

The MEPUC concept adapts the C-arm fluoroscope to image-guided surgery.

PubMed

Suhm, Norbert; Müller, Paul; Bopp, Urs; Messmer, Peter; Regazzoni, Pietro

2004-06-01

Image-guided surgery requires surgeons to be able to manipulate the imaging modality themselves and without delay. Intraoperative fluoroscopic imaging does not meet this requirement as the C-arm fluoroscope cannot be operated or positioned by the surgeons themselves. The Motorized Exact Positioning Unit for C-arm (MEPUC) concept aims to optimize the workflow of positioning the C-arm fluoroscope. The hardware component of the MEPUC equips the fluoroscope with electric stepping motors. The software component allows the surgeon to control the fluoroscope's movements. The study presented here showed that translational movements within the x-y plane are most frequently performed when positioning the C-arm fluoroscope. Furthermore, reproducing a former projection was found to be a frequent task during image-guided procedures. In our opinion, the MEPUC concept adapts the fluoroscope to image-guided surgery. The most important improvement being definition of a bidirectional data exchange between the surgeon and the C-arm fluoroscope: positioning data from the surgeon to the C-arm fluoroscope and-subsequently-image information from C-arm fluoroscope to the surgeon.

Automatic 3D reconstruction of electrophysiology catheters from two-view monoplane C-arm image sequences.

PubMed

Baur, Christoph; Milletari, Fausto; Belagiannis, Vasileios; Navab, Nassir; Fallavollita, Pascal

2016-07-01

Catheter guidance is a vital task for the success of electrophysiology interventions. It is usually provided through fluoroscopic images that are taken intra-operatively. The cardiologists, who are typically equipped with C-arm systems, scan the patient from multiple views rotating the fluoroscope around one of its axes. The resulting sequences allow the cardiologists to build a mental model of the 3D position of the catheters and interest points from the multiple views. We describe and compare different 3D catheter reconstruction strategies and ultimately propose a novel and robust method for the automatic reconstruction of 3D catheters in non-synchronized fluoroscopic sequences. This approach does not purely rely on triangulation but incorporates prior knowledge about the catheters. In conjunction with an automatic detection method, we demonstrate the performance of our method compared to ground truth annotations. In our experiments that include 20 biplane datasets, we achieve an average reprojection error of 0.43 mm and an average reconstruction error of 0.67 mm compared to gold standard annotation. In clinical practice, catheters suffer from complex motion due to the combined effect of heartbeat and respiratory motion. As a result, any 3D reconstruction algorithm via triangulation is imprecise. We have proposed a new method that is fully automatic and highly accurate to reconstruct catheters in three dimensions.

Face biometrics with renewable templates

NASA Astrophysics Data System (ADS)

van der Veen, Michiel; Kevenaar, Tom; Schrijen, Geert-Jan; Akkermans, Ton H.; Zuo, Fei

2006-02-01

In recent literature, privacy protection technologies for biometric templates were proposed. Among these is the so-called helper-data system (HDS) based on reliable component selection. In this paper we integrate this approach with face biometrics such that we achieve a system in which the templates are privacy protected, and multiple templates can be derived from the same facial image for the purpose of template renewability. Extracting binary feature vectors forms an essential step in this process. Using the FERET and Caltech databases, we show that this quantization step does not significantly degrade the classification performance compared to, for example, traditional correlation-based classifiers. The binary feature vectors are integrated in the HDS leading to a privacy protected facial recognition algorithm with acceptable FAR and FRR, provided that the intra-class variation is sufficiently small. This suggests that a controlled enrollment procedure with a sufficient number of enrollment measurements is required.

A novel chaotic stream cipher and its application to palmprint template protection

NASA Astrophysics Data System (ADS)

Li, Heng-Jian; Zhang, Jia-Shu

2010-04-01

Based on a coupled nonlinear dynamic filter (NDF), a novel chaotic stream cipher is presented in this paper and employed to protect palmprint templates. The chaotic pseudorandom bit generator (PRBG) based on a coupled NDF, which is constructed in an inverse flow, can generate multiple bits at one iteration and satisfy the security requirement of cipher design. Then, the stream cipher is employed to generate cancelable competitive code palmprint biometrics for template protection. The proposed cancelable palmprint authentication system depends on two factors: the palmprint biometric and the password/token. Therefore, the system provides high-confidence and also protects the user's privacy. The experimental results of verification on the Hong Kong PolyU Palmprint Database show that the proposed approach has a large template re-issuance ability and the equal error rate can achieve 0.02%. The performance of the palmprint template protection scheme proves the good practicability and security of the proposed stream cipher.

Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine

PubMed Central

Guo, Fei; Dai, Jianhao; Zhang, Junxiang; Ma, Yichuan; Zhu, Guanghui; Shen, Junjie; Niu, Guoqi

2017-01-01

Purpose Pedicle screw fixation in the upper cervical spine is a difficult and high-risk procedure. The screw is difficult to place rapidly and accurately, and can lead to serious injury of spinal cord or vertebral artery. The aim of this study was to design an individualized 3D printing navigation template for pedicle screw fixation in the upper cervical spine. Methods Using CT thin slices data, we employed computer software to design the navigation template for pedicle screw fixation in the upper cervical spine (atlas and axis). The upper cervical spine models and navigation templates were produced by 3D printer with equal proportion, two sets for each case. In one set (Test group), pedicle screws fixation were guided by the navigation template; in the second set (Control group), the screws were fixed under fluoroscopy. According to the degree of pedicle cortex perforation and whether the screw needed to be refitted, the fixation effects were divided into 3 types: Type I, screw is fully located within the vertebral pedicle; Type II, degree of pedicle cortex perforation is <1 mm, but with good internal fixation stability and no need to renovate; Type III, degree of pedicle cortex perforation is >1 mm or with the poor internal fixation stability and in need of renovation. Type I and Type II were acceptable placements; Type III placements were unacceptable. Results A total of 19 upper cervical spine and 19 navigation templates were printed, and 37 pedicle screws were fixed in each group. Type I screw-placements in the test group totaled 32; Type II totaled 3; and Type III totaled 2; with an acceptable rate of 94.60%. Type I screw placements in the control group totaled 23; Type II totaled 3; and Type III totaled 11, with an acceptable rate of 70.27%. The acceptability rate in test group was higher than the rate in control group. The operation time and fluoroscopic frequency for each screw were decreased, compared with control group. Conclusion The individualized 3D printing navigation template for pedicle screw fixation is easy and safe, with a high success rate in the upper cervical spine surgery. PMID:28152039

Individualized 3D printing navigation template for pedicle screw fixation in upper cervical spine.

PubMed

Guo, Fei; Dai, Jianhao; Zhang, Junxiang; Ma, Yichuan; Zhu, Guanghui; Shen, Junjie; Niu, Guoqi

2017-01-01

Pedicle screw fixation in the upper cervical spine is a difficult and high-risk procedure. The screw is difficult to place rapidly and accurately, and can lead to serious injury of spinal cord or vertebral artery. The aim of this study was to design an individualized 3D printing navigation template for pedicle screw fixation in the upper cervical spine. Using CT thin slices data, we employed computer software to design the navigation template for pedicle screw fixation in the upper cervical spine (atlas and axis). The upper cervical spine models and navigation templates were produced by 3D printer with equal proportion, two sets for each case. In one set (Test group), pedicle screws fixation were guided by the navigation template; in the second set (Control group), the screws were fixed under fluoroscopy. According to the degree of pedicle cortex perforation and whether the screw needed to be refitted, the fixation effects were divided into 3 types: Type I, screw is fully located within the vertebral pedicle; Type II, degree of pedicle cortex perforation is <1 mm, but with good internal fixation stability and no need to renovate; Type III, degree of pedicle cortex perforation is >1 mm or with the poor internal fixation stability and in need of renovation. Type I and Type II were acceptable placements; Type III placements were unacceptable. A total of 19 upper cervical spine and 19 navigation templates were printed, and 37 pedicle screws were fixed in each group. Type I screw-placements in the test group totaled 32; Type II totaled 3; and Type III totaled 2; with an acceptable rate of 94.60%. Type I screw placements in the control group totaled 23; Type II totaled 3; and Type III totaled 11, with an acceptable rate of 70.27%. The acceptability rate in test group was higher than the rate in control group. The operation time and fluoroscopic frequency for each screw were decreased, compared with control group. The individualized 3D printing navigation template for pedicle screw fixation is easy and safe, with a high success rate in the upper cervical spine surgery.

WE-G-207-06: 3D Fluoroscopic Image Generation From Patient-Specific 4DCBCT-Based Motion Models Derived From Physical Phantom and Clinical Patient Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dhou, S; Cai, W; Hurwitz, M

2015-06-15

Purpose: Respiratory-correlated cone-beam CT (4DCBCT) images acquired immediately prior to treatment have the potential to represent patient motion patterns and anatomy during treatment, including both intra- and inter-fractional changes. We develop a method to generate patient-specific motion models based on 4DCBCT images acquired with existing clinical equipment and used to generate time varying volumetric images (3D fluoroscopic images) representing motion during treatment delivery. Methods: Motion models are derived by deformably registering each 4DCBCT phase to a reference phase, and performing principal component analysis (PCA) on the resulting displacement vector fields. 3D fluoroscopic images are estimated by optimizing the resulting PCAmore » coefficients iteratively through comparison of the cone-beam projections simulating kV treatment imaging and digitally reconstructed radiographs generated from the motion model. Patient and physical phantom datasets are used to evaluate the method in terms of tumor localization error compared to manually defined ground truth positions. Results: 4DCBCT-based motion models were derived and used to generate 3D fluoroscopic images at treatment time. For the patient datasets, the average tumor localization error and the 95th percentile were 1.57 and 3.13 respectively in subsets of four patient datasets. For the physical phantom datasets, the average tumor localization error and the 95th percentile were 1.14 and 2.78 respectively in two datasets. 4DCBCT motion models are shown to perform well in the context of generating 3D fluoroscopic images due to their ability to reproduce anatomical changes at treatment time. Conclusion: This study showed the feasibility of deriving 4DCBCT-based motion models and using them to generate 3D fluoroscopic images at treatment time in real clinical settings. 4DCBCT-based motion models were found to account for the 3D non-rigid motion of the patient anatomy during treatment and have the potential to localize tumor and other patient anatomical structures at treatment time even when inter-fractional changes occur. This project was supported, in part, through a Master Research Agreement with Varian Medical Systems, Inc., Palo Alto, CA. The project was also supported, in part, by Award Number R21CA156068 from the National Cancer Institute.« less

Learning-based meta-algorithm for MRI brain extraction.

PubMed

Shi, Feng; Wang, Li; Gilmore, John H; Lin, Weili; Shen, Dinggang

2011-01-01

Multiple-segmentation-and-fusion method has been widely used for brain extraction, tissue segmentation, and region of interest (ROI) localization. However, such studies are hindered in practice by their computational complexity, mainly coming from the steps of template selection and template-to-subject nonlinear registration. In this study, we address these two issues and propose a novel learning-based meta-algorithm for MRI brain extraction. Specifically, we first use exemplars to represent the entire template library, and assign the most similar exemplar to the test subject. Second, a meta-algorithm combining two existing brain extraction algorithms (BET and BSE) is proposed to conduct multiple extractions directly on test subject. Effective parameter settings for the meta-algorithm are learned from the training data and propagated to subject through exemplars. We further develop a level-set based fusion method to combine multiple candidate extractions together with a closed smooth surface, for obtaining the final result. Experimental results show that, with only a small portion of subjects for training, the proposed method is able to produce more accurate and robust brain extraction results, at Jaccard Index of 0.956 +/- 0.010 on total 340 subjects under 6-fold cross validation, compared to those by the BET and BSE even using their best parameter combinations.

Biometric templates selection and update using quality measures

NASA Astrophysics Data System (ADS)

Abboud, Ali J.; Jassim, Sabah A.

2012-06-01

To deal with severe variation in recording conditions, most biometric systems acquire multiple biometric samples, at the enrolment stage, for the same person and then extract their individual biometric feature vectors and store them in the gallery in the form of biometric template(s), labelled with the person's identity. The number of samples/templates and the choice of the most appropriate templates influence the performance of the system. The desired biometric template(s) selection technique must aim to control the run time and storage requirements while improving the recognition accuracy of the biometric system. This paper is devoted to elaborating on and discussing a new two stages approach for biometric templates selection and update. This approach uses a quality-based clustering, followed by a special criterion for the selection of an ultimate set of biometric templates from the various clusters. This approach is developed to select adaptively a specific number of templates for each individual. The number of biometric templates depends mainly on the performance of each individual (i.e. gallery size should be optimised to meet the needs of each target individual). These experiments have been conducted on two face image databases and their results will demonstrate the effectiveness of proposed quality-guided approach.

Signal template generation from acquired mammographic images for the non-prewhitening model observer with eye-filter

NASA Astrophysics Data System (ADS)

Balta, Christiana; Bouwman, Ramona W.; Sechopoulos, Ioannis; Broeders, Mireille J. M.; Karssemeijer, Nico; van Engen, Ruben E.; Veldkamp, Wouter J. H.

2017-03-01

Model observers (MOs) are being investigated for image quality assessment in full-field digital mammography (FFDM). Signal templates for the non-prewhitening MO with eye filter (NPWE) were formed using acquired FFDM images. A signal template was generated from acquired images by averaging multiple exposures resulting in a low noise signal template. Noise elimination while preserving the signal was investigated and a methodology which results in a noise-free template is proposed. In order to deal with signal location uncertainty, template shifting was implemented. The procedure to generate the template was evaluated on images of an anthropomorphic breast phantom containing microcalcification-related signals. Optimal reduction of the background noise was achieved without changing the signal. Based on a validation study in simulated images, the difference (bias) in MO performance from the ground truth signal was calculated and found to be <1%. As template generation is a building stone of the entire image quality assessment framework, the proposed method to construct templates from acquired images facilitates the use of the NPWE MO in acquired images.

Multiple template-based image matching using alpha-rooted quaternion phase correlation

NASA Astrophysics Data System (ADS)

DelMarco, Stephen

2010-04-01

In computer vision applications, image matching performed on quality-degraded imagery is difficult due to image content distortion and noise effects. State-of-the art keypoint based matchers, such as SURF and SIFT, work very well on clean imagery. However, performance can degrade significantly in the presence of high noise and clutter levels. Noise and clutter cause the formation of false features which can degrade recognition performance. To address this problem, previously we developed an extension to the classical amplitude and phase correlation forms, which provides improved robustness and tolerance to image geometric misalignments and noise. This extension, called Alpha-Rooted Phase Correlation (ARPC), combines Fourier domain-based alpha-rooting enhancement with classical phase correlation. ARPC provides tunable parameters to control the alpha-rooting enhancement. These parameter values can be optimized to tradeoff between high narrow correlation peaks, and more robust wider, but smaller peaks. Previously, we applied ARPC in the radon transform domain for logo image recognition in the presence of rotational image misalignments. In this paper, we extend ARPC to incorporate quaternion Fourier transforms, thereby creating Alpha-Rooted Quaternion Phase Correlation (ARQPC). We apply ARQPC to the logo image recognition problem. We use ARQPC to perform multiple-reference logo template matching by representing multiple same-class reference templates as quaternion-valued images. We generate recognition performance results on publicly-available logo imagery, and compare recognition results to results generated from standard approaches. We show that small deviations in reference templates of sameclass logos can lead to improved recognition performance using the joint matching inherent in ARQPC.

Marker Configuration Model-Based Roentgen Fluoroscopic Analysis.

PubMed

Garling, Eric H; Kaptein, Bart L; Geleijns, Koos; Nelissen, Rob G H H; Valstar, Edward R

2005-04-01

It remains unknown if and how the polyethylene bearing in mobile bearing knees moves during dynamic activities with respect to the tibial base plate. Marker Configuration Model-Based Roentgen Fluoroscopic Analysis (MCM-based RFA) uses a marker configuration model of inserted tantalum markers in order to accurately estimate the pose of an implant or bone using single plane Roentgen images or fluoroscopic images. The goal of this study is to assess the accuracy of (MCM-Based RFA) in a standard fluoroscopic set-up using phantom experiments and to determine the error propagation with computer simulations. The experimental set-up of the phantom study was calibrated using a calibration box equipped with 600 tantalum markers, which corrected for image distortion and determined the focus position. In the computer simulation study the influence of image distortion, MC-model accuracy, focus position, the relative distance between MC-models and MC-model configuration on the accuracy of MCM-Based RFA were assessed. The phantom study established that the in-plane accuracy of MCM-Based RFA is 0.1 mm and the out-of-plane accuracy is 0.9 mm. The rotational accuracy is 0.1 degrees. A ninth-order polynomial model was used to correct for image distortion. Marker-Based RFA was estimated to have, in a worst case scenario, an in vivo translational accuracy of 0.14 mm (x-axis), 0.17 mm (y-axis), 1.9 mm (z-axis), respectively, and a rotational accuracy of 0.3 degrees. When using fluoroscopy to study kinematics, image distortion and the accuracy of models are important factors, which influence the accuracy of the measurements. MCM-Based RFA has the potential to be an accurate, clinically useful tool for studying kinematics after total joint replacement using standard equipment.

Robust Visual Tracking Revisited: From Correlation Filter to Template Matching.

PubMed

Liu, Fanghui; Gong, Chen; Huang, Xiaolin; Zhou, Tao; Yang, Jie; Tao, Dacheng

2018-06-01

In this paper, we propose a novel matching based tracker by investigating the relationship between template matching and the recent popular correlation filter based trackers (CFTs). Compared to the correlation operation in CFTs, a sophisticated similarity metric termed mutual buddies similarity is proposed to exploit the relationship of multiple reciprocal nearest neighbors for target matching. By doing so, our tracker obtains powerful discriminative ability on distinguishing target and background as demonstrated by both empirical and theoretical analyses. Besides, instead of utilizing single template with the improper updating scheme in CFTs, we design a novel online template updating strategy named memory, which aims to select a certain amount of representative and reliable tracking results in history to construct the current stable and expressive template set. This scheme is beneficial for the proposed tracker to comprehensively understand the target appearance variations, recall some stable results. Both qualitative and quantitative evaluations on two benchmarks suggest that the proposed tracking method performs favorably against some recently developed CFTs and other competitive trackers.

Template based protein structure modeling by global optimization in CASP11.

PubMed

Joo, Keehyoung; Joung, InSuk; Lee, Sun Young; Kim, Jong Yun; Cheng, Qianyi; Manavalan, Balachandran; Joung, Jong Young; Heo, Seungryong; Lee, Juyong; Nam, Mikyung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2016-09-01

For the template-based modeling (TBM) of CASP11 targets, we have developed three new protein modeling protocols (nns for server prediction and LEE and LEER for human prediction) by improving upon our previous CASP protocols (CASP7 through CASP10). We applied the powerful global optimization method of conformational space annealing to three stages of optimization, including multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain remodeling. For more successful fold recognition, a new alignment method called CRFalign was developed. It can incorporate sensitive positional and environmental dependence in alignment scores as well as strong nonlinear correlations among various features. Modifications and adjustments were made to the form of the energy function and weight parameters pertaining to the chain building procedure. For the side-chain remodeling step, residue-type dependence was introduced to the cutoff value that determines the entry of a rotamer to the side-chain modeling library. The improved performance of the nns server method is attributed to successful fold recognition achieved by combining several methods including CRFalign and to the current modeling formulation that can incorporate native-like structural aspects present in multiple templates. The LEE protocol is identical to the nns one except that CASP11-released server models are used as templates. The success of LEE in utilizing CASP11 server models indicates that proper template screening and template clustering assisted by appropriate cluster ranking promises a new direction to enhance protein 3D modeling. Proteins 2016; 84(Suppl 1):221-232. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Controlling macro- and mesostructures with hierarchical porosity through combined hard and soft templating.

PubMed

Petkovich, Nicholas D; Stein, Andreas

2013-05-07

Rigid, porous objects and surfactants serve as powerful templates for the formation of mesoporous and macroporous materials. When both types of template are combined in a single synthesis, materials with intricate architectures and hierarchical porosity can be obtained. In this tutorial review, we explain how to conduct syntheses with both soft and hard templates; moreover, we describe methods to control the final structure present in the templated material. Much of the foundation for multiple templating lies in the study of materials made with only one type of template. To establish a foundation in this area, a description of hard and soft templating is given, delving into the templates available and the steps required for effective templating. This leads into an extended discussion about materials templated with both hard and soft templates. Through the use of recent examples in the literature, we aim to show the diversity of structures possible through multiple templating and the advantages these structures can provide for a wide range of applications. An emphasis is placed on how various factors-such as the type of template, type of precursor, heat-treatment temperature, confinement within a small space, and template-template interactions-impact morphology.

Fluoroscopic image-guided intervention system for transbronchial localization

NASA Astrophysics Data System (ADS)

Rai, Lav; Keast, Thomas M.; Wibowo, Henky; Yu, Kun-Chang; Draper, Jeffrey W.; Gibbs, Jason D.

2012-02-01

Reliable transbronchial access of peripheral lung lesions is desirable for the diagnosis and potential treatment of lung cancer. This procedure can be difficult, however, because accessory devices (e.g., needle or forceps) cannot be reliably localized while deployed. We present a fluoroscopic image-guided intervention (IGI) system for tracking such bronchoscopic accessories. Fluoroscopy, an imaging technology currently utilized by many bronchoscopists, has a fundamental shortcoming - many lung lesions are invisible in its images. Our IGI system aligns a digitally reconstructed radiograph (DRR) defined from a pre-operative computed tomography (CT) scan with live fluoroscopic images. Radiopaque accessory devices are readily apparent in fluoroscopic video, while lesions lacking a fluoroscopic signature but identifiable in the CT scan are superimposed in the scene. The IGI system processing steps consist of: (1) calibrating the fluoroscopic imaging system; (2) registering the CT anatomy with its depiction in the fluoroscopic scene; (3) optical tracking to continually update the DRR and target positions as the fluoroscope is moved about the patient. The end result is a continuous correlation of the DRR and projected targets with the anatomy depicted in the live fluoroscopic video feed. Because both targets and bronchoscopic devices are readily apparent in arbitrary fluoroscopic orientations, multiplane guidance is straightforward. The system tracks in real-time with no computational lag. We have measured a mean projected tracking accuracy of 1.0 mm in a phantom and present results from an in vivo animal study.

Enhanced disease characterization through multi network functional normalization in fMRI.

PubMed

Çetin, Mustafa S; Khullar, Siddharth; Damaraju, Eswar; Michael, Andrew M; Baum, Stefi A; Calhoun, Vince D

2015-01-01

Conventionally, structural topology is used for spatial normalization during the pre-processing of fMRI. The co-existence of multiple intrinsic networks which can be detected in the resting brain are well-studied. Also, these networks exhibit temporal and spatial modulation during cognitive task vs. rest which shows the existence of common spatial excitation patterns between these identified networks. Previous work (Khullar et al., 2011) has shown that structural and functional data may not have direct one-to-one correspondence and functional activation patterns in a well-defined structural region can vary across subjects even for a well-defined functional task. The results of this study and the existence of the neural activity patterns in multiple networks motivates us to investigate multiple resting-state networks as a single fusion template for functional normalization for multi groups of subjects. We extend the previous approach (Khullar et al., 2011) by co-registering multi group of subjects (healthy control and schizophrenia patients) and by utilizing multiple resting-state networks (instead of just one) as a single fusion template for functional normalization. In this paper we describe the initial steps toward using multiple resting-state networks as a single fusion template for functional normalization. A simple wavelet-based image fusion approach is presented in order to evaluate the feasibility of combining multiple functional networks. Our results showed improvements in both the significance of group statistics (healthy control and schizophrenia patients) and the spatial extent of activation when a multiple resting-state network applied as a single fusion template for functional normalization after the conventional structural normalization. Also, our results provided evidence that the improvement in significance of group statistics lead to better accuracy results for classification of healthy controls and schizophrenia patients.

Iatrogenic deep musculocutaneous radiation injury following percutaneous coronary intervention.

PubMed

Monaco, JoAn L; Bowen, Kanika; Tadros, Peter N; Witt, Peter D

2003-08-01

Radiation-induced skin injury has been reported for multiple fluoroscopic procedures. Previous studies have indicated that prolonged fluoroscopic exposure during even a single percutaneous coronary intervention (PCI) may lead to cutaneous radiation injury. We document a novel case of deep muscle damage requiring wide local debridement and muscle flap reconstruction in a 59-year-old man with a large radiation-induced wound to the lower thoracic region following 1 prolonged PCI procedure. The deep muscular iatrogenic injury described in this report may be the source of significant morbidity. Recommendations to reduce radiation-induced damage include careful examination of the skin site before each procedure, minimized fluoroscopy time, utilization of pulse fluoroscopy, employment of radiation filters, and collimator s and rotation of the location of the image intensifier.

Template-based protein structure modeling using the RaptorX web server.

PubMed

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2012-07-19

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.

Template-based protein structure modeling using the RaptorX web server

PubMed Central

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2016-01-01

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world. PMID:22814390

21 CFR 892.1650 - Image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Image-intensified fluoroscopic x-ray system. 892... fluoroscopic x-ray system. (a) Identification. An image-intensified fluoroscopic x-ray system is a device intended to visualize anatomical structures by converting a pattern of x-radiation into a visible image...

21 CFR 892.1650 - Image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Image-intensified fluoroscopic x-ray system. 892... fluoroscopic x-ray system. (a) Identification. An image-intensified fluoroscopic x-ray system is a device intended to visualize anatomical structures by converting a pattern of x-radiation into a visible image...

Prospective comparison of virtual fluoroscopy to fluoroscopy and plain radiographs for placement of lumbar pedicle screws.

PubMed

Resnick, Daniel K

2003-06-01

Fluoroscopy-based frameless stereotactic systems provide feedback to the surgeon using virtual fluoroscopic images. The real-life accuracy of these virtual images has not been compared with traditional fluoroscopy in a clinical setting. We prospectively studied 23 consecutive cases. In two cases, registration errors precluded the use of virtual fluoroscopy. Pedicle probes placed with virtual fluoroscopic imaging were imaged with traditional fluoroscopy in the remaining 21 cases. Position of the probes was judged to be ideal, acceptable but not ideal, or not acceptable based on the traditional fluoroscopic images. Virtual fluoroscopy was used to place probes in for 97 pedicles from L1 to the sacrum. Eighty-eight probes were judged to be in ideal position, eight were judged to be acceptable but not ideal, and one probe was judged to be in an unacceptable position. This probe was angled toward an adjacent disc space. Therefore, 96 of 97 probes placed using virtual fluoroscopy were found to be in an acceptable position. The positive predictive value for acceptable screw placement with virtual fluoroscopy compared with traditional fluoroscopy was 99%. A probe placed with virtual fluoroscopic guidance will be judged to be in an acceptable position when imaged with traditional fluoroscopy 99% of the time.

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10

PubMed Central

Zhang, Yang

2014-01-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. PMID:23760925

Interplay of I-TASSER and QUARK for template-based and ab initio protein structure prediction in CASP10.

PubMed

Zhang, Yang

2014-02-01

We develop and test a new pipeline in CASP10 to predict protein structures based on an interplay of I-TASSER and QUARK for both free-modeling (FM) and template-based modeling (TBM) targets. The most noteworthy observation is that sorting through the threading template pool using the QUARK-based ab initio models as probes allows the detection of distant-homology templates which might be ignored by the traditional sequence profile-based threading alignment algorithms. Further template assembly refinement by I-TASSER resulted in successful folding of two medium-sized FM targets with >150 residues. For TBM, the multiple threading alignments from LOMETS are, for the first time, incorporated into the ab initio QUARK simulations, which were further refined by I-TASSER assembly refinement. Compared with the traditional threading assembly refinement procedures, the inclusion of the threading-constrained ab initio folding models can consistently improve the quality of the full-length models as assessed by the GDT-HA and hydrogen-bonding scores. Despite the success, significant challenges still exist in domain boundary prediction and consistent folding of medium-size proteins (especially beta-proteins) for nonhomologous targets. Further developments of sensitive fold-recognition and ab initio folding methods are critical for solving these problems. Copyright © 2013 Wiley Periodicals, Inc.

SU-E-I-58: Experiences in Setting Up An Online Fluoroscopy Tracking System in a Large Healthcare System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fisher, R; Wunderle, K; Lingenfelter, M

Purpose: Transitioning from a paper based to an online system for tracking fluoroscopic case information required by state regulation and to conform to NCRP patient dose tracking suggestions. Methods: State regulations require documentation of operator, equipment, and some metric of tube output for fluoroscopy exams. This information was previously collected in paper logs, which was cumbersome and inefficient for the large number of fluoroscopic units across multiple locations within the system. The “tech notes” feature within Siemens’ Syngo workflow RIS was utilized to create an entry form for technologists to input case information, which was sent to a third partymore » vendor for archiving and display though an online web based portal. Results: Over 55k cases were logged in the first year of implementation, with approximately 6,500 cases per month once fully online. A system was built for area managers to oversee and correct data, which has increased the accuracy of inputted values. A high-dose report was built to automatically send notifications when patients exceed trigger levels. In addition to meeting regulatory requirements, the new system allows for larger scale QC in fluoroscopic cases by allowing comparison of data from specific procedures, locations, equipment, and operators so that instances that fall outside of reference levels can be identified for further evaluation. The system has also drastically improved identification of operators without documented equipment specific training. Conclusion: The transition to online fluoroscopy logs has improved efficiency in meeting state regulatory requirements as well as allowed for identification of particular procedures, equipment, and operators in need of additional attention in order to optimize patient and personnel doses, while high dose alerts improve patient care and follow up. Future efforts are focused on incorporating case information from outside of radiology, as well as on automating processes for increased efficiencies.« less

21 CFR 892.1660 - Non-image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Non-image-intensified fluoroscopic x-ray system... fluoroscopic x-ray system. (a) Identification. A non-image-intensified fluoroscopic x-ray system is a device... of x-radiation into a visible image. This generic type of device may include signal analysis and...

21 CFR 892.1660 - Non-image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Non-image-intensified fluoroscopic x-ray system... fluoroscopic x-ray system. (a) Identification. A non-image-intensified fluoroscopic x-ray system is a device... of x-radiation into a visible image. This generic type of device may include signal analysis and...

Combination of CT scanning and fluoroscopy imaging on a flat-panel CT scanner

NASA Astrophysics Data System (ADS)

Grasruck, M.; Gupta, R.; Reichardt, B.; Suess, Ch.; Schmidt, B.; Stierstorfer, K.; Popescu, S.; Brady, T.; Flohr, T.

2006-03-01

We developed and evaluated a prototype flat-panel detector based Volume CT (fpVCT) scanner. The fpVCT scanner consists of a Varian 4030CB a-Si flat-panel detector mounted in a multi slice CT-gantry (Siemens Medical Solutions). It provides a 25 cm field of view with 18 cm z-coverage at the isocenter. In addition to the standard tomographic scanning, fpVCT allows two new scan modes: (1) fluoroscopic imaging from any arbitrary rotation angle, and (2) continuous, time-resolved tomographic scanning of a dynamically changing viewing volume. Fluoroscopic imaging is feasible by modifying the standard CT gantry so that the imaging chain can be oriented along any user-selected rotation angle. Scanning with a stationary gantry, after it has been oriented, is equivalent to a conventional fluoroscopic examination. This scan mode enables combined use of high-resolution tomography and real-time fluoroscopy with a clinically usable field of view in the z direction. The second scan mode allows continuous observation of a timeevolving process such as perfusion. The gantry can be continuously rotated for up to 80 sec, with the rotation time ranging from 3 to 20 sec, to gather projection images of a dynamic process. The projection data, that provides a temporal log of the viewing volume, is then converted into multiple image stacks that capture the temporal evolution of a dynamic process. Studies using phantoms, ex vivo specimens, and live animals have confirmed that these new scanning modes are clinically usable and offer a unique view of the anatomy and physiology that heretofore has not been feasible using static CT scanning. At the current level of image quality and temporal resolution, several clinical applications such a dynamic angiography, tumor enhancement pattern and vascularity studies, organ perfusion, and interventional applications are in reach.

X-ray and optical stereo-based 3D sensor fusion system for image-guided neurosurgery.

PubMed

Kim, Duk Nyeon; Chae, You Seong; Kim, Min Young

2016-04-01

In neurosurgery, an image-guided operation is performed to confirm that the surgical instruments reach the exact lesion position. Among the multiple imaging modalities, an X-ray fluoroscope mounted on C- or O-arm is widely used for monitoring the position of surgical instruments and the target position of the patient. However, frequently used fluoroscopy can result in relatively high radiation doses, particularly for complex interventional procedures. The proposed system can reduce radiation exposure and provide the accurate three-dimensional (3D) position information of surgical instruments and the target position. X-ray and optical stereo vision systems have been proposed for the C- or O-arm. Two subsystems have same optical axis and are calibrated simultaneously. This provides easy augmentation of the camera image and the X-ray image. Further, the 3D measurement of both systems can be defined in a common coordinate space. The proposed dual stereoscopic imaging system is designed and implemented for mounting on an O-arm. The calibration error of the 3D coordinates of the optical stereo and X-ray stereo is within 0.1 mm in terms of the mean and the standard deviation. Further, image augmentation with the camera image and the X-ray image using an artificial skull phantom is achieved. As the developed dual stereoscopic imaging system provides 3D coordinates of the point of interest in both optical images and fluoroscopic images, it can be used by surgeons to confirm the position of surgical instruments in a 3D space with minimum radiation exposure and to verify whether the instruments reach the surgical target observed in fluoroscopic images.

76 FR 4897 - Submission for OMB Review; OMB Control No. 3090-0291; FSRS Registration and Prime Awardee Entity...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-27

... methods for submitting multiple FFATA subaward reports: A batch upload template using Microsoft Excel, an... three methods for submitting multiple FFATA subaward reports: A batch upload template using Microsoft Excel, an XML report submission template and an XML web service. These methods do take advantage of the...

Centroid stabilization in alignment of FOA corner cube: designing of a matched filter

NASA Astrophysics Data System (ADS)

Awwal, Abdul; Wilhelmsen, Karl; Roberts, Randy; Leach, Richard; Miller Kamm, Victoria; Ngo, Tony; Lowe-Webb, Roger

2015-02-01

The current automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. An important aspect of performing multiple shots in a day is to reduce additional time spent aligning specific beams due to perturbations in those beam images. One such alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes to represent the beam center. The FOA houses the frequency conversion crystals for third harmonic generation as the beams enters the target chamber. Beam-to-beam variations and systematic beam changes over time in the FOA corner-cube images can lead to a reduction in accuracy as well as increased convergence durations for the template based centroid detector. This work presents a systematic approach of maintaining FOA corner cube centroid templates so that stable position estimation is applied thereby leading to fast convergence of alignment control loops. In the matched filtering approach, a template is designed based on most recent images taken in the last 60 days. The results show that new filter reduces the divergence of the position estimation of FOA images.

Learned suppression for multiple distractors in visual search.

PubMed

Won, Bo-Yeong; Geng, Joy J

2018-05-07

Visual search for a target object occurs rapidly if there were no distractors to compete for attention, but this rarely happens in real-world environments. Distractors are almost always present and must be suppressed for target selection to succeed. Previous research suggests that one way this occurs is through the creation of a stimulus-specific distractor template. However, it remains unknown how information within such templates scale up with multiple distractors. Here we investigated the informational content of distractor templates created from repeated exposures to multiple distractors. We investigated this question using a visual search task in which participants searched for a gray square among colored squares. During "training," participants always saw the same set of colored distractors. During "testing," new distractor sets were interleaved with the trained distractors. The critical manipulation in each study was the distance (in color space) of the new test distractors from the trained distractors. We hypothesized that the pattern of distractor interference during testing would reveal the tuning of the suppression template: RTs should be commensurate with the degree to which distractor colors are encoded within the suppression template. Results from four experiments converged on the notion that the distractor template includes information about specific color values, but has broad "tuning," allowing suppression to generalize to new distractors. These results suggest that distractor templates, unlike target templates, encode multiple features and have broad representations, which have the advantage of generalizing suppression more easily to other potential distractors. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Long-range barcode labeling-sequencing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Feng; Zhang, Tao; Singh, Kanwar K.

Methods for sequencing single large DNA molecules by clonal multiple displacement amplification using barcoded primers. Sequences are binned based on barcode sequences and sequenced using a microdroplet-based method for sequencing large polynucleotide templates to enable assembly of haplotype-resolved complex genomes and metagenomes.

ANGIOGRAPHIC ANATOMY OF THE MAJOR ABDOMINAL ARTERIAL BLOOD SUPPLY IN THE DOG.

PubMed

Culp, William T N; Mayhew, Philipp D; Pascoe, Peter J; Zwingenberger, Allison

2015-01-01

Vascular-based interventional radiology (IR) procedures are being more regularly performed in veterinary patients for both diagnostic and therapeutic purposes. A complete description of the fluoroscopic arterial anatomy of the canine abdominal cavity has not been published. This information is essential for performance of IR procedures to allow for improved preparation before and during a particular procedure. The primary purpose of this study was to provide a fluoroscopic description of the vascular branching from the abdominal aorta in a ventro-dorsal projection with a secondary goal of producing pictorial reference images of the major abdominal arterial blood vessels. Five healthy female hound type dogs were enrolled and underwent fluoroscopic arteriography. During fluoroscopy, both nonselective and selective arteriography were performed. The nonselective arteriograms were obtained in the aorta at four locations: cranial to the celiac artery, cranial to the renal arteries, cranial to the caudal mesenteric artery, and cranial to the branching of the external iliac arteries. Selective arteriography was conducted by performing injections into the following arteries: celiac, splenic, common hepatic, cranial mesenteric, left and right renal, and caudal mesenteric. Fluoroscopic arteriography allowed for excellent characterization of the aortic ostia and the location of the lower order vascular branches. Future evaluation of vascular-based treatment options will likely increase as the understanding of the normal and pathologic anatomy improves. © 2015 American College of Veterinary Radiology.

40 CFR Appendix C to Subpart Nnn... - Method for the Determination of Product Density

Code of Federal Regulations, 2013 CFR

2013-07-01

... One square foot (12 in. by 12 in.) template, or templates that are multiples of one square foot, for... to the plant's written procedure for the designated product. 3.2Cut samples using one square foot (or multiples of one square foot) template. 3.3Weigh product and obtain area weight (lb/ft2). 3.4Measure sample...

40 CFR Appendix C to Subpart Nnn... - Method for the Determination of Product Density

Code of Federal Regulations, 2014 CFR

2014-07-01

... One square foot (12 in. by 12 in.) template, or templates that are multiples of one square foot, for... to the plant's written procedure for the designated product. 3.2Cut samples using one square foot (or multiples of one square foot) template. 3.3Weigh product and obtain area weight (lb/ft2). 3.4Measure sample...

A single appointment protocol to create a partially edentulous CAD/CAM guided surgical template: a clinical report.

PubMed

Marchack, Christopher B; Charles, Allan; Pettersson, Andreas

2011-12-01

The traditional technique for creating a CAD/CAM surgical template with a NobelGuide protocol is to fabricate a radiographic template that depicts the planned tooth position first. Multiple appointments are needed for the fabrication of the radiographic template with Cone Beam Computed Tomography (CBCT) before the surgical procedure can start. An alternative technique is described for fabricating a radiographic template at the initial examination appointment and capturing the necessary DICOM data to plan and fabricate a CAD/CAM surgical template in a 1-appointment protocol, thereby saving the patient and clinician time and reducing the need for multiple appointments. Copyright © 2011 The Editorial Council of the Journal of Prosthetic Dentistry. Published by Mosby, Inc. All rights reserved.

Perioperative patient radiation exposure in the endoscopic removal of upper urinary tract calculi.

PubMed

Jamal, Joseph E; Armenakas, Noel A; Sosa, R Ernest; Fracchia, John A

2011-11-01

The efficacy of computed tomography (CT) in detailing upper urinary tract calculi is well established. There is no established acceptable annual recommended limit for medical exposure, yet the global accepted upper limit for occupational radiation exposure is <50 millisieverts (mSv) in any one year. We sought to appreciate the CT and fluoroscopic radiation exposure to our patients undergoing endoscopic removal of upper tract calculi during the periprocedure period. All patients undergoing upper urinary endoscopic stone removal between 2005 and 2009 were identified. To calculate the cumulative radiation exposure, we included all ionizing radiation imaging performed during a periprocedure period, which we defined as ≤90 days pre- and post-therapeutic procedure. A total of 233 upper urinary tract therapeutic patient stone procedures were identified; 127 patients underwent ureteroscopy (URS) and 106 patients underwent percutaneous nephrolithotomy (PCNL). A mean 1.58 CTs were performed per patient. Ninety (38.6%) patients underwent ≥2 CTs in the periprocedure period, with an average number in this group of 2.49 CT/patient, resulting in approximately 49.8 mSv of CT radiation exposure. Patients who were undergoing URS were significantly more likely to have multiple CTs (P=0.003) than those undergoing PCNL. Median fluoroscopic procedure exposures were 43.3 mGy for patients who were undergoing PCNL and 27.6 mGy for those patients undergoing URS. CT radiation exposure in the periprocedure period for patients who were undergoing endoscopic upper tract stone removal is considerable. Added to this is the procedure-related fluoroscopic radiation exposure. Urologic surgeons should be aware of the cumulative amount of ionizing radiation received by their patients from multiple sources.

MO-D-213-07: RadShield: Semi- Automated Calculation of Air Kerma Rate and Barrier Thickness

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeLorenzo, M; Wu, D; Rutel, I

2015-06-15

Purpose: To develop the first Java-based semi-automated calculation program intended to aid professional radiation shielding design. Air-kerma rate and barrier thickness calculations are performed by implementing NCRP Report 147 formalism into a Graphical User Interface (GUI). The ultimate aim of this newly created software package is to reduce errors and improve radiographic and fluoroscopic room designs over manual approaches. Methods: Floor plans are first imported as images into the RadShield software program. These plans serve as templates for drawing barriers, occupied regions and x-ray tube locations. We have implemented sub-GUIs that allow the specification in regions and equipment for occupancymore » factors, design goals, number of patients, primary beam directions, source-to-patient distances and workload distributions. Once the user enters the above parameters, the program automatically calculates air-kerma rate at sampled points beyond all barriers. For each sample point, a corresponding minimum barrier thickness is calculated to meet the design goal. RadShield allows control over preshielding, sample point location and material types. Results: A functional GUI package was developed and tested. Examination of sample walls and source distributions yields a maximum percent difference of less than 0.1% between hand-calculated air-kerma rates and RadShield. Conclusion: The initial results demonstrated that RadShield calculates air-kerma rates and required barrier thicknesses with reliable accuracy and can be used to make radiation shielding design more efficient and accurate. This newly developed approach differs from conventional calculation methods in that it finds air-kerma rates and thickness requirements for many points outside the barriers, stores the information and selects the largest value needed to comply with NCRP Report 147 design goals. Floor plans, parameters, designs and reports can be saved and accessed later for modification and recalculation. We have confirmed that this software accurately calculates air-kerma rates and required barrier thicknesses for diagnostic radiography and fluoroscopic rooms.« less

Multiple emulsions as soft templates for the synthesis of multifunctional silicone porous particles.

PubMed

Vilanova, Neus; Kolen'ko, Yury V; Solans, Conxita; Rodríguez-Abreu, Carlos

2015-01-01

Multiple emulsion templating is a versatile strategy for the synthesis of porous particles. The present work addresses the synthesis of multifunctional poly(dimethylsiloxane) porous particles using multiple water-in-oil-in-water emulsions as soft templates with an oil phase constituted by a crosslinkable poly(dimethylsiloxane) (PDMS) oil. Herewith, the impact of the viscosity of PDMS oil (i.e., molecular weight) on the properties of both the emulsion templates and the resulting particles was evaluated. The viscosity of PDMS oil has a strong effect on the size and polydispersity of the emulsion templates as well as on the mechanical properties of the derived particles. The elastic modulus can be tuned by mixing PDMS oils of different viscosities to form bimodal crosslinked networks. Iron oxide nanoparticles can be readily incorporated into the emulsion templates to provide additional functionalities to the silicone particles, such as magnetic separation or magnetic hyperthermia. The synthesized composite magnetic particles were found to be useful as recoverable absorbent materials (e.g., for oil spills) by taking advantage of their high buoyancy and high hydrophobicity. Copyright © 2014 Elsevier Inc. All rights reserved.

Functional Connectivity in Multiple Cortical Networks Is Associated with Performance Across Cognitive Domains in Older Adults.

PubMed

Shaw, Emily E; Schultz, Aaron P; Sperling, Reisa A; Hedden, Trey

2015-10-01

Intrinsic functional connectivity MRI has become a widely used tool for measuring integrity in large-scale cortical networks. This study examined multiple cortical networks using Template-Based Rotation (TBR), a method that applies a priori network and nuisance component templates defined from an independent dataset to test datasets of interest. A priori templates were applied to a test dataset of 276 older adults (ages 65-90) from the Harvard Aging Brain Study to examine the relationship between multiple large-scale cortical networks and cognition. Factor scores derived from neuropsychological tests represented processing speed, executive function, and episodic memory. Resting-state BOLD data were acquired in two 6-min acquisitions on a 3-Tesla scanner and processed with TBR to extract individual-level metrics of network connectivity in multiple cortical networks. All results controlled for data quality metrics, including motion. Connectivity in multiple large-scale cortical networks was positively related to all cognitive domains, with a composite measure of general connectivity positively associated with general cognitive performance. Controlling for the correlations between networks, the frontoparietal control network (FPCN) and executive function demonstrated the only significant association, suggesting specificity in this relationship. Further analyses found that the FPCN mediated the relationships of the other networks with cognition, suggesting that this network may play a central role in understanding individual variation in cognition during aging.

A moving fluoroscope to capture tibiofemoral kinematics during complete cycles of free level and downhill walking as well as stair descent.

PubMed

List, Renate; Postolka, Barbara; Schütz, Pascal; Hitz, Marco; Schwilch, Peter; Gerber, Hans; Ferguson, Stephen J; Taylor, William R

2017-01-01

Videofluoroscopy has been shown to provide essential information in the evaluation of the functionality of total knee arthroplasties. However, due to the limitation in the field of view, most systems can only assess knee kinematics during highly restricted movements. To avoid the limitations of a static image intensifier, a moving fluoroscope has been presented as a standalone system that allows tracking of the knee during multiple complete cycles of level- and downhill-walking, as well as stair descent, in combination with the synchronous assessment of ground reaction forces and whole body skin marker measurements. Here, we assess the ability of the system to keep the knee in the field of view of the image intensifier. By measuring ten total knee arthroplasty subjects, we demonstrate that it is possible to maintain the knee to within 1.8 ± 1.4 cm vertically and 4.0 ± 2.6 cm horizontally of the centre of the intensifier throughout full cycles of activities of daily living. Since control of the system is based on real-time feedback of a wire sensor, the system is not dependent on repeatable gait patterns, but is rather able to capture pathological motion patterns with low inter-trial repeatability.

A moving fluoroscope to capture tibiofemoral kinematics during complete cycles of free level and downhill walking as well as stair descent

PubMed Central

Postolka, Barbara; Schütz, Pascal; Hitz, Marco; Schwilch, Peter; Gerber, Hans

2017-01-01

Videofluoroscopy has been shown to provide essential information in the evaluation of the functionality of total knee arthroplasties. However, due to the limitation in the field of view, most systems can only assess knee kinematics during highly restricted movements. To avoid the limitations of a static image intensifier, a moving fluoroscope has been presented as a standalone system that allows tracking of the knee during multiple complete cycles of level- and downhill-walking, as well as stair descent, in combination with the synchronous assessment of ground reaction forces and whole body skin marker measurements. Here, we assess the ability of the system to keep the knee in the field of view of the image intensifier. By measuring ten total knee arthroplasty subjects, we demonstrate that it is possible to maintain the knee to within 1.8 ± 1.4 cm vertically and 4.0 ± 2.6 cm horizontally of the centre of the intensifier throughout full cycles of activities of daily living. Since control of the system is based on real-time feedback of a wire sensor, the system is not dependent on repeatable gait patterns, but is rather able to capture pathological motion patterns with low inter-trial repeatability. PMID:29016647

Phosphor-Free Apple-White LEDs with Embedded Indium-Rich Nanostructures Grown on Strain Relaxed Nano-epitaxy GaN.

PubMed

Soh, C B; Liu, W; Yong, A M; Chua, S J; Chow, S Y; Tripathy, S; Tan, R J N

2010-08-01

Phosphor-free apple-white light emitting diodes have been fabricated using a dual stacked InGaN/GaN multiple quantum wells comprising of a lower set of long wavelength emitting indium-rich nanostructures incorporated in multiple quantum wells with an upper set of cyan-green emitting multiple quantum wells. The light-emitting diodes were grown on nano-epitaxially lateral overgrown GaN template formed by regrowth of GaN over SiO(2) film patterned with an anodic aluminum oxide mask with holes of 125 nm diameter and a period of 250 nm. The growth of InGaN/GaN multiple quantum wells on these stress relaxed low defect density templates improves the internal quantum efficiency by 15% for the cyan-green multiple quantum wells. Higher emission intensity with redshift in the PL peak emission wavelength is obtained for the indium-rich nanostructures incorporated in multiple quantum wells. The quantum wells grown on the nano-epitaxially lateral overgrown GaN has a weaker piezoelectric field and hence shows a minimal peak shift with application of higher injection current. An enhancement of external quantum efficiency is achieved for the apple-white light emitting diodes grown on the nano-epitaxially lateral overgrown GaN template based on the light -output power measurement. The improvement in light extraction efficiency, η(extraction,) was found to be 34% for the cyan-green emission peak and 15% from the broad long wavelength emission with optimized lattice period.

Phosphor-Free Apple-White LEDs with Embedded Indium-Rich Nanostructures Grown on Strain Relaxed Nano-epitaxy GaN

NASA Astrophysics Data System (ADS)

Soh, C. B.; Liu, W.; Yong, A. M.; Chua, S. J.; Chow, S. Y.; Tripathy, S.; Tan, R. J. N.

2010-11-01

Phosphor-free apple-white light emitting diodes have been fabricated using a dual stacked InGaN/GaN multiple quantum wells comprising of a lower set of long wavelength emitting indium-rich nanostructures incorporated in multiple quantum wells with an upper set of cyan-green emitting multiple quantum wells. The light-emitting diodes were grown on nano-epitaxially lateral overgrown GaN template formed by regrowth of GaN over SiO2 film patterned with an anodic aluminum oxide mask with holes of 125 nm diameter and a period of 250 nm. The growth of InGaN/GaN multiple quantum wells on these stress relaxed low defect density templates improves the internal quantum efficiency by 15% for the cyan-green multiple quantum wells. Higher emission intensity with redshift in the PL peak emission wavelength is obtained for the indium-rich nanostructures incorporated in multiple quantum wells. The quantum wells grown on the nano-epitaxially lateral overgrown GaN has a weaker piezoelectric field and hence shows a minimal peak shift with application of higher injection current. An enhancement of external quantum efficiency is achieved for the apple-white light emitting diodes grown on the nano-epitaxially lateral overgrown GaN template based on the light -output power measurement. The improvement in light extraction efficiency, ηextraction, was found to be 34% for the cyan-green emission peak and 15% from the broad long wavelength emission with optimized lattice period.

A method of percutaneous vertebroplasty under the guidance of two C-arm fluoroscopes

PubMed Central

Xu, Ren-Jie; Yan, Yong-Qing; Chen, Guang-Xiang; Zou, Tian-Ming; Cai, Xiao-Qiang; Wang, Dong-Lai

2014-01-01

Objective: To compare the clinical application in the percutaneous vertebroplasty under the guidance of one or two C-arm fluoroscopes. Methods: One hundred forty three elderly patients with Osteoporotic vertebral compression fractures (OVCFs) underwent percutaneous vertebroplasty under the guidance of one or two C-arm fluoroscopes. The number of pulsed imagings, the time of operation and the incidence of cement leakage were recorded. Results: The average number of pulsed imagings was 16.00±1.58 vs 13.07±2.00 per patient under the guidance of one vs two C-arm fluoroscopes. The average time of operation was 48.42±5.00 minutes vs 39.70±7.42 minutes per patient under the guidance of one vs two C-arm fluoroscopes. The incidence of cement leakage was 20% vs 15.7% of the patients under the guidance of one vs two C-arm fluoroscopes. The differences in the number of pulsed imagings and the time of operation were statistically significant. The difference in incidence of cement leakage was not statistically significant. Conclusion: The two-fluoroscopic technique reduce the labor cost, the radiation, the time of operation and the operation risk. PMID:24772138

Correlated Template-Switching Events during Minus-Strand DNA Synthesis: a Mechanism for High Negative Interference during Retroviral Recombination

PubMed Central

Anderson, Jeffrey A.; Teufel, Ronald J.; Yin, Philip D.; Hu, Wei-Shau

1998-01-01

Two models for the mechanism of retroviral recombination have been proposed: forced copy choice (minus-strand recombination) and strand displacement-assimilation (plus-strand recombination). Each minus-strand recombination event results in one template switch, whereas each plus-strand recombination event results in two template switches. Recombinant proviruses with one and more than one template switches were previously observed. Recombinants with one template switch were generated by minus-strand recombination, while recombinants containing more than one template switch may have been generated by plus-strand recombination or by correlated minus-strand recombination. We recently observed that retroviral recombination exhibits high negative interference whereby the frequency of recombinants containing multiple template-switching events is higher than expected. To delineate the mechanism that generates recombinants with more than one template switch, we devised a system that permits only minus-strand recombination. Two highly homologous vectors, WH204 and WH221, containing eight different restriction site markers were used. The primer binding site (PBS) of WH221 was deleted; although reverse transcription cannot initiate from WH221 RNA, it can serve as a template for DNA synthesis in heterozygotic virions. After one round of retroviral replication, the structures of the recombinant proviruses were examined. Recombinants containing two, three, four, and five template switches were observed at 1.4-, 10-, 65-, and 50-fold-higher frequencies, respectively, than expected. This indicates that minus-strand recombination events are correlated and can generate proviruses with multiple template switches efficiently. The frequencies of recombinants containing multiple template switches were similar to those observed in the previous system, which allowed both minus- and plus-strand recombination. Thus, the previously reported high negative interference during retroviral recombination can be caused by correlated template switches during minus-strand DNA synthesis. In addition, all examined recombinants contained an intact PBS, indicating that most of the plus-strand DNA transfer occurs after completion of the strong-stop DNA. PMID:9445017

Broadband infrared metamaterial absorber based on anodic aluminum oxide template

NASA Astrophysics Data System (ADS)

Yang, Jingfan; Qu, Shaobo; Ma, Hua; Wang, Jiafu; Yang, Shen; Pang, Yongqiang

2018-05-01

In this work, a broadband infrared metamaterial absorber is proposed based on trapezoid-shaped anodic aluminum oxide (AAO) template. Unlike traditional metamaterial absorber constructed from metal-dielectric-metal sandwich structure, our proposed absorber is composed of trapezoid-shaped AAO template with metallic nanowires inside. The infrared absorption efficiency is numerically calculated and the mechanism analysis is given in the paper. Owing to the superposition of multiple resonances produced by the nanowires with different heights, the infrared metamatrial absorber can keep high absorption efficiency during broad working wavelength band from 3.4 μm to 6.1 μm. In addition, the resonance wavelength is associated with the height of nanowires, which indicates that the resonance wavelength can be modulated flexibly through changing the heights of nanowires. This kind of design can also be adapted to other wavelength regions.

Fluoroscopic-guided radiofrequency ablation of the basivertebral nerve: application and analysis with multiple imaging modalities in an ovine model (Invited Paper)

NASA Astrophysics Data System (ADS)

Bergeron, Jeffrey A.; Eskey, Cliff J.; Attawia, Mohammed; Patel, Samit J.; Ryan, Thomas P.; Pellegrino, Richard; Sutton, Jeffrey; Crombie, John; Paul, B. T.; Hoopes, P. J.

2005-04-01

Pathologic involvement of the basivertebral nerve, an intraosseous vertebral nerve found in humans and most mammalian species, may play a role in some forms of back pain. This study was designed to assess the feasibility and effects of the percutaneous delivery of radiofrequency (RF) energy to thermally ablate the basivertebral nerve in the lumbar vertebrae of mature sheep. Using fluoroscopic guidance, a RF bipolar device was placed and a thermal dose delivered to lumbar vertebral bodies in sheep. Post-treatment assessment included multiple magnetic resonance imaging (MRI) techniques and computed tomography (CT). These data were analyzed and correlated to histopathology and morphometry findings to describe the cellular and boney structural changes resulting from the treatment. Imaging modalities MRI and CT can be implemented to non-invasively describe treatment region and volume, marrow cellular effects, and bone density alterations immediately following RF treatment and during convalescence. Such imaging can be utilized to assess treatment effects and refine the thermal dose to vertebral body volume ratio used in treatment planning. This information will be used to improve the therapeutic ratio and develop a treatment protocol for human applications.

The role of the geophysical template and environmental regimes in controlling stream-living trout populations

USGS Publications Warehouse

Penaluna, Brooke E.; Railsback, Steve F.; Dunham, Jason B.; Johnson, S.; Bilby, Richard E.; Skaugset, Arne E.

2015-01-01

The importance of multiple processes and instream factors to aquatic biota has been explored extensively, but questions remain about how local spatiotemporal variability of aquatic biota is tied to environmental regimes and the geophysical template of streams. We used an individual-based trout model to explore the relative role of the geophysical template versus environmental regimes on biomass of trout (Oncorhynchus clarkii clarkii). We parameterized the model with observed data from each of the four headwater streams (their local geophysical template and environmental regime) and then ran 12 simulations where we replaced environmental regimes (stream temperature, flow, turbidity) of a given stream with values from each neighboring stream while keeping the geophysical template fixed. We also performed single-parameter sensitivity analyses on the model results from each of the four streams. Although our modeled findings show that trout biomass is most responsive to changes in the geophysical template of streams, they also reveal that biomass is restricted by available habitat during seasonal low flow, which is a product of both the stream’s geophysical template and flow regime. Our modeled results suggest that differences in the geophysical template among streams render trout more or less sensitive to environmental change, emphasizing the importance of local fish–habitat relationships in streams.

Directional templates for real-time detection of coronal axis rotated faces

NASA Astrophysics Data System (ADS)

Perez, Claudio A.; Estevez, Pablo A.; Garate, Patricio

2004-10-01

Real-time face and iris detection on video images has gained renewed attention because of multiple possible applications in studying eye function, drowsiness detection, virtual keyboard interfaces, face recognition, video processing and multimedia retrieval. In this paper, a study is presented on using directional templates in the detection of faces rotated in the coronal axis. The templates are built by extracting the directional image information from the regions of the eyes, nose and mouth. The face position is determined by computing a line integral using the templates over the face directional image. The line integral reaches a maximum when it coincides with the face position. It is shown an improvement in localization selectivity by the increased value in the line integral computed with the directional template. Besides, improvements in the line integral value for face size and face rotation angle was also found through the computation of the line integral using the directional template. Based on these results the new templates should improve selectivity and hence provide the means to restrict computations to a fewer number of templates and restrict the region of search during the face and eye tracking procedure. The proposed method is real time, completely non invasive and was applied with no background limitation and normal illumination conditions in an indoor environment.

A novel cloning template designing method by using an artificial bee colony algorithm for edge detection of CNN based imaging sensors.

PubMed

Parmaksızoğlu, Selami; Alçı, Mustafa

2011-01-01

Cellular Neural Networks (CNNs) have been widely used recently in applications such as edge detection, noise reduction and object detection, which are among the main computer imaging processes. They can also be realized as hardware based imaging sensors. The fact that hardware CNN models produce robust and effective results has attracted the attention of researchers using these structures within image sensors. Realization of desired CNN behavior such as edge detection can be achieved by correctly setting a cloning template without changing the structure of the CNN. To achieve different behaviors effectively, designing a cloning template is one of the most important research topics in this field. In this study, the edge detecting process that is used as a preliminary process for segmentation, identification and coding applications is conducted by using CNN structures. In order to design the cloning template of goal-oriented CNN architecture, an Artificial Bee Colony (ABC) algorithm which is inspired from the foraging behavior of honeybees is used and the performance analysis of ABC for this application is examined with multiple runs. The CNN template generated by the ABC algorithm is tested by using artificial and real test images. The results are subjectively and quantitatively compared with well-known classical edge detection methods, and other CNN based edge detector cloning templates available in the imaging literature. The results show that the proposed method is more successful than other methods.

A Novel Cloning Template Designing Method by Using an Artificial Bee Colony Algorithm for Edge Detection of CNN Based Imaging Sensors

PubMed Central

Parmaksızoğlu, Selami; Alçı, Mustafa

2011-01-01

Cellular Neural Networks (CNNs) have been widely used recently in applications such as edge detection, noise reduction and object detection, which are among the main computer imaging processes. They can also be realized as hardware based imaging sensors. The fact that hardware CNN models produce robust and effective results has attracted the attention of researchers using these structures within image sensors. Realization of desired CNN behavior such as edge detection can be achieved by correctly setting a cloning template without changing the structure of the CNN. To achieve different behaviors effectively, designing a cloning template is one of the most important research topics in this field. In this study, the edge detecting process that is used as a preliminary process for segmentation, identification and coding applications is conducted by using CNN structures. In order to design the cloning template of goal-oriented CNN architecture, an Artificial Bee Colony (ABC) algorithm which is inspired from the foraging behavior of honeybees is used and the performance analysis of ABC for this application is examined with multiple runs. The CNN template generated by the ABC algorithm is tested by using artificial and real test images. The results are subjectively and quantitatively compared with well-known classical edge detection methods, and other CNN based edge detector cloning templates available in the imaging literature. The results show that the proposed method is more successful than other methods. PMID:22163903

Performing label-fusion-based segmentation using multiple automatically generated templates.

PubMed

Chakravarty, M Mallar; Steadman, Patrick; van Eede, Matthijs C; Calcott, Rebecca D; Gu, Victoria; Shaw, Philip; Raznahan, Armin; Collins, D Louis; Lerch, Jason P

2013-10-01

Classically, model-based segmentation procedures match magnetic resonance imaging (MRI) volumes to an expertly labeled atlas using nonlinear registration. The accuracy of these techniques are limited due to atlas biases, misregistration, and resampling error. Multi-atlas-based approaches are used as a remedy and involve matching each subject to a number of manually labeled templates. This approach yields numerous independent segmentations that are fused using a voxel-by-voxel label-voting procedure. In this article, we demonstrate how the multi-atlas approach can be extended to work with input atlases that are unique and extremely time consuming to construct by generating a library of multiple automatically generated templates of different brains (MAGeT Brain). We demonstrate the efficacy of our method for the mouse and human using two different nonlinear registration algorithms (ANIMAL and ANTs). The input atlases consist a high-resolution mouse brain atlas and an atlas of the human basal ganglia and thalamus derived from serial histological data. MAGeT Brain segmentation improves the identification of the mouse anterior commissure (mean Dice Kappa values (κ = 0.801), but may be encountering a ceiling effect for hippocampal segmentations. Applying MAGeT Brain to human subcortical structures improves segmentation accuracy for all structures compared to regular model-based techniques (κ = 0.845, 0.752, and 0.861 for the striatum, globus pallidus, and thalamus, respectively). Experiments performed with three manually derived input templates suggest that MAGeT Brain can approach or exceed the accuracy of multi-atlas label-fusion segmentation (κ = 0.894, 0.815, and 0.895 for the striatum, globus pallidus, and thalamus, respectively). Copyright © 2012 Wiley Periodicals, Inc.

21 CFR 1020.32 - Fluoroscopic equipment.

Code of Federal Regulations, 2011 CFR

2011-04-01

... information as required in § 1020.30(h). (h) Fluoroscopic irradiation time, display, and signal. (1)(i... irradiation time of the fluoroscopic tube. The maximum cumulative time of the timing device shall not exceed 5... preset cumulative irradiation-time. Such signal shall continue to sound while x-rays are produced until...

21 CFR 1020.32 - Fluoroscopic equipment.

Code of Federal Regulations, 2013 CFR

2013-04-01

... information as required in § 1020.30(h). (h) Fluoroscopic irradiation time, display, and signal. (1)(i... irradiation time of the fluoroscopic tube. The maximum cumulative time of the timing device shall not exceed 5... preset cumulative irradiation-time. Such signal shall continue to sound while x-rays are produced until...

21 CFR 1020.32 - Fluoroscopic equipment.

Code of Federal Regulations, 2014 CFR

2014-04-01

... information as required in § 1020.30(h). (h) Fluoroscopic irradiation time, display, and signal. (1)(i... irradiation time of the fluoroscopic tube. The maximum cumulative time of the timing device shall not exceed 5... preset cumulative irradiation-time. Such signal shall continue to sound while x-rays are produced until...

21 CFR 1020.32 - Fluoroscopic equipment.

Code of Federal Regulations, 2012 CFR

2012-04-01

... information as required in § 1020.30(h). (h) Fluoroscopic irradiation time, display, and signal. (1)(i... irradiation time of the fluoroscopic tube. The maximum cumulative time of the timing device shall not exceed 5... preset cumulative irradiation-time. Such signal shall continue to sound while x-rays are produced until...

Inspecting Pipe Radiographically Through Asbestos Insulation

NASA Technical Reports Server (NTRS)

Gianettino, David P.

1994-01-01

Welds between sections of insulated steampipe located and inspected radiographically. Unless need to repair defective weld, one avoids cost, time, and hazard of removing asbestos insulation. Enables inspectors to locate and evaluate nondestructively any weld in pipe system, without shutting down steam. Hidden weld joints first located by use of low-power fluoroscope, moved along pipe while technician observes fluoroscopic image. Low-energy x rays from fluoroscope penetrate insulation but not pipe. Weld bead appears in silhouette on fluoroscope screen. Technician then accurately marks weld sites on insulation for later inspection.

Influence of the quality of intraoperative fluoroscopic images on the spatial positioning accuracy of a CAOS system.

PubMed

Wang, Junqiang; Wang, Yu; Zhu, Gang; Chen, Xiangqian; Zhao, Xiangrui; Qiao, Huiting; Fan, Yubo

2018-06-01

Spatial positioning accuracy is a key issue in a computer-assisted orthopaedic surgery (CAOS) system. Since intraoperative fluoroscopic images are one of the most important input data to the CAOS system, the quality of these images should have a significant influence on the accuracy of the CAOS system. But the regularities and mechanism of the influence of the quality of intraoperative images on the accuracy of a CAOS system have yet to be studied. Two typical spatial positioning methods - a C-arm calibration-based method and a bi-planar positioning method - are used to study the influence of different image quality parameters, such as resolution, distortion, contrast and signal-to-noise ratio, on positioning accuracy. The error propagation rules of image error in different spatial positioning methods are analyzed by the Monte Carlo method. Correlation analysis showed that resolution and distortion had a significant influence on spatial positioning accuracy. In addition the C-arm calibration-based method was more sensitive to image distortion, while the bi-planar positioning method was more susceptible to image resolution. The image contrast and signal-to-noise ratio have no significant influence on the spatial positioning accuracy. The result of Monte Carlo analysis proved that generally the bi-planar positioning method was more sensitive to image quality than the C-arm calibration-based method. The quality of intraoperative fluoroscopic images is a key issue in the spatial positioning accuracy of a CAOS system. Although the 2 typical positioning methods have very similar mathematical principles, they showed different sensitivities to different image quality parameters. The result of this research may help to create a realistic standard for intraoperative fluoroscopic images for CAOS systems. Copyright © 2018 John Wiley & Sons, Ltd.

Object-based target templates guide attention during visual search.

PubMed

Berggren, Nick; Eimer, Martin

2018-05-03

During visual search, attention is believed to be controlled in a strictly feature-based fashion, without any guidance by object-based target representations. To challenge this received view, we measured electrophysiological markers of attentional selection (N2pc component) and working memory (sustained posterior contralateral negativity; SPCN) in search tasks where two possible targets were defined by feature conjunctions (e.g., blue circles and green squares). Critically, some search displays also contained nontargets with two target features (incorrect conjunction objects, e.g., blue squares). Because feature-based guidance cannot distinguish these objects from targets, any selective bias for targets will reflect object-based attentional control. In Experiment 1, where search displays always contained only one object with target-matching features, targets and incorrect conjunction objects elicited identical N2pc and SPCN components, demonstrating that attentional guidance was entirely feature-based. In Experiment 2, where targets and incorrect conjunction objects could appear in the same display, clear evidence for object-based attentional control was found. The target N2pc became larger than the N2pc to incorrect conjunction objects from 250 ms poststimulus, and only targets elicited SPCN components. This demonstrates that after an initial feature-based guidance phase, object-based templates are activated when they are required to distinguish target and nontarget objects. These templates modulate visual processing and control access to working memory, and their activation may coincide with the start of feature integration processes. Results also suggest that while multiple feature templates can be activated concurrently, only a single object-based target template can guide attention at any given time. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Medical Student Appraisal

PubMed Central

Sampognaro, P.J.; Mitchell, S.L.; Weeks, S.R.; Khalifian, S.; Markman, T.M.; Uebel, L.W.; Dattilo, J.R.

2013-01-01

Summary Background Pre-rounding is essential to preparing for morning rounds. Despite its importance, pre-rounding is rarely formally taught within the medical school curriculum and more often informally learned by modeling residents. The evolution of mobile applications provides opportunities to optimize this process. Objectives To evaluate three options available to medical students while pre-rounding and promote adoption of mobile resources in clinical care. Methods Six medical students formed the evaluation cohort. Students were surveyed to assess pre-rounding practices. Participants utilized paper-based pre-rounding templates for two weeks followed by two weeks of the electronic note-taking service EvernoteTM. A review of mobile applications on the iTunesTM and Google PlayTM stores was performed, with each application informally reviewed by a single student. The application ScutsheetTM was selected for formal review by all students. Data was collected from narrative responses supplied by students throughout the evaluation periods and aggregated to assess strengths and limitations of each application. Results Pre-study responses demonstrated two consistent processes: verbal sign-out of overnight events and template use to organize patient information. The paper-based template was praised for its organization and familiarity amongst residents, but perceived as limited by the requirement of re-copying data into the hospital’s electronic medical record (EMR). EvernoteTM excelled due to compatibility across multiple operating systems, including accessibility from clinical workstations and ability to copy notes into the hospital’s EMR. ScutsheetTM allowed for retention of data across multiple hospital days, but was limited by inability to export data or modify the electronic template. Aggregated user feedback identified the abilities to customize templates and copy information into the EMR as two prevailing characteristics that enhanced the efficiency of pre-rounding. Discussion Mobile devices offer the potential to enhance pre-rounding efficiency for medical students and residents. A customizable EvernoteTM-based system is described in sufficient detail for reproduction by interested students. PMID:24155792

Medical student appraisal: electronic resources for inpatient pre-rounding.

PubMed

Sampognaro, P J; Mitchell, S L; Weeks, S R; Khalifian, S; Markman, T M; Uebel, L W; Dattilo, J R

2013-01-01

Pre-rounding is essential to preparing for morning rounds. Despite its importance, pre-rounding is rarely formally taught within the medical school curriculum and more often informally learned by modeling residents. The evolution of mobile applications provides opportunities to optimize this process. To evaluate three options available to medical students while pre-rounding and promote adoption of mobile resources in clinical care. Six medical students formed the evaluation cohort. Students were surveyed to assess pre-rounding practices. Participants utilized paper-based pre-rounding templates for two weeks followed by two weeks of the electronic note-taking service Evernote. A review of mobile applications on the iTunes and Google Play stores was performed, with each application informally reviewed by a single student. The application Scutsheet was selected for formal review by all students. Data was collected from narrative responses supplied by students throughout the evaluation periods and aggregated to assess strengths and limitations of each application. Pre-study responses demonstrated two consistent processes: verbal sign-out of overnight events and template use to organize patient information. The paper-based template was praised for its organization and familiarity amongst residents, but perceived as limited by the requirement of re-copying data into the hospital's electronic medical record (EMR). Evernote excelled due to compatibility across multiple operating systems, including accessibility from clinical workstations and ability to copy notes into the hospital's EMR. Scutsheet allowed for retention of data across multiple hospital days, but was limited by inability to export data or modify the electronic template. Aggregated user feedback identified the abilities to customize templates and copy information into the EMR as two prevailing characteristics that enhanced the efficiency of pre-rounding. Mobile devices offer the potential to enhance pre-rounding efficiency for medical students and residents. A customizable Evernote-based system is described in sufficient detail for reproduction by interested students.

An automatic 2D–3D image matching method for reproducing spatial knee joint positions using single or dual fluoroscopic images

PubMed Central

Zhu, Zhonglin; Li, Guoan

2013-01-01

Fluoroscopic image technique, using either a single image or dual images, has been widely applied to measure in vivo human knee joint kinematics. However, few studies have compared the advantages of using single and dual fluoroscopic images. Furthermore, due to the size limitation of the image intensifiers, it is possible that only a portion of the knee joint could be captured by the fluoroscopy during dynamic knee joint motion. In this paper, we presented a systematic evaluation of an automatic 2D–3D image matching method in reproducing spatial knee joint positions using either single or dual fluoroscopic image techniques. The data indicated that for the femur and tibia, their spatial positions could be determined with an accuracy and precision less than 0.2 mm in translation and less than 0.4° in orientation when dual fluoroscopic images were used. Using single fluoroscopic images, the method could produce satisfactory accuracy in joint positions in the imaging plane (average up to 0.5 mm in translation and 1.3° in rotation), but large variations along the out-plane direction (in average up to 4.0 mm in translation and 2.28 in rotation). The precision of using single fluoroscopic images to determine the actual knee positions was worse than its accuracy obtained. The data also indicated that when using dual fluoroscopic image technique, if the knee joint outlines in one image were incomplete by 80%, the algorithm could still reproduce the joint positions with high precisions. PMID:21806411

Automated quantification of lumbar vertebral kinematics from dynamic fluoroscopic sequences

NASA Astrophysics Data System (ADS)

Camp, Jon; Zhao, Kristin; Morel, Etienne; White, Dan; Magnuson, Dixon; Gay, Ralph; An, Kai-Nan; Robb, Richard

2009-02-01

We hypothesize that the vertebra-to-vertebra patterns of spinal flexion and extension motion of persons with lower back pain will differ from those of persons who are pain-free. Thus, it is our goal to measure the motion of individual lumbar vertebrae noninvasively from dynamic fluoroscopic sequences. Two-dimensional normalized mutual information-based image registration was used to track frame-to-frame motion. Software was developed that required the operator to identify each vertebra on the first frame of the sequence using a four-point "caliper" placed at the posterior and anterior edges of the inferior and superior end plates of the target vertebrae. The program then resolved the individual motions of each vertebra independently throughout the entire sequence. To validate the technique, 6 cadaveric lumbar spine specimens were potted in polymethylmethacrylate and instrumented with optoelectric sensors. The specimens were then placed in a custom dynamic spine simulator and moved through flexion-extension cycles while kinematic data and fluoroscopic sequences were simultaneously acquired. We found strong correlation between the absolute flexionextension range of motion of each vertebra as recorded by the optoelectric system and as determined from the fluoroscopic sequence via registration. We conclude that this method is a viable way of noninvasively assessing twodimensional vertebral motion.

Effect of Off-Axis Fluoroscopy Imaging on Two-Dimensional Kinematics in the Lumbar Spine: A Dynamic In Vitro Validation Study

PubMed Central

Zhao, Kristin D.; Ben-Abraham, Ephraim I.; Magnuson, Dixon J.; Camp, Jon J.; Berglund, Lawrence J.; An, Kai-Nan; Bronfort, Gert; Gay, Ralph E.

2016-01-01

Spine intersegmental motion parameters and the resultant regional patterns may be useful for biomechanical classification of low back pain (LBP) as well as assessing the appropriate intervention strategy. Because of its availability and reasonable cost, two-dimensional (2D) fluoroscopy has great potential as a diagnostic and evaluative tool. However, the technique of quantifying intervertebral motion in the lumbar spine must be validated, and the sensitivity assessed. The purpose of this investigation was to (1) compare synchronous fluoroscopic and optoelectronic measures of intervertebral rotations during dynamic flexion–extension movements in vitro and (2) assess the effect of C-arm rotation to simulate off-axis patient alignment on intervertebral kinematics measures. Six cadaveric lumbar–sacrum specimens were dissected, and active marker optoelectronic sensors were rigidly attached to the bodies of L2–S1. Fluoroscopic sequences and optoelectronic kinematic data (0.15-mm linear, 0.17–0.20 deg rotational, accuracy) were obtained simultaneously. After images were obtained in a true sagittal plane, the image receptor was rotated in 5 deg increments (posterior oblique angulations) from 5 deg to 15 deg. Quantitative motion analysis (qma) software was used to determine the intersegmental rotations from the fluoroscopic images. The mean absolute rotation differences between optoelectronic values and dynamic fluoroscopic values were less than 0.5 deg for all the motion segments at each off-axis fluoroscopic rotation and were not significantly different (P > 0.05) for any of the off-axis rotations of the fluoroscope. Small misalignments of the lumbar spine relative to the fluoroscope did not introduce measurement variation in relative segmental rotations greater than that observed when the spine and fluoroscope were perpendicular to each other, suggesting that fluoroscopic measures of relative segmental rotation during flexion–extension are likely robust, even when patient alignment is not perfect. PMID:26974192

Effect of Off-Axis Fluoroscopy Imaging on Two-Dimensional Kinematics in the Lumbar Spine: A Dynamic In Vitro Validation Study.

PubMed

Zhao, Kristin D; Ben-Abraham, Ephraim I; Magnuson, Dixon J; Camp, Jon J; Berglund, Lawrence J; An, Kai-Nan; Bronfort, Gert; Gay, Ralph E

2016-05-01

Spine intersegmental motion parameters and the resultant regional patterns may be useful for biomechanical classification of low back pain (LBP) as well as assessing the appropriate intervention strategy. Because of its availability and reasonable cost, two-dimensional (2D) fluoroscopy has great potential as a diagnostic and evaluative tool. However, the technique of quantifying intervertebral motion in the lumbar spine must be validated, and the sensitivity assessed. The purpose of this investigation was to (1) compare synchronous fluoroscopic and optoelectronic measures of intervertebral rotations during dynamic flexion-extension movements in vitro and (2) assess the effect of C-arm rotation to simulate off-axis patient alignment on intervertebral kinematics measures. Six cadaveric lumbar-sacrum specimens were dissected, and active marker optoelectronic sensors were rigidly attached to the bodies of L2-S1. Fluoroscopic sequences and optoelectronic kinematic data (0.15-mm linear, 0.17-0.20 deg rotational, accuracy) were obtained simultaneously. After images were obtained in a true sagittal plane, the image receptor was rotated in 5 deg increments (posterior oblique angulations) from 5 deg to 15 deg. Quantitative motion analysis (qma) software was used to determine the intersegmental rotations from the fluoroscopic images. The mean absolute rotation differences between optoelectronic values and dynamic fluoroscopic values were less than 0.5 deg for all the motion segments at each off-axis fluoroscopic rotation and were not significantly different (P > 0.05) for any of the off-axis rotations of the fluoroscope. Small misalignments of the lumbar spine relative to the fluoroscope did not introduce measurement variation in relative segmental rotations greater than that observed when the spine and fluoroscope were perpendicular to each other, suggesting that fluoroscopic measures of relative segmental rotation during flexion-extension are likely robust, even when patient alignment is not perfect.

Ultrasound-guided lumbar puncture in pediatric patients: technical success and safety.

PubMed

Pierce, David B; Shivaram, Giri; Koo, Kevin S H; Shaw, Dennis W W; Meyer, Kirby F; Monroe, Eric J

2018-06-01

Disadvantages of fluoroscopically guided lumbar puncture include delivery of ionizing radiation and limited resolution of incompletely ossified posterior elements. Ultrasound (US) allows visualization of critical soft tissues and the cerebrospinal fluid (CSF) space without ionizing radiation. To determine the technical success and safety of US-guided lumbar puncture in pediatric patients. A retrospective review identified all patients referred to interventional radiology for lumbar puncture between June 2010 and June 2017. Patients who underwent lumbar puncture with fluoroscopic guidance alone were excluded. For the remaining procedures, technical success and procedural complications were assessed. Two hundred and one image-guided lumbar punctures in 161 patients were included. Eighty patients (43%) had previously failed landmark-based attempts. One hundred ninety-six (97.5%) patients underwent lumbar puncture. Five procedures (2.5%) were not attempted after US assessment, either due to a paucity of CSF or unsafe window for needle placement. Technical success was achieved in 187 (95.4%) of lumbar punctures attempted with US guidance. One hundred seventy-seven (90.3%) were technically successful with US alone (age range: 2 days-15 years, weight range: 1.9-53.1 kg) and an additional 10 (5.1%) were successful with US-guided thecal access and subsequent fluoroscopic confirmation. Three (1.5%) cases were unsuccessful with US guidance but were subsequently successful with fluoroscopic guidance. Of the 80 previously failed landmark-based lumbar punctures, 77 (96.3%) were successful with US guidance alone. There were no reported complications. US guidance is safe and effective for lumbar punctures and has specific advantages over fluoroscopy in pediatric patients.

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template

PubMed Central

Christensen, Signe; Horowitz, Scott; Bardwell, James C.A.; Olsen, Johan G.; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R.

2017-01-01

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. PMID:27659562

Computational Redesign of Thioredoxin Is Hypersensitive toward Minor Conformational Changes in the Backbone Template.

PubMed

Johansson, Kristoffer E; Tidemand Johansen, Nicolai; Christensen, Signe; Horowitz, Scott; Bardwell, James C A; Olsen, Johan G; Willemoës, Martin; Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper; Hamelryck, Thomas; Winther, Jakob R

2016-10-23

Despite the development of powerful computational tools, the full-sequence design of proteins still remains a challenging task. To investigate the limits and capabilities of computational tools, we conducted a study of the ability of the program Rosetta to predict sequences that recreate the authentic fold of thioredoxin. Focusing on the influence of conformational details in the template structures, we based our study on 8 experimentally determined template structures and generated 120 designs from each. For experimental evaluation, we chose six sequences from each of the eight templates by objective criteria. The 48 selected sequences were evaluated based on their progressive ability to (1) produce soluble protein in Escherichia coli and (2) yield stable monomeric protein, and (3) on the ability of the stable, soluble proteins to adopt the target fold. Of the 48 designs, we were able to synthesize 32, 20 of which resulted in soluble protein. Of these, only two were sufficiently stable to be purified. An X-ray crystal structure was solved for one of the designs, revealing a close resemblance to the target structure. We found a significant difference among the eight template structures to realize the above three criteria despite their high structural similarity. Thus, in order to improve the success rate of computational full-sequence design methods, we recommend that multiple template structures are used. Furthermore, this study shows that special care should be taken when optimizing the geometry of a structure prior to computational design when using a method that is based on rigid conformations. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cost of a recall of a single-center experience managing the Riata defibrillator lead.

PubMed

Hussain, Sarah; Moorman, Liza; Moorman, J Randall; DiMarco, John P; Malhotra, Rohit; Darby, Andrew; Bilchick, Kenneth; Mangrum, J Michael; Ferguson, John D; Mason, Pamela K

2015-01-15

Riata and Riata ST defibrillator leads (St. Jude Medical, Sylmar, California) were recalled in 2011 due to increased risk of insulation failure leading to externalized cables. Fluoroscopic screening can identify insulation failure, although the relation between mechanical failure and electrical failure is unclear. At the time of the recall, the University of Virginia developed a screening program, including fluoroscopic evaluation, education sessions, device interrogation, and remote monitoring for patients with this defibrillator lead. The aim of this study was to review the outcomes of the screening program, including costs, which were absorbed by our institution. Costs were calculated using Medicare reimbursement estimates. Forty-eight patients participated in the screening program. At initial screening, 31% were found to have evidence of insulation failure but electrical function was normal in all leads. The cost of this program was $35,358.72. The cost per diagnosis of mechanical lead failure was $2,357.25. During 2 years of follow-up, 1 patient experienced Riata lead electrical failure without fluoroscopic evidence of insulation failure. Patients were more likely to have a lead revision if there was evidence of insulation failure. Lead revisions occurred at the time of generator change in 88% of patients with insulation failure but in only 14% of patients with a fluoroscopically normal lead (p = 0.04). The cost of recall-related defibrillator lead revisions was $81,704.55. In conclusion, our Riata screening program added expense without clear benefit to patients. In fact, patients may have been put at more risk by undergoing defibrillator lead revisions based solely on the results of the fluoroscopic screening. Copyright © 2015 Elsevier Inc. All rights reserved.

Short template switch events explain mutation clusters in the human genome.

PubMed

Löytynoja, Ari; Goldman, Nick

2017-06-01

Resequencing efforts are uncovering the extent of genetic variation in humans and provide data to study the evolutionary processes shaping our genome. One recurring puzzle in both intra- and inter-species studies is the high frequency of complex mutations comprising multiple nearby base substitutions or insertion-deletions. We devised a generalized mutation model of template switching during replication that extends existing models of genome rearrangement and used this to study the role of template switch events in the origin of short mutation clusters. Applied to the human genome, our model detects thousands of template switch events during the evolution of human and chimp from their common ancestor and hundreds of events between two independently sequenced human genomes. Although many of these are consistent with a template switch mechanism previously proposed for bacteria, our model also identifies new types of mutations that create short inversions, some flanked by paired inverted repeats. The local template switch process can create numerous complex mutation patterns, including hairpin loop structures, and explains multinucleotide mutations and compensatory substitutions without invoking positive selection, speculative mechanisms, or implausible coincidence. Clustered sequence differences are challenging for current mapping and variant calling methods, and we show that many erroneous variant annotations exist in human reference data. Local template switch events may have been neglected as an explanation for complex mutations because of biases in commonly used analyses. Incorporation of our model into reference-based analysis pipelines and comparisons of de novo assembled genomes will lead to improved understanding of genome variation and evolution. © 2017 Löytynoja and Goldman; Published by Cold Spring Harbor Laboratory Press.

Precision of computer-assisted core decompression drilling of the knee.

PubMed

Beckmann, J; Goetz, J; Bäthis, H; Kalteis, T; Grifka, J; Perlick, L

2006-06-01

Core decompression by exact drilling into the ischemic areas is the treatment of choice in early stages of osteonecrosis of the femoral condyle. Computer-aided surgery might enhance the precision of the drilling and lower the radiation exposure time of both staff and patients. The aim of this study was to evaluate the precision of the fluoroscopically based VectorVision-navigation system in an in vitro model. Thirty sawbones were prepared with a defect filled up with a radiopaque gypsum sphere mimicking the osteonecrosis. 20 sawbones were drilled by guidance of an intraoperative navigation system VectorVision (BrainLAB, Munich, Germany). Ten sawbones were drilled by fluoroscopic control only. A statistically significant difference with a mean distance of 0.58 mm in the navigated group and 0.98 mm in the control group regarding the distance to the desired mid-point of the lesion could be stated. Significant difference was further found in the number of drilling corrections as well as radiation time needed. The fluoroscopic-based VectorVision-navigation system shows a high feasibility and precision of computer-guided drilling with simultaneously reduction of radiation time and therefore could be integrated into clinical routine.

Multiview human activity recognition system based on spatiotemporal template for video surveillance system

NASA Astrophysics Data System (ADS)

Kushwaha, Alok Kumar Singh; Srivastava, Rajeev

2015-09-01

An efficient view invariant framework for the recognition of human activities from an input video sequence is presented. The proposed framework is composed of three consecutive modules: (i) detect and locate people by background subtraction, (ii) view invariant spatiotemporal template creation for different activities, (iii) and finally, template matching is performed for view invariant activity recognition. The foreground objects present in a scene are extracted using change detection and background modeling. The view invariant templates are constructed using the motion history images and object shape information for different human activities in a video sequence. For matching the spatiotemporal templates for various activities, the moment invariants and Mahalanobis distance are used. The proposed approach is tested successfully on our own viewpoint dataset, KTH action recognition dataset, i3DPost multiview dataset, MSR viewpoint action dataset, VideoWeb multiview dataset, and WVU multiview human action recognition dataset. From the experimental results and analysis over the chosen datasets, it is observed that the proposed framework is robust, flexible, and efficient with respect to multiple views activity recognition, scale, and phase variations.

The application of high-resolution mass spectrometry-based data-mining tools in tandem to metabolite profiling of a triple drug combination in humans.

PubMed

Xing, Jie; Zang, Meitong; Zhang, Haiying; Zhu, Mingshe

2015-10-15

Patients are usually exposed to multiple drugs, and metabolite profiling of each drug in complex biological matrices is a big challenge. This study presented a new application of an improved high resolution mass spectrometry (HRMS)-based data-mining tools in tandem to fast and comprehensive metabolite identification of combination drugs in human. The model drug combination was metronidazole-pantoprazole-clarithromycin (MET-PAN-CLAR), which is widely used in clinic to treat ulcers caused by Helicobacter pylori. First, mass defect filter (MDF), as a targeted data processing tool, was able to recover all relevant metabolites of MET-PAN-CLAR in human plasma and urine from the full-scan MS dataset when appropriate MDF templates for each drug were defined. Second, the accurate mass-based background subtraction (BS), as an untargeted data-mining tool, worked effectively except for several trace metabolites, which were buried in the remaining background signals. Third, an integrated strategy, i.e., untargeted BS followed by improved MDF, was effective for metabolite identification of MET-PAN-CLAR. Most metabolites except for trace ones were found in the first step of BS-processed datasets, and the results led to the setup of appropriate metabolite MDF template for the subsequent MDF data processing. Trace metabolites were further recovered by MDF, which used both common MDF templates and the novel metabolite-based MDF templates. As a result, a total of 44 metabolites or related components were found for MET-PAN-CLAR in human plasma and urine using the integrated strategy. New metabolic pathways such as N-glucuronidation of PAN and dehydrogenation of CLAR were found. This study demonstrated that the combination of accurate mass-based multiple data-mining techniques in tandem, i.e., untargeted background subtraction followed by targeted mass defect filtering, can be a valuable tool for rapid metabolite profiling of combination drugs in vivo. Copyright © 2015 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Woong Hee; Kim, Jin Hyoung, E-mail: m1fenew@daum.net; Park, Jung-Hun

Purpose: Little was known about the safety and long-term efficacy of fluoroscopically guided balloon dilation for postintubation tracheal stenosis. The purpose of this study was to evaluate the safety and long-term efficacy of fluoroscopically guided balloon dilation in patients with postintubation tracheal stenosis. Methods: From February 2000 to November 2010, 14 patients underwent fluoroscopically guided balloon dilation for postintubation tracheal stenosis. Technical success, clinical success, and complications were evaluated. Patients were followed up for recurrent symptoms. Results: In all patients, fluoroscopically guided balloon dilation was technically and clinically successful with no major complications. Following the initial procedure, six patients (43more » %) remained asymptomatic during a follow-up period. Obstructive symptoms recurred in eight patients (57 %) within 6 months (mean, 1.7 months), who were treated with repeat balloon dilation (n = 4) and other therapies. Of the four patients who underwent repeat balloon dilation, three became asymptomatic. One patient became asymptomatic after a third balloon dilation. On long-term (mean, 74 months) follow-up, 71 % of patients experienced relief of symptoms following fluoroscopically guided balloon dilation. Conclusions: Fluoroscopically guided balloon dilation may be safe, is easy to perform, and resulted in effective treatment in patients with postintubation tracheal stenosis.« less

Fluoroscopic Placement of Double-Pigtail Ureteral Stents

PubMed Central

Chen, Gregory L.

2001-01-01

Purpose: Double-pigtail ureteral stent is placed cystoscopically after ureteroscopy. We describe a technique for fluoroscopic placement of ureteral stents and demonstrate its use in a non-randomized prospective study. Materials and methods: Double-pigtail stents were placed either fluoroscopically or cystoscopically in 121 consecutive patients. In the fluoroscopic method, the stent was placed over a guide wire using a stent pusher without the use of cystoscopy. Conversely, stents were placed through the working channel of the cystoscope under vision. The procedure, stent length, width, type, method, ureteral dilation, and use of a retrieval string were noted. Results: A wide range of stent sizes were used. The success with fluoroscopic placement of double-pigtail ureteral stents was 100% (89 of 89 cases). No stents migrated or required replacement. Stents were placed after ureteroscopic laser lithotripsy (53/89) and ureteroscopic tumor treatment (22/89). Cystoscopic visualization was used in 32 additional procedures requiring precise control (15 ureteral strictures and nine retrograde endopyelotomy). Conclusions: The fluoroscopic placement of ureteral stents is a safe and simple technique with a very high success rate. We have used cystoscopic placement only after incisional procedures such as retrograde endopyelotomy, stricture or ureterotomy. PMID:18493562

A pilot study of a heuristic algorithm for novel template identification from VA electronic medical record text.

PubMed

Redd, Andrew M; Gundlapalli, Adi V; Divita, Guy; Carter, Marjorie E; Tran, Le-Thuy; Samore, Matthew H

2017-07-01

Templates in text notes pose challenges for automated information extraction algorithms. We propose a method that identifies novel templates in plain text medical notes. The identification can then be used to either include or exclude templates when processing notes for information extraction. The two-module method is based on the framework of information foraging and addresses the hypothesis that documents containing templates and the templates within those documents can be identified by common features. The first module takes documents from the corpus and groups those with common templates. This is accomplished through a binned word count hierarchical clustering algorithm. The second module extracts the templates. It uses the groupings and performs a longest common subsequence (LCS) algorithm to obtain the constituent parts of the templates. The method was developed and tested on a random document corpus of 750 notes derived from a large database of US Department of Veterans Affairs (VA) electronic medical notes. The grouping module, using hierarchical clustering, identified 23 groups with 3 documents or more, consisting of 120 documents from the 750 documents in our test corpus. Of these, 18 groups had at least one common template that was present in all documents in the group for a positive predictive value of 78%. The LCS extraction module performed with 100% positive predictive value, 94% sensitivity, and 83% negative predictive value. The human review determined that in 4 groups the template covered the entire document, with the remaining 14 groups containing a common section template. Among documents with templates, the number of templates per document ranged from 1 to 14. The mean and median number of templates per group was 5.9 and 5, respectively. The grouping method was successful in finding like documents containing templates. Of the groups of documents containing templates, the LCS module was successful in deciphering text belonging to the template and text that was extraneous. Major obstacles to improved performance included documents composed of multiple templates, templates that included other templates embedded within them, and variants of templates. We demonstrate proof of concept of the grouping and extraction method of identifying templates in electronic medical records in this pilot study and propose methods to improve performance and scaling up. Published by Elsevier Inc.

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of National Ignition Facility high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retroreflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guaranteesmore » stable position estimation.« less

Centroid stabilization for laser alignment to corner cubes: designing a matched filter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awwal, Abdul A. S.; Bliss, Erlan; Brunton, Gordon

2016-11-08

Automation of image-based alignment of NIF high energy laser beams is providing the capability of executing multiple target shots per day. One important alignment is beam centration through the second and third harmonic generating crystals in the final optics assembly (FOA), which employs two retro-reflecting corner cubes as centering references for each beam. Beam-to-beam variations and systematic beam changes over time in the FOA corner cube images can lead to a reduction in accuracy as well as increased convergence durations for the template-based position detector. A systematic approach is described that maintains FOA corner cube templates and guarantees stable positionmore » estimation.« less

78 FR 65440 - Notice of Funds Availability (NOFA) Inviting Applications for the Native American CDFI Assistance...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-10-31

... of multiple mandatory documents including: (1) a PDF fillable Applicant intake form; (2) a Microsoft Excel Workbook; (3) a Microsoft Word Narrative template; and (4) other mandatory attachments. (Applicants must use the Microsoft Word Narrative template the CDFI Fund provides; alternative templates...

C-arm cone beam computed tomography needle path overlay for fluoroscopic guided vertebroplasty.

PubMed

Tam, Alda L; Mohamed, Ashraf; Pfister, Marcus; Chinndurai, Ponraj; Rohm, Esther; Hall, Andrew F; Wallace, Michael J

2010-05-01

Retrospective review. To report our early clinical experience using C-arm cone beam computed tomography (C-arm CBCT) with fluoroscopic overlay for needle guidance during vertebroplasty. C-arm CBCT is advanced three-dimensional (3-D) imaging technology that is currently available on state-of-the-art flat panel based angiography systems. The imaging information provided by C-arm CBCT allows for the acquisition and reconstruction of "CT-like" images in flat panel based angiography/interventional suites. As part of the evolution of this technology, enhancements allowing the overlay of cross-sectional imaging information can now be integrated with real time fluoroscopy. We report our early clinical experience with C-arm CBCT with fluoroscopic overlay for needle guidance during vertebroplasty. This is a retrospective review of 10 consecutive oncology patients who underwent vertebroplasty of 13 vertebral levels using C-arm CBCT with fluoroscopic overlay for needle guidance from November 2007 to December 2008. Procedural data including vertebral level, approach (transpedicular vs. extrapedicular), access (bilateral vs. unilateral) and complications were recorded. Technical success with the overlay technology was assessed based on accuracy which consisted of 4 measured parameters: distance from target to needle tip, distance from planned path to needle tip, distance from midline to needle tip, and distance from the anterior 1/3 of the vertebral body to needle tip. Success within each parameter required that the distance between the needle tip and parameter being evaluated be no more than 5 mm on multiplanar CBCT or fluoroscopy. Imaging data for 12 vertebral levels was available for review. All vertebral levels were treated using unilateral access and 9 levels were treated with an extrapedicular approach. Technical success rates were 92% for both distance from planned path and distance from midline to final needle tip, 100% when distance from needle tip to the anterior 1/3 border of the vertebral body was measured, and 75% when distance from target to needle tip was measured. There were no major complications. Minor complications consisted of 3 cases (25%) of cement extravasation. C-arm CBCT with needle path overlay for fluoroscopic guided vertebroplasty is feasible and allows for reliable unilateral therapy of both lumbar and thoracic vertebral bodies. Extrapedicular approaches were performed safely and with good accuracy of reaching the targets.

Computer vision-based diameter maps to study fluoroscopic recordings of small intestinal motility from conscious experimental animals.

PubMed

Ramírez, I; Pantrigo, J J; Montemayor, A S; López-Pérez, A E; Martín-Fontelles, M I; Brookes, S J H; Abalo, R

2017-08-01

When available, fluoroscopic recordings are a relatively cheap, non-invasive and technically straightforward way to study gastrointestinal motility. Spatiotemporal maps have been used to characterize motility of intestinal preparations in vitro, or in anesthetized animals in vivo. Here, a new automated computer-based method was used to construct spatiotemporal motility maps from fluoroscopic recordings obtained in conscious rats. Conscious, non-fasted, adult, male Wistar rats (n=8) received intragastric administration of barium contrast, and 1-2 hours later, when several loops of the small intestine were well-defined, a 2 minutes-fluoroscopic recording was obtained. Spatiotemporal diameter maps (Dmaps) were automatically calculated from the recordings. Three recordings were also manually analyzed for comparison. Frequency analysis was performed in order to calculate relevant motility parameters. In each conscious rat, a stable recording (17-20 seconds) was analyzed. The Dmaps manually and automatically obtained from the same recording were comparable, but the automated process was faster and provided higher resolution. Two frequencies of motor activity dominated; lower frequency contractions (15.2±0.9 cpm) had an amplitude approximately five times greater than higher frequency events (32.8±0.7 cpm). The automated method developed here needed little investigator input, provided high-resolution results with short computing times, and automatically compensated for breathing and other small movements, allowing recordings to be made without anesthesia. Although slow and/or infrequent events could not be detected in the short recording periods analyzed to date (17-20 seconds), this novel system enhances the analysis of in vivo motility in conscious animals. © 2017 John Wiley & Sons Ltd.

Psychophysical evaluation of the image quality of a dynamic flat-panel digital x-ray image detector using the threshold contrast detail detectability (TCDD) technique

NASA Astrophysics Data System (ADS)

Davies, Andrew G.; Cowen, Arnold R.; Bruijns, Tom J. C.

1999-05-01

We are currently in an era of active development of the digital X-ray imaging detectors that will serve the radiological communities in the new millennium. The rigorous comparative physical evaluations of such devices are therefore becoming increasingly important from both the technical and clinical perspectives. The authors have been actively involved in the evaluation of a clinical demonstration version of a flat-panel dynamic digital X-ray image detector (or FDXD). Results of objective physical evaluation of this device have been presented elsewhere at this conference. The imaging performance of FDXD under radiographic exposure conditions have been previously reported, and in this paper a psychophysical evaluation of the FDXD detector operating under continuous fluoroscopic conditions is presented. The evaluation technique employed was the threshold contrast detail detectability (TCDD) technique, which enables image quality to be measured on devices operating in the clinical environment. This approach addresses image quality in the context of both the image acquisition and display processes, and uses human observers to measure performance. The Leeds test objects TO[10] and TO[10+] were used to obtain comparative measurements of performance on the FDXD and two digital spot fluorography (DSF) systems, one utilizing a Plumbicon camera and the other a state of the art CCD camera. Measurements were taken at a range of detector entrance exposure rates, namely 6, 12, 25 and 50 (mu) R/s. In order to facilitate comparisons between the systems, all fluoroscopic image processing such as noise reduction algorithms, were disabled during the experiments. At the highest dose rate FDXD significantly outperformed the DSF comparison systems in the TCDD comparisons. At 25 and 12 (mu) R/s all three-systems performed in an equivalent manner and at the lowest exposure rate FDXD was inferior to the two DSF systems. At standard fluoroscopic exposures, FDXD performed in an equivalent manner to the DSF systems for the TCDD comparisons. This would suggest that FDXD would therefore perform adequately in a clinical fluoroscopic environment and our initial clinical experiences support this. Noise reduction processing of the fluoroscopic data acquired on FDXD was also found to further improve TCDD performance for FDXD. FDXD therefore combines acceptable fluoroscopic performance with excellent radiographic (snap shot) imaging fidelity, allowing the possibility of a universal x-ray detector to be developed, based on FDXD's technology. It is also envisaged that fluoroscopic performance will be improved by the development of digital image enhancement techniques specifically tailored to the characteristics of the FDXD detector.

The Applicability of Interactive Item Templates in Varied Knowledge Types

ERIC Educational Resources Information Center

Koong, Chorng-Shiuh; Wu, Chi-Ying

2011-01-01

A well-edited assessment can enhance student's learning motives. Applicability of items, which includes item content and template, plays a crucial role in authoring a good assessment. Templates in discussion contain not only conventional true & false, multiple choice, completion item and short answer but also of those interactive ones. Methods…

The Contextualization of Archetypes: Clinical Template Governance.

PubMed

Pedersen, Rune; Ulriksen, Gro-Hilde; Ellingsen, Gunnar

2015-01-01

This paper is a status report from a large-scale openEHR-based EPR project from the North Norway Regional Health Authority. It concerns the standardization of a regional ICT portfolio and the ongoing development of a new process oriented EPR systems encouraged by the unfolding of a national repository for openEHR archetypes. Subject of interest; the contextualization of clinical templates is governed over multiple national boundaries which is complex due to the dependency of clinical resources. From the outset of this, we are interested in how local, regional, and national organizers maneuver to standardize while applying OpenEHR technology.

SU-D-209-02: Percent Depth Dose Curves for Fluoroscopic X-Ray Beam Qualities Incorporating Copper Filtration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wunderle, K; Wayne State University School of Medicine, Detroit, MI; Godley, A

Purpose: The purpose of this investigation was to quantify percent depth dose (PDD) curves for fluoroscopic x-ray beam qualities incorporating added copper filtration. Methods: A PTW (Freiburg, Germany) MP3 water tank was used with a Standard Imaging (Middleton, WI) Exradin Model 11 Spokas Chamber to measure PDD curves for 60, 80, 100 and 120 kVp x-ray beams with copper filtration ranging from 0.0–0.9 mm at 22cm and 42cm fields of view from 0 to 150 mm of water. A free-in-air monitor chamber was used to normalize the water tank data to fluctuations in output from the fluoroscope. The measurements weremore » acquired on a Siemens (Erlangen, Germany) Artis ZeeGo fluoroscope. The fluoroscope was inverted from the typical orientation providing an x-ray beam originating from above the water tank. The water tank was positioned so that the water level was located at 60cm from the focal spot; which also represents the focal spot to interventional reference plane distance for that fluoroscope. Results: PDDs for 60, 80, 100, and 120 kVp with 0 mm of copper filtration compared well to previously published data by Fetterly et al. [Med Phys, 28, 205 (2001)] for those beam qualities given differences in fluoroscopes, geometric orientation, type of ionization chamber, and the water tank used for data collection. PDDs for 60, 80, 100, and 120 kVp with copper filtration were obtained and are presented, which have not been previously investigated and published. Conclusion: The equipment and processes used to acquire the reported data were sound and compared well with previously published data for PDDs without copper filtration. PDD data for the fluoroscopic x-ray beams incorporating copper filtration can be used as reference data for estimating organ or soft tissue dose at depth involving similar beam qualities or for comparison with mathematical models.« less

Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio folding and FG-MD-based structure refinement

PubMed Central

Xu, Dong; Zhang, Jian; Roy, Ambrish; Zhang, Yang

2011-01-01

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and FG-MD, were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for structure modeling of proteins that lack detectable template structures. For distantly homologous targets, QUARK models are found useful as a reference structure for selecting good threading alignments and guiding the I-TASSER structure assembly simulations. FG-MD is an atomic-level structural refinement program that uses structural fragments collected from the PDB structures to guide molecular dynamics simulation and improve the local structure of predicted model, including hydrogen-bonding networks, torsion angles and steric clashes. Despite considerable progress in both the template-based and template-free structure modeling, significant improvements on protein target classification, domain parsing, model selection, and ab initio folding of beta-proteins are still needed to further improve the I-TASSER pipeline. PMID:22069036

Magnetic molecularly imprinted polymers based on silica modified by deep eutectic solvents for the rapid simultaneous magnetic-based solid-phase extraction of Salvia miltiorrhiza bunge, Glycine max (Linn.) Merr and green tea.

PubMed

Li, Guizhen; Wang, Xiaoqin; Row, Kyung Ho

2018-04-01

Novel magnetic molecularly imprinted polymers (MMIPs) with multiple-template based on silica were modified by four types of deep eutectic solvents (DESs) for the rapid simultaneous magnetic solid-phase extraction (MSPE) of tanshinone Ⅰ, tanshinone ⅡA, and cryptotanshinone from Salvia miltiorrhiza bunge; glycitein, genistein, and daidzein from Glycine max (Linn.) Merr; and epicatechin, epigallocatechin gallate, and epicatechin gallate from green tea, respectively. The synthesized materials were characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscopy. Single factor experiments were to explore the relationship between the extraction efficiency and four factors (the sample solution pH, amount of DESs for modification, amount of adsorbent, and extraction time). It was showed that the DES4-MMIPs have better extraction ability than the MMIPs without DESs and the other three DESs-modified MMIPs. The best extraction recoveries with DES4-MMIP were tanshinone Ⅰ (85.57%), tanshinone ⅡA (80.58%), cryptotanshinone (92.12%), glycitein (81.65%), genistein (87.72%), daidzein (92.24%), epicatechin (86.43%), epigallocatechin gallate (80.92%), and epicatechin gallate (93.64%), respectively. The novel multiple-template MMIPs materials modified by DES for the rapid simultaneous MSPE of active compounds were proved to reduce the experimental steps than single-template technique, and increase the extraction efficiency. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

40 CFR Appendix C to Subpart Nnn... - Method for the Determination of Product Density

Code of Federal Regulations, 2011 CFR

2011-07-01

... insulation. The method is applicable to all cured board and blanket products. 2. Equipment One square foot (12 in. by 12 in.) template, or templates that are multiples of one square foot, for use in cutting... procedure for the designated product. 3.2Cut samples using one square foot (or multiples of one square foot...

40 CFR Appendix C to Subpart Nnn... - Method for the Determination of Product Density

Code of Federal Regulations, 2012 CFR

2012-07-01

.... The method is applicable to all cured board and blanket products. 2. Equipment One square foot (12 in. by 12 in.) template, or templates that are multiples of one square foot, for use in cutting... procedure for the designated product. 3.2Cut samples using one square foot (or multiples of one square foot...

40 CFR Appendix C to Subpart Nnn... - Method for the Determination of Product Density

Code of Federal Regulations, 2010 CFR

2010-07-01

.... The method is applicable to all cured board and blanket products. 2. Equipment One square foot (12 in. by 12 in.) template, or templates that are multiples of one square foot, for use in cutting... procedure for the designated product. 3.2Cut samples using one square foot (or multiples of one square foot...

Characterizing stroke lesions using digital templates and lesion quantification tools in a web-based imaging informatics system for a large-scale stroke rehabilitation clinical trial

NASA Astrophysics Data System (ADS)

Wang, Ximing; Edwardson, Matthew; Dromerick, Alexander; Winstein, Carolee; Wang, Jing; Liu, Brent

2015-03-01

Previously, we presented an Interdisciplinary Comprehensive Arm Rehabilitation Evaluation (ICARE) imaging informatics system that supports a large-scale phase III stroke rehabilitation trial. The ePR system is capable of displaying anonymized patient imaging studies and reports, and the system is accessible to multiple clinical trial sites and users across the United States via the web. However, the prior multicenter stroke rehabilitation trials lack any significant neuroimaging analysis infrastructure. In stroke related clinical trials, identification of the stroke lesion characteristics can be meaningful as recent research shows that lesion characteristics are related to stroke scale and functional recovery after stroke. To facilitate the stroke clinical trials, we hope to gain insight into specific lesion characteristics, such as vascular territory, for patients enrolled into large stroke rehabilitation trials. To enhance the system's capability for data analysis and data reporting, we have integrated new features with the system: a digital brain template display, a lesion quantification tool and a digital case report form. The digital brain templates are compiled from published vascular territory templates at each of 5 angles of incidence. These templates were updated to include territories in the brainstem using a vascular territory atlas and the Medical Image Processing, Analysis and Visualization (MIPAV) tool. The digital templates are displayed for side-by-side comparisons and transparent template overlay onto patients' images in the image viewer. The lesion quantification tool quantifies planimetric lesion area from user-defined contour. The digital case report form stores user input into a database, then displays contents in the interface to allow for reviewing, editing, and new inputs. In sum, the newly integrated system features provide the user with readily-accessible web-based tools to identify the vascular territory involved, estimate lesion area, and store these results in a web-based digital format.

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11

PubMed Central

Cao, Renzhi; Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2015-01-01

Model evaluation and selection is an important step and a big challenge in template-based protein structure prediction. Individual model quality assessment methods designed for recognizing some specific properties of protein structures often fail to consistently select good models from a model pool because of their limitations. Therefore, combining multiple complimentary quality assessment methods is useful for improving model ranking and consequently tertiary structure prediction. Here, we report the performance and analysis of our human tertiary structure predictor (MULTICOM) based on the massive integration of 14 diverse complementary quality assessment methods that was successfully benchmarked in the 11th Critical Assessment of Techniques of Protein Structure prediction (CASP11). The predictions of MULTICOM for 39 template-based domains were rigorously assessed by six scoring metrics covering global topology of Cα trace, local all-atom fitness, side chain quality, and physical reasonableness of the model. The results show that the massive integration of complementary, diverse single-model and multi-model quality assessment methods can effectively leverage the strength of single-model methods in distinguishing quality variation among similar good models and the advantage of multi-model quality assessment methods of identifying reasonable average-quality models. The overall excellent performance of the MULTICOM predictor demonstrates that integrating a large number of model quality assessment methods in conjunction with model clustering is a useful approach to improve the accuracy, diversity, and consequently robustness of template-based protein structure prediction. PMID:26369671

Centriole overduplication through the concurrent formation of multiple daughter centrioles at single maternal templates.

PubMed

Duensing, A; Liu, Y; Perdreau, S A; Kleylein-Sohn, J; Nigg, E A; Duensing, S

2007-09-20

Abnormal centrosome numbers are detected in virtually all cancers. The molecular mechanisms that underlie centrosome amplification, however, are poorly characterized. Based on the model that each maternal centriole serves as a template for the formation of one and only one daughter centriole per cell division cycle, the prevailing view is that centriole overduplication arises from successive rounds of centriole reproduction. Here, we provide evidence that a single maternal centriole can concurrently generate multiple daughter centrioles. This mechanism was initially identified in cells treated with the peptide vinyl sulfone proteasome inhibitor Z-L(3)VS. We subsequently found that the formation of more than one daughter at maternal centrioles requires cyclin E/cyclin-dependent kinase 2 as well as Polo-like kinase 4 and that overexpression of these proteins mimics this phenotype in the absence of a proteasome inhibitor. Moreover, we show that the human papillomavirus type 16 E7 oncoprotein stimulates aberrant daughter centriole numbers in part through the formation of more than one daughter centriole at single maternal templates. These results help to explain how oncogenic stimuli can rapidly induce abnormal centriole numbers within a single cell-division cycle and provide insights into the regulation of centriole duplication.

A linear concatenation strategy to construct 5'-enriched amplified cDNA libraries using multiple displacement amplification.

PubMed

Gadkar, Vijay J; Filion, Martin

2013-06-01

In various experimental systems, limiting available amounts of RNA may prevent a researcher from performing large-scale analyses of gene transcripts. One way to circumvent this is to 'pre-amplify' the starting RNA/cDNA, so that sufficient amounts are available for any downstream analysis. In the present study, we report the development of a novel protocol for constructing amplified cDNA libraries using the Phi29 DNA polymerase based multiple displacement amplification (MDA) system. Using as little as 200 ng of total RNA, we developed a linear concatenation strategy to make the single-stranded cDNA template amenable for MDA. The concatenation, made possible by the template switching property of the reverse transcriptase enzyme, resulted in the amplified cDNA library with intact 5' ends. MDA generated micrograms of template, allowing large-scale polymerase chain reaction analyses or other large-scale downstream applications. As the amplified cDNA library contains intact 5' ends, it is also compatible with 5' RACE analyses of specific gene transcripts. Empirical validation of this protocol is demonstrated on a highly characterized (tomato) and an uncharacterized (corn gromwell) experimental system.

Fluoroscopically guided closed reduction and internal fixation of fractures of the lateral portion of the humeral condyle: prospective clinical study of the technique and results in ten dogs.

PubMed

Cook, J L; Tomlinson, J L; Reed, A L

1999-01-01

To report a technique for fluoroscopically guided closed reduction with internal fixation of fractures of the lateral portion of the humeral condyle (FLHC) and determine the long-term results in 10 clinical cases. Prospective clinical case study. Ten dogs with 11 fractures. Fractures of the lateral portion of the humeral condyle were stabilized with transcondylar screws and Kirschner wires. Closed reduction and implant placement were achieved using intraoperative fluoroscopic guidance. After fracture repair, postoperative radiographs were evaluated for articular alignment and implant placement. Dogs were evaluated after surgery by means of lameness scores, elbow range of motion (ROM), radiographic assessment, and owner evaluation of function. Postoperative reduction was considered anatomic in 6 fractures with all other fractures having <1.5 mm of malreduction. Follow-up was available for 9 patients from 9 to 21 months after surgery. All of the fractures had healed. One minor (wire migration) and one major (implant failure) complication occurred. Mean lameness scores were 0 (n = 6), 0.5 (n = 2), and 1 (n = 1) at the time of final follow-up. No significant differences were found in follow-up ROM values between affected and unaffected elbows. All of the dogs in this study regained 90-100% of full function, based on owner assessment. Fluoroscopic guidance for closed reduction and internal fixation of FLHC in dogs is an effective technique.

Cryo-balloon catheter localization in fluoroscopic images

NASA Astrophysics Data System (ADS)

Kurzendorfer, Tanja; Brost, Alexander; Jakob, Carolin; Mewes, Philip W.; Bourier, Felix; Koch, Martin; Kurzidim, Klaus; Hornegger, Joachim; Strobel, Norbert

2013-03-01

Minimally invasive catheter ablation has become the preferred treatment option for atrial fibrillation. Although the standard ablation procedure involves ablation points set by radio-frequency catheters, cryo-balloon catheters have even been reported to be more advantageous in certain cases. As electro-anatomical mapping systems do not support cryo-balloon ablation procedures, X-ray guidance is needed. However, current methods to provide support for cryo-balloon catheters in fluoroscopically guided ablation procedures rely heavily on manual user interaction. To improve this, we propose a first method for automatic cryo-balloon catheter localization in fluoroscopic images based on a blob detection algorithm. Our method is evaluated on 24 clinical images from 17 patients. The method successfully detected the cryoballoon in 22 out of 24 images, yielding a success rate of 91.6 %. The successful localization achieved an accuracy of 1.00 mm +/- 0.44 mm. Even though our methods currently fails in 8.4 % of the images available, it still offers a significant improvement over manual methods. Furthermore, detecting a landmark point along the cryo-balloon catheter can be a very important step for additional post-processing operations.

A low-cost, durable, combined ultrasound and fluoroscopic phantom for cervical transforaminal injections.

PubMed

Lerman, Imanuel R; Souzdalnitski, Dmitri; Narouze, Samer

2012-01-01

This technical report describes a durable, low-cost, anatomically accurate, and easy-to-prepare combined ultrasound (US) and fluoroscopic phantom of the cervical spine. This phantom is meant to augment training in US- and fluoroscopic-guided pain medicine procedures. The combined US and fluoroscopic phantom (CUF-P) is prepared from commercially available liquid plastic that is ordinarily used to prepare synthetic fishing lures. The liquid plastic is heated and then poured into a metal canister that houses an anatomical cervical spine model. Drops of dark purple dye are added to make the phantom opaque. After cooling, tubing is attached to the CUF-P to simulate blood vessels. The CUF-P accurately simulates human tissue by imitating both the tactile texture of skin and the haptic resistance of human tissue as the needle is advanced. This phantom contains simulated fluid-filled vertebral arteries that exhibit pulsed flow under color Doppler US. Under fluoroscopic examination, the CUF-P-simulated vertebral arteries also exhibit uptake of contrast dye if mistakenly injected. The creation of a training phantom allows the pain physician to practice needle positioning technique while simultaneously visualizing both targeted and avoidable vascular structures under US and fluoroscopic guidance. This low-cost CUF-P is easy to prepare and is reusable, making it an attractive alternative to current homemade and commercially available phantom simulators.

Security enhanced BioEncoding for protecting iris codes

NASA Astrophysics Data System (ADS)

Ouda, Osama; Tsumura, Norimichi; Nakaguchi, Toshiya

2011-06-01

Improving the security of biometric template protection techniques is a key prerequisite for the widespread deployment of biometric technologies. BioEncoding is a recently proposed template protection scheme, based on the concept of cancelable biometrics, for protecting biometric templates represented as binary strings such as iris codes. The main advantage of BioEncoding over other template protection schemes is that it does not require user-specific keys and/or tokens during verification. Besides, it satisfies all the requirements of the cancelable biometrics construct without deteriorating the matching accuracy. However, although it has been shown that BioEncoding is secure enough against simple brute-force search attacks, the security of BioEncoded templates against more smart attacks, such as record multiplicity attacks, has not been sufficiently investigated. In this paper, a rigorous security analysis of BioEncoding is presented. Firstly, resistance of BioEncoded templates against brute-force attacks is revisited thoroughly. Secondly, we show that although the cancelable transformation employed in BioEncoding might be non-invertible for a single protected template, the original iris code could be inverted by correlating several templates used in different applications but created from the same iris. Accordingly, we propose an important modification to the BioEncoding transformation process in order to hinder attackers from exploiting this type of attacks. The effectiveness of adopting the suggested modification is validated and its impact on the matching accuracy is investigated empirically using CASIA-IrisV3-Interval dataset. Experimental results confirm the efficacy of the proposed approach and show that it preserves the matching accuracy of the unprotected iris recognition system.

PoLi: A Virtual Screening Pipeline Based On Template Pocket And Ligand Similarity

PubMed Central

Roy, Ambrish; Srinivasan, Bharath; Skolnick, Jeffrey

2015-01-01

Often in pharmaceutical research, the goal is to identify small molecules that can interact with and appropriately modify the biological behavior of a new protein target. Unfortunately, most proteins lack both known structures and small molecule binders, prerequisites of many virtual screening, VS, approaches. For such proteins, ligand homology modeling, LHM, that copies ligands from homologous and perhaps evolutionarily distant template proteins, has been shown to be a powerful VS approach to identify possible binding ligands. However, if we want to target a specific pocket for which there is no homologous holo template protein structure, then LHM will not work. To address this issue, in a new pocket based approach, PoLi, we generalize LHM by exploiting the fact that the number of distinct small molecule ligand binding pockets in proteins is small. PoLi identifies similar ligand binding pockets in a holo-template protein library, selectively copies relevant parts of template ligands and uses them for VS. In practice, PoLi is a hybrid structure and ligand based VS algorithm that integrates 2D fingerprint-based and 3D shape-based similarity metrics for improved virtual screening performance. On standard DUD and DUD-E benchmark databases, using modeled receptor structures, PoLi achieves an average enrichment factor of 13.4 and 9.6 respectively, in the top 1% of the screened library. In contrast, traditional docking based VS using AutoDock Vina and homology-based VS using FINDSITEfilt have an average enrichment of 1.6 (3.0) and 9.0 (7.9) on the DUD (DUD-E) sets respectively. Experimental validation of PoLi predictions on dihydrofolate reductase, DHFR, using differential scanning fluorimetry, DSF, identifies multiple ligands with diverse molecular scaffolds, thus demonstrating the advantage of PoLi over current state-of-the-art VS methods. PMID:26225536

Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index

PubMed Central

Tsai, Yu-Shuen; Aguan, Kripamoy; Pal, Nikhil R.; Chung, I-Fang

2011-01-01

Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing drug on other diseases as well as designing a single drug for multiple diseases. PMID:21909426

Template reporter bacteriophage platform and multiple bacterial detection assays based thereon

NASA Technical Reports Server (NTRS)

Goodridge, Lawrence (Inventor)

2007-01-01

The invention is a method for the development of assays for the simultaneous detection of multiple bacteria. A bacteria of interest is selected. A host bacteria containing plasmid DNA from a T even bacteriophage that infects the bacteria of interest is infected with T4 reporter bacteriophage. After infection, the progeny bacteriophage are plating onto the bacteria of interest. The invention also includes single-tube, fast and sensitive assays which utilize the novel method.

Automated antibody structure prediction using Accelrys tools: Results and best practices

PubMed Central

Fasnacht, Marc; Butenhof, Ken; Goupil-Lamy, Anne; Hernandez-Guzman, Francisco; Huang, Hongwei; Yan, Lisa

2014-01-01

We describe the methodology and results from our participation in the second Antibody Modeling Assessment experiment. During the experiment we predicted the structure of eleven unpublished antibody Fv fragments. Our prediction methods centered on template-based modeling; potential templates were selected from an antibody database based on their sequence similarity to the target in the framework regions. Depending on the quality of the templates, we constructed models of the antibody framework regions either using a single, chimeric or multiple template approach. The hypervariable loop regions in the initial models were rebuilt by grafting the corresponding regions from suitable templates onto the model. For the H3 loop region, we further refined models using ab initio methods. The final models were subjected to constrained energy minimization to resolve severe local structural problems. The analysis of the models submitted show that Accelrys tools allow for the construction of quite accurate models for the framework and the canonical CDR regions, with RMSDs to the X-ray structure on average below 1 Å for most of these regions. The results show that accurate prediction of the H3 hypervariable loops remains a challenge. Furthermore, model quality assessment of the submitted models show that the models are of quite high quality, with local geometry assessment scores similar to that of the target X-ray structures. Proteins 2014; 82:1583–1598. © 2014 The Authors. Proteins published by Wiley Periodicals, Inc. PMID:24833271

Prosthetic component segmentation with blur compensation: a fast method for 3D fluoroscopy.

PubMed

Tarroni, Giacomo; Tersi, Luca; Corsi, Cristiana; Stagni, Rita

2012-06-01

A new method for prosthetic component segmentation from fluoroscopic images is presented. The hybrid approach we propose combines diffusion filtering, region growing and level-set techniques without exploiting any a priori knowledge of the analyzed geometry. The method was evaluated on a synthetic dataset including 270 images of knee and hip prosthesis merged to real fluoroscopic data simulating different conditions of blurring and illumination gradient. The performance of the method was assessed by comparing estimated contours to references using different metrics. Results showed that the segmentation procedure is fast, accurate, independent on the operator as well as on the specific geometrical characteristics of the prosthetic component, and able to compensate for amount of blurring and illumination gradient. Importantly, the method allows a strong reduction of required user interaction time when compared to traditional segmentation techniques. Its effectiveness and robustness in different image conditions, together with simplicity and fast implementation, make this prosthetic component segmentation procedure promising and suitable for multiple clinical applications including assessment of in vivo joint kinematics in a variety of cases.

Fluoroscopic guide wire manipulation of malfunctioning peritoneal dialysis catheters initially placed by interventional radiologists.

PubMed

Kwon, Young Ho; Kwon, Se Hwan; Oh, Joo Hyeong; Jeong, Kyung Hwan; Lee, Tae Won

2014-06-01

To assess the efficacy of fluoroscopic guide wire manipulation in patients with malfunctioning peritoneal dialysis (PD) catheters that were initially placed by interventional radiologists under fluoroscopic guidance. From January 2002 to April 2012, 52 patients (mean age, 52.8 y ± 2.10s; range, 12-79 y) with malfunctioning PD catheters in whom fluoroscopic guide wire manipulation was performed were retrospectively reviewed. Technical success, clinical success, and complications were evaluated. Technical success was defined as fluoroscopically verified, successful catheter repositioning and adequate dialysate drainage after the procedure. Clinical success was defined as maintenance of PD catheter function for at least 30 days after the manipulation. During the study period, 72 manipulations (68 initial manipulations and 4 remanipulations) for malfunctioning PD catheters were done. The technical success rate was 74% (50 of 68) for initial manipulations and 75% (3 of 4) for remanipulations. The overall clinical success rate was 47% (32 of 68) for initial manipulations and 0% (0 of 4) for remanipulations. The primary causes of catheter malfunction were extraluminal obstruction by omental wrapping or adhesions in 43 of 68 cases (63.2%) and catheter malposition in 25 of 68 (36.8%) cases. There were no procedure-related major complications. Fluoroscopic guide wire manipulation in patients with malfunctioning PD catheters initially placed by interventional radiologists is a simple procedure, an effective way of prolonging PD catheter life, and a recommended procedure before invasive surgical procedures. Copyright © 2014 SIR. Published by Elsevier Inc. All rights reserved.

Real-Time Verification of a High-Dose-Rate Iridium 192 Source Position Using a Modified C-Arm Fluoroscope

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nose, Takayuki, E-mail: nose-takayuki@nms.ac.jp; Chatani, Masashi; Otani, Yuki

Purpose: High-dose-rate (HDR) brachytherapy misdeliveries can occur at any institution, and they can cause disastrous results. Even a patient's death has been reported. Misdeliveries could be avoided with real-time verification methods. In 1996, we developed a modified C-arm fluoroscopic verification of an HDR Iridium 192 source position prevent these misdeliveries. This method provided excellent image quality sufficient to detect errors, and it has been in clinical use at our institutions for 20 years. The purpose of the current study is to introduce the mechanisms and validity of our straightforward C-arm fluoroscopic verification method. Methods and Materials: Conventional X-ray fluoroscopic images aremore » degraded by spurious signals and quantum noise from Iridium 192 photons, which make source verification impractical. To improve image quality, we quadrupled the C-arm fluoroscopic X-ray dose per pulse. The pulse rate was reduced by a factor of 4 to keep the average exposure compliant with Japanese medical regulations. The images were then displayed with quarter-frame rates. Results: Sufficient quality was obtained to enable observation of the source position relative to both the applicators and the anatomy. With this method, 2 errors were detected among 2031 treatment sessions for 370 patients within a 6-year period. Conclusions: With the use of a modified C-arm fluoroscopic verification method, treatment errors that were otherwise overlooked were detected in real time. This method should be given consideration for widespread use.« less

Real-Time Verification of a High-Dose-Rate Iridium 192 Source Position Using a Modified C-Arm Fluoroscope.

PubMed

Nose, Takayuki; Chatani, Masashi; Otani, Yuki; Teshima, Teruki; Kumita, Shinichirou

2017-03-15

High-dose-rate (HDR) brachytherapy misdeliveries can occur at any institution, and they can cause disastrous results. Even a patient's death has been reported. Misdeliveries could be avoided with real-time verification methods. In 1996, we developed a modified C-arm fluoroscopic verification of an HDR Iridium 192 source position prevent these misdeliveries. This method provided excellent image quality sufficient to detect errors, and it has been in clinical use at our institutions for 20 years. The purpose of the current study is to introduce the mechanisms and validity of our straightforward C-arm fluoroscopic verification method. Conventional X-ray fluoroscopic images are degraded by spurious signals and quantum noise from Iridium 192 photons, which make source verification impractical. To improve image quality, we quadrupled the C-arm fluoroscopic X-ray dose per pulse. The pulse rate was reduced by a factor of 4 to keep the average exposure compliant with Japanese medical regulations. The images were then displayed with quarter-frame rates. Sufficient quality was obtained to enable observation of the source position relative to both the applicators and the anatomy. With this method, 2 errors were detected among 2031 treatment sessions for 370 patients within a 6-year period. With the use of a modified C-arm fluoroscopic verification method, treatment errors that were otherwise overlooked were detected in real time. This method should be given consideration for widespread use. Copyright © 2016 Elsevier Inc. All rights reserved.

Massive integration of diverse protein quality assessment methods to improve template based modeling in CASP11.

PubMed

Cao, Renzhi; Bhattacharya, Debswapna; Adhikari, Badri; Li, Jilong; Cheng, Jianlin

2016-09-01

Model evaluation and selection is an important step and a big challenge in template-based protein structure prediction. Individual model quality assessment methods designed for recognizing some specific properties of protein structures often fail to consistently select good models from a model pool because of their limitations. Therefore, combining multiple complimentary quality assessment methods is useful for improving model ranking and consequently tertiary structure prediction. Here, we report the performance and analysis of our human tertiary structure predictor (MULTICOM) based on the massive integration of 14 diverse complementary quality assessment methods that was successfully benchmarked in the 11th Critical Assessment of Techniques of Protein Structure prediction (CASP11). The predictions of MULTICOM for 39 template-based domains were rigorously assessed by six scoring metrics covering global topology of Cα trace, local all-atom fitness, side chain quality, and physical reasonableness of the model. The results show that the massive integration of complementary, diverse single-model and multi-model quality assessment methods can effectively leverage the strength of single-model methods in distinguishing quality variation among similar good models and the advantage of multi-model quality assessment methods of identifying reasonable average-quality models. The overall excellent performance of the MULTICOM predictor demonstrates that integrating a large number of model quality assessment methods in conjunction with model clustering is a useful approach to improve the accuracy, diversity, and consequently robustness of template-based protein structure prediction. Proteins 2016; 84(Suppl 1):247-259. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

White light emission of monolithic InGaN/GaN grown on morphology-controlled, nanostructured GaN templates.

PubMed

Song, Keun Man; Kim, Do-Hyun; Kim, Jong-Min; Cho, Chu-Young; Choi, Jehyuk; Kim, Kahee; Park, Jinsup; Kim, Hogyoug

2017-06-02

We demonstrated an InGaN/GaN-based, monolithic, white light-emitting diode (LED) without phosphors by using morphology-controlled active layers formed on multi-facet GaN templates containing polar and semipolar surfaces. The nanostructured surface morphology was controlled by changing the growth time, and distinct multiple photoluminescence peaks were observed at 360, 460, and 560 nm; these features were caused by InGaN/GaN-based multiple quantum wells (MQWs) on the nanostructured facets. The origin of each multi-peak was related to the different indium (In) compositions in the different planes of the quantum wells grown on the nanostructured GaN. The emitting units of MQWs in the LED structures were continuously connected, which is different from other GaN-based nanorod or nanowire LEDs. Therefore, the suggested structure had a larger active area. From the electroluminescence spectrum of the fabricated LED, monolithic white light emission with CIE color coordinates of x = 0.306 and y = 0.333 was achieved via multi-facet control combined with morphology control of the metal organic chemical vapor deposition-selective area growth of InGaN/GaN MQWs.

White light emission of monolithic InGaN/GaN grown on morphology-controlled, nanostructured GaN templates

NASA Astrophysics Data System (ADS)

Song, Keun Man; Kim, Do-Hyun; Kim, Jong-Min; Cho, Chu-Young; Choi, Jehyuk; Kim, Kahee; Park, Jinsup; Kim, Hogyoug

2017-06-01

We demonstrated an InGaN/GaN-based, monolithic, white light-emitting diode (LED) without phosphors by using morphology-controlled active layers formed on multi-facet GaN templates containing polar and semipolar surfaces. The nanostructured surface morphology was controlled by changing the growth time, and distinct multiple photoluminescence peaks were observed at 360, 460, and 560 nm; these features were caused by InGaN/GaN-based multiple quantum wells (MQWs) on the nanostructured facets. The origin of each multi-peak was related to the different indium (In) compositions in the different planes of the quantum wells grown on the nanostructured GaN. The emitting units of MQWs in the LED structures were continuously connected, which is different from other GaN-based nanorod or nanowire LEDs. Therefore, the suggested structure had a larger active area. From the electroluminescence spectrum of the fabricated LED, monolithic white light emission with CIE color coordinates of x = 0.306 and y = 0.333 was achieved via multi-facet control combined with morphology control of the metal organic chemical vapor deposition-selective area growth of InGaN/GaN MQWs.

A new method for generating an invariant iris private key based on the fuzzy vault system.

PubMed

Lee, Youn Joo; Park, Kang Ryoung; Lee, Sung Joo; Bae, Kwanghyuk; Kim, Jaihie

2008-10-01

Cryptographic systems have been widely used in many information security applications. One main challenge that these systems have faced has been how to protect private keys from attackers. Recently, biometric cryptosystems have been introduced as a reliable way of concealing private keys by using biometric data. A fuzzy vault refers to a biometric cryptosystem that can be used to effectively protect private keys and to release them only when legitimate users enter their biometric data. In biometric systems, a critical problem is storing biometric templates in a database. However, fuzzy vault systems do not need to directly store these templates since they are combined with private keys by using cryptography. Previous fuzzy vault systems were designed by using fingerprint, face, and so on. However, there has been no attempt to implement a fuzzy vault system that used an iris. In biometric applications, it is widely known that an iris can discriminate between persons better than other biometric modalities. In this paper, we propose a reliable fuzzy vault system based on local iris features. We extracted multiple iris features from multiple local regions in a given iris image, and the exact values of the unordered set were then produced using the clustering method. To align the iris templates with the new input iris data, a shift-matching technique was applied. Experimental results showed that 128-bit private keys were securely and robustly generated by using any given iris data without requiring prealignment.

Increase in fluoroscopic radiation dose in successive sessions of multistage Onyx embolization of brain arteriovenous malformations compared with the first session.

PubMed

Sheen, Jae Jon; Jiang, Yuan Yuan; Kim, Young Eun; Maeng, Jun Young; Kim, Tae-Il; Lee, Deok Hee

2018-03-23

Onyx embolization is a treatment for brain arteriovenous malformations (AVMs). However, multistage embolization usually involves the presence of radiodense Onyx cast from the previous sessions, which may influence the fluoroscopic radiation dose. We compared the fluoroscopic dose between the initial and final embolization sessions. From January 2014 to September 2016, 18 patients underwent multistage Onyx embolization (more than twice) for brain AVMs. The total fluoroscopic duration (minutes), dose-area product (DAP, Gy×cm 2 ), and cumulative air kerma (CAK, mGy) of both the frontal and lateral planes were obtained. We compared the frontal and lateral fluoroscopic dose rates (dose/time) of the final embolization session with those of the initial session. The relationship between the injected Onyx volume and radiation dose was tested. The initial and final procedures on the frontal plane showed significantly different fluoroscopic dose rates (DAP: initial 0.668 Gy×cm 2 /min, final 0.848 Gy×cm 2 /min, P=0.02; CAK: initial 12.7 mGy/min, final 23.1 mGy/min, P=0.007). Those on the lateral plane also showed a similar pattern (DAP: initial 0.365 Gy×cm 2 /min, final 0.519 Gy×cm 2 /min, P=0.03; CAK: initial 6.2 mGy/min, final 12.9 mGy/min, P=0.01). The correlation between the cumulative Onyx volume (vials) and radiation dose ratio of both planes showed an increasing trend (rho 0.4325-0.7053; P=0.0011-0.0730). Owing to the automatic exposure control function during fluoroscopy, successive Onyx embolization procedures increase the fluoroscopic radiation dose in multistage brain AVM embolization because of the presence of radiodense Onyx mass. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Computerized tomography using video recorded fluoroscopic images

NASA Technical Reports Server (NTRS)

Kak, A. C.; Jakowatz, C. V., Jr.; Baily, N. A.; Keller, R. A.

1975-01-01

A computerized tomographic imaging system is examined which employs video-recorded fluoroscopic images as input data. By hooking the video recorder to a digital computer through a suitable interface, such a system permits very rapid construction of tomograms.

Are care plans suitable for the management of multiple conditions?

PubMed Central

Young, Charlotte E.; Boyle, Frances M.; Mutch, Allyson J.

2016-01-01

Background Care plans have been part of the primary care landscape in Australia for almost two decades. With an increasing number of patients presenting with multiple chronic conditions, it is timely to consider whether care plans meet the needs of patients and clinicians. Objectives To review and benchmark existing care plan templates that include recommendations for comorbid conditions, against four key criteria: (i) patient preferences, (ii) setting priorities, (iii) identifying conflicts and synergies between conditions, and (iv) setting dates for reviewing the care plan. Design Document analysis of Australian care plan templates published from 2006 to 2014 that incorporated recommendations for managing comorbid conditions in primary care. Results Sixteen templates were reviewed. All of the care plan templates addressed patient preference, but this was not done comprehensively. Only three templates included setting priorities. None assisted in identifying conflicts and synergies between conditions. Fifteen templates included setting a date for reviewing the care plan. Conclusions Care plans are a well-used tool in primary care practice, but their current format perpetuates a single-disease approach to care, which works contrary to their intended purpose. Restructuring care plans to incorporate shared decision-making and attention to patient preferences may assist in shifting the focus back to the patient and their care needs. PMID:29090181

Perforated Tuberculosis Lymphadenitis

PubMed Central

Cataño, Juan; Cardeño, John

2013-01-01

A 26-year-old man (human immunodeficiency virus-positive and not taking highly active antiretroviral treatment [HAART]) presented to the emergency room with 2 months of malaise, 20 kg weight loss, high spiking fevers, generalized lymph nodes, night sweats, dry cough, and chest pain when swallowing. On physical examination, he had multiple cervical lymphadenopathies. Suspecting a systemic opportunistic infection, a contrasted chest computed tomography (CT) was done, showing an esophageal to mediastinum fistulae. Two days after admission, a fluoroscopic contrasted endoscopy was done that showed two esophageal fistulae from scrofula to esophagus and then, to mediastinum. A bronchoalveolar lavage and a cervical lymphadenopathy biopsy were done, both showing multiple acid-fast bacillae, where cultures grew Mycobacterium tuberculosis. PMID:23740190

Phylogeny, paleontology, and primates: do incomplete fossils bias the tree of life?

PubMed

Pattinson, David J; Thompson, Richard S; Piotrowski, Aleks K; Asher, Robert J

2015-03-01

Paleontological systematics relies heavily on morphological data that have undergone decay and fossilization. Here, we apply a heuristic means to assess how a fossil's incompleteness detracts from inferring its phylogenetic relationships. We compiled a phylogenetic matrix for primates and simulated the extinction of living species by deleting an extant taxon's molecular data and keeping only those morphological characters present in actual fossils. The choice of characters present in a given living taxon (the subject) was defined by those present in a given fossil (the template). By measuring congruence between a well-corroborated phylogeny to those incorporating artificial fossils, and by comparing real vs. random character distributions and states, we tested the information content of paleontological datasets and determined if extinction of a living species leads to bias in phylogeny reconstruction. We found a positive correlation between fossil completeness and topological congruence. Real fossil templates sampled for 36 or more of the 360 available morphological characters (including dental) performed significantly better than similarly complete templates with random states. Templates dominated by only one partition performed worse than templates with randomly sampled characters across partitions. The template based on the Eocene primate Darwinius masillae performs better than most other templates with a similar number of sampled characters, likely due to preservation of data across multiple partitions. Our results support the interpretation that Darwinius is strepsirhine, not haplorhine, and suggest that paleontological datasets are reliable in primate phylogeny reconstruction. © The Author(s) 2014. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes.

PubMed

Han, Dan; Wei, Chunying

2018-05-01

In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost. Copyright © 2017 Elsevier B.V. All rights reserved.

A motion-compensated image filter for low-dose fluoroscopy in a real-time tumor-tracking radiotherapy system

PubMed Central

Miyamoto, Naoki; Ishikawa, Masayori; Sutherland, Kenneth; Suzuki, Ryusuke; Matsuura, Taeko; Toramatsu, Chie; Takao, Seishin; Nihongi, Hideaki; Shimizu, Shinichi; Umegaki, Kikuo; Shirato, Hiroki

2015-01-01

In the real-time tumor-tracking radiotherapy system, a surrogate fiducial marker inserted in or near the tumor is detected by fluoroscopy to realize respiratory-gated radiotherapy. The imaging dose caused by fluoroscopy should be minimized. In this work, an image processing technique is proposed for tracing a moving marker in low-dose imaging. The proposed tracking technique is a combination of a motion-compensated recursive filter and template pattern matching. The proposed image filter can reduce motion artifacts resulting from the recursive process based on the determination of the region of interest for the next frame according to the current marker position in the fluoroscopic images. The effectiveness of the proposed technique and the expected clinical benefit were examined by phantom experimental studies with actual tumor trajectories generated from clinical patient data. It was demonstrated that the marker motion could be traced in low-dose imaging by applying the proposed algorithm with acceptable registration error and high pattern recognition score in all trajectories, although some trajectories were not able to be tracked with the conventional spatial filters or without image filters. The positional accuracy is expected to be kept within ±2 mm. The total computation time required to determine the marker position is a few milliseconds. The proposed image processing technique is applicable for imaging dose reduction. PMID:25129556

Food impaction after expandable metal stent placement: experience in 1,360 patients with esophageal and upper gastrointestinal tract obstruction.

PubMed

Song, Min; Song, Ho-Young; Kim, Jin Hyoung; Park, Jung-Hoon; Jung, Hwoon-Yong; Kim, Jong-Hoon; Kim, Sung-Bae

2011-09-01

To retrospectively evaluate the incidence, predictive factors, and interventional management of food impaction after expandable metallic stent placement in patients with obstruction of the esophagus or upper gastrointestinal tract caused by benign or malignant disease. Between March 1993 and March 2010, 1,360 patients (1,029 men, 331 women; age range, 21-89 y; mean age, 61 y) underwent fluoroscopically guided stent placement for dysphagia caused by esophageal or gastrointestinal tract strictures. Five types of covered expandable metal stents were used, including four types of esophageal stents (types A-D) and one type of gastroduodenal stent (type E), with types A, B, C, D, and E stents used in 180, 60, 90, 432, and 598 patients, respectively. Multivariate analysis was performed to evaluate factors predictive of food impaction. Food impaction occurred in 41 of 1,360 patients (3.0%). The food impaction rates for types A, B, C, D, and E stents were 0.6%, 1.7%, 1.1%, 3.2%, and 4.0%, respectively. Multivariate analysis showed that stent length was an independent predictor of food impaction (odds ratio, 0.839; P = .012). Of the 41 patients with food impaction, 23 underwent endoscopic management, 12 underwent fluoroscopically guided management, and six did not require management because impacted food spontaneously passed through the stent. The overall food impaction rate was 3.0%, with multiple logistic regression analysis showing that shorter stent length was the only significant predictor of food impaction. Food impaction can be managed by endoscopic or fluoroscopically guided removal or placement of a second stent. Copyright © 2011 SIR. Published by Elsevier Inc. All rights reserved.

Contrast fluoroscopic evaluation of gastrointestinal transit times with and without the use of falconry hoods in red-tailed hawks (Buteo jamaicensis).

PubMed

Doss, Grayson A; Williams, Jackie M; Mans, Christoph

2017-11-01

OBJECTIVE To evaluate gastrointestinal transit times in red-tailed hawks (Buteo jamaicensis) by use of contrast fluoroscopic imaging and investigate the effect of falconry hooding in these hawks on gastrointestinal transit time. DESIGN Prospective, randomized, blinded, complete crossover study. ANIMALS 9 healthy red-tailed hawks. PROCEDURES Hawks were gavage-fed a 30% weight-by-volume barium suspension (25 mL/kg [11.3 mL/lb]) into the crop. Fluoroscopic images were obtained at multiple time points after barium administration. Time to filling and emptying of various gastrointestinal tract organs and overall transit time were measured. The effect of hooding (hooded vs nonhooded) on these variables was assessed in a randomized complete crossover design. RESULTS In nonhooded birds, overall gastrointestinal transit time ranged from 30 to 180 minutes (mean ± SD, 100 ± 52 min). Time to complete crop emptying ranged from 30 to 180 minutes (83 ± 49 min). Contrast medium was present in the ventriculus in all birds within 5 minutes of administration and in the small intestines within 5 to 15 minutes (median, 5 min). Hooding of red-tailed hawks resulted in a significant delay of complete crop emptying (no hood, 83 ± 49 minutes; hood, 133 ± 48 minutes), but no significant effects of hooding were found on other measured variables. CONCLUSIONS AND CLINICAL RELEVANCE These results indicated that overall gastrointestinal transit times are faster in red-tailed hawks than has been reported for psittacines and that the use of a falconry hood in red-tailed hawks may result in delayed crop emptying. Hooding did not exert significant effects on overall gastrointestinal transit time in this raptorial species.

Engineering Strain for Improved III-Nitride Optoelectronic Device Performance

NASA Astrophysics Data System (ADS)

Van Den Broeck, Dennis Marnix

Due to growing environmental and economic concerns, renewable energy generation and high-efficiency lighting are becoming even more important in the scientific community. III-Nitride devices have been essential in production of high-brightness light-emitting diodes (LEDs) and are now entering the photovoltaic (PV) realm as the technology advances. InGaN/GaN multiple quantum well LEDs emitting in the blue/green region have emerged as promising candidates for next-generation lighting technologies. Due to the large lattice mismatch between InN and GaN, large electric fields exist within the quantum well layers and result in low rates of radiative recombination, especially for the green spectral region. This is commonly referred to as the "green gap" and results in poor external quantum efficiencies for light-emitting diodes and laser diodes. In order to mitigate the compressive stress of InGaN QWs, a novel growth technique is developed in order to grown thick, strain-relaxed In yGa1-yN templates for 0.08 < y < 0.11. By inserting 2 nm GaN interlayers into the growing InyGa1-yN film, and subsequently annealing the structure, "semibulk" InGaN templates were achieved with vastly superior crystal and optical properties than bulk InGaN films. These semibulk InGaN templates were then utilized as new templates for multiple quantum well active layers, effectively reducing the compressive strain in the InGaN wells due to the larger lattice constant of the InGaN template with respect to a GaN template. A zero-stress balance method was used in order to realize a strain-balanced multiple quantum well structure, which again showed improved optical characteristics when compared to fully-strain active regions. The semibulk InGaN template was then implemented into "strain-compensated" LED structures, where light emission was achieved with very little leakage current. Discussion of these strain-compensated devices compared to conventional LEDs is detailed.

Integrating evidence and individual preferences using a web-based multi-criteria decision analytic tool: an application to prostate cancer screening.

PubMed

Cunich, Michelle; Salkeld, Glenn; Dowie, Jack; Henderson, Joan; Bayram, Clare; Britt, Helena; Howard, Kirsten

2011-01-01

Annalisa© (AL) is a web-based decision-support template grounded in multi-criteria decision analysis (MCDA). It uses a simple expected value algorithm to calculate a score for each option by taking into account the individual's preferences for different criteria (as importance weights) and the evidence of the performance of each option on each criterion. Given the uncertainty surrounding the trade offs between benefits and harms for prostate cancer screening, this topic was chosen as the vehicle to introduce this new decision-support template. The aim of the study was to introduce a new decision-support template, AL, and to develop and pilot a decision-support tool for prostate cancer screening using it. A decision-support tool for prostate cancer screening (ALProst) was implemented in the AL template. ALProst incorporated evidence on both the benefits and the potential harms of prostate cancer screening (the 'attributes') from published randomized controlled trials (RCTs). Individual weights for each attribute were elicited during interviews. By combining the individual's preferences and the evidence, the best option for the user was identified on the basis of quantified scores. A convenience sample of computer-proficient primary-care physicians (general practitioners [GPs] in Australia) from the Sydney Metropolitan area (Australia) were invited to complete a face-to-face interview involving the decision-support tool. Preference for undergoing prostate-specific antigen testing for prostate cancer, both personally and for their patients, was sought prior to seeing the tool. After gaining hands-on experience with using the tool, GPs were asked to comment on the merits of the template and the tool. Preference for presenting the benefits of prostate cancer screening as the relative or absolute risk reduction in prostate cancer-specific mortality was also sought. Of 60 GPs approached, ten (six men and four women) completed an interview (16.7% response rate). Most GPs agreed/strongly agreed with positive statements about the ease with which they could use AL (seven GPs), and understand the information in, and format of, AL (nine and eight, respectively). Eight agreed/strongly agreed that ALProst would be a useful tool for discussing prostate cancer screening with their patients. GPs were also asked to nominate difficult clinical decisions that they, and their patients, have had to make; responses included cancer screening (including prostate cancer); treating patients with multiple illnesses/diseases; managing multiple cardiovascular disease risk factors; and managing patients who are receiving multiple medications. The common element was the need to consider multiple factors in making these complex decisions. AL is distinguishable from most other decision-support templates available today by its underlying conceptual framework, MCDA, and its power to combine individual preferences with evidence to derive the best option for the user quantitatively. It therefore becomes potentially useful for all decisions at all levels in the healthcare system. Moreover, it will provide a universal graphic 'language' that can overcome the burden to patients of encountering a plethora of widely varying decision aids for different conditions during their lifetime.

New Jersey's Thomas Edison and the fluoroscope.

PubMed

Tselos, G D

1995-11-01

Thomas Edison played a major role in the development of early x-ray technology in 1896, notably increasing tube power and reliability and making the fluoroscope a practical instrument. Eventually, Edison would move x-ray technology from the laboratory to the marketplace.

Percutaneous Relief of Tension Pneumomediastinum in a Child

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chau, Helen Hoi-lun; Kwok, Philip Chong-hei; Lai, Albert Kwok-hung

2003-11-15

The purpose of this article was to describe the experience of relieving tension pneumomediastinum by a fluoroscopic-guided percutaneous method. We inserted a percutaneous drainage catheter with a Heimlich valve under fluoroscopic guidance to relieve the tension pneumomediastinum in a 2-year-old girl who suffered from dermatomyositis with lung involvement. This allowed immediate relief without the need for surgery. The procedure was repeated for relapsed tension pneumomediastinum. Good immediate results were achieved in each attempt. We conclude that percutaneous relief of pneumomediastinum under fluoroscopic guidance can be performed safely and rapidly in patients not fit for surgery.

Heuristic estimation of electromagnetically tracked catheter shape for image-guided vascular procedures

NASA Astrophysics Data System (ADS)

Mefleh, Fuad N.; Baker, G. Hamilton; Kwartowitz, David M.

2014-03-01

In our previous work we presented a novel image-guided surgery (IGS) system, Kit for Navigation by Image Focused Exploration (KNIFE).1,2 KNIFE has been demonstrated to be effective in guiding mock clinical procedures with the tip of an electromagnetically tracked catheter overlaid onto a pre-captured bi-plane fluoroscopic loop. Representation of the catheter in KNIFE differs greatly from what is captured by the fluoroscope, due to distortions and other properties of fluoroscopic images. When imaged by a fluoroscope, catheters can be visualized due to the inclusion of radiopaque materials (i.e. Bi, Ba, W) in the polymer blend.3 However, in KNIFE catheter location is determined using a single tracking seed located in the catheter tip that is represented as a single point overlaid on pre-captured fluoroscopic images. To bridge the gap in catheter representation between KNIFE and traditional methods we constructed a catheter with five tracking seeds positioned along the distal 70 mm of the catheter. We have currently investigated the use of four spline interpolation methods for estimation of true catheter shape and have assesed the error in their estimation of true catheter shape. In this work we present a method for the evaluation of interpolation algorithms with respect to catheter shape determination.

Efficient segmentation of 3D fluoroscopic datasets from mobile C-arm

NASA Astrophysics Data System (ADS)

Styner, Martin A.; Talib, Haydar; Singh, Digvijay; Nolte, Lutz-Peter

2004-05-01

The emerging mobile fluoroscopic 3D technology linked with a navigation system combines the advantages of CT-based and C-arm-based navigation. The intra-operative, automatic segmentation of 3D fluoroscopy datasets enables the combined visualization of surgical instruments and anatomical structures for enhanced planning, surgical eye-navigation and landmark digitization. We performed a thorough evaluation of several segmentation algorithms using a large set of data from different anatomical regions and man-made phantom objects. The analyzed segmentation methods include automatic thresholding, morphological operations, an adapted region growing method and an implicit 3D geodesic snake method. In regard to computational efficiency, all methods performed within acceptable limits on a standard Desktop PC (30sec-5min). In general, the best results were obtained with datasets from long bones, followed by extremities. The segmentations of spine, pelvis and shoulder datasets were generally of poorer quality. As expected, the threshold-based methods produced the worst results. The combined thresholding and morphological operations methods were considered appropriate for a smaller set of clean images. The region growing method performed generally much better in regard to computational efficiency and segmentation correctness, especially for datasets of joints, and lumbar and cervical spine regions. The less efficient implicit snake method was able to additionally remove wrongly segmented skin tissue regions. This study presents a step towards efficient intra-operative segmentation of 3D fluoroscopy datasets, but there is room for improvement. Next, we plan to study model-based approaches for datasets from the knee and hip joint region, which would be thenceforth applied to all anatomical regions in our continuing development of an ideal segmentation procedure for 3D fluoroscopic images.

Feature-based respiratory motion tracking in native fluoroscopic sequences for dynamic roadmaps during minimally invasive procedures in the thorax and abdomen

NASA Astrophysics Data System (ADS)

Wagner, Martin G.; Laeseke, Paul F.; Schubert, Tilman; Slagowski, Jordan M.; Speidel, Michael A.; Mistretta, Charles A.

2017-03-01

Fluoroscopic image guidance for minimally invasive procedures in the thorax and abdomen suffers from respiratory and cardiac motion, which can cause severe subtraction artifacts and inaccurate image guidance. This work proposes novel techniques for respiratory motion tracking in native fluoroscopic images as well as a model based estimation of vessel deformation. This would allow compensation for respiratory motion during the procedure and therefore simplify the workflow for minimally invasive procedures such as liver embolization. The method first establishes dynamic motion models for both the contrast-enhanced vasculature and curvilinear background features based on a native (non-contrast) and a contrast-enhanced image sequence acquired prior to device manipulation, under free breathing conditions. The model of vascular motion is generated by applying the diffeomorphic demons algorithm to an automatic segmentation of the subtraction sequence. The model of curvilinear background features is based on feature tracking in the native sequence. The two models establish the relationship between the respiratory state, which is inferred from curvilinear background features, and the vascular morphology during that same respiratory state. During subsequent fluoroscopy, curvilinear feature detection is applied to determine the appropriate vessel mask to display. The result is a dynamic motioncompensated vessel mask superimposed on the fluoroscopic image. Quantitative evaluation of the proposed methods was performed using a digital 4D CT-phantom (XCAT), which provides realistic human anatomy including sophisticated respiratory and cardiac motion models. Four groups of datasets were generated, where different parameters (cycle length, maximum diaphragm motion and maximum chest expansion) were modified within each image sequence. Each group contains 4 datasets consisting of the initial native and contrast enhanced sequences as well as a sequence, where the respiratory motion is tracked. The respiratory motion tracking error was between 1.00 % and 1.09 %. The estimated dynamic vessel masks yielded a Sørensen-Dice coefficient between 0.94 and 0.96. Finally, the accuracy of the vessel contours was measured in terms of the 99th percentile of the error, which ranged between 0.64 and 0.96 mm. The presented results show that the approach is feasible for respiratory motion tracking and compensation and could therefore considerably improve the workflow of minimally invasive procedures in the thorax and abdomen

TH-E-209-01: Fluoroscopic Dose Monitoring and Patient Follow-Up Program at Massachusetts General Hospital

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, B.

2016-06-15

Radiation dose monitoring solutions have opened up new opportunities for medical physicists to be more involved in modern clinical radiology practices. In particular, with the help of comprehensive radiation dose data, data-driven protocol management and informed case follow up are now feasible. Significant challenges remain however and the problems faced by medical physicists are highly heterogeneous. Imaging systems from multiple vendors and a wide range of vintages co-exist in the same department and employ data communication protocols that are not fully standardized or implemented making harmonization complex. Many different solutions for radiation dose monitoring have been implemented by imaging facilitiesmore » over the past few years. Such systems are based on commercial software, home-grown IT solutions, manual PACS data dumping, etc., and diverse pathways can be used to bring the data to impact clinical practice. The speakers will share their experiences with creating or tailoring radiation dose monitoring/management systems and procedures over the past few years, which vary significantly in design and scope. Topics to cover: (1) fluoroscopic dose monitoring and high radiation event handling from a large academic hospital; (2) dose monitoring and protocol optimization in pediatric radiology; and (3) development of a home-grown IT solution and dose data analysis framework. Learning Objectives: Describe the scope and range of radiation dose monitoring and protocol management in a modern radiology practice Review examples of data available from a variety of systems and how it managed and conveyed. Reflect on the role of the physicist in radiation dose awareness.« less

21 CFR 1020.32 - Fluoroscopic equipment.

Code of Federal Regulations, 2010 CFR

2010-04-01

.... Radiation therapy simulation systems shall be exempt from this requirement provided the systems are intended... 10, 2006, other than radiation therapy simulation systems, the following applies: (A) Neither the... fluoroscopic equipment manufactured on or after June 10, 2006, other than radiation therapy simulation systems...

Registration of angiographic image on real-time fluoroscopic image for image-guided percutaneous coronary intervention.

PubMed

Kim, Dongkue; Park, Sangsoo; Jeong, Myung Ho; Ryu, Jeha

2018-02-01

In percutaneous coronary intervention (PCI), cardiologists must study two different X-ray image sources: a fluoroscopic image and an angiogram. Manipulating a guidewire while alternately monitoring the two separate images on separate screens requires a deep understanding of the anatomy of coronary vessels and substantial training. We propose 2D/2D spatiotemporal image registration of the two images in a single image in order to provide cardiologists with enhanced visual guidance in PCI. The proposed 2D/2D spatiotemporal registration method uses a cross-correlation of two ECG series in each image to temporally synchronize two separate images and register an angiographic image onto the fluoroscopic image. A guidewire centerline is then extracted from the fluoroscopic image in real time, and the alignment of the centerline with vessel outlines of the chosen angiographic image is optimized using the iterative closest point algorithm for spatial registration. A proof-of-concept evaluation with a phantom coronary vessel model with engineering students showed an error reduction rate greater than 74% on wrong insertion to nontarget branches compared to the non-registration method and more than 47% reduction in the task completion time in performing guidewire manipulation for very difficult tasks. Evaluation with a small number of experienced doctors shows a potentially significant reduction in both task completion time and error rate for difficult tasks. The total registration time with real procedure X-ray (angiographic and fluoroscopic) images takes [Formula: see text] 60 ms, which is within the fluoroscopic image acquisition rate of 15 Hz. By providing cardiologists with better visual guidance in PCI, the proposed spatiotemporal image registration method is shown to be useful in advancing the guidewire to the coronary vessel branches, especially those difficult to insert into.

Framework for adaptive multiscale analysis of nonhomogeneous point processes.

PubMed

Helgason, Hannes; Bartroff, Jay; Abry, Patrice

2011-01-01

We develop the methodology for hypothesis testing and model selection in nonhomogeneous Poisson processes, with an eye toward the application of modeling and variability detection in heart beat data. Modeling the process' non-constant rate function using templates of simple basis functions, we develop the generalized likelihood ratio statistic for a given template and a multiple testing scheme to model-select from a family of templates. A dynamic programming algorithm inspired by network flows is used to compute the maximum likelihood template in a multiscale manner. In a numerical example, the proposed procedure is nearly as powerful as the super-optimal procedures that know the true template size and true partition, respectively. Extensions to general history-dependent point processes is discussed.

Image quality evaluation and patient dose assessment of medical fluoroscopic X-ray systems: a national study.

PubMed

Economides, S; Hourdakis, C J; Kalivas, N; Kalathaki, M; Simantirakis, G; Tritakis, P; Manousaridis, G; Vogiatzi, S; Kipouros, P; Boziari, A; Kamenopoulou, V

2008-01-01

This study presents the results from a survey conducted by the Greek Atomic Energy Commission (GAEC), during the period 1998-2003, in 530 public and private owned fluoroscopic X-ray systems in Greece. Certain operational parameters for conventional and remote control systems were assessed, according to a quality control protocol developed by GAEC on the basis of the current literature. Public (91.5%) and private (81.5%) owned fluoroscopic units exhibit high-contrast resolution values over 1 lp mm(-1). Moreover, 88.5 and 87.1% of the fluoroscopic units installed in the public and private sector, respectively, present Maximum Patient Entrance Kerma Rate values lower than 100 mGy min(-1). Additionally, 68.3% of the units assessed were found to perform within the acceptance limits. Finally, the third quartile of the Entrance Surface Dose Rate distribution was estimated according to the Dose Reference Level definition and found equal to 35 mGy min(-1).

Full-Waveform Envelope Templates for Low Magnitude Discrimination and Yield Estimation at Local and Regional Distances with Application to the North Korean Nuclear Tests

NASA Astrophysics Data System (ADS)

Yoo, S. H.

2017-12-01

Monitoring seismologists have successfully used seismic coda for event discrimination and yield estimation for over a decade. In practice seismologists typically analyze long-duration, S-coda signals with high signal-to-noise ratios (SNR) at regional and teleseismic distances, since the single back-scattering model reasonably predicts decay of the late coda. However, seismic monitoring requirements are shifting towards smaller, locally recorded events that exhibit low SNR and short signal lengths. To be successful at characterizing events recorded at local distances, we must utilize the direct-phase arrivals, as well as the earlier part of the coda, which is dominated by multiple forward scattering. To remedy this problem, we have developed a new hybrid method known as full-waveform envelope template matching to improve predicted envelope fits over the entire waveform and account for direct-wave and early coda complexity. We accomplish this by including a multiple forward-scattering approximation in the envelope modeling of the early coda. The new hybrid envelope templates are designed to fit local and regional full waveforms and produce low-variance amplitude estimates, which will improve yield estimation and discrimination between earthquakes and explosions. To demonstrate the new technique, we applied our full-waveform envelope template-matching method to the six known North Korean (DPRK) underground nuclear tests and four aftershock events following the September 2017 test. We successfully discriminated the event types and estimated the yield for all six nuclear tests. We also applied the same technique to the 2015 Tianjin explosions in China, and another suspected low-yield explosion at the DPRK test site on May 12, 2010. Our results show that the new full-waveform envelope template-matching method significantly improves upon longstanding single-scattering coda prediction techniques. More importantly, the new method allows monitoring seismologists to extend coda-based techniques to lower magnitude thresholds and low-yield local explosions.

RECURSIVE PROTEIN MODELING: A DIVIDE AND CONQUER STRATEGY FOR PROTEIN STRUCTURE PREDICTION AND ITS CASE STUDY IN CASP9

PubMed Central

CHENG, JIANLIN; EICKHOLT, JESSE; WANG, ZHENG; DENG, XIN

2013-01-01

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of structural modeling, two types of modeling techniques — template-based modeling and template-free modeling — have been developed. Template-based modeling can often generate a moderate- to high-resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling, such as fragment-based assembly, may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e. certain) and template-free (i.e. uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can signicantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction. PMID:22809379

White emission from non-planar InGaN/GaN MQW LEDs grown on GaN template with truncated hexagonal pyramids.

PubMed

Lee, Ming-Lun; Yeh, Yu-Hsiang; Tu, Shang-Ju; Chen, P C; Lai, Wei-Chih; Sheu, Jinn-Kong

2015-04-06

Non-planar InGaN/GaN multiple quantum well (MQW) structures are grown on a GaN template with truncated hexagonal pyramids (THPs) featuring c-plane and r-plane surfaces. The THP array is formed by the regrowth of the GaN layer on a selective-area Si-implanted GaN template. Transmission electron microscopy shows that the InGaN/GaN epitaxial layers regrown on the THPs exhibit different growth rates and indium compositions of the InGaN layer between the c-plane and r-plane surfaces. Consequently, InGaN/GaN MQW light-emitting diodes grown on the GaN THP array emit multiple wavelengths approaching near white light.

DNA Sequences from Formalin-Fixed Nematodes: Integrating Molecular and Morphological Approaches to Taxonomy

PubMed Central

Thomas, W. Kelley; Vida, J. T.; Frisse, Linda M.; Mundo, Manuel; Baldwin, James G.

1997-01-01

To effectively integrate DNA sequence analysis and classical nematode taxonomy, we must be able to obtain DNA sequences from formalin-fixed specimens. Microdissected sections of nematodes were removed from specimens fixed in formalin, using standard protocols and without destroying morphological features. The fixed sections provided sufficient template for multiple polymerase chain reaction-based DNA sequence analyses. PMID:19274156

Fluoroscopic studies of the upper gastrointestinal tract: techniques and indications.

PubMed

Sánchez-Carpintero de la Vega, M; García Villar, C

Fluoroscopic studies of the gastrointestinal tract are becoming increasing less common due to the introduction of other imaging techniques such as computed tomography and magnetic resonance imaging and to the increased availability of endoscopy. Nevertheless, fluoroscopic studies of the gastrointestinal tract continue to appear in clinical guidelines and some of their indications are still valid. These studies are dynamic, operator-dependent examinations that require training to obtain the maximum diagnostic performance. This review aims to describe the technique and bring the indications for this imaging modality up to date. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

SU-E-J-42: Motion Adaptive Image Filter for Low Dose X-Ray Fluoroscopy in the Real-Time Tumor-Tracking Radiotherapy System.

PubMed

Miyamoto, N; Ishikawa, M; Sutherland, K; Suzuki, R; Matsuura, T; Takao, S; Toramatsu, C; Nihongi, H; Shimizu, S; Onimaru, R; Umegaki, K; Shirato, H

2012-06-01

In the real-time tumor-tracking radiotherapy system, fiducial markers are detected by X-ray fluoroscopy. The fluoroscopic parameters should be optimized as low as possible in order to reduce unnecessary imaging dose. However, the fiducial markers could not be recognized due to effect of statistical noise in low dose imaging. Image processing is envisioned to be a solution to improve image quality and to maintain tracking accuracy. In this study, a recursive image filter adapted to target motion is proposed. A fluoroscopy system was used for the experiment. A spherical gold marker was used as a fiducial marker. About 450 fluoroscopic images of the marker were recorded. In order to mimic respiratory motion of the marker, the images were shifted sequentially. The tube voltage, current and exposure duration were fixed at 65 kV, 50 mA and 2.5 msec as low dose imaging condition, respectively. The tube current was 100 mA as high dose imaging. A pattern recognition score (PRS) ranging from 0 to 100 and image registration error were investigated by performing template pattern matching to each sequential image. The results with and without image processing were compared. In low dose imaging, theimage registration error and the PRS without the image processing were 2.15±1.21 pixel and 46.67±6.40, respectively. Those with the image processing were 1.48±0.82 pixel and 67.80±4.51, respectively. There was nosignificant difference in the image registration error and the PRS between the results of low dose imaging with the image processing and that of high dose imaging without the image processing. The results showed that the recursive filter was effective in order to maintain marker tracking stability and accuracy in low dose fluoroscopy. © 2012 American Association of Physicists in Medicine.

Integration of EEG lead placement templates into traditional technologist-based staffing models reduces costs in continuous video-EEG monitoring service.

PubMed

Kolls, Brad J; Lai, Amy H; Srinivas, Anang A; Reid, Robert R

2014-06-01

The purpose of this study was to determine the relative cost reductions within different staffing models for continuous video-electroencephalography (cvEEG) service by introducing a template system for 10/20 lead application. We compared six staffing models using decision tree modeling based on historical service line utilization data from the cvEEG service at our center. Templates were integrated into technologist-based service lines in six different ways. The six models studied were templates for all studies, templates for intensive care unit (ICU) studies, templates for on-call studies, templates for studies of ≤ 24-hour duration, technologists for on-call studies, and technologists for all studies. Cost was linearly related to the study volume for all models with the "templates for all" model incurring the lowest cost. The "technologists for all" model carried the greatest cost. Direct cost comparison shows that any introduction of templates results in cost savings, with the templates being used for patients located in the ICU being the second most cost efficient and the most practical of the combined models to implement. Cost difference between the highest and lowest cost models under the base case produced an annual estimated savings of $267,574. Implementation of the ICU template model at our institution under base case conditions would result in a $205,230 savings over our current "technologist for all" model. Any implementation of templates into a technologist-based cvEEG service line results in cost savings, with the most significant annual savings coming from using the templates for all studies, but the most practical implementation approach with the second highest cost reduction being the template used in the ICU. The lowered costs determined in this work suggest that a template-based cvEEG service could be supported at smaller centers with significantly reduced costs and could allow for broader use of cvEEG patient monitoring.

Multi-template polymerase chain reaction.

PubMed

Kalle, Elena; Kubista, Mikael; Rensing, Christopher

2014-12-01

PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

Toward Simultaneous Real-Time Fluoroscopic and Nuclear Imaging in the Intervention Room.

PubMed

Beijst, Casper; Elschot, Mattijs; Viergever, Max A; de Jong, Hugo W A M

2016-01-01

To investigate the technical feasibility of hybrid simultaneous fluoroscopic and nuclear imaging. An x-ray tube, an x-ray detector, and a gamma camera were positioned in one line, enabling imaging of the same field of view. Since a straightforward combination of these elements would block the lines of view, a gamma camera setup was developed to be able to view around the x-ray tube. A prototype was built by using a mobile C-arm and a gamma camera with a four-pinhole collimator. By using the prototype, test images were acquired and sensitivity, resolution, and coregistration error were analyzed. Nuclear images (two frames per second) were acquired simultaneously with fluoroscopic images. Depending on the distance from point source to detector, the system resolution was 1.5-1.9-cm full width at half maximum, the sensitivity was (0.6-1.5) × 10(-5) counts per decay, and the coregistration error was -0.13 to 0.15 cm. With good spatial and temporal alignment of both modalities throughout the field of view, fluoroscopic images can be shown in grayscale and corresponding nuclear images in color overlay. Measurements obtained with the hybrid imaging prototype device that combines simultaneous fluoroscopic and nuclear imaging of the same field of view have demonstrated the feasibility of real-time simultaneous hybrid imaging in the intervention room. © RSNA, 2015

The effect of electronic health record software design on resident documentation and compliance with evidence-based medicine.

PubMed

Rodriguez Torres, Yasaira; Huang, Jordan; Mihlstin, Melanie; Juzych, Mark S; Kromrei, Heidi; Hwang, Frank S

2017-01-01

This study aimed to determine the role of electronic health record software in resident education by evaluating documentation of 30 elements extracted from the American Academy of Ophthalmology Dry Eye Syndrome Preferred Practice Pattern. The Kresge Eye Institute transitioned to using electronic health record software in June 2013. We evaluated the charts of 331 patients examined in the resident ophthalmology clinic between September 1, 2011, and March 31, 2014, for an initial evaluation for dry eye syndrome. We compared documentation rates for the 30 evidence-based elements between electronic health record chart note templates among the ophthalmology residents. Overall, significant changes in documentation occurred when transitioning to a new version of the electronic health record software with average compliance ranging from 67.4% to 73.6% (p < 0.0005). Electronic Health Record A had high compliance (>90%) in 13 elements while Electronic Health Record B had high compliance (>90%) in 11 elements. The presence of dialog boxes was responsible for significant changes in documentation of adnexa, puncta, proptosis, skin examination, contact lens wear, and smoking exposure. Significant differences in documentation were correlated with electronic health record template design rather than individual resident or residents' year in training. Our results show that electronic health record template design influences documentation across all resident years. Decreased documentation likely results from "mouse click fatigue" as residents had to access multiple dialog boxes to complete documentation. These findings highlight the importance of EHR template design to improve resident documentation and integration of evidence-based medicine into their clinical notes.

A new template matching method based on contour information

NASA Astrophysics Data System (ADS)

Cai, Huiying; Zhu, Feng; Wu, Qingxiao; Li, Sicong

2014-11-01

Template matching is a significant approach in machine vision due to its effectiveness and robustness. However, most of the template matching methods are so time consuming that they can't be used to many real time applications. The closed contour matching method is a popular kind of template matching methods. This paper presents a new closed contour template matching method which is suitable for two dimensional objects. Coarse-to-fine searching strategy is used to improve the matching efficiency and a partial computation elimination scheme is proposed to further speed up the searching process. The method consists of offline model construction and online matching. In the process of model construction, triples and distance image are obtained from the template image. A certain number of triples which are composed by three points are created from the contour information that is extracted from the template image. The rule to select the three points is that the template contour is divided equally into three parts by these points. The distance image is obtained here by distance transform. Each point on the distance image represents the nearest distance between current point and the points on the template contour. During the process of matching, triples of the searching image are created with the same rule as the triples of the model. Through the similarity that is invariant to rotation, translation and scaling between triangles, the triples corresponding to the triples of the model are found. Then we can obtain the initial RST (rotation, translation and scaling) parameters mapping the searching contour to the template contour. In order to speed up the searching process, the points on the searching contour are sampled to reduce the number of the triples. To verify the RST parameters, the searching contour is projected into the distance image, and the mean distance can be computed rapidly by simple operations of addition and multiplication. In the fine searching process, the initial RST parameters are discrete to obtain the final accurate pose of the object. Experimental results show that the proposed method is reasonable and efficient, and can be used in many real time applications.

Methods for Multiplex Template Sampling in Digital PCR Assays

PubMed Central

Petriv, Oleh I.; Heyries, Kevin A.; VanInsberghe, Michael; Walker, David; Hansen, Carl L.

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision. PMID:24854517

Methods for multiplex template sampling in digital PCR assays.

PubMed

Petriv, Oleh I; Heyries, Kevin A; VanInsberghe, Michael; Walker, David; Hansen, Carl L

2014-01-01

The efficient use of digital PCR (dPCR) for precision copy number analysis requires high concentrations of target molecules that may be difficult or impossible to obtain from clinical samples. To solve this problem we present a strategy, called Multiplex Template Sampling (MTS), that effectively increases template concentrations by detecting multiple regions of fragmented target molecules. Three alternative assay approaches are presented for implementing MTS analysis of chromosome 21, providing a 10-fold concentration enhancement while preserving assay precision.

Formation of template-switching artifacts by linear amplification.

PubMed

Chakravarti, Dhrubajyoti; Mailander, Paula C

2008-07-01

Linear amplification is a method of synthesizing single-stranded DNA from either a single-stranded DNA or one strand of a double-stranded DNA. In this protocol, molecules of a single primer DNA are extended by multiple rounds of DNA synthesis at high temperature using thermostable DNA polymerases. Although linear amplification generates the intended full-length single-stranded product, it is more efficient over single-stranded templates than double-stranded templates. We analyzed linear amplification over single- or double-stranded mouse H-ras DNA (exon 1-2 region). The single-stranded H-ras template yielded only the intended product. However, when the double-stranded template was used, additional artifact products were observed. Increasing the concentration of the double-stranded template produced relatively higher amounts of these artifact products. One of the artifact DNA bands could be mapped and analyzed by sequencing. It contained three template-switching products. These DNAs were formed by incomplete DNA strand extension over the template strand, followed by switching to the complementary strand at a specific Ade nucleotide within a putative hairpin sequence, from which DNA synthesis continued over the complementary strand.

Accuracy of in vivo palpation-guided acromioclavicular joint injection assessed with contrast material and fluoroscopic evaluations.

PubMed

Scillia, Anthony; Issa, Kimona; McInerney, Vincent K; Milman, Edward; Baltazar, Romulo; Dasti, Umer; Festa, Anthony

2015-08-01

The purpose of this study was to evaluate the accuracy of in vivo acromioclavicular (AC) joint injections without fluoroscopic guidance and assess whether patient demographics affected the accuracy of injections. A consecutive cohort of patients who presented with painful acromioclavicular joints was prospectively evaluated. All patients had clinical and radiographic evidence of AC arthritis, had failed conservative measures, and thus had received intraarticular corticosteroid injections. All injections were performed by experienced fellowship-trained musculoskeletal radiologists and by blinded digital palpation technique. Accuracy of injections was assessed with biplanar fluoroscopic views. Forty-one AC injections in 22 males and 16 females with a mean age of 51 years (range 18 to 78) were identified. Twenty-three injections were in the right shoulder and 18 in the left. Only 15 injections were confirmed to be in the intraarticular AC joint, yielding an accuracy of 36.5%. There were no significant differences in the mean age (54 vs. 52 years; p = 0.58), male-to-female ratio (p = 0.73), and side of the injection between the accurate and inaccurate injections, respectively. Based on the findings of the present study, the authors encourage the use of image guidance for corticosteroid treatment of the AC joint. Level IV Therapeutic Case Series.

[Measurement of screw length through drilling technique in osteosynthesis of the proximal humerus fractures].

PubMed

Avcı, Cem Coşkun; Gülabi, Deniz; Sağlam, Necdet; Kurtulmuş, Tuhan; Saka, Gürsel

2013-01-01

This study aims to investigate the efficacy of screw length measurement through drilling technique on the reduction of intraarticular screw penetration and fluoroscopy time in osteosynthesis of proximal humerus fractures. Between January 2008 and June 2012, 98 patients (34 males, 64 females; mean age 64.4 years; range 35 to 81 years) who underwent osteosynthesis using locking anatomical proximal humerus plates (PHILOS) in our clinic with the diagnosis of Neer type 2, 3 or 4 were included. Two different surgical techniques were used to measure proximal screw length in the plate and patients were divided into two groups based on the technique used. In group 1, screw length was determined by a 3 mm blunt tipped Kirschner wire without fluoroscopic control. In group 2, bilateral fluoroscopic images for each screw at least were obtained. Intraarticular screw penetration was detected in five patients (10.6%) in group 1, and in 19 patients (37.3%) in group 2. The mean fluoroscopic imaging time was 10.6 seconds in group 1 and 24.8 seconds in group 2, indicating a statistically significant difference. Screw length measurement through the drilling technique significantly reduces the intraarticular screw penetration and fluoroscopy time in osteosynthesis of proximal humerus fractures using PHILOS plates.

21 CFR 892.1650 - Image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Image-intensified fluoroscopic x-ray system. 892.1650 Section 892.1650 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... through electronic amplification. This generic type of device may include signal analysis and display...

21 CFR 892.1650 - Image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Image-intensified fluoroscopic x-ray system. 892.1650 Section 892.1650 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... through electronic amplification. This generic type of device may include signal analysis and display...

21 CFR 892.1650 - Image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Image-intensified fluoroscopic x-ray system. 892.1650 Section 892.1650 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... through electronic amplification. This generic type of device may include signal analysis and display...

Development of Total Knee Replacement Digital Templating Software

NASA Astrophysics Data System (ADS)

Yusof, Siti Fairuz; Sulaiman, Riza; Thian Seng, Lee; Mohd. Kassim, Abdul Yazid; Abdullah, Suhail; Yusof, Shahril; Omar, Masbah; Abdul Hamid, Hamzaini

In this study, by taking full advantage of digital X-ray and computer technology, we have developed a semi-automated procedure to template knee implants, by making use of digital templating method. Using this approach, a software system called OrthoKneeTMhas been designed and developed. The system is to be utilities as a study in the Department of Orthopaedic and Traumatology in medical faculty, UKM (FPUKM). OrthoKneeTMtemplating process employs uses a technique similar to those used by many surgeons, using acetate templates over X-ray films. Using template technique makes it easy to template various implant from every Implant manufacturers who have with a comprehensive database of templates. The templating functionality includes, template (knee) and manufactures templates (Smith & Nephew; and Zimmer). From an image of patient x-ray OrthoKneeTMtemplates help in quickly and easily reads to the approximate template size needed. The visual templating features then allow us quickly review multiple template sizes against the X-ray and thus obtain the nearly precise view of the implant size required. The system can assist by templating on one patient image and will generate reports that can accompany patient notes. The software system was implemented in Visual basic 6.0 Pro using the object-oriented techniques to manage the graphics and objects. The approaches for image scaling will be discussed. Several of measurement in orthopedic diagnosis process have been studied and added in this software as measurement tools features using mathematic theorem and equations. The study compared the results of the semi-automated (using digital templating) method to the conventional method to demonstrate the accuracy of the system.

Assessment of Homology Templates and an Anesthetic Binding Site within the γ-Aminobutyric Acid Receptor

PubMed Central

Bertaccini, Edward J.; Yoluk, Ozge; Lindahl, Erik R.; Trudell, James R.

2013-01-01

Background Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). While its molecular structure remains unknown, significant progress has been made towards understanding its interactions with anesthetics via molecular modeling. Methods The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50’s. Results Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between alpha and beta subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Conclusion Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed correlation of ligand docking scores with experimentally measured GABAaR potentiation. PMID:23770602

Assessment of homology templates and an anesthetic binding site within the γ-aminobutyric acid receptor.

PubMed

Bertaccini, Edward J; Yoluk, Ozge; Lindahl, Erik R; Trudell, James R

2013-11-01

Anesthetics mediate portions of their activity via modulation of the γ-aminobutyric acid receptor (GABAaR). Although its molecular structure remains unknown, significant progress has been made toward understanding its interactions with anesthetics via molecular modeling. The structure of the torpedo acetylcholine receptor (nAChRα), the structures of the α4 and β2 subunits of the human nAChR, the structures of the eukaryotic glutamate-gated chloride channel (GluCl), and the prokaryotic pH-sensing channels, from Gloeobacter violaceus and Erwinia chrysanthemi, were aligned with the SAlign and 3DMA algorithms. A multiple sequence alignment from these structures and those of the GABAaR was performed with ClustalW. The Modeler and Rosetta algorithms independently created three-dimensional constructs of the GABAaR from the GluCl template. The CDocker algorithm docked a congeneric series of propofol derivatives into the binding pocket and scored calculated binding affinities for correlation with known GABAaR potentiation EC50s. Multiple structure alignments of templates revealed a clear consensus of residue locations relevant to anesthetic effects except for torpedo nAChR. Within the GABAaR models generated from GluCl, the residues notable for modulating anesthetic action within transmembrane segments 1, 2, and 3 converged on the intersubunit interface between α and β subunits. Docking scores of a propofol derivative series into this binding site showed strong linear correlation with GABAaR potentiation EC50. Consensus structural alignment based on homologous templates revealed an intersubunit anesthetic binding cavity within the transmembrane domain of the GABAaR, which showed a correlation of ligand docking scores with experimentally measured GABAaR potentiation.

Radiation Dose Estimation for Pediatric Patients Undergoing Cardiac Catheterization

NASA Astrophysics Data System (ADS)

Wang, Chu

Patients undergoing cardiac catheterization are potentially at risk of radiation-induced health effects from the interventional fluoroscopic X-ray imaging used throughout the clinical procedure. The amount of radiation exposure is highly dependent on the complexity of the procedure and the level of optimization in imaging parameters applied by the clinician. For cardiac catheterization, patient radiation dosimetry, for key organs as well as whole-body effective, is challenging due to the lack of fixed imaging protocols, unlike other common X-ray based imaging modalities. Pediatric patients are at a greater risk compared to adults due to their greater cellular radio-sensitivities as well as longer remaining life-expectancy following the radiation exposure. In terms of radiation dosimetry, they are often more challenging due to greater variation in body size, which often triggers a wider range of imaging parameters in modern imaging systems with automatic dose rate modulation. The overall objective of this dissertation was to develop a comprehensive method of radiation dose estimation for pediatric patients undergoing cardiac catheterization. In this dissertation, the research is divided into two main parts: the Physics Component and the Clinical Component. A proof-of-principle study focused on two patient age groups (Newborn and Five-year-old), one popular biplane imaging system, and the clinical practice of two pediatric cardiologists at one large academic medical center. The Physics Component includes experiments relevant to the physical measurement of patient organ dose using high-sensitivity MOSFET dosimeters placed in anthropomorphic pediatric phantoms. First, the three-dimensional angular dependence of MOSFET detectors in scatter medium under fluoroscopic irradiation was characterized. A custom-made spherical scatter phantom was used to measure response variations in three-dimensional angular orientations. The results were to be used as angular dependence correction factors for the MOSFET organ dose measurements in the following studies. Minor angular dependence (< +/-20% at all angles tested, < +/-10% at clinically relevant angles in cardiac catheterization) was observed. Second, the cardiac dose for common fluoroscopic imaging techniques for pediatric patients in the two age groups was measured. Imaging technique settings with variations of individual key imaging parameters were tested to observe the quantitative effect of imaging optimization or lack thereof. Along with each measurement, the two standard system output indices, the Air Kerma (AK) and Dose-Area Product (DAP), were also recorded and compared to the measured cardiac and skin doses -- the lack of correlation between the indices and the organ doses shed light to the substantial limitation of the indices in representing patient radiation dose, at least within the scope of this dissertation. Third, the effective dose (ED) for Posterior-Anterior and Lateral fluoroscopic imaging techniques for pediatric patients in the two age groups was determined. In addition, the dosimetric effect of removing the anti-scatter grid was studied, for which a factor-of-two ED rate reduction was observed for the imaging techniques. The Clinical Component involved analytical research to develop a validated retrospective cardiac dose reconstruction formulation and to propose the new Optimization Index which evaluates the level of optimization of the clinician's imaging usage during a procedure; and small sample group of actual procedures were used to demonstrate applicability of these formulations. In its entirety, the research represents a first-of-its-kind comprehensive approach in radiation dosimetry for pediatric cardiac catheterization; and separately, it is also modular enough that each individual section can serve as study templates for small-scale dosimetric studies of similar purposes. The data collected and algorithmic formulations developed can be of use in areas of personalized patient dosimetry, clinician training, image quality studies and radiation-associated health effect research.

Georeferencing the Large-Scale Aerial Photographs of a Great Lakes Coastal Wetland: A Modified Photogrammetric Method

USGS Publications Warehouse

Murphy, Marilyn K.; Kowalski, Kurt P.; Grapentine, Joel L.

2010-01-01

The geocontrol template method was developed to georeference multiple, overlapping analog aerial photographs without reliance upon conventionally obtained horizontal ground control. The method was tested as part of a long-term wetland habitat restoration project at a Lake Erie coastal wetland complex in the U.S. Fish and Wildlife Service Ottawa National Wildlife Refuge. As in most coastal wetlands, annually identifiable ground-control features required to georeference photo-interpreted data are difficult to find. The geocontrol template method relies on the following four components: (a) an uncontrolled aerial photo mosaic of the study area, (b) global positioning system (GPS) derived horizontal coordinates of each photo’s principal point, (c) a geocontrol template created by the transfer of fiducial markings and calculated principal points to clear acetate from individual photographs arranged in a mosaic, and (d) the root-mean-square-error testing of the system to ensure an acceptable level of planimetric accuracy. Once created for a study area, the geocontrol template can be registered in geographic information system (GIS) software to facilitate interpretation of multiple images without individual image registration. The geocontrol template enables precise georeferencing of single images within larger blocks of photographs using a repeatable and consistent method.

SU-E-I-26: Estimation of Micro-Angiographic Fluoroscope (MAF) Gain Settings for Digital Subtraction Angiography (DSA) Based on the Fluoroscopic Exposure.

PubMed

Ionita, C; Loughran, B; Nagesh, S Setlur; Jain, A; Bednarek, D; Rudin, S

2012-06-01

The MAF is a new high-resolution detector which is being clinically evaluated in neuro-vascular procedures. The detector contains a large-dynamic-range, high-sensitivity light image intensifier with variable gain. Since the MAF is a research prototype only partially integrated with the clinical system, x-ray technique parameters must be set manually. To improve workflow we developed an automatic method to estimate and set the proper LII voltage (MAF gain) for DSA acquisition based on the fluoroscopic parameters. The detector entrance exposure (XD) can be written as the x-ray tube output exposure (Xo) times an object attenuation factor and an inverse-square correction. If the object attenuation, scatter and distances are unchanged and the effect of x-ray kVp changes are neglected, then the DSA XD can be expressed as the ratio of Xo(DSA)/Xo(Fluoroscopy) multiplied with XD(fluoroscopy). We measured Xo for fluoroscopy and DSA for mAs and kVp ranges appropriate to neuro- vascular interventions and fit the data with a 2D function. To estimate the XD(Fluoroscopy) we derived a curve of XD versus LII-voltage for a mid- dynamic-range average pixel gray-level. Since the MAF system during clinical fluoroscopy automatically adjusts the LII voltage until the desired gray-level value is achieved, by reading that voltage we can estimate the XD(Fluoroscopy). Using the 2D-fit function, Xo(DSA) is automatically calculated for the kVp and mA values set and XD(DSA) can be estimated using the relation above. Using the inverse LII calibration curve, the proper LII-voltage can be determined for the desired average gray-level. The algorithm was implemented and evaluated in thirty-two in-vivo DSA runs on rabbits. The proper LII voltage was selected in all cases with no failures. Using the fluoroscopic LII gain setting to determine the appropriate DSA setting can greatly improve the workflow in clinical evaluations of the MAF. NIH Grants R01-EB008425, R01-EB002873 and an equipment grant from Toshiba Medical Systems Corp. © 2012 American Association of Physicists in Medicine.

A spreadsheet template compatible with Microsoft Excel and iWork Numbers that returns the simultaneous confidence intervals for all pairwise differences between multiple sample means.

PubMed

Brown, Angus M

2010-04-01

The objective of the method described in this paper is to develop a spreadsheet template for the purpose of comparing multiple sample means. An initial analysis of variance (ANOVA) test on the data returns F--the test statistic. If F is larger than the critical F value drawn from the F distribution at the appropriate degrees of freedom, convention dictates rejection of the null hypothesis and allows subsequent multiple comparison testing to determine where the inequalities between the sample means lie. A variety of multiple comparison methods are described that return the 95% confidence intervals for differences between means using an inclusive pairwise comparison of the sample means. 2009 Elsevier Ireland Ltd. All rights reserved.

Principal component reconstruction (PCR) for cine CBCT with motion learning from 2D fluoroscopy.

PubMed

Gao, Hao; Zhang, Yawei; Ren, Lei; Yin, Fang-Fang

2018-01-01

This work aims to generate cine CT images (i.e., 4D images with high-temporal resolution) based on a novel principal component reconstruction (PCR) technique with motion learning from 2D fluoroscopic training images. In the proposed PCR method, the matrix factorization is utilized as an explicit low-rank regularization of 4D images that are represented as a product of spatial principal components and temporal motion coefficients. The key hypothesis of PCR is that temporal coefficients from 4D images can be reasonably approximated by temporal coefficients learned from 2D fluoroscopic training projections. For this purpose, we can acquire fluoroscopic training projections for a few breathing periods at fixed gantry angles that are free from geometric distortion due to gantry rotation, that is, fluoroscopy-based motion learning. Such training projections can provide an effective characterization of the breathing motion. The temporal coefficients can be extracted from these training projections and used as priors for PCR, even though principal components from training projections are certainly not the same for these 4D images to be reconstructed. For this purpose, training data are synchronized with reconstruction data using identical real-time breathing position intervals for projection binning. In terms of image reconstruction, with a priori temporal coefficients, the data fidelity for PCR changes from nonlinear to linear, and consequently, the PCR method is robust and can be solved efficiently. PCR is formulated as a convex optimization problem with the sum of linear data fidelity with respect to spatial principal components and spatiotemporal total variation regularization imposed on 4D image phases. The solution algorithm of PCR is developed based on alternating direction method of multipliers. The implementation is fully parallelized on GPU with NVIDIA CUDA toolbox and each reconstruction takes about a few minutes. The proposed PCR method is validated and compared with a state-of-art method, that is, PICCS, using both simulation and experimental data with the on-board cone-beam CT setting. The results demonstrated the feasibility of PCR for cine CBCT and significantly improved reconstruction quality of PCR from PICCS for cine CBCT. With a priori estimated temporal motion coefficients using fluoroscopic training projections, the PCR method can accurately reconstruct spatial principal components, and then generate cine CT images as a product of temporal motion coefficients and spatial principal components. © 2017 American Association of Physicists in Medicine.

Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications.

PubMed

Sho, Shonan; Court, Colin M; Winograd, Paul; Lee, Sangjun; Hou, Shuang; Graeber, Thomas G; Tseng, Hsian-Rong; Tomlinson, James S

2017-07-01

Sequencing analysis of circulating tumor cells (CTCs) enables "liquid biopsy" to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies. Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score. Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA. The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5-10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template.

21 CFR 1020.31 - Radiographic equipment.

Code of Federal Regulations, 2012 CFR

2012-04-01

... fluoroscopic imaging or for recording images from the fluoroscopic image receptor, or computed tomography x-ray... and time, a preset number of pulses, or a preset radiation exposure to the image receptor. (i) Except... provided to indicate when the axis of the x-ray beam is perpendicular to the plane of the image receptor...

21 CFR 1020.31 - Radiographic equipment.

Code of Federal Regulations, 2013 CFR

2013-04-01

... fluoroscopic imaging or for recording images from the fluoroscopic image receptor, or computed tomography x-ray... and time, a preset number of pulses, or a preset radiation exposure to the image receptor. (i) Except... provided to indicate when the axis of the x-ray beam is perpendicular to the plane of the image receptor...

21 CFR 1020.31 - Radiographic equipment.

Code of Federal Regulations, 2014 CFR

2014-04-01

... fluoroscopic imaging or for recording images from the fluoroscopic image receptor, or computed tomography x-ray... and time, a preset number of pulses, or a preset radiation exposure to the image receptor. (i) Except... provided to indicate when the axis of the x-ray beam is perpendicular to the plane of the image receptor...

Template-based structure modeling of protein-protein interactions

PubMed Central

Szilagyi, Andras; Zhang, Yang

2014-01-01

The structure of protein-protein complexes can be constructed by using the known structure of other protein complexes as a template. The complex structure templates are generally detected either by homology-based sequence alignments or, given the structure of monomer components, by structure-based comparisons. Critical improvements have been made in recent years by utilizing interface recognition and by recombining monomer and complex template libraries. Encouraging progress has also been witnessed in genome-wide applications of template-based modeling, with modeling accuracy comparable to high-throughput experimental data. Nevertheless, bottlenecks exist due to the incompleteness of the proteinprotein complex structure library and the lack of methods for distant homologous template identification and full-length complex structure refinement. PMID:24721449

Design considerations for a new, high resolution Micro-Angiographic Fluoroscope based on a CMOS sensor (MAF-CMOS).

PubMed

Loughran, Brendan; Swetadri Vasan, S N; Singh, Vivek; Ionita, Ciprian N; Jain, Amit; Bednarek, Daniel R; Titus, Albert; Rudin, Stephen

2013-03-06

The detectors that are used for endovascular image-guided interventions (EIGI), particularly for neurovascular interventions, do not provide clinicians with adequate visualization to ensure the best possible treatment outcomes. Developing an improved x-ray imaging detector requires the determination of estimated clinical x-ray entrance exposures to the detector. The range of exposures to the detector in clinical studies was found for the three modes of operation: fluoroscopic mode, high frame-rate digital angiographic mode (HD fluoroscopic mode), and DSA mode. Using these estimated detector exposure ranges and available CMOS detector technical specifications, design requirements were developed to pursue a quantum limited, high resolution, dynamic x-ray detector based on a CMOS sensor with 50 μm pixel size. For the proposed MAF-CMOS, the estimated charge collected within the full exposure range was found to be within the estimated full well capacity of the pixels. Expected instrumentation noise for the proposed detector was estimated to be 50-1,300 electrons. Adding a gain stage such as a light image intensifier would minimize the effect of the estimated instrumentation noise on total image noise but may not be necessary to ensure quantum limited detector operation at low exposure levels. A recursive temporal filter may decrease the effective total noise by 2 to 3 times, allowing for the improved signal to noise ratios at the lowest estimated exposures despite consequent loss in temporal resolution. This work can serve as a guide for further development of dynamic x-ray imaging prototypes or improvements for existing dynamic x-ray imaging systems.

Fast skin dose estimation system for interventional radiology

PubMed Central

Takata, Takeshi; Kotoku, Jun’ichi; Maejima, Hideyuki; Kumagai, Shinobu; Arai, Norikazu; Kobayashi, Takenori; Shiraishi, Kenshiro; Yamamoto, Masayoshi; Kondo, Hiroshi; Furui, Shigeru

2018-01-01

Abstract To minimise the radiation dermatitis related to interventional radiology (IR), rapid and accurate dose estimation has been sought for all procedures. We propose a technique for estimating the patient skin dose rapidly and accurately using Monte Carlo (MC) simulation with a graphical processing unit (GPU, GTX 1080; Nvidia Corp.). The skin dose distribution is simulated based on an individual patient’s computed tomography (CT) dataset for fluoroscopic conditions after the CT dataset has been segmented into air, water and bone based on pixel values. The skin is assumed to be one layer at the outer surface of the body. Fluoroscopic conditions are obtained from a log file of a fluoroscopic examination. Estimating the absorbed skin dose distribution requires calibration of the dose simulated by our system. For this purpose, a linear function was used to approximate the relation between the simulated dose and the measured dose using radiophotoluminescence (RPL) glass dosimeters in a water-equivalent phantom. Differences of maximum skin dose between our system and the Particle and Heavy Ion Transport code System (PHITS) were as high as 6.1%. The relative statistical error (2 σ) for the simulated dose obtained using our system was ≤3.5%. Using a GPU, the simulation on the chest CT dataset aiming at the heart was within 3.49 s on average: the GPU is 122 times faster than a CPU (Core i7–7700K; Intel Corp.). Our system (using the GPU, the log file, and the CT dataset) estimated the skin dose more rapidly and more accurately than conventional methods. PMID:29136194

Fast skin dose estimation system for interventional radiology.

PubMed

Takata, Takeshi; Kotoku, Jun'ichi; Maejima, Hideyuki; Kumagai, Shinobu; Arai, Norikazu; Kobayashi, Takenori; Shiraishi, Kenshiro; Yamamoto, Masayoshi; Kondo, Hiroshi; Furui, Shigeru

2018-03-01

To minimise the radiation dermatitis related to interventional radiology (IR), rapid and accurate dose estimation has been sought for all procedures. We propose a technique for estimating the patient skin dose rapidly and accurately using Monte Carlo (MC) simulation with a graphical processing unit (GPU, GTX 1080; Nvidia Corp.). The skin dose distribution is simulated based on an individual patient's computed tomography (CT) dataset for fluoroscopic conditions after the CT dataset has been segmented into air, water and bone based on pixel values. The skin is assumed to be one layer at the outer surface of the body. Fluoroscopic conditions are obtained from a log file of a fluoroscopic examination. Estimating the absorbed skin dose distribution requires calibration of the dose simulated by our system. For this purpose, a linear function was used to approximate the relation between the simulated dose and the measured dose using radiophotoluminescence (RPL) glass dosimeters in a water-equivalent phantom. Differences of maximum skin dose between our system and the Particle and Heavy Ion Transport code System (PHITS) were as high as 6.1%. The relative statistical error (2 σ) for the simulated dose obtained using our system was ≤3.5%. Using a GPU, the simulation on the chest CT dataset aiming at the heart was within 3.49 s on average: the GPU is 122 times faster than a CPU (Core i7-7700K; Intel Corp.). Our system (using the GPU, the log file, and the CT dataset) estimated the skin dose more rapidly and more accurately than conventional methods.

Performance of local optimization in single-plane fluoroscopic analysis for total knee arthroplasty.

PubMed

Prins, A H; Kaptein, B L; Stoel, B C; Lahaye, D J P; Valstar, E R

2015-11-05

Fluoroscopy-derived joint kinematics plays an important role in the evaluation of knee prostheses. Fluoroscopic analysis requires estimation of the 3D prosthesis pose from its 2D silhouette in the fluoroscopic image, by optimizing a dissimilarity measure. Currently, extensive user-interaction is needed, which makes analysis labor-intensive and operator-dependent. The aim of this study was to review five optimization methods for 3D pose estimation and to assess their performance in finding the correct solution. Two derivative-free optimizers (DHSAnn and IIPM) and three gradient-based optimizers (LevMar, DoNLP2 and IpOpt) were evaluated. For the latter three optimizers two different implementations were evaluated: one with a numerically approximated gradient and one with an analytically derived gradient for computational efficiency. On phantom data, all methods were able to find the 3D pose within 1mm and 1° in more than 85% of cases. IpOpt had the highest success-rate: 97%. On clinical data, the success rates were higher than 85% for the in-plane positions, but not for the rotations. IpOpt was the most expensive method and the application of an analytically derived gradients accelerated the gradient-based methods by a factor 3-4 without any differences in success rate. In conclusion, 85% of the frames can be analyzed automatically in clinical data and only 15% of the frames require manual supervision. The optimal success-rate on phantom data (97% with IpOpt) on phantom data indicates that even less supervision may become feasible. Copyright © 2015 Elsevier Ltd. All rights reserved.

Fluoroscopic guidance for placing a double lumen endotracheal tube in adults.

PubMed

Calenda, Emile; Baste, Jean Marc; Hajjej, Ridha; Rezig, Najiba; Moriceau, Jerome; Diallo, Yaya; Sghaeir, Slim; Danielou, Eric; Peillon, Christophe

2014-09-01

The aim of this study was to assess the right placement of the double lumen endotracheal tube with fluoroscopic guidance, which is used in first intention prior to the fiberscope in our institution. This was a prospective observational study. The study was conducted in vascular and thoracic operating rooms. We enrolled 205 patients scheduled for thoracic surgery, with ASA physical statuses of I (n = 37), II (n = 84), III (n = 80), and IV (n = 4). Thoracic procedures were biopsy (n = 20), wedge (n = 34), culminectomy (n = 6), lobectomy (n = 82), pneumonectomy (n = 4), sympathectomy (n = 9), symphysis (n = 47), and thymectomy (n = 3). The intubation with a double lumen tube was performed with the help of a laryngoscope. Tracheal and bronchial balloons were inflated and auscultation was performed after right and left exclusions. One shot was performed to locate the position of the bronchial tube and the hook. Fluoroscopic guidance was used to relocate the tube in case of a wrong position. When the fluoroscopic guidance failed to position the tube, a fiberscope was used. Perioperative collapse of the lung was assessed by the surgeon during the surgery. Correct fluoroscopic image was obtained after the first attempt in 58.5% of patients therefore a misplaced position was encountered in 41.5%. The fluoroscopic guidance allowed an exact repositioning in 99.5% of cases, and the mean duration of the procedure was 8 minutes. A fiberscope was required to move the hook for one patient. We did not notice a moving of the double lumen endotracheal tube during the surgery. The surgeon satisfaction was 100%. The fluoroscopy evidenced the right position of the double lumen tube and allowed a right repositioning in 99.5% of patients with a very simple implementation. Copyright © 2014. Published by Elsevier B.V.

Effect of fluoroscopic X-ray beam spectrum on air-kerma measurement accuracy: implications for establishing correction coefficients on interventional fluoroscopes with KAP meters.

PubMed

Wunderle, Kevin A; Rakowski, Joseph T; Dong, Frank F

2016-05-08

The first goal of this study was to investigate the accuracy of the displayed reference plane air kerma (Ka,r) or air kerma-area product (Pk,a) over a broad spectrum of X-ray beam qualities on clinically used interventional fluoroscopes incorporating air kerma-area product meters (KAP meters) to measure X-ray output. The second goal was to investigate the accuracy of a correction coefficient (CC) determined at a single beam quality and applied to the measured Ka,r over a broad spectrum of beam qualities. Eleven state-of-the-art interventional fluoroscopes were evaluated, consisting of eight Siemens Artis zee and Artis Q systems and three Philips Allura FD systems. A separate calibrated 60 cc ionization chamber (external chamber) was used to determine the accuracy of the KAP meter over a broad range of clinically used beam qualities. For typical adult beam qualities, applying a single CC deter-mined at 100 kVp with copper (Cu) in the beam resulted in a deviation of < 5% due to beam quality variation. This result indicates that applying a CC determined using The American Association of Physicists in Medicine Task Group 190 protocol or a similar protocol provides very good accuracy as compared to the allowed ± 35% deviation of the KAP meter in this limited beam quality range. For interventional fluoroscopes dedicated to or routinely used to perform pediatric interventions, using a CC established with a low kVp (~ 55-60 kVp) and large amount of Cu filtration (~ 0.6-0.9 mm) may result in greater accuracy as compared to using the 100 kVp values. KAP meter responses indicate that fluoroscope vendors are likely normalizing or otherwise influencing the KAP meter output data. Although this may provide improved accuracy in some instances, there is the potential for large discrete errors to occur, and these errors may be difficult to identify.

GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors

PubMed Central

Esguerra, Mauricio; Siretskiy, Alexey; Bello, Xabier; Sallander, Jessica; Gutiérrez-de-Terán, Hugo

2016-01-01

GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results. PMID:27166369

Automated Epileptiform Spike Detection via Affinity Propagation-Based Template Matching

PubMed Central

Thomas, John; Jin, Jing; Dauwels, Justin; Cash, Sydney S.; Westover, M. Brandon

2018-01-01

Interictal epileptiform spikes are the key diagnostic biomarkers for epilepsy. The clinical gold standard of spike detection is visual inspection performed by neurologists. This is a tedious, time-consuming, and expert-centered process. The development of automated spike detection systems is necessary in order to provide a faster and more reliable diagnosis of epilepsy. In this paper, we propose an efficient template matching spike detector based on a combination of spike and background waveform templates. We generate a template library by clustering a collection of spikes and background waveforms extracted from a database of 50 patients with epilepsy. We benchmark the performance of five clustering techniques based on the receiver operating characteristic (ROC) curves. In addition, background templates are integrated with existing spike templates to improve the overall performance. The affinity propagation-based template matching system with a combination of spike and background templates is shown to outperform the other four conventional methods with the highest area-under-curve (AUC) of 0.953. PMID:29060543

Template-Based 3D Reconstruction of Non-rigid Deformable Object from Monocular Video

NASA Astrophysics Data System (ADS)

Liu, Yang; Peng, Xiaodong; Zhou, Wugen; Liu, Bo; Gerndt, Andreas

2018-06-01

In this paper, we propose a template-based 3D surface reconstruction system of non-rigid deformable objects from monocular video sequence. Firstly, we generate a semi-dense template of the target object with structure from motion method using a subsequence video. This video can be captured by rigid moving camera orienting the static target object or by a static camera observing the rigid moving target object. Then, with the reference template mesh as input and based on the framework of classical template-based methods, we solve an energy minimization problem to get the correspondence between the template and every frame to get the time-varying mesh to present the deformation of objects. The energy terms combine photometric cost, temporal and spatial smoothness cost as well as as-rigid-as-possible cost which can enable elastic deformation. In this paper, an easy and controllable solution to generate the semi-dense template for complex objects is presented. Besides, we use an effective iterative Schur based linear solver for the energy minimization problem. The experimental evaluation presents qualitative deformation objects reconstruction results with real sequences. Compare against the results with other templates as input, the reconstructions based on our template have more accurate and detailed results for certain regions. The experimental results show that the linear solver we used performs better efficiency compared to traditional conjugate gradient based solver.

Developing a Template for Electronic Portfolios in Career and Technical Education

ERIC Educational Resources Information Center

Fowler, Matthew

2012-01-01

The purposes of this multiple case study were to determine if manufacturing and services sector employers found value in the use of an ePortfolio in the hiring process, and to develop a suggested template for an ePortfolio format to be used within career and technical education. Electronic portfolios "allow students to showcase their…

Highly uniform residual layers for arrays of 3D nanoimprinted cavities in Fabry-Pérot-filter-array-based nanospectrometers

NASA Astrophysics Data System (ADS)

Memon, Imran; Shen, Yannan; Khan, Abdullah; Woidt, Carsten; Hillmer, Hartmut

2016-04-01

Miniaturized optical spectrometers can be implemented by an array of Fabry-Pérot (FP) filters. FP filters are composed of two highly reflecting parallel mirrors and a resonance cavity. Each filter transmits a small spectral band (filter line) depending on its individual cavity height. The optical nanospectrometer, a miniaturized FP-based spectrometer, implements 3D NanoImprint technology for the fabrication of multiple FP filter cavities in a single process step. However, it is challenging to avoid the dependency of residual layer (RL) thickness on the shape of the printed patterns in NanoImprint. Since in a nanospectrometer the filter cavities vary in height between neighboring FP filters and, thus, the volume of each cavity varies causing that the RL varies slightly or noticeably between different filters. This is one of the few disadvantages of NanoImprint using soft templates such as substrate conformal imprint lithography which is used in this paper. The advantages of large area soft templates can be revealed substantially if the problem of laterally inhomogeneous RLs can be avoided or reduced considerably. In the case of the nanospectrometer, non-uniform RLs lead to random variations in the designed cavity heights resulting in the shift of desired filter lines. To achieve highly uniform RLs, we report a volume-equalized template design with the lateral distribution of 64 different cavity heights into several units with each unit comprising four cavity heights. The average volume of each unit is kept constant to obtain uniform filling of imprint material per unit area. The imprint results, based on the volume-equalized template, demonstrate highly uniform RLs of 110 nm thickness.

21 CFR 892.1660 - Non-image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Non-image-intensified fluoroscopic x-ray system. 892.1660 Section 892.1660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... of x-radiation into a visible image. This generic type of device may include signal analysis and...

21 CFR 892.1660 - Non-image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Non-image-intensified fluoroscopic x-ray system. 892.1660 Section 892.1660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... of x-radiation into a visible image. This generic type of device may include signal analysis and...

21 CFR 892.1660 - Non-image-intensified fluoroscopic x-ray system.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Non-image-intensified fluoroscopic x-ray system. 892.1660 Section 892.1660 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN... of x-radiation into a visible image. This generic type of device may include signal analysis and...

28 CFR 552.13 - X-ray, major instrument, fluoroscope, or surgical intrusion.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 2 2010-07-01 2010-07-01 false X-ray, major instrument, fluoroscope, or... INSTITUTIONAL MANAGEMENT CUSTODY Searches of Housing Units, Inmates, and Inmate Work Areas § 552.13 X-ray, major... reasons only, with the inmate's consent. (b) The institution physician may authorize use of an X-ray for...

28 CFR 552.13 - X-ray, major instrument, fluoroscope, or surgical intrusion.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 28 Judicial Administration 2 2013-07-01 2013-07-01 false X-ray, major instrument, fluoroscope, or... INSTITUTIONAL MANAGEMENT CUSTODY Searches of Housing Units, Inmates, and Inmate Work Areas § 552.13 X-ray, major... reasons only, with the inmate's consent. (b) The institution physician may authorize use of an X-ray for...

28 CFR 552.13 - X-ray, major instrument, fluoroscope, or surgical intrusion.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 28 Judicial Administration 2 2014-07-01 2014-07-01 false X-ray, major instrument, fluoroscope, or... INSTITUTIONAL MANAGEMENT CUSTODY Searches of Housing Units, Inmates, and Inmate Work Areas § 552.13 X-ray, major... reasons only, with the inmate's consent. (b) The institution physician may authorize use of an X-ray for...

28 CFR 552.13 - X-ray, major instrument, fluoroscope, or surgical intrusion.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 2 2011-07-01 2011-07-01 false X-ray, major instrument, fluoroscope, or... INSTITUTIONAL MANAGEMENT CUSTODY Searches of Housing Units, Inmates, and Inmate Work Areas § 552.13 X-ray, major... reasons only, with the inmate's consent. (b) The institution physician may authorize use of an X-ray for...

28 CFR 552.13 - X-ray, major instrument, fluoroscope, or surgical intrusion.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 2 2012-07-01 2012-07-01 false X-ray, major instrument, fluoroscope, or... INSTITUTIONAL MANAGEMENT CUSTODY Searches of Housing Units, Inmates, and Inmate Work Areas § 552.13 X-ray, major... reasons only, with the inmate's consent. (b) The institution physician may authorize use of an X-ray for...

Robust multiple cue fusion-based high-speed and nonrigid object tracking algorithm for short track speed skating

NASA Astrophysics Data System (ADS)

Liu, Chenguang; Cheng, Heng-Da; Zhang, Yingtao; Wang, Yuxuan; Xian, Min

2016-01-01

This paper presents a methodology for tracking multiple skaters in short track speed skating competitions. Nonrigid skaters move at high speed with severe occlusions happening frequently among them. The camera is panned quickly in order to capture the skaters in a large and dynamic scene. To automatically track the skaters and precisely output their trajectories becomes a challenging task in object tracking. We employ the global rink information to compensate camera motion and obtain the global spatial information of skaters, utilize random forest to fuse multiple cues and predict the blob of each skater, and finally apply a silhouette- and edge-based template-matching and blob-evolving method to labelling pixels to a skater. The effectiveness and robustness of the proposed method are verified through thorough experiments.

Real-Time Tracking by Double Templates Matching Based on Timed Motion History Image with HSV Feature

PubMed Central

Li, Zhiyong; Li, Pengfei; Yu, Xiaoping; Hashem, Mervat

2014-01-01

It is a challenge to represent the target appearance model for moving object tracking under complex environment. This study presents a novel method with appearance model described by double templates based on timed motion history image with HSV color histogram feature (tMHI-HSV). The main components include offline template and online template initialization, tMHI-HSV-based candidate patches feature histograms calculation, double templates matching (DTM) for object location, and templates updating. Firstly, we initialize the target object region and calculate its HSV color histogram feature as offline template and online template. Secondly, the tMHI-HSV is used to segment the motion region and calculate these candidate object patches' color histograms to represent their appearance models. Finally, we utilize the DTM method to trace the target and update the offline template and online template real-timely. The experimental results show that the proposed method can efficiently handle the scale variation and pose change of the rigid and nonrigid objects, even in illumination change and occlusion visual environment. PMID:24592185

Aspergillus meningitis and discitis from low-back procedures in an immunocompetent patient.

PubMed

Kolbe, A B Larson; McKinney, A M; Kendi, A Tuba Karagulle; Misselt, D

2007-07-01

We present a case of an immunocompetent patient who developed Aspergillus meningitis, subsequent to discitis, presumed to be from an epidural steroid injection. Magnetic resonance imaging (MRI) of the lumbar spine confirmed the diagnosis of discitis. Fluoroscopic-guided aspiration of the disc showed growth of Aspergillus fumigatus. MRI of the brain revealed involvement of the right third cranial nerve. Repeat MRIs demonstrated multiple leptomeningeal masses consistent with granulomatous meningitis. Meningitis is a rare complication of discitis, discogram, or epidural steroid injection. Aspergillus usually only infects immunocompromised patients, but rarely can affect immunocompetent patients.

Template based rotation: A method for functional connectivity analysis with a priori templates☆

PubMed Central

Schultz, Aaron P.; Chhatwal, Jasmeer P.; Huijbers, Willem; Hedden, Trey; van Dijk, Koene R.A.; McLaren, Donald G.; Ward, Andrew M.; Wigman, Sarah; Sperling, Reisa A.

2014-01-01

Functional connectivity magnetic resonance imaging (fcMRI) is a powerful tool for understanding the network level organization of the brain in research settings and is increasingly being used to study large-scale neuronal network degeneration in clinical trial settings. Presently, a variety of techniques, including seed-based correlation analysis and group independent components analysis (with either dual regression or back projection) are commonly employed to compute functional connectivity metrics. In the present report, we introduce template based rotation,1 a novel analytic approach optimized for use with a priori network parcellations, which may be particularly useful in clinical trial settings. Template based rotation was designed to leverage the stable spatial patterns of intrinsic connectivity derived from out-of-sample datasets by mapping data from novel sessions onto the previously defined a priori templates. We first demonstrate the feasibility of using previously defined a priori templates in connectivity analyses, and then compare the performance of template based rotation to seed based and dual regression methods by applying these analytic approaches to an fMRI dataset of normal young and elderly subjects. We observed that template based rotation and dual regression are approximately equivalent in detecting fcMRI differences between young and old subjects, demonstrating similar effect sizes for group differences and similar reliability metrics across 12 cortical networks. Both template based rotation and dual-regression demonstrated larger effect sizes and comparable reliabilities as compared to seed based correlation analysis, though all three methods yielded similar patterns of network differences. When performing inter-network and sub-network connectivity analyses, we observed that template based rotation offered greater flexibility, larger group differences, and more stable connectivity estimates as compared to dual regression and seed based analyses. This flexibility owes to the reduced spatial and temporal orthogonality constraints of template based rotation as compared to dual regression. These results suggest that template based rotation can provide a useful alternative to existing fcMRI analytic methods, particularly in clinical trial settings where predefined outcome measures and conserved network descriptions across groups are at a premium. PMID:25150630

Instantiation and registration of statistical shape models of the femur and pelvis using 3D ultrasound imaging.

PubMed

Barratt, Dean C; Chan, Carolyn S K; Edwards, Philip J; Penney, Graeme P; Slomczykowski, Mike; Carter, Timothy J; Hawkes, David J

2008-06-01

Statistical shape modelling potentially provides a powerful tool for generating patient-specific, 3D representations of bony anatomy for computer-aided orthopaedic surgery (CAOS) without the need for a preoperative CT scan. Furthermore, freehand 3D ultrasound (US) provides a non-invasive method for digitising bone surfaces in the operating theatre that enables a much greater region to be sampled compared with conventional direct-contact (i.e., pointer-based) digitisation techniques. In this paper, we describe how these approaches can be combined to simultaneously generate and register a patient-specific model of the femur and pelvis to the patient during surgery. In our implementation, a statistical deformation model (SDM) was constructed for the femur and pelvis by performing a principal component analysis on the B-spline control points that parameterise the freeform deformations required to non-rigidly register a training set of CT scans to a carefully segmented template CT scan. The segmented template bone surface, represented by a triangulated surface mesh, is instantiated and registered to a cloud of US-derived surface points using an iterative scheme in which the weights corresponding to the first five principal modes of variation of the SDM are optimised in addition to the rigid-body parameters. The accuracy of the method was evaluated using clinically realistic data obtained on three intact human cadavers (three whole pelves and six femurs). For each bone, a high-resolution CT scan and rigid-body registration transformation, calculated using bone-implanted fiducial markers, served as the gold standard bone geometry and registration transformation, respectively. After aligning the final instantiated model and CT-derived surfaces using the iterative closest point (ICP) algorithm, the average root-mean-square distance between the surfaces was 3.5mm over the whole bone and 3.7mm in the region of surgical interest. The corresponding distances after aligning the surfaces using the marker-based registration transformation were 4.6 and 4.5mm, respectively. We conclude that despite limitations on the regions of bone accessible using US imaging, this technique has potential as a cost-effective and non-invasive method to enable surgical navigation during CAOS procedures, without the additional radiation dose associated with performing a preoperative CT scan or intraoperative fluoroscopic imaging. However, further development is required to investigate errors using error measures relevant to specific surgical procedures.

Radiation exposure and safety practices during pediatric central line placement

PubMed Central

Saeman, Melody R.; Burkhalter, Lorrie S.; Blackburn, Timothy J.; Murphy, Joseph T.

2015-01-01

Purpose Pediatric surgeons routinely use fluoroscopy for central venous line (CVL) placement. We examined radiation safety practices and patient/surgeon exposure during fluoroscopic CVL. Methods Fluoroscopic CVL procedures performed by 11 pediatric surgeons in 2012 were reviewed. Fluoroscopic time (FT), patient exposure (mGy), and procedural data were collected. Anthropomorphic phantom simulations were used to calculate scatter and dose (mSv). Surgeons were surveyed regarding safety practices. Results 386 procedures were reviewed. Median FT was 12.8 seconds. Median patient estimated effective dose was 0.13 mSv. Median annual FT per surgeon was 15.4 minutes. Simulations showed no significant difference (p = 0.14) between reported exposures (median 3.5 mGy/min) and the modeled regression exposures from the C-arm default mode (median 3.4 mGy/min). Median calculated surgeon exposure was 1.5 mGy/year. Eight of 11 surgeons responded to the survey. Only three reported 100% lead protection and frequent dosimeter use. Conclusion We found non-standard radiation training, safety practices, and dose monitoring for the 11 surgeons. Based on simulations, the C-arm default setting was typically used instead of low dose. While most CVL procedures have low patient/surgeon doses, every effort should be used to minimize patient and occupational exposure, suggesting the need for formal hands-on training for non-radiologist providers using fluoroscopy. PMID:25837269

From Extraction of Local Structures of Protein Energy Landscapes to Improved Decoy Selection in Template-Free Protein Structure Prediction.

PubMed

Akhter, Nasrin; Shehu, Amarda

2018-01-19

Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging. Repeatedly, research has shown that the protein energy functions whose minima are sought in the generation of decoys are unreliable indicators of nativeness. The prevalent approach ignores energy altogether and clusters decoys by conformational similarity. Complementary recent efforts design protein-specific scoring functions or train machine learning models on labeled decoys. In this paper, we show that an informative consideration of energy can be carried out under the energy landscape view. Specifically, we leverage local structures known as basins in the energy landscape probed by a template-free method. We propose and compare various strategies of basin-based decoy selection that we demonstrate are superior to clustering-based strategies. The presented results point to further directions of research for improving decoy selection, including the ability to properly consider the multiplicity of native conformations of proteins.

Pyrosequencing for Microbial Identification and Characterization

PubMed Central

Cummings, Patrick J.; Ahmed, Ray; Durocher, Jeffrey A.; Jessen, Adam; Vardi, Tamar; Obom, Kristina M.

2013-01-01

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns. PMID:23995536

Pyrosequencing for microbial identification and characterization.

PubMed

Cummings, Patrick J; Ahmed, Ray; Durocher, Jeffrey A; Jessen, Adam; Vardi, Tamar; Obom, Kristina M

2013-08-22

Pyrosequencing is a versatile technique that facilitates microbial genome sequencing that can be used to identify bacterial species, discriminate bacterial strains and detect genetic mutations that confer resistance to anti-microbial agents. The advantages of pyrosequencing for microbiology applications include rapid and reliable high-throughput screening and accurate identification of microbes and microbial genome mutations. Pyrosequencing involves sequencing of DNA by synthesizing the complementary strand a single base at a time, while determining the specific nucleotide being incorporated during the synthesis reaction. The reaction occurs on immobilized single stranded template DNA where the four deoxyribonucleotides (dNTP) are added sequentially and the unincorporated dNTPs are enzymatically degraded before addition of the next dNTP to the synthesis reaction. Detection of the specific base incorporated into the template is monitored by generation of chemiluminescent signals. The order of dNTPs that produce the chemiluminescent signals determines the DNA sequence of the template. The real-time sequencing capability of pyrosequencing technology enables rapid microbial identification in a single assay. In addition, the pyrosequencing instrument, can analyze the full genetic diversity of anti-microbial drug resistance, including typing of SNPs, point mutations, insertions, and deletions, as well as quantification of multiple gene copies that may occur in some anti-microbial resistance patterns.

Controllable Synthesis of Tunable Microstructures of Self-Supporting Graphene Films from Opened Bubble to Cube via in Situ Template-Modulating.

PubMed

Li, Na; Yang, Qiao; Liu, Xing; Huang, Xuankai; Zhang, Haiyan; Wang, Chengxin

2017-12-06

Three-dimensional (3D) microstructured building units have replaced layer-to-layer stacked designs in transparent graphene films to fully exploit the advantages of two-dimensional graphene. However, it is still challenging to precisely control the size and microstructures of these building blocks to develop multifunctional graphene-based materials that satisfy the performance requirements of diverse applications. In this study, we propose a controllable method to regulate the microstructures of building units to form structures ranging from opened bubbles and cubes, while the size decreased from 20 to 3 μm, via an in situ template-modulating technology. NaCl was used as either a liquid or solid template by changing the dc bias. The reduced size and dense arrangement of the building units not only provide an improved mass loading for the transparent films but also build multiple pathways for fast ion/electron transmission, enhancing their promise for various practical applications. Generally, we provide a convenient protocol for finely regulating the microstructure and size of these building units, resulting in multifunctional films with a controllable transmittance, which enables the use of these graphene-based architectures as transparent electrodes in various applications and extends the family of multifunctional materials that will present new possibilities for electronics and other devices.

Amplified electrochemiluminescence detection of DNA based on novel quantum dots signal probe by multiple cycling amplification strategy.

PubMed

Tan, Lu; Ge, Junjun; Jiao, Meng; Jie, Guifen; Niu, Shuyan

2018-06-01

In the present work, we designed a unique enzyme-aided multiple amplification strategy for sensitive electrochemiluminescence (ECL) detection of DNA by using the amplified gold nanoparticles (GNPS)-polyamidoamine (PAMAM)-CdSe quantum dots (QDs) signal probe. Firstly, the novel GNPS-PAMAM dendrimers nanostructure with good biocompatibility and electroconductibility contains many amino groups, which can load a large number of CdSe QDs to develop amplified ECL signal probe. Then, the presence of target DNA activated the enzyme-assisted polymerization strand-displacement cycling reaction, and a large number of the hairpin template was opened. Subsequently, the opened stem further interacted with the capture hairpin (HP) DNA on the electrode, and the GNPS-PAMAM-CdSe signal probe hybridized with the exposed stem of the HP to trigger the second new polymerization reaction. Meanwhile, the first cycle was generating abundant DNA triggers which could directly open the template. As a result of the cascade amplification technique, a large number of CdSe QDs signal probe could be assembled on the electrode, generating much amplified ECL signal for sensitive detection of target DNA. Thus, this novel QDs-based amplified ECL strategy holds great promise for DNA detection and can be further exploited for sensing applications in clinical diagnostics. Copyright © 2018 Elsevier B.V. All rights reserved.

Accelerating simulation for the multiple-point statistics algorithm using vector quantization

NASA Astrophysics Data System (ADS)

Zuo, Chen; Pan, Zhibin; Liang, Hao

2018-03-01

Multiple-point statistics (MPS) is a prominent algorithm to simulate categorical variables based on a sequential simulation procedure. Assuming training images (TIs) as prior conceptual models, MPS extracts patterns from TIs using a template and records their occurrences in a database. However, complex patterns increase the size of the database and require considerable time to retrieve the desired elements. In order to speed up simulation and improve simulation quality over state-of-the-art MPS methods, we propose an accelerating simulation for MPS using vector quantization (VQ), called VQ-MPS. First, a variable representation is presented to make categorical variables applicable for vector quantization. Second, we adopt a tree-structured VQ to compress the database so that stationary simulations are realized. Finally, a transformed template and classified VQ are used to address nonstationarity. A two-dimensional (2D) stationary channelized reservoir image is used to validate the proposed VQ-MPS. In comparison with several existing MPS programs, our method exhibits significantly better performance in terms of computational time, pattern reproductions, and spatial uncertainty. Further demonstrations consist of a 2D four facies simulation, two 2D nonstationary channel simulations, and a three-dimensional (3D) rock simulation. The results reveal that our proposed method is also capable of solving multifacies, nonstationarity, and 3D simulations based on 2D TIs.

Multiple primer extension by DNA polymerase on a novel plastic DNA array coated with a biocompatible polymer

PubMed Central

Kinoshita, Kenji; Fujimoto, Kentaro; Yakabe, Toru; Saito, Shin; Hamaguchi, Yuzo; Kikuchi, Takayuki; Nonaka, Ken; Murata, Shigenori; Masuda, Daisuke; Takada, Wataru; Funaoka, Sohei; Arai, Susumu; Nakanishi, Hisao; Yokoyama, Kanehisa; Fujiwara, Kazuhiko; Matsubara, Kenichi

2007-01-01

DNA microarrays are routinely used to monitor gene expression profiling and single nucleotide polymorphisms (SNPs). However, for practically useful high performance, the detection sensitivity is still not adequate, leaving low expression genes undetected. To resolve this issue, we have developed a new plastic S-BIO® PrimeSurface® with a biocompatible polymer; its surface chemistry offers an extraordinarily stable thermal property for a lack of pre-activated glass slide surface. The oligonucleotides immobilized on this substrate are robust in boiling water and show no significant loss of hybridization activity during dissociation treatment. This allowed us to hybridize the templates, extend the 3′ end of the immobilized DNA primers on the S-Bio® by DNA polymerase using deoxynucleotidyl triphosphates (dNTP) as extender units, release the templates by denaturalization and use the same templates for a second round of reactions similar to that of the PCR method. By repeating this cycle, the picomolar concentration range of the template oligonucleotide can be detected as stable signals via the incorporation of labeled dUTP into primers. This method of Multiple Primer EXtension (MPEX) could be further extended as an alternative route for producing DNA microarrays for SNP analyses via simple template preparation such as reverse transcript cDNA or restriction enzyme treatment of genome DNA. PMID:17135189

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.

PubMed

Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Czaplewski, Cezary; Liwo, Adam

2015-06-22

A new approach to the prediction of protein structures that uses distance and backbone virtual-bond dihedral angle restraints derived from template-based models and simulations with the united residue (UNRES) force field is proposed. The approach combines the accuracy and reliability of template-based methods for the segments of the target sequence with high similarity to those having known structures with the ability of UNRES to pack the domains correctly. Multiplexed replica-exchange molecular dynamics with restraints derived from template-based models of a given target, in which each restraint is weighted according to the accuracy of the prediction of the corresponding section of the molecule, is used to search the conformational space, and the weighted histogram analysis method and cluster analysis are applied to determine the families of the most probable conformations, from which candidate predictions are selected. To test the capability of the method to recover template-based models from restraints, five single-domain proteins with structures that have been well-predicted by template-based methods were used; it was found that the resulting structures were of the same quality as the best of the original models. To assess whether the new approach can improve template-based predictions with incorrectly predicted domain packing, four such targets were selected from the CASP10 targets; for three of them the new approach resulted in significantly better predictions compared with the original template-based models. The new approach can be used to predict the structures of proteins for which good templates can be found for sections of the sequence or an overall good template can be found for the entire sequence but the prediction quality is remarkably weaker in putative domain-linker regions.

Lyotropic liquid crystalline L3 phase silicated nanoporous monolithic composites and their production

DOEpatents

McGrath, Kathryn M.; Dabbs, Daniel M.; Aksay, Ilhan A.; Gruner, Sol M.

2003-10-28

A mesoporous ceramic material is provided having a pore size diameter in the range of about 10-100 nanometers produced by templating with a ceramic precursor a lyotropic liquid crystalline L.sub.3 phase consisting of a three-dimensional, random, nonperiodic network packing of a multiple connected continuous membrane. A preferred process for producing the inesoporous ceramic material includes producing a template of a lyotropic liquid crystalline L.sub.3 phase by mixing a surfactant, a co-surfactant and hydrochloric acid, coating the template with an inorganic ceramic precursor by adding to the L.sub.3 phase tetramethoxysilane (TMOS) or tetraethoxysilane (TEOS) and then converting the coated template to a ceramic by removing any remaining liquids.

Comparison of image quality and radiation exposure from C-arm fluoroscopes when used for imaging the spine.

PubMed

Prasarn, Mark L; Coyne, Ellen; Schreck, Michael; Rodgers, Jamie D; Rechtine, Glenn R

2013-07-15

Cadaveric imaging study. We sought to compare the fluoroscopic images produced by 4 different fluoroscopes for image quality and radiation exposure when used for imaging the spine. There are no previous published studies comparing mobile C-arm machines commonly used in clinical practice for imaging the spine. Anterior-posterior and lateral images of the cervical, thoracic, and lumbar spine were obtained from a cadaver placed supine on a radiolucent table. The fluoroscopy units used for the study included (1) GE OEC 9900 Elite (2010 model; General Electric Healthcare, Waukesha, WI), (2) Philips BV Pulsera (2009 model; Philips Healthcare, Andover, MA), (3) Philips BV Pulsera (2010 model; Philips Healthcare, Andover, MA), and (4) Siemens Arcadis Avantic (2010 model; Siemens Medical Solutions, Malvern, PA). The images were then downloaded, placed into a randomizer program, and evaluated by a group of spine surgeons and neuroradiologists independently. The reviewers, who were blinded to the fluoroscope the images were from, ranked them from best to worst using a numeric system. In addition, the images were rated according to a quality scale from 1 to 5, with 1 representing the best image quality. The radiation exposure level for the fluoroscopy units was also compared and was based on energy emission. According to the mean values for rank, the following order of best to worst was observed: (1) GE OEC > (2) Philips 2010 > (3) Philips 2009 > (4) Siemans. The exact same order was found when examining the image quality ratings. When comparing the radiation exposure level difference, it was observed that the OEC was the lowest, and there was a minimum 30% decrease in energy emission from the OEC versus the other C-arms studied. This is the first time that the spine image quality and radiation exposure of commonly used C-arm machines have been compared. The OEC was ranked the best, produced the best quality images, and had the least amount of radiation.

Radio-nuclide mixture identification using medium energy resolution detectors

DOEpatents

Nelson, Karl Einar

2013-09-17

According to one embodiment, a method for identifying radio-nuclides includes receiving spectral data, extracting a feature set from the spectral data comparable to a plurality of templates in a template library, and using a branch and bound method to determine a probable template match based on the feature set and templates in the template library. In another embodiment, a device for identifying unknown radio-nuclides includes a processor, a multi-channel analyzer, and a memory operatively coupled to the processor, the memory having computer readable code stored thereon. The computer readable code is configured, when executed by the processor, to receive spectral data, to extract a feature set from the spectral data comparable to a plurality of templates in a template library, and to use a branch and bound method to determine a probable template match based on the feature set and templates in the template library.

Identifying Drug-Target Interactions with Decision Templates.

PubMed

Yan, Xiao-Ying; Zhang, Shao-Wu

2018-01-01

During the development process of new drugs, identification of the drug-target interactions wins primary concerns. However, the chemical or biological experiments bear the limitation in coverage as well as the huge cost of both time and money. Based on drug similarity and target similarity, chemogenomic methods can be able to predict potential drug-target interactions (DTIs) on a large scale and have no luxurious need about target structures or ligand entries. In order to reflect the cases that the drugs having variant structures interact with common targets and the targets having dissimilar sequences interact with same drugs. In addition, though several other similarity metrics have been developed to predict DTIs, the combination of multiple similarity metrics (especially heterogeneous similarities) is too naïve to sufficiently explore the multiple similarities. In this paper, based on Gene Ontology and pathway annotation, we introduce two novel target similarity metrics to address above issues. More importantly, we propose a more effective strategy via decision template to integrate multiple classifiers designed with multiple similarity metrics. In the scenarios that predict existing targets for new drugs and predict approved drugs for new protein targets, the results on the DTI benchmark datasets show that our target similarity metrics are able to enhance the predictive accuracies in two scenarios. And the elaborate fusion strategy of multiple classifiers has better predictive power than the naïve combination of multiple similarity metrics. Compared with other two state-of-the-art approaches on the four popular benchmark datasets of binary drug-target interactions, our method achieves the best results in terms of AUC and AUPR for predicting available targets for new drugs (S2), and predicting approved drugs for new protein targets (S3).These results demonstrate that our method can effectively predict the drug-target interactions. The software package can freely available at https://github.com/NwpuSY/DT_all.git for academic users. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Selecting appropriate gastroenteric contrast media for diagnostic fluoroscopic imaging in infants and children: a practical approach.

PubMed

Callahan, Michael J; Talmadge, Jennifer M; MacDougall, Robert D; Kleinman, Patricia L; Taylor, George A; Buonomo, Carlo

2017-04-01

In our experience, questions about the appropriate use of enteric contrast media for pediatric fluoroscopic studies are common. The purpose of this article is to provide a comprehensive review of enteric contrast media used for pediatric fluoroscopy, highlighting the routine use of these media at a large tertiary care pediatric teaching hospital.

Actual Time Required for Dynamic Fluoroscopic Intraoperative Cholangiography

PubMed Central

Whitwam, Paul; Turner, David; Kennedy, Kathy; Hashmi, Syed

2005-01-01

Objectives: This study was undertaken to determine the actual amount of time a dynamic fluoroscopic intraoperative cholangiogram adds to a laparoscopic cholecystectomy. A secondary objective was to define the information gained from this procedure. Methods: A consecutive case study of 52 patients undergoing laparoscopic cholecystectomy was used. Time was recorded from placement of a laparoscopic hemoclip across the cystic duct at its junction with the gallbladder until successful completion of the intraoperative cholangiogram. The mean, median, and range of times for these cases, as well as the results and false-negative rates, were determined. Results: Cholangiography was successfully completed in 96% of patients. The mean time added to laparoscopic cholecystectomy by the addition of dynamic fluoroscopic intraoperative cholangiography was 4.3 minutes. The median time was 3.0 minutes. The times ranged from 2.0 minutes to 16.0 minutes. Choledocholithiasis was present in 15.4% of these patients. The false-positive rate was zero in this study. Conclusions: Dynamic fluoroscopic intraoperative cholangiogram was fast and efficient. The information gained was significant in that 15% of patients proceeded on to laparoscopic common bile duct exploration. We conclude that intraoperative cholangiography should be a routine addition to laparoscopic cholecystectomy. PMID:15984705

Evaluation of lumbar transforaminal epidural injections with needle placement and contrast flow patterns: a prospective, descriptive report.

PubMed

Manchikanti, Laxmaiah; Cash, Kim A; Pampati, Vidyasagar; Damron, Kim S; McManus, Carla D

2004-04-01

Transforaminal epidural steroid injection is one of the commonly employed modalities of treatment in managing nerve root pain. However, there have been no controlled prospective evaluations of epidural and nerve root contrast distribution patterns and other aspects of fluoroscopically directed lumbosacral transforaminal epidural steroid injections. To evaluate contrast flow patterns and intravascular needle placement of fluoroscopically guided lumbosacral transforaminal epidural injections. A prospective, observational study. A total of 100 consecutive patients undergoing fluoroscopically guided transforaminal epidural steroid injections were evaluated. The contrast flow patterns, ventral or dorsal epidural filling, nerve root filling, C-arm time, and intravascular needle placement were evaluated. Ventral epidural filling was seen in 88% of the procedures, in contrast to dorsal filling noted in 9% of the procedures. Nerve root filling was seen in 97% of the procedures. Total intravenous placement of the needle was noted in 22% of the procedures, whereas negative flashback and aspiration was noted in 5% of the procedures. Lumbosacral transforaminal epidural injections, performed under fluoroscopic visualization, provide excellent nerve root filling and ventral epidural filling patterns. However, unrecognized intravascular needle placement with negative flashback or aspiration was noted in 5% of the procedures.

Echocardiographic and Fluoroscopic Fusion Imaging for Procedural Guidance: An Overview and Early Clinical Experience.

PubMed

Thaden, Jeremy J; Sanon, Saurabh; Geske, Jeffrey B; Eleid, Mackram F; Nijhof, Niels; Malouf, Joseph F; Rihal, Charanjit S; Bruce, Charles J

2016-06-01

There has been significant growth in the volume and complexity of percutaneous structural heart procedures in the past decade. Increasing procedural complexity and accompanying reliance on multimodality imaging have fueled the development of fusion imaging to facilitate procedural guidance. The first clinically available system capable of echocardiographic and fluoroscopic fusion for real-time guidance of structural heart procedures was approved by the US Food and Drug Administration in 2012. Echocardiographic-fluoroscopic fusion imaging combines the precise catheter and device visualization of fluoroscopy with the soft tissue anatomy and color flow Doppler information afforded by echocardiography in a single image. This allows the interventionalist to perform precise catheter manipulations under fluoroscopy guidance while visualizing critical tissue anatomy provided by echocardiography. However, there are few data available addressing this technology's strengths and limitations in routine clinical practice. The authors provide a critical review of currently available echocardiographic-fluoroscopic fusion imaging for guidance of structural heart interventions to highlight its strengths, limitations, and potential clinical applications and to guide further research into value of this emerging technology. Copyright © 2016 American Society of Echocardiography. Published by Elsevier Inc. All rights reserved.

Python Waveform Cross-Correlation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Templeton, Dennise

PyWCC is a tool to compute seismic waveform cross-correlation coefficients on single-component or multiple-component seismic data across a network of seismic sensors. PyWCC compares waveform data templates with continuous seismic data, associates the resulting detections, identifies the template with the highest cross-correlation coefficient, and outputs a catalog of detections above a user-defined absolute cross-correlation threshold value.

Multi-site genetic analysis of diffusion images and voxelwise heritability analysis: A pilot project of the ENIGMA–DTI working group

PubMed Central

Jahanshad, Neda; Kochunov, Peter; Sprooten, Emma; Mandl, René C.; Nichols, Thomas E.; Almassy, Laura; Blangero, John; Brouwer, Rachel M.; Curran, Joanne E.; de Zubicaray, Greig I.; Duggirala, Ravi; Fox, Peter T.; Hong, L. Elliot; Landman, Bennett A.; Martin, Nicholas G.; McMahon, Katie L.; Medland, Sarah E.; Mitchell, Braxton D.; Olvera, Rene L.; Peterson, Charles P.; Starr, John M.; Sussmann, Jessika E.; Toga, Arthur W.; Wardlaw, Joanna M.; Wright, Margaret J.; Hulshoff Pol, Hilleke E.; Bastin, Mark E.; McIntosh, Andrew M.; Deary, Ian J.; Thompson, Paul M.; Glahn, David C.

2013-01-01

The ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium was set up to analyze brain measures and genotypes from multiple sites across the world to improve the power to detect genetic variants that influence the brain. Diffusion tensor imaging (DTI) yields quantitative measures sensitive to brain development and degeneration, and some common genetic variants may be associated with white matter integrity or connectivity. DTI measures, such as the fractional anisotropy (FA) of water diffusion, may be useful for identifying genetic variants that influence brain microstructure. However, genome-wide association studies (GWAS) require large populations to obtain sufficient power to detect and replicate significant effects, motivating a multi-site consortium effort. As part of an ENIGMA–DTI working group, we analyzed high-resolution FA images from multiple imaging sites across North America, Australia, and Europe, to address the challenge of harmonizing imaging data collected at multiple sites. Four hundred images of healthy adults aged 18–85 from four sites were used to create a template and corresponding skeletonized FA image as a common reference space. Using twin and pedigree samples of different ethnicities, we used our common template to evaluate the heritability of tract-derived FA measures. We show that our template is reliable for integrating multiple datasets by combining results through meta-analysis and unifying the data through exploratory mega-analyses. Our results may help prioritize regions of the FA map that are consistently influenced by additive genetic factors for future genetic discovery studies. Protocols and templates are publicly available at (http://enigma.loni.ucla.edu/ongoing/dti-working-group/). PMID:23629049

Image Fusion and 3D Roadmapping in Endovascular Surgery.

PubMed

Jones, Douglas W; Stangenberg, Lars; Swerdlow, Nicholas J; Alef, Matthew; Lo, Ruby; Shuja, Fahad; Schermerhorn, Marc L

2018-05-21

Practitioners of endovascular surgery have historically utilized two-dimensional (2D) intraoperative fluoroscopic imaging, with intra-vascular contrast opacification, to treat complex three-dimensional (3D) pathology. Recently, major technical developments in intraoperative imaging have made image fusion techniques possible: the creation of a 3D patient-specific vascular roadmap based on preoperative imaging which aligns with intraoperative fluoroscopy, with many potential benefits. First, a 3D model is segmented from preoperative imaging, typically a CT scan. The model is then used to plan for the procedure, with placement of specific markers and storing of C-arm angles that will be used for intra-operative guidance. At the time of the procedure, an intraoperative cone-beam CT is performed and the 3D model is registered to the patient's on-table anatomy. Finally, the system is used for live guidance where the 3D model is codisplayed overlying fluoroscopic images. Copyright © 2018. Published by Elsevier Inc.

Evaluation of low-dose limits in 3D-2D rigid registration for surgical guidance

NASA Astrophysics Data System (ADS)

Uneri, A.; Wang, A. S.; Otake, Y.; Kleinszig, G.; Vogt, S.; Khanna, A. J.; Gallia, G. L.; Gokaslan, Z. L.; Siewerdsen, J. H.

2014-09-01

An algorithm for intensity-based 3D-2D registration of CT and C-arm fluoroscopy is evaluated for use in surgical guidance, specifically considering the low-dose limits of the fluoroscopic x-ray projections. The registration method is based on a framework using the covariance matrix adaptation evolution strategy (CMA-ES) to identify the 3D patient pose that maximizes the gradient information similarity metric. Registration performance was evaluated in an anthropomorphic head phantom emulating intracranial neurosurgery, using target registration error (TRE) to characterize accuracy and robustness in terms of 95% confidence upper bound in comparison to that of an infrared surgical tracking system. Three clinical scenarios were considered: (1) single-view image + guidance, wherein a single x-ray projection is used for visualization and 3D-2D guidance; (2) dual-view image + guidance, wherein one projection is acquired for visualization, combined with a second (lower-dose) projection acquired at a different C-arm angle for 3D-2D guidance; and (3) dual-view guidance, wherein both projections are acquired at low dose for the purpose of 3D-2D guidance alone (not visualization). In each case, registration accuracy was evaluated as a function of the entrance surface dose associated with the projection view(s). Results indicate that images acquired at a dose as low as 4 μGy (approximately one-tenth the dose of a typical fluoroscopic frame) were sufficient to provide TRE comparable or superior to that of conventional surgical tracking, allowing 3D-2D guidance at a level of dose that is at most 10% greater than conventional fluoroscopy (scenario #2) and potentially reducing the dose to approximately 20% of the level in a conventional fluoroscopically guided procedure (scenario #3).

Assessing the applicability of template-based protein docking in the twilight zone.

PubMed

Negroni, Jacopo; Mosca, Roberto; Aloy, Patrick

2014-09-02

The structural modeling of protein interactions in the absence of close homologous templates is a challenging task. Recently, template-based docking methods have emerged to exploit local structural similarities to help ab-initio protocols provide reliable 3D models for protein interactions. In this work, we critically assess the performance of template-based docking in the twilight zone. Our results show that, while it is possible to find templates for nearly all known interactions, the quality of the obtained models is rather limited. We can increase the precision of the models at expenses of coverage, but it drastically reduces the potential applicability of the method, as illustrated by the whole-interactome modeling of nine organisms. Template-based docking is likely to play an important role in the structural characterization of the interaction space, but we still need to improve the repertoire of structural templates onto which we can reliably model protein complexes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Use of a Nitinol Wire Stent for Management of Severe Tracheal Stenosis in an Eclectus Parrot (Eclectus roratus).

PubMed

Mejia-Fava, Johanna; Holmes, Shannon P; Radlinsky, MaryAnn; Johnson, Dan; Ellis, Angela E; Mayer, Jörg; Schnellbacher, Rodney; Divers, Stephen J

2015-09-01

A 25-year-old, female eclectus parrot (Eclectus roratus) presented for dyspnea 3 weeks after anesthesia and surgery for egg yolk coelomitis. Radiography, computed tomography, and tracheoscopy revealed multiple tracheal strictures spanning a length of 2.6 cm in the mid to distal trachea. Histopathologic examination revealed mild fibrosis, inflammation, and hyperplasia consistent with acquired tracheal strictures. Tracheal resection was not considered possible because of the length of the affected trachea. The strictures were resected endoscopically, and repeated balloon dilation under fluoroscopic guidance over the course of 10 months resulted in immediate but unsustained improvement. Computed tomography was used to measure the stenotic area. A 4 × 36-mm, custom-made, nitinol wire stent was inserted into the trachea under fluoroscopic guidance. After stent placement, intermittent episodes of mild to moderate dyspnea continued, and these responded to nebulization with a combination of saline, acetylcysteine, and dexamethasone. Multiple attempts to wean the patient off nebulization therapy and to switch to a corticosteroid-free combination were unsuccessful. The parrot eventually developed complications, was euthanatized, and necropsy was performed. Histologically, the tracheal mucosa had widespread erosion to ulceration, with accumulation of intraluminal exudate and bacteria, severe degeneration of skeletal muscle and tracheal rings, prominent fibrosis, and mild to moderate, submucosal inflammation. Clinicopathologic findings in this case suggested tracheomalacia, which has not been previously described in birds. Custom-made tracheal stents can be used for severe tracheal stenosis in birds when tracheal resection and anastomosis is not possible. Complications of tracheal stent placement in birds may include tracheitis and tracheomalacia. To our knowledge, this is the first report of tracheal stent placement in an avian species.

Fluoroscopic Sacroiliac Joint Injection: Is Oblique Angulation Really Necessary?

PubMed

Khuba, Sandeep; Agarwal, Anil; Gautam, Sujeet; Kumar, Sanjay

2016-01-01

The conventional technique for sacroiliac (SI) joint injection involves aligning the anterior and posterior aspects of the SI joint under fluoroscopic guidance and then entering the SI joint in the most caudal aspect. We wish to highlight that there is no added advantage to aligning both the anterior and posterior joint lines of the SI joint as it is time consuming, associated with additional radiation exposure, and may make the entry into the posterior SI joint technically more difficult. Observational study. Pain Clinic, Department of Anesthesiology. With the patient lying prone on fluoroscopy table, SI joint injection is performed with a 22 G, 10 cm spinal needle in a true anteroposterior (AP) view, where anterior and posterior SI joint spaces are seen as separate entities, where the medial joint space represents the posterior SI joint and the lateral joint space represents the anterior SI joint. The distal 1 cm of the medial joint space is entered under AP view. If the SI joint is seen as a straight line rather than 2 joint spaces in the AP view then the image intensifier of the fluoroscope was tilted cranially to elongate the image of the lower part of the posterior SI joint, thus facilitating entry into this part of the joint which was confirmed by administering 0.3 to 0.5 mL of radiopaque contrast medium. Sixty SI joints of 58 patients were injected under an AP fluoroscopic view. Forty-two (70%) SI joints were seen as 2 separate medial and lateral joint spaces and were entered in distal 1 cm of the medial joint space. In 18 (30%) joints seen as a straight line rather than 2 separate spaces, the image intensifier of the fluoroscope was tilted cranially to elongate the image of the lower part of the posterior SI joint and then the SI joint was entered in its distal 1 cm. Confirmation of entry into the SI joint was confirmed by with 0.3 to 0.5 mL of radiopaque contrast medium. In 4 cases the joints did not show the correct radiopaque contrast spread (3/42 and 1/18) although the needle seemed to be in the joint space. Small sample size. Aligning the anterior and posterior aspects of SI joint for fluoroscopic guided SI joint injection is not necessary for the success of the block.Key words: Sacroiliac joint, injection, anteroposterior view, oblique angulation, fluoroscopic technique.

Multi-modal imaging, model-based tracking, and mixed reality visualisation for orthopaedic surgery

PubMed Central

Fuerst, Bernhard; Tateno, Keisuke; Johnson, Alex; Fotouhi, Javad; Osgood, Greg; Tombari, Federico; Navab, Nassir

2017-01-01

Orthopaedic surgeons are still following the decades old workflow of using dozens of two-dimensional fluoroscopic images to drill through complex 3D structures, e.g. pelvis. This Letter presents a mixed reality support system, which incorporates multi-modal data fusion and model-based surgical tool tracking for creating a mixed reality environment supporting screw placement in orthopaedic surgery. A red–green–blue–depth camera is rigidly attached to a mobile C-arm and is calibrated to the cone-beam computed tomography (CBCT) imaging space via iterative closest point algorithm. This allows real-time automatic fusion of reconstructed surface and/or 3D point clouds and synthetic fluoroscopic images obtained through CBCT imaging. An adapted 3D model-based tracking algorithm with automatic tool segmentation allows for tracking of the surgical tools occluded by hand. This proposed interactive 3D mixed reality environment provides an intuitive understanding of the surgical site and supports surgeons in quickly localising the entry point and orienting the surgical tool during screw placement. The authors validate the augmentation by measuring target registration error and also evaluate the tracking accuracy in the presence of partial occlusion. PMID:29184659

HEU Holdup Measurements in the 321-M Draw Bench, Straightener, and Fluoroscope Components

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dewberry, R.A.

The Analytical Development Section of Savannah River Technology Center (SRTC) was requested by the Facilities Disposition Division (FDD) to determine the holdup of enriched uranium in the 321-M facility as part of an overall deactivation project of the facility. This report covers holdup measurements of uranium residue on the draw bench, straightener, and the fluoroscope components of the 321-M facility.

Reduction of radiation exposure while maintaining high-quality fluoroscopic images during interventional cardiology using novel x-ray tube technology with extra beam filtering.

PubMed

den Boer, A; de Feyter, P J; Hummel, W A; Keane, D; Roelandt, J R

1994-06-01

Radiographic technology plays an integral role in interventional cardiology. The number of interventions continues to increase, and the associated radiation exposure to patients and personnel is of major concern. This study was undertaken to determine whether a newly developed x-ray tube deploying grid-switched pulsed fluoroscopy and extra beam filtering can achieve a reduction in radiation exposure while maintaining fluoroscopic images of high quality. Three fluoroscopic techniques were compared: continuous fluoroscopy, pulsed fluoroscopy, and a newly developed high-output pulsed fluoroscopy with extra filtering. To ascertain differences in the quality of images and to determine differences in patient entrance and investigator radiation exposure, the radiated volume curve was measured to determine the required high voltage levels (kVpeak) for different object sizes for each fluoroscopic mode. The fluoroscopic data of 124 patient procedures were combined. The data were analyzed for radiographic projections, image intensifier field size, and x-ray tube kilovoltage levels (kVpeak). On the basis of this analysis, a reference procedure was constructed. The reference procedure was tested on a phantom or dummy patient by all three fluoroscopic modes. The phantom was so designed that the kilovoltage requirements for each projection were comparable to those needed for the average patient. Radiation exposure of the operator and patient was measured during each mode. The patient entrance dose was measured in air, and the operator dose was measured by 18 dosimeters on a dummy operator. Pulsed compared with continuous fluoroscopy could be performed with improved image quality at lower kilovoltages. The patient entrance dose was reduced by 21% and the operator dose by 54%. High-output pulsed fluoroscopy with extra beam filtering compared with continuous fluoroscopy improved the image quality, lowered the kilovoltage requirements, and reduced the patient entrance dose by 55% and the operator dose by 69%. High-output pulsed fluoroscopy with a grid-switched tube and extra filtering improves the image quality and significantly reduces both the operator dose and patient dose.

Patient-bounded extrapolation using low-dose priors for volume-of-interest imaging in C-arm CT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia, Y.; Maier, A.; Berger, M.

2015-04-15

Purpose: Three-dimensional (3D) volume-of-interest (VOI) imaging with C-arm systems provides anatomical information in a predefined 3D target region at a considerably low x-ray dose. However, VOI imaging involves laterally truncated projections from which conventional reconstruction algorithms generally yield images with severe truncation artifacts. Heuristic based extrapolation methods, e.g., water cylinder extrapolation, typically rely on techniques that complete the truncated data by means of a continuity assumption and thus appear to be ad-hoc. It is our goal to improve the image quality of VOI imaging by exploiting existing patient-specific prior information in the workflow. Methods: A necessary initial step prior tomore » a 3D acquisition is to isocenter the patient with respect to the target to be scanned. To this end, low-dose fluoroscopic x-ray acquisitions are usually applied from anterior–posterior (AP) and medio-lateral (ML) views. Based on this, the patient is isocentered by repositioning the table. In this work, we present a patient-bounded extrapolation method that makes use of these noncollimated fluoroscopic images to improve image quality in 3D VOI reconstruction. The algorithm first extracts the 2D patient contours from the noncollimated AP and ML fluoroscopic images. These 2D contours are then combined to estimate a volumetric model of the patient. Forward-projecting the shape of the model at the eventually acquired C-arm rotation views gives the patient boundary information in the projection domain. In this manner, we are in the position to substantially improve image quality by enforcing the extrapolated line profiles to end at the known patient boundaries, derived from the 3D shape model estimate. Results: The proposed method was evaluated on eight clinical datasets with different degrees of truncation. The proposed algorithm achieved a relative root mean square error (rRMSE) of about 1.0% with respect to the reference reconstruction on nontruncated data, even in the presence of severe truncation, compared to a rRMSE of 8.0% when applying a state-of-the-art heuristic extrapolation technique. Conclusions: The method we proposed in this paper leads to a major improvement in image quality for 3D C-arm based VOI imaging. It involves no additional radiation when using fluoroscopic images that are acquired during the patient isocentering process. The model estimation can be readily integrated into the existing interventional workflow without additional hardware.« less

Template-assisted electrostatic spray deposition as a new route to mesoporous, macroporous, and hierarchically porous oxide films.

PubMed

Sokolov, S; Paul, B; Ortel, E; Fischer, A; Kraehnert, R

2011-03-01

A novel film coating technique, template-assisted electrostatic spray deposition (TAESD), was developed for the synthesis of porous metal oxide films and tested on TiO(2). Organic templates are codeposited with the titania precursor by electrostatic spray deposition and then removed during calcination. Resultant films are highly porous with pores casted by uniformly sized templates, which introduced a new level of control over the pore morphology for the ESD method. Employing the amphiphilic block copolymer Pluronic P123, PMMA latex spheres, or a combination of the two, mesoporous, macroporous, and hierarchically porous TiO(2) films are obtained. Decoupled from other coating parameters, film thickness can be controlled by deposition time or depositing multiple layers while maintaining the coating's structure and integrity.

A Bayesian approach to the creation of a study-customized neonatal brain atlas

PubMed Central

Zhang, Yajing; Chang, Linda; Ceritoglu, Can; Skranes, Jon; Ernst, Thomas; Mori, Susumu; Miller, Michael I.; Oishi, Kenichi

2014-01-01

Atlas-based image analysis (ABA), in which an anatomical “parcellation map” is used for parcel-by-parcel image quantification, is widely used to analyze anatomical and functional changes related to brain development, aging, and various diseases. The parcellation maps are often created based on common MRI templates, which allow users to transform the template to target images, or vice versa, to perform parcel-by-parcel statistics, and report the scientific findings based on common anatomical parcels. The use of a study-specific template, which represents the anatomical features of the study population better than common templates, is preferable for accurate anatomical labeling; however, the creation of a parcellation map for a study-specific template is extremely labor intensive, and the definitions of anatomical boundaries are not necessarily compatible with those of the common template. In this study, we employed a Volume-based Template Estimation (VTE) method to create a neonatal brain template customized to a study population, while keeping the anatomical parcellation identical to that of a common MRI atlas. The VTE was used to morph the standardized parcellation map of the JHU-neonate-SS atlas to capture the anatomical features of a study population. The resultant “study-customized” T1-weighted and diffusion tensor imaging (DTI) template, with three-dimensional anatomical parcellation that defined 122 brain regions, was compared with the JHU-neonate-SS atlas, in terms of the registration accuracy. A pronounced increase in the accuracy of cortical parcellation and superior tensor alignment were observed when the customized template was used. With the customized atlas-based analysis, the fractional anisotropy (FA) detected closely approximated the manual measurements. This tool provides a solution for achieving normalization-based measurements with increased accuracy, while reporting scientific findings in a consistent framework. PMID:25026155

Measuring Use of Evidence-Based Psychotherapy for PTSD in VA Residential Treatment Settings with Clinician Survey and Electronic Medical Record Templates.

PubMed

Shiner, Brian; Leonard Westgate, Christine; Simiola, Vanessa; Thompson, Richard; Schnurr, Paula P; Cook, Joan M

2018-03-14

Available studies on implementation of evidence-based psychotherapy (EBP) for patients attending Department of Veterans Affairs (VA) residential post-traumatic stress disorder (PTSD) programs rely on therapist self-report of EBP delivery. Patient-level data on receipt of EBP are needed both to corroborate therapist self-report and to understand patient factors that predict receipt of EBPs for PTSD. We identified 159 therapists from 38 VA residential PTSD programs who responded to a survey about EBP implementation during the 2015 fiscal year (FY15). Therapists self-reported their use of two EBPs, including prolonged exposure delivered in an individual format (PE-I) and cognitive processing therapy delivered in individual and group formats (CPT-I and CPT-G). Using electronic medical record (EMR) templates mandated for EBP documentation in FY15, we measured contemporaneous patient-level receipt of EBPs for PTSD. We assessed the degree of correlation between therapist self-reported EBP delivery and patient receipt of EBT as measured by EMR templates using polychoric correlation coefficients. We determined patient and therapist factors that predicted the receipt of EBPs with multivariable logistic regression, using random effects and robust standard error estimation, and controlling for site. The Veterans IRB of Northern New England provided a waiver of informed consent; as this was a retrospective review, no patients or therapists were contacted, and all data were stored, transmitted, and analyzed on secure VA servers. The VA Connecticut Health Care System Human Research Protection Program approved secondary use of therapist survey data for this project. When EMR template use became mandated in FY15, the proportion of patients in residential PTSD programs who received at least one EBP session that was recorded with an EMR template increased dramatically from 8.8% to 33.9%. There was adequate correlation and between survey-based and EMR-based measures of EBP receipt, with polychoric correlation values of 0.77 for PE-I, 0.69 for CPT-I, and 0.82 for CPT-G. Multiple patient factors were positive (e.g., female gender) and negative (e.g., depressive disorders) predictors of receipt of EBPs, even after controlling for site. Among therapist factors, only EBP consultant or trainer status was a positive predictor of EBP provision and only therapist race was a negative predictor of EBT provision after controlling for site. Following a FY15 mandate, EMR templates documenting EBP delivery were widely used by therapists working in VA residential PTSD programs. EBP receipt measured using EMR templates was consistent with therapist self-report of EBT delivery. There were several patient-level predictors of EBP receipt and therapist-level predictors of EBP delivery. However, therapists most likely to deliver EBPs were clustered at a limited number of sites.

Effects of Modeling, Story Templates, and Self-Graphing in the Use of Story Elements by Students with Moderate Intellectual Disability

ERIC Educational Resources Information Center

Pennington, Robert; Koehler, Mallory

2017-01-01

There is limited research on teaching narrative writing skills to students with moderate to severe intellectual disability. In the current study, we used a multiple probe across participants single case design to evaluate the effects of an intervention package comprised of modeling, story templates, and self-graphing, on the inclusion of story…

Sensitive SERS detection of DNA methyltransferase by target triggering primer generation-based multiple signal amplification strategy.

PubMed

Li, Ying; Yu, Chuanfeng; Han, Huixia; Zhao, Caisheng; Zhang, Xiaoru

2016-07-15

A novel and sensitive surface-enhanced Raman scattering (SERS) method is proposed for the assay of DNA methyltransferase (MTase) activity and evaluation of inhibitors by developing a target triggering primer generation-based multiple signal amplification strategy. By using of a duplex substrate for Dam MTase, two hairpin templates and a Raman probe, multiple signal amplification mode is achieved. Once recognized by Dam MTase, the duplex substrate can be cleaved by Dpn I endonuclease and two primers are released for triggering the multiple signal amplification reaction. Consequently, a wide dynamic range and remarkably high sensitivity are obtained under isothermal conditions. The detection limit is 2.57×10(-4)UmL(-1). This assay exhibits an excellent selectivity and is successfully applied in the screening of inhibitors for Dam MTase. In addition, this novel sensing system is potentially universal as the recognition element can be conveniently designed for other target analytes by changing the substrate of DNA MTase. Copyright © 2016 Elsevier B.V. All rights reserved.

A contrast and registration template for magnetic resonance image data guided dental implant placement

NASA Astrophysics Data System (ADS)

Eggers, Georg; Cosgarea, Raluca; Rieker, Marcus; Kress, Bodo; Dickhaus, Hartmut; Mühling, Joachim

2009-02-01

An oral imaging template was developed to address the shortcomings of MR image data for image guided dental implant planning and placement. The template was conctructed as a gadolinium filled plastic shell to give contrast to the dentition and also to be accurately re-attachable for use in image guided dental implant placement. The result of segmentation and modelling of the dentition from MR Image data with the template was compared to plaster casts of the dentition. In a phantom study dental implant placement was performed based on MR image data. MR imaging with the contrast template allowed complete representation of the existing dentition. In the phantom study, a commercially available system for image guided dental implant placement was used. Transformation of the imaging contrast template into a surgical drill guide based on the MR image data resulted in pilot burr hole placement with an accuracy of 2 mm. MRI based imaging of the existing dentition for proper image guided planning is possible with the proposed template. Using the image data and the template resulted in less accurate pilot burr hole placement in comparison to CT-based image guided implant placement.

Leaded eyeglasses substantially reduce radiation exposure of the surgeon's eyes during acquisition of typical fluoroscopic views of the hip and pelvis.

PubMed

Burns, Sean; Thornton, Raymond; Dauer, Lawrence T; Quinn, Brian; Miodownik, Daniel; Hak, David J

2013-07-17

Despite recommendations to do so, few orthopaedists wear leaded glasses when performing operative fluoroscopy. Radiation exposure to the ocular lens causes cataracts, and regulatory limits for maximum annual occupational exposure to the eye continue to be revised downward. Using anthropomorphic patient and surgeon phantoms, radiation dose at the surgeon phantom's lens was measured with and without leaded glasses during fluoroscopic acquisition of sixteen common pelvic and hip views. The magnitude of lens dose reduction from leaded glasses was calculated by dividing the unprotected dose by the dose measured behind leaded glasses. On average, the use of leaded glasses reduced radiation to the surgeon phantom's eye by tenfold, a 90% reduction in dose. However, there was widespread variation in the amount of radiation that reached the phantom surgeon's eye among the various radiographic projections we studied. Without leaded glasses, the dose measured at the surgeon's lens varied more than 250-fold among these sixteen different views. In addition to protecting the surgeon's eye from the deleterious effects of radiation, the use of leaded glasses could permit an orthopaedist to perform fluoroscopic views on up to ten times more patients before reaching the annual dose limit of 20 mSv of radiation to the eye recommended by the International Commission on Radiological Protection. Personal safety and adherence to limits of occupational radiation exposure should compel orthopaedists to wear leaded glasses for fluoroscopic procedures if other protective barriers are not in use. Leaded glasses are a powerful tool for reducing the orthopaedic surgeon's lens exposure to radiation during acquisition of common intraoperative fluoroscopic views.

Evaluation of methods to produce an image library for automatic patient model localization for dose mapping during fluoroscopically guided procedures

NASA Astrophysics Data System (ADS)

Kilian-Meneghin, Josh; Xiong, Z.; Rudin, S.; Oines, A.; Bednarek, D. R.

2017-03-01

The purpose of this work is to evaluate methods for producing a library of 2D-radiographic images to be correlated to clinical images obtained during a fluoroscopically-guided procedure for automated patient-model localization. The localization algorithm will be used to improve the accuracy of the skin-dose map superimposed on the 3D patient- model of the real-time Dose-Tracking-System (DTS). For the library, 2D images were generated from CT datasets of the SK-150 anthropomorphic phantom using two methods: Schmid's 3D-visualization tool and Plastimatch's digitally-reconstructed-radiograph (DRR) code. Those images, as well as a standard 2D-radiographic image, were correlated to a 2D-fluoroscopic image of a phantom, which represented the clinical-fluoroscopic image, using the Corr2 function in Matlab. The Corr2 function takes two images and outputs the relative correlation between them, which is fed into the localization algorithm. Higher correlation means better alignment of the 3D patient-model with the patient image. In this instance, it was determined that the localization algorithm will succeed when Corr2 returns a correlation of at least 50%. The 3D-visualization tool images returned 55-80% correlation relative to the fluoroscopic-image, which was comparable to the correlation for the radiograph. The DRR images returned 61-90% correlation, again comparable to the radiograph. Both methods prove to be sufficient for the localization algorithm and can be produced quickly; however, the DRR method produces more accurate grey-levels. Using the DRR code, a library at varying angles can be produced for the localization algorithm.

Edge enhancement algorithm for low-dose X-ray fluoroscopic imaging.

PubMed

Lee, Min Seok; Park, Chul Hee; Kang, Moon Gi

2017-12-01

Low-dose X-ray fluoroscopy has continually evolved to reduce radiation risk to patients during clinical diagnosis and surgery. However, the reduction in dose exposure causes quality degradation of the acquired images. In general, an X-ray device has a time-average pre-processor to remove the generated quantum noise. However, this pre-processor causes blurring and artifacts within the moving edge regions, and noise remains in the image. During high-pass filtering (HPF) to enhance edge detail, this noise in the image is amplified. In this study, a 2D edge enhancement algorithm comprising region adaptive HPF with the transient improvement (TI) method, as well as artifacts and noise reduction (ANR), was developed for degraded X-ray fluoroscopic images. The proposed method was applied in a static scene pre-processed by a low-dose X-ray fluoroscopy device. First, the sharpness of the X-ray image was improved using region adaptive HPF with the TI method, which facilitates sharpening of edge details without overshoot problems. Then, an ANR filter that uses an edge directional kernel was developed to remove the artifacts and noise that can occur during sharpening, while preserving edge details. The quantitative and qualitative results obtained by applying the developed method to low-dose X-ray fluoroscopic images and visually and numerically comparing the final images with images improved using conventional edge enhancement techniques indicate that the proposed method outperforms existing edge enhancement methods in terms of objective criteria and subjective visual perception of the actual X-ray fluoroscopic image. The developed edge enhancement algorithm performed well when applied to actual low-dose X-ray fluoroscopic images, not only by improving the sharpness, but also by removing artifacts and noise, including overshoot. Copyright © 2017 Elsevier B.V. All rights reserved.

A Novel BA Complex Network Model on Color Template Matching

PubMed Central

Han, Risheng; Yue, Guangxue; Ding, Hui

2014-01-01

A novel BA complex network model of color space is proposed based on two fundamental rules of BA scale-free network model: growth and preferential attachment. The scale-free characteristic of color space is discovered by analyzing evolving process of template's color distribution. And then the template's BA complex network model can be used to select important color pixels which have much larger effects than other color pixels in matching process. The proposed BA complex network model of color space can be easily integrated into many traditional template matching algorithms, such as SSD based matching and SAD based matching. Experiments show the performance of color template matching results can be improved based on the proposed algorithm. To the best of our knowledge, this is the first study about how to model the color space of images using a proper complex network model and apply the complex network model to template matching. PMID:25243235

A novel BA complex network model on color template matching.

PubMed

Han, Risheng; Shen, Shigen; Yue, Guangxue; Ding, Hui

2014-01-01

A novel BA complex network model of color space is proposed based on two fundamental rules of BA scale-free network model: growth and preferential attachment. The scale-free characteristic of color space is discovered by analyzing evolving process of template's color distribution. And then the template's BA complex network model can be used to select important color pixels which have much larger effects than other color pixels in matching process. The proposed BA complex network model of color space can be easily integrated into many traditional template matching algorithms, such as SSD based matching and SAD based matching. Experiments show the performance of color template matching results can be improved based on the proposed algorithm. To the best of our knowledge, this is the first study about how to model the color space of images using a proper complex network model and apply the complex network model to template matching.

A Modified Personalized Image-Based Drill Guide Template for Atlantoaxial Pedicle Screw Placement: A Clinical Study

PubMed Central

Jiang, Lianghai; Dong, Liang; Tan, Mingsheng; Qi, Yingna; Yang, Feng; Yi, Ping; Tang, Xiangsheng

2017-01-01

Background Atlantoaxial posterior pedicle screw fixation has been widely used for treatment of atlantoaxial instability (AAI). However, precise and safe insertion of atlantoaxial pedicle screws remains challenging. This study presents a modified drill guide template based on a previous template for atlantoaxial pedicle screw placement. Material/Methods Our study included 54 patients (34 males and 20 females) with AAI. All the patients underwent posterior atlantoaxial pedicle screw fixation: 25 patients underwent surgery with the use of a modified drill guide template (template group) and 29 patients underwent surgery via the conventional method (conventional group). In the template group, a modified drill guide template was designed for each patient. The modified drill guide template and intraoperative fluoroscopy were used for surgery in the template group, while only intraoperative fluoroscopy was used in the conventional group. Results Of the 54 patients, 52 (96.3%) completed the follow-up for more than 12 months. The template group had significantly lower intraoperative fluoroscopy frequency (p<0.001) and higher accuracy of screw insertion (p=0.045) than the conventional group. There were no significant differences in surgical duration, intraoperative blood loss, or improvement of neurological function between the 2 groups (p>0.05). Conclusions Based on the results of this study, it is feasible to use the modified drill guide template for atlantoaxial pedicle screw placement. Using the template can significantly lower the screw malposition rate and the frequency of intraoperative fluoroscopy. PMID:28301445

Light Weight Biomorphous Cellular Ceramics from Cellulose Templates

NASA Technical Reports Server (NTRS)

Singh, Mrityunjay; Yee, Bo-Moon; Gray, Hugh R. (Technical Monitor)

2003-01-01

Bimorphous ceramics are a new class of materials that can be fabricated from the cellulose templates derived from natural biopolymers. These biopolymers are abundantly available in nature and are produced by the photosynthesis process. The wood cellulose derived carbon templates have three- dimensional interconnectivity. A wide variety of non-oxide and oxide based ceramics have been fabricated by template conversion using infiltration and reaction-based processes. The cellular anatomy of the cellulose templates plays a key role in determining the processing parameters (pyrolysis, infiltration conditions, etc.) and resulting ceramic materials. The processing approach, microstructure, and mechanical properties of the biomorphous cellular ceramics (silicon carbide and oxide based) have been discussed.

Simulation-based educational curriculum for fluoroscopically guided lumbar puncture improves operator confidence and reduces patient dose.

PubMed

Faulkner, Austin R; Bourgeois, Austin C; Bradley, Yong C; Hudson, Kathleen B; Heidel, R Eric; Pasciak, Alexander S

2015-05-01

Fluoroscopically guided lumbar puncture (FGLP) is a commonly performed procedure with increased success rates relative to bedside technique. However, FGLP also exposes both patient and staff to ionizing radiation. The purpose of this study was to determine if the use of a simulation-based FGLP training program using an original, inexpensive lumbar spine phantom could improve operator confidence and efficiency, while also reducing patient dose. A didactic and simulation-based FGLP curriculum was designed, including a 1-hour lecture and hands-on training with a lumbar spine phantom prototype developed at our institution. Six incoming post-graduate year 2 (PGY-2) radiology residents completed a short survey before taking the course, and each resident practiced 20 simulated FGLPs using the phantom before their first clinical procedure. Data from the 114 lumbar punctures (LPs) performed by the six trained residents (prospective cohort) were compared to data from 514 LPs performed by 17 residents who did not receive simulation-based training (retrospective cohort). Fluoroscopy time (FT), FGLP success rate, and indication were compared. There was a statistically significant reduction in average FT for the 114 procedures performed by the prospective study cohort compared to the 514 procedures performed by the retrospective cohort. This held true for all procedures in aggregate, LPs for myelography, and all procedures performed for a diagnostic indication. Aggregate FT for the prospective group (0.87 ± 0.68 minutes) was significantly lower compared to the retrospective group (1.09 ± 0.65 minutes) and resulted in a 25% reduction in average FT (P = .002). There was no statistically significant difference in the number of failed FGLPs between the two groups. Our simulation-based FGLP curriculum resulted in improved operator confidence and reduced FT. These changes suggest that resident procedure efficiency was improved, whereas patient dose was reduced. The FGLP training program was implemented by radiology residents and required a minimal investment of time and resources. The LP spine phantom used during training was inexpensive, durable, and effective. In addition, the phantom is compatible with multiple modalities including fluoroscopy, computed tomography, and ultrasound and could be easily adapted to other applications such as facet injections or joint arthrograms. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Defining ecological and economical hydropoweroperations: a framework for managing dam releasesto meet multiple conflicting objectives

USGS Publications Warehouse

Irwin, Elise R.

2014-01-01

Hydroelectric dams are a flexible source of power, provide flood control, and contribute to the economic growth of local communities through real-estate and recreation. Yet the impoundment of rivers can alter and fragment miles of critical riverine habitat needed for other competing needs such as downstream consumptive water use, fish and wildlife population viability, or other forms of recreation. Multiple conflicting interests can compromise progressive management especially with recognized uncertainties related to whether management actions will fulfill the objectives of policy makers, resource managers and/or facility owners. Decision analytic tools were used in a stakeholder-driven process to develop and implement a template for evaluation and prediction of the effects of water resource management of multiple-use systems under the context provided by R.L. Harris Dam on the Tallapoosa River, Alabama, USA. The approach provided a transparent and structured framework for decision-making and incorporated both existing and new data to meet multiple management objectives. Success of the template has been evaluated by the stakeholder governing body in an adaptive resource management framework since 2005 and is ongoing. Consequences of management of discharge at the dam were evaluated annually relative to stakeholder satisfaction to allow for adjustment of both management scenarios and objectives. This template can be applied to attempt to resolve conflict inherent in many dam-regulated systems where management decisions impact diverse values of stakeholders.

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

PubMed

Xu, Dong; Zhang, Yang

2012-07-01

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

Protein structure modeling and refinement by global optimization in CASP12.

PubMed

Hong, Seung Hwan; Joung, InSuk; Flores-Canales, Jose C; Manavalan, Balachandran; Cheng, Qianyi; Heo, Seungryong; Kim, Jong Yun; Lee, Sun Young; Nam, Mikyung; Joo, Keehyoung; Lee, In-Ho; Lee, Sung Jong; Lee, Jooyoung

2018-03-01

For protein structure modeling in the CASP12 experiment, we have developed a new protocol based on our previous CASP11 approach. The global optimization method of conformational space annealing (CSA) was applied to 3 stages of modeling: multiple sequence-structure alignment, three-dimensional (3D) chain building, and side-chain re-modeling. For better template selection and model selection, we updated our model quality assessment (QA) method with the newly developed SVMQA (support vector machine for quality assessment). For 3D chain building, we updated our energy function by including restraints generated from predicted residue-residue contacts. New energy terms for the predicted secondary structure and predicted solvent accessible surface area were also introduced. For difficult targets, we proposed a new method, LEEab, where the template term played a less significant role than it did in LEE, complemented by increased contributions from other terms such as the predicted contact term. For TBM (template-based modeling) targets, LEE performed better than LEEab, but for FM targets, LEEab was better. For model refinement, we modified our CASP11 molecular dynamics (MD) based protocol by using explicit solvents and tuning down restraint weights. Refinement results from MD simulations that used a new augmented statistical energy term in the force field were quite promising. Finally, when using inaccurate information (such as the predicted contacts), it was important to use the Lorentzian function for which the maximal penalty arising from wrong information is always bounded. © 2017 Wiley Periodicals, Inc.

Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.

PubMed

Peterson, Lenna X; Shin, Woong-Hee; Kim, Hyungrae; Kihara, Daisuke

2018-03-01

We report our group's performance for protein-protein complex structure prediction and scoring in Round 37 of the Critical Assessment of PRediction of Interactions (CAPRI), an objective assessment of protein-protein complex modeling. We demonstrated noticeable improvement in both prediction and scoring compared to previous rounds of CAPRI, with our human predictor group near the top of the rankings and our server scorer group at the top. This is the first time in CAPRI that a server has been the top scorer group. To predict protein-protein complex structures, we used both multi-chain template-based modeling (TBM) and our protein-protein docking program, LZerD. LZerD represents protein surfaces using 3D Zernike descriptors (3DZD), which are based on a mathematical series expansion of a 3D function. Because 3DZD are a soft representation of the protein surface, LZerD is tolerant to small conformational changes, making it well suited to docking unbound and TBM structures. The key to our improved performance in CAPRI Round 37 was to combine multi-chain TBM and docking. As opposed to our previous strategy of performing docking for all target complexes, we used TBM when multi-chain templates were available and docking otherwise. We also describe the combination of multiple scoring functions used by our server scorer group, which achieved the top rank for the scorer phase. © 2017 Wiley Periodicals, Inc.

Risk of breast cancer following low-dose radiation exposure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boice, J.D. Jr.; Land, C.E.; Shore, R.E.

1979-06-01

Risk of breast cancer following radiation exposure was studied, based on surveys of tuberculosis patients who had multiple fluoroscopic examinations of the chest, mastitis patients given radiotherapy, and atomic bomb survivors. Analysis suggests that the risk is greatest for persons exposed as adolescents, although exposure at all ages carries some risk. The dose-response relationship was consistent with linearity in all studies. Direct evidence of radiation risk at doses under 0.5 Gy (50 rad) is apparent among A-bomb survivors. Fractionation does not appear to diminish risk, nor does time since exposure (even after 45 years of observation). The interval between exposuremore » and the clinical appearance of radiogenic breast cancer may be mediated by hormonal or other age-related factors but is unrelated to dose. Age-specific absolute risk estimtes for all studies are remarkably similar. The best estimate of risk among American women exposed after age 20 is 6.6 excess cancers/10/sup 4/ WY-Gy (10/sup 6/ WY-rad).« less

Three-dimensional CT enterography using oral gastrografin in patients with small bowel obstruction: comparison with axial CT images or fluoroscopic findings.

PubMed

Hong, Seong Sook; Kim, Ah Young; Kwon, Seok Beom; Kim, Pyo Nyun; Lee, Moon-Gyu; Ha, Hyun Kwon

2010-10-01

To evaluate the feasibility of 3D CT enterography using oral gastrografin in patients with small bowel obstruction (SBO), focusing on improving diagnostic performance as compared with the use of axial CT imagings and fluoroscopic findings. For a 10-month period, 18 patients with known SBO detected clinically and radiologically were enrolled. In all patients, gastrografin was ingested prior to CT enterography. Twelve patients underwent a fluoroscopic examination. Images were randomly assessed for confidence for the level, for the cause of SBO, and for the assessment of the interpretability of each image by two gastrointestinal radiologists. The results were considered statistically significant using the Wilcoxon rank sum test. All patients (100%) well tolerated the administration of oral gastrografin. The use of 3D CT enterography significantly improved diagnostic confidence for the interpretation of the level, cause of SBO, and the assessment of the interpretability of each image as compared with the use of axial CT images (P < 0.05). 3D CT enterography was superior as compared to fluoroscopic examination (P < 0.05). The use of gastrografin for 3D CT enterography is a safe and feasible technique for precise evaluation of known or suspected SBO.

Value of Examination Under Fluoroscopy for the Assessment of Sacroiliac Joint Dysfunction.

PubMed

Eskander, Jonathan P; Ripoll, Juan G; Calixto, Frank; Beakley, Burton D; Baker, Jeffrey T; Healy, Patrick J; Gunduz, O H; Shi, Lizheng; Clodfelter, Jamie A; Liu, Jinan; Kaye, Alan D; Sharma, Sanjay

2015-01-01

Pain emanating from the sacroiliac (SI) joint can have variable radiation patterns. Single physical examination tests for SI joint pain are inconsistent with multiple tests increasing both sensitivity and specificity. To evaluate the use of fluoroscopy in the diagnosis of SI joint pain. Prospective double blind comparison study. Pain clinic and radiology setting in urban Veterans Administration (VA) in New Orleans, Louisiana. Twenty-two adult men, patients at a southeastern United States VA interventional pain clinic, presented with unilateral low back pain of more than 2 months' duration. Patients with previous back surgery were excluded from the study. Each patient was given a Gapping test, Patrick (FABERE) test, and Gaenslen test. A second blinded physician placed each patient prone under fluoroscopic guidance, asking each patient to point to the most painful area. Pain was provoked by applying pressure with the heel of the palm in that area to determine the point of maximum tenderness. The area was marked with a radio-opaque object and was placed on the mark with a fluoroscopic imgage. A site within 1 cm of the SI joint was considered as a positive test. This was followed by a diagnostic injection under fluoroscopy with 1 mL 2% lidocaine. A positive result was considered as more than 2 hours of greater than 75% reduction in pain. Then, in 2-3 days this was followed by a therapeutic injection under fluoroscopy with 1 mL 0.5% bupivacaine and 40 mg methylprednisolone. Each patient was reassessed after 6 weeks. The sensitivity and specificity in addition to the positive and negative predictive values were determined for both the conventional examinations, as well as the examination under fluoroscopy. Finally, a receiver operating characteristic (ROC) curve was constructed to evaluate test performance. The sensitivity and specificity of the fluoroscopic examination were 0.82 and 0.80 respectively; Positive predictive value and negative predictive value were 0.93 and 0.57 respectively. The area under ROC curve was 0.812 which is considered a "good" test; however the area under ROC for the conventional examination were between 0.52-0.58 which is considered "poor to fail". Variation in anatomy of the SI joint, small sample size. Multiple structures of the SI joint complex can result in clinical symptoms of pain. These include intra-articular structures (degenerative arthritis, and inflammatory conditions) as well as extra-articular structures (ligaments, muscles, etc.).

[Arthroscopy-guided fracture management. Ankle joint and calcaneus].

PubMed

Schoepp, C; Rixen, D

2013-04-01

Arthroscopic fracture management of the ankle and calcaneus requires a differentiated approach. The aim is to minimize surgical soft tissue damage and to visualize anatomical fracture reduction arthroscopically. Moreover, additional cartilage damage can be detected and treated. The arthroscopic approach is limited by deep impressions of the joint surface needing cancellous bone grafting, by multiple fracture lines on the articular side and by high-grade soft tissue damage. An alternative to the minimally invasive arthroscopic approach is open arthroscopic reduction in conventional osteosynthesis. This facilitates correct assessment of surgical reduction of complex calcaneal fractures, otherwise remaining non-anatomical reduction might not be fluoroscopically detected during surgery.

Template-directed synthesis of linear porphyrin oligomers: classical, Vernier and mutual Vernier† †Electronic supplementary information (ESI) available: Synthesis and characterization of new compounds, ladder complexes, UV-vis-NIR titrations and binding data for reference compounds and for the formation of linear oligomer complexes, calculation of effective molarities, analytical GPC calibration and molar absorption coefficients. See DOI: 10.1039/c6sc05355f Click here for additional data file.

PubMed Central

Kamonsutthipaijit, Nuntaporn

2017-01-01

Three different types of template-directed syntheses of linear porphyrin oligomers are presented. In the classical approach the product has the same number of binding sites as the template, whereas in Vernier reactions the product has the lowest common multiple of the numbers of binding sites in the template and the building block. Mutual Vernier templating is like Vernier templating except that both strands of the Vernier complex undergo coupling simultaneously, so that it becomes impossible to say which is the ‘template’ and which is the ‘building block’. The template-directed synthesis of monodisperse linear oligomers is more difficult than that of cyclic oligomers, because the products of linear templating have reactive ends. All three types of templating are demonstrated here, and used to prepare a nickel(ii) porphyrin dodecamer with 4-pyridyl substituents on all twelve porphyrin units. The stabilities and cooperativities of the double-strand complexes involved in these reactions were investigated by UV-vis-NIR titration. The four-rung ladder duplex has a stability constant of about 2 × 1018 M–1 in dichloromethane at 298 K. PMID:28553508

A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling.

PubMed

Li, Jilong; Cheng, Jianlin

2016-05-10

Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution. MTMG stochastically resamples the positions for Cα atoms of the residues whose positions are uncertain from the distribution, and accepts or rejects new position according to a simulated annealing protocol, which effectively removes atomic clashes commonly encountered in multi-template comparative modeling. We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP11 targets, respectively. Using multiple templates with MTMG improves the GDT-TS score and TM-score of structural models by 2.96-6.37% and 2.42-5.19% on the three datasets over using single templates. MTMG's performance was comparable to Modeller in terms of GDT-TS score, TM-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach. The MTMG software is freely available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/mtmg.html.

A Stochastic Point Cloud Sampling Method for Multi-Template Protein Comparative Modeling

PubMed Central

Li, Jilong; Cheng, Jianlin

2016-01-01

Generating tertiary structural models for a target protein from the known structure of its homologous template proteins and their pairwise sequence alignment is a key step in protein comparative modeling. Here, we developed a new stochastic point cloud sampling method, called MTMG, for multi-template protein model generation. The method first superposes the backbones of template structures, and the Cα atoms of the superposed templates form a point cloud for each position of a target protein, which are represented by a three-dimensional multivariate normal distribution. MTMG stochastically resamples the positions for Cα atoms of the residues whose positions are uncertain from the distribution, and accepts or rejects new position according to a simulated annealing protocol, which effectively removes atomic clashes commonly encountered in multi-template comparative modeling. We benchmarked MTMG on 1,033 sequence alignments generated for CASP9, CASP10 and CASP11 targets, respectively. Using multiple templates with MTMG improves the GDT-TS score and TM-score of structural models by 2.96–6.37% and 2.42–5.19% on the three datasets over using single templates. MTMG’s performance was comparable to Modeller in terms of GDT-TS score, TM-score, and GDT-HA score, while the average RMSD was improved by a new sampling approach. The MTMG software is freely available at: http://sysbio.rnet.missouri.edu/multicom_toolbox/mtmg.html. PMID:27161489

Strain mapping in TEM using precession electron diffraction

DOEpatents

Taheri, Mitra Lenore; Leff, Asher Calvin

2017-02-14

A sample material is scanned with a transmission electron microscope (TEM) over multiple steps having a predetermined size at a predetermined angle. Each scan at a predetermined step and angle is compared to a template, wherein the template is generated from parameters of the material and the scanning. The data is then analyzed using local mis-orientation mapping and/or Nye's tensor analysis to provide information about local strain states.

Accurate template-based modeling in CASP12 using the IntFOLD4-TS, ModFOLD6, and ReFOLD methods.

PubMed

McGuffin, Liam J; Shuid, Ahmad N; Kempster, Robert; Maghrabi, Ali H A; Nealon, John O; Salehe, Bajuna R; Atkins, Jennifer D; Roche, Daniel B

2018-03-01

Our aim in CASP12 was to improve our Template-Based Modeling (TBM) methods through better model selection, accuracy self-estimate (ASE) scores and refinement. To meet this aim, we developed two new automated methods, which we used to score, rank, and improve upon the provided server models. Firstly, the ModFOLD6_rank method, for improved global Quality Assessment (QA), model ranking and the detection of local errors. Secondly, the ReFOLD method for fixing errors through iterative QA guided refinement. For our automated predictions we developed the IntFOLD4-TS protocol, which integrates the ModFOLD6_rank method for scoring the multiple-template models that were generated using a number of alternative sequence-structure alignments. Overall, our selection of top models and ASE scores using ModFOLD6_rank was an improvement on our previous approaches. In addition, it was worthwhile attempting to repair the detected errors in the top selected models using ReFOLD, which gave us an overall gain in performance. According to the assessors' formula, the IntFOLD4 server ranked 3rd/5th (average Z-score > 0.0/-2.0) on the server only targets, and our manual predictions (McGuffin group) ranked 1st/2nd (average Z-score > -2.0/0.0) compared to all other groups. © 2017 Wiley Periodicals, Inc.

Understanding the General Packing Rearrangements Required for Successful Template Based Modeling of Protein Structure from a CASP Experiment

PubMed Central

Day, Ryan; Joo, Hyun; Chavan, Archana; Lennox, Kristin P.; Chen, Ann; Dahl, David B.; Vannucci, Marina; Tsai, Jerry W.

2012-01-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. PMID:23266765

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment.

PubMed

Day, Ryan; Joo, Hyun; Chavan, Archana C; Lennox, Kristin P; Chen, Y Ann; Dahl, David B; Vannucci, Marina; Tsai, Jerry W

2013-02-01

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling. Copyright © 2012 Elsevier Ltd. All rights reserved.

Heteroatom-doped highly porous carbon from human urine.

PubMed

Chaudhari, Nitin Kaduba; Song, Min Young; Yu, Jong-Sung

2014-06-09

Human urine, otherwise potentially polluting waste, is an universal unused resource in organic form disposed by the human body. We present for the first time "proof of concept" of a convenient, perhaps economically beneficial, and innovative template-free route to synthesize highly porous carbon containing heteroatoms such as N, S, Si, and P from human urine waste as a single precursor for carbon and multiple heteroatoms. High porosity is created through removal of inherently-present salt particles in as-prepared "Urine Carbon" (URC), and multiple heteroatoms are naturally doped into the carbon, making it unnecessary to employ troublesome expensive pore-generating templates as well as extra costly heteroatom-containing organic precursors. Additionally, isolation of rock salts is an extra bonus of present work. The technique is simple, but successful, offering naturally doped conductive hierarchical porous URC, which leads to superior electrocatalytic ORR activity comparable to state of the art Pt/C catalyst along with much improved durability and methanol tolerance, demonstrating that the URC can be a promising alternative to costly Pt-based electrocatalyst for ORR. The ORR activity can be addressed in terms of heteroatom doping, surface properties and electrical conductivity of the carbon framework.

Heteroatom-doped highly porous carbon from human urine

NASA Astrophysics Data System (ADS)

Chaudhari, Nitin Kaduba; Song, Min Young; Yu, Jong-Sung

2014-06-01

Human urine, otherwise potentially polluting waste, is an universal unused resource in organic form disposed by the human body. We present for the first time ``proof of concept'' of a convenient, perhaps economically beneficial, and innovative template-free route to synthesize highly porous carbon containing heteroatoms such as N, S, Si, and P from human urine waste as a single precursor for carbon and multiple heteroatoms. High porosity is created through removal of inherently-present salt particles in as-prepared ``Urine Carbon'' (URC), and multiple heteroatoms are naturally doped into the carbon, making it unnecessary to employ troublesome expensive pore-generating templates as well as extra costly heteroatom-containing organic precursors. Additionally, isolation of rock salts is an extra bonus of present work. The technique is simple, but successful, offering naturally doped conductive hierarchical porous URC, which leads to superior electrocatalytic ORR activity comparable to state of the art Pt/C catalyst along with much improved durability and methanol tolerance, demonstrating that the URC can be a promising alternative to costly Pt-based electrocatalyst for ORR. The ORR activity can be addressed in terms of heteroatom doping, surface properties and electrical conductivity of the carbon framework.

Nanostructured and thermoresponsive recombinant biopolymer-based microcapsules for the delivery of active molecules.

PubMed

Costa, Rui R; Custódio, Catarina A; Arias, Francisco J; Rodríguez-Cabello, José C; Mano, João F

2013-10-01

Multilayer capsules conceived at the nano- and microscales are receiving increasing interest due to their potential role as carriers of biomolecules for drug delivery and tissue engineering. Herein we report the construction of microcapsules by the sequential adsorption of chitosan and a biomimetic elastin-like recombinamer into nanostructured layers on inorganic microparticle templates. The release profile of bovine serum albumin, which was studied at 25 and 37 °C, shows higher retention and Fickian diffusion at physiological temperature. The self-assembled multilayers act as a barrier and allowed for sustained release over 14 days. The capsules studied are non-cytotoxic towards L929 cells, thereby suggesting multiple applications in the fields of biotechnology and bioengineering, where high control of the delivery of therapeutics and growth/differentiation factors is required. In this paper, the construction of microcapsules by sequential adsorption of chitosan and a biomimetic, elastin-like recombinamer into nanostructured layers on inorganic microparticle templates is reported. The layers demonstrated sustained drug release over 14 days. These microcapsules are non-cytotoxic toward L929 cells, suggesting multiple applications where high control of drug or growth factor delivery is required. Copyright © 2013 Elsevier Inc. All rights reserved.

Heteroatom-doped highly porous carbon from human urine

PubMed Central

Chaudhari, Nitin Kaduba; Song, Min Young; Yu, Jong-Sung

2014-01-01

Human urine, otherwise potentially polluting waste, is an universal unused resource in organic form disposed by the human body. We present for the first time “proof of concept” of a convenient, perhaps economically beneficial, and innovative template-free route to synthesize highly porous carbon containing heteroatoms such as N, S, Si, and P from human urine waste as a single precursor for carbon and multiple heteroatoms. High porosity is created through removal of inherently-present salt particles in as-prepared “Urine Carbon” (URC), and multiple heteroatoms are naturally doped into the carbon, making it unnecessary to employ troublesome expensive pore-generating templates as well as extra costly heteroatom-containing organic precursors. Additionally, isolation of rock salts is an extra bonus of present work. The technique is simple, but successful, offering naturally doped conductive hierarchical porous URC, which leads to superior electrocatalytic ORR activity comparable to state of the art Pt/C catalyst along with much improved durability and methanol tolerance, demonstrating that the URC can be a promising alternative to costly Pt-based electrocatalyst for ORR. The ORR activity can be addressed in terms of heteroatom doping, surface properties and electrical conductivity of the carbon framework. PMID:24909133

Comparing a volume based template approach and ultrasound guided freehand approach in multicatheter interstitial accelerated partial breast irradiation.

PubMed

Koh, Vicky Y; Buhari, Shaik A; Tan, Poh Wee; Tan, Yun Inn; Leong, Yuh Fun; Earnest, Arul; Tang, Johann I

2014-06-01

Currently, there are two described methods of catheter insertion for women undergoing multicatheter interstitial accelerated partial breast irradiation (APBI). These are a volume based template approach (template) and a non-template ultrasound guidance freehand approach (non-template). We aim to compare dosimetric endpoints between the template and non-template approach. Twenty patients, who received adjuvant multicatheter interstitial APBI between August 2008 to March 2010 formed the study cohort. Dosimetric planning was based on the RTOG 04-13 protocol. For standardization, the planning target volume evaluation (PTV-Eval) and organs at risk were contoured with the assistance of the attending surgeon. Dosimetric endpoints include D90 of the PTV-Eval, Dose Homogeneity Index (DHI), V200, maximum skin dose (MSD), and maximum chest wall dose (MCD). A median of 18 catheters was used per patient. The dose prescribed was 34 Gy in 10 fractions BID over 5 days. The average breast volume was 846 cm(3) (526-1384) for the entire cohort and there was no difference between the two groups (p = 0.6). Insertion time was significantly longer for the non-template approach (mean 150 minutes) compared to the template approach (mean: 90 minutes) (p = 0.02). The planning time was also significantly longer for the non-template approach (mean: 240 minutes) compared to the template approach (mean: 150 minutes) (p < 0.01). The template approach yielded a higher D90 (mean: 95%) compared to the non-template approach (mean: 92%) (p < 0.01). There were no differences in DHI (p = 0.14), V200 (p = 0.21), MSD (p = 0.7), and MCD (p = 0.8). Compared to the non-template approach, the template approach offered significant shorter insertion and planning times with significantly improved dosimetric PTV-Eval coverage without significantly compromising organs at risk dosimetrically.

Cloud-based preoperative planning for total hip arthroplasty: a study of accuracy, efficiency, and compliance.

PubMed

Maratt, Joseph D; Srinivasan, Ramesh C; Dahl, William J; Schilling, Peter L; Urquhart, Andrew G

2012-08-01

As digital radiography becomes more prevalent, several systems for digital preoperative planning have become available. The purpose of this study was to evaluate the accuracy and efficiency of an inexpensive, cloud-based digital templating system, which is comparable with acetate templating. However, cloud-based templating is substantially faster and more convenient than acetate templating or locally installed software. Although this is a practical solution for this particular medical application, regulatory changes are necessary before the tremendous advantages of cloud-based storage and computing can be realized in medical research and clinical practice. Copyright 2012, SLACK Incorporated.

[Preliminary safety and stability assessment of orthodontic miniscrew implantation guided by surgical template based on cone-beam CT images].

PubMed

Qiu, L L; Li, S; Bai, Y X

2016-06-01

To develop surgical templates for orthodontic miniscrew implantation based on cone-beam CT(CBCT)three-dimensional(3D)images and to evaluate the safety and stability of implantation guided by the templates. DICOM data obtained in patients who had CBCT scans taken were processed using Mimics software, and 3D images of teeth and maxillary bone were acquired. Meanwhile, 3D images of miniscrews were acquired using Solidworks software and processed with Mimics software. Virtual position of miniscrews was determined based on 3D images of teeth, bone, and miniscrews. 3D virtual templates were designed according to the virtual implantation plans. STL files were output and the real templates were fabricated with stereolithographic appliance(SLA). Postoperative CBCT scans were used to evaluate the implantation safety and the stability of miniscrews were investigated. All the templates were positioned accurately and kept stable throughout the implantation process. No root damage was found. The deviations were(1.73±0.65)mm at the corona, and(1.28±0.82)mm at the apex, respectively. The stability of miniscrews was fairly well. Surgical templates for miniscrew implantation could be acquired based on 3D CBCT images and fabricated with SLA. Implantation guided by these templates was safe and stable.

How Accurate Are Infrared Luminosities from Monochromatic Photometric Extrapolation?

NASA Astrophysics Data System (ADS)

Lin, Zesen; Fang, Guanwen; Kong, Xu

2016-12-01

Template-based extrapolations from only one photometric band can be a cost-effective method to estimate the total infrared (IR) luminosities ({L}{IR}) of galaxies. By utilizing multi-wavelength data that covers across 0.35-500 μm in GOODS-North and GOODS-South fields, we investigate the accuracy of this monochromatic extrapolated {L}{IR} based on three IR spectral energy distribution (SED) templates out to z˜ 3.5. We find that the Chary & Elbaz template provides the best estimate of {L}{IR} in Herschel/Photodetector Array Camera and Spectrometer (PACS) bands, while the Dale & Helou template performs best in Herschel/Spectral and Photometric Imaging Receiver (SPIRE) bands. To estimate {L}{IR}, we suggest that extrapolations from the available longest wavelength PACS band based on the Chary & Elbaz template can be a good estimator. Moreover, if the PACS measurement is unavailable, extrapolations from SPIRE observations but based on the Dale & Helou template can also provide a statistically unbiased estimate for galaxies at z≲ 2. The emission with a rest-frame 10-100 μm range of IR SED can be well described by all three templates, but only the Dale & Helou template shows a nearly unbiased estimate of the emission of the rest-frame submillimeter part.

The capability of fluoroscopic systems to determine differential Roentgen-ray absorption

NASA Technical Reports Server (NTRS)

Baily, N. A.; Crepeau, R. L.

1975-01-01

A clinical fluoroscopic unit used in conjunction with a TV image digitization system was investigated to determine its capability to evaluate differential absorption between two areas in the same field. Fractional contrasts and minimum detectability for air, several concentrations of Renografin-60, and aluminum were studied using phantoms of various thicknesses. Results showed that the videometric response, when treated as contrast, shows a linear response with absorber thickness up to considerable thicknesses.

A virtual fluoroscopy system to verify seed positioning accuracy during prostate permanent seed implants.

PubMed

Sarkar, V; Gutierrez, A N; Stathakis, S; Swanson, G P; Papanikolaou, N

2009-01-01

The purpose of this project was to develop a software platform to produce a virtual fluoroscopic image as an aid for permanent prostate seed implants. Seed location information from a pre-plan was extracted and used as input to in-house developed software to produce a virtual fluoroscopic image. In order to account for differences in patient positioning on the day of treatment, the user was given the ability to make changes to the virtual image. The system has been shown to work as expected for all test cases. The system allows for quick (on average less than 10 sec) generation of a virtual fluoroscopic image of the planned seed pattern. The image can be used as a verification tool to aid the physician in evaluating how close the implant is to the planned distribution throughout the procedure and enable remedial action should a large deviation be observed.

Region based feature extraction from non-cooperative iris images using triplet half-band filter bank

NASA Astrophysics Data System (ADS)

Barpanda, Soubhagya Sankar; Majhi, Banshidhar; Sa, Pankaj Kumar

2015-09-01

In this paper, we have proposed energy based features using a multi-resolution analysis (MRA) on iris template. The MRA is based on our suggested triplet half-band filter bank (THFB). The THFB derivation process is discussed in detail. The iris template is divided into six equispaced sub-templates and two level decomposition has been made to each sub-template using THFB except second one. The reason for discarding the second template is due to the fact that it mostly contains the noise due to eyelids, eyelashes, and occlusion due to segmentation failure. Subsequently, energy features are derived from the decomposed coefficients of each sub-template. The proposed feature has been experimented on standard databases like CASIAv3, UBIRISv1, and IITD and mostly on iris images which encounter a segmentation failure. Comparative analysis has been done with existing features based on Gabor transform, Fourier transform, and CDF 9/7 filter bank. The proposed scheme shows superior performance with respect to FAR, GAR and AUC.

The Control of Single-color and Multiple-color Visual Search by Attentional Templates in Working Memory and in Long-term Memory.

PubMed

Grubert, Anna; Carlisle, Nancy B; Eimer, Martin

2016-12-01

The question whether target selection in visual search can be effectively controlled by simultaneous attentional templates for multiple features is still under dispute. We investigated whether multiple-color attentional guidance is possible when target colors remain constant and can thus be represented in long-term memory but not when they change frequently and have to be held in working memory. Participants searched for one, two, or three possible target colors that were specified by cue displays at the start of each trial. In constant-color blocks, the same colors remained task-relevant throughout. In variable-color blocks, target colors changed between trials. The contralateral delay activity (CDA) to cue displays increased in amplitude as a function of color memory load in variable-color blocks, which indicates that cued target colors were held in working memory. In constant-color blocks, the CDA was much smaller, suggesting that color representations were primarily stored in long-term memory. N2pc components to targets were measured as a marker of attentional target selection. Target N2pcs were attenuated and delayed during multiple-color search, demonstrating less efficient attentional deployment to color-defined target objects relative to single-color search. Importantly, these costs were the same in constant-color and variable-color blocks. These results demonstrate that attentional guidance by multiple-feature as compared with single-feature templates is less efficient both when target features remain constant and can be represented in long-term memory and when they change across trials and therefore have to be maintained in working memory.

Environmental Learning Centers: A Template.

ERIC Educational Resources Information Center

Vozick, Eric

1999-01-01

Provides a working model, or template, for community-based environmental learning centers (ELCs). The template presents a philosophy as well as a plan for staff and administration operations, educational programming, and financial support. The template also addresses "green" construction and maintenance of buildings and grounds and…

N7 logic via patterning using templated DSA: implementation aspects

NASA Astrophysics Data System (ADS)

Bekaert, J.; Doise, J.; Gronheid, R.; Ryckaert, J.; Vandenberghe, G.; Fenger, G.; Her, Y. J.; Cao, Y.

2015-07-01

In recent years, major advancements have been made in the directed self-assembly (DSA) of block copolymers (BCP). Insertion of DSA for IC fabrication is seriously considered for the 7 nm node. At this node the DSA technology could alleviate costs for multiple patterning and limit the number of masks that would be required per layer. At imec, multiple approaches for inserting DSA into the 7 nm node are considered. One of the most straightforward approaches for implementation would be for via patterning through templated DSA; a grapho-epitaxy flow using cylindrical phase BCP material resulting in contact hole multiplication within a litho-defined pre-pattern. To be implemented for 7 nm node via patterning, not only the appropriate process flow needs to be available, but also DSA-aware mask decomposition is required. In this paper, several aspects of the imec approach for implementing templated DSA will be discussed, including experimental demonstration of density effect mitigation, DSA hole pattern transfer and double DSA patterning, creation of a compact DSA model. Using an actual 7 nm node logic layout, we derive DSA-friendly design rules in a logical way from a lithographer's view point. A concrete assessment is provided on how DSA-friendly design could potentially reduce the number of Via masks for a place-and-routed N7 logic pattern.

Liquid crystal templating as an approach to spatially and temporally organise soft matter.

PubMed

van der Asdonk, Pim; Kouwer, Paul H J

2017-10-02

Chemistry quickly moves from a molecular science to a systems science. This requires spatial and temporal control over the organisation of molecules and molecular assemblies. Whilst Nature almost by default (transiently) organises her components at multiple different length scales, scientists struggle to realise even relatively straightforward patterns. In the past decades, supramolecular chemistry has taught us the rules to precisely engineer molecular assembly at the nanometre scale. At higher length scales, however, we are bound to top-down nanotechnology techniques to realise order. For soft, biological matter, many of these top-down techniques come with serious limitations since the molecules generally show low susceptibilities to the applied stimuli. A new method is based on liquid crystal templating. In this hierarchical approach, a liquid crystalline host serves as the scaffold to order polymers or assemblies. Being a liquid crystal, the host material can be ordered at many different length scales and on top of that, is highly susceptible to many external stimuli, which can even be used to manipulate the liquid crystal organisation in time. As a result, we anticipate large control over the organisation of the materials inside the liquid crystalline host. Recently, liquid crystal templating was also realised in water. This suddenly makes this tool highly applicable to start organising more delicate biological materials or even small organisms. We review the scope and limitations of liquid crystal templating and look out to where the technique may lead us.

Evidence for the packaging of multiple copies of Tf1 mRNA into particles and the trans priming of reverse transcription.

PubMed

Haag, A L; Lin, J H; Levin, H L

2000-08-01

Long terminal repeat (LTR)-containing retrotransposons and retroviruses are close relatives that possess similar mechanisms of reverse transcription. The particles of retroviruses package two copies of viral mRNA that both function as templates for the reverse transcription of the element. We studied the LTR-retrotransposon Tf1 of Schizosaccharomyces pombe to test whether multiple copies of transposon mRNA participate in the production of cDNA. Using the unique self-priming property of Tf1, we obtained evidence that multiple copies of Tf1 mRNA were packaged into virus-like particles. By coexpressing two distinct versions of Tf1, we found that the bulk of reverse transcription that was initiated on one mRNA template was subsequently transferred to others. In addition, the first 11 nucleotides of one mRNA were able to prime, in trans, the reverse transcription of another mRNA.

Intraoperative panoramic image using alignment grid, is it accurate?

PubMed

Apivatthakakul, T; Duanghakrung, M; Luevitoonvechkit, S; Patumasutra, S

2013-07-01

Minimally invasive orthopedic trauma surgery relies heavily on intraoperative fluoroscopic images to evaluate the quality of fracture reduction and fixation. However, fluoroscopic images have a narrow field of view and often cannot visualize the entire long bone axis. To compare the coronal femoral alignment between conventional X-rays to that achieved with a new method of acquiring a panoramic intraoperative image. Twenty-four cadaveric femurs with simple diaphyseal fractures were fixed with an angulated broad DCP to create coronal plane malalignment. An intraoperative alignment grid was used to help stitch different fluoroscopic images together to produce a panoramic image. A conventional X-ray of the entire femur was then performed. The coronal plane angulation in the panoramic images was then compared to the conventional X-rays using a Wilcoxon signed rank test. The mean angle measured from the panoramic view was 173.9° (range 169.3°-178.0°) with median of 173.2°. The mean angle measured from the conventional X-ray was 173.4° (range 167.7°-178.7°) with a median angle of 173.5°. There was no significant difference between both methods of measurement (P = 0.48). Panoramic images produced by stitching fluoroscopic images together with help of an alignment grid demonstrated the same accuracy at evaluating the coronal plane alignment of femur fractures as conventional X-rays.

Fluoroscopically Guided Epidural Injections of the Cervical and Lumbar Spine.

PubMed

Shim, Euddeum; Lee, Joon Woo; Lee, Eugene; Ahn, Joong Mo; Kang, Yusuhn; Kang, Heung Sik

2017-01-01

Advances in imaging and the development of injection techniques have enabled spinal intervention to become an important tool in managing chronic spinal pain. Epidural steroid injection (ESI) is one of the most widely used spinal interventions; it directly delivers drugs into the epidural space to relieve pain originating from degenerative spine disorders-central canal stenoses and neural foraminal stenoses-or disk herniations. Knowledge of the normal anatomy of the epidural space is essential to perform an effective and safe ESI and to recognize possible complications. Although computed tomographic (CT) or combined CT-fluoroscopic guidance has been increasingly used in ESI, conventional fluoroscopic guidance is generally performed. In ESI, drugs are delivered into the epidural space by interlaminar or transforaminal routes in the cervical spine or by interlaminar, transforaminal, or caudal routes in the lumbar spine. Epidurography is usually performed before drug delivery to verify the proper position of the needle in the epidural space. A small amount of contrast agent is injected with fluoroscopic guidance. Familiarity with the findings on a typical "true" epidurogram (demonstrating correct needle placement in the epidural space) permits proper performance of ESI. Findings on "false" epidurograms (demonstrating incorrect needle placement) include muscular staining and evidence of intravascular injection, inadvertent facet joint injection, dural puncture, subdural injection, and intraneural or intradiscal injection. © RSNA, 2016 An earlier incorrect version of this article appeared online. This article was corrected on December 22, 2016.

Scale-space for empty catheter segmentation in PCI fluoroscopic images.

PubMed

Bacchuwar, Ketan; Cousty, Jean; Vaillant, Régis; Najman, Laurent

2017-07-01

In this article, we present a method for empty guiding catheter segmentation in fluoroscopic X-ray images. The guiding catheter, being a commonly visible landmark, its segmentation is an important and a difficult brick for Percutaneous Coronary Intervention (PCI) procedure modeling. In number of clinical situations, the catheter is empty and appears as a low contrasted structure with two parallel and partially disconnected edges. To segment it, we work on the level-set scale-space of image, the min tree, to extract curve blobs. We then propose a novel structural scale-space, a hierarchy built on these curve blobs. The deep connected component, i.e. the cluster of curve blobs on this hierarchy, that maximizes the likelihood to be an empty catheter is retained as final segmentation. We evaluate the performance of the algorithm on a database of 1250 fluoroscopic images from 6 patients. As a result, we obtain very good qualitative and quantitative segmentation performance, with mean precision and recall of 80.48 and 63.04% respectively. We develop a novel structural scale-space to segment a structured object, the empty catheter, in challenging situations where the information content is very sparse in the images. Fully-automatic empty catheter segmentation in X-ray fluoroscopic images is an important and preliminary step in PCI procedure modeling, as it aids in tagging the arrival and removal location of other interventional tools.

Fluoroscopic and radiographic evaluation of tracheal collapse in dogs: 62 cases (2001-2006).

PubMed

Macready, Dawn M; Johnson, Lynelle R; Pollard, Rachel E

2007-06-15

To compare the use of radiography and fluoroscopy for detection and grading of tracheal collapse in dogs. Retrospective case series. Animals-62 dogs with tracheal collapse. For each dog, tracheal collapse was confirmed fluoroscopically and lateral cervical and thoracic radiographic views were reviewed. A board-certified radiologist (who was unaware of the dogs' clinical history) evaluated the cervical, thoracic inlet, thoracic, carinal, and main stem bronchial regions in all fluoroscopic videos and radiographic images for evidence of collapse. Cervical, thoracic inlet, thoracic, and carinal regions in both radio-graphic and fluoroscopic studies were graded for collapse (0%, 25%, 50%, 75%, or 100% decrease in diameter). Lateral cervical and thoracic radiographic images were available for 54 dogs, and inspiratory and expiratory lateral cervical and thoracic radiographic images were available for 8 dogs. For detection of tracheal collapse, assessment of radiographic views was sensitive and had the best negative predictive value in the cervical and thoracic inlet regions. Assessment of radiographic views was most specific and had the best positive predictive value in the thoracic inlet, thoracic, carina, and main stem bronchial regions. Radiography underestimated the degree of collapse in all areas. Review of inspiratory and expiratory views improved the accuracy of radiography for tracheal collapse diagnosis only slightly. Compared with fluoroscopy, radiography underestimated the frequency and degree of tracheal collapse. However, radiography appears to be useful for screening dogs with potential tracheal collapse.

RNA-Mediated Epigenetic Programming of Genome Rearrangements

PubMed Central

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F.

2012-01-01

RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha’s somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells. PMID:21801022

The role of an occlusal template during the placement of preformed metal crowns in children under general anaesthesia: a randomised control trial.

PubMed

Pani, S C; Dimashkieh, M; Mojaleed, F; Al Shammery, F

2015-12-01

This aim was to evaluate preformed metal crowns (PMC) placed under general anaesthesia using an occlusal template in comparison to crowns placed without the use of a template. CONSORT protocols were followed in the design of the study. A total of 60 children between 4-7 years requiring pulpotomy and PMC for all primary molars met the inclusion criteria for this study. The control group comprised patients for whom the PMC were placed without the use of an occlusal template, while in the test group crowns were placed using a polyvinyl siloxane occlusal template. Patients were followed up at 24 h, 7 days, 3 and 6 months. The time taken for the placement of crowns, instances of post-operative discomfort, success or failure of the pulp therapy and loss of any crowns were compared between the groups. The mean time taken for completion of the procedure in the control group was significantly greater than the template group (t = 2.566, p = 0.013). Significantly fewer patients in the template group reported symptoms of discomfort or high points at the 24-h recall; however, these differences were not significant at the 1-week, 3- or 6-month recall. The use of an occlusal template for the placement of multiple PMC under general anaesthesia reduces the time taken for their placement and reduces the incidence of immediate post-operative discomfort.

Photovoltaic panel extraction from very high-resolution aerial imagery using region-line primitive association analysis and template matching

NASA Astrophysics Data System (ADS)

Wang, Min; Cui, Qi; Sun, Yujie; Wang, Qiao

2018-07-01

In object-based image analysis (OBIA), object classification performance is jointly determined by image segmentation, sample or rule setting, and classifiers. Typically, as a crucial step to obtain object primitives, image segmentation quality significantly influences subsequent feature extraction and analyses. By contrast, template matching extracts specific objects from images and prevents shape defects caused by image segmentation. However, creating or editing templates is tedious and sometimes results in incomplete or inaccurate templates. In this study, we combine OBIA and template matching techniques to address these problems and aim for accurate photovoltaic panel (PVP) extraction from very high-resolution (VHR) aerial imagery. The proposed method is based on the previously proposed region-line primitive association framework, in which complementary information between region (segment) and line (straight line) primitives is utilized to achieve a more powerful performance than routine OBIA. Several novel concepts, including the mutual fitting ratio and best-fitting template based on region-line primitive association analyses, are proposed. Automatic template generation and matching method for PVP extraction from VHR imagery are designed for concept and model validation. Results show that the proposed method can successfully extract PVPs without any user-specified matching template or training sample. High user independency and accuracy are the main characteristics of the proposed method in comparison with routine OBIA and template matching techniques.

Navigation for fluoroscopy-guided cryo-balloon ablation procedures of atrial fibrillation

NASA Astrophysics Data System (ADS)

Bourier, Felix; Brost, Alexander; Kleinoeder, Andreas; Kurzendorfer, Tanja; Koch, Martin; Kiraly, Attila; Schneider, Hans-Juergen; Hornegger, Joachim; Strobel, Norbert; Kurzidim, Klaus

2012-02-01

Atrial fibrillation (AFib), the most common arrhythmia, has been identified as a major cause of stroke. The current standard in interventional treatment of AFib is the pulmonary vein isolation (PVI). PVI is guided by fluoroscopy or non-fluoroscopic electro-anatomic mapping systems (EAMS). Either classic point-to-point radio-frequency (RF)- catheter ablation or so-called single-shot-devices like cryo-balloons are used to achieve electrically isolation of the pulmonary veins and the left atrium (LA). Fluoroscopy-based systems render overlay images from pre-operative 3-D data sets which are then merged with fluoroscopic imaging, thereby adding detailed 3-D information to conventional fluoroscopy. EAMS provide tracking and visualization of RF catheters by means of electro-magnetic tracking. Unfortunately, current navigation systems, fluoroscopy-based or EAMS, do not provide tools to localize and visualize single shot devices like cryo-balloon catheters in 3-D. We present a prototype software for fluoroscopy-guided ablation procedures that is capable of superimposing 3-D datasets as well as reconstructing cyro-balloon catheters in 3-D. The 3-D cyro-balloon reconstruction was evaluated on 9 clinical data sets, yielded a reprojected 2-D error of 1.72 mm +/- 1.02 mm.

Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

PubMed Central

Xu, Dong; Zhang, Yang

2012-01-01

Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

A spin transfer torque magnetoresistance random access memory-based high-density and ultralow-power associative memory for fully data-adaptive nearest neighbor search with current-mode similarity evaluation and time-domain minimum searching

NASA Astrophysics Data System (ADS)

Ma, Yitao; Miura, Sadahiko; Honjo, Hiroaki; Ikeda, Shoji; Hanyu, Takahiro; Ohno, Hideo; Endoh, Tetsuo

2017-04-01

A high-density nonvolatile associative memory (NV-AM) based on spin transfer torque magnetoresistive random access memory (STT-MRAM), which achieves highly concurrent and ultralow-power nearest neighbor search with full adaptivity of the template data format, has been proposed and fabricated using the 90 nm CMOS/70 nm perpendicular-magnetic-tunnel-junction hybrid process. A truly compact current-mode circuitry is developed to realize flexibly controllable and high-parallel similarity evaluation, which makes the NV-AM adaptable to any dimensionality and component-bit of template data. A compact dual-stage time-domain minimum searching circuit is also developed, which can freely extend the system for more template data by connecting multiple NM-AM cores without additional circuits for integrated processing. Both the embedded STT-MRAM module and the computing circuit modules in this NV-AM chip are synchronously power-gated to completely eliminate standby power and maximally reduce operation power by only activating the currently accessed circuit blocks. The operations of a prototype chip at 40 MHz are demonstrated by measurement. The average operation power is only 130 µW, and the circuit density is less than 11 µm2/bit. Compared with the latest conventional works in both volatile and nonvolatile approaches, more than 31.3% circuit area reductions and 99.2% power improvements are achieved, respectively. Further power performance analyses are discussed, which verify the special superiority of the proposed NV-AM in low-power and large-memory-based VLSIs.

Research on Signature Verification Method Based on Discrete Fréchet Distance

NASA Astrophysics Data System (ADS)

Fang, J. L.; Wu, W.

2018-05-01

This paper proposes a multi-feature signature template based on discrete Fréchet distance, which breaks through the limitation of traditional signature authentication using a single signature feature. It solves the online handwritten signature authentication signature global feature template extraction calculation workload, signature feature selection unreasonable problem. In this experiment, the false recognition rate (FAR) and false rejection rate (FRR) of the statistical signature are calculated and the average equal error rate (AEER) is calculated. The feasibility of the combined template scheme is verified by comparing the average equal error rate of the combination template and the original template.

Integrated on-line system for DNA sequencing by capillary electrophoresis: From template to called bases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ton, H.; Yeung, E.S.

1997-02-15

An integrated on-line prototype for coupling a microreactor to capillary electrophoresis for DNA sequencing has been demonstrated. A dye-labeled terminator cycle-sequencing reaction is performed in a fused-silica capillary. Subsequently, the sequencing ladder is directly injected into a size-exclusion chromatographic column operated at nearly 95{degree}C for purification. On-line injection to a capillary for electrophoresis is accomplished at a junction set at nearly 70{degree}C. High temperature at the purification column and injection junction prevents the renaturation of DNA fragments during on-line transfer without affecting the separation. The high solubility of DNA in and the relatively low ionic strength of 1 x TEmore » buffer permit both effective purification and electrokinetic injection of the DNA sample. The system is compatible with highly efficient separations by a replaceable poly(ethylene oxide) polymer solution in uncoated capillary tubes. Future automation and adaptation to a multiple-capillary array system should allow high-speed, high-throughput DNA sequencing from templates to called bases in one step. 32 refs., 5 figs.« less

Accurate 3D kinematic measurement of temporomandibular joint using X-ray fluoroscopic images

NASA Astrophysics Data System (ADS)

Yamazaki, Takaharu; Matsumoto, Akiko; Sugamoto, Kazuomi; Matsumoto, Ken; Kakimoto, Naoya; Yura, Yoshiaki

2014-04-01

Accurate measurement and analysis of 3D kinematics of temporomandibular joint (TMJ) is very important for assisting clinical diagnosis and treatment of prosthodontics and orthodontics, and oral surgery. This study presents a new 3D kinematic measurement technique of the TMJ using X-ray fluoroscopic images, which can easily obtain the TMJ kinematic data in natural motion. In vivo kinematics of the TMJ (maxilla and mandibular bone) is determined using a feature-based 2D/3D registration, which uses beads silhouette on fluoroscopic images and 3D surface bone models with beads. The 3D surface models of maxilla and mandibular bone with beads were created from CT scans data of the subject using the mouthpiece with the seven strategically placed beads. In order to validate the accuracy of pose estimation for the maxilla and mandibular bone, computer simulation test was performed using five patterns of synthetic tantalum beads silhouette images. In the clinical applications, dynamic movement during jaw opening and closing was conducted, and the relative pose of the mandibular bone with respect to the maxilla bone was determined. The results of computer simulation test showed that the root mean square errors were sufficiently smaller than 1.0 mm and 1.0 degree. In the results of clinical application, during jaw opening from 0.0 to 36.8 degree of rotation, mandibular condyle exhibited 19.8 mm of anterior sliding relative to maxillary articular fossa, and these measurement values were clinically similar to the previous reports. Consequently, present technique was thought to be suitable for the 3D TMJ kinematic analysis.

The Effectiveness and Risks of Fluoroscopically-Guided Cervical Medial Branch Thermal Radiofrequency Neurotomy: A Systematic Review with Comprehensive Analysis of the Published Data.

PubMed

Engel, Andrew; Rappard, George; King, Wade; Kennedy, David J

2016-04-01

To determine the effectiveness and risks of fluoroscopically-guided cervical medial branch thermal radiofrequency neurotomy (CMBTRFN) for treating chronic neck pain of zygapophysial joint origin. Systematic review of the literature with comprehensive analysis of the published data. Four reviewers formally trained in evidence-based medicine searched the literature on CMBTRFN. Each assessed the methodologies of studies found and appraised the quality of evidence presented. The primary outcomes assessed were 100% relief of pain 6 and 12 months after treatment. Other outcomes were noted if reported. The evidence was evaluated in accordance with the Grades of Recommendation, Assessment, Development, and Evaluation (GRADE) system. The searches yielded eight primary publications on the effectiveness of the procedure. The evidence shows a majority of patients were pain free at 6 months and over a third were pain free at 1 year. The number needed to treat for complete pain relief at 6 months is 2. The evidence of effectiveness is of high quality according to the GRADE system. Twelve papers were found reporting unwanted effects, most of which are minor and temporary. No serious complications have ever been reported from procedures performed according to the published guidelines. The evidence of risks is of low quality according to the GRADE system. If performed as described in the International Spine Intervention Society Guidelines, fluoroscopically-guided CMBTRFN is effective for abolishing zygapophysial joint pain and carries only minor risks. © 2015 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

X-ray beam equalization for digital fluoroscopy

NASA Astrophysics Data System (ADS)

Molloi, Sabee Y.; Tang, Jerry; Marcin, Martin R.; Zhou, Yifang; Anvar, Behzad

1996-04-01

The concept of radiographic equalization has previously been investigated. However, a suitable technique for digital fluoroscopic applications has not been developed. The previously reported scanning equalization techniques cannot be applied to fluoroscopic applications due to their exposure time limitations. On the other hand, area beam equalization techniques are more suited for digital fluoroscopic applications. The purpose of this study is to develop an x- ray beam equalization technique for digital fluoroscopic applications that will produce an equalized radiograph with minimal image artifacts and tube loading. Preliminary unequalized images of a humanoid chest phantom were acquired using a digital fluoroscopic system. Using this preliminary image as a guide, an 8 by 8 array of square pistons were used to generate masks in a mold with CeO2. The CeO2 attenuator thicknesses were calculated using the gray level information from the unequalized image. The generated mask was positioned close to the focal spot (magnification of 8.0) in order to minimize edge artifacts from the mask. The masks were generated manually in order to investigate the piston and matrix size requirements. The development of an automated version of mask generation and positioning is in progress. The results of manual mask generation and positioning show that it is possible to generate equalized radiographs with minimal perceptible artifacts. The equalization of x-ray transmission across the field exiting from the object significantly improved the image quality by preserving local contrast throughout the image. Furthermore, the reduction in dynamic range significantly reduced the effect of x-ray scatter and veiling glare from high transmission to low transmission areas. Also, the x-ray tube loading due to the mask assembly itself was negligible. In conclusion it is possible to produce area beam compensation that will be compatible with digital fluoroscopy with minimal compensation artifacts. The compensation process produces an image with equalized signal to noise ratio in all parts of the image.

Fluoroscopically guided infiltration of the cervical nerve root: an indirect approach through the ipsilateral facet joint.

PubMed

Kelekis, Alexios; Filippiadis, Dimitrios K; Velonakis, Georgios; Martin, Jean-Baptist; Oikonomopoulos, Nikolaos; Brountzos, Elias; Kelekis, Nikolaos

2014-01-01

Transforaminal infiltrations in the cervical spine are governed by a higher rate of vascular puncture than in the lumbar spine. The purpose of our study is to assess the safety and efficacy of percutaneous, fluoroscopically guided nerve root infiltrations in cases of cervical radiculopathy. An indirect postero-lateral approach was performed through the ipsilateral facet joint. During the last 2 years, 25 patients experiencing cervical radiculopathy underwent percutaneous, fluoroscopically guided nerve root infiltrations by means of an indirect postero-lateral approach through the ipsilateral facet joint. The intra-articular position of the needle (22-gauge spinal needle) was fluoroscopically verified after injection of a small amount of contrast medium which also verified dispersion of the contrast medium periradicularly and in the epidural space. Then a mixture of long-acting glucocorticosteroid diluted in normal saline (1.5/1 mL) was injected intra-articularly. A questionnaire with a Numeric Visual Scale (NVS) scale helped assess pain relief, life quality, and mobility improvement. A mean of 2.3 sessions was performed in the patients of our study. In the vast majority of our patients 19/25 (76%), the second infiltration was performed within 7-10 days of the first one. Comparing the pain scores prior (mean value 8.80 ± 1.080 NVS units) and after (mean value 1.84 ± 1.405 NVS units), there was a mean decrease of 6.96 ± 1.695 NVS units [median value 7 NVS units (P < 0.001) in terms of pain reduction, effect upon mobility, and life quality. There were no clinically significant complications noted in our study. Fluoroscopically guided transforaminal infiltrations through the ipsilateral facet joint seem to be a feasible, efficacious, and safe approach for the treatment of patients with cervical radiculopathy. This approach facilitates needle placement and minimizes risk of complications.

Fluoroscopically guided nose tube drainage of mediastinal abscesses in post-operative gastro-oesophageal anastomotic leakage.

PubMed

Xu, Q Y; Yin, G W; Chen, S X; Jiang, F; Bai, X J; Wu, J D

2012-11-01

The aim of this study was to retrospectively evaluate the technical success rates and clinical effectiveness of fluoroscopically guided nose tube drainage of mediastinal abscesses and a nasojejunum feeding tube in post-operative gastro-oesophageal anastomotic leakage (GEAL). From January 2006 to June 2011, 18 cases of post-operative GEAL with mediastinal abscesses after oesophagectomy with intrathoracic oesophagogastric anastomotic procedures for oesophageal and cardiac carcinoma were treated by insertion of a nose drainage tube and nasojejunum feeding tube under fluoroscopic guidance. We evaluated the feasibility of two-tube insertion to facilitate leakage site closure and complete resolution of the abscess, and the patients' nutritional benefit was also evaluated by checking the serum albumin level between pre- and post-enteral feeding via the feeding tube. The two tubes were placed successfully under fluoroscopic guidance in 18 patients (100%). The procedure time for two-tube insertion ranged from 20 to 40 min (mean 30 min). 17 patients (94%) achieved leakage site closure after two-tube insertion and had a good tolerance of two tubes in the nasal cavity. The serum albumin level was significant, increased from pre-enteral feeding (2.49 ± 0.42 g dl(-1)) to the post-enteral feeding (3.58 ± 0.47 g dl(-1)) via the feeding tube (p<0.001). The duration of follow-up ranged from 1 to 49 months (mean 19 months). The insertion of nose tube drainage and a nasojejunum feeding tube under fluoroscopic guidance is safe, and it provides effective relief from mediastinal abscesses in GEAL after oesophagectomy. Moreover, our findings indicate that two-tube insertion may be used as a selective procedure to treat mediastinal abscesses in post-operative GEAL. Advances in knowledge Directive drainage of mediastinal abscesses in post-operative GEAL may be an effective treatment.

Retina verification system based on biometric graph matching.

PubMed

Lajevardi, Seyed Mehdi; Arakala, Arathi; Davis, Stephen A; Horadam, Kathy J

2013-09-01

This paper presents an automatic retina verification framework based on the biometric graph matching (BGM) algorithm. The retinal vasculature is extracted using a family of matched filters in the frequency domain and morphological operators. Then, retinal templates are defined as formal spatial graphs derived from the retinal vasculature. The BGM algorithm, a noisy graph matching algorithm, robust to translation, non-linear distortion, and small rotations, is used to compare retinal templates. The BGM algorithm uses graph topology to define three distance measures between a pair of graphs, two of which are new. A support vector machine (SVM) classifier is used to distinguish between genuine and imposter comparisons. Using single as well as multiple graph measures, the classifier achieves complete separation on a training set of images from the VARIA database (60% of the data), equaling the state-of-the-art for retina verification. Because the available data set is small, kernel density estimation (KDE) of the genuine and imposter score distributions of the training set are used to measure performance of the BGM algorithm. In the one dimensional case, the KDE model is validated with the testing set. A 0 EER on testing shows that the KDE model is a good fit for the empirical distribution. For the multiple graph measures, a novel combination of the SVM boundary and the KDE model is used to obtain a fair comparison with the KDE model for the single measure. A clear benefit in using multiple graph measures over a single measure to distinguish genuine and imposter comparisons is demonstrated by a drop in theoretical error of between 60% and more than two orders of magnitude.

AquaPathogen X--A template database for tracking field isolates of aquatic pathogens

USGS Publications Warehouse

Emmenegger, Evi; Kurath, Gael

2012-01-01

AquaPathogen X is a template database for recording information on individual isolates of aquatic pathogens and is available for download from the U.S. Geological Survey (USGS) Western Fisheries Research Center (WFRC) website (http://wfrc.usgs.gov). This template database can accommodate the nucleotide sequence data generated in molecular epidemiological studies along with the myriad of abiotic and biotic traits associated with isolates of various pathogens (for example, viruses, parasites, or bacteria) from multiple aquatic animal host species (for example, fish, shellfish, or shrimp). The simultaneous cataloging of isolates from different aquatic pathogens is a unique feature to the AquaPathogen X database, which can be used in surveillance of emerging aquatic animal diseases and clarification of main risk factors associated with pathogen incursions into new water systems. As a template database, the data fields are empty upon download and can be modified to user specifications. For example, an application of the template database that stores the epidemiological profiles of fish virus isolates, called Fish ViroTrak (fig. 1), was also developed (Emmenegger and others, 2011).

MRI non-uniformity correction through interleaved bias estimation and B-spline deformation with a template.

PubMed

Fletcher, E; Carmichael, O; Decarli, C

2012-01-01

We propose a template-based method for correcting field inhomogeneity biases in magnetic resonance images (MRI) of the human brain. At each algorithm iteration, the update of a B-spline deformation between an unbiased template image and the subject image is interleaved with estimation of a bias field based on the current template-to-image alignment. The bias field is modeled using a spatially smooth thin-plate spline interpolation based on ratios of local image patch intensity means between the deformed template and subject images. This is used to iteratively correct subject image intensities which are then used to improve the template-to-image deformation. Experiments on synthetic and real data sets of images with and without Alzheimer's disease suggest that the approach may have advantages over the popular N3 technique for modeling bias fields and narrowing intensity ranges of gray matter, white matter, and cerebrospinal fluid. This bias field correction method has the potential to be more accurate than correction schemes based solely on intrinsic image properties or hypothetical image intensity distributions.

MRI Non-Uniformity Correction Through Interleaved Bias Estimation and B-Spline Deformation with a Template*

PubMed Central

Fletcher, E.; Carmichael, O.; DeCarli, C.

2013-01-01

We propose a template-based method for correcting field inhomogeneity biases in magnetic resonance images (MRI) of the human brain. At each algorithm iteration, the update of a B-spline deformation between an unbiased template image and the subject image is interleaved with estimation of a bias field based on the current template-to-image alignment. The bias field is modeled using a spatially smooth thin-plate spline interpolation based on ratios of local image patch intensity means between the deformed template and subject images. This is used to iteratively correct subject image intensities which are then used to improve the template-to-image deformation. Experiments on synthetic and real data sets of images with and without Alzheimer’s disease suggest that the approach may have advantages over the popular N3 technique for modeling bias fields and narrowing intensity ranges of gray matter, white matter, and cerebrospinal fluid. This bias field correction method has the potential to be more accurate than correction schemes based solely on intrinsic image properties or hypothetical image intensity distributions. PMID:23365843

Synthesis of Three-dimensional Polymer Nanostructures via Chemical Vapor Deposition

NASA Astrophysics Data System (ADS)

Cheng, Kenneth

Chemical vapor deposition (CVD) is a widely practiced methodology for preparing thin film polymer coatings, and the coatings can be applied to a broad range of materials, including three-dimensional solid structures and low-vapor pressure liquids. Reactive poly(p-xylylene) (PPX) coatings prepared by CVD can be used as a powerful tool for surface functionalization and bio-conjugation. The first portion of this dissertation serves to extend the use of CVD-based reactive PPX coatings as a surface functionalization strategy for the conjugation of biomolecules. Micro-structured PPX coatings having multiple surface reactive groups were fabricated. Multiple orthogonal click reactions were then employed to selectively immobilize galactose and mannobiose to the micro-structured polymer coatings. The presence of different types of carbohydrate enables lectins binding for examining ligands/cell receptor interactions. This dissertation also demonstrates the use of CVD-based reactive PPX coatings as intermediate layers to immobilize adenoviral vectors onto tissue scaffolds. The ability to tether adenoviral vectors on tissue scaffolds localizes the transduction near the scaffold surface and reduces acute toxicity and hepatic pathology cause by direct administration of the viral vector, providing a safe and efficient gene therapy delivery strategy. In the second portion of this dissertation, we explore the CVD of PPX onto surfaces coated with a thin layer of liquid crystal (LC). Instead of forming a conformal PPX coating encapsulating the LC layer, PPX assembled into an array of high-aspect ratio nanofibers inside the LC layer. The LC layer was demonstrated to act as a template where the anisotropic internal ordering of the LC facilitated the formation of nanofibers. The diameter of the nanofibers was in the range of 100 nm and could be tuned by type of LC template used, and the length of the nanofibers could be precisely controlled by varying the thickness of the LC film. The overall shape of the nanofibers could be controlled by the internal ordering of the LC template, as exemplified by the assembly of helical nanofibers using cholesteric LC as the template. PPX nanofibers could be applied to a broad range of materials, such as curved surface, metal meshes and microparticles. We successfully created nanofibers with different surface functionalities and utilized them to capture molecules of interest. We also demonstrated the synthesis of twisted nanofibers using chiral-substituted precursors. The direction and the degree of twisting of nanofibers could be controlled by the handedness and the enantiomeric excess of the chiral precursor. Finally, we showed that the LC-templated CVD method could be extended to fabricating nanofibers made of other CVD-based polymer systems, such as poly(lutidine) and poly(p-phenylene vinylene). Our work opens a new platform for designing functional polymer nanostructures with programmable geometry, alignment and chemistry. The polymer nanostructures can be attractive for applications ranging from sensors, affinity filtration, and catalytic supports.

A simple method for the generation of organ and vessel contours from roentgenographic or fluoroscopic images

NASA Technical Reports Server (NTRS)

Newell, J. D.; Keller, R. A.; Baily, N. A.

1974-01-01

A simple method for outlining or contouring any area defined by a change in film density or fluoroscopic screen intensity is described. The entire process, except for the positioning of an electronic window, is accomplished using a small computer having appropriate softwave. The electronic window is operator positioned over the area to be processed. The only requirement is that the window be large enough to encompass the total area to be considered.

Transcatheter direct mitral valve annuloplasty with the Cardioband system for the treatment of functional mitral regurgitation.

PubMed

Taramasso, Maurizio; Inderbitzin, Devdas T; Guidotti, Andrea; Nietlispach, Fabian; Gaemperli, Oliver; Zuber, Michel; Maisano, Francesco

2016-01-01

Direct mitral valve annuloplasty is a transcatheter mitral valve repair approach that mimics the conventional surgical approach to treat functional mitral regurgitation. The Cardioband system (Valtech Cardio, Inc., Or-Yehuda, Israel) is delivered by a trans-septal approach and the implant is performed on the atrial side of the mitral annulus, under live echo and fluoroscopic guidance using multiple anchor elements. The Cardioband system obtained CE mark approval in October 2015, and initial clinical experiences are promising with regard to feasibility, safety and efficacy. © The Author 2016. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors.

PubMed

Won, Jonghun; Lee, Gyu Rie; Park, Hahnbeom; Seok, Chaok

2018-06-07

The second extracellular loops (ECL2s) of G-protein-coupled receptors (GPCRs) are often involved in GPCR functions, and their structures have important implications in drug discovery. However, structure prediction of ECL2 is difficult because of its long length and the structural diversity among different GPCRs. In this study, a new ECL2 conformational sampling method involving both template-based and ab initio sampling was developed. Inspired by the observation of similar ECL2 structures of closely related GPCRs, a template-based sampling method employing loop structure templates selected from the structure database was developed. A new metric for evaluating similarity of the target loop to templates was introduced for template selection. An ab initio loop sampling method was also developed to treat cases without highly similar templates. The ab initio method is based on the previously developed fragment assembly and loop closure method. A new sampling component that takes advantage of secondary structure prediction was added. In addition, a conserved disulfide bridge restraining ECL2 conformation was predicted and analytically incorporated into sampling, reducing the effective dimension of the conformational search space. The sampling method was combined with an existing energy function for comparison with previously reported loop structure prediction methods, and the benchmark test demonstrated outstanding performance.

Base Preferences in Non-Templated Nucleotide Incorporation by MMLV-Derived Reverse Transcriptases

PubMed Central

Zajac, Pawel; Islam, Saiful; Hochgerner, Hannah; Lönnerberg, Peter; Linnarsson, Sten

2013-01-01

Reverse transcriptases derived from Moloney Murine Leukemia Virus (MMLV) have an intrinsic terminal transferase activity, which causes the addition of a few non-templated nucleotides at the 3´ end of cDNA, with a preference for cytosine. This mechanism can be exploited to make the reverse transcriptase switch template from the RNA molecule to a secondary oligonucleotide during first-strand cDNA synthesis, and thereby to introduce arbitrary barcode or adaptor sequences in the cDNA. Because the mechanism is relatively efficient and occurs in a single reaction, it has recently found use in several protocols for single-cell RNA sequencing. However, the base preference of the terminal transferase activity is not known in detail, which may lead to inefficiencies in template switching when starting from tiny amounts of mRNA. Here, we used fully degenerate oligos to determine the exact base preference at the template switching site up to a distance of ten nucleotides. We found a strong preference for guanosine at the first non-templated nucleotide, with a greatly reduced bias at progressively more distant positions. Based on this result, and a number of careful optimizations, we report conditions for efficient template switching for cDNA amplification from single cells. PMID:24392002

Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints

PubMed Central

Day, Ryan; Qu, Xiaotao; Swanson, Rosemarie; Bohannan, Zach; Bliss, Robert

2011-01-01

Abstract Most current template-based structure prediction methods concentrate on finding the correct backbone conformation and then packing sidechains within that backbone. Our packing-based method derives distance constraints from conserved relative packing groups (RPGs). In our refinement approach, the RPGs provide a level of resolution that restrains global topology while allowing conformational sampling. In this study, we test our template-based structure prediction method using 51 prediction units from CASP7 experiments. RPG-based constraints are able to substantially improve approximately two-thirds of starting templates. Upon deeper investigation, we find that true positive spatial constraints, especially those non-local in sequence, derived from the RPGs were important to building nearer native models. Surprisingly, the fraction of incorrect or false positive constraints does not strongly influence the quality of the final candidate. This result indicates that our RPG-based true positive constraints sample the self-consistent, cooperative interactions of the native structure. The lack of such reinforcing cooperativity explains the weaker effect of false positive constraints. Generally, these findings are encouraging indications that RPGs will improve template-based structure prediction. PMID:21210729

Biplane reconstruction and visualization of virtual endoscopic and fluoroscopic views for interventional device navigation

NASA Astrophysics Data System (ADS)

Wagner, Martin G.; Strother, Charles M.; Schafer, Sebastian; Mistretta, Charles A.

2016-03-01

Biplane fluoroscopic imaging is an important tool for minimally invasive procedures for the treatment of cerebrovascular diseases. However, finding a good working angle for the C-arms of the angiography system as well as navigating based on the 2D projection images can be a difficult task. The purpose of this work is to propose a novel 4D reconstruction algorithm for interventional devices from biplane fluoroscopy images and to propose new techniques for a better visualization of the results. The proposed reconstruction methods binarizes the fluoroscopic images using a dedicated noise reduction algorithm for curvilinear structures and a global thresholding approach. A topology preserving thinning algorithm is then applied and a path search algorithm minimizing the curvature of the device is used to extract the 2D device centerlines. Finally, the 3D device path is reconstructed using epipolar geometry. The point correspondences are determined by a monotonic mapping function that minimizes the reconstruction error. The three dimensional reconstruction of the device path allows the rendering of virtual fluoroscopy images from arbitrary angles as well as 3D visualizations like virtual endoscopic views or glass pipe renderings, where the vessel wall is rendered with a semi-transparent material. This work also proposes a combination of different visualization techniques in order to increase the usability and spatial orientation for the user. A combination of synchronized endoscopic and glass pipe views is proposed, where the virtual endoscopic camera position is determined based on the device tip location as well as the previous camera position using a Kalman filter in order to create a smooth path. Additionally, vessel centerlines are displayed and the path to the target is highlighted. Finally, the virtual endoscopic camera position is also visualized in the glass pipe view to further improve the spatial orientation. The proposed techniques could considerably improve the workflow of minimally invasive procedures for the treatment of cerebrovascular diseases.

White matter atlas of the human spinal cord with estimation of partial volume effect.

PubMed

Lévy, S; Benhamou, M; Naaman, C; Rainville, P; Callot, V; Cohen-Adad, J

2015-10-01

Template-based analysis has proven to be an efficient, objective and reproducible way of extracting relevant information from multi-parametric MRI data. Using common atlases, it is possible to quantify MRI metrics within specific regions without the need for manual segmentation. This method is therefore free from user-bias and amenable to group studies. While template-based analysis is common procedure for the brain, there is currently no atlas of the white matter (WM) spinal pathways. The goals of this study were: (i) to create an atlas of the white matter tracts compatible with the MNI-Poly-AMU template and (ii) to propose methods to quantify metrics within the atlas that account for partial volume effect. The WM atlas was generated by: (i) digitalizing an existing WM atlas from a well-known source (Gray's Anatomy), (ii) registering this atlas to the MNI-Poly-AMU template at the corresponding slice (C4 vertebral level), (iii) propagating the atlas throughout all slices of the template (C1 to T6) using regularized diffeomorphic transformations and (iv) computing partial volume values for each voxel and each tract. Several approaches were implemented and validated to quantify metrics within the atlas, including weighted-average and Gaussian mixture models. Proof-of-concept application was done in five subjects for quantifying magnetization transfer ratio (MTR) in each tract of the atlas. The resulting WM atlas showed consistent topological organization and smooth transitions along the rostro-caudal axis. The median MTR across tracts was 26.2. Significant differences were detected across tracts, vertebral levels and subjects, but not across laterality (right-left). Among the different tested approaches to extract metrics, the maximum a posteriori showed highest performance with respect to noise, inter-tract variability, tract size and partial volume effect. This new WM atlas of the human spinal cord overcomes the biases associated with manual delineation and partial volume effect. Combined with multi-parametric data, the atlas can be applied to study demyelination and degeneration in diseases such as multiple sclerosis and will facilitate the conduction of longitudinal and multi-center studies. Copyright © 2015 Elsevier Inc. All rights reserved.

Remote site-selective C–H activation directed by a catalytic bifunctional template

PubMed Central

Zhang, Zhipeng; Tanaka, Keita; Yu, Jin-Quan

2017-01-01

Converting C–H bonds directly into carbon-carbon and carbon-heteroatom bonds can significantly improve step-economy in synthesis by providing alternative disconnections to traditional functional group manipulations. In this context, directed C–H activation reactions have been extensively explored for regioselective functionalization1-5. Though applicability can be severely curtailed by distance from the directing group and the shape of the molecule, a number of approaches have been developed to overcome this limitation6-12. For instance, recognition of the distal and geometric relationship between an existing functional group and multiple C–H bonds has recently been exploited to achieve meta-selective C–H activation by use of a covalently attached U-shaped template13-17. However, stoichiometric installation of the template is not feasible in the absence of an appropriate functional group handle. Here we report the design of a catalytic, bifunctional template that binds heterocyclic substrate via reversible coordination instead of covalent linkage, allowing remote site-selective C–H olefination of heterocycles. The two metal centers coordinated to this template play different roles; anchoring substrates to the proximity of catalyst and cleaving the remote C–H bonds respectively. Using this strategy, we demonstrate remote site-selective C–H olefination of heterocyclic substrates which do not have functional group handles for covalently attaching templates. PMID:28273068

Research data collection methods: from paper to tablet computers.

PubMed

Wilcox, Adam B; Gallagher, Kathleen D; Boden-Albala, Bernadette; Bakken, Suzanne R

2012-07-01

Primary data collection is a critical activity in clinical research. Even with significant advances in technical capabilities, clear benefits of use, and even user preferences for using electronic systems for collecting primary data, paper-based data collection is still common in clinical research settings. However, with recent developments in both clinical research and tablet computer technology, the comparative advantages and disadvantages of data collection methods should be determined. To describe case studies using multiple methods of data collection, including next-generation tablets, and consider their various advantages and disadvantages. We reviewed 5 modern case studies using primary data collection, using methods ranging from paper to next-generation tablet computers. We performed semistructured telephone interviews with each project, which considered factors relevant to data collection. We address specific issues with workflow, implementation and security for these different methods, and identify differences in implementation that led to different technology considerations for each case study. There remain multiple methods for primary data collection, each with its own strengths and weaknesses. Two recent methods are electronic health record templates and next-generation tablet computers. Electronic health record templates can link data directly to medical records, but are notably difficult to use. Current tablet computers are substantially different from previous technologies with regard to user familiarity and software cost. The use of cloud-based storage for tablet computers, however, creates a specific challenge for clinical research that must be considered but can be overcome.

AIDA: ab initio domain assembly for automated multi-domain protein structure prediction and domain–domain interaction prediction

PubMed Central

Xu, Dong; Jaroszewski, Lukasz; Li, Zhanwen; Godzik, Adam

2015-01-01

Motivation: Most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. Template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. Results: We have developed a fast docking algorithm ab initio domain assembly (AIDA) for assembling multi-domain protein structures, guided by the ab initio folding potential. This approach can be extended to discontinuous domains (i.e. domains with ‘inserted’ domains). When tested on experimentally solved structures of multi-domain proteins, the relative domain positions were accurately found among top 5000 models in 86% of cases. AIDA server can use domain assignments provided by the user or predict them from the provided sequence. The latter approach is particularly useful for automated protein structure prediction servers. The blind test consisting of 95 CASP10 targets shows that domain boundaries could be successfully determined for 97% of targets. Availability and implementation: The AIDA package as well as the benchmark sets used here are available for download at http://ffas.burnham.org/AIDA/. Contact: adam@sanfordburnham.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25701568

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription.

PubMed

Liu, Ning; Tian, Ru; Loeb, Daniel D

2003-02-18

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis.

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

PubMed

Wang, Yi; Wang, Yan; Ma, Ai-Jing; Li, Dong-Xun; Luo, Li-Juan; Liu, Dong-Xin; Jin, Dong; Liu, Kai; Ye, Chang-Yun

2015-07-08

We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

Speech recognition: Acoustic-phonetic knowledge acquisition and representation

NASA Astrophysics Data System (ADS)

Zue, Victor W.

1988-09-01

The long-term research goal is to develop and implement speaker-independent continuous speech recognition systems. It is believed that the proper utilization of speech-specific knowledge is essential for such advanced systems. This research is thus directed toward the acquisition, quantification, and representation, of acoustic-phonetic and lexical knowledge, and the application of this knowledge to speech recognition algorithms. In addition, we are exploring new speech recognition alternatives based on artificial intelligence and connectionist techniques. We developed a statistical model for predicting the acoustic realization of stop consonants in various positions in the syllable template. A unification-based grammatical formalism was developed for incorporating this model into the lexical access algorithm. We provided an information-theoretic justification for the hierarchical structure of the syllable template. We analyzed segmented duration for vowels and fricatives in continuous speech. Based on contextual information, we developed durational models for vowels and fricatives that account for over 70 percent of the variance, using data from multiple, unknown speakers. We rigorously evaluated the ability of human spectrogram readers to identify stop consonants spoken by many talkers and in a variety of phonetic contexts. Incorporating the declarative knowledge used by the readers, we developed a knowledge-based system for stop identification. We achieved comparable system performance to that to the readers.

Next generation distal locking for intramedullary nails using an electromagnetic X-ray-radiation-free real-time navigation system.

PubMed

Hoffmann, Michael; Schröder, Malte; Lehmann, Wolfgang; Kammal, Michael; Rueger, Johannes Maria; Herrman Ruecker, Andreas

2012-07-01

Distal locking marks one challenging step during intramedullary nailing that can lead to an increased irradiation and prolonged operation times. The aim of this study was to evaluate the reliability and efficacy of an X-ray-radiation-free real-time navigation system for distal locking procedures. A prospective randomized cadaver study with 50 standard free-hand fluoroscopic-guided and 50 electromagnetic-guided distal locking procedures was performed. All procedures were timed using a stopwatch. Intraoperative fluoroscopy exposure time and absorbed radiation dose (mGy) readings were documented. All tibial nails were locked with two mediolateral and one anteroposterior screw. Successful distal locking was accomplished once correct placement of all three screws was confirmed. Successful distal locking was achieved in 98 cases. No complications were encountered using the electromagnetic navigation system. Eight complications arose during free-hand fluoroscopic distal locking. Undetected secondary drill slippage on the ipsilateral cortex accounted for most problems followed by undetected intradrilling misdirection causing a fissural fracture of the contralateral cortex while screw insertion in one case. Compared with the free-hand fluoroscopic technique, electromagnetically navigated distal locking provides a median time benefit of 244 seconds without using ionizing radiation. Compared with the standard free-hand fluoroscopic technique, the electromagnetic guidance system used in this study showed high reliability and was associated with less complications, took significantly less time, and used no radiation exposure for distal locking procedures. Therapeutic study, level II.

Dosimetry during intramedullary nailing of the tibia.

PubMed

Kirousis, George; Delis, Harry; Megas, Panagiotis; Lambiris, Elias; Panayiotakis, George

2009-10-01

Intramedullary nailing under fluoroscopic guidance is a common operation. We studied the intraoperative radiation dose received by both the patient and the personnel. 25 intramedullary nailing procedures of the tibia were studied. All patients suffered from tibial fractures and were treated using the Grosse-Kempf intramedullary nail, with free-hand technique for fixation of the distal screws, under fluoroscopic guidance. The exposure, at selected positions, was recorded using an ion chamber, while the dose area product (DAP) was measured with a DAP meter, attached to the tube head. Thermoluminescent dosimeters (TLDs) were used to derive the occupational dose to the personnel, and also to monitor the surface dose on the gonads of some of the patients. The mean operation time was 101 (48-240) min, with a mean fluoroscopic time of 72 seconds and a mean DAP value of 75 cGy x cm(2). The surface dose to the gonads of the patients was less than 8.8 mGy during any procedure, and thus cannot be considered to be a contraindication for the use of this technique. Occupational dose differed substantially between members of the operating personnel, the maximum dose recorded being to the operator of the fluoroscopic equipment (0.11 mSv). Our findings underscore the care required by the primary operator not to exceed the dose constraint of 10 mSv per year. The rest of the operating personnel, although they do not receive very high doses, should focus on the dose optimization of the technique.

Adopting Ultrasound Guidance for Prone Percutaneous Nephrolithotomy: Evaluating the Learning Curve for the Experienced Surgeon

PubMed Central

Usawachintachit, Manint; Masic, Selma; Allen, Isabel E.; Li, Jianxing

2016-01-01

Abstract Objectives: To define the learning curve associated with adopting ultrasound guidance for prone percutaneous nephrolithotomy (PCNL) for the experienced surgeon. Methods: A prospective cohort study of consecutive patients undergoing PCNL with ultrasound guidance for renal tract access and dilation was performed. Clinical data reviewed included success in gaining renal access with ultrasound guidance, total fluoroscopic screening time, and radiation exposure dose. PCNL cases performed with fluoroscopic guidance matched for stone size served as control cases. Results: One hundred consecutive ultrasound-guided procedures performed by a single experienced endourologist were divided into five experience groups. Significant improvement in renal access success rate with ultrasound was seen after 20 cases (p < 0.05). Total fluoroscopic screening time, radiation exposure dose, and operative time were also statistically significantly improved over the study period. When compared with fluoroscopy-guided PCNL, significant decreases in total fluoroscopic screening time (33.4 ± 35.3 seconds vs 157.5 ± 84.9 seconds, p < 0.05) and radiation exposure (7.0 ± 8.7 mGy vs 47.8 ± 45.9 mGy, p < 0.05) were seen. No differences in complication rates were found. Conclusions: Ultrasound-guided renal access for PCNL can be performed effectively after 20 cases. Transition to the use of ultrasound will quickly reduce radiation exposure for patients and intraoperative personnel. PMID:27150671

A Template for Open Inquiry: Using Questions to Encourage and Support Inquiry in Earth and Space Science

ERIC Educational Resources Information Center

Hermann, Ronald S.; Miranda, Rommel J.

2010-01-01

This article provides an instructional approach to helping students generate open-inquiry research questions, which the authors call the "open-inquiry question template." This template was created based on their experience teaching high school science and preservice university methods courses. To help teachers implement this template, they…

Reducing Individual Variation for fMRI Studies in Children by Minimizing Template Related Errors

PubMed Central

Weng, Jian; Dong, Shanshan; He, Hongjian; Chen, Feiyan; Peng, Xiaogang

2015-01-01

Spatial normalization is an essential process for group comparisons in functional MRI studies. In practice, there is a risk of normalization errors particularly in studies involving children, seniors or diseased populations and in regions with high individual variation. One way to minimize normalization errors is to create a study-specific template based on a large sample size. However, studies with a large sample size are not always feasible, particularly for children studies. The performance of templates with a small sample size has not been evaluated in fMRI studies in children. In the current study, this issue was encountered in a working memory task with 29 children in two groups. We compared the performance of different templates: a study-specific template created by the experimental population, a Chinese children template and the widely used adult MNI template. We observed distinct differences in the right orbitofrontal region among the three templates in between-group comparisons. The study-specific template and the Chinese children template were more sensitive for the detection of between-group differences in the orbitofrontal cortex than the MNI template. Proper templates could effectively reduce individual variation. Further analysis revealed a correlation between the BOLD contrast size and the norm index of the affine transformation matrix, i.e., the SFN, which characterizes the difference between a template and a native image and differs significantly across subjects. Thereby, we proposed and tested another method to reduce individual variation that included the SFN as a covariate in group-wise statistics. This correction exhibits outstanding performance in enhancing detection power in group-level tests. A training effect of abacus-based mental calculation was also demonstrated, with significantly elevated activation in the right orbitofrontal region that correlated with behavioral response time across subjects in the trained group. PMID:26207985

Addressing recent docking challenges: A hybrid strategy to integrate template-based and free protein-protein docking.

PubMed

Yan, Yumeng; Wen, Zeyu; Wang, Xinxiang; Huang, Sheng-You

2017-03-01

Protein-protein docking is an important computational tool for predicting protein-protein interactions. With the rapid development of proteomics projects, more and more experimental binding information ranging from mutagenesis data to three-dimensional structures of protein complexes are becoming available. Therefore, how to appropriately incorporate the biological information into traditional ab initio docking has been an important issue and challenge in the field of protein-protein docking. To address these challenges, we have developed a Hybrid DOCKing protocol of template-based and template-free approaches, referred to as HDOCK. The basic procedure of HDOCK is to model the structures of individual components based on the template complex by a template-based method if a template is available; otherwise, the component structures will be modeled based on monomer proteins by regular homology modeling. Then, the complex structure of the component models is predicted by traditional protein-protein docking. With the HDOCK protocol, we have participated in the CPARI experiment for rounds 28-35. Out of the 25 CASP-CAPRI targets for oligomer modeling, our HDOCK protocol predicted correct models for 16 targets, ranking one of the top algorithms in this challenge. Our docking method also made correct predictions on other CAPRI challenges such as protein-peptide binding for 6 out of 8 targets and water predictions for 2 out of 2 targets. The advantage of our hybrid docking approach over pure template-based docking was further confirmed by a comparative evaluation on 20 CASP-CAPRI targets. Proteins 2017; 85:497-512. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Template-Based Modeling of Protein-RNA Interactions.

PubMed

Zheng, Jinfang; Kundrotas, Petras J; Vakser, Ilya A; Liu, Shiyong

2016-09-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes.

High incidence of non-random template strand segregation and asymmetric fate determination in dividing stem cells and their progeny.

PubMed

Conboy, Michael J; Karasov, Ariela O; Rando, Thomas A

2007-05-01

Decades ago, the "immortal strand hypothesis" was proposed as a means by which stem cells might limit acquiring mutations that could give rise to cancer, while continuing to proliferate for the life of an organism. Originally based on observations in embryonic cells, and later studied in terms of stem cell self-renewal, this hypothesis has remained largely unaccepted because of few additional reports, the rarity of the cells displaying template strand segregation, and alternative interpretations of experiments involving single labels or different types of labels to follow template strands. Using sequential pulses of halogenated thymidine analogs (bromodeoxyuridine [BrdU], chlorodeoxyuridine [CldU], and iododeoxyuridine [IdU]), and analyzing stem cell progeny during induced regeneration in vivo, we observed extraordinarily high frequencies of segregation of older and younger template strands during a period of proliferative expansion of muscle stem cells. Furthermore, template strand co-segregation was strongly associated with asymmetric cell divisions yielding daughters with divergent fates. Daughter cells inheriting the older templates retained the more immature phenotype, whereas daughters inheriting the newer templates acquired a more differentiated phenotype. These data provide compelling evidence of template strand co-segregation based on template age and associated with cell fate determination, suggest that template strand age is monitored during stem cell lineage progression, and raise important caveats for the interpretation of label-retaining cells.

Comparison of Arterial Spin-labeling Perfusion Images at Different Spatial Normalization Methods Based on Voxel-based Statistical Analysis.

PubMed

Tani, Kazuki; Mio, Motohira; Toyofuku, Tatsuo; Kato, Shinichi; Masumoto, Tomoya; Ijichi, Tetsuya; Matsushima, Masatoshi; Morimoto, Shoichi; Hirata, Takumi

2017-01-01

Spatial normalization is a significant image pre-processing operation in statistical parametric mapping (SPM) analysis. The purpose of this study was to clarify the optimal method of spatial normalization for improving diagnostic accuracy in SPM analysis of arterial spin-labeling (ASL) perfusion images. We evaluated the SPM results of five spatial normalization methods obtained by comparing patients with Alzheimer's disease or normal pressure hydrocephalus complicated with dementia and cognitively healthy subjects. We used the following methods: 3DT1-conventional based on spatial normalization using anatomical images; 3DT1-DARTEL based on spatial normalization with DARTEL using anatomical images; 3DT1-conventional template and 3DT1-DARTEL template, created by averaging cognitively healthy subjects spatially normalized using the above methods; and ASL-DARTEL template created by averaging cognitively healthy subjects spatially normalized with DARTEL using ASL images only. Our results showed that ASL-DARTEL template was small compared with the other two templates. Our SPM results obtained with ASL-DARTEL template method were inaccurate. Also, there were no significant differences between 3DT1-conventional and 3DT1-DARTEL template methods. In contrast, the 3DT1-DARTEL method showed higher detection sensitivity, and precise anatomical location. Our SPM results suggest that we should perform spatial normalization with DARTEL using anatomical images.

Image-driven Population Analysis through Mixture Modeling

PubMed Central

Sabuncu, Mert R.; Balci, Serdar K.; Shenton, Martha E.; Golland, Polina

2009-01-01

We present iCluster, a fast and efficient algorithm that clusters a set of images while co-registering them using a parameterized, nonlinear transformation model. The output of the algorithm is a small number of template images that represent different modes in a population. This is in contrast with traditional, hypothesis-driven computational anatomy approaches that assume a single template to construct an atlas. We derive the algorithm based on a generative model of an image population as a mixture of deformable template images. We validate and explore our method in four experiments. In the first experiment, we use synthetic data to explore the behavior of the algorithm and inform a design choice on parameter settings. In the second experiment, we demonstrate the utility of having multiple atlases for the application of localizing temporal lobe brain structures in a pool of subjects that contains healthy controls and schizophrenia patients. Next, we employ iCluster to partition a data set of 415 whole brain MR volumes of subjects aged 18 through 96 years into three anatomical subgroups. Our analysis suggests that these subgroups mainly correspond to age groups. The templates reveal significant structural differences across these age groups that confirm previous findings in aging research. In the final experiment, we run iCluster on a group of 15 patients with dementia and 15 age-matched healthy controls. The algorithm produces two modes, one of which contains dementia patients only. These results suggest that the algorithm can be used to discover sub-populations that correspond to interesting structural or functional “modes.” PMID:19336293

Tensorial dynamic time warping with articulation index representation for efficient audio-template learning.

PubMed

Le, Long N; Jones, Douglas L

2018-03-01

Audio classification techniques often depend on the availability of a large labeled training dataset for successful performance. However, in many application domains of audio classification (e.g., wildlife monitoring), obtaining labeled data is still a costly and laborious process. Motivated by this observation, a technique is proposed to efficiently learn a clean template from a few labeled, but likely corrupted (by noise and interferences), data samples. This learning can be done efficiently via tensorial dynamic time warping on the articulation index-based time-frequency representations of audio data. The learned template can then be used in audio classification following the standard template-based approach. Experimental results show that the proposed approach outperforms both (1) the recurrent neural network approach and (2) the state-of-the-art in the template-based approach on a wildlife detection application with few training samples.

Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates.

PubMed

Cao, Youfang; Wang, Lianjie; Xu, Kexue; Kou, Chunhai; Zhang, Yulei; Wei, Guifang; He, Junjian; Wang, Yunfang; Zhao, Liping

2005-07-26

A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process. Primer sequence is converted to a vector of the full potential hydrogen numbers (3 for G or C, 2 for A or T), while template sequence is converted to a vector of the actual hydrogen bond numbers formed after primer annealing. The former is considered as source information and the latter destination information. An information coefficient is calculated as a measure for fidelity of this information transfer process and thus a measure of similarity between primer and potential annealing site on template. Successful prediction of PCR products from whole genomic sequences with a computer program based on the algorithm demonstrated the potential of this new algorithm in areas like in silico PCR and gene finding.

Infrared dim moving target tracking via sparsity-based discriminative classifier and convolutional network

NASA Astrophysics Data System (ADS)

Qian, Kun; Zhou, Huixin; Wang, Bingjian; Song, Shangzhen; Zhao, Dong

2017-11-01

Infrared dim and small target tracking is a great challenging task. The main challenge for target tracking is to account for appearance change of an object, which submerges in the cluttered background. An efficient appearance model that exploits both the global template and local representation over infrared image sequences is constructed for dim moving target tracking. A Sparsity-based Discriminative Classifier (SDC) and a Convolutional Network-based Generative Model (CNGM) are combined with a prior model. In the SDC model, a sparse representation-based algorithm is adopted to calculate the confidence value that assigns more weights to target templates than negative background templates. In the CNGM model, simple cell feature maps are obtained by calculating the convolution between target templates and fixed filters, which are extracted from the target region at the first frame. These maps measure similarities between each filter and local intensity patterns across the target template, therefore encoding its local structural information. Then, all the maps form a representation, preserving the inner geometric layout of a candidate template. Furthermore, the fixed target template set is processed via an efficient prior model. The same operation is applied to candidate templates in the CNGM model. The online update scheme not only accounts for appearance variations but also alleviates the migration problem. At last, collaborative confidence values of particles are utilized to generate particles' importance weights. Experiments on various infrared sequences have validated the tracking capability of the presented algorithm. Experimental results show that this algorithm runs in real-time and provides a higher accuracy than state of the art algorithms.

Template-guided vs. non-guided drilling in site preparation of dental implants.

PubMed

Scherer, Uta; Stoetzer, Marcus; Ruecker, Martin; Gellrich, Nils-Claudius; von See, Constantin

2015-07-01

Clinical success of oral implants is related to primary stability and osseointegration. These parameters are associated with delicate surgical techniques. We herein studied whether template-guided drilling has a significant influence on drillholes diameter and accuracy in an in vitro model. Fresh cadaveric porcine mandibles were used for drilling experiments of four experimental groups. Each group consisted of three operators, comparing guide templates for drilling with free-handed procedure. Operators without surgical knowledge were grouped together, contrasting highly experienced oral surgeons in other groups. A total of 180 drilling actions were performed, and diameters were recorded at multiple depth levels, with a precision measuring instrument. Template-guided drilling procedure improved accuracy on a very significant level in comparison with free-handed drilling operation (p ≤ 0.001). Inaccuracy of free-handed drilling became more significant in relation to measurement depth. High homogenic uniformity of template-guided drillholes was significantly stronger than unguided drilling operations by highly experienced oral surgeons (p ≤ 0.001). Template-guided drilling procedure leads to significantly enhanced accuracy. Significant results compared to free-handed drilling actions were achieved, irrespective of the clinical experience level of the operator. Template-guided drilling procedures lead to a more predictable clinical diameter. It shows that any set of instruments has to be carefully chosen to match the specific implant system. The current in vitro study is implicating an improvement of implant bed preparation but needs to be confirmed in clinical studies.

Periodic Two-Dimensional GaAs and InGaAs Quantum Rings Grown on GaAs (001) by Droplet Epitaxy.

PubMed

Tung, Kar Hoo Patrick; Huang, Jian; Danner, Aaron

2016-06-01

Growth of ordered GaAs and InGaAs quantum rings (QRs) in a patterned SiO2 nanohole template by molecular beam epitaxy (MBE) using droplet epitaxy (DE) process is demonstrated. DE is an MBE growth technique used to fabricate quantum nanostructures of high crystal quality by supplying group III and group V elements in separate phases. In this work, ordered QRs grown on an ordered nanohole template are compared to self-assembled QRs grown with the same DE technique without the nanohole template. This study allows us to understand and compare the surface kinetics of Ga and InGa droplets when a template is present. It is found that template-grown GaAs QRs form clustered rings which can be attributed to low mobility of Ga droplets resulting in multiple nucleation sites for QR formation when As is supplied. However, the case of template-grown InGaAs QRs only one ring is formed per nanohole; no clustering is observed. The outer QR diameter is a close match to the nanohole template diameter. This can be attributed to more mobile InGa droplets, which coalesce from an Ostwald ripening to form a single large droplet before As is supplied. Thus, well-patterned InGaAs QRs are demonstrated and the kinetics of their growth are better understood which could potentially lead to improvements in the future devices that require the unique properties of patterned QRs.

HDOCK: a web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy

PubMed Central

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong

2017-01-01

Abstract Protein–protein and protein–DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein–protein and protein–DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10–20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein–protein and protein–DNA benchmarks and performed better than template-based modeling on the three protein–RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. PMID:28521030

A Template-Based Protein Structure Reconstruction Method Using Deep Autoencoder Learning.

PubMed

Li, Haiou; Lyu, Qiang; Cheng, Jianlin

2016-12-01

Protein structure prediction is an important problem in computational biology, and is widely applied to various biomedical problems such as protein function study, protein design, and drug design. In this work, we developed a novel deep learning approach based on a deeply stacked denoising autoencoder for protein structure reconstruction. We applied our approach to a template-based protein structure prediction using only the 3D structural coordinates of homologous template proteins as input. The templates were identified for a target protein by a PSI-BLAST search. 3DRobot (a program that automatically generates diverse and well-packed protein structure decoys) was used to generate initial decoy models for the target from the templates. A stacked denoising autoencoder was trained on the decoys to obtain a deep learning model for the target protein. The trained deep model was then used to reconstruct the final structural model for the target sequence. With target proteins that have highly similar template proteins as benchmarks, the GDT-TS score of the predicted structures is greater than 0.7, suggesting that the deep autoencoder is a promising method for protein structure reconstruction.

Sacrificial template method of fabricating a nanotube

DOEpatents

Yang, Peidong [Berkeley, CA; He, Rongrui [Berkeley, CA; Goldberger, Joshua [Berkeley, CA; Fan, Rong [El Cerrito, CA; Wu, Yi-Ying [Albany, CA; Li, Deyu [Albany, CA; Majumdar, Arun [Orinda, CA

2007-05-01

Methods of fabricating uniform nanotubes are described in which nanotubes were synthesized as sheaths over nanowire templates, such as using a chemical vapor deposition process. For example, single-crystalline zinc oxide (ZnO) nanowires are utilized as templates over which gallium nitride (GaN) is epitaxially grown. The ZnO templates are then removed, such as by thermal reduction and evaporation. The completed single-crystalline GaN nanotubes preferably have inner diameters ranging from 30 nm to 200 nm, and wall thicknesses between 5 and 50 nm. Transmission electron microscopy studies show that the resultant nanotubes are single-crystalline with a wurtzite structure, and are oriented along the <001> direction. The present invention exemplifies single-crystalline nanotubes of materials with a non-layered crystal structure. Similar "epitaxial-casting" approaches could be used to produce arrays and single-crystalline nanotubes of other solid materials and semiconductors. Furthermore, the fabrication of multi-sheath nanotubes are described as well as nanotubes having multiple longitudinal segments.

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

PubMed

Karczyńska, Agnieszka S; Czaplewski, Cezary; Krupa, Paweł; Mozolewska, Magdalena A; Joo, Keehyoung; Lee, Jooyoung; Liwo, Adam

2017-12-05

Molecular simulations restrained to single or multiple templates are commonly used in protein-structure modeling. However, the restraints introduce additional barriers, thus impairing the ergodicity of simulations, which can affect the quality of the resulting models. In this work, the effect of restraint types and simulation schemes on ergodicity and model quality was investigated by performing template-restrained canonical molecular dynamics (MD), multiplexed replica-exchange molecular dynamics, and Hamiltonian replica exchange molecular dynamics (HREMD) simulations with the coarse-grained UNRES force field on nine selected proteins, with pseudo-harmonic log-Gaussian (unbounded) or Lorentzian (bounded) restraint functions. The best ergodicity was exhibited by HREMD. It has been found that non-ergodicity does not affect model quality if good templates are used to generate restraints. However, when poor-quality restraints not covering the entire protein are used, the improved ergodicity of HREMD can lead to significantly improved protein models. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

THRIVE: threshold homomorphic encryption based secure and privacy preserving biometric verification system

NASA Astrophysics Data System (ADS)

Karabat, Cagatay; Kiraz, Mehmet Sabir; Erdogan, Hakan; Savas, Erkay

2015-12-01

In this paper, we introduce a new biometric verification and template protection system which we call THRIVE. The system includes novel enrollment and authentication protocols based on threshold homomorphic encryption where a private key is shared between a user and a verifier. In the THRIVE system, only encrypted binary biometric templates are stored in a database and verification is performed via homomorphically randomized templates, thus, original templates are never revealed during authentication. Due to the underlying threshold homomorphic encryption scheme, a malicious database owner cannot perform full decryption on encrypted templates of the users in the database. In addition, security of the THRIVE system is enhanced using a two-factor authentication scheme involving user's private key and biometric data. Using simulation-based techniques, the proposed system is proven secure in the malicious model. The proposed system is suitable for applications where the user does not want to reveal her biometrics to the verifier in plain form, but needs to prove her identity by using biometrics. The system can be used with any biometric modality where a feature extraction method yields a fixed size binary template and a query template is verified when its Hamming distance to the database template is less than a threshold. The overall connection time for the proposed THRIVE system is estimated to be 336 ms on average for 256-bit biometric templates on a desktop PC running with quad core 3.2 GHz CPUs at 10 Mbit/s up/down link connection speed. Consequently, the proposed system can be efficiently used in real-life applications.

Linear pi-Acceptor-Templated Dynamic Clipping to Macrobicycles and[2]Rotaxanes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klivansky, Liana M.; Koshkakaryan, Gayane; Cao, Dennis

2009-04-30

Functional rotaxanes are one of the representative nanoscale molecular machines that have found applications in many areas, including molecular electronics, nanoelectromechanical systems (NEMS), photo controllable smart surfaces, and nanovalves. With the advent of molecular recognition and self-assembly, such molecular compounds can now be obtained efficiently through template-directed synthesis. One of the common strategies of making [2]rotaxanes involves the clipping of a macrocycle around a preformed dumbbell-shaped template in a [1+1] or [2+2] manner. While early examples were based on irreversible kinetic pathway through covalent bond formation, recent advances on reversible dynamic covalent chemistry (DCC) has attracted great attention to thismore » field. By virtue of thermodynamically controlled equilibria, DCC has provided highly efficient and versatile synthetic routes in the selection of specific products from a complex system. Among the several reversible reactions in the category of DCC reactions, the imine formation has proven to be very versatile in macrocyclization to give complex interlocked molecular compounds. Cryptands are three dimensional bicyclic hosts with preorganized cavities capable of inclusion of ions and small molecules. Replacing the nitrogen bridgeheads in common cryptands with aromatic ring systems gives cyclophane-based macrobicycles. The introduction of aromatic ring systems into a preorganized cage-like geometry facilitates ion-{pi} interactions and {pi}-{pi} interactions, resulting in novel metal sandwiches, fluoride receptors, and host-guest complexes. In particular, the seminal work by Gibson, Huang and coworkers on cryptand complexation with paraquat and diquat guests have resulted in the efficient synthesis of mechanically interlocked rotaxanes. The synthesis of cyclophane-based macrobicycles, however, was mostly realized through multiple reaction steps and in high-dilution conditions, which often suffered from low yield and tedious workup. Thus, a one-step, five-component [2+3] clipping reaction that can give the desired macrobicycle is highly desirable. We are motivated by a {pi}-guest templating protocol, because not only {pi}-{pi} interactions can contribute to the formation of macrobicycles, but also the resulting host-guest system holds great promise as a forerunner in the construction of interlocked molecules. (Scheme 1c) Very simple precursors, namely 1,3,5-benzenetrialdehyde (1) and 2,2{prime}-(ethylenedioxy)diethylamine (2) were chosen as the components for desired macrobicycle. (Scheme 2) The formation of six imine bonds would connect the five components to give a macrobicycle while extending the conjugation in the C{sub 3}-symmetric aromatic 'ceiling' and 'floor', which is suitable for enhancing the {pi}-{pi} interactions with a complementary aromatic template. Meanwhile, the ethylene glycol 'pillars' can provide sufficient flexibility, proper spacing, and polar binding sites to assist guest encapsulation. Initial screening of ?-templates engaged several C{sub 3} symmetric aromatic compounds in order to match the symmetry of the desired macrobicycle, which only resulted in nonspecific mixtures. It was found instead that linear bipyridinium (BPY) containing guests effectively templated the [2+3] clipping reaction. Based on this protocol, a [2]rotaxane was successfully assembled as the single product from the six-component reaction.« less

Video-guided calibration of an augmented reality mobile C-arm.

PubMed

Chen, Xin; Naik, Hemal; Wang, Lejing; Navab, Nassir; Fallavollita, Pascal

2014-11-01

The augmented reality (AR) fluoroscope augments an X-ray image by video and provides the surgeon with a real-time in situ overlay of the anatomy. The overlay alignment is crucial for diagnostic and intra-operative guidance, so precise calibration of the AR fluoroscope is required. The first and most complex step of the calibration procedure is the determination of the X-ray source position. Currently, this is achieved using a biplane phantom with movable metallic rings on its top layer and fixed X-ray opaque markers on its bottom layer. The metallic rings must be moved to positions where at least two pairs of rings and markers are isocentric in the X-ray image. The current "trial and error" calibration process currently requires acquisition of many X-ray images, a task that is both time consuming and radiation intensive. An improved process was developed and tested for C-arm calibration. Video guidance was used to drive the calibration procedure to minimize both X-ray exposure and the time involved. For this, a homography between X-ray and video images is estimated. This homography is valid for the plane at which the metallic rings are positioned and is employed to guide the calibration procedure. Eight users having varying calibration experience (i.e., 2 experts, 2 semi-experts, 4 novices) were asked to participate in the evaluation. The video-guided technique reduced the number of intra-operative X-ray calibration images by 89% and decreased the total time required by 59%. A video-based C-arm calibration method has been developed that improves the usability of the AR fluoroscope with a friendlier interface, reduced calibration time and clinically acceptable radiation doses.

How much articular displacement can be detected using fluoroscopy for tibial plateau fractures?

PubMed

Haller, Justin M; O'Toole, Robert; Graves, Matthew; Barei, David; Gardner, Michael; Kubiak, Erik; Nascone, Jason; Nork, Sean; Presson, Angela P; Higgins, Thomas F

2015-11-01

While there is conflicting evidence regarding the importance of anatomic reduction for tibial plateau fractures, there are currently no studies that analyse our ability to grade reduction based on fluoroscopic imaging. The purpose of this study was to determine the accuracy of fluoroscopy in judging tibial plateau articular reduction. Ten embalmed human cadavers were selected. The lateral plateau was sagitally sectioned, and the joint was reduced under direct visualization. Lateral, anterior-posterior (AP), and joint line fluoroscopic views were obtained. The same fluoroscopic views were obtained with 2mm displacement and 5mm displacement. The images were randomised, and eight orthopaedic traumatologists were asked whether the plateau was reduced. Within each pair of conditions (view and displacement from 0mm to 5mm) sensitivity, specificity, and intraclass correlations (ICC) were evaluated. The AP-lateral view with 5mm displacement yielded the highest accuracy for detecting reduction at 90% (95% CI: 83-94%). For the other conditions, accuracy ranged from (37-83%). Sensitivity was highest for the reduced lateral view (79%, 95% CI: 57-91%). Specificity was highest in the AP-lateral view 98% (95% CI: 93-99%) for 5mm step-off. ICC was perfect for the AP-lateral view with 5mm displacement, but otherwise agreement ranged from poor to moderate at ICC=0.09-0.46. Finally, there was no additional benefit to including the joint-line view with the AP and lateral views. Using both AP and lateral views for 5mm displacement had the highest accuracy, specificity, and ICC. Outside of this scenario, agreement was poor to moderate and accuracy was low. Applying this clinically, direct visualization of the articular surface may be necessary to ensure malreduction less than 5mm. Copyright © 2015 Elsevier Ltd. All rights reserved.

Proposed Optimal Fluoroscopic Targets for Cooled Radiofrequency Neurotomy of the Sacral Lateral Branches to Improve Clinical Outcomes: An Anatomical Study.

PubMed

Stout, Alison; Dreyfuss, Paul; Swain, Nathan; Roberts, Shannon; Loh, Eldon; Agur, Anne

2017-11-23

Current sacroiliac joint (SIJ) cooled radiofrequency (RF) is based on fluoroscopic anatomy of lateral branches (LBs) in three specimens. Recent studies confirm significant variation in LB positions. To determine if common fluoroscopic needle placements for cooled SIJ RF are adequate to lesion all S1-3 LBs. If not, would different targets improve lesion accuracy? The LBs of 20 cadavers were dissected bilaterally (40 SIJs), and 26 G radiopaque wires were sutured to the LBs. With a 10-mm radius ruler centered at each foramen, standard targets were assessed, as judged by a clockface on the right, for S1 and S2 at 2:30, 4:00, and 5:30 positions and at S3 at 2:30 and 4:00. Mirror image targets were assessed on the left. Assuming an 8-mm lesion diameter, the percentage of LBs that would not be ablated for each level was determined. Imaging through the superior end plate of S1 was compared against segment specific (SS) imaging. Nine point four percent of LBs would not be ablated at S1 vs 0.99% at S2 vs 35% at S3, and 60% of the 40 SIJs would be completely denervated using current targets. SS imaging did not improve results. Alternate target locations could improve the miss rate to 2.8% at S1 and 0% at S3 and would ablate all LBs in 95% of SIJs. Using a conservative 8-mm lesion measurement, contemporary cooled RF needle targets are inadequate to lesion all target LBs. Modifications to current targets are recommended to increase the effectiveness of the procedure. © 2017 American Academy of Pain Medicine. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules.

PubMed

Usanov, Dmitry L; Chan, Alix I; Maianti, Juan Pablo; Liu, David R

2018-07-01

DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC 50  = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery.

Evidence for the Packaging of Multiple Copies of Tf1 mRNA into Particles and the trans Priming of Reverse Transcription

PubMed Central

Haag, Amanda Leigh; Lin, Jia-Hwei; Levin, Henry L.

2000-01-01

Long terminal repeat (LTR)-containing retrotransposons and retroviruses are close relatives that possess similar mechanisms of reverse transcription. The particles of retroviruses package two copies of viral mRNA that both function as templates for the reverse transcription of the element. We studied the LTR-retrotransposon Tf1 of Schizosaccharomyces pombe to test whether multiple copies of transposon mRNA participate in the production of cDNA. Using the unique self-priming property of Tf1, we obtained evidence that multiple copies of Tf1 mRNA were packaged into virus-like particles. By coexpressing two distinct versions of Tf1, we found that the bulk of reverse transcription that was initiated on one mRNA template was subsequently transferred to others. In addition, the first 11 nucleotides of one mRNA were able to prime, in trans, the reverse transcription of another mRNA. PMID:10888658

Multiple Antibiotic Resistance Plasmids Allow Scalable,
PCR-Mediated DNA Manipulation and Near-Zero Background Cloning

PubMed Central

Arnak, Remigiusz; Altun, Burcin; Tosato, Valentina

2016-01-01

Summary We have constructed two plasmids that can be used for cloning as templates for PCR- -based gene disruption, mutagenesis and the construction of DNA chromosome translocation cassettes. To our knowledge, these plasmids are the first vectors that confer resistance to ampicillin, kanamycin and hygromycin B in bacteria, and to geneticin (G418) and hygromycin B in Saccharomyces cerevisiae simultaneously. The option of simultaneously using up to three resistance markers provides a highly stringent control of recombinant selection and the almost complete elimination of background resistance, while unique restriction sites allow easy cloning of chosen genetic material. Moreover, we successfully used these new vectors as PCR templates for the induction of chromosome translocation in budding yeast by the bridge-induced translocation system. Cells in which translocation was induced carried chromosomal rearrangements as expected and exhibited resistance to both, G418 and hygromycin B. These features make our constructs very handy tools for many molecular biology applications. PMID:27956856

Three-dimensional Aerographite-GaN hybrid networks: Single step fabrication of porous and mechanically flexible materials for multifunctional applications

PubMed Central

Schuchardt, Arnim; Braniste, Tudor; Mishra, Yogendra K.; Deng, Mao; Mecklenburg, Matthias; Stevens-Kalceff, Marion A.; Raevschi, Simion; Schulte, Karl; Kienle, Lorenz; Adelung, Rainer; Tiginyanu, Ion

2015-01-01

Three dimensional (3D) elastic hybrid networks built from interconnected nano- and microstructure building units, in the form of semiconducting-carbonaceous materials, are potential candidates for advanced technological applications. However, fabrication of these 3D hybrid networks by simple and versatile methods is a challenging task due to the involvement of complex and multiple synthesis processes. In this paper, we demonstrate the growth of Aerographite-GaN 3D hybrid networks using ultralight and extremely porous carbon based Aerographite material as templates by a single step hydride vapor phase epitaxy process. The GaN nano- and microstructures grow on the surface of Aerographite tubes and follow the network architecture of the Aerographite template without agglomeration. The synthesized 3D networks are integrated with the properties from both, i.e., nanoscale GaN structures and Aerographite in the form of flexible and semiconducting composites which could be exploited as next generation materials for electronic, photonic, and sensors applications. PMID:25744694

Wolf Attack Probability: A Theoretical Security Measure in Biometric Authentication Systems

NASA Astrophysics Data System (ADS)

Une, Masashi; Otsuka, Akira; Imai, Hideki

This paper will propose a wolf attack probability (WAP) as a new measure for evaluating security of biometric authentication systems. The wolf attack is an attempt to impersonate a victim by feeding “wolves” into the system to be attacked. The “wolf” means an input value which can be falsely accepted as a match with multiple templates. WAP is defined as a maximum success probability of the wolf attack with one wolf sample. In this paper, we give a rigorous definition of the new security measure which gives strength estimation of an individual biometric authentication system against impersonation attacks. We show that if one reestimates using our WAP measure, a typical fingerprint algorithm turns out to be much weaker than theoretically estimated by Ratha et al. Moreover, we apply the wolf attack to a finger-vein-pattern based algorithm. Surprisingly, we show that there exists an extremely strong wolf which falsely matches all templates for any threshold value.

Constructing statistically unbiased cortical surface templates using feature-space covariance

NASA Astrophysics Data System (ADS)

Parvathaneni, Prasanna; Lyu, Ilwoo; Huo, Yuankai; Blaber, Justin; Hainline, Allison E.; Kang, Hakmook; Woodward, Neil D.; Landman, Bennett A.

2018-03-01

The choice of surface template plays an important role in cross-sectional subject analyses involving cortical brain surfaces because there is a tendency toward registration bias given variations in inter-individual and inter-group sulcal and gyral patterns. In order to account for the bias and spatial smoothing, we propose a feature-based unbiased average template surface. In contrast to prior approaches, we factor in the sample population covariance and assign weights based on feature information to minimize the influence of covariance in the sampled population. The mean surface is computed by applying the weights obtained from an inverse covariance matrix, which guarantees that multiple representations from similar groups (e.g., involving imaging, demographic, diagnosis information) are down-weighted to yield an unbiased mean in feature space. Results are validated by applying this approach in two different applications. For evaluation, the proposed unbiased weighted surface mean is compared with un-weighted means both qualitatively and quantitatively (mean squared error and absolute relative distance of both the means with baseline). In first application, we validated the stability of the proposed optimal mean on a scan-rescan reproducibility dataset by incrementally adding duplicate subjects. In the second application, we used clinical research data to evaluate the difference between the weighted and unweighted mean when different number of subjects were included in control versus schizophrenia groups. In both cases, the proposed method achieved greater stability that indicated reduced impacts of sampling bias. The weighted mean is built based on covariance information in feature space as opposed to spatial location, thus making this a generic approach to be applicable to any feature of interest.

Optimization of MRI-based scoring scales of brain injury severity in children with unilateral cerebral palsy.

PubMed

Pagnozzi, Alex M; Fiori, Simona; Boyd, Roslyn N; Guzzetta, Andrea; Doecke, James; Gal, Yaniv; Rose, Stephen; Dowson, Nicholas

2016-02-01

Several scoring systems for measuring brain injury severity have been developed to standardize the classification of MRI results, which allows for the prediction of functional outcomes to help plan effective interventions for children with cerebral palsy. The aim of this study is to use statistical techniques to optimize the clinical utility of a recently proposed template-based scoring method by weighting individual anatomical scores of injury, while maintaining its simplicity by retaining only a subset of scored anatomical regions. Seventy-six children with unilateral cerebral palsy were evaluated in terms of upper limb motor function using the Assisting Hand Assessment measure and injuries visible on MRI using a semiquantitative approach. This cohort included 52 children with periventricular white matter injury and 24 with cortical and deep gray matter injuries. A subset of the template-derived cerebral regions was selected using a data-driven region selection algorithm. Linear regression was performed using this subset, with interaction effects excluded. Linear regression improved multiple correlations between MRI-based and Assisting Hand Assessment scores for both periventricular white matter (R squared increased to 0.45 from 0, P < 0.0001) and cortical and deep gray matter (0.84 from 0.44, P < 0.0001) cohorts. In both cohorts, the data-driven approach retained fewer than 8 of the 40 template-derived anatomical regions. The equal or better prediction of the clinically meaningful Assisting Hand Assessment measure using fewer anatomical regions highlights the potential of these developments to enable enhanced quantification of injury and prediction of patient motor outcome, while maintaining the clinical expediency of the scoring approach.

Mechanical Energy Harvesting Performance of Ferroelectric Polymer Nanowires Grown via Template‐Wetting

PubMed Central

Whiter, Richard A.; Boughey, Chess; Smith, Michael

2018-01-01

Abstract Nanowires of the ferroelectric co‐polymer poly(vinylidenefluoride‐co‐triufloroethylene) [P(VDF‐TrFE)] are fabricated from solution within nanoporous templates of both “hard” anodic aluminium oxide (AAO) and “soft” polyimide (PI) through a facile and scalable template‐wetting process. The confined geometry afforded by the pores of the templates leads directly to highly crystalline P(VDF‐TrFE) nanowires in a macroscopic “poled” state that precludes the need for external electrical poling procedure typically required for piezoelectric performance. The energy‐harvesting performance of nanogenerators based on these template‐grown nanowires are extensively studied and analyzed in combination with finite element modelling. Both experimental results and computational models probing the role of the templates in determining overall nanogenerator performance, including both materials and device efficiencies, are presented. It is found that although P(VDF‐TrFE) nanowires grown in PI templates exhibit a lower material efficiency due to lower crystallinity as compared to nanowires grown in AAO templates, the overall device efficiency was higher for the PI‐template‐based nanogenerator because of the lower stiffness of the PI template as compared to the AAO template. This work provides a clear framework to assess the energy conversion efficiency of template‐grown piezoelectric nanowires and paves the way towards optimization of template‐based nanogenerator devices.

Assessment of primer/template mismatch effects on real-time PCR amplification of target taxa for GMO quantification.

PubMed

Ghedira, Rim; Papazova, Nina; Vuylsteke, Marnik; Ruttink, Tom; Taverniers, Isabel; De Loose, Marc

2009-10-28

GMO quantification, based on real-time PCR, relies on the amplification of an event-specific transgene assay and a species-specific reference assay. The uniformity of the nucleotide sequences targeted by both assays across various transgenic varieties is an important prerequisite for correct quantification. Single nucleotide polymorphisms (SNPs) frequently occur in the maize genome and might lead to nucleotide variation in regions used to design primers and probes for reference assays. Further, they may affect the annealing of the primer to the template and reduce the efficiency of DNA amplification. We assessed the effect of a minor DNA template modification, such as a single base pair mismatch in the primer attachment site, on real-time PCR quantification. A model system was used based on the introduction of artificial mismatches between the forward primer and the DNA template in the reference assay targeting the maize starch synthase (SSIIb) gene. The results show that the presence of a mismatch between the primer and the DNA template causes partial to complete failure of the amplification of the initial DNA template depending on the type and location of the nucleotide mismatch. With this study, we show that the presence of a primer/template mismatch affects the estimated total DNA quantity to a varying degree.

Base pairing among three cis-acting sequences contributes to template switching during hepadnavirus reverse transcription

PubMed Central

Liu, Ning; Tian, Ru; Loeb, Daniel D.

2003-01-01

Synthesis of the relaxed-circular (RC) DNA genome of hepadnaviruses requires two template switches during plus-strand DNA synthesis: primer translocation and circularization. Although primer translocation and circularization use different donor and acceptor sequences, and are distinct temporally, they share the common theme of switching from one end of the minus-strand template to the other end. Studies of duck hepatitis B virus have indicated that, in addition to the donor and acceptor sequences, three other cis-acting sequences, named 3E, M, and 5E, are required for the synthesis of RC DNA by contributing to primer translocation and circularization. The mechanism by which 3E, M, and 5E act was not known. We present evidence that these sequences function by base pairing with each other within the minus-strand template. 3E base-pairs with one portion of M (M3) and 5E base-pairs with an adjacent portion of M (M5). We found that disrupting base pairing between 3E and M3 and between 5E and M5 inhibited primer translocation and circularization. More importantly, restoring base pairing with mutant sequences restored the production of RC DNA. These results are consistent with the model that, within duck hepatitis B virus capsids, the ends of the minus-strand template are juxtaposed via base pairing to facilitate the two template switches during plus-strand DNA synthesis. PMID:12578983

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

2015-10-01

In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

The fidelity of replication of the three-base-pair set adenine/thymine, hypoxanthine/cytosine and 6-thiopurine/5-methyl-2-pyrimidinone with T7 DNA polymerase

PubMed Central

2004-01-01

With the goal of constructing a genetic alphabet consisting of a set of three base pairs, the fidelity of replication of the three base pairs TH (5-methyl-2-pyrimidinone)/HS (6-thiopurine; thiohypoxanthine), C/H (hypoxanthine) and T/A was evaluated using T7 DNA polymerase, a polymerase with a strong 3′→5′ exonuclease activity. An evaluation of the suitability of a new base pair for replication should include both the contribution of the fidelity of a polymerase activity and the contribution of proofreading by a 3′→5′ exonuclease activity. Using a steady-state kinetics method that included the contribution of the 3′→5′ exonuclease activity, the fidelity of replication was determined. The method determined the ratio of the apparent rate constant for the addition of a deoxynucleotide to the primer across from a template base by the polymerase activity and the rate constant for removal of the added deoxynucleotide from the primer by the 3′→5′ exonuclease activity. This ratio was designated the eni (efficiency of net incorporation). The eni of the base pair C/H was equal to or greater than the eni of T/A. The eni of the base pair TH/HS was 0.1 times that of A/T for TH in the template and 0.01 times that of A/T for HS in the template. The ratio of the eni of a mismatched deoxynucleotide to the eni of a matched deoxynucleotide was a measure of the error frequency. The error frequencies were as follows: thymine or TH opposite a template hypoxanthine, 2×10−6; HS opposite a template cytosine, <3×10−4. The remaining 24 mismatched combinations of bases gave no detectable net incorporation. Two mismatches, hypoxanthine opposite a template thymine or a template TH, showed trace incorporation in the presence of a standard dNTP complementary to the next template base. T7 DNA polymerase extended the primer beyond each of the matched base pairs of the set. The level of fidelity of replication of the three base pairs with T7 DNA polymerase suggests that they are adequate for a three-base-pair alphabet for DNA replication. PMID:15078225

Development of a Human Brain Diffusion Tensor Template

PubMed Central

Peng, Huiling; Orlichenko, Anton; Dawe, Robert J.; Agam, Gady; Zhang, Shengwei; Arfanakis, Konstantinos

2009-01-01

The development of a brain template for diffusion tensor imaging (DTI) is crucial for comparisons of neuronal structural integrity and brain connectivity across populations, as well as for the development of a white matter atlas. Previous efforts to produce a DTI brain template have been compromised by factors related to image quality, the effectiveness of the image registration approach, the appropriateness of subject inclusion criteria, the completeness and accuracy of the information summarized in the final template. The purpose of this work was to develop a DTI human brain template using techniques that address the shortcomings of previous efforts. Therefore, data containing minimal artifacts were first obtained on 67 healthy human subjects selected from an age-group with relatively similar diffusion characteristics (20–40 years of age), using an appropriate DTI acquisition protocol. Non-linear image registration based on mean diffusion-weighted and fractional anisotropy images was employed. DTI brain templates containing median and mean tensors were produced in ICBM-152 space and made publicly available. The resulting set of DTI templates is characterized by higher image sharpness, provides the ability to distinguish smaller white matter fiber structures, contains fewer image artifacts, than previously developed templates, and to our knowledge, is one of only two templates produced based on a relatively large number of subjects. Furthermore, median tensors were shown to better preserve the diffusion characteristics at the group level than mean tensors. Finally, white matter fiber tractography was applied on the template and several fiber-bundles were traced. PMID:19341801

Development of a human brain diffusion tensor template.

PubMed

Peng, Huiling; Orlichenko, Anton; Dawe, Robert J; Agam, Gady; Zhang, Shengwei; Arfanakis, Konstantinos

2009-07-15

The development of a brain template for diffusion tensor imaging (DTI) is crucial for comparisons of neuronal structural integrity and brain connectivity across populations, as well as for the development of a white matter atlas. Previous efforts to produce a DTI brain template have been compromised by factors related to image quality, the effectiveness of the image registration approach, the appropriateness of subject inclusion criteria, and the completeness and accuracy of the information summarized in the final template. The purpose of this work was to develop a DTI human brain template using techniques that address the shortcomings of previous efforts. Therefore, data containing minimal artifacts were first obtained on 67 healthy human subjects selected from an age-group with relatively similar diffusion characteristics (20-40 years of age), using an appropriate DTI acquisition protocol. Non-linear image registration based on mean diffusion-weighted and fractional anisotropy images was employed. DTI brain templates containing median and mean tensors were produced in ICBM-152 space and made publicly available. The resulting set of DTI templates is characterized by higher image sharpness, provides the ability to distinguish smaller white matter fiber structures, contains fewer image artifacts, than previously developed templates, and to our knowledge, is one of only two templates produced based on a relatively large number of subjects. Furthermore, median tensors were shown to better preserve the diffusion characteristics at the group level than mean tensors. Finally, white matter fiber tractography was applied on the template and several fiber-bundles were traced.

Effects of 99mTc-TRODAT-1 drug template on image quantitative analysis

PubMed Central

Yang, Bang-Hung; Chou, Yuan-Hwa; Wang, Shyh-Jen; Chen, Jyh-Cheng

2018-01-01

99mTc-TRODAT-1 is a type of drug that can bind to dopamine transporters in living organisms and is often used in SPCT imaging for observation of changes in the activity uptake of dopamine in the striatum. Therefore, it is currently widely used in studies on clinical diagnosis of Parkinson’s disease (PD) and movement-related disorders. In conventional 99mTc-TRODAT-1 SPECT image evaluation, visual inspection or manual selection of ROI for semiquantitative analysis is mainly used to observe and evaluate the degree of striatal defects. However, these methods are dependent on the subjective opinions of observers, which lead to human errors, have shortcomings such as long duration, increased effort, and have low reproducibility. To solve this problem, this study aimed to establish an automatic semiquantitative analytical method for 99mTc-TRODAT-1. This method combines three drug templates (one built-in SPECT template in SPM software and two self-generated MRI-based and HMPAO-based TRODAT-1 templates) for the semiquantitative analysis of the striatal phantom and clinical images. At the same time, the results of automatic analysis of the three templates were compared with results from a conventional manual analysis for examining the feasibility of automatic analysis and the effects of drug templates on automatic semiquantitative analysis results. After comparison, it was found that the MRI-based TRODAT-1 template generated from MRI images is the most suitable template for 99mTc-TRODAT-1 automatic semiquantitative analysis. PMID:29543874

Three-Station Three-dimensional Bolus-Chase MR Angiography with Real-time Fluoroscopic Tracking

PubMed Central

Johnson, Casey P.; Weavers, Paul T.; Borisch, Eric A.; Grimm, Roger C.; Hulshizer, Thomas C.; LaPlante, Christine C.; Rossman, Phillip J.; Glockner, James F.; Young, Phillip M.

2014-01-01

Purpose To determine the feasibility of using real-time fluoroscopic tracking for bolus-chase magnetic resonance (MR) angiography of peripheral vasculature to image three stations from the aortoiliac bifurcation to the pedal arteries. Materials and Methods This prospective study was institutional review board approved and HIPAA compliant. Eight healthy volunteers (three men; mean age, 48 years; age range, 30–81 years) and 13 patients suspected of having peripheral arterial disease (five men; mean age, 67 years; age range, 47–81 years) were enrolled and provided informed consent. All subjects were imaged with the fluoroscopic tracking MR angiographic protocol. Ten patients also underwent a clinical computed tomographic (CT) angiographic runoff examination. Two readers scored the MR angiographic studies for vessel signal intensity and sharpness and presence of confounding artifacts and venous contamination at 35 arterial segments. Mean aggregate scores were assessed. The paired MR angiographic and CT angiographic studies also were scored for visualization of disease, reader confidence, and overall diagnostic quality and were compared by using a Wilcoxon signed rank test. Results Real-time fluoroscopic tracking performed well technically in all studies. Vessel segments were scored good to excellent in all but the following categories: For vessel signal intensity and sharpness, the abdominal aorta, iliac arteries, distal plantar arteries, and plantar arch were scored as fair to good; and for presence of confounding artifacts, the abdominal aorta and iliac arteries were scored as fair. The MR angiograms and CT angiograms did not differ significantly in any scoring category (reader 1: P = .50, .39, and .39; reader 2: P = .41, .61, and .33, respectively). CT scores were substantially better in 20% (four of 20) and 25% (five of 20) of the pooled evaluations for the visualization of disease and overall image quality categories, respectively, versus 5% (one of 20) for MR scores in both categories. Conclusion Three-station bolus-chase MR angiography with real-time fluoroscopic tracking provided high-spatial-resolution arteriograms of the peripheral vasculature, enabled precise triggering of table motion, and compared well with CT angiograms. © RSNA, 2014 Online supplemental material is available for this article. PMID:24635676

WE-DE-201-08: Multi-Source Rotating Shield Brachytherapy Apparatus for Prostate Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dadkhah, H; Wu, X; Kim, Y

Purpose: To introduce a novel multi-source rotating shield brachytherapy (RSBT) apparatus for the precise simultaneous angular and linear positioning of all partially-shielded 153Gd radiation sources in interstitial needles for treating prostate cancer. The mechanism is designed to lower the detrimental dose to healthy tissues, the urethra in particular, relative to conventional high-dose-rate brachytherapy (HDR-BT) techniques. Methods: Following needle implantation, the delivery system is docked to the patient template. Each needle is coupled to a multi-source afterloader catheter by a connector passing through a shaft. The shafts are rotated by translating a moving template between two stationary templates. Shaft walls asmore » well as moving template holes are threaded such that the resistive friction produced between the two parts exerts enough force on the shafts to bring about the rotation. Rotation of the shaft is then transmitted to the shielded source via several keys. Thus, shaft angular position is fully correlated with the position of the moving template. The catheter angles are simultaneously incremented throughout treatment as needed, and only a single 360° rotation of all catheters is needed for a full treatment. For each rotation angle, source depth in each needle is controlled by a multi-source afterloader, which is proposed as an array of belt-driven linear actuators, each of which drives a source wire. Results: Optimized treatment plans based on Monte Carlo dose calculations demonstrated RSBT with the proposed apparatus reduced urethral D{sub 1cc} below that of conventional HDR-BT by 35% for urethral dose gradient volume within 3 mm of the urethra surface. Treatment time to deliver 20 Gy with multi-source RSBT apparatus using nineteen 62.4 GBq {sup 153}Gd sources is 117 min. Conclusions: The proposed RSBT delivery apparatus in conjunction with multiple nitinol catheter-mounted platinum-shielded {sup 153}Gd sources enables a mechanically feasible urethra-sparing treatment technique for prostate cancer in a clinically reasonable timeframe.« less

Research progress in radiation detectors, pattern recognition programs, and radiation damage determination in DNA

NASA Technical Reports Server (NTRS)

Baily, N. A.

1973-01-01

The radiological implications of statistical variations in energy deposition by ionizing radiation were investigated in the conduct of the following experiments: (1) study of the production of secondary particles generated by the passage of the primary radiation through bone and muscle; (2) the study of the ratio of nonreparable to reparable damage in DNA as a function of different energy deposition patterns generated by X rays versus heavy fast charged particles; (3) the use of electronic radiography systems for direct fluoroscopic tomography and for the synthesis of multiple planes and; (4) the determination of the characteristics of systems response to split fields having different contrast levels, and of minimum detectable contrast levels between the halves under realistic clinical situations.

THTM: A template matching algorithm based on HOG descriptor and two-stage matching

NASA Astrophysics Data System (ADS)

Jiang, Yuanjie; Ruan, Li; Xiao, Limin; Liu, Xi; Yuan, Feng; Wang, Haitao

2018-04-01

We propose a novel method for template matching named THTM - a template matching algorithm based on HOG (histogram of gradient) and two-stage matching. We rely on the fast construction of HOG and the two-stage matching that jointly lead to a high accuracy approach for matching. TMTM give enough attention on HOG and creatively propose a twice-stage matching while traditional method only matches once. Our contribution is to apply HOG to template matching successfully and present two-stage matching, which is prominent to improve the matching accuracy based on HOG descriptor. We analyze key features of THTM and perform compared to other commonly used alternatives on a challenging real-world datasets. Experiments show that our method outperforms the comparison method.

Real-time image-processing algorithm for markerless tumour tracking using X-ray fluoroscopic imaging.

PubMed

Mori, S

2014-05-01

To ensure accuracy in respiratory-gating treatment, X-ray fluoroscopic imaging is used to detect tumour position in real time. Detection accuracy is strongly dependent on image quality, particularly positional differences between the patient and treatment couch. We developed a new algorithm to improve the quality of images obtained in X-ray fluoroscopic imaging and report the preliminary results. Two oblique X-ray fluoroscopic images were acquired using a dynamic flat panel detector (DFPD) for two patients with lung cancer. The weighting factor was applied to the DFPD image in respective columns, because most anatomical structures, as well as the treatment couch and port cover edge, were aligned in the superior-inferior direction when the patient lay on the treatment couch. The weighting factors for the respective columns were varied until the standard deviation of the pixel values within the image region was minimized. Once the weighting factors were calculated, the quality of the DFPD image was improved by applying the factors to multiframe images. Applying the image-processing algorithm produced substantial improvement in the quality of images, and the image contrast was increased. The treatment couch and irradiation port edge, which were not related to a patient's position, were removed. The average image-processing time was 1.1 ms, showing that this fast image processing can be applied to real-time tumour-tracking systems. These findings indicate that this image-processing algorithm improves the image quality in patients with lung cancer and successfully removes objects not related to the patient. Our image-processing algorithm might be useful in improving gated-treatment accuracy.

Dosimetry during intramedullary nailing of the tibia

PubMed Central

2009-01-01

Background Intramedullary nailing under fluoroscopic guidance is a common operation. We studied the intraoperative radiation dose received by both the patient and the personnel. Patients and methods 25 intramedullary nailing procedures of the tibia were studied. All patients suffered from tibial fractures and were treated using the Grosse-Kempf intramedullary nail, with free-hand technique for fixation of the distal screws, under fluoroscopic guidance. The exposure, at selected positions, was recorded using an ion chamber, while the dose area product (DAP) was measured with a DAP meter, attached to the tube head. Thermoluminescent dosimeters (TLDs) were used to derive the occupational dose to the personnel, and also to monitor the surface dose on the gonads of some of the patients. Results The mean operation time was 101 (48–240) min, with a mean fluoroscopic time of 72 seconds and a mean DAP value of 75 cGy·cm2. The surface dose to the gonads of the patients was less than 8.8 mGy during any procedure, and thus cannot be considered to be a contraindication for the use of this technique. Occupational dose differed substantially between members of the operating personnel, the maximum dose recorded being to the operator of the fluoroscopic equipment (0.11 mSv). Interpretation Our findings underscore the care required by the primary operator not to exceed the dose constraint of 10 mSv per year. The rest of the operating personnel, although they do not receive very high doses, should focus on the dose optimization of the technique. PMID:19916691

Three-dimensional curvilinear device reconstruction from two fluoroscopic views

NASA Astrophysics Data System (ADS)

Delmas, Charlotte; Berger, Marie-Odile; Kerrien, Erwan; Riddell, Cyril; Trousset, Yves; Anxionnat, René; Bracard, Serge

2015-03-01

In interventional radiology, navigating devices under the sole guidance of fluoroscopic images inside a complex architecture of tortuous and narrow vessels like the cerebral vascular tree is a difficult task. Visualizing the device in 3D could facilitate this navigation. For curvilinear devices such as guide-wires and catheters, a 3D reconstruction may be achieved using two simultaneous fluoroscopic views, as available on a biplane acquisition system. The purpose of this paper is to present a new automatic three-dimensional curve reconstruction method that has the potential to reconstruct complex 3D curves and does not require a perfect segmentation of the endovascular device. Using epipolar geometry, our algorithm translates the point correspondence problem into a segment correspondence problem. Candidate 3D curves can be formed and evaluated independently after identifying all possible combinations of compatible 3D segments. Correspondence is then inherently solved by looking in 3D space for the most coherent curve in terms of continuity and curvature. This problem can be cast into a graph problem where the most coherent curve corresponds to the shortest path of a weighted graph. We present quantitative results of curve reconstructions performed from numerically simulated projections of tortuous 3D curves extracted from cerebral vascular trees affected with brain arteriovenous malformations as well as fluoroscopic image pairs of a guide-wire from both phantom and clinical sets. Our method was able to select the correct 3D segments in 97.5% of simulated cases thus demonstrating its ability to handle complex 3D curves and can deal with imperfect 2D segmentation.

CaTiO.sub.3 Interfacial template structure on semiconductor-based material and the growth of electroceramic thin-films in the perovskite class

DOEpatents

McKee, Rodney Allen; Walker, Frederick Joseph

1998-01-01

A structure including a film of a desired perovskite oxide which overlies and is fully commensurate with the material surface of a semiconductor-based substrate and an associated process for constructing the structure involves the build up of an interfacial template film of perovskite between the material surface and the desired perovskite film. The lattice parameters of the material surface and the perovskite of the template film are taken into account so that during the growth of the perovskite template film upon the material surface, the orientation of the perovskite of the template is rotated 45.degree. with respect to the orientation of the underlying material surface and thereby effects a transition in the lattice structure from fcc (of the semiconductor-based material) to the simple cubic lattice structure of perovskite while the fully commensurate periodicity between the perovskite template film and the underlying material surface is maintained. The film-growth techniques of the invention can be used to fabricate solid state electrical components wherein a perovskite film is built up upon a semiconductor-based material and the perovskite film is adapted to exhibit ferroelectric, piezoelectric, pyroelectric, electro-optic or large dielectric properties during use of the component.

Template-Based Modeling of Protein-RNA Interactions

PubMed Central

Zheng, Jinfang; Kundrotas, Petras J.; Vakser, Ilya A.

2016-01-01

Protein-RNA complexes formed by specific recognition between RNA and RNA-binding proteins play an important role in biological processes. More than a thousand of such proteins in human are curated and many novel RNA-binding proteins are to be discovered. Due to limitations of experimental approaches, computational techniques are needed for characterization of protein-RNA interactions. Although much progress has been made, adequate methodologies reliably providing atomic resolution structural details are still lacking. Although protein-RNA free docking approaches proved to be useful, in general, the template-based approaches provide higher quality of predictions. Templates are key to building a high quality model. Sequence/structure relationships were studied based on a representative set of binary protein-RNA complexes from PDB. Several approaches were tested for pairwise target/template alignment. The analysis revealed a transition point between random and correct binding modes. The results showed that structural alignment is better than sequence alignment in identifying good templates, suitable for generating protein-RNA complexes close to the native structure, and outperforms free docking, successfully predicting complexes where the free docking fails, including cases of significant conformational change upon binding. A template-based protein-RNA interaction modeling protocol PRIME was developed and benchmarked on a representative set of complexes. PMID:27662342

Biometric template transformation: a security analysis

NASA Astrophysics Data System (ADS)

Nagar, Abhishek; Nandakumar, Karthik; Jain, Anil K.

2010-01-01

One of the critical steps in designing a secure biometric system is protecting the templates of the users that are stored either in a central database or on smart cards. If a biometric template is compromised, it leads to serious security and privacy threats because unlike passwords, it is not possible for a legitimate user to revoke his biometric identifiers and switch to another set of uncompromised identifiers. One methodology for biometric template protection is the template transformation approach, where the template, consisting of the features extracted from the biometric trait, is transformed using parameters derived from a user specific password or key. Only the transformed template is stored and matching is performed directly in the transformed domain. In this paper, we formally investigate the security strength of template transformation techniques and define six metrics that facilitate a holistic security evaluation. Furthermore, we analyze the security of two wellknown template transformation techniques, namely, Biohashing and cancelable fingerprint templates based on the proposed metrics. Our analysis indicates that both these schemes are vulnerable to intrusion and linkage attacks because it is relatively easy to obtain either a close approximation of the original template (Biohashing) or a pre-image of the transformed template (cancelable fingerprints). We argue that the security strength of template transformation techniques must consider also consider the computational complexity of obtaining a complete pre-image of the transformed template in addition to the complexity of recovering the original biometric template.

Evaluation of MRI and cannabinoid type 1 receptor PET templates constructed using DARTEL for spatial normalization of rat brains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kronfeld, Andrea; Müller-Forell, Wibke; Buchholz, Hans-Georg

Purpose: Image registration is one prerequisite for the analysis of brain regions in magnetic-resonance-imaging (MRI) or positron-emission-tomography (PET) studies. Diffeomorphic anatomical registration through exponentiated Lie algebra (DARTEL) is a nonlinear, diffeomorphic algorithm for image registration and construction of image templates. The goal of this small animal study was (1) the evaluation of a MRI and calculation of several cannabinoid type 1 (CB1) receptor PET templates constructed using DARTEL and (2) the analysis of the image registration accuracy of MR and PET images to their DARTEL templates with reference to analytical and iterative PET reconstruction algorithms. Methods: Five male Sprague Dawleymore » rats were investigated for template construction using MRI and [{sup 18}F]MK-9470 PET for CB1 receptor representation. PET images were reconstructed using the algorithms filtered back-projection, ordered subset expectation maximization in 2D, and maximum a posteriori in 3D. Landmarks were defined on each MR image, and templates were constructed under different settings, i.e., based on different tissue class images [gray matter (GM), white matter (WM), and GM + WM] and regularization forms (“linear elastic energy,” “membrane energy,” and “bending energy”). Registration accuracy for MRI and PET templates was evaluated by means of the distance between landmark coordinates. Results: The best MRI template was constructed based on gray and white matter images and the regularization form linear elastic energy. In this case, most distances between landmark coordinates were <1 mm. Accordingly, MRI-based spatial normalization was most accurate, but results of the PET-based spatial normalization were quite comparable. Conclusions: Image registration using DARTEL provides a standardized and automatic framework for small animal brain data analysis. The authors were able to show that this method works with high reliability and validity. Using DARTEL templates together with nonlinear registration algorithms allows for accurate spatial normalization of combined MRI/PET or PET-only studies.« less

Template-based de novo design for type II kinase inhibitors and its extented application to acetylcholinesterase inhibitors.

PubMed

Su, Bo-Han; Huang, Yi-Syuan; Chang, Chia-Yun; Tu, Yi-Shu; Tseng, Yufeng J

2013-10-31

There is a compelling need to discover type II inhibitors targeting the unique DFG-out inactive kinase conformation since they are likely to possess greater potency and selectivity relative to traditional type I inhibitors. Using a known inhibitor, such as a currently available and approved drug or inhibitor, as a template to design new drugs via computational de novo design is helpful when working with known ligand-receptor interactions. This study proposes a new template-based de novo design protocol to discover new inhibitors that preserve and also optimize the binding interactions of the type II kinase template. First, sorafenib (Nexavar) and nilotinib (Tasigna), two type II inhibitors with different ligand-receptor interactions, were selected as the template compounds. The five-step protocol can reassemble each drug from a large fragment library. Our procedure demonstrates that the selected template compounds can be successfully reassembled while the key ligand-receptor interactions are preserved. Furthermore, to demonstrate that the algorithm is able to construct more potent compounds, we considered kinase inhibitors and other protein dataset, acetylcholinesterase (AChE) inhibitors. The de novo optimization was initiated using a template compound possessing a less than optimal activity from a series of aminoisoquinoline and TAK-285 inhibiting type II kinases, and E2020 derivatives inhibiting AChE respectively. Three compounds with greater potency than the template compound were discovered that were also included in the original congeneric series. This template-based lead optimization protocol with the fragment library can help to design compounds with preferred binding interactions of known inhibitors automatically and further optimize the compounds in the binding pockets.

A framework of multitemplate ensemble for fingerprint verification

NASA Astrophysics Data System (ADS)

Yin, Yilong; Ning, Yanbin; Ren, Chunxiao; Liu, Li

2012-12-01

How to improve performance of an automatic fingerprint verification system (AFVS) is always a big challenge in biometric verification field. Recently, it becomes popular to improve the performance of AFVS using ensemble learning approach to fuse related information of fingerprints. In this article, we propose a novel framework of fingerprint verification which is based on the multitemplate ensemble method. This framework is consisted of three stages. In the first stage, enrollment stage, we adopt an effective template selection method to select those fingerprints which best represent a finger, and then, a polyhedron is created by the matching results of multiple template fingerprints and a virtual centroid of the polyhedron is given. In the second stage, verification stage, we measure the distance between the centroid of the polyhedron and a query image. In the final stage, a fusion rule is used to choose a proper distance from a distance set. The experimental results on the FVC2004 database prove the improvement on the effectiveness of the new framework in fingerprint verification. With a minutiae-based matching method, the average EER of four databases in FVC2004 drops from 10.85 to 0.88, and with a ridge-based matching method, the average EER of these four databases also decreases from 14.58 to 2.51.

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy.

PubMed

Yan, Yumeng; Zhang, Di; Zhou, Pei; Li, Botong; Huang, Sheng-You

2017-07-03

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Fluoroscopically Guided Peritendinous Corticosteroid Injection for Proximal Hamstring Tendinopathy

PubMed Central

Nicholson, Luke T.; DiSegna, Steven; Newman, Joel S.; Miller, Suzanne L.

2014-01-01

Background: Proximal hamstring tendinopathy is an uncommon but debilitating cause of posterior thigh pain in athletes subjected to repetitive eccentric hamstring contraction, such as runners. Minimal data exist evaluating treatment options for proximal hamstring tendinopathy. Purpose: This retrospective study evaluates the effectiveness of fluoroscopically guided corticosteroid injections in treating proximal hamstring tendinopathy. Study Design: Case series; Level of evidence, 4. Methods: Eighteen athletes with 22 cases of magnetic resonance imaging–confirmed proximal hamstring tendinopathy were treated with corticosteroid injection and later contacted to evaluate the efficacy of the injection with the use of a questionnaire. Results: The visual analog score decreased from 7.22 preinjection to 3.94 postinjection (P < .001), level of athletic participation increased from 28.76% to 68.82% (P < .001) at a mean follow-up of 21 months, and 38.8% of patients experienced complete resolution at a mean follow-up of 24.8 months. The mean lower extremity function score at the time of follow-up was 60. Conclusion: A trial of fluoroscopically guided corticosteroid injection is warranted in patients presenting with symptoms of proximal hamstring tendinopathy refractory to conservative therapy. PMID:26535310

Fluoroscopically Guided Peritendinous Corticosteroid Injection for Proximal Hamstring Tendinopathy: A Retrospective Review.

PubMed

Nicholson, Luke T; DiSegna, Steven; Newman, Joel S; Miller, Suzanne L

2014-03-01

Proximal hamstring tendinopathy is an uncommon but debilitating cause of posterior thigh pain in athletes subjected to repetitive eccentric hamstring contraction, such as runners. Minimal data exist evaluating treatment options for proximal hamstring tendinopathy. This retrospective study evaluates the effectiveness of fluoroscopically guided corticosteroid injections in treating proximal hamstring tendinopathy. Case series; Level of evidence, 4. Eighteen athletes with 22 cases of magnetic resonance imaging-confirmed proximal hamstring tendinopathy were treated with corticosteroid injection and later contacted to evaluate the efficacy of the injection with the use of a questionnaire. The visual analog score decreased from 7.22 preinjection to 3.94 postinjection (P < .001), level of athletic participation increased from 28.76% to 68.82% (P < .001) at a mean follow-up of 21 months, and 38.8% of patients experienced complete resolution at a mean follow-up of 24.8 months. The mean lower extremity function score at the time of follow-up was 60. A trial of fluoroscopically guided corticosteroid injection is warranted in patients presenting with symptoms of proximal hamstring tendinopathy refractory to conservative therapy.

Reconfigurable Photonic Crystals Enabled by Multistimuli-Responsive Shape Memory Polymers Possessing Room Temperature Shape Processability.

PubMed

Fang, Yin; Leo, Sin-Yen; Ni, Yongliang; Wang, Junyu; Wang, Bingchen; Yu, Long; Dong, Zhe; Dai, Yuqiong; Basile, Vito; Taylor, Curtis; Jiang, Peng

2017-02-15

Traditional shape memory polymers (SMPs) are mostly thermoresponsive, and their applications in nano-optics are hindered by heat-demanding programming and recovery processes. By integrating a polyurethane-based shape memory copolymer with templating nanofabrication, reconfigurable/rewritable macroporous photonic crystals have been demonstrated. This SMP coupled with the unique macroporous structure enables unusual all-room-temperature shape memory cycles. "Cold" programming involving microscopic order-disorder transitions of the templated macropores is achieved by mechanically deforming the macroporous SMP membranes. The rapid recovery of the permanent, highly ordered photonic crystal structure from the temporary, disordered configuration can be triggered by multiple stimuli including a large variety of vapors and solvents, heat, and microwave radiation. Importantly, the striking chromogenic effects associated with these athermal and thermal processes render a sensitive and noninvasive optical methodology for quantitatively characterizing the intriguing nanoscopic shape memory effects. Some critical parameters/mechanisms that could significantly affect the final performance of SMP-based reconfigurable photonic crystals including strain recovery ratio, dynamics and reversibility of shape recovery, as well as capillary condensation of vapors in macropores, which play a crucial role in vapor-triggered recovery, can be evaluated using this new optical technology.

Software Template for Instruction in Mathematics

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Moebes, Travis A.; Beall, Anna

2005-01-01

Intelligent Math Tutor (IMT) is a software system that serves as a template for creating software for teaching mathematics. IMT can be easily connected to artificial-intelligence software and other analysis software through input and output of files. IMT provides an easy-to-use interface for generating courses that include tests that contain both multiple-choice and fill-in-the-blank questions, and enables tracking of test scores. IMT makes it easy to generate software for Web-based courses or to manufacture compact disks containing executable course software. IMT also can function as a Web-based application program, with features that run quickly on the Web, while retaining the intelligence of a high-level language application program with many graphics. IMT can be used to write application programs in text, graphics, and/or sound, so that the programs can be tailored to the needs of most handicapped persons. The course software generated by IMT follows a "back to basics" approach of teaching mathematics by inducing the student to apply creative mathematical techniques in the process of learning. Students are thereby made to discover mathematical fundamentals and thereby come to understand mathematics more deeply than they could through simple memorization.

Repair of Clustered Damage and DNA Polymerase Iota.

PubMed

Belousova, E A; Lavrik, O I

2015-08-01

Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

The construction of MRI brain/head templates for Chinese children from 7 to 16 years of age

PubMed Central

Xie, Wanze; Richards, John E.; Lei, Du; Zhu, Hongyan; Lee, Kang; Gong, Qiyong

2015-01-01

Population-specific brain templates that provide detailed brain information are beneficial to both structural and functional neuroimaging research. However, age-specific MRI templates have not been constructed for Chinese or any Asian developmental populations. This study developed novel T1-weighted average brain and head templates for Chinese children from 7 to 16 years of age in two-year increments using high quality magnetic resonance imaging (MRI) and well-validated image analysis techniques. A total of 138 Chinese children (51 F/87 M) were included in this study. The internally and externally validated registrations show that these Chinese age-specific templates fit Chinese children’s MR images significantly better than age-specific templates created from U.S. children, or adult templates based on either Chinese or North American adults. It implies that age-inappropriate (e.g., the Chinese56 template, the US20–24 template) and nationality-inappropriate brain templates (e.g., U.S. children’s templates, the US20–24 template) do not provide optimal reference MRIs for processing MR brain images of Chinese pediatric populations. Thus, our age-specific MRI templates are the first of the kind and should be useful in neuroimaging studies with children from Chinese or other Asian populations. These templates can also serve as the foundations for the construction of more comprehensive sets of nationality-specific templates for Asian developmental populations. These templates are available for use in our database. PMID:26343862

Rational design of mesoporous metals and related nanomaterials by a soft-template approach.

PubMed

Yamauchi, Yusuke; Kuroda, Kazuyuki

2008-04-07

We review recent developments in the preparation of mesoporous metals and related metal-based nanomaterials. Among the many types of mesoporous materials, mesoporous metals hold promise for a wide range of potential applications, such as in electronic devices, magnetic recording media, and metal catalysts, owing to their metallic frameworks. Mesoporous metals with highly ordered networks and narrow pore-size distributions have traditionally been produced by using mesoporous silica as a hard template. This method involves the formation of an original template followed by deposition of metals within the mesopores and subsequent removal of the template. Another synthetic method is the direct-template approach from lyotropic liquid crystals (LLCs) made of nonionic surfactants at high concentrations. Direct-template synthesis creates a novel avenue for the production of mesoporous metals as well as related metal-based nanomaterials. Many mesoporous metals have been prepared by the chemical or electrochemical reduction of metal salts dissolved in aqueous LLC domains. As a soft template, LLCs are more versatile and therefore more advantageous than hard templates. It is possible to produce various nanostructures (e.g., lamellar, 2D hexagonal (p6mm), and 3D cubic (Ia\\3d)), nanoparticles, and nanotubes simply by controlling the composition of the reaction bath.

RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

PubMed

Piatkowski, Pawel; Kasprzak, Joanna M; Kumar, Deepak; Magnus, Marcin; Chojnowski, Grzegorz; Bujnicki, Janusz M

2016-01-01

RNA encompasses an essential part of all known forms of life. The functions of many RNA molecules are dependent on their ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. To address this problem, computational structure prediction methods were developed that either utilize information derived from known structures of other RNA molecules (by way of template-based modeling) or attempt to simulate the physical process of RNA structure formation (by way of template-free modeling). All computational methods suffer from various limitations that make theoretical models less reliable than high-resolution experimentally determined structures. This chapter provides a protocol for computational modeling of RNA 3D structure that overcomes major limitations by combining two complementary approaches: template-based modeling that is capable of predicting global architectures based on similarity to other molecules but often fails to predict local unique features, and template-free modeling that can predict the local folding, but is limited to modeling the structure of relatively small molecules. Here, we combine the use of a template-based method ModeRNA with a template-free method SimRNA. ModeRNA requires a sequence alignment of the target RNA sequence to be modeled with a template of the known structure; it generates a model that predicts the structure of a conserved core and provides a starting point for modeling of variable regions. SimRNA can be used to fold small RNAs (<80 nt) without any additional structural information, and to refold parts of models for larger RNAs that have a correctly modeled core. ModeRNA can be either downloaded, compiled and run locally or run through a web interface at http://genesilico.pl/modernaserver/ . SimRNA is currently available to download for local use as a precompiled software package at http://genesilico.pl/software/stand-alone/simrna and as a web server at http://genesilico.pl/SimRNAweb . For model optimization we use QRNAS, available at http://genesilico.pl/qrnas .

An approach to automated particle picking from electron micrographs based on reduced representation templates.

PubMed

Volkmann, Niels

2004-01-01

Reduced representation templates are used in a real-space pattern matching framework to facilitate automatic particle picking from electron micrographs. The procedure consists of five parts. First, reduced templates are constructed either from models or directly from the data. Second, a real-space pattern matching algorithm is applied using the reduced representations as templates. Third, peaks are selected from the resulting score map using peak-shape characteristics. Fourth, the surviving peaks are tested for distance constraints. Fifth, a correlation-based outlier screening is applied. Test applications to a data set of keyhole limpet hemocyanin particles indicate that the method is robust and reliable.

Zinc oxide nanostructures as low-cost templates for neuronal circuit

NASA Astrophysics Data System (ADS)

Kritharidou, A.; Georgoussi, Z.; Tsamis, C.; Makarona, E.

2013-05-01

ZnO nanostructures were explored as templates for the development of topography-mediated neuronal cultures. Nanostructures of varying features were produced on 4" Si substrates via a rapid, facile and low-cost technique that allows the systematic investigation of nanotopographically-mediated formation of neuronal cultures. The developed ZnO-nanowire based templates were seeded with Neuro-2A mouse neuroblastoma cells and their viability over the course of 1 to 4 days was assessed. Our studies demonstrate that the ZnO-templates can support neuronal cell growth and proliferation suggesting that ZnO substrate can be used for the development of neuronal cell-based platform technologies.

Evaluation of accuracy in implant site preparation performed in single- or multi-step drilling procedures.

PubMed

Marheineke, Nadine; Scherer, Uta; Rücker, Martin; von See, Constantin; Rahlf, Björn; Gellrich, Nils-Claudius; Stoetzer, Marcus

2018-06-01

Dental implant failure and insufficient osseointegration are proven results of mechanical and thermal damage during the surgery process. We herein performed a comparative study of a less invasive single-step drilling preparation protocol and a conventional multiple drilling sequence. Accuracy of drilling holes was precisely analyzed and the influence of different levels of expertise of the handlers and additional use of drill template guidance was evaluated. Six experimental groups, deployed in an osseous study model, were representing template-guided and freehanded drilling actions in a stepwise drilling procedure in comparison to a single-drill protocol. Each experimental condition was studied by the drilling actions of respectively three persons without surgical knowledge as well as three highly experienced oral surgeons. Drilling actions were performed and diameters were recorded with a precision measuring instrument. Less experienced operators were able to significantly increase the drilling accuracy using a guiding template, especially when multi-step preparations are performed. Improved accuracy without template guidance was observed when experienced operators were executing single-step versus multi-step technique. Single-step drilling protocols have shown to produce more accurate results than multi-step procedures. The outcome of any protocol can be further improved by use of guiding templates. Operator experience can be a contributing factor. Single-step preparations are less invasive and are promoting osseointegration. Even highly experienced surgeons are achieving higher levels of accuracy by combining this technique with template guidance. Hereby template guidance enables a reduction of hands-on time and side effects during surgery and lead to a more predictable clinical diameter.

Wide-band tunable photonic bandgap device and laser in dye-doped liquid crystal refilled cholesteric liquid crystal polymer template system

NASA Astrophysics Data System (ADS)

Lin, Jia-De; Lin, Hong-Lin; Lin, Hsin-Yu; Wei, Guan-Jhong; Lee, Chia-Rong

2017-02-01

The scientists in the field of liquid crystal (LC) have paid significant attention in the exploration of novel cholesteric LC (CLC) polymer template (simply called template) in recent years. The self-assembling nanostructural template with chirality can effectively overcome the limitation in the optical features of traditional CLCs, such as enhancement of reflectivity over 50%, multiple photonic bandgaps (PBGs), and changeable optical characteristics by flexibly replacing the refilling LC materials, and so on. This work fabricates two gradient-pitched CLC templates with two opposite handednesses, which are then merged as a spatially tunable and highly reflective CLC template sample. This sample can simultaneously reflect right- and left-circularly polarized lights and the tunable spectral range includes the entire visible region. By increasing the temperature of the template sample exceeding the clearing point of the refilling LC, the light scattering significantly decreases and the reflectance effectively increase to exceed 50% in the entire visible region. This device has a maximum reflectance over 85% and a wide-band spatial tunability in PBG between 400 nm and 800 nm which covers the entire visible region. Not only the sample can be employed as a wide-band spatially tunable filter, but also the system doping with two suitable laser dyes which emitted fluorescence can cover entire visible region can develop a low-threshold, mirror-less laser with a spatial tunability at spectral regions including blue to red region (from 484 nm to 634 nm) and simultaneous lasing emission of left- and right-circular polarizations.

Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea.

PubMed

Shuttleworth, Gillian; Fogg, Mark J; Kurpiewski, Michael R; Jen-Jacobson, Linda; Connolly, Bernard A

2004-03-26

Archaeal family B DNA polymerases contain a specialised pocket that binds tightly to template-strand uracil, causing the stalling of DNA replication. The mechanism of this unique "template-strand proof-reading" has been studied using equilibrium binding measurements, DNA footprinting, van't Hoff analysis and calorimetry. Binding assays have shown that the polymerase preferentially binds to uracil in single as opposed to double-stranded DNA. Tightest binding is observed using primer-templates that contain uracil four bases in front of the primer-template junction, corresponding to the observed stalling position. Ethylation interference analysis of primer-templates shows that the two phosphates, immediately flanking the uracil (NpUpN), are important for binding; contacts are also made to phosphates in the primer-strand. Microcalorimetry and van't Hoff analysis have given a fuller understanding of the thermodynamic parameters involved in uracil recognition. All the results are consistent with a "read-ahead" mechanism, in which the replicating polymerase scans the template, ahead of the replication fork, for the presence of uracil and halts polymerisation on detecting this base. Post-stalling events, serving to eliminate uracil, await full elucidation.

iTemplate: A template-based eye movement data analysis approach.

PubMed

Xiao, Naiqi G; Lee, Kang

2018-02-08

Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method. Using a linear transformation algorithm, this method registers the eye movement data from each individual stimulus to a template. Thus, users only need to create one set of AOIs for the template in order to analyze eye movement data, rather than creating a unique set of AOIs for all individual stimuli. This change greatly reduces the error caused by the variance from manually created AOIs and boosts the efficiency of the data analysis. Furthermore, this method can help researchers prepare eye movement data for some advanced analysis approaches, such as iMap. We have developed software (iTemplate) with a graphic user interface to make this analysis method available to researchers.

Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths

PubMed Central

Gül, O. Tolga; Pugliese, Kaitlin M.; Choi, Yongki; Sims, Patrick C.; Pan, Deng; Rajapakse, Arith J.; Weiss, Gregory A.; Collins, Philip G.

2016-01-01

As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein’s activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF’s base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures. PMID:27348011

Single Molecule Bioelectronics and Their Application to Amplification-Free Measurement of DNA Lengths.

PubMed

Gül, O Tolga; Pugliese, Kaitlin M; Choi, Yongki; Sims, Patrick C; Pan, Deng; Rajapakse, Arith J; Weiss, Gregory A; Collins, Philip G

2016-06-24

As biosensing devices shrink smaller and smaller, they approach a scale in which single molecule electronic sensing becomes possible. Here, we review the operation of single-enzyme transistors made using single-walled carbon nanotubes. These novel hybrid devices transduce the motions and catalytic activity of a single protein into an electronic signal for real-time monitoring of the protein's activity. Analysis of these electronic signals reveals new insights into enzyme function and proves the electronic technique to be complementary to other single-molecule methods based on fluorescence. As one example of the nanocircuit technique, we have studied the Klenow Fragment (KF) of DNA polymerase I as it catalytically processes single-stranded DNA templates. The fidelity of DNA polymerases makes them a key component in many DNA sequencing techniques, and here we demonstrate that KF nanocircuits readily resolve DNA polymerization with single-base sensitivity. Consequently, template lengths can be directly counted from electronic recordings of KF's base-by-base activity. After measuring as few as 20 copies, the template length can be determined with <1 base pair resolution, and different template lengths can be identified and enumerated in solutions containing template mixtures.

Storyboard method of end-user programming with natural language configuration

DOEpatents

Bouchard, Ann M; Osbourn, Gordon C

2013-11-19

A technique for end-user programming includes populating a template with graphically illustrated actions and then invoking a command to generate a screen element based on the template. The screen element is rendered within a computing environment and provides a mechanism for triggering execution of a sequence of user actions. The sequence of user actions is based at least in part on the graphically illustrated actions populated into the template.

Constructing inverse V-type TiO2-based photocatalyst via bio-template approach to enhance the photosynthetic water oxidation

NASA Astrophysics Data System (ADS)

Jiang, Jinghui; Zhou, Han; Ding, Jian; Zhang, Fan; Fan, Tongxiang; Zhang, Di

2015-08-01

Bio-template approach was employed to construct inverse V-type TiO2-based photocatalyst with well distributed AgBr in TiO2 matrix by making dead Troides Helena wings with inverse V-type scales as the template. A cross-linked titanium precursor with homogenous hydrolytic rate, good liquidity, and low viscosity was employed to facilitate a perfect duplication of the template and the dispersion of AgBr based on appropriate pretreatment of the template by alkali and acid. The as-synthesized inverse V-type TiO2/AgBr can be turned into inverse V-type TiO2/Ag0 from AgBr photolysis during photocatalysis to achieve in situ deposition of Ag0 in TiO2 matrix, by this approach, to avoid the deformation of surface microstructure inherited from the template. The result showed that the cooperation of perfect inverse V-type structure and the well distributed TiO2/Ag0 microstructures can efficiently boost the photosynthetic water oxidation compared to non-inverse V-type TiO2/Ag0 and TiO2/Ag0 without using template. The anti-reflection function of inverse V-type structure and the plasmatic effect of Ag0 might be able to account for the enhanced photon capture and efficient photoelectric conversion.

Fluoroscopic tomography. [for body section synthesis

NASA Technical Reports Server (NTRS)

Baily, N. A.; Crepeau, R. L.; Lasser, E. C.

1974-01-01

A fluoroscopic tomography system capable of synthesizing body sections at a number of levels within the body has been developed. The synthesized body sections may lie either in a range of planes parallel to, tilted with respect to, skewed with respect to, or both tilted and skewed with respect to the plane of motion of the X-ray tube target. In addition, body sections can be presented which are contoured to the patient's anatomy. That is to say, they may even encompass such complex surfaces as a quadratic hyperplane. In addition, tomograms of organs in motion can be imaged.

Rapid and selective extraction of multiple macrolide antibiotics in foodstuff samples based on magnetic molecularly imprinted polymers.

PubMed

Zhou, Yusun; Zhou, Tingting; Jin, Hua; Jing, Tao; Song, Bin; Zhou, Yikai; Mei, Surong; Lee, Yong-Ill

2015-05-01

Magnetic molecularly imprinted polymers (MMIPs) were prepared based on surface molecular imprinting using erythromycin (ERY) as template molecule and Fe3O4 nanoparticles as support substrate. The MMIPs possessed high adsorption capacity of 94.1 mg/g for ERY and the imprinting factor was 11.9 indicating good imprinted effect for ERY. Selective evaluation demonstrated favorable selectivity of MMIPs for multiple macrolide antibiotics (MACs). Using MMIPs as adsorptive material, a rapid and convenient magnetic solid-phase extraction (MSPE) procedure was established for simultaneous and selective separation of six MACs in pork, fish and shrimp samples, then the MACs was subjected to high-performance liquid chromatography-ultraviolet (HPLC-UV) analysis. At different fortified concentrations, the extraction recoveries could reach 89.1% and the relative standard deviations were lower than 12.4%. Chromatogram revealed the response signals of MACs in spiked samples were greatly enhanced and matrix interferences were effectively eliminated after treatment with MSPE. The proposed MSPE procedure coupled with HPLC-UV realized selective and sensitive determination of multiple MACs in foodstuff samples. Copyright © 2015 Elsevier B.V. All rights reserved.

An in vivo MRI Template Set for Morphometry, Tissue Segmentation, and fMRI Localization in Rats

PubMed Central

Valdés-Hernández, Pedro Antonio; Sumiyoshi, Akira; Nonaka, Hiroi; Haga, Risa; Aubert-Vásquez, Eduardo; Ogawa, Takeshi; Iturria-Medina, Yasser; Riera, Jorge J.; Kawashima, Ryuta

2011-01-01

Over the last decade, several papers have focused on the construction of highly detailed mouse high field magnetic resonance image (MRI) templates via non-linear registration to unbiased reference spaces, allowing for a variety of neuroimaging applications such as robust morphometric analyses. However, work in rats has only provided medium field MRI averages based on linear registration to biased spaces with the sole purpose of approximate functional MRI (fMRI) localization. This precludes any morphometric analysis in spite of the need of exploring in detail the neuroanatomical substrates of diseases in a recent advent of rat models. In this paper we present a new in vivo rat T2 MRI template set, comprising average images of both intensity and shape, obtained via non-linear registration. Also, unlike previous rat template sets, we include white and gray matter probabilistic segmentations, expanding its use to those applications demanding prior-based tissue segmentation, e.g., statistical parametric mapping (SPM) voxel-based morphometry. We also provide a preliminary digitalization of latest Paxinos and Watson atlas for anatomical and functional interpretations within the cerebral cortex. We confirmed that, like with previous templates, forepaw and hindpaw fMRI activations can be correctly localized in the expected atlas structure. To exemplify the use of our new MRI template set, were reported the volumes of brain tissues and cortical structures and probed their relationships with ontogenetic development. Other in vivo applications in the near future can be tensor-, deformation-, or voxel-based morphometry, morphological connectivity, and diffusion tensor-based anatomical connectivity. Our template set, freely available through the SPM extension website, could be an important tool for future longitudinal and/or functional extensive preclinical studies. PMID:22275894

Effect of Body Mass Index on Digital Templating for Total Hip Arthroplasty.

PubMed

Sershon, Robert A; Diaz, Alejandro; Bohl, Daniel D; Levine, Brett R

2017-03-01

Digital templating is becoming more prevalent in orthopedics. Recent investigations report high accuracy using digital templating in total hip arthroplasty (THA); however, the effect of body mass index (BMI) on templating accuracy is not well described. Digital radiographs of 603 consecutive patients (645 hips) undergoing primary THA by a single surgeon were digitally templated using OrthoView (Jacksonville, FL). A 25-mm metallic sphere was used as a calibration marker. Preoperative digital hip templates were compared with the final implant size. Hips were stratified into groups based on BMI: BMI <30 (315), BMI 30-35 (132), BMI 35-40 (97), and BMI >40 (101). Accuracy between templating and final size did not vary by BMI for acetabular or femoral components. Digital templating was within 2 sizes of the final acetabular and femoral implants in 99.1% and 97.1% of cases, respectively. Digital templating is an effective means of predicting the final size of THA components. BMI does not appear to play a major role in altering THA digital templating accuracy. Copyright © 2016 Elsevier Inc. All rights reserved.

Formation of oligonucleotide-PNA-chimeras by template-directed ligation

NASA Technical Reports Server (NTRS)

Koppitz, M.; Nielsen, P. E.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1998-01-01

DNA sequences have previously been reported to act as templates for the synthesis of PNA, and vice versa. A continuous evolutionary transition from an informational replicating system based on one polymer to a system based on the other would be facilitated if it were possible to form chimeras, that is molecules that contain monomers of both types. Here we show that ligation to form chimeras proceeds efficiently both on PNA and on DNA templates. The efficiency of ligation is primarily determined by the number of backbone bonds at the ligation site and the relative orientation of template and substrate strands. The most efficient reactions result in the formation of chimeras with ligation junctions resembling the structures of the backbones of PNA and DNA and with antiparallel alignment of both components of the chimera with the template, that is, ligations involving formation of 3'-phosphoramidate and 5'-ester bonds. However, double helices involving PNA are stable both with antiparallel and parallel orientation of the two strands. Ligation on PNA but not on DNA templates is, therefore, sometimes possible on templates with reversed orientation. The relevance of these findings to discussions of possible transitions between genetic systems is discussed.

Authentication of two samples of ancient Chinese coins with component element depth analysis by confocal 3D XRF

NASA Astrophysics Data System (ADS)

Zhou, Peng; Liu, Zhiguo; Lin, Xiaoyan; Liu, Xin; Ye, Lei; Wang, Xingyi; Pan, Kai; Li, Yude

2018-05-01

Two samples of ancient Chinese coins were analyzed with a confocal three-dimensional micro-X-ray fluoroscope. The depth distributions of elemental iron (Fe), calcium (Ca) and copper (Cu) were obtained based on this non-destructive measurement method. One coin, named "Chongning Tongbao", was certified as genuine in accordance with the available archaeological data, whereas another coin, named "Zhenglong Yuanbao", was identified as a reproduction.

Rolling Circle Amplification of Complete Nematode Mitochondrial Genomes

PubMed Central

Tang, Sha; Hyman, Bradley C.

2005-01-01

To enable investigation of nematode mitochondrial DNA evolution, methodology has been developed to amplify intact nematode mitochondrial genomes in preparative yields using a rolling circle replication strategy. Successful reactions were generated from whole cell template DNA prepared by alkaline lysis of the rhabditid nematode Caenorhabditis elegans and a mermithid nematode, Thaumamermis cosgrovei. These taxa, representing the two major nematode classes Chromodorea and Enoplea, maintain mitochondrial genomes of 13.8 kb and 20.0 kb, respectively. Efficient amplifications were conducted on template DNA isolated from individual or pooled nematodes that were alive or stored at -80°C. Unexpectedly, these experiments revealed that multiple T. cosgrovei mitochondrial DNA haplotypes are maintained in our local population. Rolling circle amplification products can be used as templates for standard PCR reactions with specific primers that target mitochondrial genes or for direct DNA sequencing. PMID:19262866

Multiple regression based imputation for individualizing template human model from a small number of measured dimensions.

PubMed

Nohara, Ryuki; Endo, Yui; Murai, Akihiko; Takemura, Hiroshi; Kouchi, Makiko; Tada, Mitsunori

2016-08-01

Individual human models are usually created by direct 3D scanning or deforming a template model according to the measured dimensions. In this paper, we propose a method to estimate all the necessary dimensions (full set) for the human model individualization from a small number of measured dimensions (subset) and human dimension database. For this purpose, we solved multiple regression equation from the dimension database given full set dimensions as the objective variable and subset dimensions as the explanatory variables. Thus, the full set dimensions are obtained by simply multiplying the subset dimensions to the coefficient matrix of the regression equation. We verified the accuracy of our method by imputing hand, foot, and whole body dimensions from their dimension database. The leave-one-out cross validation is employed in this evaluation. The mean absolute errors (MAE) between the measured and the estimated dimensions computed from 4 dimensions (hand length, breadth, middle finger breadth at proximal, and middle finger depth at proximal) in the hand, 2 dimensions (foot length, breadth, and lateral malleolus height) in the foot, and 1 dimension (height) and weight in the whole body are computed. The average MAE of non-measured dimensions were 4.58% in the hand, 4.42% in the foot, and 3.54% in the whole body, while that of measured dimensions were 0.00%.

Population differences in brain morphology: Need for population specific brain template.

PubMed

Rao, Naren P; Jeelani, Haris; Achalia, Rashmin; Achalia, Garima; Jacob, Arpitha; Bharath, Rose Dawn; Varambally, Shivarama; Venkatasubramanian, Ganesan; K Yalavarthy, Phaneendra

2017-07-30

Brain templates provide a standard anatomical platform for population based morphometric assessments. Typically, standard brain templates for such assessments are created using Caucasian brains, which may not be ideal to analyze brains from other ethnicities. To effectively demonstrate this, we compared brain morphometric differences between T1 weighted structural MRI images of 27 healthy Indian and Caucasian subjects of similar age and same sex ratio. Furthermore, a population specific brain template was created from MRI images of healthy Indian subjects and compared with standard Montreal Neurological Institute (MNI-152) template. We also examined the accuracy of registration of by acquiring a different T1 weighted MRI data set and registering them to newly created Indian template and MNI-152 template. The statistical analysis indicates significant difference in global brain measures and regional brain structures of Indian and Caucasian subjects. Specifically, the global brain measurements of the Indian brain template were smaller than that of the MNI template. Also, Indian brain images were better realigned to the newly created template than to the MNI-152 template. The notable variations in Indian and Caucasian brains convey the need to build a population specific Indian brain template and atlas. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Predict Brain MR Image Registration via Sparse Learning of Appearance and Transformation

PubMed Central

Wang, Qian; Kim, Minjeong; Shi, Yonghong; Wu, Guorong; Shen, Dinggang

2014-01-01

We propose a new approach to register the subject image with the template by leveraging a set of intermediate images that are pre-aligned to the template. We argue that, if points in the subject and the intermediate images share similar local appearances, they may have common correspondence in the template. In this way, we learn the sparse representation of a certain subject point to reveal several similar candidate points in the intermediate images. Each selected intermediate candidate can bridge the correspondence from the subject point to the template space, thus predicting the transformation associated with the subject point at the confidence level that relates to the learned sparse coefficient. Following this strategy, we first predict transformations at selected key points, and retain multiple predictions on each key point, instead of allowing only a single correspondence. Then, by utilizing all key points and their predictions with varying confidences, we adaptively reconstruct the dense transformation field that warps the subject to the template. We further embed the prediction-reconstruction protocol above into a multi-resolution hierarchy. In the final, we refine our estimated transformation field via existing registration method in effective manners. We apply our method to registering brain MR images, and conclude that the proposed framework is competent to improve registration performances substantially. PMID:25476412

3D Bioprinting of Developmentally Inspired Templates for Whole Bone Organ Engineering.

PubMed

Daly, Andrew C; Cunniffe, Gráinne M; Sathy, Binulal N; Jeon, Oju; Alsberg, Eben; Kelly, Daniel J

2016-09-01

The ability to print defined patterns of cells and extracellular-matrix components in three dimensions has enabled the engineering of simple biological tissues; however, bioprinting functional solid organs is beyond the capabilities of current biofabrication technologies. An alternative approach would be to bioprint the developmental precursor to an adult organ, using this engineered rudiment as a template for subsequent organogenesis in vivo. This study demonstrates that developmentally inspired hypertrophic cartilage templates can be engineered in vitro using stem cells within a supporting gamma-irradiated alginate bioink incorporating Arg-Gly-Asp adhesion peptides. Furthermore, these soft tissue templates can be reinforced with a network of printed polycaprolactone fibers, resulting in a ≈350 fold increase in construct compressive modulus providing the necessary stiffness to implant such immature cartilaginous rudiments into load bearing locations. As a proof-of-principal, multiple-tool biofabrication is used to engineer a mechanically reinforced cartilaginous template mimicking the geometry of a vertebral body, which in vivo supported the development of a vascularized bone organ containing trabecular-like endochondral bone with a supporting marrow structure. Such developmental engineering approaches could be applied to the biofabrication of other solid organs by bioprinting precursors that have the capacity to mature into their adult counterparts over time in vivo. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Image quality guided approach for adaptive modelling of biometric intra-class variations

NASA Astrophysics Data System (ADS)

Abboud, Ali J.; Jassim, Sabah A.

2010-04-01

The high intra-class variability of acquired biometric data can be attributed to several factors such as quality of acquisition sensor (e.g. thermal), environmental (e.g. lighting), behavioural (e.g. change face pose). Such large fuzziness of biometric data can cause a big difference between an acquired and stored biometric data that will eventually lead to reduced performance. Many systems store multiple templates in order to account for such variations in the biometric data during enrolment stage. The number and typicality of these templates are the most important factors that affect system performance than other factors. In this paper, a novel offline approach is proposed for systematic modelling of intra-class variability and typicality in biometric data by regularly selecting new templates from a set of available biometric images. Our proposed technique is a two stage algorithm whereby in the first stage image samples are clustered in terms of their image quality profile vectors, rather than their biometric feature vectors, and in the second stage a per cluster template is selected from a small number of samples in each clusters to create an ultimate template sets. These experiments have been conducted on five face image databases and their results will demonstrate the effectiveness of proposed quality guided approach.

I-TASSER: fully automated protein structure prediction in CASP8.

PubMed

Zhang, Yang

2009-01-01

The I-TASSER algorithm for 3D protein structure prediction was tested in CASP8, with the procedure fully automated in both the Server and Human sections. The quality of the server models is close to that of human ones but the human predictions incorporate more diverse templates from other servers which improve the human predictions in some of the distant homology targets. For the first time, the sequence-based contact predictions from machine learning techniques are found helpful for both template-based modeling (TBM) and template-free modeling (FM). In TBM, although the accuracy of the sequence based contact predictions is on average lower than that from template-based ones, the novel contacts in the sequence-based predictions, which are complementary to the threading templates in the weakly or unaligned regions, are important to improve the global and local packing in these regions. Moreover, the newly developed atomic structural refinement algorithm was tested in CASP8 and found to improve the hydrogen-bonding networks and the overall TM-score, which is mainly due to its ability of removing steric clashes so that the models can be generated from cluster centroids. Nevertheless, one of the major issues of the I-TASSER pipeline is the model selection where the best models could not be appropriately recognized when the correct templates are detected only by the minority of the threading algorithms. There are also problems related with domain-splitting and mirror image recognition which mainly influences the performance of I-TASSER modeling in the FM-based structure predictions. Copyright 2009 Wiley-Liss, Inc.

[Exposition of the operator's eye lens and efficacy of radiation shielding in fluoroscopically guided interventions].

PubMed

Galster, M; Guhl, C; Uder, M; Adamus, R

2013-05-01

Efficacy of radiation protection tools for the eye lens dose of the radiologist in fluoroscopic interventions. A patient phantom was exposed using a fluoroscopic system. Dose measurements were made at the eye location of the radiologist using an ionization chamber. The setting followed typical fluoroscopic interventions. The reduction of scattered radiation by the equipment-mounted shielding (undercouch drapes and overcouch top) was evaluated. The ceiling-suspended lead acrylic glass screen was tested in scattered radiation generated by a slab phantom. The protective properties of different lead glass goggles and lead acrylic visors were evaluated by thermoluminescence measurements on a head phantom in the primary beam. The exposition of the lens of about 110 to 550 μSv during radiologic interventions is only slightly reduced by the undercouch drapes. Applying the top in addition to the drapes reduces the lens dose by a factor of 2 for PA projections. In 25°LAO the dose is reduced by a factor between 1.2 and 5. The highest doses were measured for AP angulations furthermore the efficacy of the equipment-mounted shielding is minimal. The ceiling-suspended lead screen reduced scatter by a factor of about 30. The lead glass goggles and visors reduced the lens dose up to a factor of 8 to 10. Depending on the specific design, the tested models are less effective especially for radiation from lateral with cranial angulation of the beam. Occasionally the visors even caused an increase of dose. The exposition of the eye lens can be kept below the new occupational limit recommended by the ICRP if the radiation shielding equipment is used consistently. © Georg Thieme Verlag KG Stuttgart · New York.

Adapting Human Videofluoroscopic Swallow Study Methods to Detect and Characterize Dysphagia in Murine Disease Models

PubMed Central

Lever, Teresa E.; Braun, Sabrina M.; Brooks, Ryan T.; Harris, Rebecca A.; Littrell, Loren L.; Neff, Ryan M.; Hinkel, Cameron J.; Allen, Mitchell J.; Ulsas, Mollie A.

2015-01-01

This study adapted human videofluoroscopic swallowing study (VFSS) methods for use with murine disease models for the purpose of facilitating translational dysphagia research. Successful outcomes are dependent upon three critical components: test chambers that permit self-feeding while standing unrestrained in a confined space, recipes that mask the aversive taste/odor of commercially-available oral contrast agents, and a step-by-step test protocol that permits quantification of swallow physiology. Elimination of one or more of these components will have a detrimental impact on the study results. Moreover, the energy level capability of the fluoroscopy system will determine which swallow parameters can be investigated. Most research centers have high energy fluoroscopes designed for use with people and larger animals, which results in exceptionally poor image quality when testing mice and other small rodents. Despite this limitation, we have identified seven VFSS parameters that are consistently quantifiable in mice when using a high energy fluoroscope in combination with the new murine VFSS protocol. We recently obtained a low energy fluoroscopy system with exceptionally high imaging resolution and magnification capabilities that was designed for use with mice and other small rodents. Preliminary work using this new system, in combination with the new murine VFSS protocol, has identified 13 swallow parameters that are consistently quantifiable in mice, which is nearly double the number obtained using conventional (i.e., high energy) fluoroscopes. Identification of additional swallow parameters is expected as we optimize the capabilities of this new system. Results thus far demonstrate the utility of using a low energy fluoroscopy system to detect and quantify subtle changes in swallow physiology that may otherwise be overlooked when using high energy fluoroscopes to investigate murine disease models. PMID:25866882

The accuracy and safety of fluoroscopic-guided percutaneous pedicle screws in the thoracic and lumbosacral spine in the Asian population: A CT scan analysis of 1002 screws.

PubMed

Chiu, Chee Kidd; Chan, Chris Yin Wei; Kwan, Mun Keong

2017-01-01

This study investigates the safety and accuracy of percutaneous pedicle screws placed using fluoroscopic guidance in the thoracolumbosacral spine among Asian patients. Computerized tomography scans of 128 patients who had surgery using fluoroscopic-guided percutaneous pedicle screws were selected. Medial, lateral, superior, and inferior screw perforations were classified into grade 0 (no violation), grade 1 (<2 mm perforation), grade 2 (2-4 mm perforation), and grade 3(>4 mm perforation). Anterior perforations were classified into grade 0 (no violation), grade 1 (<4 mm perforation), grade 2 (4-6 mm perforation), and grade 3(>6 mm perforation). Grade 2 and grade 3 perforation were considered as "critical" perforation. In total, 1002 percutaneous pedicle screws from 128 patients were analyzed. The mean age was 52.7 ± 16.6. There were 70 male patients and 58 female patients. The total perforation rate was 11.3% (113) with 8.4% (84) grade 1, 2.6% (26) grade 2, and 0.3% (3) grade 3 perforations. The overall "critical" perforation rate was 2.9% (29 screws) and no complications were noted. The highest perforation rates were at T4 (21.6%), T2 (19.4%), and T6 (19.2%). The total perforation rate of 11.3% with the total "critical" perforation rate of 2.9% (2.6% grade 2 and 0.3% grade 3 perforations). The highest perforation rates were found over the upper to mid-thoracic region. Fluoroscopic-guided percutaneous pedicle screws insertion among Asians has the safety and accuracy comparable to the current reported percutaneous pedicle screws and open pedicle screws techniques.

Fluoroscopically guided placement of self-expandable metallic stents and stent-grafts in the treatment of acute malignant colorectal obstruction.

PubMed

Kim, Honsoul; Kim, Seung Hyoung; Choi, Sun Young; Lee, Kwang-Hun; Won, Jong Yoon; Lee, Do Yun; Lee, Jong Tae

2008-12-01

To evaluate the technical feasibility and clinical effectiveness of fluoroscopically guided placement of self-expandable metallic stents and stent-grafts for acute malignant colorectal obstruction. Radiologic images and clinical reports of 42 patients (22 men, 20 women; age range, 28-93 years; median age, 65.5 years) who underwent fluoroscopically guided colorectal stent insertion without endoscopic assistance for acute malignant obstruction were reviewed retrospectively. Eighteen patients received bare stents as a bridge to surgery. Twenty-four patients received 27 insertions of either a bare stent (n = 15) or a stent-graft (n = 12) for palliation. The obstruction was located in the rectum (n = 8), sigmoid (n = 17), descending colon (n = 8), splenic flexure (n = 3), and transverse colon (n = 6). Clinical success, defined as more than 50% dilatation of the stent with subsequent symptomatic improvement, was achieved in 41 of the 42 patients (98%). No major procedure-related complications occurred. Minor complications occurred in eight of the 45 procedures (18%). No perioperative mortalities occurred within 1 month after surgery. In the palliative group, the median stent patency was 62 days (range, 0-1,014 days). There was no statistically significant difference in stent patency between the bare stents (range, 0-855 days; median, 68 days) and stent-grafts (range, 1-1,014 days; median, 81 days). Fluoroscopically guided placement of self-expandable metallic stents and stent-grafts for the relief of acute malignant colorectal obstruction was technically feasible without endoscopic assistance-even in lesions proximal to the splenic flexure and transverse colon-and clinically effective in both bridge to surgery and palliative management.

Fluoroscopic removal of retrievable self-expandable metal stents in patients with malignant oesophageal strictures: Experience with a non-endoscopic removal system.

PubMed

Kim, Pyeong Hwa; Song, Ho-Young; Park, Jung-Hoon; Zhou, Wei-Zhong; Na, Han Kyu; Cho, Young Chul; Jun, Eun Jung; Kim, Jun Ki; Kim, Guk Bae

2017-03-01

To evaluate clinical outcomes of fluoroscopic removal of retrievable self-expandable metal stents (SEMSs) for malignant oesophageal strictures, to compare clinical outcomes of three different removal techniques, and to identify predictive factors of successful removal by the standard technique (primary technical success). A total of 137 stents were removed from 128 patients with malignant oesophageal strictures. Primary overall technical success and removal-related complications were evaluated. Logistic regression models were constructed to identify predictive factors of primary technical success. Primary technical success rate was 78.8 % (108/137). Complications occurred in six (4.4 %) cases. Stent location in the upper oesophagus (P=0.004), stricture length over 8 cm (P=0.030), and proximal granulation tissue (P<0.001) were negative predictive factors of primary technical success. If granulation tissue was present at the proximal end, eversion technique was more frequently required (P=0.002). Fluoroscopic removal of retrievable SEMSs for malignant oesophageal strictures using three different removal techniques appeared to be safe and easy. The standard technique is safe and effective in the majority of patients. The presence of proximal granulation tissue, stent location in the upper oesophagus, and stricture length over 8 cm were negative predictive factors for primary technical success by standard extraction and may require a modified removal technique. • Fluoroscopic retrievable SEMS removal is safe and effective. • Standard removal technique by traction is effective in the majority of patients. • Three negative predictive factors of primary technical success were identified. • Caution should be exercised during the removal in those situations. • Eversion technique is effective in cases of proximal granulation tissue.

Computer assisted alignment of opening wedge high tibial osteotomy provides limited improvement of radiographic outcomes compared to flouroscopic alignment.

PubMed

Stanley, Jeremy C; Robinson, Kerian G; Devitt, Brian M; Richmond, Anneka K; Webster, Kate E; Whitehead, Timothy S; Feller, Julian A

2016-03-01

There are numerous methods available to assist surgeons in the accurate correction of varus alignment during medial opening wedge high tibial osteotomy (MOWHTO). Preoperative planning performed with radiographs or more recently intraoperative computer navigation software has been used. The aim of the study was to compare the accuracy of computer navigated versus non-navigated techniques to correct varus alignment of the knee. The preoperative and postoperative radiographs of 117 knees that underwent MOWHTO were investigated to assess radiographic limb alignment 12-months postoperatively. The desired correction was defined as a weight bearing line (Mikulicz point {MP}) 58% of the width of the tibial plateau from the medial tibial margin. Sixty-five knees were corrected using a conventional technique and 52 knees were corrected using computer navigation. The mean MP percentage was 59% in the navigated group, compared with 56% in the fluoroscopic group (p=0.183). 51.9% of the navigation knees were corrected to within five percent of the desired correction, in contrast to 38.5% of the fluoroscopically corrected knees (p=0.15). 71.2% of the navigated knees were corrected to within 10% of the desired correction, compared with 63.1% of the fluoroscopically corrected knees (p=0.36). Large preoperative deformities were more accurately corrected with navigation assistance (57% vs 49%, p=0.049). No statistically significant difference was found in the radiographic correction of varus alignment twelve months postoperatively between navigated and fluoroscopic techniques of MOWHTO. However, a subgroup analysis demonstrated that larger preoperative varus deformities may be more accurately corrected using computer navigation. Copyright © 2016 Elsevier B.V. All rights reserved.

Improved-resolution real-time skin-dose mapping for interventional fluoroscopic procedures

NASA Astrophysics Data System (ADS)

Rana, Vijay K.; Rudin, Stephen; Bednarek, Daniel R.

2014-03-01

We have developed a dose-tracking system (DTS) that provides a real-time display of the skin-dose distribution on a 3D patient graphic during fluoroscopic procedures. Radiation dose to individual points on the skin is calculated using exposure and geometry parameters from the digital bus on a Toshiba C-arm unit. To accurately define the distribution of dose, it is necessary to use a high-resolution patient graphic consisting of a large number of elements. In the original DTS version, the patient graphics were obtained from a library of population body scans which consisted of larger-sized triangular elements resulting in poor congruence between the graphic points and the x-ray beam boundary. To improve the resolution without impacting real-time performance, the number of calculations must be reduced and so we created software-designed human models and modified the DTS to read the graphic as a list of vertices of the triangular elements such that common vertices of adjacent triangles are listed once. Dose is calculated for each vertex point once instead of the number of times that a given vertex appears in multiple triangles. By reformatting the graphic file, we were able to subdivide the triangular elements by a factor of 64 times with an increase in the file size of only 1.3 times. This allows a much greater number of smaller triangular elements and improves resolution of the patient graphic without compromising the real-time performance of the DTS and also gives a smoother graphic display for better visualization of the dose distribution.

Engineering topochemical polymerizations using block copolymer templates.

PubMed

Zhu, Liangliang; Tran, Helen; Beyer, Frederick L; Walck, Scott D; Li, Xin; Agren, Hans; Killops, Kato L; Campos, Luis M

2014-09-24

With the aim to achieve rapid and efficient topochemical polymerizations in the solid state, via solution-based processing of thin films, we report the integration of a diphenyldiacetylene monomer and a poly(styrene-b-acrylic acid) block copolymer template for the generation of supramolecular architectural photopolymerizable materials. This strategy takes advantage of non-covalent interactions to template a topochemical photopolymerization that yields a polydiphenyldiacetylene (PDPDA) derivative. In thin films, it was found that hierarchical self-assembly of the diacetylene monomers by microphase segregation of the block copolymer template enhances the topochemical photopolymerization, which is complete within a 20 s exposure to UV light. Moreover, UV-active cross-linkable groups were incorporated within the block copolymer template to create micropatterns of PDPDA by photolithography, in the same step as the polymerization reaction. The materials design and processing may find potential uses in the microfabrication of sensors and other important areas that benefit from solution-based processing of flexible conjugated materials.

Nacre-like calcium carbonate controlled by ionic liquid/graphene oxide composite template.

PubMed

Yao, Chengli; Xie, Anjian; Shen, Yuhua; Zhu, Jinmiao; Li, Hongying

2015-06-01

Nacre-like calcium carbonate nanostructures have been mediated by an ionic liquid (IL)-graphene oxide (GO) composite template. The resultant crystals were characterized by scanning electron microscopy (SEM), Fourier transform infrared (FT-IR) spectroscopy, and X-ray powder diffractometry (XRD). The results showed that either 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]BF4) or graphene oxide can act as a soft template for calcium carbonate formation with unusual morphologies. Based on the time-dependent morphology changes of calcium carbonate particles, it is concluded that nacre-like calcium carbonate nanostructures can be formed gradually utilizing [BMIM]BF4/GO composite template. During the process of calcium carbonate formation, [BMIM]BF4 acted not only as solvents but also as morphology templates for the fabrication of calcium carbonate materials with nacre-like morphology. Based on the observations, the possible mechanisms were also discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Incorporating User Input in Template-Based Segmentation

PubMed Central

Vidal, Camille; Beggs, Dale; Younes, Laurent; Jain, Sanjay K.; Jedynak, Bruno

2015-01-01

We present a simple and elegant method to incorporate user input in a template-based segmentation method for diseased organs. The user provides a partial segmentation of the organ of interest, which is used to guide the template towards its target. The user also highlights some elements of the background that should be excluded from the final segmentation. We derive by likelihood maximization a registration algorithm from a simple statistical image model in which the user labels are modeled as Bernoulli random variables. The resulting registration algorithm minimizes the sum of square differences between the binary template and the user labels, while preventing the template from shrinking, and penalizing for the inclusion of background elements into the final segmentation. We assess the performance of the proposed algorithm on synthetic images in which the amount of user annotation is controlled. We demonstrate our algorithm on the segmentation of the lungs of Mycobacterium tuberculosis infected mice from μCT images. PMID:26146532

Fast Legendre moment computation for template matching

NASA Astrophysics Data System (ADS)

Li, Bing C.

2017-05-01

Normalized cross correlation (NCC) based template matching is insensitive to intensity changes and it has many applications in image processing, object detection, video tracking and pattern recognition. However, normalized cross correlation implementation is computationally expensive since it involves both correlation computation and normalization implementation. In this paper, we propose Legendre moment approach for fast normalized cross correlation implementation and show that the computational cost of this proposed approach is independent of template mask sizes which is significantly faster than traditional mask size dependent approaches, especially for large mask templates. Legendre polynomials have been widely used in solving Laplace equation in electrodynamics in spherical coordinate systems, and solving Schrodinger equation in quantum mechanics. In this paper, we extend Legendre polynomials from physics to computer vision and pattern recognition fields, and demonstrate that Legendre polynomials can help to reduce the computational cost of NCC based template matching significantly.

SU-G-BRA-05: Application of a Feature-Based Tracking Algorithm to KV X-Ray Fluoroscopic Images Toward Marker-Less Real-Time Tumor Tracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nakamura, M; Matsuo, Y; Mukumoto, N

Purpose: To detect target position on kV X-ray fluoroscopic images using a feature-based tracking algorithm, Accelerated-KAZE (AKAZE), for markerless real-time tumor tracking (RTTT). Methods: Twelve lung cancer patients treated with RTTT on the Vero4DRT (Mitsubishi Heavy Industries, Japan, and Brainlab AG, Feldkirchen, Germany) were enrolled in this study. Respiratory tumor movement was greater than 10 mm. Three to five fiducial markers were implanted around the lung tumor transbronchially for each patient. Before beam delivery, external infrared (IR) markers and the fiducial markers were monitored for 20 to 40 s with the IR camera every 16.7 ms and with an orthogonalmore » kV x-ray imaging subsystem every 80 or 160 ms, respectively. Target positions derived from the fiducial markers were determined on the orthogonal kV x-ray images, which were used as the ground truth in this study. Meanwhile, tracking positions were identified by AKAZE. Among a lot of feature points, AKAZE found high-quality feature points through sequential cross-check and distance-check between two consecutive images. Then, these 2D positional data were converted to the 3D positional data by a transformation matrix with a predefined calibration parameter. Root mean square error (RMSE) was calculated to evaluate the difference between 3D tracking and target positions. A total of 393 frames was analyzed. The experiment was conducted on a personal computer with 16 GB RAM, Intel Core i7-2600, 3.4 GHz processor. Results: Reproducibility of the target position during the same respiratory phase was 0.6 +/− 0.6 mm (range, 0.1–3.3 mm). Mean +/− SD of the RMSEs was 0.3 +/− 0.2 mm (range, 0.0–1.0 mm). Median computation time per frame was 179 msec (range, 154–247 msec). Conclusion: AKAZE successfully and quickly detected the target position on kV X-ray fluoroscopic images. Initial results indicate that the differences between 3D tracking and target position would be clinically acceptable.« less

Correlation-coefficient-based fast template matching through partial elimination.

PubMed

Mahmood, Arif; Khan, Sohaib

2012-04-01

Partial computation elimination techniques are often used for fast template matching. At a particular search location, computations are prematurely terminated as soon as it is found that this location cannot compete with an already known best match location. Due to the nonmonotonic growth pattern of the correlation-based similarity measures, partial computation elimination techniques have been traditionally considered inapplicable to speed up these measures. In this paper, we show that partial elimination techniques may be applied to a correlation coefficient by using a monotonic formulation, and we propose basic-mode and extended-mode partial correlation elimination algorithms for fast template matching. The basic-mode algorithm is more efficient on small template sizes, whereas the extended mode is faster on medium and larger templates. We also propose a strategy to decide which algorithm to use for a given data set. To achieve a high speedup, elimination algorithms require an initial guess of the peak correlation value. We propose two initialization schemes including a coarse-to-fine scheme for larger templates and a two-stage technique for small- and medium-sized templates. Our proposed algorithms are exact, i.e., having exhaustive equivalent accuracy, and are compared with the existing fast techniques using real image data sets on a wide variety of template sizes. While the actual speedups are data dependent, in most cases, our proposed algorithms have been found to be significantly faster than the other algorithms.

Nonenzymatic oligomerization reactions on templates containing inosinic acid or diaminopurine nucleotide residues

NASA Technical Reports Server (NTRS)

Kozlov, I. A.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

The template-directed oligomerization of nucleoside-5'-phosphoro-2-methyl imidazolides on standard oligonucleotide templates has been studied extensively. Here, we describe experiments with templates in which inosinic acid (I) is substituted for guanylic acid, or 2,6-diaminopurine nucleotide (D) for adenylic acid. We find that the substitution of I for G in a template is strongly inhibitory and prevents any incorporation of C into internal positions in the oligomeric products of the reaction. The substitution of D for A, on the contrary, leads to increased incorporation of U into the products. We found no evidence for the template-directed facilitation of oligomerization of A or I through A-I base pairing. The significance of these results for prebiotic chemistry is discussed.

A difference tracking algorithm based on discrete sine transform

NASA Astrophysics Data System (ADS)

Liu, HaoPeng; Yao, Yong; Lei, HeBing; Wu, HaoKun

2018-04-01

Target tracking is an important field of computer vision. The template matching tracking algorithm based on squared difference matching (SSD) and standard correlation coefficient (NCC) matching is very sensitive to the gray change of image. When the brightness or gray change, the tracking algorithm will be affected by high-frequency information. Tracking accuracy is reduced, resulting in loss of tracking target. In this paper, a differential tracking algorithm based on discrete sine transform is proposed to reduce the influence of image gray or brightness change. The algorithm that combines the discrete sine transform and the difference algorithm maps the target image into a image digital sequence. The Kalman filter predicts the target position. Using the Hamming distance determines the degree of similarity between the target and the template. The window closest to the template is determined the target to be tracked. The target to be tracked updates the template. Based on the above achieve target tracking. The algorithm is tested in this paper. Compared with SSD and NCC template matching algorithms, the algorithm tracks target stably when image gray or brightness change. And the tracking speed can meet the read-time requirement.

Template-based modeling and ab initio refinement of protein oligomer structures using GALAXY in CAPRI round 30.

PubMed

Lee, Hasup; Baek, Minkyung; Lee, Gyu Rie; Park, Sangwoo; Seok, Chaok

2017-03-01

Many proteins function as homo- or hetero-oligomers; therefore, attempts to understand and regulate protein functions require knowledge of protein oligomer structures. The number of available experimental protein structures is increasing, and oligomer structures can be predicted using the experimental structures of related proteins as templates. However, template-based models may have errors due to sequence differences between the target and template proteins, which can lead to functional differences. Such structural differences may be predicted by loop modeling of local regions or refinement of the overall structure. In CAPRI (Critical Assessment of PRotein Interactions) round 30, we used recently developed features of the GALAXY protein modeling package, including template-based structure prediction, loop modeling, model refinement, and protein-protein docking to predict protein complex structures from amino acid sequences. Out of the 25 CAPRI targets, medium and acceptable quality models were obtained for 14 and 1 target(s), respectively, for which proper oligomer or monomer templates could be detected. Symmetric interface loop modeling on oligomer model structures successfully improved model quality, while loop modeling on monomer model structures failed. Overall refinement of the predicted oligomer structures consistently improved the model quality, in particular in interface contacts. Proteins 2017; 85:399-407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Exemplary design of a DICOM structured report template for CBIR integration into radiological routine

NASA Astrophysics Data System (ADS)

Welter, Petra; Deserno, Thomas M.; Gülpers, Ralph; Wein, Berthold B.; Grouls, Christoph; Günther, Rolf W.

2010-03-01

The large and continuously growing amount of medical image data demands access methods with regards to content rather than simple text-based queries. The potential benefits of content-based image retrieval (CBIR) systems for computer-aided diagnosis (CAD) are evident and have been approved. Still, CBIR is not a well-established part of daily routine of radiologists. We have already presented a concept of CBIR integration for the radiology workflow in accordance with the Integrating the Healthcare Enterprise (IHE) framework. The retrieval result is composed as a Digital Imaging and Communication in Medicine (DICOM) Structured Reporting (SR) document. The use of DICOM SR provides interchange with PACS archive and image viewer. It offers the possibility of further data mining and automatic interpretation of CBIR results. However, existing standard templates do not address the domain of CBIR. We present a design of a SR template customized for CBIR. Our approach is based on the DICOM standard templates and makes use of the mammography and chest CAD SR templates. Reuse of approved SR sub-trees promises a reliable design which is further adopted to the CBIR domain. We analyze the special CBIR requirements and integrate the new concept of similar images into our template. Our approach also includes the new concept of a set of selected images for defining the processed images for CBIR. A commonly accepted pre-defined template for the presentation and exchange of results in a standardized format promotes the widespread application of CBIR in radiological routine.

Emergency department documentation templates: variability in template selection and association with physical examination and test ordering in dizziness presentations.

PubMed

Kerber, Kevin A; Hofer, Timothy P; Meurer, William J; Fendrick, A Mark; Morgenstern, Lewis B

2011-03-24

Clinical documentation systems, such as templates, have been associated with process utilization. The T-System emergency department (ED) templates are widely used but lacking are analyses of the templates association with processes. This system is also unique because of the many different template options available, and thus the selection of the template may also be important. We aimed to describe the selection of templates in ED dizziness presentations and to investigate the association between items on templates and process utilization. Dizziness visits were captured from a population-based study of EDs that use documentation templates. Two relevant process outcomes were assessed: head computerized tomography (CT) scan and nystagmus examination. Multivariable logistic regression was used to estimate the probability of each outcome for patients who did or did not receive a relevant-item template. Propensity scores were also used to adjust for selection effects. The final cohort was 1,485 visits. Thirty-one different templates were used. Use of a template with a head CT item was associated with an increase in the adjusted probability of head CT utilization from 12.2% (95% CI, 8.9%-16.6%) to 29.3% (95% CI, 26.0%-32.9%). The adjusted probability of documentation of a nystagmus assessment increased from 12.0% (95%CI, 8.8%-16.2%) when a nystagmus-item template was not used to 95.0% (95% CI, 92.8%-96.6%) when a nystagmus-item template was used. The associations remained significant after propensity score adjustments. Providers use many different templates in dizziness presentations. Important differences exist in the various templates and the template that is used likely impacts process utilization, even though selection may be arbitrary. The optimal design and selection of templates may offer a feasible and effective opportunity to improve care delivery.

Iris recognition based on key image feature extraction.

PubMed

Ren, X; Tian, Q; Zhang, J; Wu, S; Zeng, Y

2008-01-01

In iris recognition, feature extraction can be influenced by factors such as illumination and contrast, and thus the features extracted may be unreliable, which can cause a high rate of false results in iris pattern recognition. In order to obtain stable features, an algorithm was proposed in this paper to extract key features of a pattern from multiple images. The proposed algorithm built an iris feature template by extracting key features and performed iris identity enrolment. Simulation results showed that the selected key features have high recognition accuracy on the CASIA Iris Set, where both contrast and illumination variance exist.

CloudStackProjectsNContributions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nielsen, Roy

2017-07-12

Collection of applications and cloud templates. Project currently based on www.packer.io for automation, www.github.com/boxcutter templates and the www.github.com/csd-dev-tools/ClockworkVMs application for wrapping both of the above for easy creation of virtual systems. Will in future also contain cloud templates tuned for various services, applications and purposes.

Transdisciplinary Pedagogical Templates and Their Potential for Adaptive Reuse

ERIC Educational Resources Information Center

Dobozy, Eva; Dalziel, James

2016-01-01

This article explores the use and usefulness of carefully designed transdisciplinary pedagogical templates (TPTs) aligned to different learning theories. The TPTs are based on the Learning Design Framework outlined in the Larnaca Declaration (Dalziel et al. in this collection). The generation of pedagogical plans or templates is not new. However,…

Graphene Emerges as a Versatile Template for Materials Preparation.

PubMed

Li, Zhengjie; Wu, Sida; Lv, Wei; Shao, Jiao-Jing; Kang, Feiyu; Yang, Quan-Hong

2016-05-01

Graphene and its derivatives are emerging as a class of novel but versatile templates for the controlled preparation and functionalization of materials. In this paper a conceptual review on graphene-based templates is given, highlighting their versatile roles in materials preparation. Graphene is capable of acting as a low-dimensional hard template, where its two-dimensional morphology directs the formation of novel nanostructures. Graphene oxide and other functionalized graphenes are amphiphilic and may be seen as soft templates for formatting the growth or inducing the controlled assembly of nanostructures. In addition, nanospaces in restacked graphene can be used for confining the growth of sheet-like nanostructures, and assemblies of interlinked graphenes can behave either as skeletons for the formation of composite materials or as sacrificial templates for novel materials with a controlled network structure. In summary, flexible graphene and its derivatives together with an increasing number of assembled structures show great potentials as templates for materials production. Many challenges remain, for example precise structural control of such novel templates and the removal of the non-functional remaining templates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pacing from the right ventricular septum: is there a danger to the coronary arteries?

PubMed

Teh, Andrew W; Medi, Caroline; Rosso, Raphael; Lee, Geoffrey; Gurvitch, Ronen; Mond, Harry G

2009-07-01

Pacing from right ventricular (RV) septal sites has been suggested as an alternative to RV apical pacing in an attempt to avoid long-term adverse consequences on left ventricular function. Concern has been raised as to the relationship of the left anterior descending coronary artery (LAD) to pacing leads in these positions. We retrospectively analyzed three cases in which patients with RV active-fixation leads in situ also had coronary angiography. Multiple fluoroscopic views were used to determine the relationship of the lead tip at various pacing sites to the coronary arteries. A lead placed on the anterior wall was in close proximity to the LAD, whereas septal and free wall positioning was not. Placement of RV active-fixation leads on the septum avoids potential coronary artery compromise.

Synthesis of polybenzoxazine based nitrogen-rich porous carbons for carbon dioxide capture

NASA Astrophysics Data System (ADS)

Wan, Liu; Wang, Jianlong; Feng, Chong; Sun, Yahui; Li, Kaixi

2015-04-01

Nitrogen-rich porous carbons (NPCs) were synthesized from 1,5-dihydroxynaphthalene, urea, and formaldehyde based on benzoxazine chemistry by a soft-templating method with KOH chemical activation. They possess high surface areas of 856.8-1257.8 m2 g-1, a large pore volume of 0.15-0.65 cm3 g-1, tunable pore structure, high nitrogen content (5.21-5.32 wt%), and high char yields. The amount of the soft-templating agent F127 has multiple influences on the textural and chemical properties of the carbons, affecting the surface area and pore structure, impacting the compositions of nitrogen species and resulting in an improvement of the CO2 capture performance. At 1 bar, high CO2 uptake of 4.02 and 6.35 mmol g-1 at 25 and 0 °C was achieved for the sample NPC-2 with a molar ratio of F127 : urea = 0.010 : 1. This can be attributed to its well-developed micropore structure and abundant pyridinic nitrogen, pyrrolic nitrogen and pyridonic nitrogen functionalities. The sample NPC-2 also exhibits a remarkable selectivity for CO2/N2 separation and a fast adsorption/desorption rate and can be easily regenerated. This suggests that the polybenzoxazine-based NPCs are desirable for CO2 capture because of possessing a high micropore surface area, a large micropore volume, appropriate pore size distribution, and a large number of basic nitrogen functionalities.Nitrogen-rich porous carbons (NPCs) were synthesized from 1,5-dihydroxynaphthalene, urea, and formaldehyde based on benzoxazine chemistry by a soft-templating method with KOH chemical activation. They possess high surface areas of 856.8-1257.8 m2 g-1, a large pore volume of 0.15-0.65 cm3 g-1, tunable pore structure, high nitrogen content (5.21-5.32 wt%), and high char yields. The amount of the soft-templating agent F127 has multiple influences on the textural and chemical properties of the carbons, affecting the surface area and pore structure, impacting the compositions of nitrogen species and resulting in an improvement of the CO2 capture performance. At 1 bar, high CO2 uptake of 4.02 and 6.35 mmol g-1 at 25 and 0 °C was achieved for the sample NPC-2 with a molar ratio of F127 : urea = 0.010 : 1. This can be attributed to its well-developed micropore structure and abundant pyridinic nitrogen, pyrrolic nitrogen and pyridonic nitrogen functionalities. The sample NPC-2 also exhibits a remarkable selectivity for CO2/N2 separation and a fast adsorption/desorption rate and can be easily regenerated. This suggests that the polybenzoxazine-based NPCs are desirable for CO2 capture because of possessing a high micropore surface area, a large micropore volume, appropriate pore size distribution, and a large number of basic nitrogen functionalities. Electronic supplementary information (ESI) available: Elemental and XPS analyses and XPS peak positions and relative content of N species in the NPCs. See DOI: 10.1039/c4nr07409b

Integra-based Reconstruction of Large Scalp Wounds: A Case Report and Systematic Review of the Literature

PubMed Central

Johnson, Maxwell B.

2016-01-01

Background: Large complex scalp wounds that have traditionally required free vascularized tissue transfer have been successfully reconstructed with skin substitutes such as Integra. Although there are multiple reports of Integra-based reconstructions of scalp wounds, there has not been a comprehensive assessment of this body of literature that critically examines this method. Our goal was to conduct a systematic review to determine the effectiveness of Integra-based reconstructions of scalp wounds, with emphasis on large defects. Methods: A comprehensive systematic review was completed using key search terms, including Integra, dermal regeneration template, bovine collagen, skin substitute, forehead, and scalp. Selected articles reported characteristics of patients and their reconstructions. The primary outcome measures were wound complications and percent graft take. Results: Thirty-four articles were included in this systematic review. Wound sizes ranged from 5.7 to 610 cm2, with 35.3% of articles reporting a mean defect size >100 cm2. Thirty-two articles reported mean percent take of skin graft ≥90%. Sixteen articles reported a minor complication. There were no major complications associated with the reconstructions. Conclusions: There is a substantial evidence base for the use of Integra to reconstruct scalp wounds. To date, the dermal regeneration template is generally reserved for salvage procedures or when the patient cannot tolerate free tissue transfer. Based on the findings of this systematic review and the authors’ clinical experience, Integra can be used to achieve predictable results in large complex scalp defects. PMID:27826471

Glenohumeral joint injection: a comparative study of ultrasound and fluoroscopically guided techniques before MR arthrography.

PubMed

Rutten, Matthieu J C M; Collins, James M P; Maresch, Bas J; Smeets, Jacques H J M; Janssen, Caroline M M; Kiemeney, Lambertus A L M; Jager, Gerrit J

2009-03-01

To assess the variability in accuracy of contrast media introduction, leakage, required time and patient discomfort in four different centres, each using a different image-guided glenohumeral injection technique. Each centre included 25 consecutive patients. The ultrasound-guided anterior (USa) and posterior approach (USp), fluoroscopic-guided anterior (FLa) and posterior (FLp) approach were used. Number of injection attempts, effect of contrast leakage on diagnostic quality, and total room, radiologist and procedure times were measured. Pain was documented with a visual analogue scale (VAS) pain score. Access to the joint was achieved in all patients. A successful first attempt significantly occurred more often with US (94%) than with fluoroscopic guidance (72%). Leakage of contrast medium did not cause interpretative difficulties. With US guidance mean room, procedure and radiologist times were significantly shorter (p < 0.001). The USa approach was rated with the lowest pre- and post-injection VAS scores. The four image-guided injection techniques are successful in injection of contrast material into the glenohumeral joint. US-guided injections and especially the anterior approach are significantly less time consuming, more successful on the first attempt, cause less patient discomfort and obviate the need for radiation and iodine contrast.

Fluoroscopically guided large balloon dilatation for treating congenital esophageal stenosis in children.

PubMed

Hu, Hong-Tao; Shin, Ji Hoon; Kim, Jin-Hyoung; Jang, Jong Keon; Park, Jung-Hoon; Kim, Tae-Hyung; Nam, Deok Ho; Song, Ho-Young

2015-07-01

We aimed to evaluate the safety and clinical effectiveness of fluoroscopically guided large balloon dilatation for treating congenital esophageal stenosis in children. Our study included seven children (mean age 4.0 years) who underwent a total of ten balloon dilatation sessions. The initial balloon diameters were 10-15 mm. The technical success, clinical success (improved food intake and reduced dysphagia within 1 month following the first balloon dilatation), dysphagia recurrence, and complications were retrospectively evaluated. Technical and clinical success rates were 100 %. During the mean 38-month follow-up period after the first balloon dilatation, 3 (43 %) patients underwent only one additional balloon dilatation 4-5 months after the first balloon dilatation for dysphagia recurrence. Two of them showed improvement without further recurrence, while the remaining one underwent partial esophagectomy. Well-contained transmural esophageal rupture (type 2) occurred in two (29 %, 2/7) patients and during two (20 %, 2/10) balloon dilatation sessions. All ruptures were successfully treated conservatively. Our study showed that fluoroscopically guided large balloon dilatation seems to be a simple and effective primary treatment technique for congenital esophageal stenosis in children. Esophageal ruptures were not uncommon although they were not fatal.

Comparison of Fluoroscopy and Computed Tomography for Tracheal Lumen Diameter Measurement and Determination of Intraluminal Stent Size in Healthy Dogs

PubMed Central

Williams, Jackie M.; Krebs, Ingar A.; Riedesel, Elizabeth A.; Zhao, Qianqian

2015-01-01

Tracheal collapse is a progressive airway disease that can ultimately result in complete airway obstruction. Intraluminal tracheal stents are a minimally invasive and viable treatment for tracheal collapse once the disease becomes refractory to medical management. Intraluminal stent size is chosen based on the maximum measured tracheal diameter during maximum inflation. The purpose of this prospective, cross-sectional study was to compare tracheal lumen diameter measurements and subsequent selected stent size using both fluoroscopy and CT and to evaluate inter- and intraobserver variability of the measurements. Seventeen healthy Beagles were anesthetized and imaged with fluoroscopy and CT with positive pressure ventilation to 20 cm H2O. Fluoroscopic and CT maximum tracheal diameters were measured by 3 readers. Three individual measurements were made at 8 pre-determined tracheal sites for dorsoventral (height) and laterolateral (width) dimensions. Tracheal diameters and stent sizes (based on the maximum tracheal diameter + 10%) were analyzed using a linear mixed model. CT tracheal lumen diameters were larger compared to fluoroscopy at all locations. When comparing modalities, fluoroscopic and CT stent sizes were statistically different. Greater overall variation in tracheal diameter measurement (height or width) existed for fluoroscopy compared to CT, both within and among observers. The greater tracheal diameter and lower measurement variability supported the use of CT for appropriate stent selection to minimize complications in veterinary patients. PMID:26784924

Template-based protein-protein docking exploiting pairwise interfacial residue restraints.

PubMed

Xue, Li C; Rodrigues, João P G L M; Dobbs, Drena; Honavar, Vasant; Bonvin, Alexandre M J J

2017-05-01

Although many advanced and sophisticated ab initio approaches for modeling protein-protein complexes have been proposed in past decades, template-based modeling (TBM) remains the most accurate and widely used approach, given a reliable template is available. However, there are many different ways to exploit template information in the modeling process. Here, we systematically evaluate and benchmark a TBM method that uses conserved interfacial residue pairs as docking distance restraints [referred to as alpha carbon-alpha carbon (CA-CA)-guided docking]. We compare it with two other template-based protein-protein modeling approaches, including a conserved non-pairwise interfacial residue restrained docking approach [referred to as the ambiguous interaction restraint (AIR)-guided docking] and a simple superposition-based modeling approach. Our results show that, for most cases, the CA-CA-guided docking method outperforms both superposition with refinement and the AIR-guided docking method. We emphasize the superiority of the CA-CA-guided docking on cases with medium to large conformational changes, and interactions mediated through loops, tails or disordered regions. Our results also underscore the importance of a proper refinement of superimposition models to reduce steric clashes. In summary, we provide a benchmarked TBM protocol that uses conserved pairwise interface distance as restraints in generating realistic 3D protein-protein interaction models, when reliable templates are available. The described CA-CA-guided docking protocol is based on the HADDOCK platform, which allows users to incorporate additional prior knowledge of the target system to further improve the quality of the resulting models. © The Author 2016. Published by Oxford University Press.

A retrospective analysis of early and late outcome of biodegradable stent placement in the management of refractory anastomotic colorectal strictures.

PubMed

Repici, A; Pagano, N; Rando, G; Carlino, A; Vitetta, E; Ferrara, E; Strangio, G; Zullo, A; Hassan, C

2013-07-01

Benign colorectal strictures are treated conventionally by endoscopic dilation. Experience using SEMS for benign colonic strictures is limited, and outcomes to date have been disappointing. Refractory colorectal strictures remain challenging to be treated with surgery. Polydioxanone-based stent are biodegradable (BD) stent CE approved for esophageal strictures. This study was designed to investigate retrospectively the safety and the efficacy of these stents for the management of strictures refractory to multiple sessions of dilation. Patients with postsurgical benign strictures located within 20 cm from anal verge, refractory to mechanical or pneumatic dilation (at least 3 sessions) were included in this analysis. Clinical success was defined as the absence of occlusive symptoms and the ability to pass through the stricture with a regular size colonoscope. All patients were predilated before stent placement. Stents were released under fluoroscopic control. All patients were under stool softeners for 3 months. Follow-up was scheduled with endoscopic and fluoroscopic controls within 90 days from stent deployment and afterwards by telephone interview and/or ambulatory consultation. Eleven patients (7 males, mean age 62.3 ± 8.5 years) were included. Technical success was achieved in all the patients. Stent migration was observed in four patients within the first 2 weeks after stent placement. Stent migration was followed by recurrence of stricture and obstructive symptoms in all the cases. Among the seven patients who completed the process of stent biodegradation, five of them had complete resolution of the stricture and relief of symptoms. Two of 11 patients required surgical treatment during the follow-up period (mean 19.8 (range 42-15) months). The overall success rate of the BD stent was 45 %. This retrospective analysis of a limited number of patients demonstrated that nondedicated esophageal BD stents are associated with high risk of migration and clinical success in less than 50 % of patients. Dedicated stents with large diameter and antimigration findings could potentially improve the outcome of patients with refractory benign colorectal strictures.

Fabrication of Defined Polydopamine Nanostructures by DNA Origami-Templated Polymerization.

PubMed

Tokura, Yu; Harvey, Sean; Chen, Chaojian; Wu, Yuzhou; Ng, David Y W; Weil, Tanja

2018-02-05

A versatile, bottom-up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage-mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase-mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as "supramolecular glue" for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami-controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Variance in predicted cup size by 2-dimensional vs 3-dimensional computerized tomography-based templating in primary total hip arthroplasty.

PubMed

Osmani, Feroz A; Thakkar, Savyasachi; Ramme, Austin; Elbuluk, Ameer; Wojack, Paul; Vigdorchik, Jonathan M

2017-12-01

Preoperative total hip arthroplasty templating can be performed with radiographs using acetate prints, digital viewing software, or with computed tomography (CT) images. Our hypothesis is that 3D templating is more precise and accurate with cup size prediction as compared to 2D templating with acetate prints and digital templating software. Data collected from 45 patients undergoing robotic-assisted total hip arthroplasty compared cup sizes templated on acetate prints and OrthoView software to MAKOplasty software that uses CT scan. Kappa analysis determined strength of agreement between each templating modality and the final size used. t tests compared mean cup-size variance from the final size for each templating technique. Interclass correlation coefficient (ICC) determined reliability of digital and acetate planning by comparing predictions of the operating surgeon and a blinded adult reconstructive fellow. The Kappa values for CT-guided, digital, and acetate templating with the final size was 0.974, 0.233, and 0.262, respectively. Both digital and acetate templating significantly overpredicted cup size, compared to CT-guided methods ( P < .001). There was no significant difference between digital and acetate templating ( P  = .117). Interclass correlation coefficient value for digital and acetate templating was 0.928 and 0.931, respectively. CT-guided planning more accurately predicts hip implant cup size when compared to the significant overpredictions of digital and acetate templating. CT-guided templating may also lead to better outcomes due to bone stock preservation from a smaller and more accurate cup size predicted than that of digital and acetate predictions.

Estimating B1+ in the breast at 7 T using a generic template.

PubMed

van Rijssel, Michael J; Pluim, Josien P W; Luijten, Peter R; Gilhuijs, Kenneth G A; Raaijmakers, Alexander J E; Klomp, Dennis W J

2018-05-01

Dynamic contrast-enhanced MRI is the workhorse of breast MRI, where the diagnosis of lesions is largely based on the enhancement curve shape. However, this curve shape is biased by RF transmit (B 1 + ) field inhomogeneities. B 1 + field information is required in order to correct these. The use of a generic, coil-specific B 1 + template is proposed and tested. Finite-difference time-domain simulations for B 1 + were performed for healthy female volunteers with a wide range of breast anatomies. A generic B 1 + template was constructed by averaging simulations based on four volunteers. Three-dimensional B 1 + maps were acquired in 15 other volunteers. Root mean square error (RMSE) metrics were calculated between individual simulations and the template, and between individual measurements and the template. The agreement between the proposed template approach and a B 1 + mapping method was compared against the agreement between acquisition and reacquisition using the same mapping protocol. RMSE values (% of nominal flip angle) comparing individual simulations with the template were in the range 2.00-4.01%, with mean 2.68%. RMSE values comparing individual measurements with the template were in the range8.1-16%, with mean 11.7%. The agreement between the proposed template approach and a B 1 + mapping method was only slightly worse than the agreement between two consecutive acquisitions using the same mapping protocol in one volunteer: the range of agreement increased from ±16% of the nominal angle for repeated measurement to ±22% for the B 1 + template. With local RF transmit coils, intersubject differences in B 1 + fields of the breast are comparable to the accuracy of B 1 + mapping methods, even at 7 T. Consequently, a single generic B 1 + template suits subjects over a wide range of breast anatomies, eliminating the need for a time-consuming B 1 + mapping protocol. © 2018 The Authors. NMR in Biomedicine published by John Wiley & Sons Ltd.

Estimating B 1 + in the breast at 7 T using a generic template

PubMed Central

Pluim, Josien P. W.; Luijten, Peter R.; Gilhuijs, Kenneth G. A.; Raaijmakers, Alexander J. E.; Klomp, Dennis W. J.

2018-01-01

Dynamic contrast‐enhanced MRI is the workhorse of breast MRI, where the diagnosis of lesions is largely based on the enhancement curve shape. However, this curve shape is biased by RF transmit (B 1 +) field inhomogeneities. B 1 + field information is required in order to correct these. The use of a generic, coil‐specific B 1 + template is proposed and tested. Finite‐difference time‐domain simulations for B 1 + were performed for healthy female volunteers with a wide range of breast anatomies. A generic B 1 + template was constructed by averaging simulations based on four volunteers. Three‐dimensional B 1 + maps were acquired in 15 other volunteers. Root mean square error (RMSE) metrics were calculated between individual simulations and the template, and between individual measurements and the template. The agreement between the proposed template approach and a B 1 + mapping method was compared against the agreement between acquisition and reacquisition using the same mapping protocol. RMSE values (% of nominal flip angle) comparing individual simulations with the template were in the range 2.00‐4.01%, with mean 2.68%. RMSE values comparing individual measurements with the template were in the range8.1‐16%, with mean 11.7%. The agreement between the proposed template approach and a B 1 + mapping method was only slightly worse than the agreement between two consecutive acquisitions using the same mapping protocol in one volunteer: the range of agreement increased from ±16% of the nominal angle for repeated measurement to ±22% for the B 1 + template. With local RF transmit coils, intersubject differences in B 1 + fields of the breast are comparable to the accuracy of B 1 + mapping methods, even at 7 T. Consequently, a single generic B 1 + template suits subjects over a wide range of breast anatomies, eliminating the need for a time‐consuming B 1 + mapping protocol. PMID:29570887

Image Guidance Technologies for Interventional Pain Procedures: Ultrasound, Fluoroscopy, and CT.

PubMed

Wang, Dajie

2018-01-26

Chronic pain is a common medical condition. Patients who suffer uncontrolled chronic pain may require interventions including spinal injections and various nerve blocks. Interventional procedures have evolved and improved over time since epidural injection was first introduced for low back pain and sciatica in 1901. One of the major contributors in the improvement of these interventions is the advancement of imaging guidance technologies. The utilization of image guidance has dramatically improved the accuracy and safety of these interventions. The first image guidance technology adopted by pain specialists was fluoroscopy. This was followed by CT and ultrasound. Fluoroscopy can be used to visualize bony structures of the spine. It is still the most commonly used guidance technology in spinal injections. In the recent years, ultrasound guidance has been increasingly adopted by interventionists to perform various injections. Because its ability to visualize soft tissue, vessels, and nerves, this guidance technology appears to be a better option than fluoroscopy for interventions including SGB and celiac plexus blocks, when visualization of the vessels may prevent intravascular injection. The current evidence indicates the efficacies of these interventions are similar between ultrasound guidance and fluoroscopy guidance for SGB and celiac plexus blocks. For facet injections and interlaminar epidural steroid injections, it is important to visualize bony structures in order to perform these procedures accurately and safely. It is worth noting that facet joint injections can be done under ultrasound guidance with equivalent efficacy to fluoroscopic guidance. However, obese patients may present challenge for ultrasound guidance due to its poor visualization of deep anatomical structures. Regarding transforaminal epidural steroid injections, there are limited evidence to support that ultrasound guidance technology has equivalent efficacy and less complications comparing to fluoroscopy. However, further studies are required to prove the efficacy of ultrasound-guided transforaminal epidural injections. SI joint is unique due to its multiplanar orientation, irregular joint gap, partial ankylosis, and thick dorsal and interosseous ligament. Therefore, it can be difficult to access the joint space with fluoroscopic guidance and ultrasound guidance. CT scan, with its cross-sectional images, can identify posterior joint gap, is most likely the best guidance technology for this intervention. Intercostal nerves lie in the subcostal grove close to the plural space. Significant risk of pneumothorax is associated with intercostal blocks. Ultrasound can provide visualization of ribs and pleura. Therefore, it may improve the accuracy of the injection and reduce the risk of pneumothorax. At present time, most pain specialists are familiar with fluoroscopic guidance techniques, and fluoroscopic machines are readily available in the pain clinics. In the contrast, CT guidance can only be performed in specially equipped facilities. Ultrasound machine is generally portable and inexpensive in comparison to CT scanner and fluoroscopic machine. As pain specialists continue to improve their patient care, ultrasound and CT guidance will undoubtedly be incorporated more into the pain management practice. This review is based on a paucity of clinical evidence to compare these guidance technologies; clearly, more clinical studies is needed to further elucidate the pro and cons of each guidance method for various pain management interventions.

Guidelines for conducting pharmaceutical budget impact analyses for submission to public drug plans in Canada.

PubMed

Marshall, Deborah A; Douglas, Patrick R; Drummond, Michael F; Torrance, George W; Macleod, Stuart; Manti, Orlando; Cheruvu, Lokanadha; Corvari, Ron

2008-01-01

Until now, there has been no standardized method of performing and presenting budget impact analyses (BIAs) in Canada. Nevertheless, most drug plan managers have been requiring this economic data to inform drug reimbursement decisions. This paper describes the process used to develop the Canadian BIA Guidelines; describes the Guidelines themselves, including the model template; and compares this guidance with other guidance on BIAs. The intended audience includes those who develop, submit or use BIA models, and drug plan managers who evaluate BIA submissions. The Patented Medicine Prices Review Board (PMPRB) initiated the development of the Canadian BIA Guidelines on behalf of the National Prescription Drug Utilisation Information System (NPDUIS). The findings and recommendations from a needs assessment with respect to BIA submissions were reviewed to inform guideline development. In addition, a literature review was performed to identify existing BIA guidance. The detailed guidance was developed on this basis, and with the input of the NPDUIS Advisory Committee, including drug plan managers from multiple provinces in Canada and a representative from the Canadian Agency for Drugs and Technologies in Health. A Microsoft Excel-based interactive model template was designed to support BIA model development. Input regarding the guidelines and model template was sought from each NPDUIS Advisory Committee member to ensure compatibility with existing drug plan needs. Decisions were made by consensus through multiple rounds of review and discussion. Finally, BIA guidance in Canadian provinces and other countries were compared on the basis of multiple criteria. The BIA guidelines consist of three major sections: Analytic Framework, Inputs and Data Sources, and Reporting Format. The Analytic Framework section contains a discussion of nine general issues surrounding BIAs (model design, analytic perspective, time horizon, target population, costing, scenarios to be compared, the characterisation of uncertainty, discounting, and validation methods). The Inputs and Data Sources section addresses methods for market size estimation, comparator selection, scenario forecasting and drug price estimation. The Reporting Format section describes methods for BIA reporting. The new Canadian BIA Guidelines represent a significant departure from the limited guidance that was previously available from some of the provinces, because they include specific details of the methods of performing BIAs. The Canadian BIA Guidelines differ from the Principles of Good Research Practice for BIAs developed by the International Society for Pharmacoeconomic and Outcomes Research (ISPOR), which provide more general guidance. The Canadian BIA Guidelines and template build upon existing guidance to address the specific requirements of each of the participating drug plans in Canada. Both have been endorsed by the NPDUIS Steering Committee and the PMPRB for the standardization of BIA submissions.

The value of physical examination in the diagnosis of hip osteoarthritis.

PubMed

Chong, Timothy; Don, Darren W; Kao, Ming-Chih; Wong, Dexter; Mitra, Raj

2013-01-01

To compare the sensitivity of physical examination (internal rotation of the hip) with radiographs (using the Kellgren-Lawrence grading scale) in the diagnosis of clinically significant hip osteoarthritis. Case Series, Retrospective chart review of hip pain patients that underwent fluoroscopically guided hip steroid and anesthetic injections. 10 patients with hip pain patients seen at an academic outpatient center over a 2 year period were analyzed. Fluoroscopically guided hip steroid and anesthetic injection. Pain relief and change in VAS pain score after intra-articular hip steroid and lidocaine injection was the main outcome measure. Based on Fisher's exact test, there was no association between severity of radiographic hip arthritis and pain relief with intra-articular anesthetic/steroid injection (p=0.45). Physical examination (provocative hip internal rotation) however was associated with a significant decrease in VAS pain score after intra-articular lidocaine and corticosteroid hip injection (p=0.022). Simple hip radiographs alone are not sufficient to diagnose clinically significant hip osteoarthritis. Physical examination (hip internal rotation) was found to be more accurate than simple radiographs in the diagnosis of clinically significant hip osteoarthritis. Radiographs seem to best utilized when they are an extension of the physical examination and patient history.

Patterning nanofibrils through the templated growth of multiple modified amyloid peptides

PubMed Central

Sakai, Hiroki; Watanabe, Ken; Kudoh, Fuki; Kamada, Rui; Chuman, Yoshiro; Sakaguchi, Kazuyasu

2016-01-01

There has been considerable interest in the patterning of functionalized nanowires because of the potential applications of these materials to the construction of nanodevices. A variety of biomolecular building blocks containing amyloid peptides have been used to functionalize nanowires. However, the patterning of self-assembled nanowires can be challenging because of the difficulties associated with controlling the self-assembly of these functionalized building blocks. Herein, we present a versatile approach for the patterning of nanowires based on the combination of templated fibril growth with a versatile functionalization method using our structure-controllable amyloid peptides (SCAPs). Using this approach, we have succeeded in the formation of multi-type nanowires with tandem domain structures in high yields. Given that the mixing-SCAP method can lead to the formation of tandem fibrils, it is noteworthy that our method allowed us to control the initiation of fibril formation from the gold nanoparticles, which were attached to a short fibril as initiation points. This approach could be used to prepare a wide variety of fibril patterns, and therefore holds great potential for the development of novel self-assembled nanodevices. PMID:27559011

Ultrasensitive detection of nucleic acids and proteins using quartz crystal microbalance and surface plasmon resonance sensors based on target-triggering multiple signal amplification strategy.

PubMed

Sun, Wenbo; Song, Weiling; Guo, Xiaoyan; Wang, Zonghua

2017-07-25

In this study, quartz crystal microbalance (QCM) and surface plasmon resonance (SPR) sensors were combined with template enhanced hybridization processes (TEHP), rolling circle amplification (RCA) and biocatalytic precipitation (BCP) for ultrasensitive detection of DNA and protein. The DNA complementary to the aptamer was released by the specific binding of the aptamer to the target protein and then hybridized with the capture probe and the assistant DNA to form a ternary "Y" junction structure. The initiation chain was generated by the template-enhanced hybridization process which leaded to the rolling circle amplification reaction, and a large number of repeating unit sequences were formed. Hybridized with the enzyme-labeled probes, the biocatalytic precipitation reaction was further carried out, resulting in a large amount of insoluble precipitates and amplifying the detection signal. Under the optimum conditions, detection limits as low as 43 aM for target DNA and 53 aM for lysozyme were achieved. In addition, this method also showed good selectivity and sensitivity in human serum. Copyright © 2017 Elsevier B.V. All rights reserved.

Warping an atlas derived from serial histology to 5 high-resolution MRIs.

PubMed

Tullo, Stephanie; Devenyi, Gabriel A; Patel, Raihaan; Park, Min Tae M; Collins, D Louis; Chakravarty, M Mallar

2018-06-19

Previous work from our group demonstrated the use of multiple input atlases to a modified multi-atlas framework (MAGeT-Brain) to improve subject-based segmentation accuracy. Currently, segmentation of the striatum, globus pallidus and thalamus are generated from a single high-resolution and -contrast MRI atlas derived from annotated serial histological sections. Here, we warp this atlas to five high-resolution MRI templates to create five de novo atlases. The overall goal of this work is to use these newly warped atlases as input to MAGeT-Brain in an effort to consolidate and improve the workflow presented in previous manuscripts from our group, allowing for simultaneous multi-structure segmentation. The work presented details the methodology used for the creation of the atlases using a technique previously proposed, where atlas labels are modified to mimic the intensity and contrast profile of MRI to facilitate atlas-to-template nonlinear transformation estimation. Dice's Kappa metric was used to demonstrate high quality registration and segmentation accuracy of the atlases. The final atlases are available at https://github.com/CobraLab/atlases/tree/master/5-atlas-subcortical.

Evaluation of the UF/NCI hybrid computational phantoms for use in organ dosimetry of pediatric patients undergoing fluoroscopically guided cardiac procedures

NASA Astrophysics Data System (ADS)

Marshall, Emily L.; Borrego, David; Tran, Trung; Fudge, James C.; Bolch, Wesley E.

2018-03-01

Epidemiologic data demonstrate that pediatric patients face a higher relative risk of radiation induced cancers than their adult counterparts at equivalent exposures. Infants and children with congenital heart defects are a critical patient population exposed to ionizing radiation during life-saving procedures. These patients will likely incur numerous procedures throughout their lifespan, each time increasing their cumulative radiation absorbed dose. As continued improvements in long-term prognosis of congenital heart defect patients is achieved, a better understanding of organ radiation dose following treatment becomes increasingly vital. Dosimetry of these patients can be accomplished using Monte Carlo radiation transport simulations, coupled with modern anatomical patient models. The aim of this study was to evaluate the performance of the University of Florida/National Cancer Institute (UF/NCI) pediatric hybrid computational phantom library for organ dose assessment of patients that have undergone fluoroscopically guided cardiac catheterizations. In this study, two types of simulations were modeled. A dose assessment was performed on 29 patient-specific voxel phantoms (taken as representing the patient’s true anatomy), height/weight-matched hybrid library phantoms, and age-matched reference phantoms. Two exposure studies were conducted for each phantom type. First, a parametric study was constructed by the attending pediatric interventional cardiologist at the University of Florida to model the range of parameters seen clinically. Second, four clinical cardiac procedures were simulated based upon internal logfiles captured by a Toshiba Infinix-i Cardiac Bi-Plane fluoroscopic unit. Performance of the phantom library was quantified by computing both the percent difference in individual organ doses, as well as the organ dose root mean square values for overall phantom assessment between the matched phantoms (UF/NCI library or reference) and the patient-specific phantoms. The UF/NCI hybrid phantoms performed at percent differences of between 15% and 30% for the parametric set of irradiation events. Among internal logfile reconstructed procedures, the UF/NCI hybrid phantoms performed with RMS organ dose values between 7% and 29%. Percent improvement in organ dosimetry via the use of hybrid library phantoms over the reference phantoms ranged from 6.6% to 93%. The use of a hybrid phantom library, Monte Carlo radiation transport methods, and clinical information on irradiation events provide a means for tracking organ dose in these radiosensitive patients undergoing fluoroscopically guided cardiac procedures. This work was supported by Advanced Laboratory for Radiation Dosimetry Studies, University of Florida, American Association of University Women, National Cancer Institute Grant 1F31 CA159464.

A visual tracking method based on improved online multiple instance learning

NASA Astrophysics Data System (ADS)

He, Xianhui; Wei, Yuxing

2016-09-01

Visual tracking is an active research topic in the field of computer vision and has been well studied in the last decades. The method based on multiple instance learning (MIL) was recently introduced into the tracking task, which can solve the problem that template drift well. However, MIL method has relatively poor performance in running efficiency and accuracy, due to its strong classifiers updating strategy is complicated, and the speed of the classifiers update is not always same with the change of the targets' appearance. In this paper, we present a novel online effective MIL (EMIL) tracker. A new update strategy for strong classifier was proposed to improve the running efficiency of MIL method. In addition, to improve the t racking accuracy and stability of the MIL method, a new dynamic mechanism for learning rate renewal of the classifier and variable search window were proposed. Experimental results show that our method performs good performance under the complex scenes, with strong stability and high efficiency.

Development and validation of a 48-target analytical method for high-throughput monitoring of genetically modified organisms.

PubMed

Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

2015-01-05

The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection.

Development and Validation of A 48-Target Analytical Method for High-throughput Monitoring of Genetically Modified Organisms

PubMed Central

Li, Xiaofei; Wu, Yuhua; Li, Jun; Li, Yunjing; Long, Likun; Li, Feiwu; Wu, Gang

2015-01-01

The rapid increase in the number of genetically modified (GM) varieties has led to a demand for high-throughput methods to detect genetically modified organisms (GMOs). We describe a new dynamic array-based high throughput method to simultaneously detect 48 targets in 48 samples on a Fludigm system. The test targets included species-specific genes, common screening elements, most of the Chinese-approved GM events, and several unapproved events. The 48 TaqMan assays successfully amplified products from both single-event samples and complex samples with a GMO DNA amount of 0.05 ng, and displayed high specificity. To improve the sensitivity of detection, a preamplification step for 48 pooled targets was added to enrich the amount of template before performing dynamic chip assays. This dynamic chip-based method allowed the synchronous high-throughput detection of multiple targets in multiple samples. Thus, it represents an efficient, qualitative method for GMO multi-detection. PMID:25556930

Enhanced ICBM Diffusion Tensor Template of the Human Brain

PubMed Central

Zhang, Shengwei; Peng, Huiling; Dawe, Robert J.; Arfanakis, Konstantinos

2010-01-01

Development of a diffusion tensor (DT) template that is representative of the micro-architecture of the human brain is crucial for comparisons of neuronal structural integrity and brain connectivity across populations, as well as for the generation of a detailed white matter atlas. Furthermore, a DT template in ICBM space may simplify consolidation of information from DT, anatomical and functional MRI studies. The previously developed “IIT DT brain template” was produced in ICBM-152 space, based on a large number of subjects from a limited age-range, using data with minimal image artifacts, and non-linear registration. That template was characterized by higher image sharpness, provided the ability to distinguish smaller white matter fiber structures, and contained fewer image artifacts, than several previously published DT templates. However, low-dimensional registration was used in the development of that template, which led to a mismatch of DT information across subjects, eventually manifested as loss of local diffusion information and errors in the final tensors. Also, low-dimensional registration led to a mismatch of the anatomy in the IIT and ICBM-152 templates. In this work, a significantly improved DT brain template in ICBM-152 space was developed, using high-dimensional non-linear registration and the raw data collected for the purposes of the IIT template. The accuracy of inter-subject DT matching was significantly increased compared to that achieved for the development of the IIT template. Consequently, the new template contained DT information that was more representative of single-subject human brain data, and was characterized by higher image sharpness than the IIT template. Furthermore, a bootstrap approach demonstrated that the variance of tensor characteristics was lower in the new template. Additionally, compared to the IIT template, brain anatomy in the new template more accurately matched ICBM-152 space. Finally, spatial normalization of a number of DT datasets through registration to the new and existing IIT templates was improved when using the new template. PMID:20851772

Development of a rapid, sensitive and specific diagnostic assay for fish Aquareovirus based on RT-PCR.

PubMed

Seng, E K; Fang, Q; Lam, T J; Sin, Y M

2004-06-15

A rapid, sensitive and highly specific detection method for Aquareovirus based on reverse-transcription polymerase chain reaction (RT-PCR) was developed. Based on multiple sequence alignment of the cloned sequences of a local isolates, the Threadfin reovirus (TFV) and Guppy reovirus (GPV) with Grass carp reovirus (GCRV), a pair of degenerate primers was selected carefully and synthesized. Using this primer combination, only one specific product, approximately 450 bp in length was obtained when RT-PCR was carried out using the genomic double-stranded RNA (dsRNA) of TFV, GPV and GCRV. Similar results were also obtained when Chum salmon reovirus (CSRV) and Striped bass reovirus (SBRV) dsRNA were used as templates. No products were observed when nucleic acids other than the dsRNA of the aquareoviruses described above were used as RT-PCR templates. This technique could detect not only TFV but also GPV and GCRV in low titer virus-infected cell cultured cells. Furthermore, this method has also been shown to be able to diagnose GPV-infected guppy (Poecilia reticulata) that exhibit clinical symptoms as well as GPV-carrier guppy. Collectively, these results showed that the RT-PCR amplification method using specific degenerate primers described below is very useful for rapid and accurate detection of a variety of aquareovirus strains isolated from different host species and origin.

Mechanism of chimera formation during the Multiple Displacement Amplification reaction.

PubMed

Lasken, Roger S; Stockwell, Timothy B

2007-04-12

Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2-21 nucleotides (nts) in the new templates. Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications.

Layer-by-layer hollow photosensitizer microcapsule design via a manganese carbonate hard template for photodynamic therapy in cells.

PubMed

Simioni, Andreza Ribeiro; de Jesus, Priscila Costa Carvalho; Tedesco, Antonio Claudio

2018-06-01

Microcapsules fabricated using layer-by-layer self-assembly have unique properties, making them attractive for drug delivery applications. The technique has been improved, allowing the deposition of multiple layers of oppositely charged polyelectrolytes on spherical, colloidal templates. These templates can be decomposed by coating multiple layers, resulting in hollow shells. In this paper, we describe a novel drug delivery system for loading photosensitizer drugs into hollow multilayered microcapsules for photoprocess applications. Manganese carbonate particles were prepared by mixing NH 4 HCO 3 and MnSO 4 and performing consecutive polyelectrolyte adsorption processes onto these templates using poly-(sodium 4-styrene sulfonate) and poly-(allylamine hydrocholoride). A photosensitizer was also incorporated into the layers. Hollow spheres were fabricated by removing the cores in the acidic solution. The hollow, multilayered microcapsules were studied by scanning electron microscopy, steady-state, and time-resolved techniques. Their biological activity was evaluated in vitro with cancer cells using a conventional MTT assay. The synthesized CaCO 3 microparticles were uniform, non-aggregated, and highly porous spheres. The phthalocyanine derivatives loaded in the microcapsules maintained their photophysical behaviour after encapsulation. The spectroscopic results presented here showed excellent photophysical behaviour of the studied drug. We observed a desirable increase in singlet oxygen production, which is favourable for the PDT protocol. Cell viability after treatment was determined and the proposed microcapsules caused 80% cell death compared to the control. The results demonstrate that photosensitizer adsorption into the CaCO 3 microparticle voids together with the layer-by-layer assembly of biopolymers provide a method for the fabrication of biocompatible microcapsules for use as biomaterials. Copyright © 2018 Elsevier B.V. All rights reserved.

Mechanism of chimera formation during the Multiple Displacement Amplification reaction

PubMed Central

Lasken, Roger S; Stockwell, Timothy B

2007-01-01

Background Multiple Displacement Amplification (MDA) is a method used for amplifying limiting DNA sources. The high molecular weight amplified DNA is ideal for DNA library construction. While this has enabled genomic sequencing from one or a few cells of unculturable microorganisms, the process is complicated by the tendency of MDA to generate chimeric DNA rearrangements in the amplified DNA. Determining the source of the DNA rearrangements would be an important step towards reducing or eliminating them. Results Here, we characterize the major types of chimeras formed by carrying out an MDA whole genome amplification from a single E. coli cell and sequencing by the 454 Life Sciences method. Analysis of 475 chimeras revealed the predominant reaction mechanisms that create the DNA rearrangements. The highly branched DNA synthesized in MDA can assume many alternative secondary structures. DNA strands extended on an initial template can be displaced becoming available to prime on a second template creating the chimeras. Evidence supports a model in which branch migration can displace 3'-ends freeing them to prime on the new templates. More than 85% of the resulting DNA rearrangements were inverted sequences with intervening deletions that the model predicts. Intramolecular rearrangements were favored, with displaced 3'-ends reannealing to single stranded 5'-strands contained within the same branched DNA molecule. In over 70% of the chimeric junctions, the 3' termini had initiated priming at complimentary sequences of 2–21 nucleotides (nts) in the new templates. Conclusion Formation of chimeras is an important limitation to the MDA method, particularly for whole genome sequencing. Identification of the mechanism for chimera formation provides new insight into the MDA reaction and suggests methods to reduce chimeras. The 454 sequencing approach used here will provide a rapid method to assess the utility of reaction modifications. PMID:17430586

Automating Embedded Analysis Capabilities and Managing Software Complexity in Multiphysics Simulation, Part I: Template-Based Generic Programming

DOE PAGES

Pawlowski, Roger P.; Phipps, Eric T.; Salinger, Andrew G.

2012-01-01

An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.

Rapid and Sensitive Detection of Vibrio parahaemolyticus and Vibrio vulnificus by Multiple Endonuclease Restriction Real-Time Loop-Mediated Isothermal Amplification Technique.

PubMed

Wang, Yi; Li, Dongxun; Wang, Yan; Li, Kewei; Ye, Changyun

2016-01-19

Vibrio parahaemolyticus and Vibrio vulnificus are two marine seafood-borne pathogens causing severe illnesses in humans and aquatic animals. In this study, a recently developed novel multiple endonuclease restriction real-time loop-mediated isothermal amplification technology (MERT-LAMP) were successfully developed and evaluated for simultaneous detection of V. parahaemolyticus and V. vulnificus strains in only a single reaction. Two MERT-LAMP primer sets were designed to specifically target toxR gene of V. parahaemolyticus and rpoS gene of V. vulnificus. The MERT-LAMP reactions were conducted at 62 °C, and the positive results were produced in as short as 19 min with the genomic DNA templates extracted from the V. parahaemolyticus and V. vulnificus strains. The two target pathogens present in the same sample could be simultaneously detected and correctly differentiated based on distinct fluorescence curves in a real-time format. The sensitivity of MERT-LAMP assay was 250 fg and 125 fg DNA per reaction with genomic templates of V. parahaemolyticus and V. vulnificus strains, which was in conformity with conventional LAMP detection. Compared with PCR-based techniques, the MERT-LAMP technology was 100- and 10-fold more sensitive than that of PCR and qPCR methods. Moreover, the limit of detection of MERT-LAMP approach for V. parahaemolyticus isolates and V. vulnificus isolates detection in artificially-contaminated oyster samples was 92 CFU and 83 CFU per reaction. In conclusion, the MERT-LAMP assay presented here was a rapid, specific, and sensitive tool for the detection of V. parahaemolyticus and V. vulnificus, and could be adopted for simultaneous screening of V. parahaemolyticus and V. vulnificus in a wide variety of samples.

A LabVIEW based template for user created experiment automation.

PubMed

Kim, D J; Fisk, Z

2012-12-01

We have developed an expandable software template to automate user created experiments. The LabVIEW based template is easily modifiable to add together user created measurements, controls, and data logging with virtually any type of laboratory equipment. We use reentrant sequential selection to implement sequence script making it possible to wrap a long series of the user created experiments and execute them in sequence. Details of software structure and application examples for scanning probe microscope and automated transport experiments using custom built laboratory electronics and a cryostat are described.

[Manufacture method and clinical application of minimally invasive dental implant guide template based on registration technology].

PubMed

Lin, Zeming; He, Bingwei; Chen, Jiang; D u, Zhibin; Zheng, Jingyi; Li, Yanqin

2012-08-01

To guide doctors in precisely positioning surgical operation, a new production method of minimally invasive implant guide template was presented. The mandible of patient was scanned by CT scanner, and three-dimensional jaw bone model was constructed based on CT images data The professional dental implant software Simplant was used to simulate the plant based on the three-dimensional CT model to determine the location and depth of implants. In the same time, the dental plaster models were scanned by stereo vision system to build the oral mucosa model. Next, curvature registration technology was used to fuse the oral mucosa model and the CT model, then the designed position of implant in the oral mucosa could be determined. The minimally invasive implant guide template was designed in 3-Matic software according to the design position of implant and the oral mucosa model. Finally, the template was produced by rapid prototyping. The three-dimensional registration technology was useful to fuse the CT data and the dental plaster data, and the template was accurate that could provide the doctors a guidance in the actual planting without cut-off mucosa. The guide template which fabricated by comprehensive utilization of three-dimensional registration, Simplant simulation and rapid prototyping positioning are accurate and can achieve the minimally invasive and accuracy implant surgery, this technique is worthy of clinical use.

Precursor Mediated Synthesis of Nanostructured Silicas: From Precursor-Surfactant Ion Pairs to Structured Materials.

PubMed

Hesemann, Peter; Nguyen, Thy Phung; Hankari, Samir El

2014-04-11

The synthesis of nanostructured anionic-surfactant-templated mesoporous silica (AMS) recently appeared as a new strategy for the formation of nanostructured silica based materials. This method is based on the use of anionic surfactants together with a co-structure-directing agent (CSDA), mostly a silylated ammonium precursor. The presence of this CSDA is necessary in order to create ionic interactions between template and silica forming phases and to ensure sufficient affinity between the two phases. This synthetic strategy was for the first time applied in view of the synthesis of surface functionalized silica bearing ammonium groups and was then extended on the formation of materials functionalized with anionic carboxylate and bifunctional amine-carboxylate groups. In the field of silica hybrid materials, the "anionic templating" strategy has recently been applied for the synthesis of silica hybrid materials from cationic precursors. Starting from di- or oligosilylated imidazolium and ammonium precursors, only template directed hydrolysis-polycondensation reactions involving complementary anionic surfactants allowed accessing structured ionosilica hybrid materials. The mechanistic particularity of this approach resides in the formation of precursor-surfactant ion pairs in the hydrolysis-polycondensation mixture. This review gives a systematic overview over the various types of materials accessed from this cooperative ionic templating approach and highlights the high potential of this original strategy for the formation of nanostructured silica based materials which appears as a complementary strategy to conventional soft templating approaches.

Directed deposition of inorganic oxide networks on patterned polymer templates

NASA Astrophysics Data System (ADS)

Ford, Thomas James Robert

Inspired by nature, we have successfully directed the deposition of inorganic oxide materials on polymer templates via a combination of top-down and bottom-up fabrication methods. We have functionally mimicked the hierarchical silica exoskeletons of diatoms, where specialized proteins chaperone the condensation of silicic acid into nanoscale silica networks confined by microscopic vesicle walls. We replaced the proteins with functionally analogous polyamines and vesicles with lithographically defined polymer templates. We grafted the polyamines either to the surface or throughout the template by changing the template chemistry and altering our grafting strategy. Exposure to an inorganic oxide precursor solution led to electrostatic aggregation at the polyamine chains, catalyzing hydrolysis and condensation to form long-range inorganic oxide nanoparticle networks. Grafted to epoxy surfaces, swelling effects and the hyperbranched brush morphology lead to the formation of nanofruit features that generated thin, conformal inorganic coatings. When the polyamines were grafted throughout hydrogel templates, we obtained composite networks that yielded faithful inorganic replicas of the original patterns. By varying the polyamine chain length and combustion parameters, we controlled the nanoparticle size, morphology, and crystalline phase. The polyamine morphology affected the resulting inorganic network in both fabrication schemes and we could control the depostion over multiple length scales. Because our methods were compatible with a variety of lithographic methods, we were able to generate inorganic replicas of 1D, 2D, and 3D polymer structures. These may be used for a wide range of applications, including sensing, catalysis, photonic, phononic, photovoltaic, and others that require well-defined inorganic structures.

Volume estimation using food specific shape templates in mobile image-based dietary assessment

NASA Astrophysics Data System (ADS)

Chae, Junghoon; Woo, Insoo; Kim, SungYe; Maciejewski, Ross; Zhu, Fengqing; Delp, Edward J.; Boushey, Carol J.; Ebert, David S.

2011-03-01

As obesity concerns mount, dietary assessment methods for prevention and intervention are being developed. These methods include recording, cataloging and analyzing daily dietary records to monitor energy and nutrient intakes. Given the ubiquity of mobile devices with built-in cameras, one possible means of improving dietary assessment is through photographing foods and inputting these images into a system that can determine the nutrient content of foods in the images. One of the critical issues in such the image-based dietary assessment tool is the accurate and consistent estimation of food portion sizes. The objective of our study is to automatically estimate food volumes through the use of food specific shape templates. In our system, users capture food images using a mobile phone camera. Based on information (i.e., food name and code) determined through food segmentation and classification of the food images, our system choose a particular food template shape corresponding to each segmented food. Finally, our system reconstructs the three-dimensional properties of the food shape from a single image by extracting feature points in order to size the food shape template. By employing this template-based approach, our system automatically estimates food portion size, providing a consistent method for estimation food volume.

Open tubular capillary columns with basic templates made by the generalized preparation protocol in capillary electrochromatography chiral separation and template structural effects on chiral separation capability.

PubMed

Zaidi, Shabi Abbas; Lee, Seung Mi; Cheong, Won Jo

2011-03-04

Some open tubular (OT) molecule imprinted polymer (MIP) silica capillary columns have been prepared using atenolol, sulpiride, methyl benzylamine (MBA) and (1-naphthyl)-ethylamine (NEA) as templates by the pre-established generalized preparation protocol. The four MIP thin layers of different templates showed quite different morphologies. The racemic selectivity of each MIP column for the template enantiomers was optimized by changing eluent composition and pH. The template structural effects on chiral separation performance have been examined. This work verifies the versatility of the generalized preparation protocol for OT-MIP silica capillary columns by extending its boundary toward templates with basic functional group moieties. This study is the very first report to demonstrate a generalized MIP preparation protocol that is valid for both acidic and basic templates. The chiral separation performances of atenolol and sulpiride by the MIPs of this study were found better than or comparable to those of atenolol and sulpiride obtained by non-MIP separation techniques and those of some basic template enantiomers obtained by MIP based techniques. Copyright © 2011 Elsevier B.V. All rights reserved.

How I do it-optimizing radiofrequency ablation in spinal metastases using iCT and navigation.

PubMed

Kavakebi, Pujan; Freyschlag, C F; Thomé, C

2017-10-01

Exact positioning of the radiofrequency ablation (RFA) probe for tumor treatment under fluoroscopic guidance can be difficult because of potentially small inaccessible lesions and the radiation dose to the medical staff in RFA. In addition, vertebroplasty (VP) can be significantly high. Description and workflow of RFA in spinal metastasis using iCT (intraoperative computed tomography) and 3D-navigation-based probe placement followed by VP. RFA and VP can be successfully combined with iCT-based navigation, which leads to a reduction of radiation to the staff and optimal probe positioning due to 3D navigation.

Unusual anchor pins placement and protocol deviations during computer-based implant placement in a patient with severe mandibular bone atrophy. A case report.

PubMed

Pozzi, A; Tallarico, M; Barlattani, A

2012-06-01

The aim of the study was to describe an unusual method to stabilize the surgical template during the treatment of a severely resorbed edentulous mandible by means of computer-guided implant surgery. Pre-operative computer-based planning revealed the difficulty to stabilize the surgical template in a 67-year-old healthy woman. A deviation of the original NobelGuide™ protocol was performed to ensure the stability of the surgical template: four anchor pins were used to stabilize the surgical template, two in the buccal side of the anterior template and two unusual pins were placed in the lingual site. Four straight TiUnite® Nobel Biocare™ implants were then placed, according to a modified All-on-4™ concept procedure, to avoid graft procedures and to reduce the cumulative chair-side treatment time and costs. A temporary restoration was placed immediately after implant placement. Three months later a definitive, full acrylic restoration was delivered.

Dual soft-template system based on colloidal chemistry for the synthesis of hollow mesoporous silica nanoparticles.

PubMed

Li, Yunqi; Bastakoti, Bishnu Prasad; Imura, Masataka; Tang, Jing; Aldalbahi, Ali; Torad, Nagy L; Yamauchi, Yusuke

2015-04-20

A new dual soft-template system comprising the asymmetric triblock copolymer poly(styrene-b-2-vinyl pyridine-b-ethylene oxide) (PS-b-P2VP-b-PEO) and the cationic surfactant cetyltrimethylammonium bromide (CTAB) is used to synthesize hollow mesoporous silica (HMS) nanoparticles with a center void of around 17 nm. The stable PS-b-P2VP-b-PEO polymeric micelle serves as a template to form the hollow interior, while the CTAB surfactant serves as a template to form mesopores in the shells. The P2VP blocks on the polymeric micelles can interact with positively charged CTA(+) ions via negatively charged hydrolyzed silica species. Thus, dual soft-templates clearly have different roles for the preparation of the HMS nanoparticles. Interestingly, the thicknesses of the mesoporous shell are tunable by varying the amounts of TEOS and CTAB. This study provides new insight on the preparation of mesoporous materials based on colloidal chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

View-Invariant Gait Recognition Through Genetic Template Segmentation

NASA Astrophysics Data System (ADS)

Isaac, Ebenezer R. H. P.; Elias, Susan; Rajagopalan, Srinivasan; Easwarakumar, K. S.

2017-08-01

Template-based model-free approach provides by far the most successful solution to the gait recognition problem in literature. Recent work discusses how isolating the head and leg portion of the template increase the performance of a gait recognition system making it robust against covariates like clothing and carrying conditions. However, most involve a manual definition of the boundaries. The method we propose, the genetic template segmentation (GTS), employs the genetic algorithm to automate the boundary selection process. This method was tested on the GEI, GEnI and AEI templates. GEI seems to exhibit the best result when segmented with our approach. Experimental results depict that our approach significantly outperforms the existing implementations of view-invariant gait recognition.

MO-DE-BRA-04: Hands-On Fluoroscopy Safety Training with Real-Time Patient and Staff Dosimetry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vanderhoek, M; Bevins, N

Purpose: Fluoroscopically guided interventions (FGI) are routinely performed across many different hospital departments. However, many involved staff members have minimal training regarding safe and optimal use of fluoroscopy systems. We developed and taught a hands-on fluoroscopy safety class incorporating real-time patient and staff dosimetry in order to promote safer and more optimal use of fluoroscopy during FGI. Methods: The hands-on fluoroscopy safety class is taught in an FGI suite, unique to each department. A patient equivalent phantom is set on the patient table with an ion chamber positioned at the x-ray beam entrance to the phantom. This provides a surrogatemore » measure of patient entrance dose. Multiple solid state dosimeters (RaySafe i2 dosimetry systemTM) are deployed at different distances from the phantom (0.1, 1, 3 meters), which provide surrogate measures of staff dose. Instructors direct participating clinical staff to operate the fluoroscopy system as they view live fluoroscopic images, patient entrance dose, and staff doses in real-time. During class, instructors work with clinical staff to investigate how patient entrance dose, staff doses, and image quality are affected by different parameters, including pulse rate, magnification, collimation, beam angulation, imaging mode, system geometry, distance, and shielding. Results: Real-time dose visualization enables clinical staff to directly see and learn how to optimize their use of their own fluoroscopy system to minimize patient and staff dose, yet maintain sufficient image quality for FGI. As a direct result of the class, multiple hospital departments have implemented changes to their imaging protocols, including reduction of the default fluoroscopy pulse rate and increased use of collimation and lower dose fluoroscopy modes. Conclusion: Hands-on fluoroscopy safety training substantially benefits from real-time patient and staff dosimetry incorporated into the class. Real-time dose display helps clinical staff visualize, internalize, and ultimately utilize the safety techniques learned during the training. RaySafe/Unfors/Fluke lent us a portable version of their RaySafe i2 Dosimetry System for 6 months.« less

Training femoral neck screw insertion skills to surgical trainees: computer-assisted surgery versus conventional fluoroscopic technique.

PubMed

Nousiainen, Markku T; Omoto, Daniel M; Zingg, Patrick O; Weil, Yoram A; Mardam-Bey, Sami W; Eward, William C

2013-02-01

: Femoral neck fractures are among the most common orthopaedic injuries impacting the health care system. Surgical management of such fractures with cannulated screws is a commonly performed procedure. The acquisition of surgical skills necessary to perform this procedure typically involves learning on real patients with fluoroscopic guidance. This study attempts to determine if a novel computer-navigated training model improves the learning of this basic surgical skill. A multicenter, prospective, randomized, and controlled study was conducted using surgical trainees with no prior experience in surgically managing femoral neck fractures. After a training session, participants underwent a pretest by performing the surgical task (screw placement) on a simulated hip fracture using fluoroscopic guidance. Immediately after, participants were randomized into either undergoing a training session using conventional fluoroscopy or computer-based navigation. Immediate posttest, retention (4 weeks later), and transfer tests were performed. Performance during the tests was determined by radiographic analysis of hardware placement. Screw placement by trainees was ultimately equal to the level of an expert surgeon with either training technique. Participants who trained with computer navigation took fewer attempts to position hardware and used less fluoroscopy time than those trained with fluoroscopy. When those trained with fluoroscopy used computer navigation at the transfer test, less fluoroscopy time and dosage was used. The concurrent augmented feedback provided by computer navigation did not affect the learning of this basic surgical skill in surgical novices. No compromise in learning occurred if the surgical novice trained with one type of technology and transferred to using the other. The findings of this study suggest that computer navigation may be safely used to train surgical novices in a basic procedure. This model avoids using both live patients and harmful radiation without a compromise in the acquisition of a 3-dimensional technical skill.

Live Virus Vaccines Based on a Yellow Fever Vaccine Backbone: Standardized Template with Key Considerations for a Risk/Benefit Assessment*

PubMed Central

Monath, Thomas P.; Seligman, Stephen J.; Robertson, James S.; Guy, Bruno; Hayes, Edward B.; Condit, Richard C.; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

2015-01-01

The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called “chimeric virus vaccines”). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were replaced by the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of information. The Brighton Collaboration V3SWG template may also be useful as a guide to the evaluation of other recombinant viral vector vaccines. PMID:25446819

C-arm positioning using virtual fluoroscopy for image-guided surgery

NASA Astrophysics Data System (ADS)

de Silva, T.; Punnoose, J.; Uneri, A.; Goerres, J.; Jacobson, M.; Ketcha, M. D.; Manbachi, A.; Vogt, S.; Kleinszig, G.; Khanna, A. J.; Wolinsky, J.-P.; Osgood, G.; Siewerdsen, J. H.

2017-03-01

Introduction: Fluoroscopically guided procedures often involve repeated acquisitions for C-arm positioning at the cost of radiation exposure and time in the operating room. A virtual fluoroscopy system is reported with the potential of reducing dose and time spent in C-arm positioning, utilizing three key advances: robust 3D-2D registration to a preoperative CT; real-time forward projection on GPU; and a motorized mobile C-arm with encoder feedback on C-arm orientation. Method: Geometric calibration of the C-arm was performed offline in two rotational directions (orbit α, orbit β). Patient registration was performed using image-based 3D-2D registration with an initially acquired radiograph of the patient. This approach for patient registration eliminated the requirement for external tracking devices inside the operating room, allowing virtual fluoroscopy using commonly available systems in fluoroscopically guided procedures within standard surgical workflow. Geometric accuracy was evaluated in terms of projection distance error (PDE) in anatomical fiducials. A pilot study was conducted to evaluate the utility of virtual fluoroscopy to aid C-arm positioning in image guided surgery, assessing potential improvements in time, dose, and agreement between the virtual and desired view. Results: The overall geometric accuracy of DRRs in comparison to the actual radiographs at various C-arm positions was PDE (mean ± std) = 1.6 ± 1.1 mm. The conventional approach required on average 8.0 ± 4.5 radiographs spent "fluoro hunting" to obtain the desired view. Positioning accuracy improved from 2.6o ± 2.3o (in α) and 4.1o ± 5.1o (in β) in the conventional approach to 1.5o ± 1.3o and 1.8o ± 1.7o, respectively, with the virtual fluoroscopy approach. Conclusion: Virtual fluoroscopy could improve accuracy of C-arm positioning and save time and radiation dose in the operating room. Such a system could be valuable to training of fluoroscopy technicians as well as intraoperative use in fluoroscopically guided procedures.

Live virus vaccines based on a yellow fever vaccine backbone: standardized template with key considerations for a risk/benefit assessment.

PubMed

Monath, Thomas P; Seligman, Stephen J; Robertson, James S; Guy, Bruno; Hayes, Edward B; Condit, Richard C; Excler, Jean Louis; Mac, Lisa Marie; Carbery, Baevin; Chen, Robert T

2015-01-01

The Brighton Collaboration Viral Vector Vaccines Safety Working Group (V3SWG) was formed to evaluate the safety of live, recombinant viral vaccines incorporating genes from heterologous viruses inserted into the backbone of another virus (so-called "chimeric virus vaccines"). Many viral vector vaccines are in advanced clinical trials. The first such vaccine to be approved for marketing (to date in Australia, Thailand, Malaysia, and the Philippines) is a vaccine against the flavivirus, Japanese encephalitis (JE), which employs a licensed vaccine (yellow fever 17D) as a vector. In this vaccine, two envelope proteins (prM-E) of YF 17D virus were exchanged for the corresponding genes of JE virus, with additional attenuating mutations incorporated into the JE gene inserts. Similar vaccines have been constructed by inserting prM-E genes of dengue and West Nile into YF 17D virus and are in late stage clinical studies. The dengue vaccine is, however, more complex in that it requires a mixture of four live vectors each expressing one of the four dengue serotypes. This vaccine has been evaluated in multiple clinical trials. No significant safety concerns have been found. The Phase 3 trials met their endpoints in terms of overall reduction of confirmed dengue fever, and, most importantly a significant reduction in severe dengue and hospitalization due to dengue. However, based on results that have been published so far, efficacy in preventing serotype 2 infection is less than that for the other three serotypes. In the development of these chimeric vaccines, an important series of comparative studies of safety and efficacy were made using the parental YF 17D vaccine virus as a benchmark. In this paper, we use a standardized template describing the key characteristics of the novel flavivirus vaccine vectors, in comparison to the parental YF 17D vaccine. The template facilitates scientific discourse among key stakeholders by increasing the transparency and comparability of information. The Brighton Collaboration V3SWG template may also be useful as a guide to the evaluation of other recombinant viral vector vaccines. Copyright © 2014. Published by Elsevier Ltd.

Theory of adsorption in a polydisperse templated porous material: Hard sphere systems

NASA Astrophysics Data System (ADS)

RŻysko, Wojciech; Sokołowski, Stefan; Pizio, Orest

2002-03-01

A theoretical description of adsorption in a templated porous material, formed by an equilibrium quench of a polydisperse fluid composed of matrix and template particles and subsequent removal of the template particles is presented. The approach is based on the solution of the replica Ornstein-Zernike equations with Percus-Yevick and hypernetted chain closures. The method of solution uses expansions of size-dependent correlation functions into Fourier series, as described by Lado [J. Chem. Phys. 108, 6441 (1998)]. Specific calculations have been carried out for model systems, composed of hard spheres.

The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family.

PubMed

van der Linden, Lonneke; Vives-Adrián, Laia; Selisko, Barbara; Ferrer-Orta, Cristina; Liu, Xinran; Lanke, Kjerstin; Ulferts, Rachel; De Palma, Armando M; Tanchis, Federica; Goris, Nesya; Lefebvre, David; De Clercq, Kris; Leyssen, Pieter; Lacroix, Céline; Pürstinger, Gerhard; Coutard, Bruno; Canard, Bruno; Boehr, David D; Arnold, Jamie J; Cameron, Craig E; Verdaguer, Nuria; Neyts, Johan; van Kuppeveld, Frank J M

2015-03-01

The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71) for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy. Nucleoside-based inhibitors have broad-spectrum activity but often exhibit off-target effects. Most non-nucleoside inhibitors (NNIs) target surface cavities, which are structurally more flexible than the nucleotide-binding pocket, and hence have a more narrow spectrum of activity and are more prone to resistance development. Here, we report a novel NNI, GPC-N114 (2,2'-[(4-chloro-1,2-phenylene)bis(oxy)]bis(5-nitro-benzonitrile)) with broad-spectrum activity against enteroviruses and cardioviruses (another genus in the picornavirus family). Surprisingly, coxsackievirus B3 (CVB3) and poliovirus displayed a high genetic barrier to resistance against GPC-N114. By contrast, EMCV, a cardiovirus, rapidly acquired resistance due to mutations in 3Dpol. In vitro polymerase activity assays showed that GPC-N114 i) inhibited the elongation activity of recombinant CVB3 and EMCV 3Dpol, (ii) had reduced activity against EMCV 3Dpol with the resistance mutations, and (iii) was most efficient in inhibiting 3Dpol when added before the RNA template-primer duplex. Elucidation of a crystal structure of the inhibitor bound to CVB3 3Dpol confirmed the RNA-binding channel as the target for GPC-N114. Docking studies of the compound into the crystal structures of the compound-resistant EMCV 3Dpol mutants suggested that the resistant phenotype is due to subtle changes that interfere with the binding of GPC-N114 but not of the RNA template-primer. In conclusion, this study presents the first NNI that targets the RNA template channel of the picornavirus polymerase and identifies a new pocket that can be used for the design of broad-spectrum inhibitors. Moreover, this study provides important new insight into the plasticity of picornavirus polymerases at the template binding site.

The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family

PubMed Central

van der Linden, Lonneke; Vives-Adrián, Laia; Selisko, Barbara; Ferrer-Orta, Cristina; Liu, Xinran; Lanke, Kjerstin; Ulferts, Rachel; De Palma, Armando M.; Tanchis, Federica; Goris, Nesya; Lefebvre, David; De Clercq, Kris; Leyssen, Pieter; Lacroix, Céline; Pürstinger, Gerhard; Coutard, Bruno; Canard, Bruno; Boehr, David D.; Arnold, Jamie J.; Cameron, Craig E.; Verdaguer, Nuria

2015-01-01

The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71) for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy. Nucleoside-based inhibitors have broad-spectrum activity but often exhibit off-target effects. Most non-nucleoside inhibitors (NNIs) target surface cavities, which are structurally more flexible than the nucleotide-binding pocket, and hence have a more narrow spectrum of activity and are more prone to resistance development. Here, we report a novel NNI, GPC-N114 (2,2'-[(4-chloro-1,2-phenylene)bis(oxy)]bis(5-nitro-benzonitrile)) with broad-spectrum activity against enteroviruses and cardioviruses (another genus in the picornavirus family). Surprisingly, coxsackievirus B3 (CVB3) and poliovirus displayed a high genetic barrier to resistance against GPC-N114. By contrast, EMCV, a cardiovirus, rapidly acquired resistance due to mutations in 3Dpol. In vitro polymerase activity assays showed that GPC-N114 i) inhibited the elongation activity of recombinant CVB3 and EMCV 3Dpol, (ii) had reduced activity against EMCV 3Dpol with the resistance mutations, and (iii) was most efficient in inhibiting 3Dpol when added before the RNA template-primer duplex. Elucidation of a crystal structure of the inhibitor bound to CVB3 3Dpol confirmed the RNA-binding channel as the target for GPC-N114. Docking studies of the compound into the crystal structures of the compound-resistant EMCV 3Dpol mutants suggested that the resistant phenotype is due to subtle changes that interfere with the binding of GPC-N114 but not of the RNA template-primer. In conclusion, this study presents the first NNI that targets the RNA template channel of the picornavirus polymerase and identifies a new pocket that can be used for the design of broad-spectrum inhibitors. Moreover, this study provides important new insight into the plasticity of picornavirus polymerases at the template binding site. PMID:25799064

Enhanced project management tool

NASA Technical Reports Server (NTRS)

Hsu, Chen-Jung (Inventor); Patel, Hemil N. (Inventor); Maluf, David A. (Inventor); Moh Hashim, Jairon C. (Inventor); Tran, Khai Peter B. (Inventor)

2012-01-01

A system for managing a project that includes multiple tasks and a plurality of workers. Input information includes characterizations based upon a human model, a team model and a product model. Periodic reports, such as one or more of a monthly report, a task plan report, a schedule report, a budget report and a risk management report, are generated and made available for display or further analysis or collection into a customized report template. An extensible database allows searching for information based upon context and upon content. Seven different types of project risks are addressed, including non-availability of required skill mix of workers. The system can be configured to exchange data and results with corresponding portions of similar project analyses, and to provide user-specific access to specified information.