A Novel Artificial Bee Colony Algorithm Based on Internal-Feedback Strategy for Image Template Matching

PubMed Central

Gong, Li-Gang

2014-01-01

Image template matching refers to the technique of locating a given reference image over a source image such that they are the most similar. It is a fundamental mission in the field of visual target recognition. In general, there are two critical aspects of a template matching scheme. One is similarity measurement and the other is best-match location search. In this work, we choose the well-known normalized cross correlation model as a similarity criterion. The searching procedure for the best-match location is carried out through an internal-feedback artificial bee colony (IF-ABC) algorithm. IF-ABC algorithm is highlighted by its effort to fight against premature convergence. This purpose is achieved through discarding the conventional roulette selection procedure in the ABC algorithm so as to provide each employed bee an equal chance to be followed by the onlooker bees in the local search phase. Besides that, we also suggest efficiently utilizing the internal convergence states as feedback guidance for searching intensity in the subsequent cycles of iteration. We have investigated four ideal template matching cases as well as four actual cases using different searching algorithms. Our simulation results show that the IF-ABC algorithm is more effective and robust for this template matching mission than the conventional ABC and two state-of-the-art modified ABC algorithms do. PMID:24892107

Monocular correspondence detection for symmetrical objects by template matching

NASA Astrophysics Data System (ADS)

Vilmar, G.; Besslich, Philipp W., Jr.

1990-09-01

We describe a possibility to reconstruct 3-D information from a single view of an 3-D bilateral symmetric object. The symmetry assumption allows us to obtain a " second view" from a different viewpoint by a simple reflection of the monocular image. Therefore we have to solve the correspondence problem in a special case where known feature-based or area-based binocular approaches fail. In principle our approach is based on a frequency domain template matching of the features on the epipolar lines. During a training period our system " learns" the assignment of correspondence models to image features. The object shape is interpolated when no template matches to the image features. This fact is an important advantage of this methodology because no " real world" image holds the symmetry assumption perfectly. To simplify the training process we used single views on human faces (e. g. passport photos) but our system is trainable on any other kind of objects.

Rapid and Robust Cross-Correlation-Based Seismic Phase Identification Using an Approximate Nearest Neighbor Method

NASA Astrophysics Data System (ADS)

Tibi, R.; Young, C. J.; Gonzales, A.; Ballard, S.; Encarnacao, A. V.

2016-12-01

The matched filtering technique involving the cross-correlation of a waveform of interest with archived signals from a template library has proven to be a powerful tool for detecting events in regions with repeating seismicity. However, waveform correlation is computationally expensive, and therefore impractical for large template sets unless dedicated distributed computing hardware and software are used. In this study, we introduce an Approximate Nearest Neighbor (ANN) approach that enables the use of very large template libraries for waveform correlation without requiring a complex distributed computing system. Our method begins with a projection into a reduced dimensionality space based on correlation with a randomized subset of the full template archive. Searching for a specified number of nearest neighbors is accomplished by using randomized K-dimensional trees. We used the approach to search for matches to each of 2700 analyst-reviewed signal detections reported for May 2010 for the IMS station MKAR. The template library in this case consists of a dataset of more than 200,000 analyst-reviewed signal detections for the same station from 2002-2014 (excluding May 2010). Of these signal detections, 60% are teleseismic first P, and 15% regional phases (Pn, Pg, Sn, and Lg). The analyses performed on a standard desktop computer shows that the proposed approach performs the search of the large template libraries about 20 times faster than the standard full linear search, while achieving recall rates greater than 80%, with the recall rate increasing for higher correlation values. To decide whether to confirm a match, we use a hybrid method involving a cluster approach for queries with two or more matches, and correlation score for single matches. Of the signal detections that passed our confirmation process, 52% were teleseismic first P, and 30% were regional phases.

Improvement in Visual Target Tracking for a Mobile Robot

NASA Technical Reports Server (NTRS)

Kim, Won; Ansar, Adnan; Madison, Richard

2006-01-01

In an improvement of the visual-target-tracking software used aboard a mobile robot (rover) of the type used to explore the Martian surface, an affine-matching algorithm has been replaced by a combination of a normalized- cross-correlation (NCC) algorithm and a template-image-magnification algorithm. Although neither NCC nor template-image magnification is new, the use of both of them to increase the degree of reliability with which features can be matched is new. In operation, a template image of a target is obtained from a previous rover position, then the magnification of the template image is based on the estimated change in the target distance from the previous rover position to the current rover position (see figure). For this purpose, the target distance at the previous rover position is determined by stereoscopy, while the target distance at the current rover position is calculated from an estimate of the current pose of the rover. The template image is then magnified by an amount corresponding to the estimated target distance to obtain a best template image to match with the image acquired at the current rover position.

Object Detection Based on Template Matching through Use of Best-So-Far ABC

PubMed Central

2014-01-01

Best-so-far ABC is a modified version of the artificial bee colony (ABC) algorithm used for optimization tasks. This algorithm is one of the swarm intelligence (SI) algorithms proposed in recent literature, in which the results demonstrated that the best-so-far ABC can produce higher quality solutions with faster convergence than either the ordinary ABC or the current state-of-the-art ABC-based algorithm. In this work, we aim to apply the best-so-far ABC-based approach for object detection based on template matching by using the difference between the RGB level histograms corresponding to the target object and the template object as the objective function. Results confirm that the proposed method was successful in both detecting objects and optimizing the time used to reach the solution. PMID:24812556

A new algorithm for distorted fingerprints matching based on normalized fuzzy similarity measure.

PubMed

Chen, Xinjian; Tian, Jie; Yang, Xin

2006-03-01

Coping with nonlinear distortions in fingerprint matching is a challenging task. This paper proposes a novel algorithm, normalized fuzzy similarity measure (NFSM), to deal with the nonlinear distortions. The proposed algorithm has two main steps. First, the template and input fingerprints were aligned. In this process, the local topological structure matching was introduced to improve the robustness of global alignment. Second, the method NFSM was introduced to compute the similarity between the template and input fingerprints. The proposed algorithm was evaluated on fingerprints databases of FVC2004. Experimental results confirm that NFSM is a reliable and effective algorithm for fingerprint matching with nonliner distortions. The algorithm gives considerably higher matching scores compared to conventional matching algorithms for the deformed fingerprints.

Optimizing Multi-Station Template Matching to Identify and Characterize Induced Seismicity in Ohio

NASA Astrophysics Data System (ADS)

Brudzinski, M. R.; Skoumal, R.; Currie, B. S.

2014-12-01

As oil and gas well completions utilizing multi-stage hydraulic fracturing have become more commonplace, the potential for seismicity induced by the deep disposal of frac-related flowback waters and the hydraulic fracturing process itself has become increasingly important. While it is rare for these processes to induce felt seismicity, the recent increase in the number of deep injection wells and volumes injected have been suspected to have contributed to a substantial increase of events = M 3 in the continental U.S. over the past decade. Earthquake template matching using multi-station waveform cross-correlation is an adept tool for investigating potentially induced sequences due to its proficiency at identifying similar/repeating seismic events. We have sought to refine this approach by investigating a variety of seismic sequences and determining the optimal parameters (station combinations, template lengths and offsets, filter frequencies, data access method, etc.) for identifying induced seismicity. When applied to a sequence near a wastewater injection well in Youngstown, Ohio, our optimized template matching routine yielded 566 events while other template matching studies found ~100-200 events. We also identified 77 events on 4-12 March 2014 that are temporally and spatially correlated with active hydraulic fracturing in Poland Township, Ohio. We find similar improvement in characterizing sequences in Washington and Harrison Counties, which appear to be related to wastewater injection and hydraulic fracturing, respectively. In the Youngstown and Poland Township cases, focal mechanisms and double difference relocation using the cross-correlation matrix finds left-lateral faults striking roughly east-west near the top of the basement. We have also used template matching to determine isolated earthquakes near several other wastewater injection wells are unlikely to be induced based on a lack of similar/repeating sequences. Optimized template matching utilizes high-quality reliable stations within pre-existing seismic networks and is therefore a cost-efficient monitoring strategy for identifying and characterizing potentially induced seismic sequences.

Adaptive elastic segmentation of brain MRI via shape-model-guided evolutionary programming.

PubMed

Pitiot, Alain; Toga, Arthur W; Thompson, Paul M

2002-08-01

This paper presents a fully automated segmentation method for medical images. The goal is to localize and parameterize a variety of types of structure in these images for subsequent quantitative analysis. We propose a new hybrid strategy that combines a general elastic template matching approach and an evolutionary heuristic. The evolutionary algorithm uses prior statistical information about the shape of the target structure to control the behavior of a number of deformable templates. Each template, modeled in the form of a B-spline, is warped in a potential field which is itself dynamically adapted. Such a hybrid scheme proves to be promising: by maintaining a population of templates, we cover a large domain of the solution space under the global guidance of the evolutionary heuristic, and thoroughly explore interesting areas. We address key issues of automated image segmentation systems. The potential fields are initially designed based on the spatial features of the edges in the input image, and are subjected to spatially adaptive diffusion to guarantee the deformation of the template. This also improves its global consistency and convergence speed. The deformation algorithm can modify the internal structure of the templates to allow a better match. We investigate in detail the preprocessing phase that the images undergo before they can be used more effectively in the iterative elastic matching procedure: a texture classifier, trained via linear discriminant analysis of a learning set, is used to enhance the contrast of the target structure with respect to surrounding tissues. We show how these techniques interact within a statistically driven evolutionary scheme to achieve a better tradeoff between template flexibility and sensitivity to noise and outliers. We focus on understanding the features of template matching that are most beneficial in terms of the achieved match. Examples from simulated and real image data are discussed, with considerations of algorithmic efficiency.

Rapid earthquake detection through GPU-Based template matching

NASA Astrophysics Data System (ADS)

Mu, Dawei; Lee, En-Jui; Chen, Po

2017-12-01

The template-matching algorithm (TMA) has been widely adopted for improving the reliability of earthquake detection. The TMA is based on calculating the normalized cross-correlation coefficient (NCC) between a collection of selected template waveforms and the continuous waveform recordings of seismic instruments. In realistic applications, the computational cost of the TMA is much higher than that of traditional techniques. In this study, we provide an analysis of the TMA and show how the GPU architecture provides an almost ideal environment for accelerating the TMA and NCC-based pattern recognition algorithms in general. So far, our best-performing GPU code has achieved a speedup factor of more than 800 with respect to a common sequential CPU code. We demonstrate the performance of our GPU code using seismic waveform recordings from the ML 6.6 Meinong earthquake sequence in Taiwan.

[Algorithm of locally adaptive region growing based on multi-template matching applied to automated detection of hemorrhages].

PubMed

Gao, Wei-Wei; Shen, Jian-Xin; Wang, Yu-Liang; Liang, Chun; Zuo, Jing

2013-02-01

In order to automatically detect hemorrhages in fundus images, and develop an automated diabetic retinopathy screening system, a novel algorithm named locally adaptive region growing based on multi-template matching was established and studied. Firstly, spectral signature of major anatomical structures in fundus was studied, so that the right channel among RGB channels could be selected for different segmentation objects. Secondly, the fundus image was preprocessed by means of HSV brightness correction and contrast limited adaptive histogram equalization (CLAHE). Then, seeds of region growing were founded out by removing optic disc and vessel from the resulting image of normalized cross-correlation (NCC) template matching on the previous preprocessed image with several templates. Finally, locally adaptive region growing segmentation was used to find out the exact contours of hemorrhages, and the automated detection of the lesions was accomplished. The approach was tested on 90 different resolution fundus images with variable color, brightness and quality. Results suggest that the approach could fast and effectively detect hemorrhages in fundus images, and it is stable and robust. As a result, the approach can meet the clinical demands.

From scores to face templates: a model-based approach.

PubMed

Mohanty, Pranab; Sarkar, Sudeep; Kasturi, Rangachar

2007-12-01

Regeneration of templates from match scores has security and privacy implications related to any biometric authentication system. We propose a novel paradigm to reconstruct face templates from match scores using a linear approach. It proceeds by first modeling the behavior of the given face recognition algorithm by an affine transformation. The goal of the modeling is to approximate the distances computed by a face recognition algorithm between two faces by distances between points, representing these faces, in an affine space. Given this space, templates from an independent image set (break-in) are matched only once with the enrolled template of the targeted subject and match scores are recorded. These scores are then used to embed the targeted subject in the approximating affine (non-orthogonal) space. Given the coordinates of the targeted subject in the affine space, the original template of the targeted subject is reconstructed using the inverse of the affine transformation. We demonstrate our ideas using three, fundamentally different, face recognition algorithms: Principal Component Analysis (PCA) with Mahalanobis cosine distance measure, Bayesian intra-extrapersonal classifier (BIC), and a feature-based commercial algorithm. To demonstrate the independence of the break-in set with the gallery set, we select face templates from two different databases: Face Recognition Grand Challenge (FRGC) and Facial Recognition Technology (FERET) Database (FERET). With an operational point set at 1 percent False Acceptance Rate (FAR) and 99 percent True Acceptance Rate (TAR) for 1,196 enrollments (FERET gallery), we show that at most 600 attempts (score computations) are required to achieve a 73 percent chance of breaking in as a randomly chosen target subject for the commercial face recognition system. With similar operational set up, we achieve a 72 percent and 100 percent chance of breaking in for the Bayesian and PCA based face recognition systems, respectively. With three different levels of score quantization, we achieve 69 percent, 68 percent and 49 percent probability of break-in, indicating the robustness of our proposed scheme to score quantization. We also show that the proposed reconstruction scheme has 47 percent more probability of breaking in as a randomly chosen target subject for the commercial system as compared to a hill climbing approach with the same number of attempts. Given that the proposed template reconstruction method uses distinct face templates to reconstruct faces, this work exposes a more severe form of vulnerability than a hill climbing kind of attack where incrementally different versions of the same face are used. Also, the ability of the proposed approach to reconstruct actual face templates of the users increases privacy concerns in biometric systems.

Mapping of a standard documentation template to the ICF core sets for arthritis and low back pain.

PubMed

Escorpizo, Reuben; Davis, Kandace; Stumbo, Teri

2010-12-01

To identify the contents of a documentation template in The Guide to Physical Therapist Practice using the International Classification of Functioning, Disability, and Health (ICF) Core Sets for rheumatoid arthritis, osteoarthritis, and low back pain (LBP) as reference. Concepts were identified from items of an outpatient documentation template and mapped to the ICF using established linking rules. The ICF categories that were linked were compared with existing arthritis and LBP Core Sets. Based on the ICF, the template had the highest number (29%) of linked categories under Activities and participation while Body structures had the least (17%). ICF categories in the arthritis and LBP Core Sets had a 37-55% match with the ICF categories found in the template. We found 164 concepts that were not classified or not defined and 37 as personal factors. The arthritis and LBP Core Sets were reflected in the contents of the template. ICF categories in the Core Sets were reflected in the template (demonstrating up to 55% match). Potential integration of ICF in documentation templates could be explored and examined in the future to enhance clinical encounters and multidisciplinary communication. Copyright © 2010 John Wiley & Sons, Ltd.

Fast image matching algorithm based on projection characteristics

NASA Astrophysics Data System (ADS)

Zhou, Lijuan; Yue, Xiaobo; Zhou, Lijun

2011-06-01

Based on analyzing the traditional template matching algorithm, this paper identified the key factors restricting the speed of matching and put forward a brand new fast matching algorithm based on projection. Projecting the grayscale image, this algorithm converts the two-dimensional information of the image into one-dimensional one, and then matches and identifies through one-dimensional correlation, meanwhile, because of normalization has been done, when the image brightness or signal amplitude increasing in proportion, it could also perform correct matching. Experimental results show that the projection characteristics based image registration method proposed in this article could greatly improve the matching speed, which ensuring the matching accuracy as well.

Automated Threshold Selection for Template-Based Sonar Target Detection

DTIC Science & Technology

2017-08-01

test based on the distribution of the matched filter correlations. From the matched filter output we evaluate target sized areas and surrounding...synthetic aperture sonar data that were part of the evaluation . Figure 3 shows a nearly uniform seafloor. Figure 4 is more complex, with

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.

Object matching using a locally affine invariant and linear programming techniques.

PubMed

Li, Hongsheng; Huang, Xiaolei; He, Lei

2013-02-01

In this paper, we introduce a new matching method based on a novel locally affine-invariant geometric constraint and linear programming techniques. To model and solve the matching problem in a linear programming formulation, all geometric constraints should be able to be exactly or approximately reformulated into a linear form. This is a major difficulty for this kind of matching algorithm. We propose a novel locally affine-invariant constraint which can be exactly linearized and requires a lot fewer auxiliary variables than other linear programming-based methods do. The key idea behind it is that each point in the template point set can be exactly represented by an affine combination of its neighboring points, whose weights can be solved easily by least squares. Errors of reconstructing each matched point using such weights are used to penalize the disagreement of geometric relationships between the template points and the matched points. The resulting overall objective function can be solved efficiently by linear programming techniques. Our experimental results on both rigid and nonrigid object matching show the effectiveness of the proposed algorithm.

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.

A Fast Approach to Automatic Detection of Brain Lesions

PubMed Central

Koley, Subhranil; Chakraborty, Chandan; Mainero, Caterina; Fischl, Bruce; Aganj, Iman

2017-01-01

Template matching is a popular approach to computer-aided detection of brain lesions from magnetic resonance (MR) images. The outcomes are often sufficient for localizing lesions and assisting clinicians in diagnosis. However, processing large MR volumes with three-dimensional (3D) templates is demanding in terms of computational resources, hence the importance of the reduction of computational complexity of template matching, particularly in situations in which time is crucial (e.g. emergent stroke). In view of this, we make use of 3D Gaussian templates with varying radii and propose a new method to compute the normalized cross-correlation coefficient as a similarity metric between the MR volume and the template to detect brain lesions. Contrary to the conventional fast Fourier transform (FFT) based approach, whose runtime grows as O(N logN) with the number of voxels, the proposed method computes the cross-correlation in O(N). We show through our experiments that the proposed method outperforms the FFT approach in terms of computational time, and retains comparable accuracy. PMID:29082383

Dendritic cell recognition using template matching based on one-dimensional (1D) Fourier descriptors (FD)

NASA Astrophysics Data System (ADS)

Muhd Suberi, Anis Azwani; Wan Zakaria, Wan Nurshazwani; Tomari, Razali; Lau, Mei Xia

2016-07-01

Identification of Dendritic Cell (DC) particularly in the cancer microenvironment is a unique disclosure since fighting tumor from the harnessing immune system has been a novel treatment under investigation. Nowadays, the staining procedure in sorting DC can affect their viability. In this paper, a computer aided system is proposed for automatic classification of DC in peripheral blood mononuclear cell (PBMC) images. Initially, the images undergo a few steps in preprocessing to remove uneven illumination and artifacts around the cells. In segmentation, morphological operators and Canny edge are implemented to isolate the cell shapes and extract the contours. Following that, information from the contours are extracted based on Fourier descriptors, derived from one dimensional (1D) shape signatures. Eventually, cells are classified as DC by comparing template matching (TM) of established template and target images. The results show that the proposed scheme is reliable and effective to recognize DC.

Human Actions Analysis: Templates Generation, Matching and Visualization Applied to Motion Capture of Highly-Skilled Karate Athletes

PubMed Central

Piekarczyk, Marcin; Ogiela, Marek R.

2017-01-01

The aim of this paper is to propose and evaluate the novel method of template generation, matching, comparing and visualization applied to motion capture (kinematic) analysis. To evaluate our approach, we have used motion capture recordings (MoCap) of two highly-skilled black belt karate athletes consisting of 560 recordings of various karate techniques acquired with wearable sensors. We have evaluated the quality of generated templates; we have validated the matching algorithm that calculates similarities and differences between various MoCap data; and we have examined visualizations of important differences and similarities between MoCap data. We have concluded that our algorithms works the best when we are dealing with relatively short (2–4 s) actions that might be averaged and aligned with the dynamic time warping framework. In practice, the methodology is designed to optimize the performance of some full body techniques performed in various sport disciplines, for example combat sports and martial arts. We can also use this approach to generate templates or to compare the correct performance of techniques between various top sportsmen in order to generate a knowledge base of reference MoCap videos. The motion template generated by our method can be used for action recognition purposes. We have used the DTW classifier with angle-based features to classify various karate kicks. We have performed leave-one-out action recognition for the Shorin-ryu and Oyama karate master separately. In this case, 100% actions were correctly classified. In another experiment, we used templates generated from Oyama master recordings to classify Shorin-ryu master recordings and vice versa. In this experiment, the overall recognition rate was 94.2%, which is a very good result for this type of complex action. PMID:29125560

Alignment and bit extraction for secure fingerprint biometrics

NASA Astrophysics Data System (ADS)

Nagar, A.; Rane, S.; Vetro, A.

2010-01-01

Security of biometric templates stored in a system is important because a stolen template can compromise system security as well as user privacy. Therefore, a number of secure biometrics schemes have been proposed that facilitate matching of feature templates without the need for a stored biometric sample. However, most of these schemes suffer from poor matching performance owing to the difficulty of designing biometric features that remain robust over repeated biometric measurements. This paper describes a scheme to extract binary features from fingerprints using minutia points and fingerprint ridges. The features are amenable to direct matching based on binary Hamming distance, but are especially suitable for use in secure biometric cryptosystems that use standard error correcting codes. Given all binary features, a method for retaining only the most discriminable features is presented which improves the Genuine Accept Rate (GAR) from 82% to 90% at a False Accept Rate (FAR) of 0.1% on a well-known public database. Additionally, incorporating singular points such as a core or delta feature is shown to improve the matching tradeoff.

[Using neural networks based template matching method to obtain redshifts of normal galaxies].

PubMed

Xu, Xin; Luo, A-li; Wu, Fu-chao; Zhao, Yong-heng

2005-06-01

Galaxies can be divided into two classes: normal galaxy (NG) and active galaxy (AG). In order to determine NG redshifts, an automatic effective method is proposed in this paper, which consists of the following three main steps: (1) From the template of normal galaxy, the two sets of samples are simulated, one with the redshift of 0.0-0.3, the other of 0.3-0.5, then the PCA is used to extract the main components, and train samples are projected to the main component subspace to obtain characteristic spectra. (2) The characteristic spectra are used to train a Probabilistic Neural Network to obtain a Bayes classifier. (3) An unknown real NG spectrum is first inputted to this Bayes classifier to determine the possible range of redshift, then the template matching is invoked to locate the redshift value within the estimated range. Compared with the traditional template matching technique with an unconstrained range, our proposed method not only halves the computational load, but also increases the estimation accuracy. As a result, the proposed method is particularly useful for automatic spectrum processing produced from a large-scale sky survey project.

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.

An improved finger-vein recognition algorithm based on template matching

NASA Astrophysics Data System (ADS)

Liu, Yueyue; Di, Si; Jin, Jian; Huang, Daoping

2016-10-01

Finger-vein recognition has became the most popular biometric identify methods. The investigation on the recognition algorithms always is the key point in this field. So far, there are many applicable algorithms have been developed. However, there are still some problems in practice, such as the variance of the finger position which may lead to the image distortion and shifting; during the identification process, some matching parameters determined according to experience may also reduce the adaptability of algorithm. Focus on above mentioned problems, this paper proposes an improved finger-vein recognition algorithm based on template matching. In order to enhance the robustness of the algorithm for the image distortion, the least squares error method is adopted to correct the oblique finger. During the feature extraction, local adaptive threshold method is adopted. As regard as the matching scores, we optimized the translation preferences as well as matching distance between the input images and register images on the basis of Naoto Miura algorithm. Experimental results indicate that the proposed method can improve the robustness effectively under the finger shifting and rotation conditions.

Component-based target recognition inspired by human vision

NASA Astrophysics Data System (ADS)

Zheng, Yufeng; Agyepong, Kwabena

2009-05-01

In contrast with machine vision, human can recognize an object from complex background with great flexibility. For example, given the task of finding and circling all cars (no further information) in a picture, you may build a virtual image in mind from the task (or target) description before looking at the picture. Specifically, the virtual car image may be composed of the key components such as driver cabin and wheels. In this paper, we propose a component-based target recognition method by simulating the human recognition process. The component templates (equivalent to the virtual image in mind) of the target (car) are manually decomposed from the target feature image. Meanwhile, the edges of the testing image can be extracted by using a difference of Gaussian (DOG) model that simulates the spatiotemporal response in visual process. A phase correlation matching algorithm is then applied to match the templates with the testing edge image. If all key component templates are matched with the examining object, then this object is recognized as the target. Besides the recognition accuracy, we will also investigate if this method works with part targets (half cars). In our experiments, several natural pictures taken on streets were used to test the proposed method. The preliminary results show that the component-based recognition method is very promising.

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

A flexible and robust approach for segmenting cell nuclei from 2D microscopy images using supervised learning and template matching

PubMed Central

Chen, Cheng; Wang, Wei; Ozolek, John A.; Rohde, Gustavo K.

2013-01-01

We describe a new supervised learning-based template matching approach for segmenting cell nuclei from microscopy images. The method uses examples selected by a user for building a statistical model which captures the texture and shape variations of the nuclear structures from a given dataset to be segmented. Segmentation of subsequent, unlabeled, images is then performed by finding the model instance that best matches (in the normalized cross correlation sense) local neighborhood in the input image. We demonstrate the application of our method to segmenting nuclei from a variety of imaging modalities, and quantitatively compare our results to several other methods. Quantitative results using both simulated and real image data show that, while certain methods may work well for certain imaging modalities, our software is able to obtain high accuracy across several imaging modalities studied. Results also demonstrate that, relative to several existing methods, the template-based method we propose presents increased robustness in the sense of better handling variations in illumination, variations in texture from different imaging modalities, providing more smooth and accurate segmentation borders, as well as handling better cluttered nuclei. PMID:23568787

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

A multibiometric face recognition fusion framework with template protection

NASA Astrophysics Data System (ADS)

Chindaro, S.; Deravi, F.; Zhou, Z.; Ng, M. W. R.; Castro Neves, M.; Zhou, X.; Kelkboom, E.

2010-04-01

In this work we present a multibiometric face recognition framework based on combining information from 2D with 3D facial features. The 3D biometrics channel is protected by a privacy enhancing technology, which uses error correcting codes and cryptographic primitives to safeguard the privacy of the users of the biometric system at the same time enabling accurate matching through fusion with 2D. Experiments are conducted to compare the matching performance of such multibiometric systems with the individual biometric channels working alone and with unprotected multibiometric systems. The results show that the proposed hybrid system incorporating template protection, match and in some cases exceed the performance of corresponding unprotected equivalents, in addition to offering the additional privacy protection.

Template matching for auditing hospital cost and quality.

PubMed

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Mukherjee, Nabanita; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-10-01

Develop an improved method for auditing hospital cost and quality. Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, Texas, and New York between 2004 and 2006. A template of 300 representative patients was constructed and then used to match 300 patients at hospitals that had a minimum of 500 patients over a 3-year study period. From each of 217 hospitals we chose 300 patients most resembling the template using multivariate matching. The matching algorithm found close matches on procedures and patient characteristics, far more balanced than measured covariates would be in a randomized clinical trial. These matched samples displayed little to no differences across hospitals in common patient characteristics yet found large and statistically significant hospital variation in mortality, complications, failure-to-rescue, readmissions, length of stay, ICU days, cost, and surgical procedure length. Similar patients at different hospitals had substantially different outcomes. The template-matched sample can produce fair, directly standardized audits that evaluate hospitals on patients with similar characteristics, thereby making benchmarking more believable. Through examining matched samples of individual patients, administrators can better detect poor performance at their hospitals and better understand why these problems are occurring. © Health Research and Educational Trust.

A hospital-specific template for benchmarking its cost and quality.

PubMed

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-10-01

Develop an improved method for auditing hospital cost and quality tailored to a specific hospital's patient population. Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, New York, and Texas between 2004 and 2006. A template of 300 representative patients from a single index hospital was constructed and used to match 300 patients at 43 hospitals that had a minimum of 500 patients over a 3-year study period. From each of 43 hospitals we chose 300 patients most resembling the template using multivariate matching. We found close matches on procedures and patient characteristics, far more balanced than would be expected in a randomized trial. There were little to no differences between the index hospital's template and the 43 hospitals on most patient characteristics yet large and significant differences in mortality, failure-to-rescue, and cost. Matching can produce fair, directly standardized audits. From the perspective of the index hospital, "hospital-specific" template matching provides the fairness of direct standardization with the specific institutional relevance of indirect standardization. Using this approach, hospitals will be better able to examine their performance, and better determine why they are achieving the results they observe. © Health Research and Educational Trust.

Multiple template-based fluoroscopic tracking of lung tumor mass without implanted fiducial markers

NASA Astrophysics Data System (ADS)

Cui, Ying; Dy, Jennifer G.; Sharp, Gregory C.; Alexander, Brian; Jiang, Steve B.

2007-10-01

Precise lung tumor localization in real time is particularly important for some motion management techniques, such as respiratory gating or beam tracking with a dynamic multi-leaf collimator, due to the reduced clinical tumor volume (CTV) to planning target volume (PTV) margin and/or the escalated dose. There might be large uncertainties in deriving tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using a template matching method (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007 Phys. Med. Biol. 52 741-55). In this paper, we present an extension of this method to multiple-template matching for directly tracking the lung tumor mass in fluoroscopy video. The basic idea is as follows: (i) during the patient setup session, a pair of orthogonal fluoroscopic image sequences are taken and processed off-line to generate a set of reference templates that correspond to different breathing phases and tumor positions; (ii) during treatment delivery, fluoroscopic images are continuously acquired and processed; (iii) the similarity between each reference template and the processed incoming image is calculated; (iv) the tumor position in the incoming image is then estimated by combining the tumor centroid coordinates in reference templates with proper weights based on the measured similarities. With different handling of image processing and similarity calculation, two such multiple-template tracking techniques have been developed: one based on motion-enhanced templates and Pearson's correlation score while the other based on eigen templates and mean-squared error. The developed techniques have been tested on six sequences of fluoroscopic images from six lung cancer patients against the reference tumor positions manually determined by a radiation oncologist. The tumor centroid coordinates automatically detected using both methods agree well with the manually marked reference locations. The eigenspace tracking method performs slightly better than the motion-enhanced method, with average localization errors less than 2 pixels (1 mm) and the error at a 95% confidence level of about 2-4 pixels (1-2 mm). This work demonstrates the feasibility of direct tracking of a lung tumor mass in fluoroscopic images without implanted fiducial markers using multiple reference templates.

Content analysis of physical examination templates in electronic health records using SNOMED CT.

PubMed

Gøeg, Kirstine Rosenbeck; Chen, Rong; Højen, Anne Randorff; Elberg, Pia

2014-10-01

Most electronic health record (EHR) systems are built on proprietary information models and terminology, which makes achieving semantic interoperability a challenge. Solving interoperability problems requires well-defined standards. In contrast, the need to support clinical work practice requires a local customization of EHR systems. Consequently, contrasting goals may be evident in EHR template design because customization means that local EHR organizations can define their own templates, whereas standardization implies consensus at some level. To explore the complexity of balancing these two goals, this study analyzes the differences and similarities between templates in use today. A similarity analysis was developed on the basis of SNOMED CT. The analysis was performed on four physical examination templates from Denmark and Sweden. The semantic relationships in SNOMED CT were used to quantify similarities and differences. Moreover, the analysis used these identified similarities to investigate the common content of a physical examination template. The analysis showed that there were both similarities and differences in physical examination templates, and the size of the templates varied from 18 to 49 fields. In the SNOMED CT analysis, exact matches and terminology similarities were represented in all template pairs. The number of exact matches ranged from 7 to 24. Moreover, the number of unrelated fields differed a lot from 1/18 to 22/35. Cross-country comparisons tended to have more unrelated content than within-country comparisons. On the basis of identified similarities, it was possible to define the common content of a physical examination. Nevertheless, a complete view on the physical examination required the inclusion of both exact matches and terminology similarities. This study revealed that a core set of items representing the physical examination templates can be generated when the analysis takes into account not only exact matches but also terminology similarities. This core set of items could be a starting point for standardization and semantic interoperability. However, both unmatched terms and terminology matched terms pose a challenge for standardization. Future work will include using local templates as a point of departure in standardization to see if local requirements can be maintained in a standardized framework. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Template Matching for Auditing Hospital Cost and Quality

PubMed Central

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Mukherjee, Nabanita; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-01-01

Objective Develop an improved method for auditing hospital cost and quality. Data Sources/Setting Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, Texas, and New York between 2004 and 2006. Study Design A template of 300 representative patients was constructed and then used to match 300 patients at hospitals that had a minimum of 500 patients over a 3-year study period. Data Collection/Extraction Methods From each of 217 hospitals we chose 300 patients most resembling the template using multivariate matching. Principal Findings The matching algorithm found close matches on procedures and patient characteristics, far more balanced than measured covariates would be in a randomized clinical trial. These matched samples displayed little to no differences across hospitals in common patient characteristics yet found large and statistically significant hospital variation in mortality, complications, failure-to-rescue, readmissions, length of stay, ICU days, cost, and surgical procedure length. Similar patients at different hospitals had substantially different outcomes. Conclusion The template-matched sample can produce fair, directly standardized audits that evaluate hospitals on patients with similar characteristics, thereby making benchmarking more believable. Through examining matched samples of individual patients, administrators can better detect poor performance at their hospitals and better understand why these problems are occurring. PMID:24588413

Adding a Zero-Crossing Count to Spectral Information in Template-Based Speech Recognition

DTIC Science & Technology

1982-01-01

incorporation of zero-crossing information into the spectral representation used in a template-matching system ( cIcADA ). An analysis of zero-crossing data for an...procedure to be used. The work described in this paper was done using the CICADA system developed at Carnegie-Mellon University [Alleva 81, Waibel 801... CICADA uses a representation based on a compression of the short-term spectrum according to a 16 coefficient mel scale. Let us consider the CICADA

Template match using local feature with view invariance

NASA Astrophysics Data System (ADS)

Lu, Cen; Zhou, Gang

2013-10-01

Matching the template image in the target image is the fundamental task in the field of computer vision. Aiming at the deficiency in the traditional image matching methods and inaccurate matching in scene image with rotation, illumination and view changing, a novel matching algorithm using local features are proposed in this paper. The local histograms of the edge pixels (LHoE) are extracted as the invariable feature to resist view and brightness changing. The merits of the LHoE is that the edge points have been little affected with view changing, and the LHoE can resist not only illumination variance but also the polution of noise. For the process of matching are excuded only on the edge points, the computation burden are highly reduced. Additionally, our approach is conceptually simple, easy to implement and do not need the training phase. The view changing can be considered as the combination of rotation, illumination and shear transformation. Experimental results on simulated and real data demonstrated that the proposed approach is superior to NCC(Normalized cross-correlation) and Histogram-based methods with view changing.

Rapid and Robust Cross-Correlation-Based Seismic Signal Identification Using an Approximate Nearest Neighbor Method

DOE PAGES

Tibi, Rigobert; Young, Christopher; Gonzales, Antonio; ...

2017-07-04

The matched filtering technique that uses the cross correlation of a waveform of interest with archived signals from a template library has proven to be a powerful tool for detecting events in regions with repeating seismicity. However, waveform correlation is computationally expensive and therefore impractical for large template sets unless dedicated distributed computing hardware and software are used. In this paper, we introduce an approximate nearest neighbor (ANN) approach that enables the use of very large template libraries for waveform correlation. Our method begins with a projection into a reduced dimensionality space, based on correlation with a randomized subset ofmore » the full template archive. Searching for a specified number of nearest neighbors for a query waveform is accomplished by iteratively comparing it with the neighbors of its immediate neighbors. We used the approach to search for matches to each of ~2300 analyst-reviewed signal detections reported in May 2010 for the International Monitoring System station MKAR. The template library in this case consists of a data set of more than 200,000 analyst-reviewed signal detections for the same station from February 2002 to July 2016 (excluding May 2010). Of these signal detections, 73% are teleseismic first P and 17% regional phases (Pn, Pg, Sn, and Lg). Finally, the analyses performed on a standard desktop computer show that the proposed ANN approach performs a search of the large template libraries about 25 times faster than the standard full linear search and achieves recall rates greater than 80%, with the recall rate increasing for higher correlation thresholds.« less

Rapid and Robust Cross-Correlation-Based Seismic Signal Identification Using an Approximate Nearest Neighbor Method

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

Tibi, Rigobert; Young, Christopher; Gonzales, Antonio

The matched filtering technique that uses the cross correlation of a waveform of interest with archived signals from a template library has proven to be a powerful tool for detecting events in regions with repeating seismicity. However, waveform correlation is computationally expensive and therefore impractical for large template sets unless dedicated distributed computing hardware and software are used. In this paper, we introduce an approximate nearest neighbor (ANN) approach that enables the use of very large template libraries for waveform correlation. Our method begins with a projection into a reduced dimensionality space, based on correlation with a randomized subset ofmore » the full template archive. Searching for a specified number of nearest neighbors for a query waveform is accomplished by iteratively comparing it with the neighbors of its immediate neighbors. We used the approach to search for matches to each of ~2300 analyst-reviewed signal detections reported in May 2010 for the International Monitoring System station MKAR. The template library in this case consists of a data set of more than 200,000 analyst-reviewed signal detections for the same station from February 2002 to July 2016 (excluding May 2010). Of these signal detections, 73% are teleseismic first P and 17% regional phases (Pn, Pg, Sn, and Lg). Finally, the analyses performed on a standard desktop computer show that the proposed ANN approach performs a search of the large template libraries about 25 times faster than the standard full linear search and achieves recall rates greater than 80%, with the recall rate increasing for higher correlation thresholds.« less

CONEDEP: COnvolutional Neural network based Earthquake DEtection and Phase Picking

NASA Astrophysics Data System (ADS)

Zhou, Y.; Huang, Y.; Yue, H.; Zhou, S.; An, S.; Yun, N.

2017-12-01

We developed an automatic local earthquake detection and phase picking algorithm based on Fully Convolutional Neural network (FCN). The FCN algorithm detects and segments certain features (phases) in 3 component seismograms to realize efficient picking. We use STA/LTA algorithm and template matching algorithm to construct the training set from seismograms recorded 1 month before and after the Wenchuan earthquake. Precise P and S phases are identified and labeled to construct the training set. Noise data are produced by combining back-ground noise and artificial synthetic noise to form the equivalent scale of noise set as the signal set. Training is performed on GPUs to achieve efficient convergence. Our algorithm has significantly improved performance in terms of the detection rate and precision in comparison with STA/LTA and template matching algorithms.

GASS-WEB: a web server for identifying enzyme active sites based on genetic algorithms.

PubMed

Moraes, João P A; Pappa, Gisele L; Pires, Douglas E V; Izidoro, Sandro C

2017-07-03

Enzyme active sites are important and conserved functional regions of proteins whose identification can be an invaluable step toward protein function prediction. Most of the existing methods for this task are based on active site similarity and present limitations including performing only exact matches on template residues, template size restraints, despite not being capable of finding inter-domain active sites. To fill this gap, we proposed GASS-WEB, a user-friendly web server that uses GASS (Genetic Active Site Search), a method based on an evolutionary algorithm to search for similar active sites in proteins. GASS-WEB can be used under two different scenarios: (i) given a protein of interest, to match a set of specific active site templates; or (ii) given an active site template, looking for it in a database of protein structures. The method has shown to be very effective on a range of experiments and was able to correctly identify >90% of the catalogued active sites from the Catalytic Site Atlas. It also managed to achieve a Matthew correlation coefficient of 0.63 using the Critical Assessment of protein Structure Prediction (CASP 10) dataset. In our analysis, GASS was ranking fourth among 18 methods. GASS-WEB is freely available at http://gass.unifei.edu.br/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

System and method for detection of dispersed broadband signals

DOEpatents

Qian, S.; Dunham, M.E.

1999-06-08

A system and method for detecting the presence of dispersed broadband signals in real time are disclosed. The present invention utilizes a bank of matched filters for detecting the received dispersed broadband signals. Each matched filter uses a respective robust time template that has been designed to approximate the dispersed broadband signals of interest, and each time template varies across a spectrum of possible dispersed broadband signal time templates. The received dispersed broadband signal x(t) is received by each of the matched filters, and if one or more matches occurs, then the received data is determined to have signal data of interest. This signal data can then be analyzed and/or transmitted to Earth for analysis, as desired. The system and method of the present invention will prove extremely useful in many fields, including satellite communications, plasma physics, and interstellar research. The varying time templates used in the bank of matched filters are determined as follows. The robust time domain template is assumed to take the form w(t)=A(t)cos[l brace]2[phi](t)[r brace]. Since the instantaneous frequency f(t) is known to be equal to the derivative of the phase [phi](t), the trajectory of a joint time-frequency representation of x(t) is used as an approximation of [phi][prime](t). 10 figs.

System and method for detection of dispersed broadband signals

DOEpatents

Qian, Shie; Dunham, Mark E.

1999-06-08

A system and method for detecting the presence of dispersed broadband signals in real time. The present invention utilizes a bank of matched filters for detecting the received dispersed broadband signals. Each matched filter uses a respective robust time template that has been designed to approximate the dispersed broadband signals of interest, and each time template varies across a spectrum of possible dispersed broadband signal time templates. The received dispersed broadband signal x(t) is received by each of the matched filters, and if one or more matches occurs, then the received data is determined to have signal data of interest. This signal data can then be analyzed and/or transmitted to Earth for analysis, as desired. The system and method of the present invention will prove extremely useful in many fields, including satellite communications, plasma physics, and interstellar research. The varying time templates used in the bank of matched filters are determined as follows. The robust time domain template is assumed to take the form w(t)=A(t)cos{2.phi.(t)}. Since the instantaneous frequency f(t) is known to be equal to the derivative of the phase .phi.(t), the trajectory of a joint time-frequency representation of x(t) is used as an approximation of .phi.'(t).

A Hospital-Specific Template for Benchmarking its Cost and Quality

PubMed Central

Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

2014-01-01

Objective Develop an improved method for auditing hospital cost and quality tailored to a specific hospital’s patient population. Data Sources/Setting Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, New York, and Texas between 2004 and 2006. Study Design A template of 300 representative patients from a single index hospital was constructed and used to match 300 patients at 43 hospitals that had a minimum of 500 patients over a 3-year study period. Data Collection/Extraction Methods From each of 43 hospitals we chose 300 patients most resembling the template using multivariate matching. Principal Findings We found close matches on procedures and patient characteristics, far more balanced than would be expected in a randomized trial. There were little to no differences between the index hospital’s template and the 43 hospitals on most patient characteristics yet large and significant differences in mortality, failure-to-rescue, and cost. Conclusion Matching can produce fair, directly standardized audits. From the perspective of the index hospital, “hospital-specific” template matching provides the fairness of direct standardization with the specific institutional relevance of indirect standardization. Using this approach, hospitals will be better able to examine their performance, and better determine why they are achieving the results they observe. PMID:25201167

A model-based 3D template matching technique for pose acquisition of an uncooperative space object.

PubMed

Opromolla, Roberto; Fasano, Giancarmine; Rufino, Giancarlo; Grassi, Michele

2015-03-16

This paper presents a customized three-dimensional template matching technique for autonomous pose determination of uncooperative targets. This topic is relevant to advanced space applications, like active debris removal and on-orbit servicing. The proposed technique is model-based and produces estimates of the target pose without any prior pose information, by processing three-dimensional point clouds provided by a LIDAR. These estimates are then used to initialize a pose tracking algorithm. Peculiar features of the proposed approach are the use of a reduced number of templates and the idea of building the database of templates on-line, thus significantly reducing the amount of on-board stored data with respect to traditional techniques. An algorithm variant is also introduced aimed at further accelerating the pose acquisition time and reducing the computational cost. Technique performance is investigated within a realistic numerical simulation environment comprising a target model, LIDAR operation and various target-chaser relative dynamics scenarios, relevant to close-proximity flight operations. Specifically, the capability of the proposed techniques to provide a pose solution suitable to initialize the tracking algorithm is demonstrated, as well as their robustness against highly variable pose conditions determined by the relative dynamics. Finally, a criterion for autonomous failure detection of the presented techniques is presented.

Hybrid geometric-random template-placement algorithm for gravitational wave searches from compact binary coalescences

NASA Astrophysics Data System (ADS)

Roy, Soumen; Sengupta, Anand S.; Thakor, Nilay

2017-05-01

Astrophysical compact binary systems consisting of neutron stars and black holes are an important class of gravitational wave (GW) sources for advanced LIGO detectors. Accurate theoretical waveform models from the inspiral, merger, and ringdown phases of such systems are used to filter detector data under the template-based matched-filtering paradigm. An efficient grid over the parameter space at a fixed minimal match has a direct impact on the overall time taken by these searches. We present a new hybrid geometric-random template placement algorithm for signals described by parameters of two masses and one spin magnitude. Such template banks could potentially be used in GW searches from binary neutron stars and neutron star-black hole systems. The template placement is robust and is able to automatically accommodate curvature and boundary effects with no fine-tuning. We also compare these banks against vanilla stochastic template banks and show that while both are equally efficient in the fitting-factor sense, the bank sizes are ˜25 % larger in the stochastic method. Further, we show that the generation of the proposed hybrid banks can be sped up by nearly an order of magnitude over the stochastic bank. Generic issues related to optimal implementation are discussed in detail. These improvements are expected to directly reduce the computational cost of gravitational wave searches.

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.

Improving and Assessing Planet Sensitivity of the GPI Exoplanet Survey with a Forward Model Matched Filter

NASA Astrophysics Data System (ADS)

Ruffio, Jean-Baptiste; Macintosh, Bruce; Wang, Jason J.; Pueyo, Laurent; Nielsen, Eric L.; De Rosa, Robert J.; Czekala, Ian; Marley, Mark S.; Arriaga, Pauline; Bailey, Vanessa P.; Barman, Travis; Bulger, Joanna; Chilcote, Jeffrey; Cotten, Tara; Doyon, Rene; Duchêne, Gaspard; Fitzgerald, Michael P.; Follette, Katherine B.; Gerard, Benjamin L.; Goodsell, Stephen J.; Graham, James R.; Greenbaum, Alexandra Z.; Hibon, Pascale; Hung, Li-Wei; Ingraham, Patrick; Kalas, Paul; Konopacky, Quinn; Larkin, James E.; Maire, Jérôme; Marchis, Franck; Marois, Christian; Metchev, Stanimir; Millar-Blanchaer, Maxwell A.; Morzinski, Katie M.; Oppenheimer, Rebecca; Palmer, David; Patience, Jennifer; Perrin, Marshall; Poyneer, Lisa; Rajan, Abhijith; Rameau, Julien; Rantakyrö, Fredrik T.; Savransky, Dmitry; Schneider, Adam C.; Sivaramakrishnan, Anand; Song, Inseok; Soummer, Remi; Thomas, Sandrine; Wallace, J. Kent; Ward-Duong, Kimberly; Wiktorowicz, Sloane; Wolff, Schuyler

2017-06-01

We present a new matched-filter algorithm for direct detection of point sources in the immediate vicinity of bright stars. The stellar point-spread function (PSF) is first subtracted using a Karhunen-Loéve image processing (KLIP) algorithm with angular and spectral differential imaging (ADI and SDI). The KLIP-induced distortion of the astrophysical signal is included in the matched-filter template by computing a forward model of the PSF at every position in the image. To optimize the performance of the algorithm, we conduct extensive planet injection and recovery tests and tune the exoplanet spectra template and KLIP reduction aggressiveness to maximize the signal-to-noise ratio (S/N) of the recovered planets. We show that only two spectral templates are necessary to recover any young Jovian exoplanets with minimal S/N loss. We also developed a complete pipeline for the automated detection of point-source candidates, the calculation of receiver operating characteristics (ROC), contrast curves based on false positives, and completeness contours. We process in a uniform manner more than 330 data sets from the Gemini Planet Imager Exoplanet Survey and assess GPI typical sensitivity as a function of the star and the hypothetical companion spectral type. This work allows for the first time a comparison of different detection algorithms at a survey scale accounting for both planet completeness and false-positive rate. We show that the new forward model matched filter allows the detection of 50% fainter objects than a conventional cross-correlation technique with a Gaussian PSF template for the same false-positive rate.

Automatic capture of attention by conceptually generated working memory templates.

PubMed

Sun, Sol Z; Shen, Jenny; Shaw, Mark; Cant, Jonathan S; Ferber, Susanne

2015-08-01

Many theories of attention propose that the contents of working memory (WM) can act as an attentional template, which biases processing in favor of perceptually similar inputs. While support has been found for this claim, it is unclear how attentional templates are generated when searching real-world environments. We hypothesized that in naturalistic settings, attentional templates are commonly generated from conceptual knowledge, an idea consistent with sensorimotor models of knowledge representation. Participants performed a visual search task in the delay period of a WM task, where the item in memory was either a colored disk or a word associated with a color concept (e.g., "Rose," associated with red). During search, we manipulated whether a singleton distractor in the array matched the contents of WM. Overall, we found that search times were impaired in the presence of a memory-matching distractor. Furthermore, the degree of impairment did not differ based on the contents of WM. Put differently, regardless of whether participants were maintaining a perceptually colored disk identical to the singleton distractor, or whether they were simply maintaining a word associated with the color of the distractor, the magnitude of attentional capture was the same. Our results suggest that attentional templates can be generated from conceptual knowledge, in the physical absence of the visual feature.

Learning templates for artistic portrait lighting analysis.

PubMed

Chen, Xiaowu; Jin, Xin; Wu, Hongyu; Zhao, Qinping

2015-02-01

Lighting is a key factor in creating impressive artistic portraits. In this paper, we propose to analyze portrait lighting by learning templates of lighting styles. Inspired by the experience of artists, we first define several novel features that describe the local contrasts in various face regions. The most informative features are then selected with a stepwise feature pursuit algorithm to derive the templates of various lighting styles. After that, the matching scores that measure the similarity between a testing portrait and those templates are calculated for lighting style classification. Furthermore, we train a regression model by the subjective scores and the feature responses of a template to predict the score of a portrait lighting quality. Based on the templates, a novel face illumination descriptor is defined to measure the difference between two portrait lightings. Experimental results show that the learned templates can well describe the lighting styles, whereas the proposed approach can assess the lighting quality of artistic portraits as human being does.

A coarse-to-fine kernel matching approach for mean-shift based visual tracking

NASA Astrophysics Data System (ADS)

Liangfu, L.; Zuren, F.; Weidong, C.; Ming, J.

2009-03-01

Mean shift is an efficient pattern match algorithm. It is widely used in visual tracking fields since it need not perform whole search in the image space. It employs gradient optimization method to reduce the time of feature matching and realize rapid object localization, and uses Bhattacharyya coefficient as the similarity measure between object template and candidate template. This thesis presents a mean shift algorithm based on coarse-to-fine search for the best kernel matching. This paper researches for object tracking with large motion area based on mean shift. To realize efficient tracking of such an object, we present a kernel matching method from coarseness to fine. If the motion areas of the object between two frames are very large and they are not overlapped in image space, then the traditional mean shift method can only obtain local optimal value by iterative computing in the old object window area, so the real tracking position cannot be obtained and the object tracking will be disabled. Our proposed algorithm can efficiently use a similarity measure function to realize the rough location of motion object, then use mean shift method to obtain the accurate local optimal value by iterative computing, which successfully realizes object tracking with large motion. Experimental results show its good performance in accuracy and speed when compared with background-weighted histogram algorithm in the literature.

Automatic generation of endocardial surface meshes with 1-to-1 correspondence from cine-MR images

NASA Astrophysics Data System (ADS)

Su, Yi; Teo, S.-K.; Lim, C. W.; Zhong, L.; Tan, R. S.

2015-03-01

In this work, we develop an automatic method to generate a set of 4D 1-to-1 corresponding surface meshes of the left ventricle (LV) endocardial surface which are motion registered over the whole cardiac cycle. These 4D meshes have 1- to-1 point correspondence over the entire set, and is suitable for advanced computational processing, such as shape analysis, motion analysis and finite element modelling. The inputs to the method are the set of 3D LV endocardial surface meshes of the different frames/phases of the cardiac cycle. Each of these meshes is reconstructed independently from border-delineated MR images and they have no correspondence in terms of number of vertices/points and mesh connectivity. To generate point correspondence, the first frame of the LV mesh model is used as a template to be matched to the shape of the meshes in the subsequent phases. There are two stages in the mesh correspondence process: (1) a coarse matching phase, and (2) a fine matching phase. In the coarse matching phase, an initial rough matching between the template and the target is achieved using a radial basis function (RBF) morphing process. The feature points on the template and target meshes are automatically identified using a 16-segment nomenclature of the LV. In the fine matching phase, a progressive mesh projection process is used to conform the rough estimate to fit the exact shape of the target. In addition, an optimization-based smoothing process is used to achieve superior mesh quality and continuous point motion.

An eFTD-VP framework for efficiently generating patient-specific anatomically detailed facial soft tissue FE mesh for craniomaxillofacial surgery simulation

PubMed Central

Zhang, Xiaoyan; Kim, Daeseung; Shen, Shunyao; Yuan, Peng; Liu, Siting; Tang, Zhen; Zhang, Guangming; Zhou, Xiaobo; Gateno, Jaime

2017-01-01

Accurate surgical planning and prediction of craniomaxillofacial surgery outcome requires simulation of soft tissue changes following osteotomy. This can only be achieved by using an anatomically detailed facial soft tissue model. The current state-of-the-art of model generation is not appropriate to clinical applications due to the time-intensive nature of manual segmentation and volumetric mesh generation. The conventional patient-specific finite element (FE) mesh generation methods are to deform a template FE mesh to match the shape of a patient based on registration. However, these methods commonly produce element distortion. Additionally, the mesh density for patients depends on that of the template model. It could not be adjusted to conduct mesh density sensitivity analysis. In this study, we propose a new framework of patient-specific facial soft tissue FE mesh generation. The goal of the developed method is to efficiently generate a high-quality patient-specific hexahedral FE mesh with adjustable mesh density while preserving the accuracy in anatomical structure correspondence. Our FE mesh is generated by eFace template deformation followed by volumetric parametrization. First, the patient-specific anatomically detailed facial soft tissue model (including skin, mucosa, and muscles) is generated by deforming an eFace template model. The adaptation of the eFace template model is achieved by using a hybrid landmark-based morphing and dense surface fitting approach followed by a thin-plate spline interpolation. Then, high-quality hexahedral mesh is constructed by using volumetric parameterization. The user can control the resolution of hexahedron mesh to best reflect clinicians’ need. Our approach was validated using 30 patient models and 4 visible human datasets. The generated patient-specific FE mesh showed high surface matching accuracy, element quality, and internal structure matching accuracy. They can be directly and effectively used for clinical simulation of facial soft tissue change. PMID:29027022

An eFTD-VP framework for efficiently generating patient-specific anatomically detailed facial soft tissue FE mesh for craniomaxillofacial surgery simulation.

PubMed

Zhang, Xiaoyan; Kim, Daeseung; Shen, Shunyao; Yuan, Peng; Liu, Siting; Tang, Zhen; Zhang, Guangming; Zhou, Xiaobo; Gateno, Jaime; Liebschner, Michael A K; Xia, James J

2018-04-01

Accurate surgical planning and prediction of craniomaxillofacial surgery outcome requires simulation of soft tissue changes following osteotomy. This can only be achieved by using an anatomically detailed facial soft tissue model. The current state-of-the-art of model generation is not appropriate to clinical applications due to the time-intensive nature of manual segmentation and volumetric mesh generation. The conventional patient-specific finite element (FE) mesh generation methods are to deform a template FE mesh to match the shape of a patient based on registration. However, these methods commonly produce element distortion. Additionally, the mesh density for patients depends on that of the template model. It could not be adjusted to conduct mesh density sensitivity analysis. In this study, we propose a new framework of patient-specific facial soft tissue FE mesh generation. The goal of the developed method is to efficiently generate a high-quality patient-specific hexahedral FE mesh with adjustable mesh density while preserving the accuracy in anatomical structure correspondence. Our FE mesh is generated by eFace template deformation followed by volumetric parametrization. First, the patient-specific anatomically detailed facial soft tissue model (including skin, mucosa, and muscles) is generated by deforming an eFace template model. The adaptation of the eFace template model is achieved by using a hybrid landmark-based morphing and dense surface fitting approach followed by a thin-plate spline interpolation. Then, high-quality hexahedral mesh is constructed by using volumetric parameterization. The user can control the resolution of hexahedron mesh to best reflect clinicians' need. Our approach was validated using 30 patient models and 4 visible human datasets. The generated patient-specific FE mesh showed high surface matching accuracy, element quality, and internal structure matching accuracy. They can be directly and effectively used for clinical simulation of facial soft tissue change.

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.

Improving and Assessing Planet Sensitivity of the GPI Exoplanet Survey with a Forward Model Matched Filter

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

Ruffio, Jean-Baptiste; Macintosh, Bruce; Nielsen, Eric L.

We present a new matched-filter algorithm for direct detection of point sources in the immediate vicinity of bright stars. The stellar point-spread function (PSF) is first subtracted using a Karhunen-Loéve image processing (KLIP) algorithm with angular and spectral differential imaging (ADI and SDI). The KLIP-induced distortion of the astrophysical signal is included in the matched-filter template by computing a forward model of the PSF at every position in the image. To optimize the performance of the algorithm, we conduct extensive planet injection and recovery tests and tune the exoplanet spectra template and KLIP reduction aggressiveness to maximize the signal-to-noise ratiomore » (S/N) of the recovered planets. We show that only two spectral templates are necessary to recover any young Jovian exoplanets with minimal S/N loss. We also developed a complete pipeline for the automated detection of point-source candidates, the calculation of receiver operating characteristics (ROC), contrast curves based on false positives, and completeness contours. We process in a uniform manner more than 330 data sets from the Gemini Planet Imager Exoplanet Survey and assess GPI typical sensitivity as a function of the star and the hypothetical companion spectral type. This work allows for the first time a comparison of different detection algorithms at a survey scale accounting for both planet completeness and false-positive rate. We show that the new forward model matched filter allows the detection of 50% fainter objects than a conventional cross-correlation technique with a Gaussian PSF template for the same false-positive rate.« less

A KARAOKE System Singing Evaluation Method that More Closely Matches Human Evaluation

NASA Astrophysics Data System (ADS)

Takeuchi, Hideyo; Hoguro, Masahiro; Umezaki, Taizo

KARAOKE is a popular amusement for old and young. Many KARAOKE machines have singing evaluation function. However, it is often said that the scores given by KARAOKE machines do not match human evaluation. In this paper a KARAOKE scoring method strongly correlated with human evaluation is proposed. This paper proposes a way to evaluate songs based on the distance between singing pitch and musical scale, employing a vibrato extraction method based on template matching of spectrum. The results show that correlation coefficients between scores given by the proposed system and human evaluation are -0.76∼-0.89.

Study of moving object detecting and tracking algorithm for video surveillance system

NASA Astrophysics Data System (ADS)

Wang, Tao; Zhang, Rongfu

2010-10-01

This paper describes a specific process of moving target detecting and tracking in the video surveillance.Obtain high-quality background is the key to achieving differential target detecting in the video surveillance.The paper is based on a block segmentation method to build clear background,and using the method of background difference to detecing moving target,after a series of treatment we can be extracted the more comprehensive object from original image,then using the smallest bounding rectangle to locate the object.In the video surveillance system, the delay of camera and other reasons lead to tracking lag,the model of Kalman filter based on template matching was proposed,using deduced and estimated capacity of Kalman,the center of smallest bounding rectangle for predictive value,predicted the position in the next moment may appare,followed by template matching in the region as the center of this position,by calculate the cross-correlation similarity of current image and reference image,can determine the best matching center.As narrowed the scope of searching,thereby reduced the searching time,so there be achieve fast-tracking.

Detection and Counting of Orchard Trees from Vhr Images Using a Geometrical-Optical Model and Marked Template Matching

NASA Astrophysics Data System (ADS)

Maillard, Philippe; Gomes, Marília F.

2016-06-01

This article presents an original algorithm created to detect and count trees in orchards using very high resolution images. The algorithm is based on an adaptation of the "template matching" image processing approach, in which the template is based on a "geometricaloptical" model created from a series of parameters, such as illumination angles, maximum and ambient radiance, and tree size specifications. The algorithm is tested on four images from different regions of the world and different crop types. These images all have < 1 meter spatial resolution and were downloaded from the GoogleEarth application. Results show that the algorithm is very efficient at detecting and counting trees as long as their spectral and spatial characteristics are relatively constant. For walnut, mango and orange trees, the overall accuracy was clearly above 90%. However, the overall success rate for apple trees fell under 75%. It appears that the openness of the apple tree crown is most probably responsible for this poorer result. The algorithm is fully explained with a step-by-step description. At this stage, the algorithm still requires quite a bit of user interaction. The automatic determination of most of the required parameters is under development.

Effects of Channel Modification on Detection and Dating of Fault Scarps

NASA Astrophysics Data System (ADS)

Sare, R.; Hilley, G. E.

2016-12-01

Template matching of scarp-like features could potentially generate morphologic age estimates for individual scarps over entire regions, but data noise and scarp modification limits detection of fault scarps by this method. Template functions based on diffusion in the cross-scarp direction may fail to accurately date scarps near channel boundaries. Where channels reduce scarp amplitudes, or where cross-scarp noise is significant, signal-to-noise ratios decrease and the scarp may be poorly resolved. In this contribution, we explore the bias in morphologic age of a complex scarp produced by systematic changes in fault scarp curvature. For example, fault scarps may be modified by encroaching channel banks and mass failure, lateral diffusion of material into a channel, or undercutting parallel to the base of a scarp. We quantify such biases on morphologic age estimates using a block offset model subject to two-dimensional linear diffusion. We carry out a synthetic study of the effects of two-dimensional transport on morphologic age calculated using a profile model, and compare these results to a well- studied and constrained site along the San Andreas Fault at Wallace Creek, CA. This study serves as a first step towards defining regions of high confidence in template matching results based on scarp length, channel geometry, and near-scarp topography.

Performance evaluation of non-targeted peak-based cross-sample analysis for comprehensive two-dimensional gas chromatography-mass spectrometry data and application to processed hazelnut profiling.

PubMed

Kiefl, Johannes; Cordero, Chiara; Nicolotti, Luca; Schieberle, Peter; Reichenbach, Stephen E; Bicchi, Carlo

2012-06-22

The continuous interest in non-targeted profiling induced the development of tools for automated cross-sample analysis. Such tools were found to be selective or not comprehensive thus delivering a biased view on the qualitative/quantitative peak distribution across 2D sample chromatograms. Therefore, the performance of non-targeted approaches needs to be critically evaluated. This study focused on the development of a validation procedure for non-targeted, peak-based, GC×GC-MS data profiling. The procedure introduced performance parameters such as specificity, precision, accuracy, and uncertainty for a profiling method known as Comprehensive Template Matching. The performance was assessed by applying a three-week validation protocol based on CITAC/EURACHEM guidelines. Optimized ¹D and ²D retention times search windows, MS match factor threshold, detection threshold, and template threshold were evolved from two training sets by a semi-automated learning process. The effectiveness of proposed settings to consistently match 2D peak patterns was established by evaluating the rate of mismatched peaks and was expressed in terms of results accuracy. The study utilized 23 different 2D peak patterns providing the chemical fingerprints of raw and roasted hazelnuts (Corylus avellana L.) from different geographical origins, of diverse varieties and different roasting degrees. The validation results show that non-targeted peak-based profiling can be reliable with error rates lower than 10% independent of the degree of analytical variance. The optimized Comprehensive Template Matching procedure was employed to study hazelnut roasting profiles and in particular to find marker compounds strongly dependent on the thermal treatment, and to establish the correlation of potential marker compounds to geographical origin and variety/cultivar and finally to reveal the characteristic release of aroma active compounds. Copyright © 2012 Elsevier B.V. All rights reserved.

RNA-templated single-base mutation detection based on T4 DNA ligase and reverse molecular beacon.

PubMed

Tang, Hongxing; Yang, Xiaohai; Wang, Kemin; Tan, Weihong; Li, Huimin; He, Lifang; Liu, Bin

2008-06-15

A novel RNA-templated single-base mutation detection method based on T4 DNA ligase and reverse molecular beacon (rMB) has been developed and successfully applied to identification of single-base mutation in codon 273 of the p53 gene. The discrimination was carried out using allele-specific primers, which flanked the variable position in the target RNA and was ligated using T4 DNA ligase only when the primers perfectly matched the RNA template. The allele-specific primers also carried complementary stem structures with end-labels (fluorophore TAMRA, quencher DABCYL), which formed a molecular beacon after RNase H digestion. One-base mismatch can be discriminated by analyzing the change of fluorescence intensity before and after RNase H digestion. This method has several advantages for practical applications, such as direct discrimination of single-base mismatch of the RNA extracted from cell; no requirement of PCR amplification; performance of homogeneous detection; and easily design of detection probes.

A narrow band pattern-matching model of vowel perception

NASA Astrophysics Data System (ADS)

Hillenbrand, James M.; Houde, Robert A.

2003-02-01

The purpose of this paper is to propose and evaluate a new model of vowel perception which assumes that vowel identity is recognized by a template-matching process involving the comparison of narrow band input spectra with a set of smoothed spectral-shape templates that are learned through ordinary exposure to speech. In the present simulation of this process, the input spectra are computed over a sufficiently long window to resolve individual harmonics of voiced speech. Prior to template creation and pattern matching, the narrow band spectra are amplitude equalized by a spectrum-level normalization process, and the information-bearing spectral peaks are enhanced by a ``flooring'' procedure that zeroes out spectral values below a threshold function consisting of a center-weighted running average of spectral amplitudes. Templates for each vowel category are created simply by averaging the narrow band spectra of like vowels spoken by a panel of talkers. In the present implementation, separate templates are used for men, women, and children. The pattern matching is implemented with a simple city-block distance measure given by the sum of the channel-by-channel differences between the narrow band input spectrum (level-equalized and floored) and each vowel template. Spectral movement is taken into account by computing the distance measure at several points throughout the course of the vowel. The input spectrum is assigned to the vowel template that results in the smallest difference accumulated over the sequence of spectral slices. The model was evaluated using a large database consisting of 12 vowels in /hVd/ context spoken by 45 men, 48 women, and 46 children. The narrow band model classified vowels in this database with a degree of accuracy (91.4%) approaching that of human listeners.

Visual working memory simultaneously guides facilitation and inhibition during visual search.

PubMed

Dube, Blaire; Basciano, April; Emrich, Stephen M; Al-Aidroos, Naseem

2016-07-01

During visual search, visual working memory (VWM) supports the guidance of attention in two ways: It stores the identity of the search target, facilitating the selection of matching stimuli in the search array, and it maintains a record of the distractors processed during search so that they can be inhibited. In two experiments, we investigated whether the full contents of VWM can be used to support both of these abilities simultaneously. In Experiment 1, participants completed a preview search task in which (a) a subset of search distractors appeared before the remainder of the search items, affording participants the opportunity to inhibit them, and (b) the search target varied from trial to trial, requiring the search target template to be maintained in VWM. We observed the established signature of VWM-based inhibition-reduced ability to ignore previewed distractors when the number of distractors exceeds VWM's capacity-suggesting that VWM can serve this role while also representing the target template. In Experiment 2, we replicated Experiment 1, but added to the search displays a singleton distractor that sometimes matched the color (a task-irrelevant feature) of the search target, to evaluate capture. We again observed the signature of VWM-based preview inhibition along with attentional capture by (and, thus, facilitation of) singletons matching the target template. These findings indicate that more than one VWM representation can bias attention at a time, and that these representations can separately affect selection through either facilitation or inhibition, placing constraints on existing models of the VWM-based guidance of attention.

Robust Observation Detection for Single Object Tracking: Deterministic and Probabilistic Patch-Based Approaches

PubMed Central

Zulkifley, Mohd Asyraf; Rawlinson, David; Moran, Bill

2012-01-01

In video analytics, robust observation detection is very important as the content of the videos varies a lot, especially for tracking implementation. Contrary to the image processing field, the problems of blurring, moderate deformation, low illumination surroundings, illumination change and homogenous texture are normally encountered in video analytics. Patch-Based Observation Detection (PBOD) is developed to improve detection robustness to complex scenes by fusing both feature- and template-based recognition methods. While we believe that feature-based detectors are more distinctive, however, for finding the matching between the frames are best achieved by a collection of points as in template-based detectors. Two methods of PBOD—the deterministic and probabilistic approaches—have been tested to find the best mode of detection. Both algorithms start by building comparison vectors at each detected points of interest. The vectors are matched to build candidate patches based on their respective coordination. For the deterministic method, patch matching is done in 2-level test where threshold-based position and size smoothing are applied to the patch with the highest correlation value. For the second approach, patch matching is done probabilistically by modelling the histograms of the patches by Poisson distributions for both RGB and HSV colour models. Then, maximum likelihood is applied for position smoothing while a Bayesian approach is applied for size smoothing. The result showed that probabilistic PBOD outperforms the deterministic approach with average distance error of 10.03% compared with 21.03%. This algorithm is best implemented as a complement to other simpler detection methods due to heavy processing requirement. PMID:23202226

Particle Filtering with Region-based Matching for Tracking of Partially Occluded and Scaled Targets*

PubMed Central

Nakhmani, Arie; Tannenbaum, Allen

2012-01-01

Visual tracking of arbitrary targets in clutter is important for a wide range of military and civilian applications. We propose a general framework for the tracking of scaled and partially occluded targets, which do not necessarily have prominent features. The algorithm proposed in the present paper utilizes a modified normalized cross-correlation as the likelihood for a particle filter. The algorithm divides the template, selected by the user in the first video frame, into numerous patches. The matching process of these patches by particle filtering allows one to handle the target’s occlusions and scaling. Experimental results with fixed rectangular templates show that the method is reliable for videos with nonstationary, noisy, and cluttered background, and provides accurate trajectories in cases of target translation, scaling, and occlusion. PMID:22506088

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.

Improving the convergence rate in affine registration of PET and SPECT brain images using histogram equalization.

PubMed

Salas-Gonzalez, D; Górriz, J M; Ramírez, J; Padilla, P; Illán, I A

2013-01-01

A procedure to improve the convergence rate for affine registration methods of medical brain images when the images differ greatly from the template is presented. The methodology is based on a histogram matching of the source images with respect to the reference brain template before proceeding with the affine registration. The preprocessed source brain images are spatially normalized to a template using a general affine model with 12 parameters. A sum of squared differences between the source images and the template is considered as objective function, and a Gauss-Newton optimization algorithm is used to find the minimum of the cost function. Using histogram equalization as a preprocessing step improves the convergence rate in the affine registration algorithm of brain images as we show in this work using SPECT and PET brain images.

Task demands determine the specificity of the search template.

PubMed

Bravo, Mary J; Farid, Hany

2012-01-01

When searching for an object, an observer holds a representation of the target in mind while scanning the scene. If the observer repeats the search, performance may become more efficient as the observer hones this target representation, or "search template," to match the specific demands of the search task. An effective search template must have two characteristics: It must reliably discriminate the target from the distractors, and it must tolerate variability in the appearance of the target. The present experiment examined how the tolerance of the search template is affected by the search task. Two groups of 18 observers trained on the same set of stimuli blocked either by target image (block-by-image group) or by target category (block-by-category group). One or two days after training, both groups were tested on a related search task. The pattern of test results revealed that the two groups of observers had developed different search templates, and that the templates of the block-by-category observers better captured the general characteristics of the category. These results demonstrate that observers match their search templates to the demands of the search task.

Rules versus Prototype Matching: Strategies of Perception of Emotional Facial Expressions in the Autism Spectrum

ERIC Educational Resources Information Center

Rutherford, M. D.; McIntosh, Daniel N.

2007-01-01

When perceiving emotional facial expressions, people with autistic spectrum disorders (ASD) appear to focus on individual facial features rather than configurations. This paper tests whether individuals with ASD use these features in a rule-based strategy of emotional perception, rather than a typical, template-based strategy by considering…

Automated side-chain model building and sequence assignment by template matching.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm is described for automated building of side chains in an electron-density map once a main-chain model is built and for alignment of the protein sequence to the map. The procedure is based on a comparison of electron density at the expected side-chain positions with electron-density templates. The templates are constructed from average amino-acid side-chain densities in 574 refined protein structures. For each contiguous segment of main chain, a matrix with entries corresponding to an estimate of the probability that each of the 20 amino acids is located at each position of the main-chain model is obtained. The probability that this segment corresponds to each possible alignment with the sequence of the protein is estimated using a Bayesian approach and high-confidence matches are kept. Once side-chain identities are determined, the most probable rotamer for each side chain is built into the model. The automated procedure has been implemented in the RESOLVE software. Combined with automated main-chain model building, the procedure produces a preliminary model suitable for refinement and extension by an experienced crystallographer.

The Role of Color in Search Templates for Real-world Target Objects.

PubMed

Nako, Rebecca; Smith, Tim J; Eimer, Martin

2016-11-01

During visual search, target representations (attentional templates) control the allocation of attention to template-matching objects. The activation of new attentional templates can be prompted by verbal or pictorial target specifications. We measured the N2pc component of the ERP as a temporal marker of attentional target selection to determine the role of color signals in search templates for real-world search target objects that are set up in response to word or picture cues. On each trial run, a word cue (e.g., "apple") was followed by three search displays that contained the cued target object among three distractors. The selection of the first target was based on the word cue only, whereas selection of the two subsequent targets could be controlled by templates set up after the first visual presentation of the target (picture cue). In different trial runs, search displays either contained objects in their natural colors or monochromatic objects. These two display types were presented in different blocks (Experiment 1) or in random order within each block (Experiment 2). RTs were faster, and target N2pc components emerged earlier for the second and third display of each trial run relative to the first display, demonstrating that pictures are more effective than word cues in guiding search. N2pc components were triggered more rapidly for targets in the second and third display in trial runs with colored displays. This demonstrates that when visual target attributes are fully specified by picture cues, the additional presence of color signals in target templates facilitates the speed with which attention is allocated to template-matching objects. No such selection benefits for colored targets were found when search templates were set up in response to word cues. Experiment 2 showed that color templates activated by word cues can even impair the attentional selection of noncolored targets. Results provide new insights into the status of color during the guidance of visual search for real-world target objects. Color is a powerful guiding feature when the precise visual properties of these objects are known but seems to be less important when search targets are specified by word cues.

Integrity Determination for Image Rendering Vision Navigation

DTIC Science & Technology

2016-03-01

identifying an object within a scene, tracking a SIFT feature between frames or matching images and/or features for stereo vision applications. This... object level, either in 2-D or 3-D, versus individual features. There is a breadth of information, largely from the machine vision community...matching or image rendering image correspondence approach is based upon using either 2-D or 3-D object models or templates to perform object detection or

3D Facial Pattern Analysis for Autism

DTIC Science & Technology

2010-07-01

each individual’s data were scaled by the geometric mean of all possible linear distances between landmarks, following. The first two principal...over traditional template matching in that it can represent geometrical and non- geometrical changes of an object in the parametric template space...set of vertex templates can be generated from the root template by geometric or non- geometric transformation. Let Mtt ,...1 be M normalized vertex

Local structure preserving sparse coding for infrared target recognition

PubMed Central

Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

2017-01-01

Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

Estimation of Cirrus and Stratus Cloud Heights Using Landsat Imagery

NASA Technical Reports Server (NTRS)

Inomata, Yasushi; Feind, R. E.; Welch, R. M.

1996-01-01

A new method based upon high-spatial-resolution imagery is presented that matches cloud and shadow regions to estimate cirrus and stratus cloud heights. The distance between the cloud and the matching shadow pattern is accomplished using the 2D cross-correlation function from which the cloud height is derived. The distance between the matching cloud-shadow patterns is verified manually. The derived heights also are validated through comparison with a temperature-based retrieval of cloud height. It is also demonstrated that an estimate of cloud thickness can be retrieved if both the sunside and anti-sunside of the cloud-shadow pair are apparent. The technique requires some intepretation to determine the cloud height level retrieved (i.e., the top, base, or mid-level). It is concluded that the method is accurate to within several pixels, equivalent to cloud height variations of about +/- 250 m. The results show that precise placement of the templates is unnecessary, so that the development of a semi-automated procedure is possible. Cloud templates of about 64 pixels on a side or larger produce consistent results. The procedure was repeated for imagery degraded to simulate lower spatial resolutions. The results suggest that spatial resolution of 150-200 m or better is necessary in order to obtain stable cloud height retrievals.

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.

Foot-mounted inertial measurement unit for activity classification.

PubMed

Ghobadi, Mostafa; Esfahani, Ehsan T

2014-01-01

This paper proposes a classification technique for daily base activity recognition for human monitoring during physical therapy in home. The proposed method estimates the foot motion using single inertial measurement unit, then segments the motion into steps classify them by template-matching as walking, stairs up or stairs down steps. The results show a high accuracy of activity recognition. Unlike previous works which are limited to activity recognition, the proposed approach is more qualitative by providing similarity index of any activity to its desired template which can be used to assess subjects improvement.

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.

Dance-the-Music: an educational platform for the modeling, recognition and audiovisual monitoring of dance steps using spatiotemporal motion templates

NASA Astrophysics Data System (ADS)

Maes, Pieter-Jan; Amelynck, Denis; Leman, Marc

2012-12-01

In this article, a computational platform is presented, entitled "Dance-the-Music", that can be used in a dance educational context to explore and learn the basics of dance steps. By introducing a method based on spatiotemporal motion templates, the platform facilitates to train basic step models from sequentially repeated dance figures performed by a dance teacher. Movements are captured with an optical motion capture system. The teachers' models can be visualized from a first-person perspective to instruct students how to perform the specific dance steps in the correct manner. Moreover, recognition algorithms-based on a template matching method-can determine the quality of a student's performance in real time by means of multimodal monitoring techniques. The results of an evaluation study suggest that the Dance-the-Music is effective in helping dance students to master the basics of dance figures.

V2S: Voice to Sign Language Translation System for Malaysian Deaf People

NASA Astrophysics Data System (ADS)

Mean Foong, Oi; Low, Tang Jung; La, Wai Wan

The process of learning and understand the sign language may be cumbersome to some, and therefore, this paper proposes a solution to this problem by providing a voice (English Language) to sign language translation system using Speech and Image processing technique. Speech processing which includes Speech Recognition is the study of recognizing the words being spoken, regardless of whom the speaker is. This project uses template-based recognition as the main approach in which the V2S system first needs to be trained with speech pattern based on some generic spectral parameter set. These spectral parameter set will then be stored as template in a database. The system will perform the recognition process through matching the parameter set of the input speech with the stored templates to finally display the sign language in video format. Empirical results show that the system has 80.3% recognition rate.

The ontogeny of kin-recognition mechanisms in Belding's ground squirrels.

PubMed

Mateo, Jill M

2017-05-01

Despite extensive research on the functions and mechanisms of kin recognition, little is known about developmental changes in the abilities mediating such recognition. Belding's ground squirrels, Urocitellus beldingi, use at least two mechanisms of kin recognition in nepotistic contexts: familiarity and phenotype matching. Because recognition templates develop from early associations with familiar kin (and/or with self), familiarity-based recognition should precede phenotype-matching recognition even though one template is thought to be used for both mechanisms. I used a cross-fostering design to produce individuals that differed in relatedness and familiarity. Two pups (one female and one male) were exchanged reciprocally between two litters within 48-h of birth. Every five days, from 15 to 30-d of age, young were exposed to bedding and oral-gland odors from their familiar foster mother and an unfamiliar unrelated female (familiarity test) and from their unfamiliar genetic mother and another unfamiliar unrelated female (phenotype-matching test). As expected, discrimination of odors based on familiarity was evident at all ages tested, whereas discrimination based on relatedness was not evident until 30-d. My results provide a first estimate for when phenotype-matching mechanisms are used by young Belding's ground squirrels, and thus when they can recognize unfamiliar kin such as older sisters or grandmothers. Belding's ground squirrels are the first species for which the development of the production, perception and action components is well understood. Copyright © 2017 Elsevier Inc. All rights reserved.

Inhibitory motor control based on complex stopping goals relies on the same brain network as simple stopping

PubMed Central

Wessel, Jan R.; Aron, Adam R.

2014-01-01

Much research has modeled action-stopping using the stop-signal task (SST), in which an impending response has to be stopped when an explicit stop-signal occurs. A limitation of the SST is that real-world action-stopping rarely involves explicit stop-signals. Instead, the stopping-system engages when environmental features match more complex stopping goals. For example, when stepping into the street, one monitors path, velocity, size, and types of objects; and only stops if there is a vehicle approaching. Here, we developed a task in which participants compared the visual features of a multidimensional go-stimulus to a complex stopping-template, and stopped their go-response if all features matched the template. We used independent component analysis of EEG data to show that the same motor inhibition brain network that explains action-stopping in the SST also implements motor inhibition in the complex-stopping task. Furthermore, we found that partial feature overlap between go-stimulus and stopping-template lead to motor slowing, which also corresponded with greater stopping-network activity. This shows that the same brain system for action-stopping to explicit stop-signals is recruited to slow or stop behavior when stimuli match a complex stopping goal. The results imply a generalizability of the brain’s network for simple action-stopping to more ecologically valid scenarios. PMID:25270603

MARZ: Manual and automatic redshifting software

NASA Astrophysics Data System (ADS)

Hinton, S. R.; Davis, Tamara M.; Lidman, C.; Glazebrook, K.; Lewis, G. F.

2016-04-01

The Australian Dark Energy Survey (OzDES) is a 100-night spectroscopic survey underway on the Anglo-Australian Telescope using the fibre-fed 2-degree-field (2dF) spectrograph. We have developed a new redshifting application MARZ with greater usability, flexibility, and the capacity to analyse a wider range of object types than the RUNZ software package previously used for redshifting spectra from 2dF. MARZ is an open-source, client-based, Javascript web-application which provides an intuitive interface and powerful automatic matching capabilities on spectra generated from the AAOmega spectrograph to produce high quality spectroscopic redshift measurements. The software can be run interactively or via the command line, and is easily adaptable to other instruments and pipelines if conforming to the current FITS file standard is not possible. Behind the scenes, a modified version of the AUTOZ cross-correlation algorithm is used to match input spectra against a variety of stellar and galaxy templates, and automatic matching performance for OzDES spectra has increased from 54% (RUNZ) to 91% (MARZ). Spectra not matched correctly by the automatic algorithm can be easily redshifted manually by cycling automatic results, manual template comparison, or marking spectral features.

A template-finding algorithm and a comprehensive benchmark for homology modeling of proteins

PubMed Central

Vallat, Brinda Kizhakke; Pillardy, Jaroslaw; Elber, Ron

2010-01-01

The first step in homology modeling is to identify a template protein for the target sequence. The template structure is used in later phases of the calculation to construct an atomically detailed model for the target. We have built from the Protein Data Bank a large-scale learning set that includes tens of millions of pair matches that can be either a true template or a false one. Discriminatory learning (learning from positive and negative examples) is employed to train a decision tree. Each branch of the tree is a mathematical programming model. The decision tree is tested on an independent set from PDB entries and on the sequences of CASP7. It provides significant enrichment of true templates (between 50-100 percent) when compared to PSI-BLAST. The model is further verified by building atomically detailed structures for each of the tentative true templates with modeller. The probability that a true match does not yield an acceptable structural model (within 6Å RMSD from the native structure), decays linearly as a function of the TM structural-alignment score. PMID:18300226

Mapped Landmark Algorithm for Precision Landing

NASA Technical Reports Server (NTRS)

Johnson, Andrew; Ansar, Adnan; Matthies, Larry

2007-01-01

A report discusses a computer vision algorithm for position estimation to enable precision landing during planetary descent. The Descent Image Motion Estimation System for the Mars Exploration Rovers has been used as a starting point for creating code for precision, terrain-relative navigation during planetary landing. The algorithm is designed to be general because it handles images taken at different scales and resolutions relative to the map, and can produce mapped landmark matches for any planetary terrain of sufficient texture. These matches provide a measurement of horizontal position relative to a known landing site specified on the surface map. Multiple mapped landmarks generated per image allow for automatic detection and elimination of bad matches. Attitude and position can be generated from each image; this image-based attitude measurement can be used by the onboard navigation filter to improve the attitude estimate, which will improve the position estimates. The algorithm uses normalized correlation of grayscale images, producing precise, sub-pixel images. The algorithm has been broken into two sub-algorithms: (1) FFT Map Matching (see figure), which matches a single large template by correlation in the frequency domain, and (2) Mapped Landmark Refinement, which matches many small templates by correlation in the spatial domain. Each relies on feature selection, the homography transform, and 3D image correlation. The algorithm is implemented in C++ and is rated at Technology Readiness Level (TRL) 4.

Probabilistic multi-resolution human classification

NASA Astrophysics Data System (ADS)

Tu, Jun; Ran, H.

2006-02-01

Recently there has been some interest in using infrared cameras for human detection because of the sharply decreasing prices of infrared cameras. The training data used in our work for developing the probabilistic template consists images known to contain humans in different poses and orientation but having the same height. Multiresolution templates are performed. They are based on contour and edges. This is done so that the model does not learn the intensity variations among the background pixels and intensity variations among the foreground pixels. Each template at every level is then translated so that the centroid of the non-zero pixels matches the geometrical center of the image. After this normalization step, for each pixel of the template, the probability of it being pedestrian is calculated based on the how frequently it appears as 1 in the training data. We also use periodicity gait to verify the pedestrian in a Bayesian manner for the whole blob in a probabilistic way. The videos had quite a lot of variations in the scenes, sizes of people, amount of occlusions and clutter in the backgrounds as is clearly evident. Preliminary experiments show the robustness.

Nonlinear matching measure for the analysis of on-off type DNA microarray images

NASA Astrophysics Data System (ADS)

Kim, Jong D.; Park, Misun; Kim, Jongwon

2003-07-01

In this paper, we propose a new nonlinear matching measure for automatic analysis of the on-off type DNA microarray images in which the hybridized spots are detected by the template matching method. The targeting spots of HPV DNA chips are designed for genotyping the human papilloma virus(HPV). The proposed measure is obtained by binarythresholding over the whole template region and taking the number of white pixels inside the spotted area. This measure is evaluated in terms of the accuracy of the estimated marker location to show better performance than the normalized covariance.

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

Reconstruction of ECG signals in presence of corruption.

PubMed

Ganeshapillai, Gartheeban; Liu, Jessica F; Guttag, John

2011-01-01

We present an approach to identifying and reconstructing corrupted regions in a multi-parameter physiological signal. The method, which uses information in correlated signals, is specifically designed to preserve clinically significant aspects of the signals. We use template matching to jointly segment the multi-parameter signal, morphological dissimilarity to estimate the quality of the signal segment, similarity search using features on a database of templates to find the closest match, and time-warping to reconstruct the corrupted segment with the matching template. In experiments carried out on the MIT-BIH Arrhythmia Database, a two-parameter database with many clinically significant arrhythmias, our method improved the classification accuracy of the beat type by more than 7 times on a signal corrupted with white Gaussian noise, and increased the similarity to the original signal, as measured by the normalized residual distance, by more than 2.5 times.

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

Colbert, C.; Moles, D.R.

This paper reports that the authors developed for the Air Force the Mark VI Personal Identity Verifier (PIV) for controlling access to a fixed or mobile ICBM site, a computer terminal, or mainframe. The Mark VI records the digitized silhouettes of four fingers of each hand on an AT and T smart card. Like fingerprints, finger shapes, lengths, and widths constitute an unguessable biometric password. A Security Officer enrolls an authorized person who places each hand, in turn, on a backlighted panel. An overhead scanning camera records the right and left hand reference templates on the smart card. The Securitymore » Officer adds to the card: name, personal identification number (PIN), and access restrictions such as permitted days of the week, times of day, and doors. To gain access, cardowner inserts card into a reader slot and places either hand on the panel. Resulting access template is matched to the reference template by three sameness algorithms. The final match score is an average of 12 scores (each of the four fingers, matched for shape, length, and width), expressing the degree of sameness. (A perfect match would score 100.00.) The final match score is compared to a predetermined score (threshold), generating an accept or reject decision.« less

Knowledge-based image processing for on-off type DNA microarray

NASA Astrophysics Data System (ADS)

Kim, Jong D.; Kim, Seo K.; Cho, Jeong S.; Kim, Jongwon

2002-06-01

This paper addresses the image processing technique for discriminating whether the probes are hybrized with target DNA in the Human Papilloma Virus (HPV) DNA Chip designed for genotyping HPV. In addition to the probes, the HPV DNA chip has markers that always react with the sample DNA. The positions of probe-dots in the final scanned image are fixed relative to the marker-dot locations with a small variation according to the accuracy of the dotter and the scanner. The probes are duplicated 4 times for the diagnostic stability. The prior knowledges such as the maker relative distance and the duplication information of probes is integrated into the template matching technique with the normalized correlation measure. Results show that the employment of both of the prior knowledges is to simply average the template matching measures over the positions of the markers and probes. The eventual proposed scheme yields stable marker locating and probe classification.

Database extraction strategies for low-template evidence.

PubMed

Bleka, Øyvind; Dørum, Guro; Haned, Hinda; Gill, Peter

2014-03-01

Often in forensic cases, the profile of at least one of the contributors to a DNA evidence sample is unknown and a database search is needed to discover possible perpetrators. In this article we consider two types of search strategies to extract suspects from a database using methods based on probability arguments. The performance of the proposed match scores is demonstrated by carrying out a study of each match score relative to the level of allele drop-out in the crime sample, simulating low-template DNA. The efficiency was measured by random man simulation and we compared the performance using the SGM Plus kit and the ESX 17 kit for the Norwegian population, demonstrating that the latter has greatly enhanced power to discover perpetrators of crime in large national DNA databases. The code for the database extraction strategies will be prepared for release in the R-package forensim. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Fuzzy Matching Based on Gray-scale Difference for Quantum Images

NASA Astrophysics Data System (ADS)

Luo, GaoFeng; Zhou, Ri-Gui; Liu, XingAo; Hu, WenWen; Luo, Jia

2018-05-01

Quantum image processing has recently emerged as an essential problem in practical tasks, e.g. real-time image matching. Previous studies have shown that the superposition and entanglement of quantum can greatly improve the efficiency of complex image processing. In this paper, a fuzzy quantum image matching scheme based on gray-scale difference is proposed to find out the target region in a reference image, which is very similar to the template image. Firstly, we employ the proposed enhanced quantum representation (NEQR) to store digital images. Then some certain quantum operations are used to evaluate the gray-scale difference between two quantum images by thresholding. If all of the obtained gray-scale differences are not greater than the threshold value, it indicates a successful fuzzy matching of quantum images. Theoretical analysis and experiments show that the proposed scheme performs fuzzy matching at a low cost and also enables exponentially significant speedup via quantum parallel computation.

Unconstrained and contactless hand geometry biometrics.

PubMed

de-Santos-Sierra, Alberto; Sánchez-Ávila, Carmen; Del Pozo, Gonzalo Bailador; Guerra-Casanova, Javier

2011-01-01

This paper presents a hand biometric system for contact-less, platform-free scenarios, proposing innovative methods in feature extraction, template creation and template matching. The evaluation of the proposed method considers both the use of three contact-less publicly available hand databases, and the comparison of the performance to two competitive pattern recognition techniques existing in literature: namely support vector machines (SVM) and k-nearest neighbour (k-NN). Results highlight the fact that the proposed method outcomes existing approaches in literature in terms of computational cost, accuracy in human identification, number of extracted features and number of samples for template creation. The proposed method is a suitable solution for human identification in contact-less scenarios based on hand biometrics, providing a feasible solution to devices with limited hardware requirements like mobile devices.

Unconstrained and Contactless Hand Geometry Biometrics

PubMed Central

de-Santos-Sierra, Alberto; Sánchez-Ávila, Carmen; del Pozo, Gonzalo Bailador; Guerra-Casanova, Javier

2011-01-01

This paper presents a hand biometric system for contact-less, platform-free scenarios, proposing innovative methods in feature extraction, template creation and template matching. The evaluation of the proposed method considers both the use of three contact-less publicly available hand databases, and the comparison of the performance to two competitive pattern recognition techniques existing in literature: namely Support Vector Machines (SVM) and k-Nearest Neighbour (k-NN). Results highlight the fact that the proposed method outcomes existing approaches in literature in terms of computational cost, accuracy in human identification, number of extracted features and number of samples for template creation. The proposed method is a suitable solution for human identification in contact-less scenarios based on hand biometrics, providing a feasible solution to devices with limited hardware requirements like mobile devices. PMID:22346634

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).

Automatic tracking of arbitrarily shaped implanted markers in kilovoltage projection images: A feasibility study

PubMed Central

Regmi, Rajesh; Lovelock, D. Michael; Hunt, Margie; Zhang, Pengpeng; Pham, Hai; Xiong, Jianping; Yorke, Ellen D.; Goodman, Karyn A.; Rimner, Andreas; Mostafavi, Hassan; Mageras, Gig S.

2014-01-01

Purpose: Certain types of commonly used fiducial markers take on irregular shapes upon implantation in soft tissue. This poses a challenge for methods that assume a predefined shape of markers when automatically tracking such markers in kilovoltage (kV) radiographs. The authors have developed a method of automatically tracking regularly and irregularly shaped markers using kV projection images and assessed its potential for detecting intrafractional target motion during rotational treatment. Methods: Template-based matching used a normalized cross-correlation with simplex minimization. Templates were created from computed tomography (CT) images for phantom studies and from end-expiration breath-hold planning CT for patient studies. The kV images were processed using a Sobel filter to enhance marker visibility. To correct for changes in intermarker relative positions between simulation and treatment that can introduce errors in automatic matching, marker offsets in three dimensions were manually determined from an approximately orthogonal pair of kV images. Two studies in anthropomorphic phantom were carried out, one using a gold cylindrical marker representing regular shape, another using a Visicoil marker representing irregular shape. Automatic matching of templates to cone beam CT (CBCT) projection images was performed to known marker positions in phantom. In patient data, automatic matching was compared to manual matching as an approximate ground truth. Positional discrepancy between automatic and manual matching of less than 2 mm was assumed as the criterion for successful tracking. Tracking success rates were examined in kV projection images from 22 CBCT scans of four pancreas, six gastroesophageal junction, and one lung cancer patients. Each patient had at least one irregularly shaped radiopaque marker implanted in or near the tumor. In addition, automatic tracking was tested in intrafraction kV images of three lung cancer patients with irregularly shaped markers during 11 volumetric modulated arc treatments. Purpose-built software developed at our institution was used to create marker templates and track the markers embedded in kV images. Results: Phantom studies showed mean ± standard deviation measurement uncertainty of automatic registration to be 0.14 ± 0.07 mm and 0.17 ± 0.08 mm for Visicoil and gold cylindrical markers, respectively. The mean success rate of automatic tracking with CBCT projections (11 frames per second, fps) of pancreas, gastroesophageal junction, and lung cancer patients was 100%, 99.1% (range 98%–100%), and 100%, respectively. With intrafraction images (approx. 0.2 fps) of lung cancer patients, the success rate was 98.2% (range 97%–100%), and 94.3% (range 93%–97%) using templates from 1.25 mm and 2.5 mm slice spacing CT scans, respectively. Correction of intermarker relative position was found to improve the success rate in two out of eight patients analyzed. Conclusions: The proposed method can track arbitrary marker shapes in kV images using templates generated from a breath-hold CT acquired at simulation. The studies indicate its feasibility for tracking tumor motion during rotational treatment. Investigation of the causes of misregistration suggests that its rate of incidence can be reduced with higher frequency of image acquisition, templates made from smaller CT slice spacing, and correction of changes in intermarker relative positions when they occur. PMID:24989384

Automatic tracking of arbitrarily shaped implanted markers in kilovoltage projection images: A feasibility study

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

Regmi, Rajesh; Lovelock, D. Michael; Hunt, Margie

Purpose: Certain types of commonly used fiducial markers take on irregular shapes upon implantation in soft tissue. This poses a challenge for methods that assume a predefined shape of markers when automatically tracking such markers in kilovoltage (kV) radiographs. The authors have developed a method of automatically tracking regularly and irregularly shaped markers using kV projection images and assessed its potential for detecting intrafractional target motion during rotational treatment. Methods: Template-based matching used a normalized cross-correlation with simplex minimization. Templates were created from computed tomography (CT) images for phantom studies and from end-expiration breath-hold planning CT for patient studies. Themore » kV images were processed using a Sobel filter to enhance marker visibility. To correct for changes in intermarker relative positions between simulation and treatment that can introduce errors in automatic matching, marker offsets in three dimensions were manually determined from an approximately orthogonal pair of kV images. Two studies in anthropomorphic phantom were carried out, one using a gold cylindrical marker representing regular shape, another using a Visicoil marker representing irregular shape. Automatic matching of templates to cone beam CT (CBCT) projection images was performed to known marker positions in phantom. In patient data, automatic matching was compared to manual matching as an approximate ground truth. Positional discrepancy between automatic and manual matching of less than 2 mm was assumed as the criterion for successful tracking. Tracking success rates were examined in kV projection images from 22 CBCT scans of four pancreas, six gastroesophageal junction, and one lung cancer patients. Each patient had at least one irregularly shaped radiopaque marker implanted in or near the tumor. In addition, automatic tracking was tested in intrafraction kV images of three lung cancer patients with irregularly shaped markers during 11 volumetric modulated arc treatments. Purpose-built software developed at our institution was used to create marker templates and track the markers embedded in kV images. Results: Phantom studies showed mean ± standard deviation measurement uncertainty of automatic registration to be 0.14 ± 0.07 mm and 0.17 ± 0.08 mm for Visicoil and gold cylindrical markers, respectively. The mean success rate of automatic tracking with CBCT projections (11 frames per second, fps) of pancreas, gastroesophageal junction, and lung cancer patients was 100%, 99.1% (range 98%–100%), and 100%, respectively. With intrafraction images (approx. 0.2 fps) of lung cancer patients, the success rate was 98.2% (range 97%–100%), and 94.3% (range 93%–97%) using templates from 1.25 mm and 2.5 mm slice spacing CT scans, respectively. Correction of intermarker relative position was found to improve the success rate in two out of eight patients analyzed. Conclusions: The proposed method can track arbitrary marker shapes in kV images using templates generated from a breath-hold CT acquired at simulation. The studies indicate its feasibility for tracking tumor motion during rotational treatment. Investigation of the causes of misregistration suggests that its rate of incidence can be reduced with higher frequency of image acquisition, templates made from smaller CT slice spacing, and correction of changes in intermarker relative positions when they occur.« less

Privacy protection schemes for fingerprint recognition systems

NASA Astrophysics Data System (ADS)

Marasco, Emanuela; Cukic, Bojan

2015-05-01

The deployment of fingerprint recognition systems has always raised concerns related to personal privacy. A fingerprint is permanently associated with an individual and, generally, it cannot be reset if compromised in one application. Given that fingerprints are not a secret, potential misuses besides personal recognition represent privacy threats and may lead to public distrust. Privacy mechanisms control access to personal information and limit the likelihood of intrusions. In this paper, image- and feature-level schemes for privacy protection in fingerprint recognition systems are reviewed. Storing only key features of a biometric signature can reduce the likelihood of biometric data being used for unintended purposes. In biometric cryptosystems and biometric-based key release, the biometric component verifies the identity of the user, while the cryptographic key protects the communication channel. Transformation-based approaches only a transformed version of the original biometric signature is stored. Different applications can use different transforms. Matching is performed in the transformed domain which enable the preservation of low error rates. Since such templates do not reveal information about individuals, they are referred to as cancelable templates. A compromised template can be re-issued using a different transform. At image-level, de-identification schemes can remove identifiers disclosed for objectives unrelated to the original purpose, while permitting other authorized uses of personal information. Fingerprint images can be de-identified by, for example, mixing fingerprints or removing gender signature. In both cases, degradation of matching performance is minimized.

An efficient indexing scheme for binary feature based biometric database

NASA Astrophysics Data System (ADS)

Gupta, P.; Sana, A.; Mehrotra, H.; Hwang, C. Jinshong

2007-04-01

The paper proposes an efficient indexing scheme for binary feature template using B+ tree. In this scheme the input image is decomposed into approximation, vertical, horizontal and diagonal coefficients using the discrete wavelet transform. The binarized approximation coefficient at second level is divided into four quadrants of equal size and Hamming distance (HD) for each quadrant with respect to sample template of all ones is measured. This HD value of each quadrant is used to generate upper and lower range values which are inserted into B+ tree. The nodes of tree at first level contain the lower and upper range values generated from HD of first quadrant. Similarly, lower and upper range values for the three quadrants are stored in the second, third and fourth level respectively. Finally leaf node contains the set of identifiers. At the time of identification, the test image is used to generate HD for four quadrants. Then the B+ tree is traversed based on the value of HD at every node and terminates to leaf nodes with set of identifiers. The feature vector for each identifier is retrieved from the particular bin of secondary memory and matched with test feature template to get top matches. The proposed scheme is implemented on ear biometric database collected at IIT Kanpur. The system is giving an overall accuracy of 95.8% at penetration rate of 34%.

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

Scibelli, Samantha; Newberg, Heidi Jo; Carlin, Jeffrey L.

We present a census of the 12,060 spectra of blue objects ((g – r){sub 0} < –0.25) in the Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8). As part of the data release, all of the spectra were cross-correlated with 48 template spectra of stars, galaxies, and QSOs to determine the best match. We compared the blue spectra by eye to the templates assigned in SDSS DR8. 10,856 of the objects matched their assigned template, 170 could not be classified due to low signal-to-noise ratio, and 1034 were given new classifications. We identify 7458 DA white dwarfs, 1145 DBmore » white dwarfs, 273 rarer white dwarfs (including carbon, DZ, DQ, and magnetic), 294 subdwarf O stars, 648 subdwarf B stars, 679 blue horizontal branch stars, 1026 blue stragglers, 13 cataclysmic variables, 129 white dwarf-M dwarf binaries, 36 objects with spectra similar to DO white dwarfs, 179, quasi-stellar objects (QSOs), and 10 galaxies. We provide two tables of these objects, sample spectra that match the templates, figures showing all of the spectra that were grouped by eye, and diagnostic plots that show the positions, colors, apparent magnitudes, proper motions, etc., for each classification. Future surveys will be able to use templates similar to stars in each of the classes we identify to automatically classify blue stars, including rare types.« less

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

Scibelli, Samantha; Newberg, Heidi Jo; Carlin, Jeffrey L.

In this work, we present a census of the 12,060 spectra of blue objects (more » $$(g-r)_0<-0.25$$) in the Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8). As part of the data release, all of the spectra were cross-correlated with 48 template spectra of stars, galaxies and QSOs to determine the best match. We compared the blue spectra by eye to the templates assigned in SDSS DR8. 10,856 of the objects matched their assigned template, 170 could not be classified due to low signal-to-noise (S/N), and 1034 were given new classifications. We identify 7458 DA white dwarfs, 1145 DB white dwarfs, 273 rarer white dwarfs (including carbon, DZ, DQ, and magnetic), 294 subdwarf O stars, 648 subdwarf B stars, 679 blue horizontal branch stars, 1026 blue stragglers, 13 cataclysmic variables, 129 white dwarf - M dwarf binaries, 36 objects with spectra similar to DO white dwarfs, 179 QSOs, and 10 galaxies. We provide two tables of these objects, sample spectra that match the templates, figures showing all of the spectra that were grouped by eye, and diagnostic plots that show the positions, colors, apparent magnitudes, proper motions, etc. for each classification. In conclusion, future surveys will be able to use templates similar to stars in each of the classes we identify to classify blue stars, including rare types, automatically.« less

CENSUS OF BLUE STARS IN SDSS DR8

DOE PAGES

Scibelli, Samantha; Newberg, Heidi Jo; Carlin, Jeffrey L.; ...

2014-12-02

In this work, we present a census of the 12,060 spectra of blue objects (more » $$(g-r)_0<-0.25$$) in the Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8). As part of the data release, all of the spectra were cross-correlated with 48 template spectra of stars, galaxies and QSOs to determine the best match. We compared the blue spectra by eye to the templates assigned in SDSS DR8. 10,856 of the objects matched their assigned template, 170 could not be classified due to low signal-to-noise (S/N), and 1034 were given new classifications. We identify 7458 DA white dwarfs, 1145 DB white dwarfs, 273 rarer white dwarfs (including carbon, DZ, DQ, and magnetic), 294 subdwarf O stars, 648 subdwarf B stars, 679 blue horizontal branch stars, 1026 blue stragglers, 13 cataclysmic variables, 129 white dwarf - M dwarf binaries, 36 objects with spectra similar to DO white dwarfs, 179 QSOs, and 10 galaxies. We provide two tables of these objects, sample spectra that match the templates, figures showing all of the spectra that were grouped by eye, and diagnostic plots that show the positions, colors, apparent magnitudes, proper motions, etc. for each classification. In conclusion, future surveys will be able to use templates similar to stars in each of the classes we identify to classify blue stars, including rare types, automatically.« less

3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake.

PubMed

Jacob, Mathews; Blu, Thierry; Vaillant, Cedric; Maddocks, John H; Unser, Michael

2006-01-01

We introduce a three-dimensional (3-D) parametric active contour algorithm for the shape estimation of DNA molecules from stereo cryo-electron micrographs. We estimate the shape by matching the projections of a 3-D global shape model with the micrographs; we choose the global model as a 3-D filament with a B-spline skeleton and a specified radial profile. The active contour algorithm iteratively updates the B-spline coefficients, which requires us to evaluate the projections and match them with the micrographs at every iteration. Since the evaluation of the projections of the global model is computationally expensive, we propose a fast algorithm based on locally approximating it by elongated blob-like templates. We introduce the concept of projection-steerability and derive a projection-steerable elongated template. Since the two-dimensional projections of such a blob at any 3-D orientation can be expressed as a linear combination of a few basis functions, matching the projections of such a 3-D template involves evaluating a weighted sum of inner products between the basis functions and the micrographs. The weights are simple functions of the 3-D orientation and the inner-products are evaluated efficiently by separable filtering. We choose an internal energy term that penalizes the average curvature magnitude. Since the exact length of the DNA molecule is known a priori, we introduce a constraint energy term that forces the curve to have this specified length. The sum of these energies along with the image energy derived from the matching process is minimized using the conjugate gradients algorithm. We validate the algorithm using real, as well as simulated, data and show that it performs well.

Automatic script identification from images using cluster-based templates

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

Hochberg, J.; Kerns, L.; Kelly, P.

We have developed a technique for automatically identifying the script used to generate a document that is stored electronically in bit image form. Our approach differs from previous work in that the distinctions among scripts are discovered by an automatic learning procedure, without any handson analysis. We first develop a set of representative symbols (templates) for each script in our database (Cyrillic, Roman, etc.). We do this by identifying all textual symbols in a set of training documents, scaling each symbol to a fixed size, clustering similar symbols, pruning minor clusters, and finding each cluster`s centroid. To identify a newmore » document`s script, we identify and scale a subset of symbols from the document and compare them to the templates for each script. We choose the script whose templates provide the best match. Our current system distinguishes among the Armenian, Burmese, Chinese, Cyrillic, Ethiopic, Greek, Hebrew, Japanese, Korean, Roman, and Thai scripts with over 90% accuracy.« less

Template protection and its implementation in 3D face recognition systems

NASA Astrophysics Data System (ADS)

Zhou, Xuebing

2007-04-01

As biometric recognition systems are widely applied in various application areas, security and privacy risks have recently attracted the attention of the biometric community. Template protection techniques prevent stored reference data from revealing private biometric information and enhance the security of biometrics systems against attacks such as identity theft and cross matching. This paper concentrates on a template protection algorithm that merges methods from cryptography, error correction coding and biometrics. The key component of the algorithm is to convert biometric templates into binary vectors. It is shown that the binary vectors should be robust, uniformly distributed, statistically independent and collision-free so that authentication performance can be optimized and information leakage can be avoided. Depending on statistical character of the biometric template, different approaches for transforming biometric templates into compact binary vectors are presented. The proposed methods are integrated into a 3D face recognition system and tested on the 3D facial images of the FRGC database. It is shown that the resulting binary vectors provide an authentication performance that is similar to the original 3D face templates. A high security level is achieved with reasonable false acceptance and false rejection rates of the system, based on an efficient statistical analysis. The algorithm estimates the statistical character of biometric templates from a number of biometric samples in the enrollment database. For the FRGC 3D face database, the small distinction of robustness and discriminative power between the classification results under the assumption of uniquely distributed templates and the ones under the assumption of Gaussian distributed templates is shown in our tests.

Data-analysis driven comparison of analytic and numerical coalescing binary waveforms: Nonspinning case

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

Pan Yi; Buonanno, Alessandra; McWilliams, Sean T.

2008-01-15

We compare waveforms obtained by numerically evolving nonspinning binary black holes to post-Newtonian (PN) template families currently used in the search for gravitational waves by ground-based detectors. We find that the time-domain 3.5PN template family, which includes the inspiral phase, has fitting factors (FFs) {>=}0.96 for binary systems with total mass M=10-20M{sub {center_dot}}. The time-domain 3.5PN effective-one-body template family, which includes the inspiral, merger, and ring-down phases, gives satisfactory signal-matching performance with FFs {>=}0.96 for binary systems with total mass M=10-120M{sub {center_dot}}. If we introduce a cutoff frequency properly adjusted to the final black-hole ring-down frequency, we find that themore » frequency-domain stationary-phase-approximated template family at 3.5PN order has FFs {>=}0.96 for binary systems with total mass M=10-20M{sub {center_dot}}. However, to obtain high matching performances for larger binary masses, we need to either extend this family to unphysical regions of the parameter space or introduce a 4PN order coefficient in the frequency-domain gravitational wave (GW) phase. Finally, we find that the phenomenological Buonanno-Chen-Vallisneri family has FFs {>=}0.97 with total mass M=10-120M{sub {center_dot}}. The main analyses use the noise-spectral density of LIGO, but several tests are extended to VIRGO and advanced LIGO noise-spectral densities.« less

Modeling IrisCode and its variants as convex polyhedral cones and its security implications.

PubMed

Kong, Adams Wai-Kin

2013-03-01

IrisCode, developed by Daugman, in 1993, is the most influential iris recognition algorithm. A thorough understanding of IrisCode is essential, because over 100 million persons have been enrolled by this algorithm and many biometric personal identification and template protection methods have been developed based on IrisCode. This paper indicates that a template produced by IrisCode or its variants is a convex polyhedral cone in a hyperspace. Its central ray, being a rough representation of the original biometric signal, can be computed by a simple algorithm, which can often be implemented in one Matlab command line. The central ray is an expected ray and also an optimal ray of an objective function on a group of distributions. This algorithm is derived from geometric properties of a convex polyhedral cone but does not rely on any prior knowledge (e.g., iris images). The experimental results show that biometric templates, including iris and palmprint templates, produced by different recognition methods can be matched through the central rays in their convex polyhedral cones and that templates protected by a method extended from IrisCode can be broken into. These experimental results indicate that, without a thorough security analysis, convex polyhedral cone templates cannot be assumed secure. Additionally, the simplicity of the algorithm implies that even junior hackers without knowledge of advanced image processing and biometric databases can still break into protected templates and reveal relationships among templates produced by different recognition methods.

Automated extraction of pleural effusion in three-dimensional thoracic CT images

NASA Astrophysics Data System (ADS)

Kido, Shoji; Tsunomori, Akinori

2009-02-01

It is important for diagnosis of pulmonary diseases to measure volume of accumulating pleural effusion in threedimensional thoracic CT images quantitatively. However, automated extraction of pulmonary effusion correctly is difficult. Conventional extraction algorithm using a gray-level based threshold can not extract pleural effusion from thoracic wall or mediastinum correctly, because density of pleural effusion in CT images is similar to those of thoracic wall or mediastinum. So, we have developed an automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion. Our method used a template of lung obtained from a normal lung for segmentation of lungs with pleural effusions. Registration process consisted of two steps. First step was a global matching processing between normal and abnormal lungs of organs such as bronchi, bones (ribs, sternum and vertebrae) and upper surfaces of livers which were extracted using a region-growing algorithm. Second step was a local matching processing between normal and abnormal lungs which were deformed by the parameter obtained from the global matching processing. Finally, we segmented a lung with pleural effusion by use of the template which was deformed by two parameters obtained from the global matching processing and the local matching processing. We compared our method with a conventional extraction method using a gray-level based threshold and two published methods. The extraction rates of pleural effusions obtained from our method were much higher than those obtained from other methods. Automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion is promising for diagnosis of pulmonary diseases by providing quantitative volume of accumulating pleural effusion.

VizieR Online Data Catalog: Census of blue stars in SDSS DR8 (Scibelli+, 2014)

NASA Astrophysics Data System (ADS)

Scibelli, S.; Newberg, H. J.; Carlin, J. L.; Yanny, B.

2015-02-01

We present a census of the 12060 spectra of blue objects ((g-r)0<-0.25) in the Sloan Digital Sky Survey (SDSS) Data Release 8 (DR8). As part of the data release, all of the spectra were cross-correlated with 48 template spectra of stars, galaxies, and QSOs to determine the best match. We compared the blue spectra by eye to the templates assigned in SDSS DR8. 10856 of the objects matched their assigned template, 170 could not be classified due to low signal-to-noise ratio, and 1034 were given new classifications. We identify 7458 DA white dwarfs, 1145 DB white dwarfs, 273 rarer white dwarfs (including carbon, DZ, DQ, and magnetic), 294 subdwarf O stars, 648 subdwarf B stars, 679 blue horizontal branch stars, 1026 blue stragglers, 13 cataclysmic variables, 129 white dwarf-M dwarf binaries, 36 objects with spectra similar to DO white dwarfs, 179, quasi-stellar objects (QSOs), and 10 galaxies. We provide two tables of these objects, sample spectra that match the templates, figures showing all of the spectra that were grouped by eye, and diagnostic plots that show the positions, colors, apparent magnitudes, proper motions, etc., for each classification. (3 data files).

Effect of eccentricity on searches for gravitational waves from coalescing compact binaries in ground-based detectors

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

Brown, Duncan A.; Zimmerman, Peter J.

2010-01-15

Inspiralling compact binaries are expected to circularize before their gravitational-wave signals reach the sensitive frequency band of ground-based detectors. Current searches for gravitational waves from compact binaries using the LIGO and Virgo detectors therefore use circular templates to construct matched filters. Binary formation models have been proposed which suggest that some systems detectable by the LIGO-Virgo network may have non-negligible eccentricity. We investigate the ability of the restricted 3.5 post-Newtonian order TaylorF2 template bank, used by LIGO and Virgo to search for gravitational waves from compact binaries with masses M{<=}35M{sub {center_dot},} to detect binaries with nonzero eccentricity. We model themore » gravitational waves from eccentric binaries using the x-model post-Newtonian formalism proposed by Hinder et al.[I. Hinder, F. Hermann, P. Laguna, and D. Shoemaker, arXiv:0806.1037v1]. We find that small residual eccentricities (e{sub 0} < or approx. 0.05 at 40 Hz) do not significantly affect the ability of current LIGO searches to detect gravitational waves from coalescing compact binaries with total mass 2M{sub {center_dot}<}M<15M{sub {center_dot}.} For eccentricities e{sub 0} > or approx. 0.1, the loss in matched filter signal-to-noise ratio due to eccentricity can be significant and so templates which include eccentric effects will be required to perform optimal searches for such systems.« less

System and method for constructing filters for detecting signals whose frequency content varies with time

DOEpatents

Qian, S.; Dunham, M.E.

1996-11-12

A system and method are disclosed for constructing a bank of filters which detect the presence of signals whose frequency content varies with time. The present invention includes a novel system and method for developing one or more time templates designed to match the received signals of interest and the bank of matched filters use the one or more time templates to detect the received signals. Each matched filter compares the received signal x(t) with a respective, unique time template that has been designed to approximate a form of the signals of interest. The robust time domain template is assumed to be of the order of w(t)=A(t)cos(2{pi}{phi}(t)) and the present invention uses the trajectory of a joint time-frequency representation of x(t) as an approximation of the instantaneous frequency function {phi}{prime}(t). First, numerous data samples of the received signal x(t) are collected. A joint time frequency representation is then applied to represent the signal, preferably using the time frequency distribution series. The joint time-frequency transformation represents the analyzed signal energy at time t and frequency f, P(t,f), which is a three-dimensional plot of time vs. frequency vs. signal energy. Then P(t,f) is reduced to a multivalued function f(t), a two dimensional plot of time vs. frequency, using a thresholding process. Curve fitting steps are then performed on the time/frequency plot, preferably using Levenberg-Marquardt curve fitting techniques, to derive a general instantaneous frequency function {phi}{prime}(t) which best fits the multivalued function f(t). Integrating {phi}{prime}(t) along t yields {phi}{prime}(t), which is then inserted into the form of the time template equation. A suitable amplitude A(t) is also preferably determined. Once the time template has been determined, one or more filters are developed which each use a version or form of the time template. 7 figs.

Study of image matching algorithm and sub-pixel fitting algorithm in target tracking

NASA Astrophysics Data System (ADS)

Yang, Ming-dong; Jia, Jianjun; Qiang, Jia; Wang, Jian-yu

2015-03-01

Image correlation matching is a tracking method that searched a region most approximate to the target template based on the correlation measure between two images. Because there is no need to segment the image, and the computation of this method is little. Image correlation matching is a basic method of target tracking. This paper mainly studies the image matching algorithm of gray scale image, which precision is at sub-pixel level. The matching algorithm used in this paper is SAD (Sum of Absolute Difference) method. This method excels in real-time systems because of its low computation complexity. The SAD method is introduced firstly and the most frequently used sub-pixel fitting algorithms are introduced at the meantime. These fitting algorithms can't be used in real-time systems because they are too complex. However, target tracking often requires high real-time performance, we put forward a fitting algorithm named paraboloidal fitting algorithm based on the consideration above, this algorithm is simple and realized easily in real-time system. The result of this algorithm is compared with that of surface fitting algorithm through image matching simulation. By comparison, the precision difference between these two algorithms is little, it's less than 0.01pixel. In order to research the influence of target rotation on precision of image matching, the experiment of camera rotation was carried on. The detector used in the camera is a CMOS detector. It is fixed to an arc pendulum table, take pictures when the camera rotated different angles. Choose a subarea in the original picture as the template, and search the best matching spot using image matching algorithm mentioned above. The result shows that the matching error is bigger when the target rotation angle is larger. It's an approximate linear relation. Finally, the influence of noise on matching precision was researched. Gaussian noise and pepper and salt noise were added in the image respectively, and the image was processed by mean filter and median filter, then image matching was processed. The result show that when the noise is little, mean filter and median filter can achieve a good result. But when the noise density of salt and pepper noise is bigger than 0.4, or the variance of Gaussian noise is bigger than 0.0015, the result of image matching will be wrong.

Extracting Information from Narratives: An Application to Aviation Safety Reports

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

Posse, Christian; Matzke, Brett D.; Anderson, Catherine M.

2005-05-12

Aviation safety reports are the best available source of information about why a flight incident happened. However, stream of consciousness permeates the narratives making difficult the automation of the information extraction task. We propose an approach and infrastructure based on a common pattern specification language to capture relevant information via normalized template expression matching in context. Template expression matching handles variants of multi-word expressions. Normalization improves the likelihood of correct hits by standardizing and cleaning the vocabulary used in narratives. Checking for the presence of negative modifiers in the proximity of a potential hit reduces the chance of false hits.more » We present the above approach in the context of a specific application, which is the extraction of human performance factors from NASA ASRS reports. While knowledge infusion from experts plays a critical role during the learning phase, early results show that in a production mode, the automated process provides information that is consistent with analyses by human subjects.« less

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.

Automatic target detection using binary template matching

NASA Astrophysics Data System (ADS)

Jun, Dong-San; Sun, Sun-Gu; Park, HyunWook

2005-03-01

This paper presents a new automatic target detection (ATD) algorithm to detect targets such as battle tanks and armored personal carriers in ground-to-ground scenarios. Whereas most ATD algorithms were developed for forward-looking infrared (FLIR) images, we have developed an ATD algorithm for charge-coupled device (CCD) images, which have superior quality to FLIR images in daylight. The proposed algorithm uses fast binary template matching with an adaptive binarization, which is robust to various light conditions in CCD images and saves computation time. Experimental results show that the proposed method has good detection performance.

BgCut: automatic ship detection from UAV images.

PubMed

Xu, Chao; Zhang, Dongping; Zhang, Zhengning; Feng, Zhiyong

2014-01-01

Ship detection in static UAV aerial images is a fundamental challenge in sea target detection and precise positioning. In this paper, an improved universal background model based on Grabcut algorithm is proposed to segment foreground objects from sea automatically. First, a sea template library including images in different natural conditions is built to provide an initial template to the model. Then the background trimap is obtained by combing some templates matching with region growing algorithm. The output trimap initializes Grabcut background instead of manual intervention and the process of segmentation without iteration. The effectiveness of our proposed model is demonstrated by extensive experiments on a certain area of real UAV aerial images by an airborne Canon 5D Mark. The proposed algorithm is not only adaptive but also with good segmentation. Furthermore, the model in this paper can be well applied in the automated processing of industrial images for related researches.

BgCut: Automatic Ship Detection from UAV Images

PubMed Central

Zhang, Zhengning; Feng, Zhiyong

2014-01-01

Ship detection in static UAV aerial images is a fundamental challenge in sea target detection and precise positioning. In this paper, an improved universal background model based on Grabcut algorithm is proposed to segment foreground objects from sea automatically. First, a sea template library including images in different natural conditions is built to provide an initial template to the model. Then the background trimap is obtained by combing some templates matching with region growing algorithm. The output trimap initializes Grabcut background instead of manual intervention and the process of segmentation without iteration. The effectiveness of our proposed model is demonstrated by extensive experiments on a certain area of real UAV aerial images by an airborne Canon 5D Mark. The proposed algorithm is not only adaptive but also with good segmentation. Furthermore, the model in this paper can be well applied in the automated processing of industrial images for related researches. PMID:24977182

Auditing Practice Style Variation in Pediatric Inpatient Asthma Care.

PubMed

Silber, Jeffrey H; Rosenbaum, Paul R; Wang, Wei; Ludwig, Justin M; Calhoun, Shawna; Guevara, James P; Zorc, Joseph J; Zeigler, Ashley; Even-Shoshan, Orit

2016-09-01

Asthma is the most prevalent chronic illness among children, remaining a leading cause of pediatric hospitalizations and representing a major financial burden to many health care systems. To implement a new auditing process examining whether differences in hospital practice style may be associated with potential resource savings or inefficiencies in treating pediatric asthma admissions. A retrospective matched-cohort design study, matched for asthma severity, compared practice patterns for patients admitted to Children's Hospital Association hospitals contributing data to the Pediatric Hospital Information System (PHIS) database. With 3 years of PHIS data on 48 887 children, an asthma template was constructed consisting of representative children hospitalized for asthma between April 1, 2011, and March 31, 2014. The template was matched with either a 1:1, 2:1, or 3:1 ratio at each of 37 tertiary care children's hospitals, depending on available sample size. Treatment at each PHIS hospital. Cost, length of stay, and intensive care unit (ICU) utilization. After matching patients (n = 9100; mean [SD] age, 7.1 [3.6] years; 3418 [37.6%] females) to the template (n = 100, mean [SD] age, 7.2 [3.7] years; 37 [37.0%] females), there was no significant difference in observable patient characteristics at the 37 hospitals meeting the matching criteria. Despite similar characteristics of the patients, we observed large and significant variation in use of the ICUs as well as in length of stay and cost. For the same template-matched populations, comparing utilization between the 12.5th percentile (lower eighth) and 87.5th percentile (upper eighth) of hospitals, median cost varied by 87% ($3157 vs $5912 per patient; P < .001); total hospital length of stay varied by 47% (1.5 vs 2.2 days; P < .001); and ICU utilization was 254% higher (6.5% vs 23.0%; P < .001). Furthermore, the patterns of resource utilization by patient risk differed significantly across hospitals. For example, as patient risk increased one hospital displayed significantly increasing costs compared with their matched controls (comparative cost difference: lowest risk, -34.21%; highest risk, 53.27%; P < .001). In contrast, another hospital displayed significantly decreasing costs relative to their matched controls as patient risk increased (comparative cost difference: lowest risk, -10.12%; highest risk, -16.85%; P = .01). For children with asthma who had similar characteristics, we observed different hospital resource utilization; some values differed greatly, with important differences by initial patient risk. Through the template matching audit, hospitals and stakeholders can better understand where this excess variation occurs and can help to pinpoint practice styles that should be emulated or avoided.

Reducing the number of templates for aligned-spin compact binary coalescence gravitational wave searches using metric-agnostic template nudging

NASA Astrophysics Data System (ADS)

Indik, Nathaniel; Fehrmann, Henning; Harke, Franz; Krishnan, Badri; Nielsen, Alex B.

2018-06-01

Efficient multidimensional template placement is crucial in computationally intensive matched-filtering searches for gravitational waves (GWs). Here, we implement the neighboring cell algorithm (NCA) to improve the detection volume of an existing compact binary coalescence (CBC) template bank. This algorithm has already been successfully applied for a binary millisecond pulsar search in data from the Fermi satellite. It repositions templates from overdense regions to underdense regions and reduces the number of templates that would have been required by a stochastic method to achieve the same detection volume. Our method is readily generalizable to other CBC parameter spaces. Here we apply this method to the aligned-single-spin neutron star-black hole binary coalescence inspiral-merger-ringdown gravitational wave parameter space. We show that the template nudging algorithm can attain the equivalent effectualness of the stochastic method with 12% fewer templates.

Global localization of 3D point clouds in building outline maps of urban outdoor environments.

PubMed

Landsiedel, Christian; Wollherr, Dirk

2017-01-01

This paper presents a method to localize a robot in a global coordinate frame based on a sparse 2D map containing outlines of building and road network information and no location prior information. Its input is a single 3D laser scan of the surroundings of the robot. The approach extends the generic chamfer matching template matching technique from image processing by including visibility analysis in the cost function. Thus, the observed building planes are matched to the expected view of the corresponding map section instead of to the entire map, which makes a more accurate matching possible. Since this formulation operates on generic edge maps from visual sensors, the matching formulation can be expected to generalize to other input data, e.g., from monocular or stereo cameras. The method is evaluated on two large datasets collected in different real-world urban settings and compared to a baseline method from literature and to the standard chamfer matching approach, where it shows considerable performance benefits, as well as the feasibility of global localization based on sparse building outline data.

Mutual information-based template matching scheme for detection of breast masses: from mammography to digital breast tomosynthesis

PubMed Central

Mazurowski, Maciej A; Lo, Joseph Y; Harrawood, Brian P; Tourassi, Georgia D

2011-01-01

Development of a computational decision aid for a new medical imaging modality typically is a long and complicated process. It consists of collecting data in the form of images and annotations, development of image processing and pattern recognition algorithms for analysis of the new images and finally testing of the resulting system. Since new imaging modalities are developed more rapidly than ever before, any effort for decreasing the time and cost of this development process could result in maximizing the benefit of the new imaging modality to patients by making the computer aids quickly available to radiologists that interpret the images. In this paper, we make a step in this direction and investigate the possibility of translating the knowledge about the detection problem from one imaging modality to another. Specifically, we present a computer-aided detection (CAD) system for mammographic masses that uses a mutual information-based template matching scheme with intelligently selected templates. We presented principles of template matching with mutual information for mammography before. In this paper, we present an implementation of those principles in a complete computer-aided detection system. The proposed system, through an automatic optimization process, chooses the most useful templates (mammographic regions of interest) using a large database of previously collected and annotated mammograms. Through this process, the knowledge about the task of detecting masses in mammograms is incorporated in the system. Then we evaluate whether our system developed for screen-film mammograms can be successfully applied not only to other mammograms but also to digital breast tomosynthesis (DBT) reconstructed slices without adding any DBT cases for training. Our rationale is that since mutual information is known to be a robust intermodality image similarity measure, it has high potential of transferring knowledge between modalities in the context of the mass detection task. Experimental evaluation of the system on mammograms showed competitive performance compared to other mammography CAD systems recently published in the literature. When the system was applied “as-is” to DBT, its performance was notably worse than that for mammograms. However, with a simple additional preprocessing step, the performance of the system reached levels similar to that obtained for mammograms. In conclusion, the presented CAD system not only performed competitively on screen-film mammograms but it also performed robustly on DBT showing that direct transfer of knowledge across breast imaging modalities for mass detection is in fact possible. PMID:21554985

Functional annotation by sequence-weighted structure alignments: statistical analysis and case studies from the Protein 3000 structural genomics project in Japan.

PubMed

Standley, Daron M; Toh, Hiroyuki; Nakamura, Haruki

2008-09-01

A method to functionally annotate structural genomics targets, based on a novel structural alignment scoring function, is proposed. In the proposed score, position-specific scoring matrices are used to weight structurally aligned residue pairs to highlight evolutionarily conserved motifs. The functional form of the score is first optimized for discriminating domains belonging to the same Pfam family from domains belonging to different families but the same CATH or SCOP superfamily. In the optimization stage, we consider four standard weighting functions as well as our own, the "maximum substitution probability," and combinations of these functions. The optimized score achieves an area of 0.87 under the receiver-operating characteristic curve with respect to identifying Pfam families within a sequence-unique benchmark set of domain pairs. Confidence measures are then derived from the benchmark distribution of true-positive scores. The alignment method is next applied to the task of functionally annotating 230 query proteins released to the public as part of the Protein 3000 structural genomics project in Japan. Of these queries, 78 were found to align to templates with the same Pfam family as the query or had sequence identities > or = 30%. Another 49 queries were found to match more distantly related templates. Within this group, the template predicted by our method to be the closest functional relative was often not the most structurally similar. Several nontrivial cases are discussed in detail. Finally, 103 queries matched templates at the fold level, but not the family or superfamily level, and remain functionally uncharacterized. 2008 Wiley-Liss, Inc.

[Characteristics of supramolecular imprinting template on liver meridian tropism of traditional Chinese medicine based on molecular connectivity index].

PubMed

Fan, Shi-Qi; Li, Sen; Liu, Jin-Ling; Yang, Jiao; Hu, Chao; Zhu, Jun-Ping; Xiao, Xiao-Qin; Liu, Wen-Long; He, Fu-Yuan

2017-01-01

The molecular connectivity index was adopted to explore the characteristics of supramolecular imprinting template of herbs distributed to liver meridian, in order to provide scientific basis for traditional Chinese medicines(TCMs) distributed to liver meridian. In this paper, with "12th five-year plan" national planning textbooks Science of Traditional Chinese Medicine and Chemistry of Traditional Chinese Medicine as the blueprint, literatures and TCMSP sub-databases in TCM pharmacology of northwest science and technology university of agriculture and forestry were retrieved to collect and summarize active constituents of TCM distributed to liver meridian, and calculate the molecular connectivity index. The average molecular connectivity index of ingredients distributed to liver meridian was 9.47, which was close to flavonoid glycosides' (9.17±2.11) and terpenes (9.30±3.62). Therefore, it is inferred that template molecule of liver meridian is similar to physicochemical property of flavonoid glycosides and terpenes, which could be best matched with imprinting template of liver meridian. Copyright© by the Chinese Pharmaceutical Association.

Using dynamic programming to improve fiducial marker localization

NASA Astrophysics Data System (ADS)

Wan, Hanlin; Ge, Jiajia; Parikh, Parag

2014-04-01

Fiducial markers are used in a wide range of medical imaging applications. In radiation therapy, they are often implanted near tumors and used as motion surrogates that are tracked with fluoroscopy. We propose a novel and robust method based on dynamic programming (DP) for retrospectively localizing radiopaque fiducial markers in fluoroscopic images. Our method was compared to template matching (TM) algorithms on 407 data sets from 24 patients. We found that the performance of TM varied dramatically depending on the template used (ranging from 47% to 92% of data sets with a mean error <1 mm). DP by itself requires no template and performed as well as the best TM method, localizing the markers in 91% of the data sets with a mean error <1 mm. Finally, by combining DP and TM, we were able to localize the markers in 99% of the data sets with a mean error <1 mm, regardless of the template used. Our results show that DP can be a powerful tool for analyzing tumor motion, capable of accurately locating fiducial markers in fluoroscopic images regardless of marker type, shape, and size.

Compressed ECG biometric: a fast, secured and efficient method for identification of CVD patient.

PubMed

Sufi, Fahim; Khalil, Ibrahim; Mahmood, Abdun

2011-12-01

Adoption of compression technology is often required for wireless cardiovascular monitoring, due to the enormous size of Electrocardiography (ECG) signal and limited bandwidth of Internet. However, compressed ECG must be decompressed before performing human identification using present research on ECG based biometric techniques. This additional step of decompression creates a significant processing delay for identification task. This becomes an obvious burden on a system, if this needs to be done for a trillion of compressed ECG per hour by the hospital. Even though the hospital might be able to come up with an expensive infrastructure to tame the exuberant processing, for small intermediate nodes in a multihop network identification preceded by decompression is confronting. In this paper, we report a technique by which a person can be identified directly from his / her compressed ECG. This technique completely obviates the step of decompression and therefore upholds biometric identification less intimidating for the smaller nodes in a multihop network. The biometric template created by this new technique is lower in size compared to the existing ECG based biometrics as well as other forms of biometrics like face, finger, retina etc. (up to 8302 times lower than face template and 9 times lower than existing ECG based biometric template). Lower size of the template substantially reduces the one-to-many matching time for biometric recognition, resulting in a faster biometric authentication mechanism.

Automatic tracking of red blood cells in micro channels using OpenCV

NASA Astrophysics Data System (ADS)

Rodrigues, Vânia; Rodrigues, Pedro J.; Pereira, Ana I.; Lima, Rui

2013-10-01

The present study aims to developan automatic method able to track red blood cells (RBCs) trajectories flowing through a microchannel using the Open Source Computer Vision (OpenCV). The developed method is based on optical flux calculation assisted by the maximization of the template-matching product. The experimental results show a good functional performance of this method.

Computer-aided diagnosis of cavernous malformations in brain MR images.

PubMed

Wang, Huiquan; Ahmed, S Nizam; Mandal, Mrinal

2018-06-01

Cavernous malformation or cavernoma is one of the most common epileptogenic lesions. It is a type of brain vessel abnormality that can cause serious symptoms such as seizures, intracerebral hemorrhage, and various neurological disorders. Manual detection of cavernomas by physicians in a large set of brain MRI slices is a time-consuming and labor-intensive task and often delays diagnosis. In this paper, we propose a computer-aided diagnosis (CAD) system for cavernomas based on T2-weighted axial plane MRI image analysis. The proposed technique first extracts the brain area based on atlas registration and active contour model, and then performs template matching to obtain candidate cavernoma regions. Texture, the histogram of oriented gradients and local binary pattern features of each candidate region are calculated, and principal component analysis is applied to reduce the feature dimensionality. Support vector machines (SVMs) are finally used to classify each region into cavernoma or non-cavernoma so that most of the false positives (obtained by template matching) are eliminated. The performance of the proposed CAD system is evaluated and experimental results show that it provides superior performance in cavernoma detection compared to existing techniques. Copyright © 2018 Elsevier Ltd. All rights reserved.

Window-based method for approximating the Hausdorff in three-dimensional range imagery

DOEpatents

Koch, Mark W [Albuquerque, NM

2009-06-02

One approach to pattern recognition is to use a template from a database of objects and match it to a probe image containing the unknown. Accordingly, the Hausdorff distance can be used to measure the similarity of two sets of points. In particular, the Hausdorff can measure the goodness of a match in the presence of occlusion, clutter, and noise. However, existing 3D algorithms for calculating the Hausdorff are computationally intensive, making them impractical for pattern recognition that requires scanning of large databases. The present invention is directed to a new method that can efficiently, in time and memory, compute the Hausdorff for 3D range imagery. The method uses a window-based approach.

Low-resolution gamma-ray spectrometry for an information barrier based on a multi-criteria template-matching approach

NASA Astrophysics Data System (ADS)

Göttsche, Malte; Schirm, Janet; Glaser, Alexander

2016-12-01

Gamma-ray spectrometry has been successfully employed to identify unique items containing special nuclear materials. Template information barriers have been developed in the past to confirm items as warheads by comparing their gamma signature to the signature of true warheads. Their development has, however, not been fully transparent, and they may not be sensitive to some relevant evasion scenarios. We develop a fully open template information barrier concept, based on low-resolution measurements, which, by design, reduces the extent of revealed sensitive information. The concept is based on three signatures of an item to be compared to a recorded template. The similarity of the spectrum is assessed by a modification of the Kolmogorov-Smirnov test to confirm the isotopic composition. The total gamma count rate must agree with the template as a measure of the projected surface of the object. In order to detect the diversion of fissile material from the interior of an item, a polyethylene mask is placed in front of the detector. Neutrons from spontaneous and induced fission events in the item produce 2.223 MeV gamma rays from neutron capture by hydrogen-1 in the mask. This peak is detected and its intensity scales with the item's fissile mass. The analysis based on MCNP Monte Carlo simulations of various plutonium configurations suggests that this concept can distinguish a valid item from a variety of invalid ones. The concept intentionally avoids any assumptions about specific spectral features, such as looking for specific gamma peaks of specific isotopes, thereby facilitating a fully unclassified discussion. By making all aspects public and allowing interested participants to contribute to the development and benchmarking, we enable a more open and inclusive discourse on this matter.

3-Dimensional printing guide template assisted percutaneous vertebroplasty: Technical note.

PubMed

Li, Jian; Lin, JiSheng; Yang, Yong; Xu, JunChuan; Fei, Qi

2018-06-01

Percutaneous vertebroplasty (PVP) is currently considered as an effective treatment for pain caused by acute osteoporotic vertebral compression fracture. Recently, puncture-related complications are increasingly reported. It's important to find a precise technique to reduce the puncture-related complications. We report a case and discussed the novel surgical technique with step-by-step operating procedures, to introduce the precise PVP assisted by a 3-dimensional printing guide template. Based on the preoperative CT scan and infrared scan data, a well-designed individual guide template could be established in a 3-dimensional reconstruction software and printed out by a 3-dimensional printer. In real operation, by matching the guide template to patient's back skin, cement needles' insertion orientation and depth were easily established. Only 14 times C-arm fluoroscopy with HDF mode (total exposure dose was 4.5 mSv) were required during the procedure. The operation took only 17 min. Cement distribution in the vertebral body was very good without any puncture-related complications. Pain was significantly relieved after surgery. In conclusion, the novel precise 3-dimensional printing guide template system may allow (1) comprehensive visualization of the fractured vertebral body and the individual surgical planning, (2) the perfect fitting between skin and guide template to ensure the puncture stability and accuracy, and (3) increased puncture precision and decreased puncture-related complications, surgical time and radiation exposure. Copyright © 2018 Elsevier Ltd. All rights reserved.

A Matched Field Processing Framework for Coherent Detection Over Local and Regional Networks (Postprint)

DTIC Science & Technology

2011-12-30

the term " superresolution "). The single-phase matched field statistic for a given template was also demonstrated to be a viable detection statistic... Superresolution with seismic arrays using empirical matched field processing, Geophys. J. Int. 182: 1455–1477. Kim, K.-H. and Park, Y. (2010): The 20

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

DOE PAGES

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

2016-08-31

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Immunophenotype Discovery, Hierarchical Organization, and Template-Based Classification of Flow Cytometry Samples

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

Azad, Ariful; Rajwa, Bartek; Pothen, Alex

We describe algorithms for discovering immunophenotypes from large collections of flow cytometry samples and using them to organize the samples into a hierarchy based on phenotypic similarity. The hierarchical organization is helpful for effective and robust cytometry data mining, including the creation of collections of cell populations’ characteristic of different classes of samples, robust classification, and anomaly detection. We summarize a set of samples belonging to a biological class or category with a statistically derived template for the class. Whereas individual samples are represented in terms of their cell populations (clusters), a template consists of generic meta-populations (a group ofmore » homogeneous cell populations obtained from the samples in a class) that describe key phenotypes shared among all those samples. We organize an FC data collection in a hierarchical data structure that supports the identification of immunophenotypes relevant to clinical diagnosis. A robust template-based classification scheme is also developed, but our primary focus is in the discovery of phenotypic signatures and inter-sample relationships in an FC data collection. This collective analysis approach is more efficient and robust since templates describe phenotypic signatures common to cell populations in several samples while ignoring noise and small sample-specific variations. We have applied the template-based scheme to analyze several datasets, including one representing a healthy immune system and one of acute myeloid leukemia (AML) samples. The last task is challenging due to the phenotypic heterogeneity of the several subtypes of AML. However, we identified thirteen immunophenotypes corresponding to subtypes of AML and were able to distinguish acute promyelocytic leukemia (APL) samples with the markers provided. Clinically, this is helpful since APL has a different treatment regimen from other subtypes of AML. Core algorithms used in our data analysis are available in the flowMatch package at www.bioconductor.org. It has been downloaded nearly 6,000 times since 2014.« less

Mouse EEG spike detection based on the adapted continuous wavelet transform

NASA Astrophysics Data System (ADS)

Tieng, Quang M.; Kharatishvili, Irina; Chen, Min; Reutens, David C.

2016-04-01

Objective. Electroencephalography (EEG) is an important tool in the diagnosis of epilepsy. Interictal spikes on EEG are used to monitor the development of epilepsy and the effects of drug therapy. EEG recordings are generally long and the data voluminous. Thus developing a sensitive and reliable automated algorithm for analyzing EEG data is necessary. Approach. A new algorithm for detecting and classifying interictal spikes in mouse EEG recordings is proposed, based on the adapted continuous wavelet transform (CWT). The construction of the adapted mother wavelet is founded on a template obtained from a sample comprising the first few minutes of an EEG data set. Main Result. The algorithm was tested with EEG data from a mouse model of epilepsy and experimental results showed that the algorithm could distinguish EEG spikes from other transient waveforms with a high degree of sensitivity and specificity. Significance. Differing from existing approaches, the proposed approach combines wavelet denoising, to isolate transient signals, with adapted CWT-based template matching, to detect true interictal spikes. Using the adapted wavelet constructed from a predefined template, the adapted CWT is calculated on small EEG segments to fit dynamical changes in the EEG recording.

Monoplane 3D-2D registration of cerebral angiograms based on multi-objective stratified optimization

NASA Astrophysics Data System (ADS)

Aksoy, T.; Špiclin, Ž.; Pernuš, F.; Unal, G.

2017-12-01

Registration of 3D pre-interventional to 2D intra-interventional medical images has an increasingly important role in surgical planning, navigation and treatment, because it enables the physician to co-locate depth information given by pre-interventional 3D images with the live information in intra-interventional 2D images such as x-ray. Most tasks during image-guided interventions are carried out under a monoplane x-ray, which is a highly ill-posed problem for state-of-the-art 3D to 2D registration methods. To address the problem of rigid 3D-2D monoplane registration we propose a novel multi-objective stratified parameter optimization, wherein a small set of high-magnitude intensity gradients are matched between the 3D and 2D images. The stratified parameter optimization matches rotation templates to depth templates, first sampled from projected 3D gradients and second from the 2D image gradients, so as to recover 3D rigid-body rotations and out-of-plane translation. The objective for matching was the gradient magnitude correlation coefficient, which is invariant to in-plane translation. The in-plane translations are then found by locating the maximum of the gradient phase correlation between the best matching pair of rotation and depth templates. On twenty pairs of 3D and 2D images of ten patients undergoing cerebral endovascular image-guided intervention the 3D to monoplane 2D registration experiments were setup with a rather high range of initial mean target registration error from 0 to 100 mm. The proposed method effectively reduced the registration error to below 2 mm, which was further refined by a fast iterative method and resulted in a high final registration accuracy (0.40 mm) and high success rate (> 96%). Taking into account a fast execution time below 10 s, the observed performance of the proposed method shows a high potential for application into clinical image-guidance systems.

Object-Based Dense Matching Method for Maintaining Structure Characteristics of Linear Buildings

PubMed Central

Yan, Yiming; Qiu, Mingjie; Zhao, Chunhui; Wang, Liguo

2018-01-01

In this paper, we proposed a novel object-based dense matching method specially for the high-precision disparity map of building objects in urban areas, which can maintain accurate object structure characteristics. The proposed framework mainly includes three stages. Firstly, an improved edge line extraction method is proposed for the edge segments to fit closely to building outlines. Secondly, a fusion method is proposed for the outlines under the constraint of straight lines, which can maintain the building structural attribute with parallel or vertical edges, which is very useful for the dense matching method. Finally, we proposed an edge constraint and outline compensation (ECAOC) dense matching method to maintain building object structural characteristics in the disparity map. In the proposed method, the improved edge lines are used to optimize matching search scope and matching template window, and the high-precision building outlines are used to compensate the shape feature of building objects. Our method can greatly increase the matching accuracy of building objects in urban areas, especially at building edges. For the outline extraction experiments, our fusion method verifies the superiority and robustness on panchromatic images of different satellites and different resolutions. For the dense matching experiments, our ECOAC method shows great advantages for matching accuracy of building objects in urban areas compared with three other methods. PMID:29596393

Biometric template revocation

NASA Astrophysics Data System (ADS)

Arndt, Craig M.

2004-08-01

Biometric are a powerful technology for identifying humans both locally and at a distance. In order to perform identification or verification biometric systems capture an image of some biometric of a user or subject. The image is then converted mathematical to representation of the person call a template. Since we know that every human in the world is different each human will have different biometric images (different fingerprints, or faces, etc.). This is what makes biometrics useful for identification. However unlike a credit card number or a password to can be given to a person and later revoked if it is compromised and biometric is with the person for life. The problem then is to develop biometric templates witch can be easily revoked and reissued which are also unique to the user and can be easily used for identification and verification. In this paper we develop and present a method to generate a set of templates which are fully unique to the individual and also revocable. By using bases set compression algorithms in an n-dimensional orthogonal space we can represent a give biometric image in an infinite number of equally valued and unique ways. The verification and biometric matching system would be presented with a given template and revocation code. The code will then representing where in the sequence of n-dimensional vectors to start the recognition.

Source mechanism of small long-period events at Mount St. Helens in July 2005 using template matching, phase-weighted stacking, and full-waveform inversion

USGS Publications Warehouse

Matoza, Robin S.; Chouet, Bernard A.; Dawson, Phillip B.; Shearer, Peter M.; Haney, Matthew M.; Waite, Gregory P.; Moran, Seth C.; Mikesell, T. Dylan

2015-01-01

Long-period (LP, 0.5-5 Hz) seismicity, observed at volcanoes worldwide, is a recognized signature of unrest and eruption. Cyclic LP “drumbeating” was the characteristic seismicity accompanying the sustained dome-building phase of the 2004–2008 eruption of Mount St. Helens (MSH), WA. However, together with the LP drumbeating was a near-continuous, randomly occurring series of tiny LP seismic events (LP “subevents”), which may hold important additional information on the mechanism of seismogenesis at restless volcanoes. We employ template matching, phase-weighted stacking, and full-waveform inversion to image the source mechanism of one multiplet of these LP subevents at MSH in July 2005. The signal-to-noise ratios of the individual events are too low to produce reliable waveform-inversion results, but the events are repetitive and can be stacked. We apply network-based template matching to 8 days of continuous velocity waveform data from 29 June to 7 July 2005 using a master event to detect 822 network triggers. We stack waveforms for 359 high-quality triggers at each station and component, using a combination of linear and phase-weighted stacking to produce clean stacks for use in waveform inversion. The derived source mechanism pointsto the volumetric oscillation (~10 m3) of a subhorizontal crack located at shallow depth (~30 m) in an area to the south of Crater Glacier in the southern portion of the breached MSH crater. A possible excitation mechanism is the sudden condensation of metastable steam from a shallow pressurized hydrothermal system as it encounters cool meteoric water in the outer parts of the edifice, perhaps supplied from snow melt.

Systematic detection of seismic events at Mount St. Helens with an ultra-dense array

NASA Astrophysics Data System (ADS)

Meng, X.; Hartog, J. R.; Schmandt, B.; Hotovec-Ellis, A. J.; Hansen, S. M.; Vidale, J. E.; Vanderplas, J.

2016-12-01

During the summer of 2014, an ultra-dense array of 900 geophones was deployed around the crater of Mount St. Helens and continuously operated for 15 days. This dataset provides us an unprecedented opportunity to systematically detect seismic events around an active volcano and study their underlying mechanisms. We use a waveform-based matched filter technique to detect seismic events from this dataset. Due to the large volume of continuous data ( 1 TB), we performed the detection on the GPU cluster Stampede (https://www.tacc.utexas.edu/systems/stampede). We build a suite of template events from three catalogs: 1) the standard Pacific Northwest Seismic Network (PNSN) catalog (45 events); 2) the catalog from Hansen&Schmandt (2015) obtained with a reverse-time imaging method (212 events); and 3) the catalog identified with a matched filter technique using the PNSN permanent stations (190 events). By searching for template matches in the ultra-dense array, we find 2237 events. We then calibrate precise relative magnitudes for template and detected events, using a principal component fit to measure waveform amplitude ratios. The magnitude of completeness and b-value of the detected catalog is -0.5 and 1.1, respectively. Our detected catalog shows several intensive swarms, which are likely driven by fluid pressure transients in conduits or slip transients on faults underneath the volcano. We are currently relocating the detected catalog with HypoDD and measuring the seismic velocity changes at Mount St. Helens using the coda wave interferometry of detected repeating earthquakes. The accurate temporal-spatial migration pattern of seismicity and seismic property changes should shed light on the physical processes beneath Mount St. Helens.

Testing sensory evidence against mnemonic templates

PubMed Central

Myers, Nicholas E; Rohenkohl, Gustavo; Wyart, Valentin; Woolrich, Mark W; Nobre, Anna C; Stokes, Mark G

2015-01-01

Most perceptual decisions require comparisons between current input and an internal template. Classic studies propose that templates are encoded in sustained activity of sensory neurons. However, stimulus encoding is itself dynamic, tracing a complex trajectory through activity space. Which part of this trajectory is pre-activated to reflect the template? Here we recorded magneto- and electroencephalography during a visual target-detection task, and used pattern analyses to decode template, stimulus, and decision-variable representation. Our findings ran counter to the dominant model of sustained pre-activation. Instead, template information emerged transiently around stimulus onset and quickly subsided. Cross-generalization between stimulus and template coding, indicating a shared neural representation, occurred only briefly. Our results are compatible with the proposal that template representation relies on a matched filter, transforming input into task-appropriate output. This proposal was consistent with a signed difference response at the perceptual decision stage, which can be explained by a simple neural model. DOI: http://dx.doi.org/10.7554/eLife.09000.001 PMID:26653854

System and method for constructing filters for detecting signals whose frequency content varies with time

DOEpatents

Qian, Shie; Dunham, Mark E.

1996-01-01

A system and method for constructing a bank of filters which detect the presence of signals whose frequency content varies with time. The present invention includes a novel system and method for developing one or more time templates designed to match the received signals of interest and the bank of matched filters use the one or more time templates to detect the received signals. Each matched filter compares the received signal x(t) with a respective, unique time template that has been designed to approximate a form of the signals of interest. The robust time domain template is assumed to be of the order of w(t)=A(t)cos{2.pi..phi.(t)} and the present invention uses the trajectory of a joint time-frequency representation of x(t) as an approximation of the instantaneous frequency function {.phi.'(t). First, numerous data samples of the received signal x(t) are collected. A joint time frequency representation is then applied to represent the signal, preferably using the time frequency distribution series (also known as the Gabor spectrogram). The joint time-frequency transformation represents the analyzed signal energy at time t and frequency .function., P(t,f), which is a three-dimensional plot of time vs. frequency vs. signal energy. Then P(t,f) is reduced to a multivalued function f(t), a two dimensional plot of time vs. frequency, using a thresholding process. Curve fitting steps are then performed on the time/frequency plot, preferably using Levenberg-Marquardt curve fitting techniques, to derive a general instantaneous frequency function .phi.'(t) which best fits the multivalued function f(t), a trajectory of the joint time-frequency domain representation of x(t). Integrating .phi.'(t) along t yields .phi.(t), which is then inserted into the form of the time template equation. A suitable amplitude A(t) is also preferably determined. Once the time template has been determined, one or more filters are developed which each use a version or form of the time template.

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.

The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.

PubMed

Schüller, Andreas; Suhartono, Marcel; Fechner, Uli; Tanrikulu, Yusuf; Breitung, Sven; Scheffer, Ute; Göbel, Michael W; Schneider, Gisbert

2008-02-01

Principles of fragment-based molecular design are presented and discussed in the context of de novo drug design. The underlying idea is to dissect known drug molecules in fragments by straightforward pseudo-retro-synthesis. The resulting building blocks are then used for automated assembly of new molecules. A particular question has been whether this approach is actually able to perform scaffold-hopping. A prospective case study illustrates the usefulness of fragment-based de novo design for finding new scaffolds. We were able to identify a novel ligand disrupting the interaction between the Tat peptide and TAR RNA, which is part of the human immunodeficiency virus (HIV-1) mRNA. Using a single template structure (acetylpromazine) as reference molecule and a topological pharmacophore descriptor (CATS), new chemotypes were automatically generated by our de novo design software Flux. Flux features an evolutionary algorithm for fragment-based compound assembly and optimization. Pharmacophore superimposition and docking into the target RNA suggest perfect matching between the template molecule and the designed compound. Chemical synthesis was straightforward, and bioactivity of the designed molecule was confirmed in a FRET assay. This study demonstrates the practicability of de novo design to generating RNA ligands containing novel molecular scaffolds.

Real-time color/shape-based traffic signs acquisition and recognition system

NASA Astrophysics Data System (ADS)

Saponara, Sergio

2013-02-01

A real-time system is proposed to acquire from an automotive fish-eye CMOS camera the traffic signs, and provide their automatic recognition on the vehicle network. Differently from the state-of-the-art, in this work color-detection is addressed exploiting the HSI color space which is robust to lighting changes. Hence the first stage of the processing system implements fish-eye correction and RGB to HSI transformation. After color-based detection a noise deletion step is implemented and then, for the classification, a template-based correlation method is adopted to identify potential traffic signs, of different shapes, from acquired images. Starting from a segmented-image a matching with templates of the searched signs is carried out using a distance transform. These templates are organized hierarchically to reduce the number of operations and hence easing real-time processing for several types of traffic signs. Finally, for the recognition of the specific traffic sign, a technique based on extraction of signs characteristics and thresholding is adopted. Implemented on DSP platform the system recognizes traffic signs in less than 150 ms at a distance of about 15 meters from 640x480-pixel acquired images. Tests carried out with hundreds of images show a detection and recognition rate of about 93%.

Advanced Tie Feature Matching for the Registration of Mobile Mapping Imaging Data and Aerial Imagery

NASA Astrophysics Data System (ADS)

Jende, P.; Peter, M.; Gerke, M.; Vosselman, G.

2016-06-01

Mobile Mapping's ability to acquire high-resolution ground data is opposing unreliable localisation capabilities of satellite-based positioning systems in urban areas. Buildings shape canyons impeding a direct line-of-sight to navigation satellites resulting in a deficiency to accurately estimate the mobile platform's position. Consequently, acquired data products' positioning quality is considerably diminished. This issue has been widely addressed in the literature and research projects. However, a consistent compliance of sub-decimetre accuracy as well as a correction of errors in height remain unsolved. We propose a novel approach to enhance Mobile Mapping (MM) image orientation based on the utilisation of highly accurate orientation parameters derived from aerial imagery. In addition to that, the diminished exterior orientation parameters of the MM platform will be utilised as they enable the application of accurate matching techniques needed to derive reliable tie information. This tie information will then be used within an adjustment solution to correct affected MM data. This paper presents an advanced feature matching procedure as a prerequisite to the aforementioned orientation update. MM data is ortho-projected to gain a higher resemblance to aerial nadir data simplifying the images' geometry for matching. By utilising MM exterior orientation parameters, search windows may be used in conjunction with a selective keypoint detection and template matching. Originating from different sensor systems, however, difficulties arise with respect to changes in illumination, radiometry and a different original perspective. To respond to these challenges for feature detection, the procedure relies on detecting keypoints in only one image. Initial tests indicate a considerable improvement in comparison to classic detector/descriptor approaches in this particular matching scenario. This method leads to a significant reduction of outliers due to the limited availability of putative matches and the utilisation of templates instead of feature descriptors. In our experiments discussed in this paper, typical urban scenes have been used for evaluating the proposed method. Even though no additional outlier removal techniques have been used, our method yields almost 90% of correct correspondences. However, repetitive image patterns may still induce ambiguities which cannot be fully averted by this technique. Hence and besides, possible advancements will be briefly presented.

Multi-template analysis of human perirhinal cortex in brain MRI: Explicitly accounting for anatomical variability

PubMed Central

Xie, Long; Pluta, John B.; Das, Sandhitsu R.; Wisse, Laura E.M.; Wang, Hongzhi; Mancuso, Lauren; Kliot, Dasha; Avants, Brian B.; Ding, Song-Lin; Manjón, José V.; Wolk, David A.; Yushkevich, Paul A.

2016-01-01

Rational The human perirhinal cortex (PRC) plays critical roles in episodic and semantic memory and visual perception. The PRC consists of Brodmann areas 35 and 36 (BA35, BA36). In Alzheimer's disease (AD), BA35 is the first cortical site affected by neurofibrillary tangle pathology, which is closely linked to neural injury in AD. Large anatomical variability, manifested in the form of different cortical folding and branching patterns, makes it difficult to segment the PRC in MRI scans. Pathology studies have found that in ~97% of specimens, the PRC falls into one of three discrete anatomical variants. However, current methods for PRC segmentation and morphometry in MRI are based on single-template approaches, which may not be able to accurately model these discrete variants Methods A multi-template analysis pipeline that explicitly accounts for anatomical variability is used to automatically label the PRC and measure its thickness in T2-weighted MRI scans. The pipeline uses multi-atlas segmentation to automatically label medial temporal lobe cortices including entorhinal cortex, PRC and the parahippocampal cortex. Pairwise registration between label maps and clustering based on residual dissimilarity after registration are used to construct separate templates for the anatomical variants of the PRC. An optimal path of deformations linking these templates is used to establish correspondences between all the subjects. Experimental evaluation focuses on the ability of single-template and multi-template analyses to detect differences in the thickness of medial temporal lobe cortices between patients with amnestic mild cognitive impairment (aMCI, n=41) and age-matched controls (n=44). Results The proposed technique is able to generate templates that recover the three dominant discrete variants of PRC and establish more meaningful correspondences between subjects than a single-template approach. The largest reduction in thickness associated with aMCI, in absolute terms, was found in left BA35 using both regional and summary thickness measures. Further, statistical maps of regional thickness difference between aMCI and controls revealed different patterns for the three anatomical variants. PMID:27702610

Implementation of sobel method to detect the seed rubber plant leaves

NASA Astrophysics Data System (ADS)

Suyanto; Munte, J.

2018-03-01

This research was conducted to develop a system that can identify and recognize the type of rubber tree based on the pattern of leaves of the plant. The steps research are started with the identification of the image data acquisition, image processing, image edge detection and identification method template matching. Edge detection is using Sobel edge detection. Pattern recognition would detect image as input and compared with other images in a database called templates. Experiments carried out in one phase, identification of the leaf edge, using a rubber plant leaf image 14 are superior and 5 for each type of test images (clones) of the plant. From the experimental results obtained by the recognition rate of 91.79%.

Automated main-chain model building by template matching and iterative fragment extension.

PubMed

Terwilliger, Thomas C

2003-01-01

An algorithm for the automated macromolecular model building of polypeptide backbones is described. The procedure is hierarchical. In the initial stages, many overlapping polypeptide fragments are built. In subsequent stages, the fragments are extended and then connected. Identification of the locations of helical and beta-strand regions is carried out by FFT-based template matching. Fragment libraries of helices and beta-strands from refined protein structures are then positioned at the potential locations of helices and strands and the longest segments that fit the electron-density map are chosen. The helices and strands are then extended using fragment libraries consisting of sequences three amino acids long derived from refined protein structures. The resulting segments of polypeptide chain are then connected by choosing those which overlap at two or more C(alpha) positions. The fully automated procedure has been implemented in RESOLVE and is capable of model building at resolutions as low as 3.5 A. The algorithm is useful for building a preliminary main-chain model that can serve as a basis for refinement and side-chain addition.

SpikeGUI: software for rapid interictal discharge annotation via template matching and online machine learning.

PubMed

Jing Jin; Dauwels, Justin; Cash, Sydney; Westover, M Brandon

2014-01-01

Detection of interictal discharges is a key element of interpreting EEGs during the diagnosis and management of epilepsy. Because interpretation of clinical EEG data is time-intensive and reliant on experts who are in short supply, there is a great need for automated spike detectors. However, attempts to develop general-purpose spike detectors have so far been severely limited by a lack of expert-annotated data. Huge databases of interictal discharges are therefore in great demand for the development of general-purpose detectors. Detailed manual annotation of interictal discharges is time consuming, which severely limits the willingness of experts to participate. To address such problems, a graphical user interface "SpikeGUI" was developed in our work for the purposes of EEG viewing and rapid interictal discharge annotation. "SpikeGUI" substantially speeds up the task of annotating interictal discharges using a custom-built algorithm based on a combination of template matching and online machine learning techniques. While the algorithm is currently tailored to annotation of interictal epileptiform discharges, it can easily be generalized to other waveforms and signal types.

SpikeGUI: Software for Rapid Interictal Discharge Annotation via Template Matching and Online Machine Learning

PubMed Central

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

2015-01-01

Detection of interictal discharges is a key element of interpreting EEGs during the diagnosis and management of epilepsy. Because interpretation of clinical EEG data is time-intensive and reliant on experts who are in short supply, there is a great need for automated spike detectors. However, attempts to develop general-purpose spike detectors have so far been severely limited by a lack of expert-annotated data. Huge databases of interictal discharges are therefore in great demand for the development of general-purpose detectors. Detailed manual annotation of interictal discharges is time consuming, which severely limits the willingness of experts to participate. To address such problems, a graphical user interface “SpikeGUI” was developed in our work for the purposes of EEG viewing and rapid interictal discharge annotation. “SpikeGUI” substantially speeds up the task of annotating interictal discharges using a custom-built algorithm based on a combination of template matching and online machine learning techniques. While the algorithm is currently tailored to annotation of interictal epileptiform discharges, it can easily be generalized to other waveforms and signal types. PMID:25570976

Effect of digital template in the assistant of a giant condylar osteochondroma resection.

PubMed

Bai, Guo; He, Dongmei; Yang, Chi; Lu, Chuan; Huang, Dong; Chen, Minjie; Yuan, Jianbing

2014-05-01

Exostosis osteochondroma is usually resected with the whole condyle even part of it is not involved. This study was to report the effect of using digital template in the assistant of resection while protecting the uninvolved condyle. We used computer-aided design technique in the assistant of making preoperative plan of a patient with giant condylar osteochondroma of exogenous type, including determining the boundary between the tumor and the articular surface of condyle, and designing the virtual tumor resection plane, surgical approach, and remove-out path of the tumor. The digital osteotomy template was made by rapid prototyping technique based on the preoperative plan. Postoperative CT scan was performed and merged with the preoperative CT by the Proplan 1.3 system to evaluate the accuracy of surgical resection with the guide of digital template. The osteotomy template was attached to the lateral surface of condyle accurately, and the tumor was removed totally by the guide of the template without injuries to adjacent nerves and vessels. Postoperative CT showed that the osteochondroma was removed completely and the unaffected articular surface of condyle was preserved well. The merging of postoperative and preoperative CT by Proplan 1.3 system showed the outcome of the operation matched with the preoperative planning quite well with an error of 0.92 mm. There was no sign of recurrence after 6 months of follow-up. The application of digital template could improve the accuracy of the giant condylar tumor resection and help to preserve the uninvolved condyle. The use of digital template could reduce injuries to the nerves and vessels as well as save time for the operation.

A temperature match based optimization method for daily load prediction considering DLC effect

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

Yu, Z.

This paper presents a unique optimization method for short term load forecasting. The new method is based on the optimal template temperature match between the future and past temperatures. The optimal error reduction technique is a new concept introduced in this paper. Two case studies show that for hourly load forecasting, this method can yield results as good as the rather complicated Box-Jenkins Transfer Function method, and better than the Box-Jenkins method; for peak load prediction, this method is comparable in accuracy to the neural network method with back propagation, and can produce more accurate results than the multi-linear regressionmore » method. The DLC effect on system load is also considered in this method.« less

Application of Template Matching for Improving Classification of Urban Railroad Point Clouds

PubMed Central

Arastounia, Mostafa; Oude Elberink, Sander

2016-01-01

This study develops an integrated data-driven and model-driven approach (template matching) that clusters the urban railroad point clouds into three classes of rail track, contact cable, and catenary cable. The employed dataset covers 630 m of the Dutch urban railroad corridors in which there are four rail tracks, two contact cables, and two catenary cables. The dataset includes only geometrical information (three dimensional (3D) coordinates of the points) with no intensity data and no RGB data. The obtained results indicate that all objects of interest are successfully classified at the object level with no false positives and no false negatives. The results also show that an average 97.3% precision and an average 97.7% accuracy at the point cloud level are achieved. The high precision and high accuracy of the rail track classification (both greater than 96%) at the point cloud level stems from the great impact of the employed template matching method on excluding the false positives. The cables also achieve quite high average precision (96.8%) and accuracy (98.4%) due to their high sampling and isolated position in the railroad corridor. PMID:27973452

Moving Object Detection Using a Parallax Shift Vector Algorithm

NASA Astrophysics Data System (ADS)

Gural, Peter S.; Otto, Paul R.; Tedesco, Edward F.

2018-07-01

There are various algorithms currently in use to detect asteroids from ground-based observatories, but they are generally restricted to linear or mildly curved movement of the target object across the field of view. Space-based sensors in high inclination, low Earth orbits can induce significant parallax in a collected sequence of images, especially for objects at the typical distances of asteroids in the inner solar system. This results in a highly nonlinear motion pattern of the asteroid across the sensor, which requires a more sophisticated search pattern for detection processing. Both the classical pattern matching used in ground-based asteroid search and the more sensitive matched filtering and synthetic tracking techniques, can be adapted to account for highly complex parallax motion. A new shift vector generation methodology is discussed along with its impacts on commonly used detection algorithms, processing load, and responsiveness to asteroid track reporting. The matched filter, template generator, and pattern matcher source code for the software described herein are available via GitHub.

A fast template periodogram

NASA Astrophysics Data System (ADS)

Hoffman, John; VanderPlas, Jake; Hartman, Joel; Bakos, Gáspár

2017-09-01

This proceedings contribution presents a novel, non-linear extension to the Lomb-Scargle periodogram that allows periodograms to be generated for arbitrary signal shapes. Such periodograms are already known as "template periodograms" or "periodic matched filters," but current implementations are computationally inefficient. The "fast template periodogram" presented here improves existing techniques by a factor of ˜a few for small test cases (O(10) observations), and over three orders of magnitude for lightcurves containing O(104) observations. The fast template periodogram scales asymptotically as O(HNf log HNf + H4Nf), where H denotes the number of harmonics required to adequately approximate the template and Nf is the number of trial frequencies. Existing implementations scale as O(NobsNf), where Nobs is the number of observations in the lightcurve. An open source Python implementation is available on GitHub.

On the suitability and development of layout templates for analog layout reuse and layout-aware synthesis

NASA Astrophysics Data System (ADS)

Castro-Lopez, Rafael; Fernandez, Francisco V.; Rodriguez Vazquez, Angel

2005-06-01

Accelerating the synthesis of increasingly complex analog integrated circuits is key to bridge the widening gap between what we can integrate and what we can design while meeting ever-tightening time-to-market constraints. It is a well-known fact in the semiconductor industry that such goal can only be attained by means of adequate CAD methodologies, techniques, and accompanying tools. This is particularly important in analog physical synthesis (a.k.a. layout generation), where large sensitivities of the circuit performances to the many subtle details of layout implementation (device matching, loading and coupling effects, reliability, and area features are of utmost importance to analog designers), render complete automation a truly challenging task. To approach the problem, two directions have been traditionally considered, knowledge-based and optimization-based, both with their own pros and cons. Besides, recently reported solutions oriented to speed up the overall design flow by means of reuse-based practices or by cutting off time-consuming, error-prone spins between electrical and layout synthesis (a technique known as layout-aware synthesis), rely on a outstandingly rapid yet efficient layout generation method. This paper analyses the suitability of procedural layout generation based on templates (a knowledge-based approach) by examining the requirements that both layout reuse and layout-aware solutions impose, and how layout templates face them. The ability to capture the know-how of experienced layout designers and the turnaround times for layout instancing are considered main comparative aspects in relation to other layout generation approaches. A discussion on the benefit-cost trade-off of using layout templates is also included. In addition to this analysis, the paper delves deeper into systematic techniques to develop fully reusable layout templates for analog circuits, either for a change of the circuit sizing (i.e., layout retargeting) or a change of the fabrication process (i.e., layout migration). Several examples implemented with the Cadence's Virtuoso tool suite are provided as demonstration of the paper's contributions.

[Affine transformation-based automatic registration for peripheral digital subtraction angiography (DSA)].

PubMed

Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min

2008-07-01

In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.

Template-based combinatorial enumeration of virtual compound libraries for lipids

PubMed Central

2012-01-01

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license. PMID:23006594

Robust 3D DFT video watermarking

NASA Astrophysics Data System (ADS)

Deguillaume, Frederic; Csurka, Gabriela; O'Ruanaidh, Joseph J.; Pun, Thierry

1999-04-01

This paper proposes a new approach for digital watermarking and secure copyright protection of videos, the principal aim being to discourage illicit copying and distribution of copyrighted material. The method presented here is based on the discrete Fourier transform (DFT) of three dimensional chunks of video scene, in contrast with previous works on video watermarking where each video frame was marked separately, or where only intra-frame or motion compensation parameters were marked in MPEG compressed videos. Two kinds of information are hidden in the video: a watermark and a template. Both are encoded using an owner key to ensure the system security and are embedded in the 3D DFT magnitude of video chunks. The watermark is a copyright information encoded in the form of a spread spectrum signal. The template is a key based grid and is used to detect and invert the effect of frame-rate changes, aspect-ratio modification and rescaling of frames. The template search and matching is performed in the log-log-log map of the 3D DFT magnitude. The performance of the presented technique is evaluated experimentally and compared with a frame-by-frame 2D DFT watermarking approach.

Template-based combinatorial enumeration of virtual compound libraries for lipids.

PubMed

Sud, Manish; Fahy, Eoin; Subramaniam, Shankar

2012-09-25

A variety of software packages are available for the combinatorial enumeration of virtual libraries for small molecules, starting from specifications of core scaffolds with attachments points and lists of R-groups as SMILES or SD files. Although SD files include atomic coordinates for core scaffolds and R-groups, it is not possible to control 2-dimensional (2D) layout of the enumerated structures generated for virtual compound libraries because different packages generate different 2D representations for the same structure. We have developed a software package called LipidMapsTools for the template-based combinatorial enumeration of virtual compound libraries for lipids. Virtual libraries are enumerated for the specified lipid abbreviations using matching lists of pre-defined templates and chain abbreviations, instead of core scaffolds and lists of R-groups provided by the user. 2D structures of the enumerated lipids are drawn in a specific and consistent fashion adhering to the framework for representing lipid structures proposed by the LIPID MAPS consortium. LipidMapsTools is lightweight, relatively fast and contains no external dependencies. It is an open source package and freely available under the terms of the modified BSD license.

Toward semantic-based retrieval of visual information: a model-based approach

NASA Astrophysics Data System (ADS)

Park, Youngchoon; Golshani, Forouzan; Panchanathan, Sethuraman

2002-07-01

This paper center around the problem of automated visual content classification. To enable classification based image or visual object retrieval, we propose a new image representation scheme called visual context descriptor (VCD) that is a multidimensional vector in which each element represents the frequency of a unique visual property of an image or a region. VCD utilizes the predetermined quality dimensions (i.e., types of features and quantization level) and semantic model templates mined in priori. Not only observed visual cues, but also contextually relevant visual features are proportionally incorporated in VCD. Contextual relevance of a visual cue to a semantic class is determined by using correlation analysis of ground truth samples. Such co-occurrence analysis of visual cues requires transformation of a real-valued visual feature vector (e.g., color histogram, Gabor texture, etc.,) into a discrete event (e.g., terms in text). Good-feature to track, rule of thirds, iterative k-means clustering and TSVQ are involved in transformation of feature vectors into unified symbolic representations called visual terms. Similarity-based visual cue frequency estimation is also proposed and used for ensuring the correctness of model learning and matching since sparseness of sample data causes the unstable results of frequency estimation of visual cues. The proposed method naturally allows integration of heterogeneous visual or temporal or spatial cues in a single classification or matching framework, and can be easily integrated into a semantic knowledge base such as thesaurus, and ontology. Robust semantic visual model template creation and object based image retrieval are demonstrated based on the proposed content description scheme.

3D temporal subtraction on multislice CT images using nonlinear warping technique

NASA Astrophysics Data System (ADS)

Ishida, Takayuki; Katsuragawa, Shigehiko; Kawashita, Ikuo; Kim, Hyounseop; Itai, Yoshinori; Awai, Kazuo; Li, Qiang; Doi, Kunio

2007-03-01

The detection of very subtle lesions and/or lesions overlapped with vessels on CT images is a time consuming and difficult task for radiologists. In this study, we have developed a 3D temporal subtraction method to enhance interval changes between previous and current multislice CT images based on a nonlinear image warping technique. Our method provides a subtraction CT image which is obtained by subtraction of a previous CT image from a current CT image. Reduction of misregistration artifacts is important in the temporal subtraction method. Therefore, our computerized method includes global and local image matching techniques for accurate registration of current and previous CT images. For global image matching, we selected the corresponding previous section image for each current section image by using 2D cross-correlation between a blurred low-resolution current CT image and a blurred previous CT image. For local image matching, we applied the 3D template matching technique with translation and rotation of volumes of interests (VOIs) which were selected in the current and the previous CT images. The local shift vector for each VOI pair was determined when the cross-correlation value became the maximum in the 3D template matching. The local shift vectors at all voxels were determined by interpolation of shift vectors of VOIs, and then the previous CT image was nonlinearly warped according to the shift vector for each voxel. Finally, the warped previous CT image was subtracted from the current CT image. The 3D temporal subtraction method was applied to 19 clinical cases. The normal background structures such as vessels, ribs, and heart were removed without large misregistration artifacts. Thus, interval changes due to lung diseases were clearly enhanced as white shadows on subtraction CT images.

Visual environment recognition for robot path planning using template matched filters

NASA Astrophysics Data System (ADS)

Orozco-Rosas, Ulises; Picos, Kenia; Díaz-Ramírez, Víctor H.; Montiel, Oscar; Sepúlveda, Roberto

2017-08-01

A visual approach in environment recognition for robot navigation is proposed. This work includes a template matching filtering technique to detect obstacles and feasible paths using a single camera to sense a cluttered environment. In this problem statement, a robot can move from the start to the goal by choosing a single path between multiple possible ways. In order to generate an efficient and safe path for mobile robot navigation, the proposal employs a pseudo-bacterial potential field algorithm to derive optimal potential field functions using evolutionary computation. Simulation results are evaluated in synthetic and real scenes in terms of accuracy of environment recognition and efficiency of path planning computation.

Traffic sign recognition based on a context-aware scale-invariant feature transform approach

NASA Astrophysics Data System (ADS)

Yuan, Xue; Hao, Xiaoli; Chen, Houjin; Wei, Xueye

2013-10-01

A new context-aware scale-invariant feature transform (CASIFT) approach is proposed, which is designed for the use in traffic sign recognition (TSR) systems. The following issues remain in previous works in which SIFT is used for matching or recognition: (1) SIFT is unable to provide color information; (2) SIFT only focuses on local features while ignoring the distribution of global shapes; (3) the template with the maximum number of matching points selected as the final result is instable, especially for images with simple patterns; and (4) SIFT is liable to result in errors when different images share the same local features. In order to resolve these problems, a new CASIFT approach is proposed. The contributions of the work are as follows: (1) color angular patterns are used to provide the color distinguishing information; (2) a CASIFT which effectively combines local and global information is proposed; and (3) a method for computing the similarity between two images is proposed, which focuses on the distribution of the matching points, rather than using the traditional SIFT approach of selecting the template with maximum number of matching points as the final result. The proposed approach is particularly effective in dealing with traffic signs which have rich colors and varied global shape distribution. Experiments are performed to validate the effectiveness of the proposed approach in TSR systems, and the experimental results are satisfying even for images containing traffic signs that have been rotated, damaged, altered in color, have undergone affine transformations, or images which were photographed under different weather or illumination conditions.

2D/3D Visual Tracker for Rover Mast

NASA Technical Reports Server (NTRS)

Bajracharya, Max; Madison, Richard W.; Nesnas, Issa A.; Bandari, Esfandiar; Kunz, Clayton; Deans, Matt; Bualat, Maria

2006-01-01

A visual-tracker computer program controls an articulated mast on a Mars rover to keep a designated feature (a target) in view while the rover drives toward the target, avoiding obstacles. Several prior visual-tracker programs have been tested on rover platforms; most require very small and well-estimated motion between consecutive image frames a requirement that is not realistic for a rover on rough terrain. The present visual-tracker program is designed to handle large image motions that lead to significant changes in feature geometry and photometry between frames. When a point is selected in one of the images acquired from stereoscopic cameras on the mast, a stereo triangulation algorithm computes a three-dimensional (3D) location for the target. As the rover moves, its body-mounted cameras feed images to a visual-odometry algorithm, which tracks two-dimensional (2D) corner features and computes their old and new 3D locations. The algorithm rejects points, the 3D motions of which are inconsistent with a rigid-world constraint, and then computes the apparent change in the rover pose (i.e., translation and rotation). The mast pan and tilt angles needed to keep the target centered in the field-of-view of the cameras (thereby minimizing the area over which the 2D-tracking algorithm must operate) are computed from the estimated change in the rover pose, the 3D position of the target feature, and a model of kinematics of the mast. If the motion between the consecutive frames is still large (i.e., 3D tracking was unsuccessful), an adaptive view-based matching technique is applied to the new image. This technique uses correlation-based template matching, in which a feature template is scaled by the ratio between the depth in the original template and the depth of pixels in the new image. This is repeated over the entire search window and the best correlation results indicate the appropriate match. The program could be a core for building application programs for systems that require coordination of vision and robotic motion.

Shedding light on some possible remedies against watermark desynchronization: a case study

NASA Astrophysics Data System (ADS)

Barni, Mauro

2005-03-01

Watermark de-synchronization is perhaps the most dangerous attack against the great majority of watermarking systems proposed so far. Exhaustive search and template matching are two of the most popular solution against it, however several doubts exist about their effectiveness. As a matter of fact, a controversial point in digital watermarking is whether these techniques are of any help to cope with watermark de-synchronization introduced by geometric attacks. On one side, watermark synchronization through exhaustive search dramatically increases the false detection probability. On the other side, for the template matching approach the probability of a synchronization error must be taken into account, thus deteriorating significantly the performance of the system. It is the scope of this paper to shed some light on the above points. To do so we focus on a very simple case study, whereby we show that as long as the size of the search space (the cardinality of the geometric attack) increases polynomially with the length of the to-be-marked host feature sequence, both methods provide an effective solution to the de-synchronization problem. Interestingly, and rather surprisingly, we also show that Exhaustive Search Detection (ESD) always outperforms Template Matching Detection (TMD), though the general behavior of the two schemes is rather similar.

NOTE: Fluoroscopic gating without implanted fiducial markers for lung cancer radiotherapy based on support vector machines

NASA Astrophysics Data System (ADS)

Cui, Ying; Dy, Jennifer G.; Alexander, Brian; Jiang, Steve B.

2008-08-01

Various problems with the current state-of-the-art techniques for gated radiotherapy have prevented this new treatment modality from being widely implemented in clinical routine. These problems are caused mainly by applying various external respiratory surrogates. There might be large uncertainties in deriving the tumor position from external respiratory surrogates. While tracking implanted fiducial markers has sufficient accuracy, this procedure may not be widely accepted due to the risk of pneumothorax. Previously, we have developed a technique to generate gating signals from fluoroscopic images without implanted fiducial markers using template matching methods (Berbeco et al 2005 Phys. Med. Biol. 50 4481-90, Cui et al 2007b Phys. Med. Biol. 52 741-55). In this note, our main contribution is to provide a totally different new view of the gating problem by recasting it as a classification problem. Then, we solve this classification problem by a well-studied powerful classification method called a support vector machine (SVM). Note that the goal of an automated gating tool is to decide when to turn the beam ON or OFF. We treat ON and OFF as the two classes in our classification problem. We create our labeled training data during the patient setup session by utilizing the reference gating signal, manually determined by a radiation oncologist. We then pre-process these labeled training images and build our SVM prediction model. During treatment delivery, fluoroscopic images are continuously acquired, pre-processed and sent as an input to the SVM. Finally, our SVM model will output the predicted labels as gating signals. We test the proposed technique on five sequences of fluoroscopic images from five lung cancer patients against the reference gating signal as ground truth. We compare the performance of the SVM to our previous template matching method (Cui et al 2007b Phys. Med. Biol. 52 741-55). We find that the SVM is slightly more accurate on average (1-3%) than the template matching method, when delivering the target dose. And the average duty cycle is 4-6% longer. Given the very limited patient dataset, we cannot conclude that the SVM is more accurate and efficient than the template matching method. However, our preliminary results show that the SVM is a potentially precise and efficient algorithm for generating gating signals for radiotherapy. This work demonstrates that the gating problem can be considered as a classification problem and solved accordingly.

Perspectives of human verification via binary QRS template matching of single-lead and 12-lead electrocardiogram.

PubMed

Krasteva, Vessela; Jekova, Irena; Schmid, Ramun

2018-01-01

This study aims to validate the 12-lead electrocardiogram (ECG) as a biometric modality based on two straightforward binary QRS template matching characteristics. Different perspectives of the human verification problem are considered, regarding the optimal lead selection and stability over sample size, gender, age, heart rate (HR). A clinical 12-lead resting ECG database, including a population of 460 subjects with two-session recordings (>1 year apart) is used. Cost-effective strategies for extraction of personalized QRS patterns (100ms) and binary template matching estimate similarity in the time scale (matching time) and dissimilarity in the amplitude scale (mismatch area). The two-class person verification task, taking the decision to validate or to reject the subject identity is managed by linear discriminant analysis (LDA). Non-redundant LDA models for different lead configurations (I,II,III,aVF,aVL,aVF,V1-V6) are trained on the first half of 230 subjects by stepwise feature selection until maximization of the area under the receiver operating characteristic curve (ROC AUC). The operating point on the training ROC at equal error rate (EER) is tested on the independent dataset (second half of 230 subjects) to report unbiased validation of test-ROC AUC and true verification rate (TVR = 100-EER). The test results are further evaluated in groups by sample size, gender, age, HR. The optimal QRS pattern projection for single-lead ECG biometric modality is found in the frontal plane sector (60°-0°) with best (Test-AUC/TVR) for lead II (0.941/86.8%) and slight accuracy drop for -aVR (-0.017/-1.4%), I (-0.01/-1.5%). Chest ECG leads have degrading accuracy from V1 (0.885/80.6%) to V6 (0.799/71.8%). The multi-lead ECG improves verification: 6-chest (0.97/90.9%), 6-limb (0.986/94.3%), 12-leads (0.995/97.5%). The QRS pattern matching model shows stable performance for verification of 10 to 230 individuals; insignificant degradation of TVR in women by (1.2-3.6%), adults ≥70 years (3.7%), younger <40 years (1.9%), HR<60bpm (1.2%), HR>90bpm (3.9%), no degradation for HR change (0 to >20bpm).

Modular preoperative planning software for computer-aided oral implantology and the application of a novel stereolithographic template: a pilot study.

PubMed

Chen, Xiaojun; Yuan, Jianbing; Wang, Chengtao; Huang, Yuanliang; Kang, Lu

2010-09-01

In the field of oral implantology, there is a trend toward computer-aided implant surgery, especially the application of computerized tomography (CT)-derived surgical templates. However, because of relatively unsatisfactory match between the templates and receptor sites, conventional surgical templates may not be accurate enough for the severely resorbed edentulous cases during the procedure of transferring the preoperative plan to the actual surgery. The purpose of this study is to introduce a novel bone-tooth-combined-supported surgical guide, which is designed by utilizing a special modular software and fabricated via stereolithography technique using both laser scanning and CT imaging, thus improving the fit accuracy and reliability. A modular preoperative planning software was developed for computer-aided oral implantology. With the introduction of dynamic link libraries and some well-known free, open-source software libraries such as Visualization Toolkit (Kitware, Inc., New York, USA) and Insight Toolkit (Kitware, Inc.) a plug-in evolutive software architecture was established, allowing for expandability, accessibility, and maintainability in our system. To provide a link between the preoperative plan and the actual surgery, a novel bone-tooth-combined-supported surgical template was fabricated, utilizing laser scanning, image registration, and rapid prototyping. Clinical studies were conducted on four partially edentulous cases to make a comparison with the conventional bone-supported templates. The fixation was more stable than tooth-supported templates because laser scanning technology obtained detailed dentition information, which brought about the unique topography between the match surface of the templates and the adjacent teeth. The average distance deviations at the coronal and apical point of the implant were 0.66 mm (range: 0.3-1.2) and 0.86 mm (range: 0.4-1.2), and the average angle deviation was 1.84 degrees (range: 0.6-2.8 degrees ). This pilot study proves that the novel combined-supported templates are superior to the conventional ones. However, more clinical cases will be conducted to demonstrate their feasibility and reliability.

Developmental changes in hippocampal shape among preadolescent children.

PubMed

Lin, Muqing; Fwu, Peter T; Buss, Claudia; Davis, Elysia P; Head, Kevin; Muftuler, L Tugan; Sandman, Curt A; Su, Min-Ying

2013-11-01

It is known that the largest developmental changes in the hippocampus take place during the prenatal period and during the first two years of postnatal life. Few studies have been conducted to address the normal developmental trajectory of the hippocampus during childhood. In this study shape analysis was applied to study the normal developing hippocampus in a group of 103 typically developing 6- to 10-year-old preadolescent children. The individual brain was normalized to a template, and then the hippocampus was manually segmented and further divided into the head, body, and tail sub-regions. Three different methods were applied for hippocampal shape analysis: radial distance mapping, surface-based template registration using the robust point matching (RPM) algorithm, and volume-based template registration using the Demons algorithm. All three methods show that the older children have bilateral expanded head segments compared to the younger children. The results analyzed based on radial distance to the centerline were consistent with those analyzed using template-based registration methods. In analyses stratified by sex, it was found that the age-associated anatomical changes were similar in boys and girls, but the age-association was strongest in girls. Total hippocampal volume and sub-regional volumes analyzed using manual segmentation did not show a significant age-association. Our results suggest that shape analysis is sensitive to detect sub-regional differences that are not revealed in volumetric analysis. The three methods presented in this study may be applied in future studies to investigate the normal developmental trajectory of the hippocampus in children. They may be further applied to detect early deviations from the normal developmental trajectory in young children for evaluating susceptibility for psychopathological disorders involving hippocampus. Copyright © 2013 ISDN. Published by Elsevier Ltd. All rights reserved.

Megathrust Earthquake Swarms Contemporaneous to Slow Slip and Non-Volcanic Tremor in Southern Mexico, Detected and Analyzed through a Template Matching Approach

NASA Astrophysics Data System (ADS)

Holtkamp, S.; Brudzinski, M. R.; Cabral-Cano, E.; Arciniega-Ceballos, A.

2012-12-01

An outstanding question in geophysics is the degree to which the newly discovered types of slow fault slip are related to their destructive cousin - the earthquake. Here, we utilize a local network along the Oaxacan segment of the Middle American subduction zone to investigate the potential relationship between slow slip, non-volcanic tremor (NVT), and earthquakes along the subduction megathrust. We have developed a multi-station "template matching" waveform cross correlation technique which is able to detect and locate events several orders of magnitude smaller than would be possible using more traditional techniques. Also, our template matching procedure is capable of consistently locate events which occur during periods of increased background activity (e.g., during productive NVT, loud cultural noise, or after larger earthquakes) because the multi-station detector is finely tuned to events with similar hypocentral location and focal mechanism. The local network in the Oaxaca region allows us to focus on documented megathrust earthquake swarms, which we focus on because slow slip is hypothesized to be the cause for earthquake swarms in some tectonic environments. We identify a productive earthquake swarm in July 2006 (~600 similar earthquakes detected), which occurred during a week-long episode of productive tremor and slow slip. Families of events in this sequence were also active during larger and longer slow slip events, which provides a potential link between slow slip in the transition zone and earthquakes at the downdip end of the seismogenic portion of the megathrust. Because template matching techniques only detect similar signals, detected waveforms can be stacked together to produce higher signal to noise ratios or cross correlated against each other to produce precise relative phase arrival times. We are using the refined signals to look for evidence of expansion or propagation of hypocenters during these earthquake swarms, which could be used as a test for determining their underlying processes (e.g., fluid diffusion or slow slip).

A robust and non-invertible fingerprint template for fingerprint matching system.

PubMed

Trivedi, Amit Kumar; Thounaojam, Dalton Meitei; Pal, Shyamosree

2018-05-20

Fingerprint Recognition System is widely deployed in variety of application domain, ranging from forensic to mobile phones. Its widespread deployment in various applications were person authentication are required, has caused concern that a leaked fingerprint template may be used to reconstruct the original fingerprint and the reconstructed fingerprint can be used to circumvent all the applications the person is enrolled. In this paper, a non-invertible fingerprint template that stores only the relative geometric information about the minutiae points is proposed. The spatial location of the minutiae points in original fingerprint and its orientations are not available in the proposed template which makes it impossible to estimate the orientation of fingerprint from the template. The proposed template is invariant to rotation, translation and distortion and immune to reconstruction algorithm. The proposed system is experimented using standard FVC2000 database and yields better results in terms of EER and FMR as compared with latest techniques. Copyright © 2018 Elsevier B.V. All rights reserved.

Visual Object Recognition and Tracking of Tools

NASA Technical Reports Server (NTRS)

English, James; Chang, Chu-Yin; Tardella, Neil

2011-01-01

A method has been created to automatically build an algorithm off-line, using computer-aided design (CAD) models, and to apply this at runtime. The object type is discriminated, and the position and orientation are identified. This system can work with a single image and can provide improved performance using multiple images provided from videos. The spatial processing unit uses three stages: (1) segmentation; (2) initial type, pose, and geometry (ITPG) estimation; and (3) refined type, pose, and geometry (RTPG) calculation. The image segmentation module files all the tools in an image and isolates them from the background. For this, the system uses edge-detection and thresholding to find the pixels that are part of a tool. After the pixels are identified, nearby pixels are grouped into blobs. These blobs represent the potential tools in the image and are the product of the segmentation algorithm. The second module uses matched filtering (or template matching). This approach is used for condensing synthetic images using an image subspace that captures key information. Three degrees of orientation, three degrees of position, and any number of degrees of freedom in geometry change are included. To do this, a template-matching framework is applied. This framework uses an off-line system for calculating template images, measurement images, and the measurements of the template images. These results are used online to match segmented tools against the templates. The final module is the RTPG processor. Its role is to find the exact states of the tools given initial conditions provided by the ITPG module. The requirement that the initial conditions exist allows this module to make use of a local search (whereas the ITPG module had global scope). To perform the local search, 3D model matching is used, where a synthetic image of the object is created and compared to the sensed data. The availability of low-cost PC graphics hardware allows rapid creation of synthetic images. In this approach, a function of orientation, distance, and articulation is defined as a metric on the difference between the captured image and a synthetic image with an object in the given orientation, distance, and articulation. The synthetic image is created using a model that is looked up in an object-model database. A composable software architecture is used for implementation. Video is first preprocessed to remove sensor anomalies (like dead pixels), and then is processed sequentially by a prioritized list of tracker-identifiers.

RESOLVING THE ACTIVE GALACTIC NUCLEUS AND HOST EMISSION IN THE MID-INFRARED USING A MODEL-INDEPENDENT SPECTRAL DECOMPOSITION

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

Hernán-Caballero, Antonio; Alonso-Herrero, Almudena; Hatziminaoglou, Evanthia

2015-04-20

We present results on the spectral decomposition of 118 Spitzer Infrared Spectrograph (IRS) spectra from local active galactic nuclei (AGNs) using a large set of Spitzer/IRS spectra as templates. The templates are themselves IRS spectra from extreme cases where a single physical component (stellar, interstellar, or AGN) completely dominates the integrated mid-infrared emission. We show that a linear combination of one template for each physical component reproduces the observed IRS spectra of AGN hosts with unprecedented fidelity for a template fitting method with no need to model extinction separately. We use full probability distribution functions to estimate expectation values andmore » uncertainties for observables, and find that the decomposition results are robust against degeneracies. Furthermore, we compare the AGN spectra derived from the spectral decomposition with sub-arcsecond resolution nuclear photometry and spectroscopy from ground-based observations. We find that the AGN component derived from the decomposition closely matches the nuclear spectrum with a 1σ dispersion of 0.12 dex in luminosity and typical uncertainties of ∼0.19 in the spectral index and ∼0.1 in the silicate strength. We conclude that the emission from the host galaxy can be reliably removed from the IRS spectra of AGNs. This allows for unbiased studies of the AGN emission in intermediate- and high-redshift galaxies—currently inaccesible to ground-based observations—with archival Spitzer/IRS data and in the future with the Mid-InfraRed Instrument of the James Webb Space Telescope. The decomposition code and templates are available at http://denebola.org/ahc/deblendIRS.« less

Automatic detection of motor unit innervation zones of the external anal sphincter by multichannel surface EMG.

PubMed

Ullah, Khalil; Cescon, Corrado; Afsharipour, Babak; Merletti, Roberto

2014-12-01

A method to detect automatically the location of innervation zones (IZs) from 16-channel surface EMG (sEMG) recordings from the external anal sphincter (EAS) muscle is presented in order to guide episiotomy during child delivery. The new algorithm (2DCorr) is applied to individual motor unit action potential (MUAP) templates and is based on bidimensional cross correlation between the interpolated image of each MUAP template and two images obtained by flipping upside-down (around a horizontal axis) and left-right (around a vertical axis) the original one. The method was tested on 640 simulated MUAP templates of the sphincter muscle and compared with previously developed algorithms (Radon Transform, RT; Template Match, TM). Experimental signals were detected from the EAS of 150 subjects using an intra-anal probe with 16 equally spaced circumferential electrodes. The results of the three algorithms were compared with the actual IZ location (simulated signal) and with IZ location provided by visual analysis (VA) (experimental signals). For simulated signals, the inter quartile error range (IQR) between the estimated and the actual locations of the IZ was 0.20, 0.23, 0.42, and 2.32 interelectrode distances (IED) for the VA, 2DCorr, RT and TM methods respectively. Copyright © 2014 Elsevier Ltd. All rights reserved.

The guidance of visual search by shape features and shape configurations.

PubMed

McCants, Cody W; Berggren, Nick; Eimer, Martin

2018-03-01

Representations of target features (attentional templates) guide attentional object selection during visual search. In many search tasks, targets objects are defined not by a single feature but by the spatial configuration of their component shapes. We used electrophysiological markers of attentional selection processes to determine whether the guidance of shape configuration search is entirely part-based or sensitive to the spatial relationship between shape features. Participants searched for targets defined by the spatial arrangement of two shape components (e.g., hourglass above circle). N2pc components were triggered not only by targets but also by partially matching distractors with one target shape (e.g., hourglass above hexagon) and by distractors that contained both target shapes in the reverse arrangement (e.g., circle above hourglass), in line with part-based attentional control. Target N2pc components were delayed when a reverse distractor was present on the opposite side of the same display, suggesting that early shape-specific attentional guidance processes could not distinguish between targets and reverse distractors. The control of attention then became sensitive to spatial configuration, which resulted in a stronger attentional bias for target objects relative to reverse and partially matching distractors. Results demonstrate that search for target objects defined by the spatial arrangement of their component shapes is initially controlled in a feature-based fashion but can later be guided by templates for spatial configurations. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

An Implementation of Privacy Protection for a Surveillance Camera Using ROI Coding of JPEG2000 with Face Detection

NASA Astrophysics Data System (ADS)

Muneyasu, Mitsuji; Odani, Shuhei; Kitaura, Yoshihiro; Namba, Hitoshi

On the use of a surveillance camera, there is a case where privacy protection should be considered. This paper proposes a new privacy protection method by automatically degrading the face region in surveillance images. The proposed method consists of ROI coding of JPEG2000 and a face detection method based on template matching. The experimental result shows that the face region can be detected and hidden correctly.

One Decade of Induced Seismicity in Basel, Switzerland: A Consistent High-Resolution Catalog Obtained by Template Matching

NASA Astrophysics Data System (ADS)

Herrmann, M.; Kraft, T.; Tormann, T.; Scarabello, L.; Wiemer, S.

2017-12-01

Induced seismicity at the site of the Basel Enhanced Geothermal System (EGS) continuously decayed for six years after injection had been stopped in December 2006. Starting in May 2012, the Swiss Seismological Service was detecting a renewed increase of induced seismicity in the EGS reservoir to levels last seen in 2007 and reaching magnitudes up to ML2.0. Seismic monitoring at this EGS site is running for more than ten years now, but the details of the long-term behavior of its induced seismicity remained unexplored because a seismic event catalog that is consistent in detection sensitivity and magnitude estimation did not exist.We have created such a catalog by applying our matched filter detector to the 11-year-long seismic recordings of a borehole station at 2.7km depth. Based on 3'600 located earthquakes of the operator's borehole-network catalog, we selected about 2'500 reasonably dissimilar templates using waveform clustering. This large template set ensures an adequate coverage of the diversity of event waveforms which is due to the reservoir's highly complex fault system and the close observation distance. To cope with the increased computational demand of scanning 11-years of data with 2'500 templates, we parallelized our detector to run on a high-performance computer of the Swiss National Supercomputing Centre.We detect more than 200'000 events down to ML-2.5 during the six-day-long stimulation in December 2006 alone. Previously, only 13'000 detections found by an amplitude-threshold-based detector were known for this period. The high temporal and spatial resolution of this new catalog allows us to analyze the statistics of the induced Basel earthquakes in great detail. We resolve spatio-temporal variations of the seismicity parameters (a- and b-value) that have not been identified before and derive the first high-resolution temporal evolution of the seismic hazard for the Basel EGS reservoir.In summer 2017, our detector monitored the 10-week pressure reduction operation at the Basel-1 borehole during which the well was periodically opened. The detections drove a traffic light system based on magnitude thresholds and earthquake rates. For future EGS projects in Switzerland, our detector is planned to run in near real-time and provide the basis for an advanced traffic light system.

Morphometry Based on Effective and Accurate Correspondences of Localized Patterns (MEACOLP)

PubMed Central

Wang, Hu; Ren, Yanshuang; Bai, Lijun; Zhang, Wensheng; Tian, Jie

2012-01-01

Local features in volumetric images have been used to identify correspondences of localized anatomical structures for brain morphometry. However, the correspondences are often sparse thus ineffective in reflecting the underlying structures, making it unreliable to evaluate specific morphological differences. This paper presents a morphometry method (MEACOLP) based on correspondences with improved effectiveness and accuracy. A novel two-level scale-invariant feature transform is used to enhance the detection repeatability of local features and to recall the correspondences that might be missed in previous studies. Template patterns whose correspondences could be commonly identified in each group are constructed to serve as the basis for morphometric analysis. A matching algorithm is developed to reduce the identification errors by comparing neighboring local features and rejecting unreliable matches. The two-sample t-test is finally adopted to analyze specific properties of the template patterns. Experiments are performed on the public OASIS database to clinically analyze brain images of Alzheimer's disease (AD) and normal controls (NC). MEACOLP automatically identifies known morphological differences between AD and NC brains, and characterizes the differences well as the scaling and translation of underlying structures. Most of the significant differences are identified in only a single hemisphere, indicating that AD-related structures are characterized by strong anatomical asymmetry. In addition, classification trials to differentiate AD subjects from NC confirm that the morphological differences are reliably related to the groups of interest. PMID:22540000

Matching organic libraries with protein-substructures

NASA Astrophysics Data System (ADS)

Preissner, R.; Goede, A.; Rother, K.; Osterkamp, F.; Koert, U.; Froemmel, C.

2001-09-01

We present a general approach which allows automatic identification of sub-structures in proteins that resemble given three-dimensional templates. This paper documents its success with non-peptide templates such as β-turn mimetics. We considered well-tested turn-mimetics such as the bicyclic turned dipeptide (BTD), spiro lactam (Spiro) and the 2,5-disubstituded tetrahydrofuran (THF), a new furan-derivative which was recently developed and characterized. The detected geometric similarity between the templates and the protein patches corresponds to r.m.s.-values of 0.3 Å for more than 80% of the constituting atoms, which is typical for active site comparisons of homologous proteins. This fast automatic procedure might be of biomedical value for finding special mimicking leads for particular protein sub-structures as well as for template-assembled synthetic protein (TASP) design.

Query-by-example surgical activity detection.

PubMed

Gao, Yixin; Vedula, S Swaroop; Lee, Gyusung I; Lee, Mija R; Khudanpur, Sanjeev; Hager, Gregory D

2016-06-01

Easy acquisition of surgical data opens many opportunities to automate skill evaluation and teaching. Current technology to search tool motion data for surgical activity segments of interest is limited by the need for manual pre-processing, which can be prohibitive at scale. We developed a content-based information retrieval method, query-by-example (QBE), to automatically detect activity segments within surgical data recordings of long duration that match a query. The example segment of interest (query) and the surgical data recording (target trial) are time series of kinematics. Our approach includes an unsupervised feature learning module using a stacked denoising autoencoder (SDAE), two scoring modules based on asymmetric subsequence dynamic time warping (AS-DTW) and template matching, respectively, and a detection module. A distance matrix of the query against the trial is computed using the SDAE features, followed by AS-DTW combined with template scoring, to generate a ranked list of candidate subsequences (substrings). To evaluate the quality of the ranked list against the ground-truth, thresholding conventional DTW distances and bipartite matching are applied. We computed the recall, precision, F1-score, and a Jaccard index-based score on three experimental setups. We evaluated our QBE method using a suture throw maneuver as the query, on two tool motion datasets (JIGSAWS and MISTIC-SL) captured in a training laboratory. We observed a recall of 93, 90 and 87 % and a precision of 93, 91, and 88 % with same surgeon same trial (SSST), same surgeon different trial (SSDT) and different surgeon (DS) experiment setups on JIGSAWS, and a recall of 87, 81 and 75 % and a precision of 72, 61, and 53 % with SSST, SSDT and DS experiment setups on MISTIC-SL, respectively. We developed a novel, content-based information retrieval method to automatically detect multiple instances of an activity within long surgical recordings. Our method demonstrated adequate recall across different complexity datasets and experimental conditions.

Topics in the Detection of Gravitational Waves from Compact Binary Inspirals

NASA Astrophysics Data System (ADS)

Kapadia, Shasvath Jagat

Orbiting compact binaries - such as binary black holes, binary neutron stars and neutron star-black hole binaries - are among the most promising sources of gravitational waves observable by ground-based interferometric detectors. Despite numerous sophisticated engineering techniques, the gravitational wave signals will be buried deep within noise generated by various instrumental and environmental processes, and need to be extracted via a signal processing technique referred to as matched filtering. Matched filtering requires large banks of signal templates that are faithful representations of the true gravitational waveforms produced by astrophysical binaries. The accurate and efficient production of templates is thus crucial to the success of signal processing and data analysis. To that end, the dissertation presents a numerical technique that calibrates existing analytical (Post-Newtonian) waveforms, which are relatively inexpensive, to more accurate fiducial waveforms that are computationally expensive to generate. The resulting waveform family is significantly more accurate than the analytical waveforms, without incurring additional computational costs of production. Certain kinds of transient background noise artefacts, called "glitches'', can masquerade as gravitational wave signals for short durations and throw-off the matched-filter algorithm. Identifying glitches from true gravitational wave signals is a highly non-trivial exercise in data analysis which has been attempted with varying degrees of success. We present here a machine-learning based approach that exploits the various attributes of glitches and signals within detector data to provide a classification scheme that is a significant improvement over previous methods. The dissertation concludes by investigating the possibility of detecting a non-linear DC imprint, called the Christodoulou memory, produced in the arms of ground-based interferometers by the recently detected gravitational waves. The memory, which is even smaller in amplitude than the primary (detected) gravitational waves, will almost certainly not be seen in the current detection event. Nevertheless, future space-based detectors will likely be sensitive enough to observe the memory.

Broadband moth-eye antireflection coatings on silicon

NASA Astrophysics Data System (ADS)

Sun, Chih-Hung; Jiang, Peng; Jiang, Bin

2008-02-01

We report a bioinspired templating technique for fabricating broadband antireflection coatings that mimic antireflective moth eyes. Wafer-scale, subwavelength-structured nipple arrays are directly patterned on silicon using spin-coated silica colloidal monolayers as etching masks. The templated gratings exhibit excellent broadband antireflection properties and the normal-incidence specular reflection matches with the theoretical prediction using a rigorous coupled-wave analysis (RCWA) model. We further demonstrate that two common simulation methods, RCWA and thin-film multilayer models, generate almost identical prediction for the templated nipple arrays. This simple bottom-up technique is compatible with standard microfabrication, promising for reducing the manufacturing cost of crystalline silicon solar cells.

Vibration extraction based on fast NCC algorithm and high-speed camera.

PubMed

Lei, Xiujun; Jin, Yi; Guo, Jie; Zhu, Chang'an

2015-09-20

In this study, a high-speed camera system is developed to complete the vibration measurement in real time and to overcome the mass introduced by conventional contact measurements. The proposed system consists of a notebook computer and a high-speed camera which can capture the images as many as 1000 frames per second. In order to process the captured images in the computer, the normalized cross-correlation (NCC) template tracking algorithm with subpixel accuracy is introduced. Additionally, a modified local search algorithm based on the NCC is proposed to reduce the computation time and to increase efficiency significantly. The modified algorithm can rapidly accomplish one displacement extraction 10 times faster than the traditional template matching without installing any target panel onto the structures. Two experiments were carried out under laboratory and outdoor conditions to validate the accuracy and efficiency of the system performance in practice. The results demonstrated the high accuracy and efficiency of the camera system in extracting vibrating signals.

Enhanced brainstem and cortical evoked response amplitudes: single-trial covariance analysis.

PubMed

Galbraith, G C

2001-06-01

The purpose of the present study was to develop analytic procedures that improve the definition of sensory evoked response components. Such procedures could benefit all recordings but would especially benefit difficult recordings where many trials are contaminated by muscle and movement artifacts. First, cross-correlation and latency adjustment analyses were applied to the human brainstem frequency-following response and cortical auditory evoked response recorded on the same trials. Lagged cross-correlation functions were computed, for each of 17 subjects, between single-trial data and templates consisting of the sinusoid stimulus waveform for the brainstem response and the subject's own smoothed averaged evoked response P2 component for the cortical response. Trials were considered in the analysis only if the maximum correlation-squared (r2) exceeded .5 (negatively correlated trials were thus included). Identical correlation coefficients may be based on signals with quite different amplitudes, but it is possible to assess amplitude by the nonnormalized covariance function. Next, an algorithm is applied in which each trial with negative covariance is matched to a trial with similar, but positive, covariance and these matched-trial pairs are deleted. When an evoked response signal is present in the data, the majority of trials positively correlate with the template. Thus, a residual of positively correlated trials remains after matched covariance trials are deleted. When these residual trials are averaged, the resulting brainstem and cortical responses show greatly enhanced amplitudes. This result supports the utility of this analysis technique in clarifying and assessing evoked response signals.

Simultaneous 3D–2D image registration and C-arm calibration: Application to endovascular image-guided interventions

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

Mitrović, Uroš; Pernuš, Franjo; Likar, Boštjan

Purpose: Three-dimensional to two-dimensional (3D–2D) image registration is a key to fusion and simultaneous visualization of valuable information contained in 3D pre-interventional and 2D intra-interventional images with the final goal of image guidance of a procedure. In this paper, the authors focus on 3D–2D image registration within the context of intracranial endovascular image-guided interventions (EIGIs), where the 3D and 2D images are generally acquired with the same C-arm system. The accuracy and robustness of any 3D–2D registration method, to be used in a clinical setting, is influenced by (1) the method itself, (2) uncertainty of initial pose of the 3Dmore » image from which registration starts, (3) uncertainty of C-arm’s geometry and pose, and (4) the number of 2D intra-interventional images used for registration, which is generally one and at most two. The study of these influences requires rigorous and objective validation of any 3D–2D registration method against a highly accurate reference or “gold standard” registration, performed on clinical image datasets acquired in the context of the intervention. Methods: The registration process is split into two sequential, i.e., initial and final, registration stages. The initial stage is either machine-based or template matching. The latter aims to reduce possibly large in-plane translation errors by matching a projection of the 3D vessel model and 2D image. In the final registration stage, four state-of-the-art intrinsic image-based 3D–2D registration methods, which involve simultaneous refinement of rigid-body and C-arm parameters, are evaluated. For objective validation, the authors acquired an image database of 15 patients undergoing cerebral EIGI, for which accurate gold standard registrations were established by fiducial marker coregistration. Results: Based on target registration error, the obtained success rates of 3D to a single 2D image registration after initial machine-based and template matching and final registration involving C-arm calibration were 36%, 73%, and 93%, respectively, while registration accuracy of 0.59 mm was the best after final registration. By compensating in-plane translation errors by initial template matching, the success rates achieved after the final stage improved consistently for all methods, especially if C-arm calibration was performed simultaneously with the 3D–2D image registration. Conclusions: Because the tested methods perform simultaneous C-arm calibration and 3D–2D registration based solely on anatomical information, they have a high potential for automation and thus for an immediate integration into current interventional workflow. One of the authors’ main contributions is also comprehensive and representative validation performed under realistic conditions as encountered during cerebral EIGI.« less

Comparative Performance Analysis of Different Fingerprint Biometric Scanners for Patient Matching.

PubMed

Kasiiti, Noah; Wawira, Judy; Purkayastha, Saptarshi; Were, Martin C

2017-01-01

Unique patient identification within health services is an operational challenge in healthcare settings. Use of key identifiers, such as patient names, hospital identification numbers, national ID, and birth date are often inadequate for ensuring unique patient identification. In addition approximate string comparator algorithms, such as distance-based algorithms, have proven suboptimal for improving patient matching, especially in low-resource settings. Biometric approaches may improve unique patient identification. However, before implementing the technology in a given setting, such as health care, the right scanners should be rigorously tested to identify an optimal package for the implementation. This study aimed to investigate the effects of factors such as resolution, template size, and scan capture area on the matching performance of different fingerprint scanners for use within health care settings. Performance analysis of eight different scanners was tested using the demo application distributed as part of the Neurotech Verifinger SDK 6.0.

An improved low-frequency earthquakes catalogue in the vicinity of the late-interseismic central Alpine Fault, Southern Alps, New Zealand

NASA Astrophysics Data System (ADS)

Baratin, Laura-May; Chamberlain, Calum J.; Townend, John; Savage, Martha K.

2017-04-01

Characterising the seismicity associated with slow deformation in the vicinity of the Alpine Fault may provide constraints on the state of stress of this major transpressive margin prior to a large (≥M8) earthquake. Here, we use recently detected tectonic tremor and low-frequency earthquakes (LFEs) to examine how slow tectonic deformation is loading the Alpine Fault toward an anticipated large rupture. We initially work with a continous seismic dataset collected between 2009 and 2012 from an array of short-period seismometers, the Southern Alps Microearthquake Borehole Array. Fourteen primary LFE templates, found through visual inspection within previously identified tectonic tremor, are used in an iterative matched-filter and stacking routine. This method allows the detection of similar signals and establishes LFE families with common locations. We thus generate a 36 month catalogue of 10718 LFEs. The detections are then combined for each LFE family using phase-weighted stacking to yield a signal with the highest possible signal to noise ratio. We found phase-weighted stacking to be successful in increasing the number of LFE detections by roughly 20%. Phase-weighted stacking also provides cleaner phase arrivals of apparently impulsive nature allowing more precise phase picks. We then compute non-linear earthquake locations using a 3D velocity model and find LFEs to occur below the seismogenic zone at depths of 18-34 km, locating on or near the proposed deep extent of the Alpine Fault. To gain insight into deep fault slip behaviour, a detailed study of the spatial-temporal evolution of LFEs is required. We thus generate a more extensive catalogue of LFEs spanning the years 2009 to 2016 using a different technique to detect LFEs more efficiently. This time 638 synthetic waveforms are used as primary templates in the match-filter routine. Of those, 38 templates yield no detections over our 7-yr study period. The remaining 600 templates end up detecting between 370 and 730 events each totalling ˜310 000 detections. We then focus on only keeping the detections that robustly stack (i.e. representing real LFEs) for each synthetic template hence creating new LFE templates. From there, we rerun the match-filter routine with our new LFE templates. Finally, each LFE template and its subsequent detections form a LFE family, itself associated with a single source. Initial testing shows that this technique paired up with phase-weighted stacking increases the number of LFE families and overall detected events roughly thirtyfold. Our next step is to study in detail the spatial and temporal activity of our LFEs. This new catalogue should provide new insight into the deep central Alpine Fault structure and its slip behaviour.

Compact hybrid optoelectrical unit for image processing and recognition

NASA Astrophysics Data System (ADS)

Cheng, Gang; Jin, Guofan; Wu, Minxian; Liu, Haisong; He, Qingsheng; Yuan, ShiFu

1998-07-01

In this paper a compact opto-electric unit (CHOEU) for digital image processing and recognition is proposed. The central part of CHOEU is an incoherent optical correlator, which is realized with a SHARP QA-1200 8.4 inch active matrix TFT liquid crystal display panel which is used as two real-time spatial light modulators for both the input image and reference template. CHOEU can do two main processing works. One is digital filtering; the other is object matching. Using CHOEU an edge-detection operator is realized to extract the edges from the input images. Then the reprocessed images are sent into the object recognition unit for identifying the important targets. A novel template- matching method is proposed for gray-tome image recognition. A positive and negative cycle-encoding method is introduced to realize the absolute difference measurement pixel- matching on a correlator structure simply. The system has god fault-tolerance ability for rotation distortion, Gaussian noise disturbance or information losing. The experiments are given at the end of this paper.

SU-G-206-01: A Fully Automated CT Tool to Facilitate Phantom Image QA for Quantitative Imaging in Clinical Trials

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

Wahi-Anwar, M; Lo, P; Kim, H

Purpose: The use of Quantitative Imaging (QI) methods in Clinical Trials requires both verification of adherence to a specified protocol and an assessment of scanner performance under that protocol, which are currently accomplished manually. This work introduces automated phantom identification and image QA measure extraction towards a fully-automated CT phantom QA system to perform these functions and facilitate the use of Quantitative Imaging methods in clinical trials. Methods: This study used a retrospective cohort of CT phantom scans from existing clinical trial protocols - totaling 84 phantoms, across 3 phantom types using various scanners and protocols. The QA system identifiesmore » the input phantom scan through an ensemble of threshold-based classifiers. Each classifier - corresponding to a phantom type - contains a template slice, which is compared to the input scan on a slice-by-slice basis, resulting in slice-wise similarity metric values for each slice compared. Pre-trained thresholds (established from a training set of phantom images matching the template type) are used to filter the similarity distribution, and the slice with the most optimal local mean similarity, with local neighboring slices meeting the threshold requirement, is chosen as the classifier’s matched slice (if it existed). The classifier with the matched slice possessing the most optimal local mean similarity is then chosen as the ensemble’s best matching slice. If the best matching slice exists, image QA algorithm and ROIs corresponding to the matching classifier extracted the image QA measures. Results: Automated phantom identification performed with 84.5% accuracy and 88.8% sensitivity on 84 phantoms. Automated image quality measurements (following standard protocol) on identified water phantoms (n=35) matched user QA decisions with 100% accuracy. Conclusion: We provide a fullyautomated CT phantom QA system consistent with manual QA performance. Further work will include parallel component to automatically verify image acquisition parameters and automated adherence to specifications. Institutional research agreement, Siemens Healthcare; Past recipient, research grant support, Siemens Healthcare; Consultant, Toshiba America Medical Systems; Consultant, Samsung Electronics; NIH Grant support from: U01 CA181156.« less

An electrooculogram-based binary saccade sequence classification (BSSC) technique for augmentative communication and control.

PubMed

Keegan, Johnalan; Burke, Edward; Condron, James

2009-01-01

In the field of assistive technology, the electrooculogram (EOG) can be used as a channel of communication and the basis of a man-machine interface. For many people with severe motor disabilities, simple actions such as changing the TV channel require assistance. This paper describes a method of detecting saccadic eye movements and the use of a saccade sequence classification algorithm to facilitate communication and control. Saccades are fast eye movements that occurs when a person's gaze jumps from one fixation point to another. The classification is based on pre-defined sequences of saccades, guided by a static visual template (e.g. a page or poster). The template, consisting of a table of symbols each having a clearly identifiable fixation point, is situated within view of the user. To execute a particular command, the user moves his or her gaze through a pre-defined path of eye movements. This results in a well-formed sequence of saccades which are translated into a command if a match is found in a library of predefined sequences. A coordinate transformation algorithm is applied to each candidate sequence of recorded saccades to mitigate the effect of changes in the user's position and orientation relative to the visual template. Upon recognition of a saccade sequence from the library, its associated command is executed. A preliminary experiment in which two subjects were instructed to perform a series of command sequences consisting of 8 different commands are presented in the final sections. The system is also shown to be extensible to facilitate convenient text entry via an alphabetic visual template.

Natural Crack Sizing Based on Eddy Current Image and Electromagnetic Field Analyses

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

Endo, H.; Uchimoto, T.; Takagi, T.

2006-03-06

An eddy current testing (ECT) system with multi-coil type probes is applied to size up cracks fabricated on austenite stainless plates. We have developed muti-channel ECT system to produce data as digital images. The probes consist of transmit-receive type sensors as elements to classify crack directions, working as two scan direction modes simultaneously. Template matching applied to the ECT images determines regions of interest in sizing up cracks. Finite element based inversion sizes up the crack depth from the measured ECT signal. The present paper demonstrates this approach for fatigue crack and stress corrosion cracking.

Guided endodontics: accuracy of a novel method for guided access cavity preparation and root canal location.

PubMed

Zehnder, M S; Connert, T; Weiger, R; Krastl, G; Kühl, S

2016-10-01

To present a novel method utilizing 3D printed templates to gain guided access to root canals and to evaluate its accuracy in vitro. Sixty extracted human teeth were placed into six maxillary jaw models. Preoperative CBCT scans were matched with intra-oral scans using the coDiagnostix(™) software. Access cavities, sleeves and templates for guidance were virtually planned. Templates were produced by a 3D printer. After access cavity preparation by two operators, a postoperative CBCT scan was superimposed on the virtual planning. Accuracy was measured by calculating the deviation of planned and prepared cavities in three dimensions and angle. Ninety-five per cent confidence intervals were calculated for both operators. All root canals were accessible after cavity preparation with 'Guided Endodontics'. Deviations of planned and prepared access cavities were low with means ranging from 0.16 to 0.21 mm for different aspects at the base of the bur and 0.17-0.47 mm at the tip of the bur. Mean of angle deviation was 1.81°. Overlapping 95% confidence intervals revealed no significant difference between operators. 'Guided Endodontics' allowed an accurate access cavity preparation up to the apical third of the root utilizing printed templates for guidance. All root canals were accessible after preparation. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Improved Detection of Local Earthquakes in the Vienna Basin (Austria), using Subspace Detectors

NASA Astrophysics Data System (ADS)

Apoloner, Maria-Theresia; Caffagni, Enrico; Bokelmann, Götz

2016-04-01

The Vienna Basin in Eastern Austria is densely populated and highly-developed; it is also a region of low to moderate seismicity, yet the seismological network coverage is relatively sparse. This demands improving our capability of earthquake detection by testing new methods, enlarging the existing local earthquake catalogue. This contributes to imaging tectonic fault zones for better understanding seismic hazard, also through improved earthquake statistics (b-value, magnitude of completeness). Detection of low-magnitude earthquakes or events for which the highest amplitudes slightly exceed the signal-to-noise-ratio (SNR), may be possible by using standard methods like the short-term over long-term average (STA/LTA). However, due to sparse network coverage and high background noise, such a technique may not detect all potentially recoverable events. Yet, earthquakes originating from the same source region and relatively close to each other, should be characterized by similarity in seismic waveforms, at a given station. Therefore, waveform similarity can be exploited by using specific techniques such as correlation-template based (also known as matched filtering) or subspace detection methods (based on the subspace theory). Matching techniques basically require a reference or template event, usually characterized by high waveform coherence in the array receivers, and high SNR, which is cross-correlated with the continuous data. Instead, subspace detection methods overcome in principle the necessity of defining template events as single events, but use a subspace extracted from multiple events. This approach theoretically should be more robust in detecting signals that exhibit a strong variability (e.g. because of source or magnitude). In this study we scan the continuous data recorded in the Vienna Basin with a subspace detector to identify additional events. This will allow us to estimate the increase of the seismicity rate in the local earthquake catalogue, therefore providing an evaluation of network performance and efficiency of the method.

Adaptive template generation for amyloid PET using a deep learning approach.

PubMed

Kang, Seung Kwan; Seo, Seongho; Shin, Seong A; Byun, Min Soo; Lee, Dong Young; Kim, Yu Kyeong; Lee, Dong Soo; Lee, Jae Sung

2018-05-11

Accurate spatial normalization (SN) of amyloid positron emission tomography (PET) images for Alzheimer's disease assessment without coregistered anatomical magnetic resonance imaging (MRI) of the same individual is technically challenging. In this study, we applied deep neural networks to generate individually adaptive PET templates for robust and accurate SN of amyloid PET without using matched 3D MR images. Using 681 pairs of simultaneously acquired 11 C-PIB PET and T1-weighted 3D MRI scans of AD, MCI, and cognitively normal subjects, we trained and tested two deep neural networks [convolutional auto-encoder (CAE) and generative adversarial network (GAN)] that produce adaptive best PET templates. More specifically, the networks were trained using 685,100 pieces of augmented data generated by rotating 527 randomly selected datasets and validated using 154 datasets. The input to the supervised neural networks was the 3D PET volume in native space and the label was the spatially normalized 3D PET image using the transformation parameters obtained from MRI-based SN. The proposed deep learning approach significantly enhanced the quantitative accuracy of MRI-less amyloid PET assessment by reducing the SN error observed when an average amyloid PET template is used. Given an input image, the trained deep neural networks rapidly provide individually adaptive 3D PET templates without any discontinuity between the slices (in 0.02 s). As the proposed method does not require 3D MRI for the SN of PET images, it has great potential for use in routine analysis of amyloid PET images in clinical practice and research. © 2018 Wiley Periodicals, Inc.

VizieR Online Data Catalog: Intrinsic far-IR SED of luminous AGNs (Lyu+, 2017)

NASA Astrophysics Data System (ADS)

Lyu, J.; Rieke, G. H.

2018-01-01

The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR properties of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at ~20μm and can be matched by an Elvis+ (1994, J/ApJS/95/1)-like template with a minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at λ~20-100μm, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR. (3 data files).

The Intrinsic Far-infrared Continua of Type-1 Quasars

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

Lyu, Jianwei; Rieke, George H., E-mail: jianwei@email.arizona.edu

2017-06-01

The range of currently proposed active galactic nucleus (AGN) far-infrared templates results in uncertainties in retrieving host galaxy information from infrared observations and also undermines constraints on the outer part of the AGN torus. We discuss how to test and reconcile these templates. Physically, the fraction of the intrinsic AGN IR-processed luminosity compared with that from the central engine should be consistent with the dust-covering factor. In addition, besides reproducing the composite spectral energy distributions (SEDs) of quasars, a correct AGN IR template combined with an accurate library of star-forming galaxy templates should be able to reproduce the IR propertiesmore » of the host galaxies, such as the luminosity-dependent SED shapes and aromatic feature strengths. We develop tests based on these expected behaviors and find that the shape of the AGN intrinsic far-IR emission drops off rapidly starting at ∼20 μ m and can be matched by an Elvis et al.-like template with a minor modification. Despite the variations in the near- to mid-IR bands, AGNs in quasars and Seyfert galaxies have remarkably similar intrinsic far-IR SEDs at λ ∼ 20–100 μ m, suggesting a similar emission character of the outermost region of the circumnuclear torus. The variations of the intrinsic AGN IR SEDs among the type-1 quasar population can be explained by the changing relative strengths of four major dust components with similar characteristic temperatures, and there is evidence for compact AGN-heated dusty structures at sub-kiloparsec scales in the far-IR.« less

In induced reconstructions of Si(1 1 1) as superlattice matched epitaxial templates for InN growth

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

Kuyyalil, Jithesh; Tangi, Malleswararao; Shivaprasad, S.M., E-mail: smsprasad@jncasr.ac.in

Graphical abstract: Display Omitted Highlights: ► A novel growth method to form InN at low growth temperatures. ► Use of Si reconstruction as a growth template for group III nitrides. ► Band gap variation of InN – Moss–Burstein shift – non-parabolic conduction band for InN. ► Super lattice matching epitaxy of metal induced reconstructions with III–V unit cell. -- Abstract: Indium induced surface reconstructions of Si(1 1 1)-7 × 7 are used as templates to grow high quality InN. We grow InN on Si(1 1 1)-7 × 7, Si(1 1 1)-4 × 1-In and Si(1 1 1)-1 × 1-In reconstructedmore » surfaces and study the quality of the films formed using complementary characterization tools. InN grown on Si(1 1 1)-1 × 1-In reconstruction shows superior film quality with lowest band-edge emission having a narrow full width at half maximum, intense and narrow 0 0 0 2 X-ray diffraction, low surface roughness and carrier concentration an order lower than other samples. We attribute the high quality of the film formed at 300 °C to the integral matching of InN and super lattice dimensions, we also study the reasons for the band gap variation of InN in the literature. Present study demonstrates the proposed Superlattice Matched Epitaxy can be a general approach to grow good quality InN at much lower growth temperature on compatible In induced reconstructions of the Si surface.« less

A comparison of image processing techniques for bird recognition.

PubMed

Nadimpalli, Uma D; Price, Randy R; Hall, Steven G; Bomma, Pallavi

2006-01-01

Bird predation is one of the major concerns for fish culture in open ponds. A novel method for dispersing birds is the use of autonomous vehicles. Image recognition software can improve their efficiency. Several image processing techniques for recognition of birds have been tested. A series of morphological operations were implemented. We divided images into 3 types, Type 1, Type 2, and Type 3, based on the level of difficulty of recognizing birds. Type 1 images were clear; Type 2 images were medium clear, and Type 3 images were unclear. Local thresholding has been implemented using HSV (Hue, Saturation, and Value), GRAY, and RGB (Red, Green, and Blue) color models on all three sections of images and results were tabulated. Template matching using normal correlation and artificial neural networks (ANN) are the other methods that have been developed in this study in addition to image morphology. Template matching produced satisfactory results irrespective of the difficulty level of images, but artificial neural networks produced accuracies of 100, 60, and 50% on Type 1, Type 2, and Type 3 images, respectively. Correct classification rate can be increased by further training. Future research will focus on testing the recognition algorithms in natural or aquacultural settings on autonomous boats. Applications of such techniques to industrial, agricultural, or related areas are additional future possibilities.

Arraycount, an algorithm for automatic cell counting in microwell arrays.

PubMed

Kachouie, Nezamoddin; Kang, Lifeng; Khademhosseini, Ali

2009-09-01

Microscale technologies have emerged as a powerful tool for studying and manipulating biological systems and miniaturizing experiments. However, the lack of software complementing these techniques has made it difficult to apply them for many high-throughput experiments. This work establishes Arraycount, an approach to automatically count cells in microwell arrays. The procedure consists of fluorescent microscope imaging of cells that are seeded in microwells of a microarray system and then analyzing images via computer to recognize the array and count cells inside each microwell. To start counting, green and red fluorescent images (representing live and dead cells, respectively) are extracted from the original image and processed separately. A template-matching algorithm is proposed in which pre-defined well and cell templates are matched against the red and green images to locate microwells and cells. Subsequently, local maxima in the correlation maps are determined and local maxima maps are thresholded. At the end, the software records the cell counts for each detected microwell on the original image in high-throughput. The automated counting was shown to be accurate compared with manual counting, with a difference of approximately 1-2 cells per microwell: based on cell concentration, the absolute difference between manual and automatic counting measurements was 2.5-13%.

Evaluation of lung tumor motion management in radiation therapy with dynamic MRI

NASA Astrophysics Data System (ADS)

Park, Seyoun; Farah, Rana; Shea, Steven M.; Tryggestad, Erik; Hales, Russell; Lee, Junghoon

2017-03-01

Surrogate-based tumor motion estimation and tracing methods are commonly used in radiotherapy despite the lack of continuous real time 3D tumor and surrogate data. In this study, we propose a method to simultaneously track the tumor and external surrogates with dynamic MRI, which allows us to evaluate their reproducible correlation. Four MRIcompatible fiducials are placed on the patient's chest and upper abdomen, and multi-slice 2D cine MRIs are acquired to capture the lung and whole tumor, followed by two-slice 2D cine MRIs to simultaneously track the tumor and fiducials, all in sagittal orientation. A phase-binned 4D-MRI is first reconstructed from multi-slice MR images using body area as a respiratory surrogate and group-wise registration. The 4D-MRI provides 3D template volumes for different breathing phases. 3D tumor position is calculated by 3D-2D template matching in which 3D tumor templates in 4D-MRI reconstruction and the 2D cine MRIs from the two-slice tracking dataset are registered. 3D trajectories of the external surrogates are derived via matching a 3D geometrical model to the fiducial segmentations on the 2D cine MRIs. We tested our method on five lung cancer patients. Internal target volume from 4D-CT showed average sensitivity of 86.5% compared to the actual tumor motion for 5 min. 3D tumor motion correlated with the external surrogate signal, but showed a noticeable phase mismatch. The 3D tumor trajectory showed significant cycle-to-cycle variation, while the external surrogate was not sensitive enough to capture such variations. Additionally, there was significant phase mismatch between surrogate signals obtained from fiducials at different locations.

Evolution of kin recognition mechanisms in a fish.

PubMed

Hain, Timothy J A; Garner, Shawn R; Ramnarine, Indar W; Neff, Bryan D

2017-03-01

Both selection and phylogenetic history can influence the evolution of phenotypic traits. Here we used recently characterized variation in kin recognition mechanisms among six guppy populations to explore the phylogenetic history of this trait. Guppies can use two different kin recognition mechanisms: either phenotype matching, in which individuals are identified based on comparison with a recognition template, or familiarity, in which individuals are remembered based on previous interactions. Across the six populations, we identified four transitions in recognition mechanism: phenotype matching evolved once and was subsequently lost in a single population, whereas familiarity evolved twice. Based on a molecular clock, these transitions occurred among populations that had diverged on a timescale of hundreds of thousands of years, which is two orders of magnitude faster than previously documented transitions in recognition mechanisms. A randomization test provided no evidence that recognition mechanisms were constrained by phylogeny, suggesting that recognition mechanisms have the capacity to evolve rapidly, although the specific selection pressures that may be contributing to variation in recognition mechanisms across populations remain unknown.

Whatever you do, don't look at the...: Evaluating guidance by an exclusionary attentional template.

PubMed

Beck, Valerie M; Luck, Steven J; Hollingworth, Andrew

2018-04-01

People can use a target template consisting of one or more features to guide attention and gaze to matching objects in a search array. But can we also use feature information to guide attention away from known irrelevant items? Some studies found a benefit from foreknowledge of a distractor feature, whereas others found a cost. Importantly, previous work has largely relied on end-of-trial manual responses; it is unclear how feature-guided avoidance might unfold as candidate objects are inspected. In the current experiments, participants were cued with a distractor feature to avoid, then performed a visual search task while eye movements were recorded. Participants initially fixated a to-be-avoided object more frequently than predicted by chance, but they also demonstrated avoidance of cue-matching objects later in the trial. When provided more time between cue stimulus and search array, participants continued to be initially captured by a cued-color item. Furthermore, avoidance of cue-matching objects later in the trial was not contingent on initial capture by a cue-matching object. These results suggest that the conflicting findings in previous negative-cue experiments may be explained by a mixture of two independent processes: initial attentional capture by memory-matching items and later avoidance of known irrelevant items. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

On the construction of a new stellar classification template library for the LAMOST spectral analysis pipeline

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

Wei, Peng; Luo, Ali; Li, Yinbi

2014-05-01

The LAMOST spectral analysis pipeline, called the 1D pipeline, aims to classify and measure the spectra observed in the LAMOST survey. Through this pipeline, the observed stellar spectra are classified into different subclasses by matching with template spectra. Consequently, the performance of the stellar classification greatly depends on the quality of the template spectra. In this paper, we construct a new LAMOST stellar spectral classification template library, which is supposed to improve the precision and credibility of the present LAMOST stellar classification. About one million spectra are selected from LAMOST Data Release One to construct the new stellar templates, andmore » they are gathered in 233 groups by two criteria: (1) pseudo g – r colors obtained by convolving the LAMOST spectra with the Sloan Digital Sky Survey ugriz filter response curve, and (2) the stellar subclass given by the LAMOST pipeline. In each group, the template spectra are constructed using three steps. (1) Outliers are excluded using the Local Outlier Probabilities algorithm, and then the principal component analysis method is applied to the remaining spectra of each group. About 5% of the one million spectra are ruled out as outliers. (2) All remaining spectra are reconstructed using the first principal components of each group. (3) The weighted average spectrum is used as the template spectrum in each group. Using the previous 3 steps, we initially obtain 216 stellar template spectra. We visually inspect all template spectra, and 29 spectra are abandoned due to low spectral quality. Furthermore, the MK classification for the remaining 187 template spectra is manually determined by comparing with 3 template libraries. Meanwhile, 10 template spectra whose subclass is difficult to determine are abandoned. Finally, we obtain a new template library containing 183 LAMOST template spectra with 61 different MK classes by combining it with the current library.« less

Illumination invariant feature point matching for high-resolution planetary remote sensing images

NASA Astrophysics Data System (ADS)

Wu, Bo; Zeng, Hai; Hu, Han

2018-03-01

Despite its success with regular close-range and remote-sensing images, the scale-invariant feature transform (SIFT) algorithm is essentially not invariant to illumination differences due to the use of gradients for feature description. In planetary remote sensing imagery, which normally lacks sufficient textural information, salient regions are generally triggered by the shadow effects of keypoints, reducing the matching performance of classical SIFT. Based on the observation of dual peaks in a histogram of the dominant orientations of SIFT keypoints, this paper proposes an illumination-invariant SIFT matching method for high-resolution planetary remote sensing images. First, as the peaks in the orientation histogram are generally aligned closely with the sub-solar azimuth angle at the time of image collection, an adaptive suppression Gaussian function is tuned to level the histogram and thereby alleviate the differences in illumination caused by a changing solar angle. Next, the suppression function is incorporated into the original SIFT procedure for obtaining feature descriptors, which are used for initial image matching. Finally, as the distribution of feature descriptors changes after anisotropic suppression, and the ratio check used for matching and outlier removal in classical SIFT may produce inferior results, this paper proposes an improved matching procedure based on cross-checking and template image matching. The experimental results for several high-resolution remote sensing images from both the Moon and Mars, with illumination differences of 20°-180°, reveal that the proposed method retrieves about 40%-60% more matches than the classical SIFT method. The proposed method is of significance for matching or co-registration of planetary remote sensing images for their synergistic use in various applications. It also has the potential to be useful for flyby and rover images by integrating with the affine invariant feature detectors.

Optically Transparent Wood from a Nanoporous Cellulosic Template: Combining Functional and Structural Performance.

PubMed

Li, Yuanyuan; Fu, Qiliang; Yu, Shun; Yan, Min; Berglund, Lars

2016-04-11

Optically transparent wood (TW) with transmittance as high as 85% and haze of 71% was obtained using a delignified nanoporous wood template. The template was prepared by removing the light-absorbing lignin component, creating nanoporosity in the wood cell wall. Transparent wood was prepared by successful impregnation of lumen and the nanoscale cellulose fiber network in the cell wall with refractive-index-matched prepolymerized methyl methacrylate (MMA). During the process, the hierarchical wood structure was preserved. Optical properties of TW are tunable by changing the cellulose volume fraction. The synergy between wood and PMMA was observed for mechanical properties. Lightweight and strong transparent wood is a potential candidate for lightweight low-cost, light-transmitting buildings and transparent solar cell windows.

Nodule Detection in a Lung Region that's Segmented with Using Genetic Cellular Neural Networks and 3D Template Matching with Fuzzy Rule Based Thresholding

PubMed Central

Osman, Onur; Ucan, Osman N.

2008-01-01

Objective The purpose of this study was to develop a new method for automated lung nodule detection in serial section CT images with using the characteristics of the 3D appearance of the nodules that distinguish themselves from the vessels. Materials and Methods Lung nodules were detected in four steps. First, to reduce the number of region of interests (ROIs) and the computation time, the lung regions of the CTs were segmented using Genetic Cellular Neural Networks (G-CNN). Then, for each lung region, ROIs were specified with using the 8 directional search; +1 or -1 values were assigned to each voxel. The 3D ROI image was obtained by combining all the 2-Dimensional (2D) ROI images. A 3D template was created to find the nodule-like structures on the 3D ROI image. Convolution of the 3D ROI image with the proposed template strengthens the shapes that are similar to those of the template and it weakens the other ones. Finally, fuzzy rule based thresholding was applied and the ROI's were found. To test the system's efficiency, we used 16 cases with a total of 425 slices, which were taken from the Lung Image Database Consortium (LIDC) dataset. Results The computer aided diagnosis (CAD) system achieved 100% sensitivity with 13.375 FPs per case when the nodule thickness was greater than or equal to 5.625 mm. Conclusion Our results indicate that the detection performance of our algorithm is satisfactory, and this may well improve the performance of computer-aided detection of lung nodules. PMID:18253070

Automatic identification of resting state networks: an extended version of multiple template-matching

NASA Astrophysics Data System (ADS)

Guaje, Javier; Molina, Juan; Rudas, Jorge; Demertzi, Athena; Heine, Lizette; Tshibanda, Luaba; Soddu, Andrea; Laureys, Steven; Gómez, Francisco

2015-12-01

Functional magnetic resonance imaging in resting state (fMRI-RS) constitutes an informative protocol to investigate several pathological and pharmacological conditions. A common approach to study this data source is through the analysis of changes in the so called resting state networks (RSNs). These networks correspond to well-defined functional entities that have been associated to different low and high brain order functions. RSNs may be characterized by using Independent Component Analysis (ICA). ICA provides a decomposition of the fMRI-RS signal into sources of brain activity, but it lacks of information about the nature of the signal, i.e., if the source is artifactual or not. Recently, a multiple template-matching (MTM) approach was proposed to automatically recognize RSNs in a set of Independent Components (ICs). This method provides valuable information to assess subjects at individual level. Nevertheless, it lacks of a mechanism to quantify how much certainty there is about the existence/absence of each network. This information may be important for the assessment of patients with severely damaged brains, in which RSNs may be greatly affected as a result of the pathological condition. In this work we propose a set of changes to the original MTM that improves the RSNs recognition task and also extends the functionality of the method. The key points of this improvement is a standardization strategy and a modification of method's constraints that adds flexibility to the approach. Additionally, we also introduce an analysis to the trustworthiness measurement of each RSN obtained by using template-matching approach. This analysis consists of a thresholding strategy applied over the computed Goodness-of-Fit (GOF) between the set of templates and the ICs. The proposed method was validated on 2 two independent studies (Baltimore, 23 healthy subjects and Liege, 27 healthy subjects) with different configurations of MTM. Results suggest that the method will provide complementary information for characterization of RSNs at individual level.

Real-time automatic fiducial marker tracking in low contrast cine-MV images

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

Lin, Wei-Yang; Lin, Shu-Fang; Yang, Sheng-Chang

2013-01-15

Purpose: To develop a real-time automatic method for tracking implanted radiographic markers in low-contrast cine-MV patient images used in image-guided radiation therapy (IGRT). Methods: Intrafraction motion tracking using radiotherapy beam-line MV images have gained some attention recently in IGRT because no additional imaging dose is introduced. However, MV images have much lower contrast than kV images, therefore a robust and automatic algorithm for marker detection in MV images is a prerequisite. Previous marker detection methods are all based on template matching or its derivatives. Template matching needs to match object shape that changes significantly for different implantation and projection angle.more » While these methods require a large number of templates to cover various situations, they are often forced to use a smaller number of templates to reduce the computation load because their methods all require exhaustive search in the region of interest. The authors solve this problem by synergetic use of modern but well-tested computer vision and artificial intelligence techniques; specifically the authors detect implanted markers utilizing discriminant analysis for initialization and use mean-shift feature space analysis for sequential tracking. This novel approach avoids exhaustive search by exploiting the temporal correlation between consecutive frames and makes it possible to perform more sophisticated detection at the beginning to improve the accuracy, followed by ultrafast sequential tracking after the initialization. The method was evaluated and validated using 1149 cine-MV images from two prostate IGRT patients and compared with manual marker detection results from six researchers. The average of the manual detection results is considered as the ground truth for comparisons. Results: The average root-mean-square errors of our real-time automatic tracking method from the ground truth are 1.9 and 2.1 pixels for the two patients (0.26 mm/pixel). The standard deviations of the results from the 6 researchers are 2.3 and 2.6 pixels. The proposed framework takes about 128 ms to detect four markers in the first MV images and about 23 ms to track these markers in each of the subsequent images. Conclusions: The unified framework for tracking of multiple markers presented here can achieve marker detection accuracy similar to manual detection even in low-contrast cine-MV images. It can cope with shape deformations of fiducial markers at different gantry angles. The fast processing speed reduces the image processing portion of the system latency, therefore can improve the performance of real-time motion compensation.« less

Iris Matching Based on Personalized Weight Map.

PubMed

Dong, Wenbo; Sun, Zhenan; Tan, Tieniu

2011-09-01

Iris recognition typically involves three steps, namely, iris image preprocessing, feature extraction, and feature matching. The first two steps of iris recognition have been well studied, but the last step is less addressed. Each human iris has its unique visual pattern and local image features also vary from region to region, which leads to significant differences in robustness and distinctiveness among the feature codes derived from different iris regions. However, most state-of-the-art iris recognition methods use a uniform matching strategy, where features extracted from different regions of the same person or the same region for different individuals are considered to be equally important. This paper proposes a personalized iris matching strategy using a class-specific weight map learned from the training images of the same iris class. The weight map can be updated online during the iris recognition procedure when the successfully recognized iris images are regarded as the new training data. The weight map reflects the robustness of an encoding algorithm on different iris regions by assigning an appropriate weight to each feature code for iris matching. Such a weight map trained by sufficient iris templates is convergent and robust against various noise. Extensive and comprehensive experiments demonstrate that the proposed personalized iris matching strategy achieves much better iris recognition performance than uniform strategies, especially for poor quality iris images.

Towards mitigating the effect of sine-Gaussian noise transients on searches for gravitational waves from compact binary coalescences

NASA Astrophysics Data System (ADS)

Bose, Sukanta; Dhurandhar, Sanjeev; Gupta, Anuradha; Lundgren, Andrew

2016-12-01

Gravitational wave signals were recently detected directly by LIGO from the coalescences of two stellar mass black hole pairs. These detections have strengthened our long held belief that compact binary coalescences (CBCs) are the most promising gravitational wave detection prospects accessible to ground-based interferometric detectors. For detecting CBC signals, it is of vital importance to characterize and identify non-Gaussian and nonstationary noise in these detectors. In this work, we model two important classes of transient artifacts that contribute to this noise and adversely affect the detector sensitivity to CBC signals. One of them is the sine-Gaussian "glitch," characterized by a central frequency f0 and a quality factor Q and the other is the chirping sine-Gaussian glitch, which is characterized by f0, Q as well as a chirp parameter. We study the response that a bank of compact binary inspiral templates has to these two families of glitches when they are used to match filter data containing any of these glitches. Two important characteristics of this response are the distributions of the signal-to-noise ratio and the time lag (i.e., how long after the occurrence of a glitch the signal-to-noise ratio of a trigger arises from its matched filtering by a template peaks) of individual templates. We show how these distributions differ from those when the detector data has a real CBC signal instead of a glitch. We argue that these distinctions can be utilized to develop useful signal-artifact discriminators that add negligibly to the computational cost of a CBC search. Specifically, we show how the central frequency of a glitch can be used to set adaptive time windows around it so that any template trigger occurring in that window can be quarantined for further vetting of its supposed astrophysical nature. Second, we recommend focusing efforts on reducing the incidence of glitches with low central-frequency values because they create CBC triggers with the longest time lags. This work allows us to associate such triggers with the glitches that otherwise would have escaped attention.

A human auditory tuning curves matched wavelet function.

PubMed

Abolhassani, Mohammad D; Salimpour, Yousef

2008-01-01

This paper proposes a new quantitative approach to the problem of matching a wavelet function to a human auditory tuning curves. The auditory filter shapes were derived from the psychophysical measurements in normal-hearing listeners using the variant of the notched-noise method for brief signals in forward and simultaneous masking. These filters were used as templates for the designing a wavelet function that has the maximum matching to a tuning curve. The scaling function was calculated from the matched wavelet function and by using these functions, low pass and high pass filters were derived for the implementation of a filter bank. Therefore, new wavelet families were derived.

Action detection by double hierarchical multi-structure space-time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-03-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

Action detection by double hierarchical multi-structure space–time statistical matching model

NASA Astrophysics Data System (ADS)

Han, Jing; Zhu, Junwei; Cui, Yiyin; Bai, Lianfa; Yue, Jiang

2018-06-01

Aimed at the complex information in videos and low detection efficiency, an actions detection model based on neighboring Gaussian structure and 3D LARK features is put forward. We exploit a double hierarchical multi-structure space-time statistical matching model (DMSM) in temporal action localization. First, a neighboring Gaussian structure is presented to describe the multi-scale structural relationship. Then, a space-time statistical matching method is proposed to achieve two similarity matrices on both large and small scales, which combines double hierarchical structural constraints in model by both the neighboring Gaussian structure and the 3D LARK local structure. Finally, the double hierarchical similarity is fused and analyzed to detect actions. Besides, the multi-scale composite template extends the model application into multi-view. Experimental results of DMSM on the complex visual tracker benchmark data sets and THUMOS 2014 data sets show the promising performance. Compared with other state-of-the-art algorithm, DMSM achieves superior performances.

SU-G-JeP3-01: A Method to Quantify Lung SBRT Target Localization Accuracy Based On Digitally Reconstructed Fluoroscopy

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

Lafata, K; Ren, L; Cai, J

2016-06-15

Purpose: To develop a methodology based on digitally-reconstructed-fluoroscopy (DRF) to quantitatively assess target localization accuracy of lung SBRT, and to evaluate using both a dynamic digital phantom and a patient dataset. Methods: For each treatment field, a 10-phase DRF is generated based on the planning 4DCT. Each frame is pre-processed with a morphological top-hat filter, and corresponding beam apertures are projected to each detector plane. A template-matching algorithm based on cross-correlation is used to detect the tumor location in each frame. Tumor motion relative beam aperture is extracted in the superior-inferior direction based on each frame’s impulse response to themore » template, and the mean tumor position (MTP) is calculated as the average tumor displacement. The DRF template coordinates are then transferred to the corresponding MV-cine dataset, which is retrospectively filtered as above. The treatment MTP is calculated within each field’s projection space, relative to the DRF-defined template. The field’s localization error is defined as the difference between the DRF-derived-MTP (planning) and the MV-cine-derived-MTP (delivery). A dynamic digital phantom was used to assess the algorithm’s ability to detect intra-fractional changes in patient alignment, by simulating different spatial variations in the MV-cine and calculating the corresponding change in MTP. Inter-and-intra-fractional variation, IGRT accuracy, and filtering effects were investigated on a patient dataset. Results: Phantom results demonstrated a high accuracy in detecting both translational and rotational variation. The lowest localization error of the patient dataset was achieved at each fraction’s first field (mean=0.38mm), with Fx3 demonstrating a particularly strong correlation between intra-fractional motion-caused localization error and treatment progress. Filtering significantly improved tracking visibility in both the DRF and MV-cine images. Conclusion: We have developed and evaluated a methodology to quantify lung SBRT target localization accuracy based on digitally-reconstructed-fluoroscopy. Our approach may be useful in potentially reducing treatment margins to optimize lung SBRT outcomes. R01-184173.« less

Breast MR segmentation and lesion detection with cellular neural networks and 3D template matching.

PubMed

Ertaş, Gökhan; Gülçür, H Ozcan; Osman, Onur; Uçan, Osman N; Tunaci, Mehtap; Dursun, Memduh

2008-01-01

A novel fully automated system is introduced to facilitate lesion detection in dynamic contrast-enhanced, magnetic resonance mammography (DCE-MRM). The system extracts breast regions from pre-contrast images using a cellular neural network, generates normalized maximum intensity-time ratio (nMITR) maps and performs 3D template matching with three layers of 12x12 cells to detect lesions. A breast is considered to be properly segmented when relative overlap >0.85 and misclassification rate <0.10. Sensitivity, false-positive rate per slice and per lesion are used to assess detection performance. The system was tested with a dataset of 2064 breast MR images (344slicesx6 acquisitions over time) from 19 women containing 39 marked lesions. Ninety-seven percent of the breasts were segmented properly and all the lesions were detected correctly (detection sensitivity=100%), however, there were some false-positive detections (31%/lesion, 10%/slice).

Control of Orientation and Morphology of Crystals Grown Under Organic Templates

NASA Astrophysics Data System (ADS)

Stripe, Benjamin

Living creatures demonstrate an extraordinary ability to both grow and control the growth of inorganic crystals. These biominerals are found almost everywhere in nature from simple plants and plankton to our own teeth and bones. A great deal of research has been focused on how living creatures are able to achieve such control over the shape, size, orientation, and arrangement of these biominerals. Many studies have been done demonstrating the effects the presence of organic molecules can have on the morphology of nucleating inorganic crystals. These studies have led to the use of ordered arrays of biological molecules as templates to select the orientation of the crystals. Such experiments have had amazing success cataloging monolayers, orientations and morphologies of crystals grown beneath them. However, despite several decades of work, the exact mechanisms by which the orientation and morphology of crystals is selected by organic templates are still not known. The present study attempts to explain the complex interactions that take place at the template surface and decide the orientations and morphologies of the crystals that nucleate there. To do this, scanning electron microscopy (SEM), grazing incidence x-ray diffraction (GID), and x-ray reflectivity have been used to probe the templates and nucleating crystals in situ. The experiments described here seek to move beyond the well-studied two-component systems. In many of these two-component systems a single template and a single type of crystal are grown, and often many claims and comparisons are made about monolayer charge, crystal surface energies, stereochemical recognition, and lattice matches. However, almost all of the claims and comparisons are between systems that are different enough that assumptions about relative charge, strain, recognition, and lattice dynamics are either unfounded or poorly supported. To bridge this gap in the comparison of these different two-component systems the studies presented here are tunable three-component systems. These experiments allow for either continuously adjusting the template by means of two miscible monolayers or adjusting the growing crystals by incorporation of secondary ions. In either case, the idea is the same: we can more accurately compare two-component systems and isolate the controlling factor in the selection of orientation and morphology of the nucleating crystals. The results of these studies have shown that there is a complex interplay of charge, lattice parameters and kinetics. Despite this, we have been able to show that well-oriented growth of single non-dendritic crystals is limited to a fairly small range of surface charges and relative growth kinetics. Within this range, variations in the growing crystals can be seen based on changes in the average lattice parameters despite there being no evidence of direct epitaxy. Theories have evolved around the idea of stereochemical matching between the template and nucleating surface. These theories correlate the template molecular tilt to the orientation relative to the nucleation plane. However, these theories are not supported by the results presented in this manuscript. The data presented in this manuscript are suggestive of far more complex interfacial interactions involving an intermediary amorphous precursor, or possible networks of hydrated or hydrogen bonded ions than has been suggested in previous studies. Excitingly, it appears to be possible to control the selection of orientation using these multicomponent systems despite the complex interactions at the surface.

Delineating Concealed Faults within Cogdell Oil Field via Earthquake Detection

NASA Astrophysics Data System (ADS)

Aiken, C.; Walter, J. I.; Brudzinski, M.; Skoumal, R.; Savvaidis, A.; Frohlich, C.; Borgfeldt, T.; Dotray, P.

2016-12-01

Cogdell oil field, located within the Permian Basin of western Texas, has experienced several earthquakes ranging from magnitude 1.7 to 4.6, most of which were recorded since 2006. Using the Earthscope USArray, Gan and Frohlich [2013] relocated some of these events and found a positive correlation in the timing of increased earthquake activity and increased CO2 injection volume. However, focal depths of these earthquakes are unknown due to 70 km station spacing of the USArray. Accurate focal depths as well as new detections can delineate subsurface faults and establish whether earthquakes are occurring in the shallow sediments or in the deeper basement. To delineate subsurface fault(s) in this region, we first detect earthquakes not currently listed in the USGS catalog by applying continuous waveform-template matching algorithms to multiple seismic data sets. We utilize seismic data spanning the time frame of 2006 to 2016 - which includes data from the U.S. Geological Survey Global Seismographic Network, the USArray, and the Sweetwater, TX broadband and nodal array located 20-40 km away. The catalog of earthquakes enhanced by template matching reveals events that were well recorded by the large-N Sweetwater array, so we are experimenting with strategies for optimizing template matching using different configurations of many stations. Since earthquake activity in the Cogdell oil field is on-going (a magnitude 2.6 occurred on May 29, 2016), a temporary deployment of TexNet seismometers has been planned for the immediate vicinity of Cogdell oil field in August 2016. Results on focal depths and detection of small magnitude events are pending this small local network deployment.

Stimulation artifact correction method for estimation of early cortico-cortical evoked potentials.

PubMed

Trebaul, Lena; Rudrauf, David; Job, Anne-Sophie; Mălîia, Mihai Dragos; Popa, Irina; Barborica, Andrei; Minotti, Lorella; Mîndruţă, Ioana; Kahane, Philippe; David, Olivier

2016-05-01

Effective connectivity can be explored using direct electrical stimulations in patients suffering from drug-resistant focal epilepsies and investigated with intracranial electrodes. Responses to brief electrical pulses mimic the physiological propagation of signals and manifest as cortico-cortical evoked potentials (CCEP). The first CCEP component is believed to reflect direct connectivity with the stimulated region but the stimulation artifact, a sharp deflection occurring during a few milliseconds, frequently contaminates it. In order to recover the characteristics of early CCEP responses, we developed an artifact correction method based on electrical modeling of the electrode-tissue interface. The biophysically motivated artifact templates are then regressed out of the recorded data as in any classical template-matching removal artifact methods. Our approach is able to make the distinction between the physiological responses time-locked to the stimulation pulses and the non-physiological component. We tested the correction on simulated CCEP data in order to quantify its efficiency for different stimulation and recording parameters. We demonstrated the efficiency of the new correction method on simulations of single trial recordings for early responses contaminated with the stimulation artifact. The results highlight the importance of sampling frequency for an accurate analysis of CCEP. We then applied the approach to experimental data. The model-based template removal was compared to a correction based on the subtraction of the averaged artifact. This new correction method of stimulation artifact will enable investigators to better analyze early CCEP components and infer direct effective connectivity in future CCEP studies. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

A visible light imaging device for cardiac rate detection with reduced effect of body movement

NASA Astrophysics Data System (ADS)

Jiang, Xiaotian; Liu, Ming; Zhao, Yuejin

2014-09-01

A visible light imaging system to detect human cardiac rate is proposed in this paper. A color camera and several LEDs, acting as lighting source, were used to avoid the interference of ambient light. From people's forehead, the cardiac rate could be acquired based on photoplethysmography (PPG) theory. The template matching method was used after the capture of video. The video signal was discomposed into three signal channels (RGB) and the region of interest was chosen to take the average gray value. The green channel signal could provide an excellent waveform of pulse wave on the account of green lights' absorptive characteristics of blood. Through the fast Fourier transform, the cardiac rate was exactly achieved. But the research goal was not just to achieve the cardiac rate accurately. With the template matching method, the effects of body movement are reduced to a large extent, therefore the pulse wave can be detected even while people are in the moving state and the waveform is largely optimized. Several experiments are conducted on volunteers, and the results are compared with the ones gained by a finger clamped pulse oximeter. The contrast results between these two ways are exactly agreeable. This method to detect the cardiac rate and the pulse wave largely reduces the effects of body movement and can probably be widely used in the future.

Impact of Sensor Misplacement on Dynamic Time Warping Based Human Activity Recognition using Wearable Computers.

PubMed

Kale, Nimish; Lee, Jaeseong; Lotfian, Reza; Jafari, Roozbeh

2012-10-01

Daily living activity monitoring is important for early detection of the onset of many diseases and for improving quality of life especially in elderly. A wireless wearable network of inertial sensor nodes can be used to observe daily motions. Continuous stream of data generated by these sensor networks can be used to recognize the movements of interest. Dynamic Time Warping (DTW) is a widely used signal processing method for time-series pattern matching because of its robustness to variations in time and speed as opposed to other template matching methods. Despite this flexibility, for the application of activity recognition, DTW can only find the similarity between the template of a movement and the incoming samples, when the location and orientation of the sensor remains unchanged. Due to this restriction, small sensor misplacements can lead to a decrease in the classification accuracy. In this work, we adopt DTW distance as a feature for real-time detection of human daily activities like sit to stand in the presence of sensor misplacement. To measure this performance of DTW, we need to create a large number of sensor configurations while the sensors are rotated or misplaced. Creating a large number of closely spaced sensors is impractical. To address this problem, we use the marker based optical motion capture system and generate simulated inertial sensor data for different locations and orientations on the body. We study the performance of the DTW under these conditions to determine the worst-case sensor location variations that the algorithm can accommodate.

Multi-channel measurement for hetero-core optical fiber sensor by using CMOS camera

NASA Astrophysics Data System (ADS)

Koyama, Yuya; Nishiyama, Michiko; Watanabe, Kazuhiro

2015-07-01

Fiber optic smart structures have been developed over several decades by the recent fiber optic sensor technology. Optical intensity-based sensors, which use LD or LEDs, can be suitable for the monitor system to be simple and cost effective. In this paper, a novel fiber optic smart structure with human-like perception has been demonstrated by using intensity-based hetero-core optical fiber sensors system with the CMOS detector. The optical intensity from the hetero-core optical fiber bend sensor is obtained as luminance spots indicated by the optical power distributions. A number of optical intensity spots are simultaneously readout by taking a picture of luminance pattern. To recognize the state of fiber optic smart structure with the hetero-core optical fibers, the template matching process is employed with Sum of Absolute Differences (SAD). A fiber optic smart glove having five optic fiber nerves have been employed to monitor hand postures. Three kinds of hand postures have been recognized by means of the template matching process. A body posture monitoring has also been developed by placing the wearable hetero-core optical fiber bend sensors on the body segments. In order for the CMOS system to be a human brain-like, the luminescent spots in the obtained picture were arranged to make the pattern corresponding to the position of body segments. As a result, it was successfully demonstrated that the proposed fiber optic smart structure could recognize eight kinds of body postures. The developed system will give a capability of human brain-like processing to the existing fiber optic smart structures.

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

Tailoring thermal conductivity via three-dimensional porous alumina

PubMed Central

Abad, Begoña; Maiz, Jon; Ruiz-Clavijo, Alejandra; Caballero-Calero, Olga; Martin-Gonzalez, Marisol

2016-01-01

Three-dimensional anodic alumina templates (3D-AAO) are an astonishing framework with open highly ordered three-dimensional skeleton structures. Since these templates are architecturally different from conventional solids or porous templates, they teem with opportunities for engineering thermal properties. By establishing the mechanisms of heat transfer in these frameworks, we aim to create materials with tailored thermal properties. The effective thermal conductivity of an empty 3D-AAO membrane was measured. As the effective medium theory was not valid to extract the skeletal thermal conductivity of 3D-AAO, a simple 3D thermal conduction model was developed, based on a mixed series and parallel thermal resistor circuit, giving a skeletal thermal conductivity value of approximately 1.25 W·m−1·K−1, which matches the value of the ordinary AAO membranes prepared from the same acid solution. The effect of different filler materials as well as the variation of the number of transversal nanochannels and the length of the 3D-AAO membrane in the effective thermal conductivity of the composite was studied. Finally, the thermal conductivity of two 3D-AAO membranes filled with cobalt and bismuth telluride was also measured, which was in good agreement with the thermal model predictions. Therefore, this work proved this structure as a powerful approach to tailor thermal properties. PMID:27934930

Classifier for gravitational-wave inspiral signals in nonideal single-detector data

NASA Astrophysics Data System (ADS)

Kapadia, S. J.; Dent, T.; Dal Canton, T.

2017-11-01

We describe a multivariate classifier for candidate events in a templated search for gravitational-wave (GW) inspiral signals from neutron-star-black-hole (NS-BH) binaries, in data from ground-based detectors where sensitivity is limited by non-Gaussian noise transients. The standard signal-to-noise ratio (SNR) and chi-squared test for inspiral searches use only properties of a single matched filter at the time of an event; instead, we propose a classifier using features derived from a bank of inspiral templates around the time of each event, and also from a search using approximate sine-Gaussian templates. The classifier thus extracts additional information from strain data to discriminate inspiral signals from noise transients. We evaluate a random forest classifier on a set of single-detector events obtained from realistic simulated advanced LIGO data, using simulated NS-BH signals added to the data. The new classifier detects a factor of 1.5-2 more signals at low false positive rates as compared to the standard "reweighted SNR" statistic, and does not require the chi-squared test to be computed. Conversely, if only the SNR and chi-squared values of single-detector events are available, random forest classification performs nearly identically to the reweighted SNR.

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.

Identification of the chemical components of Saussurea involucrata by high-resolution mass spectrometry and the mass spectral trees similarity filter technique.

PubMed

Jia, Zhixin; Wu, Caisheng; Jin, Hongtao; Zhang, Jinlan

2014-11-15

Saussurea involucrata is a rare traditional Chinese medicine (TCM) that displays anti-fatigue, anti-inflammatory and anti-tumor effects. In this paper, the different chemical components of Saussurea involucrata were characterized and identified over a wide dynamic range by high-performance liquid chromatography coupled with high-resolution hybrid mass spectrometry (HPLC/HRMS/MS(n)) and the mass spectral trees similarity filter (MTSF) technique. The aerial parts of Saussurea involucrata were extracted with 75% ethanol. The partial extract was separated on a chromatography column to concentrate the low-concentration compounds. Mass data were acquired using full-scan mass analysis (resolving power 50,000) with data-dependent incorporation of dynamic exclusion analysis. The identified compounds were used as templates to construct a database of mass spectral trees. Data for the unknown compounds were matched with those templates and matching candidate structures were obtained. The detected compounds were characterized based on matching to candidate structures by the MTSF technique and were further identified by their accurate mass weight, multiple-stage analysis and fragmentation patterns and through comparison with literature data. A total of 38 compounds were identified including 19 flavones, 11 phenylpropanoids and 8 sphingolipids. Among them, 7 flavonoids, 8 phenylpropanoids and 8 sphingolipids were identified for the first time in Saussurea involucrata. HPLC/HRMS/MS(n) combined with MTSF was successfully used to discover and identify the chemical compounds in Saussurea involucrata. The results indicated that this combined technique was extremely useful for the rapid detection and identification of the chemical components in TCMs. Copyright © 2014 John Wiley & Sons, Ltd.

Robust fluoroscopic respiratory gating for lung cancer radiotherapy without implanted fiducial markers

NASA Astrophysics Data System (ADS)

Cui, Ying; Dy, Jennifer G.; Sharp, Greg C.; Alexander, Brian; Jiang, Steve B.

2007-02-01

For gated lung cancer radiotherapy, it is difficult to generate accurate gating signals due to the large uncertainties when using external surrogates and the risk of pneumothorax when using implanted fiducial markers. We have previously investigated and demonstrated the feasibility of generating gating signals using the correlation scores between the reference template image and the fluoroscopic images acquired during the treatment. In this paper, we present an in-depth study, aiming at the improvement of robustness of the algorithm and its validation using multiple sets of patient data. Three different template generating and matching methods have been developed and evaluated: (1) single template method, (2) multiple template method, and (3) template clustering method. Using the fluoroscopic data acquired during patient setup before each fraction of treatment, reference templates are built that represent the tumour position and shape in the gating window, which is assumed to be at the end-of-exhale phase. For the single template method, all the setup images within the gating window are averaged to generate a composite template. For the multiple template method, each setup image in the gating window is considered as a reference template and used to generate an ensemble of correlation scores. All the scores are then combined to generate the gating signal. For the template clustering method, clustering (grouping of similar objects together) is performed to reduce the large number of reference templates into a few representative ones. Each of these methods has been evaluated against the reference gating signal as manually determined by a radiation oncologist. Five patient datasets were used for evaluation. In each case, gated treatments were simulated at both 35% and 50% duty cycles. False positive, negative and total error rates were computed. Experiments show that the single template method is sensitive to noise; the multiple template and clustering methods are more robust to noise due to the smoothing effect of aggregation of correlation scores; and the clustering method results in the best performance in terms of computational efficiency and accuracy.

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.

SU-F-BRD-10: Lung IMRT Planning Using Standardized Beam Bouquet Templates

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

Yuan, L; Wu, Q J.; Yin, F

2014-06-15

Purpose: We investigate the feasibility of choosing from a small set of standardized templates of beam bouquets (i.e., entire beam configuration settings) for lung IMRT planning to improve planning efficiency and quality consistency, and also to facilitate automated planning. Methods: A set of beam bouquet templates is determined by learning from the beam angle settings in 60 clinical lung IMRT plans. A k-medoids cluster analysis method is used to classify the beam angle configuration into clusters. The value of the average silhouette width is used to determine the ideal number of clusters. The beam arrangements in each medoid of themore » resulting clusters are taken as the standardized beam bouquet for the cluster, with the corresponding case taken as the reference case. The resulting set of beam bouquet templates was used to re-plan 20 cases randomly selected from the database and the dosimetric quality of the plans was evaluated against the corresponding clinical plans by a paired t-test. The template for each test case was manually selected by a planner based on the match between the test and reference cases. Results: The dosimetric parameters (mean±S.D. in percentage of prescription dose) of the plans using 6 beam bouquet templates and those of the clinical plans, respectively, and the p-values (in parenthesis) are: lung Dmean: 18.8±7.0, 19.2±7.0 (0.28), esophagus Dmean: 32.0±16.3, 34.4±17.9 (0.01), heart Dmean: 19.2±16.5, 19.4±16.6 (0.74), spinal cord D2%: 47.7±18.8, 52.0±20.3 (0.01), PTV dose homogeneity (D2%-D99%): 17.1±15.4, 20.7±12.2 (0.03).The esophagus Dmean, cord D02 and PTV dose homogeneity are statistically better in the plans using the standardized templates, but the improvements (<5%) may not be clinically significant. The other dosimetric parameters are not statistically different. Conclusion: It's feasible to use a small number of standardized beam bouquet templates (e.g. 6) to generate plans with quality comparable to that of clinical plans. Partially supported by NIH/NCI under grant #R21CA161389 and a master research grant by Varian Medical System.« less

Temporal regularization of ultrasound-based liver motion estimation for image-guided radiation therapy

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

O’Shea, Tuathan P., E-mail: tuathan.oshea@icr.ac.uk; Bamber, Jeffrey C.; Harris, Emma J.

Purpose: Ultrasound-based motion estimation is an expanding subfield of image-guided radiation therapy. Although ultrasound can detect tissue motion that is a fraction of a millimeter, its accuracy is variable. For controlling linear accelerator tracking and gating, ultrasound motion estimates must remain highly accurate throughout the imaging sequence. This study presents a temporal regularization method for correlation-based template matching which aims to improve the accuracy of motion estimates. Methods: Liver ultrasound sequences (15–23 Hz imaging rate, 2.5–5.5 min length) from ten healthy volunteers under free breathing were used. Anatomical features (blood vessels) in each sequence were manually annotated for comparison withmore » normalized cross-correlation based template matching. Five sequences from a Siemens Acuson™ scanner were used for algorithm development (training set). Results from incremental tracking (IT) were compared with a temporal regularization method, which included a highly specific similarity metric and state observer, known as the α–β filter/similarity threshold (ABST). A further five sequences from an Elekta Clarity™ system were used for validation, without alteration of the tracking algorithm (validation set). Results: Overall, the ABST method produced marked improvements in vessel tracking accuracy. For the training set, the mean and 95th percentile (95%) errors (defined as the difference from manual annotations) were 1.6 and 1.4 mm, respectively (compared to 6.2 and 9.1 mm, respectively, for IT). For each sequence, the use of the state observer leads to improvement in the 95% error. For the validation set, the mean and 95% errors for the ABST method were 0.8 and 1.5 mm, respectively. Conclusions: Ultrasound-based motion estimation has potential to monitor liver translation over long time periods with high accuracy. Nonrigid motion (strain) and the quality of the ultrasound data are likely to have an impact on tracking performance. A future study will investigate spatial uniformity of motion and its effect on the motion estimation errors.« less

Supervised learning of tools for content-based search of image databases

NASA Astrophysics Data System (ADS)

Delanoy, Richard L.

1996-03-01

A computer environment, called the Toolkit for Image Mining (TIM), is being developed with the goal of enabling users with diverse interests and varied computer skills to create search tools for content-based image retrieval and other pattern matching tasks. Search tools are generated using a simple paradigm of supervised learning that is based on the user pointing at mistakes of classification made by the current search tool. As mistakes are identified, a learning algorithm uses the identified mistakes to build up a model of the user's intentions, construct a new search tool, apply the search tool to a test image, display the match results as feedback to the user, and accept new inputs from the user. Search tools are constructed in the form of functional templates, which are generalized matched filters capable of knowledge- based image processing. The ability of this system to learn the user's intentions from experience contrasts with other existing approaches to content-based image retrieval that base searches on the characteristics of a single input example or on a predefined and semantically- constrained textual query. Currently, TIM is capable of learning spectral and textural patterns, but should be adaptable to the learning of shapes, as well. Possible applications of TIM include not only content-based image retrieval, but also quantitative image analysis, the generation of metadata for annotating images, data prioritization or data reduction in bandwidth-limited situations, and the construction of components for larger, more complex computer vision algorithms.

Skull defect reconstruction based on a new hybrid level set.

PubMed

Zhang, Ziqun; Zhang, Ran; Song, Zhijian

2014-01-01

Skull defect reconstruction is an important aspect of surgical repair. Historically, a skull defect prosthesis was created by the mirroring technique, surface fitting, or formed templates. These methods are not based on the anatomy of the individual patient's skull, and therefore, the prosthesis cannot precisely correct the defect. This study presented a new hybrid level set model, taking into account both the global optimization region information and the local accuracy edge information, while avoiding re-initialization during the evolution of the level set function. Based on the new method, a skull defect was reconstructed, and the skull prosthesis was produced by rapid prototyping technology. This resulted in a skull defect prosthesis that well matched the skull defect with excellent individual adaptation.

An Improved Vision-based Algorithm for Unmanned Aerial Vehicles Autonomous Landing

NASA Astrophysics Data System (ADS)

Zhao, Yunji; Pei, Hailong

In vision-based autonomous landing system of UAV, the efficiency of target detecting and tracking will directly affect the control system. The improved algorithm of SURF(Speed Up Robust Features) will resolve the problem which is the inefficiency of the SURF algorithm in the autonomous landing system. The improved algorithm is composed of three steps: first, detect the region of the target using the Camshift; second, detect the feature points in the region of the above acquired using the SURF algorithm; third, do the matching between the template target and the region of target in frame. The results of experiment and theoretical analysis testify the efficiency of the algorithm.

Thermal imaging as a biometrics approach to facial signature authentication.

PubMed

Guzman, A M; Goryawala, M; Wang, Jin; Barreto, A; Andrian, J; Rishe, N; Adjouadi, M

2013-01-01

A new thermal imaging framework with unique feature extraction and similarity measurements for face recognition is presented. The research premise is to design specialized algorithms that would extract vasculature information, create a thermal facial signature and identify the individual. The proposed algorithm is fully integrated and consolidates the critical steps of feature extraction through the use of morphological operators, registration using the Linear Image Registration Tool and matching through unique similarity measures designed for this task. The novel approach at developing a thermal signature template using four images taken at various instants of time ensured that unforeseen changes in the vasculature over time did not affect the biometric matching process as the authentication process relied only on consistent thermal features. Thirteen subjects were used for testing the developed technique on an in-house thermal imaging system. The matching using the similarity measures showed an average accuracy of 88.46% for skeletonized signatures and 90.39% for anisotropically diffused signatures. The highly accurate results obtained in the matching process clearly demonstrate the ability of the thermal infrared system to extend in application to other thermal imaging based systems. Empirical results applying this approach to an existing database of thermal images proves this assertion.

A new combined surface and volume registration

NASA Astrophysics Data System (ADS)

Lepore, Natasha; Joshi, Anand A.; Leahy, Richard M.; Brun, Caroline; Chou, Yi-Yu; Pennec, Xavier; Lee, Agatha D.; Barysheva, Marina; De Zubicaray, Greig I.; Wright, Margaret J.; McMahon, Katie L.; Toga, Arthur W.; Thompson, Paul M.

2010-03-01

3D registration of brain MRI data is vital for many medical imaging applications. However, purely intensitybased approaches for inter-subject matching of brain structure are generally inaccurate in cortical regions, due to the highly complex network of sulci and gyri, which vary widely across subjects. Here we combine a surfacebased cortical registration with a 3D fluid one for the first time, enabling precise matching of cortical folds, but allowing large deformations in the enclosed brain volume, which guarantee diffeomorphisms. This greatly improves the matching of anatomy in cortical areas. The cortices are segmented and registered with the software Freesurfer. The deformation field is initially extended to the full 3D brain volume using a 3D harmonic mapping that preserves the matching between cortical surfaces. Finally, these deformation fields are used to initialize a 3D Riemannian fluid registration algorithm, that improves the alignment of subcortical brain regions. We validate this method on an MRI dataset from 92 healthy adult twins. Results are compared to those based on volumetric registration without surface constraints; the resulting mean templates resolve consistent anatomical features both subcortically and at the cortex, suggesting that the approach is well-suited for cross-subject integration of functional and anatomic data.

Defect analysis and detection of micro nano structured optical thin film

NASA Astrophysics Data System (ADS)

Xu, Chang; Shi, Nuo; Zhou, Lang; Shi, Qinfeng; Yang, Yang; Li, Zhuo

2017-10-01

This paper focuses on developing an automated method for detecting defects on our wavelength conversion thin film. We analyzes the operating principle of our wavelength conversion Micro/Nano thin film which absorbing visible light and emitting infrared radiation, indicates the relationship between the pixel's pattern and the radiation of the thin film, and issues the principle of defining blind pixels and their categories due to the calculated and experimental results. An effective method is issued for the automated detection based on wavelet transform and template matching. The results reveal that this method has desired accuracy and processing speed.

Thin plate spline feature point matching for organ surfaces in minimally invasive surgery imaging

NASA Astrophysics Data System (ADS)

Lin, Bingxiong; Sun, Yu; Qian, Xiaoning

2013-03-01

Robust feature point matching for images with large view angle changes in Minimally Invasive Surgery (MIS) is a challenging task due to low texture and specular reflections in these images. This paper presents a new approach that can improve feature matching performance by exploiting the inherent geometric property of the organ surfaces. Recently, intensity based template image tracking using a Thin Plate Spline (TPS) model has been extended for 3D surface tracking with stereo cameras. The intensity based tracking is also used here for 3D reconstruction of internal organ surfaces. To overcome the small displacement requirement of intensity based tracking, feature point correspondences are used for proper initialization of the nonlinear optimization in the intensity based method. Second, we generate simulated images from the reconstructed 3D surfaces under all potential view positions and orientations, and then extract feature points from these simulated images. The obtained feature points are then filtered and re-projected to the common reference image. The descriptors of the feature points under different view angles are stored to ensure that the proposed method can tolerate a large range of view angles. We evaluate the proposed method with silicon phantoms and in vivo images. The experimental results show that our method is much more robust with respect to the view angle changes than other state-of-the-art methods.

Biomimetic/Optical Sensors for Detecting Bacterial Species

NASA Technical Reports Server (NTRS)

Homer, Margie; Ksendzov, Alexander; Yen, Shiao-Pin; Ryan, Margaret; Lazazzera, Beth

2006-01-01

Biomimetic/optical sensors have been proposed as means of real-time detection of bacteria in liquid samples through real-time detection of compounds secreted by the bacteria. Bacterial species of interest would be identified through detection of signaling compounds unique to those species. The best-characterized examples of quorum-signaling compounds are acyl-homoserine lactones and peptides. Each compound, secreted by each bacterium of an affected species, serves as a signal to other bacteria of the same species to engage in a collective behavior when the population density of that species reaches a threshold level analogous to a quorum. A sensor according to the proposal would include a specially formulated biomimetic film, made of a molecularly imprinted polymer (MIP), that would respond optically to the signaling compound of interest. The MIP film would be integrated directly onto an opticalwaveguide- based ring resonator for optical readout. Optically, the sensor would resemble the one described in Chemical Sensors Based on Optical Ring Resonators (NPO-40601), NASA Tech Briefs, Vol. 29, No. 10 (October 2005), page 32. MIPs have been used before as molecular- recognition compounds, though not in the manner of the present proposal. Molecular imprinting is an approach to making molecularly selective cavities in a polymer matrix. These cavities function much as enzyme receptor sites: the chemical functionality and shape of a cavity in the polymer matrix cause the cavity to bind to specific molecules. An MIP matrix is made by polymerizing monomers in the presence of the compound of interest (template molecule). The polymer forms around the template. After the polymer solidifies, the template molecules are removed from the polymer matrix by decomplexing them from their binding sites and then dissolving them, leaving cavities that are matched to the template molecules in size, shape, and chemical functionality. The cavities thus become molecular-recognition sites that bind only to molecules matched to the sites; other molecules are excluded. In a sensor according to the proposal, the MIP would feature molecular recognition sites that would bind the specific signaling molecules selectively according to their size, shape, and chemical functionality (see figure). As the film took up the signaling molecules in the molecular recognition sites, the index of refraction and thickness of the film would change, causing a wavelength shift of the peak of the resonance spectrum. It has been estimated that by measuring this wavelength shift, it should be possible to detect as little as 10 picomoles of a peptide signaling compound.

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.

Templated biomimetic multifunctional coatings

NASA Astrophysics Data System (ADS)

Sun, Chih-Hung; Gonzalez, Adriel; Linn, Nicholas C.; Jiang, Peng; Jiang, Bin

2008-02-01

We report a bioinspired templating technique for fabricating multifunctional optical coatings that mimic both unique functionalities of antireflective moth eyes and superhydrophobic cicada wings. Subwavelength-structured fluoropolymer nipple arrays are created by a soft-lithography-like process. The utilization of fluoropolymers simultaneously enhances the antireflective performance and the hydrophobicity of the replicated films. The specular reflectivity matches the optical simulation using a thin-film multilayer model. The dependence of the size and the crystalline ordering of the replicated nipples on the resulting antireflective properties have also been investigated by experiment and modeling. These biomimetic materials may find important technological application in self-cleaning antireflection coatings.

Vocal learning beyond imitation: mechanisms of adaptive vocal development in songbirds and human infants

PubMed Central

Tchernichovski, Ofer; Marcus, Gary

2014-01-01

Studies of vocal learning in songbirds typically focus on the acquisition of sensory templates for song imitation and on the consequent process of matching song production to templates. However, functional vocal development also requires the capacity to adaptively diverge from sensory templates, and to flexibly assemble vocal units. Examples of adaptive divergence include the corrective imitation of abnormal songs, and the decreased tendency to copy overabundant syllables. Such frequency-dependent effects might mirror tradeoffs between the assimilation of group identity (culture) while establishing individual and flexibly expressive songs. Intriguingly, although the requirements for vocal plasticity vary across songbirds, and more so between birdsong and language, the capacity to flexibly assemble vocal sounds develops in a similar, stepwise manner across species. Therefore, universal features of vocal learning go well beyond the capacity to imitate. PMID:25005823

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

Automated CD-SEM recipe creation technology for mass production using CAD data

NASA Astrophysics Data System (ADS)

Kawahara, Toshikazu; Yoshida, Masamichi; Tanaka, Masashi; Ido, Sanyu; Nakano, Hiroyuki; Adachi, Naokaka; Abe, Yuichi; Nagatomo, Wataru

2011-03-01

Critical Dimension Scanning Electron Microscope (CD-SEM) recipe creation needs sample preparation necessary for matching pattern registration, and recipe creation on CD-SEM using the sample, which hinders the reduction in test production cost and time in semiconductor manufacturing factories. From the perspective of cost reduction and improvement of the test production efficiency, automated CD-SEM recipe creation without the sample preparation and the manual operation has been important in the production lines. For the automated CD-SEM recipe creation, we have introduced RecipeDirector (RD) that enables the recipe creation by using Computer-Aided Design (CAD) data and text data that includes measurement information. We have developed a system that automatically creates the CAD data and the text data necessary for the recipe creation on RD; and, for the elimination of the manual operation, we have enhanced RD so that all measurement information can be specified in the text data. As a result, we have established an automated CD-SEM recipe creation system without the sample preparation and the manual operation. For the introduction of the CD-SEM recipe creation system using RD to the production lines, the accuracy of the pattern matching was an issue. The shape of design templates for the matching created from the CAD data was different from that of SEM images in vision. Thus, a development of robust pattern matching algorithm that considers the shape difference was needed. The addition of image processing of the templates for the matching and shape processing of the CAD patterns in the lower layer has enabled the robust pattern matching. This paper describes the automated CD-SEM recipe creation technology for the production lines without the sample preparation and the manual operation using RD applied in Sony Semiconductor Kyusyu Corporation Kumamoto Technology Center (SCK Corporation Kumamoto TEC).

A new general model for predicting melting thermodynamics of complementary and mismatched B-form duplexes containing locked nucleic acids: application to probe design for digital PCR detection of somatic mutations.

PubMed

Hughesman, Curtis; Fakhfakh, Kareem; Bidshahri, Roza; Lund, H Louise; Haynes, Charles

2015-02-17

Advances in real-time polymerase chain reaction (PCR), as well as the emergence of digital PCR (dPCR) and useful modified nucleotide chemistries, including locked nucleic acids (LNAs), have created the potential to improve and expand clinical applications of PCR through their ability to better quantify and differentiate amplification products, but fully realizing this potential will require robust methods for designing dual-labeled hydrolysis probes and predicting their hybridization thermodynamics as a function of their sequence, chemistry, and template complementarity. We present here a nearest-neighbor thermodynamic model that accurately predicts the melting thermodynamics of a short oligonucleotide duplexed either to its perfect complement or to a template containing mismatched base pairs. The model may be applied to pure-DNA duplexes or to duplexes for which one strand contains any number and pattern of LNA substitutions. Perturbations to duplex stability arising from mismatched DNA:DNA or LNA:DNA base pairs are treated at the Gibbs energy level to maintain statistical significance in the regressed model parameters. This approach, when combined with the model's accounting of the temperature dependencies of the melting enthalpy and entropy, permits accurate prediction of T(m) values for pure-DNA homoduplexes or LNA-substituted heteroduplexes containing one or two independent mismatched base pairs. Terms accounting for changes in solution conditions and terminal addition of fluorescent dyes and quenchers are then introduced so that the model may be used to accurately predict and thereby tailor the T(m) of a pure-DNA or LNA-substituted hydrolysis probe when duplexed either to its perfect-match template or to a template harboring a noncomplementary base. The model, which builds on classic nearest-neighbor thermodynamics, should therefore be of use to clinicians and biologists who require probes that distinguish and quantify two closely related alleles in either a quantitative PCR or dPCR assay. This potential is demonstrated by using the model to design allele-specific probes that completely discriminate and quantify clinically relevant mutant alleles (BRAF V600E and KIT D816V) in a dPCR assay.

The Elementary Operations of Human Vision Are Not Reducible to Template-Matching

PubMed Central

Neri, Peter

2015-01-01

It is generally acknowledged that biological vision presents nonlinear characteristics, yet linear filtering accounts of visual processing are ubiquitous. The template-matching operation implemented by the linear-nonlinear cascade (linear filter followed by static nonlinearity) is the most widely adopted computational tool in systems neuroscience. This simple model achieves remarkable explanatory power while retaining analytical tractability, potentially extending its reach to a wide range of systems and levels in sensory processing. The extent of its applicability to human behaviour, however, remains unclear. Because sensory stimuli possess multiple attributes (e.g. position, orientation, size), the issue of applicability may be asked by considering each attribute one at a time in relation to a family of linear-nonlinear models, or by considering all attributes collectively in relation to a specified implementation of the linear-nonlinear cascade. We demonstrate that human visual processing can operate under conditions that are indistinguishable from linear-nonlinear transduction with respect to substantially different stimulus attributes of a uniquely specified target signal with associated behavioural task. However, no specific implementation of a linear-nonlinear cascade is able to account for the entire collection of results across attributes; a satisfactory account at this level requires the introduction of a small gain-control circuit, resulting in a model that no longer belongs to the linear-nonlinear family. Our results inform and constrain efforts at obtaining and interpreting comprehensive characterizations of the human sensory process by demonstrating its inescapably nonlinear nature, even under conditions that have been painstakingly fine-tuned to facilitate template-matching behaviour and to produce results that, at some level of inspection, do conform to linear filtering predictions. They also suggest that compliance with linear transduction may be the targeted outcome of carefully crafted nonlinear circuits, rather than default behaviour exhibited by basic components. PMID:26556758

Kinetic quantitation of cerebral PET-FDG studies without concurrent blood sampling: statistical recovery of the arterial input function.

PubMed

O'Sullivan, F; Kirrane, J; Muzi, M; O'Sullivan, J N; Spence, A M; Mankoff, D A; Krohn, K A

2010-03-01

Kinetic quantitation of dynamic positron emission tomography (PET) studies via compartmental modeling usually requires the time-course of the radio-tracer concentration in the arterial blood as an arterial input function (AIF). For human and animal imaging applications, significant practical difficulties are associated with direct arterial sampling and as a result there is substantial interest in alternative methods that require no blood sampling at the time of the study. A fixed population template input function derived from prior experience with directly sampled arterial curves is one possibility. Image-based extraction, including requisite adjustment for spillover and recovery, is another approach. The present work considers a hybrid statistical approach based on a penalty formulation in which the information derived from a priori studies is combined in a Bayesian manner with information contained in the sampled image data in order to obtain an input function estimate. The absolute scaling of the input is achieved by an empirical calibration equation involving the injected dose together with the subject's weight, height and gender. The technique is illustrated in the context of (18)F -Fluorodeoxyglucose (FDG) PET studies in humans. A collection of 79 arterially sampled FDG blood curves are used as a basis for a priori characterization of input function variability, including scaling characteristics. Data from a series of 12 dynamic cerebral FDG PET studies in normal subjects are used to evaluate the performance of the penalty-based AIF estimation technique. The focus of evaluations is on quantitation of FDG kinetics over a set of 10 regional brain structures. As well as the new method, a fixed population template AIF and a direct AIF estimate based on segmentation are also considered. Kinetics analyses resulting from these three AIFs are compared with those resulting from radially sampled AIFs. The proposed penalty-based AIF extraction method is found to achieve significant improvements over the fixed template and the segmentation methods. As well as achieving acceptable kinetic parameter accuracy, the quality of fit of the region of interest (ROI) time-course data based on the extracted AIF, matches results based on arterially sampled AIFs. In comparison, significant deviation in the estimation of FDG flux and degradation in ROI data fit are found with the template and segmentation methods. The proposed AIF extraction method is recommended for practical use.

Simultaneous tumor and surrogate motion tracking with dynamic MRI for radiation therapy planning

NASA Astrophysics Data System (ADS)

Park, Seyoun; Farah, Rana; Shea, Steven M.; Tryggestad, Erik; Hales, Russell; Lee, Junghoon

2018-01-01

Respiration-induced tumor motion is a major obstacle for achieving high-precision radiotherapy of cancers in the thoracic and abdominal regions. Surrogate-based estimation and tracking methods are commonly used in radiotherapy, but with limited understanding of quantified correlation to tumor motion. In this study, we propose a method to simultaneously track the lung tumor and external surrogates to evaluate their spatial correlation in a quantitative way using dynamic MRI, which allows real-time acquisition without ionizing radiation exposure. To capture the lung and whole tumor, four MRI-compatible fiducials are placed on the patient’s chest and upper abdomen. Two different types of acquisitions are performed in the sagittal orientation including multi-slice 2D cine MRIs to reconstruct 4D-MRI and two-slice 2D cine MRIs to simultaneously track the tumor and fiducials. A phase-binned 4D-MRI is first reconstructed from multi-slice MR images using body area as a respiratory surrogate and groupwise registration. The 4D-MRI provides 3D template volumes for different breathing phases. 3D tumor position is calculated by 3D-2D template matching in which 3D tumor templates in the 4D-MRI reconstruction and the 2D cine MRIs from the two-slice tracking dataset are registered. 3D trajectories of the external surrogates are derived via matching a 3D geometrical model of the fiducials to their segmentations on the 2D cine MRIs. We tested our method on ten lung cancer patients. Using a correlation analysis, the 3D tumor trajectory demonstrates a noticeable phase mismatch and significant cycle-to-cycle motion variation, while the external surrogate was not sensitive enough to capture such variations. Additionally, there was significant phase mismatch between surrogate signals obtained from the fiducials at different locations.

Feasibility study of patient-specific surgical templates for the fixation of pedicle screws.

PubMed

Salako, F; Aubin, C-E; Fortin, C; Labelle, H

2002-01-01

Surgery for scoliosis, as well as other posterior spinal surgeries, frequently uses pedicle screws to fix an instrumentation on the spine. Misplacement of a screw can lead to intra- and post-operative complications. The objective of this study is to design patient-specific surgical templates to guide the drilling operation. From the CT-scan of a vertebra, the optimal drilling direction and limit angles are computed from an inverse projection of the pedicle limits. The first template design uses a surface-to-surface registration method and was constructed in a CAD system by subtracting the vertebra from a rectangular prism and a cylinder with the optimal orientation. This template and the vertebra were built using rapid prototyping. The second design uses a point-to-surface registration method and has 6 adjustable screws to adjust the orientation and length of the drilling support device. A mechanism was designed to hold it in place on the spinal process. A virtual prototype was build with CATIA software. During the operation, the surgeon places either template on patient's vertebra until a perfect match is obtained before drilling. The second design seems better than the first one because it can be reused on different vertebra and is less sensible to registration errors. The next step is to build the second design and make experimental and simulations tests to evaluate the benefits of this template during a scoliosis operation.

Pen-chant: Acoustic emissions of handwriting and drawing

NASA Astrophysics Data System (ADS)

Seniuk, Andrew G.

The sounds generated by a writing instrument ('pen-chant') provide a rich and underutilized source of information for pattern recognition. We examine the feasibility of recognition of handwritten cursive text, exclusively through an analysis of acoustic emissions. We design and implement a family of recognizers using a template matching approach, with templates and similarity measures derived variously from: smoothed amplitude signal with fixed resolution, discrete sequence of magnitudes obtained from peaks in the smoothed amplitude signal, and ordered tree obtained from a scale space signal representation. Test results are presented for recognition of isolated lowercase cursive characters and for whole words. We also present qualitative results for recognizing gestures such as circling, scratch-out, check-marks, and hatching. Our first set of results, using samples provided by the author, yield recognition rates of over 70% (alphabet) and 90% (26 words), with a confidence of +/-8%, based solely on acoustic emissions. Our second set of results uses data gathered from nine writers. These results demonstrate that acoustic emissions are a rich source of information, usable---on their own or in conjunction with image-based features---to solve pattern recognition problems. In future work, this approach can be applied to writer identification, handwriting and gesture-based computer input technology, emotion recognition, and temporal analysis of sketches.

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

Multi-template image matching using alpha-rooted biquaternion phase correlation with application to logo recognition

NASA Astrophysics Data System (ADS)

DelMarco, Stephen

2011-06-01

Hypercomplex approaches are seeing increased application to signal and image processing problems. The use of multicomponent hypercomplex numbers, such as quaternions, enables the simultaneous co-processing of multiple signal or image components. This joint processing capability can provide improved exploitation of the information contained in the data, thereby leading to improved performance in detection and recognition problems. In this paper, we apply hypercomplex processing techniques to the logo image recognition problem. Specifically, we develop an image matcher by generalizing classical phase correlation to the biquaternion case. We further incorporate biquaternion Fourier domain alpha-rooting enhancement to create Alpha-Rooted Biquaternion Phase Correlation (ARBPC). We present the mathematical properties which justify use of ARBPC as an image matcher. We present numerical performance results of a logo verification problem using real-world logo data, demonstrating the performance improvement obtained using the hypercomplex approach. We compare results of the hypercomplex approach to standard multi-template matching approaches.

Three-dimensional templating arthroplasty of the humeral head.

PubMed

Cho, Sung Won; Jharia, Trambak K; Moon, Young Lae; Sim, Sung Woo; Shin, Dong Sun; Bigliani, Louis U

2013-10-01

No anatomical study has been conducted over Asian population to design humeral head prosthesis for the population concerned. This study was done to evaluate the accuracy of commercially available humeral head prosthetic designs, in replicating the humeral head anatomy. CT scan data of 48 patients were taken and their 3D CAD models were generated. Then, humeral head prosthetic design of a BF shoulder system produced by a standardized, commercially available company (Zimmer) was used for templating shoulder arthroplasty and the humeral head size having the perfect fit was assessed. These data were compared with the available data in the literature. All the humeral heads were perfectly matched by one of the sizes available. The average head size was 48.5 mm and the average head thickness was 23.5 mm. The results matched reasonably well with the available data in the literature. The humeral head anatomy can be recreated reasonably well by the commercially available humeral head prosthetic designs and sizes. Their dimensions are similar to that of the published literature.

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

Panfil, J; Patel, R; Surucu, M

Purpose: To compare markerless template-based tracking of lung tumors using dual energy (DE) cone-beam computed tomography (CBCT) projections versus single energy (SE) CBCT projections. Methods: A RANDO chest phantom with a simulated tumor in the upper right lung was used to investigate the effectiveness of tumor tracking using DE and SE CBCT projections. Planar kV projections from CBCT acquisitions were captured at 60 kVp (4 mAs) and 120 kVp (1 mAs) using the Varian TrueBeam and non-commercial iTools Capture software. Projections were taken at approximately every 0.53° while the gantry rotated. Due to limitations of the phantom, angles for whichmore » the shoulders blocked the tumor were excluded from tracking analysis. DE images were constructed using a weighted logarithmic subtraction that removed bony anatomy while preserving soft tissue structures. The tumors were tracked separately on DE and SE (120 kVp) images using a template-based tracking algorithm. The tracking results were compared to ground truth coordinates designated by a physician. Matches with a distance of greater than 3 mm from ground truth were designated as failing to track. Results: 363 frames were analyzed. The algorithm successfully tracked the tumor on 89.8% (326/363) of DE frames compared to 54.3% (197/363) of SE frames (p<0.0001). Average distance between tracking and ground truth coordinates was 1.27 +/− 0.67 mm for DE versus 1.83+/−0.74 mm for SE (p<0.0001). Conclusion: This study demonstrates the effectiveness of markerless template-based tracking using DE CBCT. DE imaging resulted in better detectability with more accurate localization on average versus SE. Supported by a grant from Varian Medical Systems.« less

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

Campbell, W; Miften, M; Jones, B

Purpose: Pancreatic SBRT relies on extremely accurate delivery of ablative radiation doses to the target, and intra-fractional tracking of fiducial markers can facilitate improvements in dose delivery. However, this requires algorithms that are able to find fiducial markers with high speed and accuracy. The purpose of this study was to develop a novel marker tracking algorithm that is robust against many of the common errors seen with traditional template matching techniques. Methods: Using CBCT projection images, a method was developed to create detailed template images of fiducial marker clusters without prior knowledge of the number of markers, their positions, ormore » their orientations. Briefly, the method (i) enhances markers in projection images, (ii) stabilizes the cluster’s position, (iii) reconstructs the cluster in 3D, and (iv) precomputes a set of static template images dependent on gantry angle. Furthermore, breathing data were used to produce 4D reconstructions of clusters, yielding dynamic template images dependent on gantry angle and breathing amplitude. To test these two approaches, static and dynamic templates were used to track the motion of marker clusters in more than 66,000 projection images from 75 CBCT scans of 15 pancreatic SBRT patients. Results: For both static and dynamic templates, the new technique was able to locate marker clusters present in projection images 100% of the time. The algorithm was also able to correctly locate markers in several instances where only some of the markers were visible due to insufficient field-of-view. In cases where clusters exhibited deformation and/or rotation during breathing, dynamic templates resulted in cross-correlation scores up to 70% higher than static templates. Conclusion: Patient-specific templates provided complete tracking of fiducial marker clusters in CBCT scans, and dynamic templates helped to provide higher cross-correlation scores for deforming/rotating clusters. This novel algorithm provides an extremely accurate method to detect fiducial markers during treatment. Research funding provided by Varian Medical Systems to Miften and Jones.« less

Discovering new events beyond the catalogue—application of empirical matched field processing to Salton Sea geothermal field seismicity

DOE PAGES

Wang, Jingbo; Templeton, Dennise C.; Harris, David B.

2015-07-30

Using empirical matched field processing (MFP), we compare 4 yr of continuous seismic data to a set of 195 master templates from within an active geothermal field and identify over 140 per cent more events than were identified using traditional detection and location techniques alone. In managed underground reservoirs, a substantial fraction of seismic events can be excluded from the official catalogue due to an inability to clearly identify seismic-phase onsets. Empirical MFP can improve the effectiveness of current seismic detection and location methodologies by using conventionally located events with higher signal-to-noise ratios as master events to define wavefield templatesmore » that could then be used to map normally discarded indistinct seismicity. Since MFP does not require picking, it can be carried out automatically and rapidly once suitable templates are defined. In this application, we extend MFP by constructing local-distance empirical master templates using Southern California Earthquake Data Center archived waveform data of events originating within the Salton Sea Geothermal Field. We compare the empirical templates to continuous seismic data collected between 1 January 2008 and 31 December 2011. The empirical MFP method successfully identifies 6249 additional events, while the original catalogue reported 4352 events. The majority of these new events are lower-magnitude events with magnitudes between M0.2–M0.8. Here, the increased spatial-temporal resolution of the microseismicity map within the geothermal field illustrates how empirical MFP, when combined with conventional methods, can significantly improve seismic network detection capabilities, which can aid in long-term sustainability and monitoring of managed underground reservoirs.« less

Discovery of a novel and potent class of F. tularensis enoyl-reductase (FabI) inhibitors by molecular shape and electrostatic matching

PubMed Central

Hevener, Kirk E.; Mehboob, Shahila; Su, Pin-Chih; Truong, Kent; Boci, Teuta; Deng, Jiangping; Ghassemi, Mahmood; Cook, James L.; Johnson, Michael E.

2011-01-01

Enoyl-acyl carrier protein (ACP) reductase, FabI, is a key enzyme in the bacterial fatty acid biosynthesis pathway (FAS II). FabI is an NADH-dependent oxidoreductase that acts to reduce enoyl-ACP substrates in a final step of the pathway. The absence of this enzyme in humans makes it an attractive target for the development of new antibacterial agents. FabI is known to be unresponsive to structure-based design efforts due to a high degree of induced fit and a mobile flexible loop encompassing the active site. Here we discuss the development, validation, and careful application of a ligand-based virtual screen used for the identification of novel inhibitors of the Francisella tularensis FabI target. In this study, four known classes of FabI inhibitors were used as templates for virtual screens that involved molecular shape and electrostatic matching. The program ROCS was used to search a high-throughput screening library for compounds that matched any of the four molecular shape queries. Matching compounds were further refined using the program EON, which compares and scores compounds by matching electrostatic properties. Using these techniques, 50 compounds were selected, ordered, and tested. The tested compounds possessed novel chemical scaffolds when compared to the input query compounds. Several hits with low micromolar activity were identified and follow-up scaffold-based searches resulted in the identification of a lead series with sub-micromolar enzyme inhibition, high ligand efficiency, and a novel scaffold. Additionally, one of the most active compounds showed promising whole-cell antibacterial activity against several Gram-positive and Gram-negative species, including the target pathogen. The results of a preliminary structure-activity relationship analysis are presented. PMID:22098466

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.

Deformable templates guided discriminative models for robust 3D brain MRI segmentation.

PubMed

Liu, Cheng-Yi; Iglesias, Juan Eugenio; Tu, Zhuowen

2013-10-01

Automatically segmenting anatomical structures from 3D brain MRI images is an important task in neuroimaging. One major challenge is to design and learn effective image models accounting for the large variability in anatomy and data acquisition protocols. A deformable template is a type of generative model that attempts to explicitly match an input image with a template (atlas), and thus, they are robust against global intensity changes. On the other hand, discriminative models combine local image features to capture complex image patterns. In this paper, we propose a robust brain image segmentation algorithm that fuses together deformable templates and informative features. It takes advantage of the adaptation capability of the generative model and the classification power of the discriminative models. The proposed algorithm achieves both robustness and efficiency, and can be used to segment brain MRI images with large anatomical variations. We perform an extensive experimental study on four datasets of T1-weighted brain MRI data from different sources (1,082 MRI scans in total) and observe consistent improvement over the state-of-the-art systems.

[Application of computer-aided osteotomy template design in treatment of developmental dysplasia of the hip with steel osteotomy].

PubMed

Tong, Kuang; Zhang, Yuanzhi; Zhang, Sheng; Yu, Bin

2013-06-01

To provide an accurate method for osteotomy in the treatment of developmental dysplasia of the hip with steel osteotomy by three-dimensional reconstruction and Reverse Engineering technique. Between January 2011 and December 2012, 13 children with developmental dysplasia of the hip underwent steel osteotomy. 3D CT scan pelvic images were obtained and transferred via a DICOM network into a computer workstation to construct 3D models of the hip using Materialise Mimics 14.1 software in STL format. These models were imported into Imageware 12.0 software for steel osteotomy simulation until a stable hip was attained in the anatomical position for dislocation or subluxation of the hip in older children. The osteotomy navigational templates were designed according to the anatomical features after a stable hip was reconstructed. These navigational templates were manufactured using a rapid prototyping technique. The reconstruction hips in these children show good matching property and acetabulum cover. The computer-aided design of osteotomy template provides personalized and accurate solutions in the treatment of developmental dysplasia of the hip with steel osteotomy in older children.

Visual Detection Under Uncertainty Operates Via an Early Static, Not Late Dynamic, Non-Linearity

PubMed Central

Neri, Peter

2010-01-01

Signals in the environment are rarely specified exactly: our visual system may know what to look for (e.g., a specific face), but not its exact configuration (e.g., where in the room, or in what orientation). Uncertainty, and the ability to deal with it, is a fundamental aspect of visual processing. The MAX model is the current gold standard for describing how human vision handles uncertainty: of all possible configurations for the signal, the observer chooses the one corresponding to the template associated with the largest response. We propose an alternative model in which the MAX operation, which is a dynamic non-linearity (depends on multiple inputs from several stimulus locations) and happens after the input stimulus has been matched to the possible templates, is replaced by an early static non-linearity (depends only on one input corresponding to one stimulus location) which is applied before template matching. By exploiting an integrated set of analytical and experimental tools, we show that this model is able to account for a number of empirical observations otherwise unaccounted for by the MAX model, and is more robust with respect to the realistic limitations imposed by the available neural hardware. We then discuss how these results, currently restricted to a simple visual detection task, may extend to a wider range of problems in sensory processing. PMID:21212835

Planning surgical reconstruction in Treacher-Collins syndrome using virtual simulation.

PubMed

Nikkhah, Dariush; Ponniah, Allan; Ruff, Cliff; Dunaway, David

2013-11-01

Treacher-Collins syndrome is a rare autosomal dominant condition of varying phenotypic expression. The surgical correction in this syndrome is difficult, and the approach varies between craniofacial departments worldwide. The authors aimed to design standardized tools for planning orbitozygomatic and mandibular reconstruction in Treacher-Collins syndrome using geometric morphometrics. The Great Ormond Street Hospital database was retrospectively identified for patients with Treacher-Collins syndrome. Thirteen children (aged 2 to 15 years) who had suitable preoperative three-dimensional computed tomographic head scans were included. Six Treacher-Collins syndrome three-dimensional computed tomographic head scans were quantitatively compared using a template of 96 anatomically defined landmarks to 26 age-matched normal dry skulls. Thin-plate spline videos illustrated the characteristic deformities of retromicrognathia and maxillary and orbitozygomatic hypoplasia in the Treacher-Collins syndrome population. Geometric morphometrics was used in the virtual reconstruction of the orbitozygomatic and mandibular region in Treacher-Collins syndrome patients. Intrarater and interrater reliability of the landmarks was acceptable and within a standard deviation of less than 1 mm on 97 percent and 100 percent of 10 repeated scans, respectively. Virtual normalization of the Treacher-Collins syndrome skull effectively describes characteristic skeletal deformities and provides a useful guide to surgical reconstruction. Size-matched stereolithographic templates derived from thin-plate spline warps can provide effective intraoperative templates for zygomatic and mandibular reconstruction in the Treacher-Collins syndrome patient. Diagnostic, V.

Template-based procedures for neural network interpretation.

PubMed

Alexander, J A.; Mozer, M C.

1999-04-01

Although neural networks often achieve impressive learning and generalization performance, their internal workings are typically all but impossible to decipher. This characteristic of the networks, their opacity, is one of the disadvantages of connectionism compared to more traditional, rule-oriented approaches to artificial intelligence. Without a thorough understanding of the network behavior, confidence in a system's results is lowered, and the transfer of learned knowledge to other processing systems - including humans - is precluded. Methods that address the opacity problem by casting network weights in symbolic terms are commonly referred to as rule extraction techniques. This work describes a principled approach to symbolic rule extraction from standard multilayer feedforward networks based on the notion of weight templates, parameterized regions of weight space corresponding to specific symbolic expressions. With an appropriate choice of representation, we show how template parameters may be efficiently identified and instantiated to yield the optimal match to the actual weights of a unit. Depending on the requirements of the application domain, the approach can accommodate n-ary disjunctions and conjunctions with O(k) complexity, simple n-of-m expressions with O(k(2)) complexity, or more general classes of recursive n-of-m expressions with O(k(L+2)) complexity, where k is the number of inputs to an unit and L the recursion level of the expression class. Compared to other approaches in the literature, our method of rule extraction offers benefits in simplicity, computational performance, and overall flexibility. Simulation results on a variety of problems demonstrate the application of our procedures as well as the strengths and the weaknesses of our general approach.

Statistical density modification using local pattern matching

DOEpatents

Terwilliger, Thomas C.

2007-01-23

A computer implemented method modifies an experimental electron density map. A set of selected known experimental and model electron density maps is provided and standard templates of electron density are created from the selected experimental and model electron density maps by clustering and averaging values of electron density in a spherical region about each point in a grid that defines each selected known experimental and model electron density maps. Histograms are also created from the selected experimental and model electron density maps that relate the value of electron density at the center of each of the spherical regions to a correlation coefficient of a density surrounding each corresponding grid point in each one of the standard templates. The standard templates and the histograms are applied to grid points on the experimental electron density map to form new estimates of electron density at each grid point in the experimental electron density map.

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

Aguiar, Ana C.; Chao, Kevin; Beroza, Gregory C.

In this paper, we compare low-frequency earthquakes (LFEs) from triggered and ambient tremor under the southern Central Range, Taiwan. We apply the PageRank algorithm used by Aguiar and Beroza (2014) that exploits the repetitive nature of the LFEs to find repeating LFEs in both ambient and triggered tremor. We use these repeaters to create LFE templates and find that the templates created from both tremor types are very similar. To test their similarity, we use both interchangeably and find that most of both the ambient and triggered tremor match the LFE templates created from either data set, suggesting that LFEsmore » for both events have a common origin. Finally, we locate the LFEs by using local earthquake P wave and S wave information and find that LFEs from triggered and ambient tremor locate to between 20 and 35 km on what we interpret as the deep extension of the Chaochou-Lishan Fault.« less

Pressure activated diaphragm bonder

DOEpatents

Evans, L.B.; Malba, V.

1997-05-27

A device is available for bonding one component to another, particularly for bonding electronic components of integrated circuits, such as chips, to a substrate. The bonder device in one embodiment includes a bottom metal block having a machined opening wherein a substrate is located, a template having machined openings which match solder patterns on the substrate, a thin diaphragm placed over the template after the chips have been positioned in the openings therein, and a top metal block positioned over the diaphragm and secured to the bottom block, with the diaphragm retained therebetween. The top block includes a countersink portion which extends over at least the area of the template and an opening through which a high pressure inert gas is supplied to exert uniform pressure distribution over the diaphragm to keep the chips in place during soldering. A heating means is provided to melt the solder patterns on the substrate and thereby solder the chips thereto. 4 figs.

Pressure activated diaphragm bonder

DOEpatents

Evans, Leland B.; Malba, Vincent

1997-01-01

A device is available for bonding one component to another, particularly for bonding electronic components of integrated circuits, such as chips, to a substrate. The bonder device in one embodiment includes a bottom metal block having a machined opening wherein a substrate is located, a template having machined openings which match solder patterns on the substrate, a thin diaphragm placed over the template after the chips have been positioned in the openings therein, and a top metal block positioned over the diaphragm and secured to the bottom block, with the diaphragm retained therebetween. The top block includes a countersink portion which extends over at least the area of the template and an opening through which a high pressure inert gas is supplied to exert uniform pressure distribution over the diaphragm to keep the chips in place during soldering. A heating means is provided to melt the solder patterns on the substrate and thereby solder the chips thereto.

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

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.

Microseismic Monitoring of Stimulating Shale Gas Reservoir in SW China: 1. An Improved Matching and Locating Technique for Downhole Monitoring

NASA Astrophysics Data System (ADS)

Meng, Xiaobo; Chen, Haichao; Niu, Fenglin; Tang, Youcai; Yin, Chen; Wu, Furong

2018-02-01

We introduce an improved matching and locating technique to detect and locate microseismic events (-4 < ML < 0) associated with hydraulic fracturing treatment. We employ a set of representative master events to act as template waveforms and detect slave events that strongly resemble master events through stacking cross correlograms of both P and S waves between the template waveforms and the continuous records of the monitoring array. Moreover, the residual moveout in the cross correlograms across the array is used to locate slave events relative to the corresponding master event. In addition, P wave polarization constraint is applied to resolve the lateral extent of slave events in the case of unfavorable array configuration. We first demonstrate the detectability and location accuracy of the proposed approach with a pseudo-synthetic data set. Compared to the matched filter analysis, the proposed approach can significantly enhance detectability at low false alarm rate and yield robust location estimates of very low SNR events, particularly along the vertical direction. Then, we apply the method to a real microseismic data set acquired in the Weiyuan shale reservoir of China in November of 2014. The expanded microseismic catalog provides more easily interpretable spatiotemporal evolution of microseismicity, which is investigated in detail in a companion paper.

Bioinspired broadband antireflection coatings on GaSb

NASA Astrophysics Data System (ADS)

Min, Wei-Lun; Betancourt, Amaury P.; Jiang, Peng; Jiang, Bin

2008-04-01

We report an inexpensive yet scalable templating technique for fabricating moth-eye antireflection gratings on gallium antimonide substrates. Non-close-packed colloidal monolayers are utilized as etching masks to pattern subwavelength-structured nipple arrays on GaSb. The resulting gratings exhibit superior broadband antireflection properties and thermal stability than conventional multilayer dielectric coatings. The specular reflection of the templated nipple arrays match with the theoretical predictions using a rigorous coupled-wave analysis model. The effect of the nipple shape and size on the antireflection properties has also been investigated by the same model. These biomimetic coatings are of great technological importance in developing efficient thermophotovoltaic cells.

Versatile buffer layer architectures based on Ge1-xSnx alloys

NASA Astrophysics Data System (ADS)

Roucka, R.; Tolle, J.; Cook, C.; Chizmeshya, A. V. G.; Kouvetakis, J.; D'Costa, V.; Menendez, J.; Chen, Zhihao D.; Zollner, S.

2005-05-01

We describe methodologies for integration of compound semiconductors with Si via buffer layers and templates based on the GeSn system. These layers exhibit atomically flat surface morphologies, low defect densities, tunable thermal expansion coefficients, and unique ductile properties, which enable them to readily absorb differential stresses produced by mismatched overlayers. They also provide a continuous selection of lattice parameters higher than that of Ge, which allows lattice matching with technologically useful III-V compounds. Using this approach we have demonstrated growth of GaAs, GeSiSn, and pure Ge layers at low temperatures on Si(100). These materials display extremely high-quality structural, morphological, and optical properties opening the possibility of versatile integration schemes directly on silicon.

Vision-based vehicle detection and tracking algorithm design

NASA Astrophysics Data System (ADS)

Hwang, Junyeon; Huh, Kunsoo; Lee, Donghwi

2009-12-01

The vision-based vehicle detection in front of an ego-vehicle is regarded as promising for driver assistance as well as for autonomous vehicle guidance. The feasibility of vehicle detection in a passenger car requires accurate and robust sensing performance. A multivehicle detection system based on stereo vision has been developed for better accuracy and robustness. This system utilizes morphological filter, feature detector, template matching, and epipolar constraint techniques in order to detect the corresponding pairs of vehicles. After the initial detection, the system executes the tracking algorithm for the vehicles. The proposed system can detect front vehicles such as the leading vehicle and side-lane vehicles. The position parameters of the vehicles located in front are obtained based on the detection information. The proposed vehicle detection system is implemented on a passenger car, and its performance is verified experimentally.

Applying an Archetype-Based Approach to Electroencephalography/Event-Related Potential Experiments in the EEGBase Resource.

PubMed

Papež, Václav; Mouček, Roman

2017-01-01

The purpose of this study is to investigate the feasibility of applying openEHR (an archetype-based approach for electronic health records representation) to modeling data stored in EEGBase, a portal for experimental electroencephalography/event-related potential (EEG/ERP) data management. The study evaluates re-usage of existing openEHR archetypes and proposes a set of new archetypes together with the openEHR templates covering the domain. The main goals of the study are to (i) link existing EEGBase data/metadata and openEHR archetype structures and (ii) propose a new openEHR archetype set describing the EEG/ERP domain since this set of archetypes currently does not exist in public repositories. The main methodology is based on the determination of the concepts obtained from EEGBase experimental data and metadata that are expressible structurally by the openEHR reference model and semantically by openEHR archetypes. In addition, templates as the third openEHR resource allow us to define constraints over archetypes. Clinical Knowledge Manager (CKM), a public openEHR archetype repository, was searched for the archetypes matching the determined concepts. According to the search results, the archetypes already existing in CKM were applied and the archetypes not existing in the CKM were newly developed. openEHR archetypes support linkage to external terminologies. To increase semantic interoperability of the new archetypes, binding with the existing odML electrophysiological terminology was assured. Further, to increase structural interoperability, also other current solutions besides EEGBase were considered during the development phase. Finally, a set of templates using the selected archetypes was created to meet EEGBase requirements. A set of eleven archetypes that encompassed the domain of experimental EEG/ERP measurements were identified. Of these, six were reused without changes, one was extended, and four were newly created. All archetypes were arranged in the templates reflecting the EEGBase metadata structure. A mechanism of odML terminology referencing was proposed to assure semantic interoperability of the archetypes. The openEHR approach was found to be useful not only for clinical purposes but also for experimental data modeling.

A randomized clinical trial comparing guided implant surgery (bone- or mucosa-supported) with mental navigation or the use of a pilot-drill template.

PubMed

Vercruyssen, Marjolein; Cox, Catherine; Coucke, Wim; Naert, Ignace; Jacobs, Reinhilde; Quirynen, Marc

2014-07-01

To assess the accuracy of guided surgery (mucosa and bone-supported) compared to mental navigation or the use of a surgical template, in fully edentulous jaws, in a randomized controlled study. Fifty-nine patients (72 jaws), requiring four to six implants (maxilla or mandible), were consecutively recruited and randomly assigned to one of the following treatment groups; guidance via Materialise Universal(®)/mucosa, Materialise Universal(®)/bone, Facilitate™/mucosa, Facilitate™/bone, or mental navigation or a pilot-drill template. The precision was assessed by matching the planning computed tomography (CT) with a post-operative cone beam CT. A significant lower mean deviation at the entry point (1.4 mm, range: 0.3-3.7), at the apex (1.6 mm, range: 0.2-3.7) and angular deviation (3.0°, range: 0.2-16°) was observed for the guiding systems when compared to mental navigation (2.7 mm, range: 0.3-8.3; 2.9 mm, range: 0.5-7.4 and 9.9°, range: 1.5-27.8) and to the surgical template group (3.0 mm, range: 0.6-6.6; 3.4 mm, range: 0.3-7.5 and 8.4°, range: 0.6-21.3°). Differences between bone and mucosa support or type of guidance were negligible. Jaw and implant location (posterior-anterior, left-right), however, had a significant influence on the accuracy when guided. Based on these findings, guided implant placement appears to offer clear accuracy benefits. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Implementing a search for gravitational waves from binary black holes with nonprecessing spin

NASA Astrophysics Data System (ADS)

Capano, Collin; Harry, Ian; Privitera, Stephen; Buonanno, Alessandra

2016-06-01

Searching for gravitational waves (GWs) from binary black holes (BBHs) with LIGO and Virgo involves matched-filtering data against a set of representative signal waveforms—a template bank—chosen to cover the full signal space of interest with as few template waveforms as possible. Although the component black holes may have significant angular momenta (spin), previous searches for BBHs have filtered LIGO and Virgo data using only waveforms where both component spins are zero. This leads to a loss of signal-to-noise ratio for signals where this is not the case. Combining the best available template placement techniques and waveform models, we construct a template bank of GW signals from BBHs with component spins χ1 ,2∈[-0.99 ,0.99 ] aligned with the orbital angular momentum, component masses m1 ,2∈[2 ,48 ]M⊙ , and total mass Mtotal≤50 M⊙ . Using effective-one-body waveforms with spin effects, we show that less than 3% of the maximum signal-to-noise ratio (SNR) of these signals is lost due to the discreetness of the bank, using the early Advanced LIGO noise curve. We use simulated Advanced LIGO noise to compare the sensitivity of this bank to a nonspinning bank covering the same parameter space. In doing so, we consider the competing effects between improved SNR and signal-based vetoes and the increase in the rate of false alarms of the aligned-spin bank due to covering a larger parameter space. We find that the aligned-spin bank can be a factor of 1.3-5 more sensitive than a nonspinning bank to BBHs with dimensionless spins >+0.6 and component masses ≳20 M⊙ . Even larger gains are obtained for systems with equally high spins but smaller component masses.

Dual exposure, two-photon, conformal phasemask lithography for three dimensional silicon inverse woodpile photonic crystals

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

Shir, Daniel J.; Nelson, Erik C.; Chanda, Debashis

2010-01-01

The authors describe the fabrication and characterization of three dimensional silicon inverse woodpile photonic crystals. A dual exposure, two-photon, conformal phasemask technique is used to create high quality polymer woodpile structures over large areas with geometries that quantitatively match expectations based on optical simulations. Depositing silicon into these templates followed by the removal of the polymer results in silicon inverse woodpile photonic crystals for which calculations indicate a wide, complete photonic bandgap over a range of structural fill fractions. Spectroscopic measurements of normal incidence reflection from both the polymer and siliconphotonic crystals reveal good optical properties.

Meta-image navigation augmenters for GPS denied mountain navigation of small UAS

NASA Astrophysics Data System (ADS)

Wang, Teng; ćelik, Koray; Somani, Arun K.

2014-06-01

We present a novel approach to use mountain drainage patterns for GPS-Denied navigation of small unmanned aerial systems (UAS) such as the ScanEagle, utilizing a down-looking fixed focus monocular imager. Our proposal allows extension of missions to GPS-denied mountain areas, with no assumption of human-made geographic objects. We leverage the analogy between mountain drainage patterns, human arteriograms, and human fingerprints, to match local drainage patterns to Graphics Processing Unit (GPU) rendered parallax occlusion maps of geo-registered radar returns (GRRR). Details of our actual GPU algorithm is beyond the subject of this paper, and is planned as a future paper. The matching occurs in real-time, while GRRR data is loaded on-board the aircraft pre-mission, so as not to require a scanning aperture radar during the mission. For recognition purposes, we represent a given mountain area with a set of spatially distributed mountain minutiae, i.e., details found in the drainage patterns, so that conventional minutiae-based fingerprint matching approaches can be used to match real-time camera image against template images in the training set. We use medical arteriography processing techniques to extract the patterns. The minutiae-based representation of mountains is achieved by first exposing mountain ridges and valleys with a series of filters and then extracting mountain minutiae from these ridges/valleys. Our results are experimentally validated on actual terrain data and show the effectiveness of minutiae-based mountain representation method. Furthermore, we study how to select landmarks for UAS navigation based on the proposed mountain representation and give a set of examples to show its feasibility. This research was in part funded by Rockwell Collins Inc.

Reconstruction based finger-knuckle-print verification with score level adaptive binary fusion.

PubMed

Gao, Guangwei; Zhang, Lei; Yang, Jian; Zhang, Lin; Zhang, David

2013-12-01

Recently, a new biometrics identifier, namely finger knuckle print (FKP), has been proposed for personal authentication with very interesting results. One of the advantages of FKP verification lies in its user friendliness in data collection. However, the user flexibility in positioning fingers also leads to a certain degree of pose variations in the collected query FKP images. The widely used Gabor filtering based competitive coding scheme is sensitive to such variations, resulting in many false rejections. We propose to alleviate this problem by reconstructing the query sample with a dictionary learned from the template samples in the gallery set. The reconstructed FKP image can reduce much the enlarged matching distance caused by finger pose variations; however, both the intra-class and inter-class distances will be reduced. We then propose a score level adaptive binary fusion rule to adaptively fuse the matching distances before and after reconstruction, aiming to reduce the false rejections without increasing much the false acceptances. Experimental results on the benchmark PolyU FKP database show that the proposed method significantly improves the FKP verification accuracy.

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.

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

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

PubMed Central

Egge, Elianne; Bittner, Lucie; Andersen, Tom; Audic, Stéphane; de Vargas, Colomban; Edvardsen, Bente

2013-01-01

Next generation sequencing of ribosomal DNA is increasingly used to assess the diversity and structure of microbial communities. Here we test the ability of 454 pyrosequencing to detect the number of species present, and assess the relative abundance in terms of cell numbers and biomass of protists in the phylum Haptophyta. We used a mock community consisting of equal number of cells of 11 haptophyte species and compared targeting DNA and RNA/cDNA, and two different V4 SSU rDNA haptophyte-biased primer pairs. Further, we tested four different bioinformatic filtering methods to reduce errors in the resulting sequence dataset. With sequencing depth of 11000–20000 reads and targeting cDNA with Haptophyta specific primers Hap454 we detected all 11 species. A rarefaction analysis of expected number of species recovered as a function of sampling depth suggested that minimum 1400 reads were required here to recover all species in the mock community. Relative read abundance did not correlate to relative cell numbers. Although the species represented with the largest biomass was also proportionally most abundant among the reads, there was generally a weak correlation between proportional read abundance and proportional biomass of the different species, both with DNA and cDNA as template. The 454 sequencing generated considerable spurious diversity, and more with cDNA than DNA as template. With initial filtering based only on match with barcode and primer we observed 100-fold more operational taxonomic units (OTUs) at 99% similarity than the number of species present in the mock community. Filtering based on quality scores, or denoising with PyroNoise resulted in ten times more OTU99% than the number of species. Denoising with AmpliconNoise reduced the number of OTU99% to match the number of species present in the mock community. Based on our analyses, we propose a strategy to more accurately depict haptophyte diversity using 454 pyrosequencing. PMID:24069303

Search algorithm complexity modeling with application to image alignment and matching

NASA Astrophysics Data System (ADS)

DelMarco, Stephen

2014-05-01

Search algorithm complexity modeling, in the form of penetration rate estimation, provides a useful way to estimate search efficiency in application domains which involve searching over a hypothesis space of reference templates or models, as in model-based object recognition, automatic target recognition, and biometric recognition. The penetration rate quantifies the expected portion of the database that must be searched, and is useful for estimating search algorithm computational requirements. In this paper we perform mathematical modeling to derive general equations for penetration rate estimates that are applicable to a wide range of recognition problems. We extend previous penetration rate analyses to use more general probabilistic modeling assumptions. In particular we provide penetration rate equations within the framework of a model-based image alignment application domain in which a prioritized hierarchical grid search is used to rank subspace bins based on matching probability. We derive general equations, and provide special cases based on simplifying assumptions. We show how previously-derived penetration rate equations are special cases of the general formulation. We apply the analysis to model-based logo image alignment in which a hierarchical grid search is used over a geometric misalignment transform hypothesis space. We present numerical results validating the modeling assumptions and derived formulation.

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

A Study of Galaxies and Quasars in the Background of the Andromeda Galaxy

NASA Astrophysics Data System (ADS)

Dhara, Atirath; McConnell, Kaela; Guhathakurta, Puragra; Roy, Namrata; Waite, Jurij

2018-01-01

The SPLASH (Spectroscopic and Photometric Landscape of Andromeda’s Stellar Halo) survey is based on wide-field ground-based optical images (KPNO 4-m/Mosaic, CFHT 3.6-m/MegaCam imager, and Subaru 8-m/Suprime-Cam), deep Hubble Space Telescope ultraviolet/optical/near infrared images (ACS and WFC3), and medium resolution spectra (Keck II 10-m/DEIMOS). The SPLASH survey data set contains two main categories of (non-M31) contaminants (SPLASH trash, if you will): foreground Milky Way stars and compact background galaxies/quasars. In this poster, we present the discovery and characterization of galaxies and quasars behind M31. Such objects were identified based on the presence of redshifted emission lines and other galaxy/quasar spectral features (e.g., Ca H+K absorption and IGM absorption). The redshift of each galaxy was measured by cross-correlating its spectrum against an emission line galaxy spectral template. The cross-correlation results (spectrum and best-fit template) were visually inspected to identify cases of incorrect matching of emission lines. Many of these incorrect redshift estimates were corrected by using the second or third highest cross-correlation peak. Quasar redshifts were determined based on cross-correlation against a quasar spectral template. Most of the galaxies in our sample are star forming galaxies with strong emission lines. We analyze their emission line flux ratios in a BPT diagram to learn more about the ionization source and metallicity. Finally, the properties of these compact galaxies behind M31 are compared to those of galaxies selected in a more standard way in the DEEP2 redshift survey to explore the effects of morphological pre-selection (compact vs. extended) on the properties of the resulting galaxy sample.This research was supported by NASA/STScI and the National Science Foundation. Most of this work was carried out by high school students working under the auspices of the Science Internship Program (SIP) at UC Santa Cruz.

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.

Structural action recognition in body sensor networks: distributed classification based on string matching.

PubMed

Ghasemzadeh, Hassan; Loseu, Vitali; Jafari, Roozbeh

2010-03-01

Mobile sensor-based systems are emerging as promising platforms for healthcare monitoring. An important goal of these systems is to extract physiological information about the subject wearing the network. Such information can be used for life logging, quality of life measures, fall detection, extraction of contextual information, and many other applications. Data collected by these sensor nodes are overwhelming, and hence, an efficient data processing technique is essential. In this paper, we present a system using inexpensive, off-the-shelf inertial sensor nodes that constructs motion transcripts from biomedical signals and identifies movements by taking collaboration between the nodes into consideration. Transcripts are built of motion primitives and aim to reduce the complexity of the original data. We then label each primitive with a unique symbol and generate a sequence of symbols, known as motion template, representing a particular action. This model leads to a distributed algorithm for action recognition using edit distance with respect to motion templates. The algorithm reduces the number of active nodes during every classification decision. We present our results using data collected from five normal subjects performing transitional movements. The results clearly illustrate the effectiveness of our framework. In particular, we obtain a classification accuracy of 84.13% with only one sensor node involved in the classification process.

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

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

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

Qiu, J; Yang, D

2015-06-15

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets,more » and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from Varian Medical System.« less

Brief Report: Imaginative Drawing in Children with Autism Spectrum Disorder and Learning Disabilities

ERIC Educational Resources Information Center

Allen, Melissa L.; Craig, Eleanore

2016-01-01

Here we examine imaginative drawing abilities in children with Autism Spectrum Disorder (ASD) and learning disabilities (LD) under several conditions: spontaneous production, with use of a template, and combining two real entities to form an "unreal" entity. Sixteen children in each group, matched on mental and chronological age, were…

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.

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.

Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR.

PubMed Central

Huang, M M; Arnheim, N; Goodman, M F

1992-01-01

Thermus aquaticus (Taq) DNA polymerase was used to measure the extension efficiency for all configurations of matched and mismatched base pairs at template-primer 3'-termini. The transition mispairs, A(primer).C, C.A, G.T, and T.G were extended 10(-3) to 10(-4)-fold less efficiently than their correctly paired counterparts. Relative efficiencies for extending transversion mispairs were 10(-4) to 10(-5) for T.C and T.T, about 10(-6) for A.A, and less than 10(-6) for G.A, A.G, G.G and C.C. The transversion mispair C(primer).T was extended with high efficiency, about 10(-2) compared to a correct A.T basepair. The unexpected ease of extending the C.T mismatch was not likely to have been caused by primer-template misalignment. Taq polymerase was observed to bind with similar affinities to each of the correctly paired and mispaired primer-template 3'-ends. Thus, the failure of Taq polymerase to extend mismatches efficiently appears to be an intrinsic property of the enzyme and not due to an inability to bind to 3'-terminal mispairs. For almost all of the mispairs, C.T being the exception, Taq polymerase exhibits about 100 to 1000-fold greater discrimination against mismatch extension compared to avian myeloblastosis reverse transcriptase and HIV-1 reverse transcriptase which extend most mismatched basepairs permissively. Relative mismatch extension efficiencies for Taq polymerase were measured at 45 degrees C, 55 degrees C and 70 degrees C and found to be independent of temperature. The mispair extension data should be important in designing experiments using PCR to distinguish between sequences that vary by a single nucleotide. Images PMID:1408758

Impaired capacity of cerebellar patients to perceive and learn two-dimensional shapes based on kinesthetic cues.

PubMed

Shimansky, Y; Saling, M; Wunderlich, D A; Bracha, V; Stelmach, G E; Bloedel, J R

1997-01-01

This study addresses the issue of the role of the cerebellum in the processing of sensory information by determining the capability of cerebellar patients to acquire and use kinesthetic cues received via the active or passive tracing of an irregular shape while blindfolded. Patients with cerebellar lesions and age-matched healthy controls were tested on four tasks: (1) learning to discriminate a reference shape from three others through the repeated tracing of the reference template; (2) reproducing the reference shape from memory by drawing blindfolded; (3) performing the same task with vision; and (4) visually recognizing the reference shape. The cues used to acquire and then to recognize the reference shape were generated under four conditions: (1) "active kinesthesia," in which cues were acquired by the blindfolded subject while actively tracing a reference template; (2) "passive kinesthesia," in which the tracing was performed while the hand was guided passively through the template; (3) "sequential vision," in which the shape was visualized by the serial exposure of small segments of its outline; and (4) "full vision," in which the entire shape was visualized. The sequential vision condition was employed to emulate the sequential way in which kinesthetic information is acquired while tracing the reference shape. The results demonstrate a substantial impairment of cerebellar patients in their capability to perceive two-dimensional irregular shapes based only on kinesthetic cues. There also is evidence that this deficit in part relates to a reduced capacity to integrate temporal sequences of sensory cues into a complete image useful for shape discrimination tasks or for reproducing the shape through drawing. Consequently, the cerebellum has an important role in this type of sensory information processing even when it is not directly associated with the execution of movements.

Automatic vertebral bodies detection of x-ray images using invariant multiscale template matching

NASA Astrophysics Data System (ADS)

Sharifi Sarabi, Mona; Villaroman, Diane; Beckett, Joel; Attiah, Mark; Marcus, Logan; Ahn, Christine; Babayan, Diana; Gaonkar, Bilwaj; Macyszyn, Luke; Raghavendra, Cauligi

2017-03-01

Lower back pain and pathologies related to it are one of the most common results for a referral to a neurosurgical clinic in the developed and the developing world. Quantitative evaluation of these pathologies is a challenge. Image based measurements of angles/vertebral heights and disks could provide a potential quantitative biomarker for tracking and measuring these pathologies. Detection of vertebral bodies is a key element and is the focus of the current work. From the variety of medical imaging techniques, MRI and CT scans have been typically used for developing image segmentation methods. However, CT scans are known to give a large dose of x-rays, increasing cancer risk [8]. MRI can be substituted for CTs when the risk is high [8] but are difficult to obtain in smaller facilities due to cost and lack of expertise in the field [2]. X-rays provide another option with its ability to control the x-ray dosage, especially for young people, and its accessibility for smaller facilities. Hence, the ability to create quantitative biomarkers from x-ray data is especially valuable. Here, we develop a multiscale template matching, inspired by [9], to detect centers of vertebral bodies from x-ray data. The immediate application of such detection lies in developing quantitative biomarkers and in querying similar images in a database. Previously, shape similarity classification methods have been used to address this problem, but these are challenging to use in the presence of variation due to gross pathology and even subtle effects [1].

DNA sequence requirements for the accurate transcription of a protein-coding plastid gene in a plastid in vitro system from mustard (Sinapis alba L.)

PubMed Central

Link, Gerhard

1984-01-01

A nuclease-treated plastid extract from mustard (Sinapis alba L.) allows efficient transcription of cloned plastid DNA templates. In this in vitro system, the major runoff transcript of the truncated gene for the 32 000 mol. wt. photosystem II protein was accurately initiated from a site close to or identical with the in vivo start site. By using plasmids with deletions in the 5'-flanking region of this gene as templates, a DNA region required for efficient and selective initiation was detected ˜28-35 nucleotides upstream of the transcription start site. This region contains the sequence element TTGACA, which matches the consensus sequence for prokaryotic `−35' promoter elements. In the absence of this region, a region ˜13-27 nucleotides upstream of the start site still enables a basic level of specific transcription. This second region contains the sequence element TATATAA, which matches the consensus sequence for the `TATA' box of genes transcribed by RNA polymerase II (or B). The region between the `TATA'-like element and the transcription start site is not sufficient but may be required for specific transcription of the plastid gene. This latter region contains the sequence element TATACT, which resembles the prokaryotic `−10' (Pribnow) box. Based on the structural and transcriptional features of the 5' upstream region, a `promoter switch' mechanism is proposed, which may account for the developmentally regulated expression of this plastid gene. ImagesFig. 1.Fig. 2.Fig. 3.Fig. 4.Figure 5. PMID:16453540

Detection of high-frequency radiation sources during the 2004 Parkfield earthquake by a matched filter analysis

NASA Astrophysics Data System (ADS)

Uchide, T.; Shearer, P. M.

2009-12-01

Introduction Uchide and Ide [SSA Spring Meeting, 2009] proposed a new framework for studying the scaling and overall nature of earthquake rupture growth in terms of cumulative moment functions. For better understanding of rupture growth processes, spatiotemporally local processes are also important. The nature of high-frequency (HF) radiation has been investigated for some time, but its role in the earthquake rupture process is still unclear. A wavelet analysis reveals that the HF radiation (e.g., 4 - 32 Hz) of the 2004 Parkfield earthquake is peaky, which implies that the sources of the HF radiation are isolated in space and time. We experiment with applying a matched filter analysis using small template events occurring near the target event rupture area to test whether it can reveal the HF radiation sources for a regular large earthquake. Method We design a matched filter for multiple components and stations. Shelly et al. [2007] attempted identifying low-frequency earthquakes (LFE) in non-volcanic tremor waveforms by stacking the correlation coefficients (CC) between the seismograms of the tremor and the LFE. Differing from their method, our event detection indicator is the CC between the seismograms of the target and template events recorded at the same stations, since the key information for detecting the sources will be the arrival-time differences and the amplitude ratios among stations. Data from both the target and template events are normalized by the maximum amplitude of the seismogram of the template event in the cross-correlation time window. This process accounts for the radiation pattern and distance between the source and stations. At each small earthquake target, high values in the CC time series suggest the possibility of HF radiation during the mainshock rupture from a similar location to the target event. Application to the 2004 Parkfield earthquake We apply the matched filter method to the 2004 Parkfield earthquake (Mw 6.0). We use seismograms recorded at the 13 stations of UPSAR [Fletcher et al, 1992]. At each station, both acceleration and velocity sensors are installed, therefore both large and small earthquakes are observable. We employ 184 earthquakes (M 2.0 - 3.5) as template events, and 0.5 s of the P waves on the vertical components and the S waves on all three components. The data are bandpass-filtered between 4 and 16 Hz. One source is detected at 4 s and 12 km northwest from the hypocenter. Although the CC has generally low values, its peak is more than five times larger than its standard deviation and thus remarkably high. This source is close to the secondary onset revealed by a back-projection analysis of 2 - 8 Hz data from Parkfield strong motion stations [Allmann and Shearer, 2007]. While the back-projection approach images the peak of HF radiation, our method detects the onset time, which is slightly different. Another source is located at 1.2 s and 2 km southeast from the hypocenter, which may correspond to deceleration of the initial rupture. Comparisons of the derived HF radiation sources to the whole rupture process will help us reveal general earthquake source dynamics.

Matched Filter Detection of Microseismicity at Ngatamariki and Rotokawa Geothermal Fields, Central North Island, New Zealand

NASA Astrophysics Data System (ADS)

Hopp, C. J.; Savage, M. K.; Townend, J.; Sherburn, S.

2016-12-01

Monitoring patterns in local microseismicity gives clues to the existence and location of subsurface structures. In the context of a geothermal reservoir, subsurface structures often indicate areas of high permeability and are vitally important in understanding fluid flow within the geothermal resource. Detecting and locating microseismic events within an area of power generation, however, is often challenging due to high levels of noise associated with nearby power plant infrastructure. In this situation, matched filter detection improves drastically upon standard earthquake detection techniques, specifically when events are likely induced by fluid injection and are therefore near-repeating. Using an earthquake catalog of 637 events which occurred between 1 January and 18 November 2015 as our initial dataset, we implemented a matched filtering routine for the Mighty River Power (MRP) geothermal fields at Rotokawa and Ngatamariki, central North Island, New Zealand. We detected nearly 21,000 additional events across both geothermal fields, a roughly 30-fold increase from the original catalog. On average, each of the 637 template events detected 45 additional events throughout the study period, with a maximum number of additional detections for a single template of 359. Cumulative detection rates for all template events, in general, do not mimic large scale changes in injection rates within the fields, however we do see indications of an increase in detection rate associated with power plant shutdown at Ngatamariki. Locations of detected events follow established patterns of historic seismicity at both Ngatamariki and Rotokawa. One large cluster of events persists in the southeastern portion of Rotokawa and is likely bounded to the northwest by a known fault dividing the injection and production sections of the field. Two distinct clusters of microseismicity occur in the North and South of Ngatamariki, the latter appearing to coincide with a structure dividing the production zone and the southern injection zone.

Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches

PubMed Central

Green, Stefan J.; Venkatramanan, Raghavee; Naqib, Ankur

2015-01-01

The polymerase chain reaction (PCR) is sensitive to mismatches between primer and template, and mismatches can lead to inefficient amplification of targeted regions of DNA template. In PCRs in which a degenerate primer pool is employed, each primer can behave differently. Therefore, inefficiencies due to different primer melting temperatures within a degenerate primer pool, in addition to mismatches between primer binding sites and primers, can lead to a distortion of the true relative abundance of targets in the original DNA pool. A theoretical analysis indicated that a combination of primer-template and primer-amplicon interactions during PCR cycles 3–12 is potentially responsible for this distortion. To test this hypothesis, we developed a novel amplification strategy, entitled “Polymerase-exonuclease (PEX) PCR”, in which primer-template interactions and primer-amplicon interactions are separated. The PEX PCR method substantially and significantly improved the evenness of recovery of sequences from a mock community of known composition, and allowed for amplification of templates with introduced mismatches near the 3’ end of the primer annealing sites. When the PEX PCR method was applied to genomic DNA extracted from complex environmental samples, a significant shift in the observed microbial community was detected. Furthermore, the PEX PCR method provides a mechanism to identify which primers in a primer pool are annealing to target gDNA. Primer utilization patterns revealed that at high annealing temperatures in the PEX PCR method, perfect match annealing predominates, while at lower annealing temperatures, primers with up to four mismatches with templates can contribute substantially to amplification. The PEX PCR method is simple to perform, is limited to PCR mixes and a single exonuclease step which can be performed without reaction cleanup, and is recommended for reactions in which degenerate primer pools are used or when mismatches between primers and template are possible. PMID:25996930

Cross-Sectional Elasticity Imaging of Arterial Wall by Comparing Measured Change in Thickness with Model Waveform

NASA Astrophysics Data System (ADS)

Tang, Jiang; Hasegawa, Hideyuki; Kanai, Hiroshi

2005-06-01

For the assessment of the elasticity of the arterial wall, we have developed the phased tracking method [H. Kanai et al.: IEEE Trans. Ultrason. Ferroelectr. Freq. Control 43 (1996) 791] for measuring the minute change in thickness due to heartbeats and the elasticity of the arterial wall with transcutaneous ultrasound. For various reasons, for example, an extremely small deformation of the wall, the minute change in wall thickness during one heartbeat is largely influenced by noise in these cases and the reliability of the elasticity distribution obtained from the maximum change in thickness deteriorates because the maximum value estimation is largely influenced by noise. To obtain a more reliable cross-sectional image of the elasticity of the arterial wall, in this paper, a matching method is proposed to evaluate the waveform of the measured change in wall thickness by comparing the measured waveform with a template waveform. The maximum deformation, which is used in the calculation of elasticity, was determined from the amplitude of the matched model waveform to reduce the influence of noise. The matched model waveform was obtained by minimizing the difference between the measured and template waveforms. Furthermore, a random error, which was obtained from the reproducibility among the heartbeats of the measured waveform, was considered useful for the evaluation of the reliability of the measured waveform.

Patient specific computerized phantoms to estimate dose in pediatric CT

NASA Astrophysics Data System (ADS)

Segars, W. P.; Sturgeon, G.; Li, X.; Cheng, L.; Ceritoglu, C.; Ratnanather, J. T.; Miller, M. I.; Tsui, B. M. W.; Frush, D.; Samei, E.

2009-02-01

We create a series of detailed computerized phantoms to estimate patient organ and effective dose in pediatric CT and investigate techniques for efficiently creating patient-specific phantoms based on imaging data. The initial anatomy of each phantom was previously developed based on manual segmentation of pediatric CT data. Each phantom was extended to include a more detailed anatomy based on morphing an existing adult phantom in our laboratory to match the framework (based on segmentation) defined for the target pediatric model. By morphing a template anatomy to match the patient data in the LDDMM framework, it was possible to create a patient specific phantom with many anatomical structures, some not visible in the CT data. The adult models contain thousands of defined structures that were transformed to define them in each pediatric anatomy. The accuracy of this method, under different conditions, was tested using a known voxelized phantom as the target. Errors were measured in terms of a distance map between the predicted organ surfaces and the known ones. We also compared calculated dose measurements to see the effect of different magnitudes of errors in morphing. Despite some variations in organ geometry, dose measurements from morphing predictions were found to agree with those calculated from the voxelized phantom thus demonstrating the feasibility of our methods.

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.

GALAHAD: 1. Pharmacophore identification by hypermolecular alignment of ligands in 3D

NASA Astrophysics Data System (ADS)

Richmond, Nicola J.; Abrams, Charlene A.; Wolohan, Philippa R. N.; Abrahamian, Edmond; Willett, Peter; Clark, Robert D.

2006-09-01

Alignment of multiple ligands based on shared pharmacophoric and pharmacosteric features is a long-recognized challenge in drug discovery and development. This is particularly true when the spatial overlap between structures is incomplete, in which case no good template molecule is likely to exist. Pair-wise rigid ligand alignment based on linear assignment (the LAMDA algorithm) has the potential to address this problem (Richmond et al. in J Mol Graph Model 23:199-209, 2004). Here we present the version of LAMDA embodied in the GALAHAD program, which carries out multi-way alignments by iterative construction of hypermolecules that retain the aggregate as well as the individual attributes of the ligands. We have also generalized the cost function from being purely atom-based to being one that operates on ionic, hydrogen bonding, hydrophobic and steric features. Finally, we have added the ability to generate useful partial-match 3D search queries from the hypermolecules obtained. By running frozen conformations through the GALAHAD program, one can utilize the extended version of LAMDA to generate pharmacophores and pharmacosteres that agree well with crystal structure alignments for a range of literature datasets, with minor adjustments of the default parameters generating even better models. Allowing for inclusion of partial match constraints in the queries yields pharmacophores that are consistently a superset of full-match pharmacophores identified in previous analyses, with the additional features representing points of potentially beneficial interaction with the target.

The shape of the face template: geometric distortions of faces and their detection in natural scenes.

PubMed

Pongakkasira, Kaewmart; Bindemann, Markus

2015-04-01

Human face detection might be driven by skin-coloured face-shaped templates. To explore this idea, this study compared the detection of faces for which the natural height-to-width ratios were preserved with distorted faces that were stretched vertically or horizontally. The impact of stretching on detection performance was not obvious when faces were equated to their unstretched counterparts in terms of their height or width dimension (Experiment 1). However, stretching impaired detection when the original and distorted faces were matched for their surface area (Experiment 2), and this was found with both vertically and horizontally stretched faces (Experiment 3). This effect was evident in accuracy, response times, and also observers' eye movements to faces. These findings demonstrate that height-to-width ratios are an important component of the cognitive template for face detection. The results also highlight important differences between face detection and face recognition. Copyright © 2015 Elsevier Ltd. All rights reserved.

Tectonic tremor and LFEs on a reverse fault in Taiwan

DOE PAGES

Aguiar, Ana C.; Chao, Kevin; Beroza, Gregory C.

2017-06-16

In this paper, we compare low-frequency earthquakes (LFEs) from triggered and ambient tremor under the southern Central Range, Taiwan. We apply the PageRank algorithm used by Aguiar and Beroza (2014) that exploits the repetitive nature of the LFEs to find repeating LFEs in both ambient and triggered tremor. We use these repeaters to create LFE templates and find that the templates created from both tremor types are very similar. To test their similarity, we use both interchangeably and find that most of both the ambient and triggered tremor match the LFE templates created from either data set, suggesting that LFEsmore » for both events have a common origin. Finally, we locate the LFEs by using local earthquake P wave and S wave information and find that LFEs from triggered and ambient tremor locate to between 20 and 35 km on what we interpret as the deep extension of the Chaochou-Lishan Fault.« less

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.

Signal detection by means of orthogonal decomposition

NASA Astrophysics Data System (ADS)

Hajdu, C. F.; Dabóczi, T.; Péceli, G.; Zamantzas, C.

2018-03-01

Matched filtering is a well-known method frequently used in digital signal processing to detect the presence of a pattern in a signal. In this paper, we suggest a time variant matched filter, which, unlike a regular matched filter, maintains a given alignment between the input signal and the template carrying the pattern, and can be realized recursively. We introduce a method to synchronize the two signals for presence detection, usable in case direct synchronization between the signal generator and the receiver is not possible or not practical. We then propose a way of realizing and extending the same filter by modifying a recursive spectral observer, which gives rise to orthogonal filter channels and also leads to another way to synchronize the two signals.

An iterative matching and locating technique for borehole microseismic monitoring

NASA Astrophysics Data System (ADS)

Chen, H.; Meng, X.; Niu, F.; Tang, Y.

2016-12-01

Microseismic monitoring has been proven to be an effective and valuable technology to image hydraulic fracture geometry. The success of hydraulic fracturing monitoring relies on the detection and characterization (i.e., location and focal mechanism estimation) of a maximum number of induced microseismic events. All the events are important to quantify the stimulated reservior volume (SRV) and characterize the newly created fracture network. Detecting and locating low magnitude events, however, are notoriously difficult, particularly at a high noisy production environment. Here we propose an iterative matching and locating technique (iMLT) to obtain a maximum detection of small events and the best determination of their locations from continuous data recorded by a single azimuth downhole geophone array. As the downhole array is located in one azimuth, the regular M&L using the P-wave cross-correlation only is not able to resolve the location of a matched event relative to the template event. We thus introduce the polarization direction in the matching, which significantly improve the lateral resolution of the M&L method based on numerical simulations with synthetic data. Our synthetic tests further indicate that the inclusion of S-wave cross-correlation data can help better constrain the focal depth of the matched events. We apply this method to a dataset recorded during hydraulic fracturing treatment of a pilot horizontal well within the shale play in southwest China. Our approach yields a more than fourfold increase in the number of located events, compared with the original event catalog from traditional downhole processing.

Kinect-based sign language recognition of static and dynamic hand movements

NASA Astrophysics Data System (ADS)

Dalawis, Rando C.; Olayao, Kenneth Deniel R.; Ramos, Evan Geoffrey I.; Samonte, Mary Jane C.

2017-02-01

A different approach of sign language recognition of static and dynamic hand movements was developed in this study using normalized correlation algorithm. The goal of this research was to translate fingerspelling sign language into text using MATLAB and Microsoft Kinect. Digital input image captured by Kinect devices are matched from template samples stored in a database. This Human Computer Interaction (HCI) prototype was developed to help people with communication disability to express their thoughts with ease. Frame segmentation and feature extraction was used to give meaning to the captured images. Sequential and random testing was used to test both static and dynamic fingerspelling gestures. The researchers explained some factors they encountered causing some misclassification of signs.

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.

Nucleic acid amplification using modular branched primers

DOEpatents

Ulanovsky, Levy; Raja, Mugasimangalam C.

2001-01-01

Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

Liquid foam templating - A route to tailor-made polymer foams.

PubMed

Andrieux, Sébastien; Quell, Aggeliki; Stubenrauch, Cosima; Drenckhan, Wiebke

2018-06-01

Solid foams with pore sizes between a few micrometres and a few millimetres are heavily exploited in a wide range of established and emerging applications. While the optimisation of foam applications requires a fine control over their structural properties (pore size distribution, pore opening, foam density, …), the great complexity of most foaming processes still defies a sound scientific understanding and therefore explicit control and prediction of these parameters. We therefore need to improve our understanding of existing processes and also develop new fabrication routes which we understand and which we can exploit to tailor-make new porous materials. One of these new routes is liquid templating in general and liquid foam templating in particular, to which this review article is dedicated. While all solid foams are generated from an initially liquid(-like) state, the particular notion of liquid foam templating implies the specific condition that the liquid foam has time to find its "equilibrium structure" before it is solidified. In other words, the characteristic time scales of the liquid foam's stability and its solidification are well separated, allowing to build on the vast know-how on liquid foams established over the last 20 years. The dispersed phase of the liquid foam determines the final pore size and pore size distribution, while the continuous phase contains the precursors of the desired porous scaffold. We review here the three key challenges which need to be addressed by this approach: (1) the control of the structure of the liquid template, (2) the matching of the time scales between the stability of the liquid template and solidification, and (3) the preservation of the structure of the template throughout the process. Focusing on the field of polymer foams, this review gives an overview of recent research on the properties of liquid foam templates and summarises a key set of studies in the emerging field of liquid foam templating. It finishes with an outlook on future developments. Occasional references to non-polymeric foams are given if the analogy provides specific insight into a physical phenomenon. Copyright © 2018 Elsevier B.V. All rights reserved.

Image registration algorithm for high-voltage electric power live line working robot based on binocular vision

NASA Astrophysics Data System (ADS)

Li, Chengqi; Ren, Zhigang; Yang, Bo; An, Qinghao; Yu, Xiangru; Li, Jinping

2017-12-01

In the process of dismounting and assembling the drop switch for the high-voltage electric power live line working (EPL2W) robot, one of the key problems is the precision of positioning for manipulators, gripper and the bolts used to fix drop switch. To solve it, we study the binocular vision system theory of the robot and the characteristic of dismounting and assembling drop switch. We propose a coarse-to-fine image registration algorithm based on image correlation, which can improve the positioning precision of manipulators and bolt significantly. The algorithm performs the following three steps: firstly, the target points are marked respectively in the right and left visions, and then the system judges whether the target point in right vision can satisfy the lowest registration accuracy by using the similarity of target points' backgrounds in right and left visions, this is a typical coarse-to-fine strategy; secondly, the system calculates the epipolar line, and then the regional sequence existing matching points is generated according to neighborhood of epipolar line, the optimal matching image is confirmed by calculating the similarity between template image in left vision and the region in regional sequence according to correlation matching; finally, the precise coordinates of target points in right and left visions are calculated according to the optimal matching image. The experiment results indicate that the positioning accuracy of image coordinate is within 2 pixels, the positioning accuracy in the world coordinate system is within 3 mm, the positioning accuracy of binocular vision satisfies the requirement dismounting and assembling the drop switch.

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…

A Spatially and Temporally Continuous LFE Catalogue for the Southern Alps, New Zealand

NASA Astrophysics Data System (ADS)

Chamberlain, C. J.; Townend, J.; Baratin, L. M.

2015-12-01

Using a brightness-based beamforming approach coupled with a matched-filter correlation method, we have developed a 6.5 year record of low-frequency earthquakes (LFEs) occuring on and near the deep extent of New Zealand's Alpine Fault. Our brightness template detection method, based on that of Frank et al. (2014), scans a pre-determined grid of possible seismic sources to automatically find LFE templates based on the stack of bandpassed squared seismic data. Previous work (Wech et al., 2012, Chamberlain et al., 2014) has shown that the depths of standard seismicity are anti-correlated with those of tremor and LFEs in the central Southern Alps: hence, by careful grid selection, shallow seismic sources can effectively be discriminated against. This beamforming approach produces many (>900) possible events. Initial beamforming detections are grouped by moveout and stacked to produce a subset of higher-quality events for use as templates in a cross-correlation detector. Events detected by cross-correlation are stacked to increase their signal-to-noise charectaristics before being located using a 3D velocity model. This method produces a spatially and temporally continuous catalogue of LFEs throughout the 6.5 year study period. The catalogue highlights quasi-continuous slow deformation occuring beneath the seismogenic zone near the Alpine Fault, punctuated by periods of increased LFE generation associated with tremor, and following large regional earthquakes. To date we have found no evidence of LFE generation north-east of Mt. Cook, the highest point in the Southern Alps, despite systematic searching throughout the region. We suggest that the along-strike cessation of tremor is due to changes in the fault's dip and the hypothesised presence of partially subducted passive margin material. This remnant passive margin would lie benath the tremor-generating region and has been linked to along-strike changes in subcrustal earthquake distributions (Boese et al., 2013).

Multi-template tensor-based morphometry: Application to analysis of Alzheimer's disease

PubMed Central

Koikkalainen, Juha; Lötjönen, Jyrki; Thurfjell, Lennart; Rueckert, Daniel; Waldemar, Gunhild; Soininen, Hilkka

2012-01-01

In this paper methods for using multiple templates in tensor-based morphometry (TBM) are presented and comparedtothe conventional single-template approach. TBM analysis requires non-rigid registrations which are often subject to registration errors. When using multiple templates and, therefore, multiple registrations, it can be assumed that the registration errors are averaged and eventually compensated. Four different methods are proposed for multi-template TBM. The methods were evaluated using magnetic resonance (MR) images of healthy controls, patients with stable or progressive mild cognitive impairment (MCI), and patients with Alzheimer's disease (AD) from the ADNI database (N=772). The performance of TBM features in classifying images was evaluated both quantitatively and qualitatively. Classification results show that the multi-template methods are statistically significantly better than the single-template method. The overall classification accuracy was 86.0% for the classification of control and AD subjects, and 72.1%for the classification of stable and progressive MCI subjects. The statistical group-level difference maps produced using multi-template TBM were smoother, formed larger continuous regions, and had larger t-values than the maps obtained with single-template TBM. PMID:21419228

Synthesis and Characterization of Templated Ion Exchange Resins for the Selective Complexion of Actinide Ions

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

Murrray, George M.; Uy, O. Manuel

The purpose of this research is to develop polymeric extractants for the selective complexation of uranyl ions (and subsequently other actinyl and actinide ions) from aqueous solutions. Selectivity for a specific actinide ion is obtained by providing the polymers with cavities lined with complexing ligands so arranged as to match the charge, coordination number, coordination geometry, and size of the actinide ion. These cavity-containing polymers are produced by using a specific actinide ion (or surrogate) as a template around which monomeric complexing ligands are polymerized. The polymers provide useful sequestering agents for removing actinide ions from wastes and will formmore » the basis for a variety of analytical techniques for actinide determination.« less

Fabrication of Nonperiodic Metasurfaces by Microlens Projection Lithography.

PubMed

Gonidec, Mathieu; Hamedi, Mahiar M; Nemiroski, Alex; Rubio, Luis M; Torres, Cesar; Whitesides, George M

2016-07-13

This paper describes a strategy that uses template-directed self-assembly of micrometer-scale microspheres to fabricate arrays of microlenses for projection photolithography of periodic, quasiperiodic, and aperiodic infrared metasurfaces. This method of "template-encoded microlens projection lithography" (TEMPL) enables rapid prototyping of planar, multiscale patterns of similarly shaped structures with critical dimensions down to ∼400 nm. Each of these structures is defined by local projection lithography with a single microsphere acting as a lens. This paper explores the use of TEMPL for the fabrication of a broad range of two-dimensional lattices with varying types of nonperiodic spatial distribution. The matching optical spectra of the fabricated and simulated metasurfaces confirm that TEMPL can produce structures that conform to expected optical behavior.

Object Tracking and Target Reacquisition Based on 3-D Range Data for Moving Vehicles

PubMed Central

Lee, Jehoon; Lankton, Shawn; Tannenbaum, Allen

2013-01-01

In this paper, we propose an approach for tracking an object of interest based on 3-D range data. We employ particle filtering and active contours to simultaneously estimate the global motion of the object and its local deformations. The proposed algorithm takes advantage of range information to deal with the challenging (but common) situation in which the tracked object disappears from the image domain entirely and reappears later. To cope with this problem, a method based on principle component analysis (PCA) of shape information is proposed. In the proposed method, if the target disappears out of frame, shape similarity energy is used to detect target candidates that match a template shape learned online from previously observed frames. Thus, we require no a priori knowledge of the target’s shape. Experimental results show the practical applicability and robustness of the proposed algorithm in realistic tracking scenarios. PMID:21486717

Vehicle detection and orientation estimation using the radon transform

NASA Astrophysics Data System (ADS)

Pelapur, Rengarajan; Bunyak, Filiz; Palaniappan, Kannappan; Seetharaman, Gunasekaran

2013-05-01

Determining the location and orientation of vehicles in satellite and airborne imagery is a challenging task given the density of cars and other vehicles and complexity of the environment in urban scenes almost anywhere in the world. We have developed a robust and accurate method for detecting vehicles using a template-based directional chamfer matching, combined with vehicle orientation estimation based on a refined segmentation, followed by a Radon transform based profile variance peak analysis approach. The same algorithm was applied to both high resolution satellite imagery and wide area aerial imagery and initial results show robustness to illumination changes and geometric appearance distortions. Nearly 80% of the orientation angle estimates for 1585 vehicles across both satellite and aerial imagery were accurate to within 15? of the ground truth. In the case of satellite imagery alone, nearly 90% of the objects have an estimated error within +/-1.0° of the ground truth.

Machine vision application in animal trajectory tracking.

PubMed

Koniar, Dušan; Hargaš, Libor; Loncová, Zuzana; Duchoň, František; Beňo, Peter

2016-04-01

This article was motivated by the doctors' demand to make a technical support in pathologies of gastrointestinal tract research [10], which would be based on machine vision tools. Proposed solution should be less expensive alternative to already existing RF (radio frequency) methods. The objective of whole experiment was to evaluate the amount of animal motion dependent on degree of pathology (gastric ulcer). In the theoretical part of the article, several methods of animal trajectory tracking are presented: two differential methods based on background subtraction, the thresholding methods based on global and local threshold and the last method used for animal tracking was the color matching with a chosen template containing a searched spectrum of colors. The methods were tested offline on five video samples. Each sample contained situation with moving guinea pig locked in a cage under various lighting conditions. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Secure and Robust Iris Recognition Using Random Projections and Sparse Representations.

PubMed

Pillai, Jaishanker K; Patel, Vishal M; Chellappa, Rama; Ratha, Nalini K

2011-09-01

Noncontact biometrics such as face and iris have additional benefits over contact-based biometrics such as fingerprint and hand geometry. However, three important challenges need to be addressed in a noncontact biometrics-based authentication system: ability to handle unconstrained acquisition, robust and accurate matching, and privacy enhancement without compromising security. In this paper, we propose a unified framework based on random projections and sparse representations, that can simultaneously address all three issues mentioned above in relation to iris biometrics. Our proposed quality measure can handle segmentation errors and a wide variety of possible artifacts during iris acquisition. We demonstrate how the proposed approach can be easily extended to handle alignment variations and recognition from iris videos, resulting in a robust and accurate system. The proposed approach includes enhancements to privacy and security by providing ways to create cancelable iris templates. Results on public data sets show significant benefits of the proposed approach.

A spline-based regression parameter set for creating customized DARTEL MRI brain templates from infancy to old age.

PubMed

Wilke, Marko

2018-02-01

This dataset contains the regression parameters derived by analyzing segmented brain MRI images (gray matter and white matter) from a large population of healthy subjects, using a multivariate adaptive regression splines approach. A total of 1919 MRI datasets ranging in age from 1-75 years from four publicly available datasets (NIH, C-MIND, fCONN, and IXI) were segmented using the CAT12 segmentation framework, writing out gray matter and white matter images normalized using an affine-only spatial normalization approach. These images were then subjected to a six-step DARTEL procedure, employing an iterative non-linear registration approach and yielding increasingly crisp intermediate images. The resulting six datasets per tissue class were then analyzed using multivariate adaptive regression splines, using the CerebroMatic toolbox. This approach allows for flexibly modelling smoothly varying trajectories while taking into account demographic (age, gender) as well as technical (field strength, data quality) predictors. The resulting regression parameters described here can be used to generate matched DARTEL or SHOOT templates for a given population under study, from infancy to old age. The dataset and the algorithm used to generate it are publicly available at https://irc.cchmc.org/software/cerebromatic.php.

Engineering Lipid Bilayer Membranes for Protein Studies

PubMed Central

Khan, Muhammad Shuja; Dosoky, Noura Sayed; Williams, John Dalton

2013-01-01

Lipid membranes regulate the flow of nutrients and communication signaling between cells and protect the sub-cellular structures. Recent attempts to fabricate artificial systems using nanostructures that mimic the physiological properties of natural lipid bilayer membranes (LBM) fused with transmembrane proteins have helped demonstrate the importance of temperature, pH, ionic strength, adsorption behavior, conformational reorientation and surface density in cellular membranes which all affect the incorporation of proteins on solid surfaces. Much of this work is performed on artificial templates made of polymer sponges or porous materials based on alumina, mica, and porous silicon (PSi) surfaces. For example, porous silicon materials have high biocompatibility, biodegradability, and photoluminescence, which allow them to be used both as a support structure for lipid bilayers or a template to measure the electrochemical functionality of living cells grown over the surface as in vivo. The variety of these media, coupled with the complex physiological conditions present in living systems, warrant a summary and prospectus detailing which artificial systems provide the most promise for different biological conditions. This study summarizes the use of electrochemical impedance spectroscopy (EIS) data on artificial biological membranes that are closely matched with previously published biological systems using both black lipid membrane and patch clamp techniques. PMID:24185908

Modulation of Posterior Alpha Activity by Spatial Attention Allows for Controlling A Continuous Brain-Computer Interface.

PubMed

Horschig, Jörn M; Oosterheert, Wouter; Oostenveld, Robert; Jensen, Ole

2015-11-01

Here we report that the modulation of alpha activity by covert attention can be used as a control signal in an online brain-computer interface, that it is reliable, and that it is robust. Subjects were instructed to orient covert visual attention to the left or right hemifield. We decoded the direction of attention from the magnetoencephalogram by a template matching classifier and provided the classification outcome to the subject in real-time using a novel graphical user interface. Training data for the templates were obtained from a Posner-cueing task conducted just before the BCI task. Eleven subjects participated in four sessions each. Eight of the subjects achieved classification rates significantly above chance level. Subjects were able to significantly increase their performance from the first to the second session. Individual patterns of posterior alpha power remained stable throughout the four sessions and did not change with increased performance. We conclude that posterior alpha power can successfully be used as a control signal in brain-computer interfaces. We also discuss several ideas for further improving the setup and propose future research based on solid hypotheses about behavioral consequences of modulating neuronal oscillations by brain computer interfacing.

Semi-automated intra-operative fluoroscopy guidance for osteotomy and external-fixator.

PubMed

Lin, Hong; Samchukov, Mikhail L; Birch, John G; Cherkashin, Alexander

2006-01-01

This paper outlines a semi-automated intra-operative fluoroscopy guidance and monitoring approach for osteotomy and external-fixator application in orthopedic surgery. Intra-operative Guidance module is one component of the "LegPerfect Suite" developed for assisting the surgical correction of lower extremity angular deformity. The Intra-operative Guidance module utilizes information from the preoperative surgical planning module as a guideline to overlay (register) its bone outline semi-automatically with the bone edge from the real-time fluoroscopic C-Arm X-Ray image in the operating room. In the registration process, scaling factor is obtained automatically through matching a fiducial template in the fluoroscopic image and a marker in the module. A triangle metal plate, placed on the operating table is used as fiducial template. The area of template image within the viewing area of the fluoroscopy machine is obtained by the image processing techniques such as edge detection and Hough transformation to extract the template from other objects in the fluoroscopy image. The area of fiducial template from fluoroscopic image is then compared with the area of the marker from the planning so as to obtain the scaling factor. After the scaling factor is obtained, the user can use simple operations by mouse to shift and rotate the preoperative planning to overlay the bone outline from planning with the bone edge from fluoroscopy image. In this way osteotomy levels and external fixator positioning on the limb can guided by the computerized preoperative plan.

Emulating the Visual Receptive Field Properties of MST Neurons with a Template Model of Heading Estimation

NASA Technical Reports Server (NTRS)

Perrone, John A.; Stone, Leland S.

1997-01-01

We have previously proposed a computational neural-network model by which the complex patterns of retinal image motion generated during locomotion (optic flow) can be processed by specialized detectors acting as templates for specific instances of self-motion. The detectors in this template model respond to global optic flow by sampling image motion over a large portion of the visual field through networks of local motion sensors with properties similar to neurons found in the middle temporal (MT) area of primate extrastriate visual cortex. The model detectors were designed to extract self-translation (heading), self-rotation, as well as the scene layout (relative distances) ahead of a moving observer, and are arranged in cortical-like heading maps to perform this function. Heading estimation from optic flow has been postulated by some to be implemented within the medial superior temporal (MST) area. Others have questioned whether MST neurons can fulfill this role because some of their receptive-field properties appear inconsistent with a role in heading estimation. To resolve this issue, we systematically compared MST single-unit responses with the outputs of model detectors under matched stimulus conditions. We found that the basic physiological properties of MST neurons can be explained by the template model. We conclude that MST neurons are well suited to support heading estimation and that the template model provides an explicit set of testable hypotheses which can guide future exploration of MST and adjacent areas within the primate superior temporal sulcus.

Minutiae Matching with Privacy Protection Based on the Combination of Garbled Circuit and Homomorphic Encryption

PubMed Central

Li, Mengxing; Zhao, Jian; Yang, Mei; Kang, Lijun; Wu, Lili

2014-01-01

Biometrics plays an important role in authentication applications since they are strongly linked to holders. With an increasing growth of e-commerce and e-government, one can expect that biometric-based authentication systems are possibly deployed over the open networks in the near future. However, due to its openness, the Internet poses a great challenge to the security and privacy of biometric authentication. Biometric data cannot be revoked, so it is of paramount importance that biometric data should be handled in a secure way. In this paper we present a scheme achieving privacy-preserving fingerprint authentication between two parties, in which fingerprint minutiae matching algorithm is completed in the encrypted domain. To improve the efficiency, we exploit homomorphic encryption as well as garbled circuits to design the protocol. Our goal is to provide protection for the security of template in storage and data privacy of two parties in transaction. The experimental results show that the proposed authentication protocol runs efficiently. Therefore, the protocol can run over open networks and help to alleviate the concerns on security and privacy of biometric applications over the open networks. PMID:24711729

Minutiae matching with privacy protection based on the combination of garbled circuit and homomorphic encryption.

PubMed

Li, Mengxing; Feng, Quan; Zhao, Jian; Yang, Mei; Kang, Lijun; Wu, Lili

2014-01-01

Biometrics plays an important role in authentication applications since they are strongly linked to holders. With an increasing growth of e-commerce and e-government, one can expect that biometric-based authentication systems are possibly deployed over the open networks in the near future. However, due to its openness, the Internet poses a great challenge to the security and privacy of biometric authentication. Biometric data cannot be revoked, so it is of paramount importance that biometric data should be handled in a secure way. In this paper we present a scheme achieving privacy-preserving fingerprint authentication between two parties, in which fingerprint minutiae matching algorithm is completed in the encrypted domain. To improve the efficiency, we exploit homomorphic encryption as well as garbled circuits to design the protocol. Our goal is to provide protection for the security of template in storage and data privacy of two parties in transaction. The experimental results show that the proposed authentication protocol runs efficiently. Therefore, the protocol can run over open networks and help to alleviate the concerns on security and privacy of biometric applications over the open networks.

Evaluation of Anti-HIV-1 Mutagenic Nucleoside Analogues*

PubMed Central

Vivet-Boudou, Valérie; Isel, Catherine; El Safadi, Yazan; Smyth, Redmond P.; Laumond, Géraldine; Moog, Christiane; Paillart, Jean-Christophe; Marquet, Roland

2015-01-01

Because of their high mutation rates, RNA viruses and retroviruses replicate close to the threshold of viability. Their existence as quasi-species has pioneered the concept of “lethal mutagenesis” that prompted us to synthesize pyrimidine nucleoside analogues with antiviral activity in cell culture consistent with an accumulation of deleterious mutations in the HIV-1 genome. However, testing all potentially mutagenic compounds in cell-based assays is tedious and costly. Here, we describe two simple in vitro biophysical/biochemical assays that allow prediction of the mutagenic potential of deoxyribonucleoside analogues. The first assay compares the thermal stabilities of matched and mismatched base pairs in DNA duplexes containing or not the nucleoside analogues as follows. A promising candidate should display a small destabilization of the matched base pair compared with the natural nucleoside and the smallest gap possible between the stabilities of the matched and mismatched base pairs. From this assay, we predicted that two of our compounds, 5-hydroxymethyl-2′-deoxyuridine and 5-hydroxymethyl-2′-deoxycytidine, should be mutagenic. The second in vitro reverse transcription assay assesses DNA synthesis opposite nucleoside analogues inserted into a template strand and subsequent extension of the newly synthesized base pairs. Once again, only 5-hydroxymethyl-2′-deoxyuridine and 5-hydroxymethyl-2′-deoxycytidine are predicted to be efficient mutagens. The predictive potential of our fast and easy first line screens was confirmed by detailed analysis of the mutation spectrum induced by the compounds in cell culture because only compounds 5-hydroxymethyl-2′-deoxyuridine and 5-hydroxymethyl-2′-deoxycytidine were found to increase the mutation frequency by 3.1- and 3.4-fold, respectively. PMID:25398876

Evaluation of anti-HIV-1 mutagenic nucleoside analogues.

PubMed

Vivet-Boudou, Valérie; Isel, Catherine; El Safadi, Yazan; Smyth, Redmond P; Laumond, Géraldine; Moog, Christiane; Paillart, Jean-Christophe; Marquet, Roland

2015-01-02

Because of their high mutation rates, RNA viruses and retroviruses replicate close to the threshold of viability. Their existence as quasi-species has pioneered the concept of "lethal mutagenesis" that prompted us to synthesize pyrimidine nucleoside analogues with antiviral activity in cell culture consistent with an accumulation of deleterious mutations in the HIV-1 genome. However, testing all potentially mutagenic compounds in cell-based assays is tedious and costly. Here, we describe two simple in vitro biophysical/biochemical assays that allow prediction of the mutagenic potential of deoxyribonucleoside analogues. The first assay compares the thermal stabilities of matched and mismatched base pairs in DNA duplexes containing or not the nucleoside analogues as follows. A promising candidate should display a small destabilization of the matched base pair compared with the natural nucleoside and the smallest gap possible between the stabilities of the matched and mismatched base pairs. From this assay, we predicted that two of our compounds, 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine, should be mutagenic. The second in vitro reverse transcription assay assesses DNA synthesis opposite nucleoside analogues inserted into a template strand and subsequent extension of the newly synthesized base pairs. Once again, only 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine are predicted to be efficient mutagens. The predictive potential of our fast and easy first line screens was confirmed by detailed analysis of the mutation spectrum induced by the compounds in cell culture because only compounds 5-hydroxymethyl-2'-deoxyuridine and 5-hydroxymethyl-2'-deoxycytidine were found to increase the mutation frequency by 3.1- and 3.4-fold, respectively. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Very low frequency earthquakes (VLFEs) detected during episodic tremor and slip (ETS) events in Cascadia using a match filter method indicate repeating events

NASA Astrophysics Data System (ADS)

Hutchison, A. A.; Ghosh, A.

2016-12-01

Very low frequency earthquakes (VLFEs) occur in transitional zones of faults, releasing seismic energy in the 0.02-0.05 Hz frequency band over a 90 s duration and typically have magntitudes within the range of Mw 3.0-4.0. VLFEs can occur down-dip of the seismogenic zone, where they can transfer stress up-dip potentially bringing the locked zone closer to a critical failure stress. VLFEs also occur up-dip of the seismogenic zone in a region along the plate interface that can rupture coseismically during large megathrust events, such as the 2011 Tohoku-Oki earthquake [Ide et al., 2011]. VLFEs were first detected in Cascadia during the 2011 episodic tremor and slip (ETS) event, occurring coincidentally with tremor [Ghosh et al., 2015]. However, during the 2014 ETS event, VLFEs were spatially and temporally asynchronous with tremor activity [Hutchison and Ghosh, 2016]. Such contrasting behaviors remind us that the mechanics behind such events remain elusive, yet they are responsible for the largest portion of the moment release during an ETS event. Here, we apply a match filter method using known VLFEs as template events to detect additional VLFEs. Using a grid-search centroid moment tensor inversion method, we invert stacks of the resulting match filter detections to ensure moment tensor solutions are similar to that of the respective template events. Our ability to successfully employ a match filter method to VLFE detection in Cascadia intrinsically indicates that these events can be repeating, implying that the same asperities are likely responsible for generating multiple VLFEs.

Theoretical accuracy in cosmological growth estimation

NASA Astrophysics Data System (ADS)

Bose, Benjamin; Koyama, Kazuya; Hellwing, Wojciech A.; Zhao, Gong-Bo; Winther, Hans A.

2017-07-01

We elucidate the importance of the consistent treatment of gravity-model specific nonlinearities when estimating the growth of cosmological structures from redshift space distortions (RSD). Within the context of standard perturbation theory (SPT), we compare the predictions of two theoretical templates with redshift space data from COLA (comoving Lagrangian acceleration) simulations in the normal branch of DGP gravity (nDGP) and general relativity (GR). Using COLA for these comparisons is validated using a suite of full N-body simulations for the same theories. The two theoretical templates correspond to the standard general relativistic perturbation equations and those same equations modeled within nDGP. Gravitational clustering nonlinear effects are accounted for by modeling the power spectrum up to one-loop order and redshift space clustering anisotropy is modeled using the Taruya, Nishimichi and Saito (TNS) RSD model. Using this approach, we attempt to recover the simulation's fiducial logarithmic growth parameter f . By assigning the simulation data with errors representing an idealized survey with a volume of 10 Gpc3/h3 , we find the GR template is unable to recover fiducial f to within 1 σ at z =1 when we match the data up to kmax=0.195 h /Mpc . On the other hand, the DGP template recovers the fiducial value within 1 σ . Further, we conduct the same analysis for sets of mock data generated for generalized models of modified gravity using SPT, where again we analyze the GR template's ability to recover the fiducial value. We find that for models with enhanced gravitational nonlinearity, the theoretical bias of the GR template becomes significant for stage IV surveys. Thus, we show that for the future large data volume galaxy surveys, the self-consistent modeling of non-GR gravity scenarios will be crucial in constraining theory parameters.

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.

GalaxyTBM: template-based modeling by building a reliable core and refining unreliable local regions.

PubMed

Ko, Junsu; Park, Hahnbeom; Seok, Chaok

2012-08-10

Protein structures can be reliably predicted by template-based modeling (TBM) when experimental structures of homologous proteins are available. However, it is challenging to obtain structures more accurate than the single best templates by either combining information from multiple templates or by modeling regions that vary among templates or are not covered by any templates. We introduce GalaxyTBM, a new TBM method in which the more reliable core region is modeled first from multiple templates and less reliable, variable local regions, such as loops or termini, are then detected and re-modeled by an ab initio method. This TBM method is based on "Seok-server," which was tested in CASP9 and assessed to be amongst the top TBM servers. The accuracy of the initial core modeling is enhanced by focusing on more conserved regions in the multiple-template selection and multiple sequence alignment stages. Additional improvement is achieved by ab initio modeling of up to 3 unreliable local regions in the fixed framework of the core structure. Overall, GalaxyTBM reproduced the performance of Seok-server, with GalaxyTBM and Seok-server resulting in average GDT-TS of 68.1 and 68.4, respectively, when tested on 68 single-domain CASP9 TBM targets. For application to multi-domain proteins, GalaxyTBM must be combined with domain-splitting methods. Application of GalaxyTBM to CASP9 targets demonstrates that accurate protein structure prediction is possible by use of a multiple-template-based approach, and ab initio modeling of variable regions can further enhance the model quality.

Fifty years of progress in speech and speaker recognition

NASA Astrophysics Data System (ADS)

Furui, Sadaoki

2004-10-01

Speech and speaker recognition technology has made very significant progress in the past 50 years. The progress can be summarized by the following changes: (1) from template matching to corpus-base statistical modeling, e.g., HMM and n-grams, (2) from filter bank/spectral resonance to Cepstral features (Cepstrum + DCepstrum + DDCepstrum), (3) from heuristic time-normalization to DTW/DP matching, (4) from gdistanceh-based to likelihood-based methods, (5) from maximum likelihood to discriminative approach, e.g., MCE/GPD and MMI, (6) from isolated word to continuous speech recognition, (7) from small vocabulary to large vocabulary recognition, (8) from context-independent units to context-dependent units for recognition, (9) from clean speech to noisy/telephone speech recognition, (10) from single speaker to speaker-independent/adaptive recognition, (11) from monologue to dialogue/conversation recognition, (12) from read speech to spontaneous speech recognition, (13) from recognition to understanding, (14) from single-modality (audio signal only) to multi-modal (audio/visual) speech recognition, (15) from hardware recognizer to software recognizer, and (16) from no commercial application to many practical commercial applications. Most of these advances have taken place in both the fields of speech recognition and speaker recognition. The majority of technological changes have been directed toward the purpose of increasing robustness of recognition, including many other additional important techniques not noted above.

Generating cancelable fingerprint templates.

PubMed

Ratha, Nalini K; Chikkerur, Sharat; Connell, Jonathan H; Bolle, Ruud M

2007-04-01

Biometrics-based authentication systems offer obvious usability advantages over traditional password and token-based authentication schemes. However, biometrics raises several privacy concerns. A biometric is permanently associated with a user and cannot be changed. Hence, if a biometric identifier is compromised, it is lost forever and possibly for every application where the biometric is used. Moreover, if the same biometric is used in multiple applications, a user can potentially be tracked from one application to the next by cross-matching biometric databases. In this paper, we demonstrate several methods to generate multiple cancelable identifiers from fingerprint images to overcome these problems. In essence, a user can be given as many biometric identifiers as needed by issuing a new transformation "key." The identifiers can be cancelled and replaced when compromised. We empirically compare the performance of several algorithms such as Cartesian, polar, and surface folding transformations of the minutiae positions. It is demonstrated through multiple experiments that we can achieve revocability and prevent cross-matching of biometric databases. It is also shown that the transforms are noninvertible by demonstrating that it is computationally as hard to recover the original biometric identifier from a transformed version as by randomly guessing. Based on these empirical results and a theoretical analysis we conclude that feature-level cancelable biometric construction is practicable in large biometric deployments.

Fast and Robust Registration of Multimodal Remote Sensing Images via Dense Orientated Gradient Feature

NASA Astrophysics Data System (ADS)

Ye, Y.

2017-09-01

This paper presents a fast and robust method for the registration of multimodal remote sensing data (e.g., optical, LiDAR, SAR and map). The proposed method is based on the hypothesis that structural similarity between images is preserved across different modalities. In the definition of the proposed method, we first develop a pixel-wise feature descriptor named Dense Orientated Gradient Histogram (DOGH), which can be computed effectively at every pixel and is robust to non-linear intensity differences between images. Then a fast similarity metric based on DOGH is built in frequency domain using the Fast Fourier Transform (FFT) technique. Finally, a template matching scheme is applied to detect tie points between images. Experimental results on different types of multimodal remote sensing images show that the proposed similarity metric has the superior matching performance and computational efficiency than the state-of-the-art methods. Moreover, based on the proposed similarity metric, we also design a fast and robust automatic registration system for multimodal images. This system has been evaluated using a pair of very large SAR and optical images (more than 20000 × 20000 pixels). Experimental results show that our system outperforms the two popular commercial software systems (i.e. ENVI and ERDAS) in both registration accuracy and computational efficiency.

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

Fast-match on particle swarm optimization with variant system mechanism

NASA Astrophysics Data System (ADS)

Wang, Yuehuang; Fang, Xin; Chen, Jie

2018-03-01

Fast-Match is a fast and effective algorithm for approximate template matching under 2D affine transformations, which can match the target with maximum similarity without knowing the target gesture. It depends on the minimum Sum-of-Absolute-Differences (SAD) error to obtain the best affine transformation. The algorithm is widely used in the field of matching images because of its fastness and robustness. In this paper, our approach is to search an approximate affine transformation over Particle Swarm Optimization (PSO) algorithm. We treat each potential transformation as a particle that possesses memory function. Each particle is given a random speed and flows throughout the 2D affine transformation space. To accelerate the algorithm and improve the abilities of seeking the global excellent result, we have introduced the variant system mechanism on this basis. The benefit is that we can avoid matching with huge amount of potential transformations and falling into local optimal condition, so that we can use a few transformations to approximate the optimal solution. The experimental results prove that our method has a faster speed and a higher accuracy performance with smaller affine transformation space.

Epitaxial growth and characterization of approximately 300-nm-thick AlInN films nearly lattice-matched to c-plane GaN grown on sapphire

NASA Astrophysics Data System (ADS)

Miyoshi, Makoto; Yamanaka, Mizuki; Egawa, Takashi; Takeuchi, Tetsuya

2018-05-01

AlInN epitaxial films with film thicknesses up to approximately 300 nm were grown nearly lattice-matched to a c-plane GaN-on-sapphire template by metalorganic chemical vapor deposition. The AlInN films showed relative good crystal qualities and flat surfaces, despite the existence of surface pits connected to dislocations in the underlying GaN film. The refractive index derived in this study agreed well with a previously reported result obtained over the whole visible wavelength region. The extinction coefficient spectrum exhibited a clear absorption edge, and the bandgap energy for AlInN nearly lattice-matched to GaN was determined to be approximately 4.0 eV.

Testosterone treatment and MMPI-2 improvement in transgender men: a prospective controlled study.

PubMed

Keo-Meier, Colton L; Herman, Levi I; Reisner, Sari L; Pardo, Seth T; Sharp, Carla; Babcock, Julia C

2015-02-01

Most transgender men desire to receive testosterone treatment in order to masculinize their bodies. In this study, we aimed to investigate the short-term effects of testosterone treatment on psychological functioning in transgender men. This is the 1st controlled prospective follow-up study to examine such effects. We examined a sample of transgender men (n = 48) and nontransgender male (n = 53) and female (n = 62) matched controls (mean age = 26.6 years; 74% White). We asked participants to complete the Minnesota Multiphasic Personality Inventory (2nd ed., or MMPI-2; Butcher, Graham, Tellegen, Dahlstrom, & Kaemmer, 2001) to assess psychological functioning at baseline and at the acute posttreatment follow-up (3 months after testosterone initiation). Regression models tested (a) Gender × Time interaction effects comparing divergent mean response profiles across measurements by gender identity; (b) changes in psychological functioning scores for acute postintervention measurements, adjusting for baseline measures, comparing transgender men with their matched nontransgender male and female controls and adjusting for baseline scores; and (c) changes in meeting clinical psychopathological thresholds. Statistically significant changes in MMPI-2 scale scores were found at 3-month follow-up after initiating testosterone treatment relative to baseline for transgender men compared with female controls (female template): reductions in Hypochondria (p < .05), Depression (p < .05), Hysteria (p < .05), and Paranoia (p < .01); and increases in Masculinity-Femininity scores (p < .01). Gender × Time interaction effects were found for Hysteria (p < .05) and Paranoia (p < .01) relative to female controls (female template) and for Hypochondria (p < .05), Depression (p < .01), Hysteria (p < .01), Psychopathic Deviate (p < .05), Paranoia (p < .01), Psychasthenia (p < .01), and Schizophrenia (p < .01) compared with male controls (male template). In addition, the proportion of transgender men presenting with co-occurring psychopathology significantly decreased from baseline compared with 3-month follow-up relative to controls (p < .05). Findings suggest that testosterone treatment resulted in increased levels of psychological functioning on multiple domains in transgender men relative to nontransgender controls. These findings differed in comparisons of transgender men with female controls using the female template and with male controls using the male template. No iatrogenic effects of testosterone were found. These findings suggest a direct positive effect of 3 months of testosterone treatment on psychological functioning in transgender men. (PsycINFO Database Record (c) 2015 APA, all rights reserved).

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.

SPLAT: Using Spectral Indices to Identify and Characterize Ultracool Stars, Brown Dwarfs and Exoplanets in Deep Surveys and as Companions to Nearby Stars

NASA Astrophysics Data System (ADS)

Aganze, Christian; Burgasser, Adam J.; Martin, Eduardo; Konopacky, Quinn; Masters, Daniel C.

2016-06-01

The majority of ultracool dwarf stars and brown dwarfs currently known were identified in wide-field red optical and infrared surveys, enabling measures of the local, typically isolated, population in a relatively shallow (<100 pc radius) volume. Constraining the properties of the wider Galactic population (scale height, radial distribution, Population II sources), and close brown dwarf and exoplanet companions to nearby stars, requires specialized instrumentation, such as high-contrast, coronagraphic spectrometers (e.g., Gemini/GPI, VLT/Sphere, Project 1640); and deep spectral surveys (e.g., HST/WFC3 parallel fields, Euclid). We present a set of quantitative methodologies to identify and robustly characterize sources for these specific populations, based on templates and tools developed as part of the SpeX Prism Library Analysis Toolkit. In particular, we define and characterize specifically-tuned sets spectral indices that optimize selection of cool dwarfs and distinguish rare populations (subdwarfs, young planetary-mass objects) based on low-resolution, limited-wavelength-coverage spectral data; and present a template-matching classification method for these instruments. We apply these techniques to HST/WFC3 parallel fields data in the WISPS and HST-3D programs, where our spectral index set allows high completeness and low contamination for searches of late M, L and T dwarfs to distances out to ~3 kpc.The material presented here is based on work supported by the National Aeronautics and Space Administration under Grant No. NNX15AI75G.

Demonstration of Advanced EMI Models for Live-Site UXO Discrimination at Former Camp Butner, North Carolina

DTIC Science & Technology

2012-05-01

GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7 . PERFORMING ORGANIZATION NAME(S...2.3.3 Classification using template matching ...................................................... 7 2.4 Details of classification schemes... 7 2.4.1 Camp Butner TEMTADS data inversion and classification scheme .......... 9

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

Fast prediction and evaluation of eccentric inspirals using reduced-order models

NASA Astrophysics Data System (ADS)

Barta, Dániel; Vasúth, Mátyás

2018-06-01

A large number of theoretically predicted waveforms are required by matched-filtering searches for the gravitational-wave signals produced by compact binary coalescence. In order to substantially alleviate the computational burden in gravitational-wave searches and parameter estimation without degrading the signal detectability, we propose a novel reduced-order-model (ROM) approach with applications to adiabatic 3PN-accurate inspiral waveforms of nonspinning sources that evolve on either highly or slightly eccentric orbits. We provide a singular-value decomposition-based reduced-basis method in the frequency domain to generate reduced-order approximations of any gravitational waves with acceptable accuracy and precision within the parameter range of the model. We construct efficient reduced bases comprised of a relatively small number of the most relevant waveforms over three-dimensional parameter-space covered by the template bank (total mass 2.15 M⊙≤M ≤215 M⊙ , mass ratio 0.01 ≤q ≤1 , and initial orbital eccentricity 0 ≤e0≤0.95 ). The ROM is designed to predict signals in the frequency band from 10 Hz to 2 kHz for aLIGO and aVirgo design sensitivity. Beside moderating the data reduction, finer sampling of fiducial templates improves the accuracy of surrogates. Considerable increase in the speedup from several hundreds to thousands can be achieved by evaluating surrogates for low-mass systems especially when combined with high-eccentricity.

A Tutor That's Up to the Task

NASA Technical Reports Server (NTRS)

2003-01-01

With assistance from NASA s Marshall Space Flight Center, a new breed of ITS for technical training and complex problem-solving has hit the market to provide students and trainees with the decision-making skills necessary to succeed to the next level. The Task Tutor Toolkit (T3), developed by Stottler Henke Associates, Inc., of San Mateo, California, is a generic tutoring system shell and scenario authoring tool that emulates expert instructors and lowers the cost and difficulty of creating scenario-based ITS for technical training. The functionality of Stottler Henke Associates T3 far exceeds that of traditional computer-based training systems, which test factual recall and narrow skills by prompting students to answer multiple-choice or fill-inthe- blank questions. The T3, on the contrary, lets students assess situations, generate solutions, make decisions, and carry out actions in realistically complex scenarios.At the beginning of each scenario, the T3 tutoring system presents a briefing that describes the situation and the goals the students should pursue. Each scenario contains a solution template that specifies a partially-ordered sequence of action patterns that match correct sequences of student actions. During each scenario, the built-in simulator notifies the tutoring system of each student action. The T3 uses this information to evaluate the student action by comparing it with the scenario s solution template and with error rules that detect incorrect actions.

3D-printed orthodontic brackets - proof of concept.

PubMed

Krey, Karl-Friedrich; Darkazanly, Nawras; Kühnert, Rolf; Ruge, Sebastian

Today, orthodontic treatment with fixed appliances is usually carried out using preprogrammed straight-wire brackets made of metal or ceramics. The goal of this study was to determine the possibility of clinically implementing a fully digital workflow with individually designed and three-dimensionally printed (3D-printed) brackets. Edgewise brackets were designed using computer-aided design (CAD) software for demonstration purposes. After segmentation of the malocclusion model generated based on intraoral scan data, the brackets were digitally positioned on the teeth and a target occlusion model created. The thus-defined tooth position was used to generate a template for an individualized arch form in the horizontal plane. The base contours of the brackets were modified to match the shape of the tooth surfaces, and a positioning guide (fabricated beforehand) was used to ensure that the brackets were bonded at the correct angle and position. The brackets, positioning guide, and retainer splint, digitally designed on the target occlusion model, were 3D printed using a Digital Light Processing (DLP) 3D printer. The archwires were individually pre-bent using the template. In the treatment sequence, it was shown for the first time that, in principle, it is possible to perform treatment with an individualized 3D-printed brackets system by using the proposed fully digital workflow. Technical aspects of the system, problems encountered in treatment, and possible future developments are discussed in this article.

Development and application of 3-chloro-1,2-propandiol electrochemical sensor based on a polyaminothiophenol modified molecularly imprinted film.

PubMed

Sun, Xiulan; Zhang, Lijuan; Zhang, Hongxia; Qian, He; Zhang, Yinzhi; Tang, Lili; Li, Zaijun

2014-05-21

In this work, a novel electrochemical sensor for 3-chloro-1,2-propandiol (3-MCPD) detection based on a gold nanoparticle-modified glassy carbon electrode (AuNP/GCE) coated with a molecular imprinted polymer (MIP) film was constructed. p-Aminothiophenol (p-ATP) and 3-MCPD were self-assembled on a AuNP/GCE surface, and then a MIP film was formed by electropolymerization. The 3-MCPD template combined with p-ATP during self-assembly and electropolymerization, and the cavities matching 3-MCPD remained after the removal of the template. The MIP sensor was characterized by cyclic voltammetry (CV), differential pulse voltammetry (DPV) and scanning electron microscopy (SEM). Many factors that affected the performance of the MIP membrane were discussed and optimized. Under optimal conditions, the DPV current was linear with the log of the 3-MCPD concentration in the range from 1.0 × 10(-17) to 1.0 × 10(-13) mol L(-1) (R(2) = 0.9939), and the detection limit was 3.8 × 10(-18) mol L(-1) (S/N = 3). The average recovery rate of 3-MCPD from spiked soy sauce samples ranged from 95.0% to 106.4% (RSD < 3.49%). Practically, the sensor showed high sensitivity, good selectivity, excellent reproducibility, and stability during the quantitative determination of 3-MCPD.

Detection and location of earthquakes along the west coast of Chile: Examining seismicity in the 2010 M 8.8 Maule and 2014 M 8.1 Iquique earthquake rupture zones.

NASA Astrophysics Data System (ADS)

Diniakos, R. S.; Bilek, S. L.; Rowe, C. A.; Draganov, D.

2015-12-01

The subduction of the Nazca Plate beneath the South American Plate along Chile has led to some of the largest earthquakes recorded on modern seismic instrumentation. These include the 1960 M 9.5 Valdivia, 2010 M 8.8 Maule, and 2014 M 8.1 Iquique earthquakes. Slip heterogeneity for both the 2010 and 2014 earthquakes has been noted in various studies. In order to explore both spatial variations in the continued aftershocks of the 2010 event, and also seismicity to the north along Iquique prior to the 2014 earthquake relative to the high slip regions, we are expanding the catalog of small earthquakes using template matching algorithms to find other small earthquakes in the region. We start with an earthquake catalog developed from regional and local array data; these events provide the templates used to search through waveform data from a temporary seismic array in Malargue, Argentina, located ~300 km west of the Maule region, which operated in 2012. Our template events are first identified on the array stations, and we use a 10-s window around the P-wave arrival as the template. We then use a waveform cross-correlation algorithm to compare the template with day-long seismograms from Malargue stations. The newly detected events are then located using the HYPOINVERSE2000 program. Initial results for 103 templates on 19 of the array stations show that we find 275 new events ,with an average of three new events for each template correlated. For these preliminary results, events from the Maule region appear to provide the most new detections, with an average of ten new events. We will present our locations for the detected events and we will compare them to patterns of high slip along the 2010 rupture zone of the M 8.8 Maule earthquake and the 2014 M 8.1 Iquique event.

Osteoarthritis classification using self organizing map based on gabor kernel and contrast-limited adaptive histogram equalization.

PubMed

Anifah, Lilik; Purnama, I Ketut Eddy; Hariadi, Mochamad; Purnomo, Mauridhi Hery

2013-01-01

Localization is the first step in osteoarthritis (OA) classification. Manual classification, however, is time-consuming, tedious, and expensive. The proposed system is designed as decision support system for medical doctors to classify the severity of knee OA. A method has been proposed here to localize a joint space area for OA and then classify it in 4 steps to classify OA into KL-Grade 0, KL-Grade 1, KL-Grade 2, KL-Grade 3 and KL-Grade 4, which are preprocessing, segmentation, feature extraction, and classification. In this proposed system, right and left knee detection was performed by employing the Contrast-Limited Adaptive Histogram Equalization (CLAHE) and the template matching. The Gabor kernel, row sum graph and moment methods were used to localize the junction space area of knee. CLAHE is used for preprocessing step, i.e.to normalize the varied intensities. The segmentation process was conducted using the Gabor kernel, template matching, row sum graph and gray level center of mass method. Here GLCM (contrast, correlation, energy, and homogeinity) features were employed as training data. Overall, 50 data were evaluated for training and 258 data for testing. Experimental results showed the best performance by using gabor kernel with parameters α=8, θ=0, Ψ=[0 π/2], γ=0,8, N=4 and with number of iterations being 5000, momentum value 0.5 and α0=0.6 for the classification process. The run gave classification accuracy rate of 93.8% for KL-Grade 0, 70% for KL-Grade 1, 4% for KL-Grade 2, 10% for KL-Grade 3 and 88.9% for KL-Grade 4.

Osteoarthritis Classification Using Self Organizing Map Based on Gabor Kernel and Contrast-Limited Adaptive Histogram Equalization

PubMed Central

Anifah, Lilik; Purnama, I Ketut Eddy; Hariadi, Mochamad; Purnomo, Mauridhi Hery

2013-01-01

Localization is the first step in osteoarthritis (OA) classification. Manual classification, however, is time-consuming, tedious, and expensive. The proposed system is designed as decision support system for medical doctors to classify the severity of knee OA. A method has been proposed here to localize a joint space area for OA and then classify it in 4 steps to classify OA into KL-Grade 0, KL-Grade 1, KL-Grade 2, KL-Grade 3 and KL-Grade 4, which are preprocessing, segmentation, feature extraction, and classification. In this proposed system, right and left knee detection was performed by employing the Contrast-Limited Adaptive Histogram Equalization (CLAHE) and the template matching. The Gabor kernel, row sum graph and moment methods were used to localize the junction space area of knee. CLAHE is used for preprocessing step, i.e.to normalize the varied intensities. The segmentation process was conducted using the Gabor kernel, template matching, row sum graph and gray level center of mass method. Here GLCM (contrast, correlation, energy, and homogeinity) features were employed as training data. Overall, 50 data were evaluated for training and 258 data for testing. Experimental results showed the best performance by using gabor kernel with parameters α=8, θ=0, Ψ=[0 π/2], γ=0,8, N=4 and with number of iterations being 5000, momentum value 0.5 and α0=0.6 for the classification process. The run gave classification accuracy rate of 93.8% for KL-Grade 0, 70% for KL-Grade 1, 4% for KL-Grade 2, 10% for KL-Grade 3 and 88.9% for KL-Grade 4. PMID:23525188

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

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.

Full-waveform detection of non-impulsive seismic events based on time-reversal methods

NASA Astrophysics Data System (ADS)

Solano, Ericka Alinne; Hjörleifsdóttir, Vala; Liu, Qinya

2017-12-01

We present a full-waveform detection method for non-impulsive seismic events, based on time-reversal principles. We use the strain Green's tensor as a matched filter, correlating it with continuous observed seismograms, to detect non-impulsive seismic events. We show that this is mathematically equivalent to an adjoint method for detecting earthquakes. We define the detection function, a scalar valued function, which depends on the stacked correlations for a group of stations. Event detections are given by the times at which the amplitude of the detection function exceeds a given value relative to the noise level. The method can make use of the whole seismic waveform or any combination of time-windows with different filters. It is expected to have an advantage compared to traditional detection methods for events that do not produce energetic and impulsive P waves, for example glacial events, landslides, volcanic events and transform-fault earthquakes for events which velocity structure along the path is relatively well known. Furthermore, the method has advantages over empirical Greens functions template matching methods, as it does not depend on records from previously detected events, and therefore is not limited to events occurring in similar regions and with similar focal mechanisms as these events. The method is not specific to any particular way of calculating the synthetic seismograms, and therefore complicated structural models can be used. This is particularly beneficial for intermediate size events that are registered on regional networks, for which the effect of lateral structure on the waveforms can be significant. To demonstrate the feasibility of the method, we apply it to two different areas located along the mid-oceanic ridge system west of Mexico where non-impulsive events have been reported. The first study area is between Clipperton and Siqueiros transform faults (9°N), during the time of two earthquake swarms, occurring in March 2012 and May 2016. The second area of interest is the Gulf of California where two swarms took place during July and September of 2015. We show that we are able to detect previously non-reported, non-impulsive events and recommend that this method be used together with more traditional template matching methods to maximize the number of detected events.

Subpixel Mapping of Hyperspectral Image Based on Linear Subpixel Feature Detection and Object Optimization

NASA Astrophysics Data System (ADS)

Liu, Zhaoxin; Zhao, Liaoying; Li, Xiaorun; Chen, Shuhan

2018-04-01

Owing to the limitation of spatial resolution of the imaging sensor and the variability of ground surfaces, mixed pixels are widesperead in hyperspectral imagery. The traditional subpixel mapping algorithms treat all mixed pixels as boundary-mixed pixels while ignoring the existence of linear subpixels. To solve this question, this paper proposed a new subpixel mapping method based on linear subpixel feature detection and object optimization. Firstly, the fraction value of each class is obtained by spectral unmixing. Secondly, the linear subpixel features are pre-determined based on the hyperspectral characteristics and the linear subpixel feature; the remaining mixed pixels are detected based on maximum linearization index analysis. The classes of linear subpixels are determined by using template matching method. Finally, the whole subpixel mapping results are iteratively optimized by binary particle swarm optimization algorithm. The performance of the proposed subpixel mapping method is evaluated via experiments based on simulated and real hyperspectral data sets. The experimental results demonstrate that the proposed method can improve the accuracy of subpixel mapping.

A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.

PubMed

Zhu, Yanan; Ouyang, Qi; Mao, Youdong

2017-07-21

Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly "knowledgeable". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.

Motion Evaluation for Rehabilitation Training of the Disabled

NASA Astrophysics Data System (ADS)

Kim, Tae-Young; Park, Jun; Lim, Cheol-Su

In this paper, a motion evaluation technique for rehabilitation training is introduced. Motion recognition technologies have been developed for determining matching motions in the training set. However, we need to measure how well and how much of the motion has been followed for training motion evaluation. We employed a Finite State Machine as a framework of motion evaluation. For similarity analysis, we used weighted angular value differences although any template matching algorithm may be used. For robustness under illumination changes, IR LED's and cameras with IR-pass filter were used. Developed technique was successfully used for rehabilitation training of the disabled. Therapists appraised the system as practically useful.

Sorted Index Numbers for Privacy Preserving Face Recognition

NASA Astrophysics Data System (ADS)

Wang, Yongjin; Hatzinakos, Dimitrios

2009-12-01

This paper presents a novel approach for changeable and privacy preserving face recognition. We first introduce a new method of biometric matching using the sorted index numbers (SINs) of feature vectors. Since it is impossible to recover any of the exact values of the original features, the transformation from original features to the SIN vectors is noninvertible. To address the irrevocable nature of biometric signals whilst obtaining stronger privacy protection, a random projection-based method is employed in conjunction with the SIN approach to generate changeable and privacy preserving biometric templates. The effectiveness of the proposed method is demonstrated on a large generic data set, which contains images from several well-known face databases. Extensive experimentation shows that the proposed solution may improve the recognition accuracy.

An Application for Driver Drowsiness Identification based on Pupil Detection using IR Camera

NASA Astrophysics Data System (ADS)

Kumar, K. S. Chidanand; Bhowmick, Brojeshwar

A Driver drowsiness identification system has been proposed that generates alarms when driver falls asleep during driving. A number of different physical phenomena can be monitored and measured in order to detect drowsiness of driver in a vehicle. This paper presents a methodology for driver drowsiness identification using IR camera by detecting and tracking pupils. The face region is first determined first using euler number and template matching. Pupils are then located in the face region. In subsequent frames of video, pupils are tracked in order to find whether the eyes are open or closed. If eyes are closed for several consecutive frames then it is concluded that the driver is fatigued and alarm is generated.

VizieR Online Data Catalog: LAMOST candidate members of star clusters (Xiang+, 2015)

NASA Astrophysics Data System (ADS)

Xiang, M. S.; Liu, X. W.; Yuan, H. B.; Huang, Y.; Huo, Z. Y.; Zhang, H. W.; Chen, B. Q.; Zhang, H. H.; Sun, N. C.; Wang, C.; Zhao, Y. H.; Shi, J. R.; Luo, A. L.; Li, G. P.; Wu, Y.; Bai, Z. R.; Zhang, Y.; Hou, Y. H.; Yuan, H. L.; Li, G. W.; Wei, Z.

2015-08-01

In this work, we describe the algorithms and implementation of LSP3, the LAMOST Stellar Parameter Pipeline at Peking University, a pipeline developed to determine the stellar parameters (radial velocity Vr, effective temperature Teff, surface gravity logg and metallicity [Fe/H]) from LAMOST spectra based on a template-matching technique. Following the data policy of LAMOST surveys, the data as well as the LSP3 pipeline will be public released as value-added products of the first data release of LAMOST (LAMOST DR1; Bai et al., 2015, A&A submitted), currently scheduled in 2014 December and can be accessed via http://lamost973.pku.edu.cn/site/node/4, along with a description file. (1 data file).

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.

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.

Speciation of nanoscale objects by nanoparticle imprinted matrices

NASA Astrophysics Data System (ADS)

Hitrik, Maria; Pisman, Yamit; Wittstock, Gunther; Mandler, Daniel

2016-07-01

The toxicity of nanoparticles is not only a function of the constituting material but depends largely on their size, shape and stabilizing shell. Hence, the speciation of nanoscale objects, namely, their detection and separation based on the different species, similarly to heavy metals, is of outmost importance. Here we demonstrate the speciation of gold nanoparticles (AuNPs) and their electrochemical detection using the concept of ``nanoparticles imprinted matrices'' (NAIM). Negatively charged AuNPs are adsorbed as templates on a conducting surface previously modified with polyethylenimine (PEI). The selective matrix is formed by the adsorption of either oleic acid (OA) or poly(acrylic acid) (PAA) on the non-occupied areas. The AuNPs are removed by electrooxidation to form complementary voids. These voids are able to recognize the AuNPs selectively based on their size. Furthermore, the selectivity could be improved by adsorbing an additional layer of 1-hexadecylamine, which deepened the voids. Interestingly, silver nanoparticles (AgNPs) were also recognized if their size matched those of the template AuNPs. The steps in assembling the NAIMs and the reuptake of the nanoparticles were characterized carefully. The prospects for the analytical use of NAIMs, which are simple, of small dimension, cost-efficient and portable, are in the sensing and separation of nanoobjects.The toxicity of nanoparticles is not only a function of the constituting material but depends largely on their size, shape and stabilizing shell. Hence, the speciation of nanoscale objects, namely, their detection and separation based on the different species, similarly to heavy metals, is of outmost importance. Here we demonstrate the speciation of gold nanoparticles (AuNPs) and their electrochemical detection using the concept of ``nanoparticles imprinted matrices'' (NAIM). Negatively charged AuNPs are adsorbed as templates on a conducting surface previously modified with polyethylenimine (PEI). The selective matrix is formed by the adsorption of either oleic acid (OA) or poly(acrylic acid) (PAA) on the non-occupied areas. The AuNPs are removed by electrooxidation to form complementary voids. These voids are able to recognize the AuNPs selectively based on their size. Furthermore, the selectivity could be improved by adsorbing an additional layer of 1-hexadecylamine, which deepened the voids. Interestingly, silver nanoparticles (AgNPs) were also recognized if their size matched those of the template AuNPs. The steps in assembling the NAIMs and the reuptake of the nanoparticles were characterized carefully. The prospects for the analytical use of NAIMs, which are simple, of small dimension, cost-efficient and portable, are in the sensing and separation of nanoobjects. Electronic supplementary information (ESI) available: S1 - instrumentation, S2 - immobilization of AuNPs, S3 - time dependent immobilization, S4 - CVs at matrix-coated substrates, S5 - CVs at AuNP-loaded matrices, S6 - peak potentials for the oxidation of AuNPs of different sizes, S7 - schematics for the change of conductive area of the matrices, S8 - probe CVs before and after AuNPs oxidation, S9 - calculation of adsorbed and reuptaken AuNPs, S10 - CVs of AuNPs adsorbed on non-imprinted matrices, S11 - SEM images of AuNPs adsorbed on non-imprinted matrices, S12 - SEM images after reuptake of AuNPs, S13 - schematic of the effect of thickening the matrix. See DOI: 10.1039/c6nr01106c

Three-dimensional MRI-linac intra-fraction guidance using multiple orthogonal cine-MRI planes

NASA Astrophysics Data System (ADS)

Bjerre, Troels; Crijns, Sjoerd; Rosenschöld, Per Munck af; Aznar, Marianne; Specht, Lena; Larsen, Rasmus; Keall, Paul

2013-07-01

The introduction of integrated MRI-radiation therapy systems will offer live intra-fraction imaging. We propose a feasible low-latency multi-plane MRI-linac guidance strategy. In this work we demonstrate how interleaved acquired, orthogonal cine-MRI planes can be used for low-latency tracking of the 3D trajectory of a soft-tissue target structure. The proposed strategy relies on acquiring a pre-treatment 3D breath-hold scan, extracting a 3D target template and performing template matching between this 3D template and pairs of orthogonal 2D cine-MRI planes intersecting the target motion path. For a 60 s free-breathing series of orthogonal cine-MRI planes, we demonstrate that the method was capable of accurately tracking the respiration related 3D motion of the left kidney. Quantitative evaluation of the method using a dataset designed for this purpose revealed a translational error of 1.15 mm for a translation of 39.9 mm. We have demonstrated how interleaved acquired, orthogonal cine-MRI planes can be used for online tracking of soft-tissue target volumes.

Binding of anions in triply interlocked coordination catenanes and dynamic allostery for dehalogenation reactions.

PubMed

Yang, Linlin; Jing, Xu; An, Bowen; He, Cheng; Yang, Yang; Duan, Chunying

2018-01-28

By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds. The presence of several kinds of individual pocket that were attributed to the triply interlocked patterns enabled the possibility of encapsulating different anions, allowing the dynamic allostery between the unlocked/locked conformers to promote the dehalogenation reaction of 3-bromo-cyclohexene efficiently, as with the use of dehalogenase enzymes. The interlocked structures could be unlocked into two individual tetrahedrons through removal of the well-matched anion templates. The stability and reversibility of the locked/unlocked structures were further confirmed by the catching/releasing process that accompanied emission switching, providing opportunities for the system to be a dynamic molecular logic system.

Optimizing microstimulation using a reinforcement learning framework.

PubMed

Brockmeier, Austin J; Choi, John S; Distasio, Marcello M; Francis, Joseph T; Príncipe, José C

2011-01-01

The ability to provide sensory feedback is desired to enhance the functionality of neuroprosthetics. Somatosensory feedback provides closed-loop control to the motor system, which is lacking in feedforward neuroprosthetics. In the case of existing somatosensory function, a template of the natural response can be used as a template of desired response elicited by electrical microstimulation. In the case of no initial training data, microstimulation parameters that produce responses close to the template must be selected in an online manner. We propose using reinforcement learning as a framework to balance the exploration of the parameter space and the continued selection of promising parameters for further stimulation. This approach avoids an explicit model of the neural response from stimulation. We explore a preliminary architecture--treating the task as a k-armed bandit--using offline data recorded for natural touch and thalamic microstimulation, and we examine the methods efficiency in exploring the parameter space while concentrating on promising parameter forms. The best matching stimulation parameters, from k = 68 different forms, are selected by the reinforcement learning algorithm consistently after 334 realizations.

Three-dimensional MRI-linac intra-fraction guidance using multiple orthogonal cine-MRI planes.

PubMed

Bjerre, Troels; Crijns, Sjoerd; af Rosenschöld, Per Munck; Aznar, Marianne; Specht, Lena; Larsen, Rasmus; Keall, Paul

2013-07-21

The introduction of integrated MRI-radiation therapy systems will offer live intra-fraction imaging. We propose a feasible low-latency multi-plane MRI-linac guidance strategy. In this work we demonstrate how interleaved acquired, orthogonal cine-MRI planes can be used for low-latency tracking of the 3D trajectory of a soft-tissue target structure. The proposed strategy relies on acquiring a pre-treatment 3D breath-hold scan, extracting a 3D target template and performing template matching between this 3D template and pairs of orthogonal 2D cine-MRI planes intersecting the target motion path. For a 60 s free-breathing series of orthogonal cine-MRI planes, we demonstrate that the method was capable of accurately tracking the respiration related 3D motion of the left kidney. Quantitative evaluation of the method using a dataset designed for this purpose revealed a translational error of 1.15 mm for a translation of 39.9 mm. We have demonstrated how interleaved acquired, orthogonal cine-MRI planes can be used for online tracking of soft-tissue target volumes.

Feasibility of using single photon counting X-ray for lung tumor position estimation based on 4D-CT.

PubMed

Aschenbrenner, Katharina P; Guthier, Christian V; Lyatskaya, Yulia; Boda-Heggemann, Judit; Wenz, Frederik; Hesser, Jürgen W

2017-09-01

In stereotactic body radiation therapy of lung tumors, reliable position estimation of the tumor is necessary in order to minimize normal tissue complication rate. While kV X-ray imaging is frequently used, continuous application during radiotherapy sessions is often not possible due to concerns about the additional dose. Thus, ultra low-dose (ULD) kV X-ray imaging based on a single photon counting detector is suggested. This paper addresses the lower limit of photons to locate the tumor reliably with an accuracy in the range of state-of-the-art methods, i.e. a few millimeters. 18 patient cases with four dimensional CT (4D-CT), which serves as a-priori information, are included in the study. ULD cone beam projections are simulated from the 4D-CTs including Poisson noise. The projections from the breathing phases which correspond to different tumor positions are compared to the ULD projection by means of Poisson log-likelihood (PML) and correlation coefficient (CC), and template matching under these metrics. The results indicate that in full thorax imaging five photons per pixel suffice for a standard deviation in tumor positions of less than half a breathing phase. Around 50 photons per pixel are needed to achieve this accuracy with the field of view restricted to the tumor region. Compared to CC, PML tends to perform better for low photon counts and shifts in patient setup. Template matching only improves the position estimation in high photon counts. The quality of the reconstruction is independent of the projection angle. The accuracy of the proposed ULD single photon counting system is in the range of a few millimeters and therefore comparable to state-of-the-art tumor tracking methods. At the same time, a reduction in photons per pixel by three to four orders of magnitude relative to commercial systems with flatpanel detectors can be achieved. This enables continuous kV image-based position estimation during all fractions since the additional dose to the patient is negligible. Copyright © 2017. Published by Elsevier GmbH.

[Spectroscopic Study of Salbutamol Molecularly Imprinted Polymers].

PubMed

Ren, Hui-peng; Guan, Yu-yu; Dai, Rong-hua; Liu, Guo-yan; Chai, Chun-yan

2016-02-01

In order to solve the problem of on-site rapid detection of salbutamol residues in feed and animal products, and develop a new method of fast detection of salbutamol on the basis of the molecular imprinting technology, this article uses the salbutamol (SAL) working as template molecule, methacrylic acid (MAA) working as functional monomer. On this basis, a new type of core-shell type salbutamol molecularly imprinted polymers were prepared with colloidal gold particles as triggering core. Superficial characteristics of the MIPs and the related compounds were investigated by ultraviolet (UV) spectra and infrared (IR) spectra, Raman spectra, Scanning electron microscopy (SEM) respectively. The results indicated that a stable hydrogen bonding complex has been formed between the carboxyl groups of SAL and MA with a matching ratio of 1:1. The complex can be easily eluted by the reagent containing hydrogen bonding. The chemical binding constant K reaches -0.245 x 10⁶ L² · mol⁻². The possible binding sites of the hydrogen bonding was formed between the hydrogen atoms of -COOH in MA and the oxygen atoms of C==O in SAL. IR and Raman spectrum showed that, compared with MA, a significant red shift of -OH absorption peak was manifested in MIPs, which proved that SAL as template molecule occurred a specific bond between MA. Red shift of stretching vibration absorption peak of C==O was also detected in the un-eluted MIPs and obvious energy loss happened, which demonstrated a possible binding sites is SAL intramolecular of C==O atom of oxygen. If the hydrogen atoms of -COOH in MA wanted to generate hydrogen bond. However, the shapes of absorption peak of other functional groups including C==C, C==O, and -OH were very similar both in MIPs and NIPs. Specific cavities were formed after the template molecules in MIPs were removed. It was proved by the adsorption experiment that the specific sites in these cavities highly match with the chemical and space structure of SAL. Besides, colloidal gold type core-shell molecularly imprinted polymers have looser surface, more cavities in the surface compared with ordinary molecularly imprinted polymers, which increased the effective area of adsorption to target molecules. So it have better performance in adsorption. Based on the principle that these cavities can specificly recognize and combine with target molecule in the test sample, and the excellent ability of colloidal gold core-shell molecularly imprinted polymers, the development of novel methods for fast determination of SAL based on the molecular imprinting technology can be expected in the near future.

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…

Metal-chelate dye-controlled organization of Cd32S14(SPh)40(4-) nanoclusters into three-dimensional molecular and covalent open architecture.

PubMed

Zheng, Nanfeng; Lu, Haiwei; Bu, Xianhui; Feng, Pingyun

2006-04-12

Chalcogenide II-VI nanoclusters are usually prepared as isolated clusters and have defied numerous efforts to join them into covalent open-framework architecture with conventional templating methods such as protonated amines or inorganic cations commonly used to direct the formation of porous frameworks. Herein, we report the first templated synthesis of II-VI covalent superlattices from large II-VI tetrahedral clusters (i.e., [Cd32S14(SPh)38]2-). Our method takes advantage of low charge density of metal-chelate dyes that is a unique match with three-dimensional II-VI semiconductor frameworks in charge density, surface hydrophilicity-hydrophobicity, and spatial organization. In addition, metal-chelate dyes also serve to tune the optical properties of resulting dye semiconductor composite materials.

[Multiplexing mapping of human cDNAs]. Final report, September 1, 1991--February 28, 1994

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

Not Available

Using PCR with automated product analysis, 329 human brain cDNA sequences have been assigned to individual human chromosomes. Primers were designed from single-pass cDNA sequences expressed sequence tags (ESTs). Primers were used in PCR reactions with DNA from somatic cell hybrid mapping panels as templates, often with multiplexing. Many ESTs mapped match sequence database records. To evaluate of these matches, the position of the primers relative to the matching region (In), the BLAST scores and the Poisson probability values of the EST/sequence record match were determined. In cases where the gene product was stringently identified by the sequence match hadmore » already been mapped, the gene locus determined by EST was consistent with the previous position which strongly supports the validity of assigning unknown genes to human chromosomes based on the EST sequence matches. In the present cases mapping the ESTs to a chromosome can also be considered to have mapped the known gene product: rolipram-sensitive cAMP phosphodiesterase, chromosome 1; protein phosphatase 2A{beta}, chromosome 4; alpha-catenin, chromosome 5; the ELE1 oncogene, chromosome 10q11.2 or q2.1-q23; MXII protein, chromosome l0q24-qter; ribosomal protein L18a homologue, chromosome 14; ribosomal protein L3, chromosome 17; and moesin, Xp11-cen. There were also ESTs mapped that were closely related to non-human sequence records. These matches therefore can be considered to identify human counterparts of known gene products, or members of known gene families. Examples of these include membrane proteins, translation-associated proteins, structural proteins, and enzymes. These data then demonstrate that single pass sequence information is sufficient to design PCR primers useful for assigning cDNA sequences to human chromosomes. When the EST sequence matches previous sequence database records, the chromosome assignments of the EST can be used to make preliminary assignments of the human gene to a chromosome.« less

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

Does an English appeal court ruling increase the risks of miscarriages of justice when complex DNA profiles are searched against the national DNA database?

PubMed

Gill, P; Bleka, Ø; Egeland, T

2014-11-01

Likelihood ratio (LR) methods to interpret multi-contributor, low template, complex DNA mixtures are becoming standard practice. The next major development will be to introduce search engines based on the new methods to interrogate very large national DNA databases, such as those held by China, the USA and the UK. Here we describe a rapid method that was used to assign a LR to each individual member of database of 5 million genotypes which can be ranked in order. Previous authors have only considered database trawls in the context of binary match or non-match criteria. However, the concept of match/non-match no longer applies within the new paradigm introduced, since the distribution of resultant LRs is continuous for practical purposes. An English appeal court decision allows scientists to routinely report complex DNA profiles using nothing more than their subjective personal 'experience of casework' and 'observations' in order to apply an expression of the rarity of an evidential sample. This ruling must be considered in context of a recent high profile English case, where an individual was extracted from a database and wrongly accused of a serious crime. In this case the DNA evidence was used to negate the overwhelming exculpatory (non-DNA) evidence. Demonstrable confirmation bias, also known as the 'CSI-effect, seriously affected the investigation. The case demonstrated that in practice, databases could be used to select and prosecute an individual, simply because he ranked high in the list of possible matches. We have identified this phenomenon as a cognitive error which we term: 'the naïve investigator effect'. We take the opportunity to test the performance of database extraction strategies either by using a simple matching allele count (MAC) method or LR. The example heard by the appeal court is used as the exemplar case. It is demonstrated that the LR search-method offers substantial benefits compared to searches based on simple matching allele count (MAC) methods. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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.

Understanding Consistency Maintenance in Service Discovery Architectures during Communication Failure

DTIC Science & Technology

2002-07-01

our general model include: (1) service user (SU), (2) service manager (SM), and (3) service cache manager ( SCM ), where the SCM is an optional...maintained by SMs that satisfy specific requirements. Where employed, the SCM operates as an intermediary, matching advertised SDs of SMs to...Directory Service Agent (optional) not applicableLookup ServiceService Cache Manager ( SCM ) Service URL Service Type Service Attributes Template URL

Toward a Natural Speech Understanding System

DTIC Science & Technology

1989-10-01

WALTER J. SENUS Technical Director Directorate of Intelligence & Reconnaissance FOR THE COMMANDER JAMES W. HYDE III V Directorate of Plans & Programs ...applicable) Human Resources Laboratory F30602-81-C-0193 8 . ADDRESS (City, State, and ZIP Code) 10. SOURCE OF FUNDING NUMBERS PROGRAM PROJECT TASK WORK...error rates for distinctive words produced in isolation by a single speaker, and their simple programming requirements. Template-matching systems rank

Dust-deficient Palomar-Green Quasars and the Diversity of AGN Intrinsic IR Emission

NASA Astrophysics Data System (ADS)

Lyu, Jianwei; Rieke, G. H.; Shi, Yong

2017-02-01

To elucidate the intrinsic broadband infrared (IR) emission properties of active galactic nuclei (AGNs), we analyze the spectral energy distributions (SEDs) of 87 z ≲ 0.5 Palomar-Green (PG) quasars. While the Elvis AGN template with a moderate far-IR correction can reasonably match the SEDs of the AGN components in ˜60% of the sample (and is superior to alternatives such as that by Assef), it fails on two quasar populations: (1) hot-dust-deficient (HDD) quasars that show very weak emission thoroughly from the near-IR to the far-IR, and (2) warm-dust-deficient (WDD) quasars that have similar hot dust emission as normal quasars but are relatively faint in the mid- and far-IR. After building composite AGN templates for these dust-deficient quasars, we successfully fit the 0.3-500 μm SEDs of the PG sample with the appropriate AGN template, an infrared template of a star-forming galaxy, and a host galaxy stellar template. 20 HDD and 12 WDD quasars are identified from the SED decomposition, including seven ambiguous cases. Compared with normal quasars, the HDD quasars have AGNs with relatively low Eddington ratios and the fraction of WDD quasars increases with AGN luminosity. Moreover, both the HDD and WDD quasar populations show relatively stronger mid-IR silicate emission. Virtually identical SED properties are also found in some quasars from z = 0.5 to 6. We propose a conceptual model to demonstrate that the observed dust deficiency of quasars can result from a change of structures of the circumnuclear tori that can occur at any cosmic epoch.

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

Lyu, Jianwei; Rieke, G. H.; Shi, Yong, E-mail: jianwei@email.arizona.edu

To elucidate the intrinsic broadband infrared (IR) emission properties of active galactic nuclei (AGNs), we analyze the spectral energy distributions (SEDs) of 87 z ≲ 0.5 Palomar-Green (PG) quasars. While the Elvis AGN template with a moderate far-IR correction can reasonably match the SEDs of the AGN components in ∼60% of the sample (and is superior to alternatives such as that by Assef), it fails on two quasar populations: (1) hot-dust-deficient (HDD) quasars that show very weak emission thoroughly from the near-IR to the far-IR, and (2) warm-dust-deficient (WDD) quasars that have similar hot dust emission as normal quasars butmore » are relatively faint in the mid- and far-IR. After building composite AGN templates for these dust-deficient quasars, we successfully fit the 0.3–500 μm SEDs of the PG sample with the appropriate AGN template, an infrared template of a star-forming galaxy, and a host galaxy stellar template. 20 HDD and 12 WDD quasars are identified from the SED decomposition, including seven ambiguous cases. Compared with normal quasars, the HDD quasars have AGNs with relatively low Eddington ratios and the fraction of WDD quasars increases with AGN luminosity. Moreover, both the HDD and WDD quasar populations show relatively stronger mid-IR silicate emission. Virtually identical SED properties are also found in some quasars from z = 0.5 to 6. We propose a conceptual model to demonstrate that the observed dust deficiency of quasars can result from a change of structures of the circumnuclear tori that can occur at any cosmic epoch.« less

Emulating the visual receptive-field properties of MST neurons with a template model of heading estimation

NASA Technical Reports Server (NTRS)

Perrone, J. A.; Stone, L. S.

1998-01-01

We have proposed previously a computational neural-network model by which the complex patterns of retinal image motion generated during locomotion (optic flow) can be processed by specialized detectors acting as templates for specific instances of self-motion. The detectors in this template model respond to global optic flow by sampling image motion over a large portion of the visual field through networks of local motion sensors with properties similar to those of neurons found in the middle temporal (MT) area of primate extrastriate visual cortex. These detectors, arranged within cortical-like maps, were designed to extract self-translation (heading) and self-rotation, as well as the scene layout (relative distances) ahead of a moving observer. We then postulated that heading from optic flow is directly encoded by individual neurons acting as heading detectors within the medial superior temporal (MST) area. Others have questioned whether individual MST neurons can perform this function because some of their receptive-field properties seem inconsistent with this role. To resolve this issue, we systematically compared MST responses with those of detectors from two different configurations of the model under matched stimulus conditions. We found that the characteristic physiological properties of MST neurons can be explained by the template model. We conclude that MST neurons are well suited to support self-motion estimation via a direct encoding of heading and that the template model provides an explicit set of testable hypotheses that can guide future exploration of MST and adjacent areas within the superior temporal sulcus.

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

Hazelaar, Colien, E-mail: c.hazelaar@vumc.nl; Dahele, Max; Mostafavi, Hassan

Purpose: Spine stereotactic body radiation therapy (SBRT) requires highly accurate positioning. We report our experience with markerless template matching and triangulation of kilovoltage images routinely acquired during spine SBRT, to determine spine position. Methods and Materials: Kilovoltage images, continuously acquired at 7, 11 or 15 frames/s during volumetric modulated spine SBRT of 18 patients, consisting of 93 fluoroscopy datasets (1 dataset/arc), were analyzed off-line. Four patients were immobilized in a head/neck mask, 14 had no immobilization. Two-dimensional (2D) templates were created for each gantry angle from planning computed tomography data and registered to prefiltered kilovoltage images to determine 2D shiftsmore » between actual and planned spine position. Registrations were considered valid if the normalized cross correlation score was ≥0.15. Multiple registrations were triangulated to determine 3D position. For each spine position dataset, average positional offset and standard deviation were calculated. To verify the accuracy and precision of the technique, mean positional offset and standard deviation for twenty stationary phantom datasets with different baseline shifts were measured. Results: For the phantom, average standard deviations were 0.18 mm for left-right (LR), 0.17 mm for superior-inferior (SI), and 0.23 mm for the anterior-posterior (AP) direction. Maximum difference in average detected and applied shift was 0.09 mm. For the 93 clinical datasets, the percentage of valid matched frames was, on average, 90.7% (range: 49.9-96.1%) per dataset. Average standard deviations for all datasets were 0.28, 0.19, and 0.28 mm for LR, SI, and AP, respectively. Spine position offsets were, on average, −0.05 (range: −1.58 to 2.18), −0.04 (range: −3.56 to 0.82), and −0.03 mm (range: −1.16 to 1.51), respectively. Average positional deviation was <1 mm in all directions in 92% of the arcs. Conclusions: Template matching and triangulation using kilovoltage images acquired during irradiation allows spine position detection with submillimeter accuracy at subsecond intervals. Although the majority of patients were not immobilized, most vertebrae were stable at the sub-mm level during spine SBRT delivery.« less

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.

Rapid top-down control over template-guided attention shifts to multiple objects.

PubMed

Grubert, Anna; Fahrenfort, Johannes; Olivers, Christian N L; Eimer, Martin

2017-02-01

Previous research has shown that when observers search for targets defined by a particular colour, attention can be directed rapidly and independently to two target objects that appear in close temporal proximity. We investigated how such rapid attention shifts are modulated by task instructions to selectively attend versus ignore one of these objects. Two search displays that both contained a colour-defined target and a distractor in a different colour were presented in rapid succession, with a stimulus onset asynchrony (SOA) of 100ms. In different blocks, participants were instructed to attend and respond to target-colour objects in the first display and to ignore these objects in the second display, or vice versa. N2pc components were measured to track the allocation of spatial attention to target-colour objects in these two displays. When participants responded to the second display, irrelevant target-colour objects in the first display still triggered N2pc components, demonstrating task-set contingent attentional capture while a feature-specific target template is active. Critically, when participants responded to the first display instead, no N2pc was elicited by target-colour items in the second display, indicating that they no longer rapidly captured attention. However, these items still elicited a longer-latency contralateral negativity (SPCN component), suggesting that attention was oriented towards template-matching objects in working memory. This dissociation between N2pc and SPCN components shows that rapid attentional capture and subsequent attentional selection processes within working memory can be independent. We suggest that early attentional orienting mechanisms can be inhibited when task-set matching objects are no longer task-relevant, and that this type of inhibitory control is a rapid but transient process. Copyright © 2016 Elsevier Inc. All rights reserved.

Foreshocks and delayed triggering of the 2016 MW7.1 Te Araroa earthquake and dynamic reinvigoration of its aftershock sequence by the MW7.8 Kaikōura earthquake, New Zealand

NASA Astrophysics Data System (ADS)

Warren-Smith, Emily; Fry, Bill; Kaneko, Yoshihiro; Chamberlain, Calum J.

2018-01-01

We analyze the preparatory period of the September 2016 MW7.1 Te Araroa foreshock-mainshock sequence in the Northern Hikurangi margin, New Zealand, and subsequent reinvigoration of Te Araroa aftershocks driven by a large distant earthquake (the November 2016 MW7.8 Kaikōura earthquake). By adopting a matched-filter detection workflow using 582 well-defined template events, we generate an improved foreshock and aftershock catalog for the Te Araroa sequence (>8,000 earthquakes over 66 d). Templates characteristic of the MW7.1 sequence (including the mainshock template) detect several highly correlating events (ML2.5-3.5) starting 12 min after a MW5.7 foreshock. These pre-cursory events occurred within ∼1 km of the mainshock and migrate bilaterally, suggesting precursory slip was triggered by the foreshock on the MW7.1 fault patch prior to mainshock failure. We extend our matched-filter routine to examine the interactions between high dynamic stresses resulting from passing surface waves of the November 2016 MW7.8 Kaikōura earthquake, and the evolution of the Te Araroa aftershock sequence. We observe a sudden spike in moment release of the aftershock sequence immediately following peak dynamic Coulomb stresses of 50-150 kPa on the MW7.1 fault plane. The triggered increase in moment release culminated in a MW5.1 event, immediately followed by a ∼3 h temporal stress shadow. Our observations document the preparatory period of a major subduction margin earthquake following a significant foreshock, and quantify dynamic reinvigoration of a distant on-going major aftershock sequence amid a period of temporal clustering of seismic activity in New Zealand.

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.

PHOTOMETRIC REDSHIFTS IN THE HAWAII-HUBBLE DEEP FIELD-NORTH (H-HDF-N)

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

Yang, G.; Xue, Y. Q.; Kong, X.

2015-01-01

We derive photometric redshifts (z {sub phot}) for sources in the entire (∼0.4 deg{sup 2}) Hawaii-Hubble Deep Field-North (H-HDF-N) field with the EAzY code, based on point-spread-function-matched photometry of 15 broad bands from the ultraviolet (U band) to mid-infrared (IRAC 4.5 μm). Our catalog consists of a total of 131,678 sources. We evaluate the z {sub phot} quality by comparing z {sub phot} with spectroscopic redshifts (z {sub spec}) when available, and find a value of normalized median absolute deviation σ{sub NMAD} = 0.029 and an outlier fraction of 5.5% (outliers are defined as sources having |z{sub phot} – z{sub spec} |/(1more » + z{sub spec} ) > 0.15) for non-X-ray sources. More specifically, we obtain σ{sub NMAD} = 0.024 with 2.7% outliers for sources brighter than R = 23 mag, σ{sub NMAD} = 0.035 with 7.4% outliers for sources fainter than R = 23 mag, σ{sub NMAD} = 0.026 with 3.9% outliers for sources having z < 1, and σ{sub NMAD} = 0.034 with 9.0% outliers for sources having z > 1. Our z {sub phot} quality shows an overall improvement over an earlier z {sub phot} work that focused only on the central H-HDF-N area. We also classify each object as a star or galaxy through template spectral energy distribution fitting and complementary morphological parameterization, resulting in 4959 stars and 126,719 galaxies. Furthermore, we match our catalog with the 2 Ms Chandra Deep Field-North main X-ray catalog. For the 462 matched non-stellar X-ray sources (281 having z {sub spec}), we improve their z {sub phot} quality by adding three additional active galactic nucleus templates, achieving σ{sub NMAD} = 0.035 and an outlier fraction of 12.5%. We make our catalog publicly available presenting both photometry and z {sub phot}, and provide guidance on how to make use of our catalog.« less

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.

Kin recognition in zebrafish: a 24-hour window for olfactory imprinting

PubMed Central

Gerlach, Gabriele; Hodgins-Davis, Andrea; Avolio, Carla; Schunter, Celia

2008-01-01

Distinguishing kin from non-kin profoundly impacts the evolution of social behaviour. Individuals able to assess the genetic relatedness of conspecifics can preferentially allocate resources towards related individuals and avoid inbreeding. We have addressed the question of how animals acquire the ability to recognize kin by studying the development of olfactory kin preference in zebrafish (Danio rerio). Previously, we showed that zebrafish use an olfactory template to recognize even unfamiliar kin through phenotype matching. Here, we show for the first time that this phenotype matching is based on a learned olfactory imprinting process in which exposure to kin individuals on day 6 post fertilization (pf) is necessary and sufficient for imprinting. Larvae that were exposed to kin before or after but not on day 6 pf did not recognize kin. Larvae isolated from all contact with conspecifics did not imprint on their own chemical cues; therefore, we see no evidence for kin recognition through self-matching in this species. Surprisingly, exposure to non-kin odour during the sensitive phase of development did not result in imprinting on the odour cues of unrelated individuals, suggesting a genetic predisposition to kin odour. Urine-born peptides expressed by genes of the immune system (MHC) are important messengers carrying information about ‘self’ and ‘other’. We suggest that phenotype matching is acquired through a time-sensitive learning process that, in zebrafish, includes a genetic predisposition potentially involving MHC genes expressed in the olfactory receptor neurons. PMID:18544507

Kin recognition in zebrafish: a 24-hour window for olfactory imprinting.

PubMed

Gerlach, Gabriele; Hodgins-Davis, Andrea; Avolio, Carla; Schunter, Celia

2008-09-22

Distinguishing kin from non-kin profoundly impacts the evolution of social behaviour. Individuals able to assess the genetic relatedness of conspecifics can preferentially allocate resources towards related individuals and avoid inbreeding. We have addressed the question of how animals acquire the ability to recognize kin by studying the development of olfactory kin preference in zebrafish (Danio rerio). Previously, we showed that zebrafish use an olfactory template to recognize even unfamiliar kin through phenotype matching. Here, we show for the first time that this phenotype matching is based on a learned olfactory imprinting process in which exposure to kin individuals on day 6 post fertilization (pf) is necessary and sufficient for imprinting. Larvae that were exposed to kin before or after but not on day 6 pf did not recognize kin. Larvae isolated from all contact with conspecifics did not imprint on their own chemical cues; therefore, we see no evidence for kin recognition through self-matching in this species. Surprisingly, exposure to non-kin odour during the sensitive phase of development did not result in imprinting on the odour cues of unrelated individuals, suggesting a genetic predisposition to kin odour. Urine-born peptides expressed by genes of the immune system (MHC) are important messengers carrying information about 'self' and 'other'. We suggest that phenotype matching is acquired through a time-sensitive learning process that, in zebrafish, includes a genetic predisposition potentially involving MHC genes expressed in the olfactory receptor neurons.

Automated framework for estimation of lung tumor locations in kV-CBCT images for tumor-based patient positioning in stereotactic lung body radiotherapy

NASA Astrophysics Data System (ADS)

Yoshidome, Satoshi; Arimura, Hidetaka; Terashima, Koutarou; Hirakawa, Masakazu; Hirose, Taka-aki; Fukunaga, Junichi; Nakamura, Yasuhiko

2017-03-01

Recently, image-guided radiotherapy (IGRT) systems using kilovolt cone-beam computed tomography (kV-CBCT) images have become more common for highly accurate patient positioning in stereotactic lung body radiotherapy (SLBRT). However, current IGRT procedures are based on bone structures and subjective correction. Therefore, the aim of this study was to evaluate the proposed framework for automated estimation of lung tumor locations in kV-CBCT images for tumor-based patient positioning in SLBRT. Twenty clinical cases are considered, involving solid, pure ground-glass opacity (GGO), mixed GGO, solitary, and non-solitary tumor types. The proposed framework consists of four steps: (1) determination of a search region for tumor location detection in a kV-CBCT image; (2) extraction of a tumor template from a planning CT image; (3) preprocessing for tumor region enhancement (edge and tumor enhancement using a Sobel filter and a blob structure enhancement (BSE) filter, respectively); and (4) tumor location estimation based on a template-matching technique. The location errors in the original, edge-, and tumor-enhanced images were found to be 1.2 ± 0.7 mm, 4.2 ± 8.0 mm, and 2.7 ± 4.6 mm, respectively. The location errors in the original images of solid, pure GGO, mixed GGO, solitary, and non-solitary types of tumors were 1.2 ± 0.7 mm, 1.3 ± 0.9 mm, 0.4 ± 0.6 mm, 1.1 ± 0.8 mm and 1.0 ± 0.7 mm, respectively. These results suggest that the proposed framework is robust as regards automatic estimation of several types of tumor locations in kV-CBCT images for tumor-based patient positioning in SLBRT.

Smartphone-Based Real-time Assessment of Swallowing Ability From the Swallowing Sound.

PubMed

Jayatilake, Dushyantha; Ueno, Tomoyuki; Teramoto, Yohei; Nakai, Kei; Hidaka, Kikue; Ayuzawa, Satoshi; Eguchi, Kiyoshi; Matsumura, Akira; Suzuki, Kenji

2015-01-01

Dysphagia can cause serious challenges to both physical and mental health. Aspiration due to dysphagia is a major health risk that could cause pneumonia and even death. The videofluoroscopic swallow study (VFSS), which is considered the gold standard for the diagnosis of dysphagia, is not widely available, expensive and causes exposure to radiation. The screening tests used for dysphagia need to be carried out by trained staff, and the evaluations are usually non-quantifiable. This paper investigates the development of the Swallowscope, a smartphone-based device and a feasible real-time swallowing sound-processing algorithm for the automatic screening, quantitative evaluation, and the visualisation of swallowing ability. The device can be used during activities of daily life with minimal intervention, making it potentially more capable of capturing aspirations and risky swallow patterns through the continuous monitoring. It also consists of a cloud-based system for the server-side analyzing and automatic sharing of the swallowing sound. The real-time algorithm we developed for the detection of dry and water swallows is based on a template matching approach. We analyzed the wavelet transformation-based spectral characteristics and the temporal characteristics of simultaneous synchronised VFSS and swallowing sound recordings of 25% barium mixed 3-ml water swallows of 70 subjects and the dry or saliva swallowing sound of 15 healthy subjects to establish the parameters of the template. With this algorithm, we achieved an overall detection accuracy of 79.3% (standard error: 4.2%) for the 92 water swallows; and a precision of 83.7% (range: 66.6%-100%) and a recall of 93.9% (range: 72.7%-100%) for the 71 episodes of dry swallows.

Smartphone-Based Real-time Assessment of Swallowing Ability From the Swallowing Sound

PubMed Central

Ueno, Tomoyuki; Teramoto, Yohei; Nakai, Kei; Hidaka, Kikue; Ayuzawa, Satoshi; Eguchi, Kiyoshi; Matsumura, Akira; Suzuki, Kenji

2015-01-01

Dysphagia can cause serious challenges to both physical and mental health. Aspiration due to dysphagia is a major health risk that could cause pneumonia and even death. The videofluoroscopic swallow study (VFSS), which is considered the gold standard for the diagnosis of dysphagia, is not widely available, expensive and causes exposure to radiation. The screening tests used for dysphagia need to be carried out by trained staff, and the evaluations are usually non-quantifiable. This paper investigates the development of the Swallowscope, a smartphone-based device and a feasible real-time swallowing sound-processing algorithm for the automatic screening, quantitative evaluation, and the visualisation of swallowing ability. The device can be used during activities of daily life with minimal intervention, making it potentially more capable of capturing aspirations and risky swallow patterns through the continuous monitoring. It also consists of a cloud-based system for the server-side analyzing and automatic sharing of the swallowing sound. The real-time algorithm we developed for the detection of dry and water swallows is based on a template matching approach. We analyzed the wavelet transformation-based spectral characteristics and the temporal characteristics of simultaneous synchronised VFSS and swallowing sound recordings of 25% barium mixed 3-ml water swallows of 70 subjects and the dry or saliva swallowing sound of 15 healthy subjects to establish the parameters of the template. With this algorithm, we achieved an overall detection accuracy of 79.3% (standard error: 4.2%) for the 92 water swallows; and a precision of 83.7% (range: 66.6%–100%) and a recall of 93.9% (range: 72.7%–100%) for the 71 episodes of dry swallows. PMID:27170905

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.

Detecting binary neutron star systems with spin in advanced gravitational-wave detectors

NASA Astrophysics Data System (ADS)

Brown, Duncan A.; Harry, Ian; Lundgren, Andrew; Nitz, Alexander H.

2012-10-01

The detection of gravitational waves from binary neutron stars is a major goal of the gravitational-wave observatories Advanced LIGO and Advanced Virgo. Previous searches for binary neutron stars with LIGO and Virgo neglected the component stars’ angular momentum (spin). We demonstrate that neglecting spin in matched-filter searches causes advanced detectors to lose more than 3% of the possible signal-to-noise ratio for 59% (6%) of sources, assuming that neutron star dimensionless spins, cJ/GM2, are uniformly distributed with magnitudes between 0 and 0.4 (0.05) and that the neutron stars have isotropically distributed spin orientations. We present a new method for constructing template banks for gravitational-wave searches for systems with spin. We present a new metric in a parameter space in which the template placement metric is globally flat. This new method can create template banks of signals with nonzero spins that are (anti-)aligned with the orbital angular momentum. We show that this search loses more than 3% of the maximum signal-to-noise for only 9% (0.2%) of binary neutron star sources with dimensionless spins between 0 and 0.4 (0.05) and isotropic spin orientations. Use of this template bank will prevent selection bias in gravitational-wave searches and allow a more accurate exploration of the distribution of spins in binary neutron stars.

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.

Automated MRI Cerebellar Size Measurements Using Active Appearance Modeling

PubMed Central

Price, Mathew; Cardenas, Valerie A.; Fein, George

2014-01-01

Although the human cerebellum has been increasingly identified as an important hub that shows potential for helping in the diagnosis of a large spectrum of disorders, such as alcoholism, autism, and fetal alcohol spectrum disorder, the high costs associated with manual segmentation, and low availability of reliable automated cerebellar segmentation tools, has resulted in a limited focus on cerebellar measurement in human neuroimaging studies. We present here the CATK (Cerebellar Analysis Toolkit), which is based on the Bayesian framework implemented in FMRIB’s FIRST. This approach involves training Active Appearance Models (AAM) using hand-delineated examples. CATK can currently delineate the cerebellar hemispheres and three vermal groups (lobules I–V, VI–VII, and VIII–X). Linear registration with the low-resolution MNI152 template is used to provide initial alignment, and Point Distribution Models (PDM) are parameterized using stellar sampling. The Bayesian approach models the relationship between shape and texture through computation of conditionals in the training set. Our method varies from the FIRST framework in that initial fitting is driven by 1D intensity profile matching, and the conditional likelihood function is subsequently used to refine fitting. The method was developed using T1-weighted images from 63 subjects that were imaged and manually labeled: 43 subjects were scanned once and were used for training models, and 20 subjects were imaged twice (with manual labeling applied to both runs) and used to assess reliability and validity. Intraclass correlation analysis shows that CATK is highly reliable (average test-retest ICCs of 0.96), and offers excellent agreement with the gold standard (average validity ICC of 0.87 against manual labels). Comparisons against an alternative atlas-based approach, SUIT (Spatially Unbiased Infratentorial Template), that registers images with a high-resolution template of the cerebellum, show that our AAM approach offers superior reliability and validity. Extensions of CATK to cerebellar hemisphere parcels is envisioned. PMID:25192657

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

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

C-oriented and {010} facets exposed BiVO4 nanowall films: template-free fabrication and their enhanced photoelectrochemical properties.

PubMed

Zhou, Min; Zhang, Shudong; Sun, Yongfu; Wu, Changzheng; Wang, Mingtai; Xie, Yi

2010-12-03

Vertically aligned BiVO(4) nanowall films on indium tin oxide (ITO) glass have been fabricated through a template-free hydrothermal method for the first time. Based on the structural understanding of both BiVO(4) and ITO, the lattice matches ({020}(BiVO4) and {040}(ITO), {200}(BiVO4) and {004}(ITO), respectively) and the similarity of metal atomic arrangement parallel to {001} planes turn out to be crucial for the fabrication of the nanowalls. Consequently, the growth of a BiVO(4) film begins from heteroepitaxy and undergoes an Ostwald ripening process to form an extended network, resulting in a c-orientation and exposing {010} facets. Through this process, it is much easier to obtain a range of nanowall films with different packing densities, as the surface state of ITO glass is alterable by adjusting the concentration of acid. The films can be directly used as an electrode, which exhibits an excellent response to visible light, especially light with low intensity, allowing for the electrical interconnection, highly active surface, appropriate orientation, and a good contact with the substrate. There are great benefits in improving the technique for detecting the weak light source signals.

Probing the bulk ionic conductivity by thin film hetero-epitaxial engineering

NASA Astrophysics Data System (ADS)

Pergolesi, Daniele; Roddatis, Vladimir; Fabbri, Emiliana; Schneider, Christof W.; Lippert, Thomas; Traversa, Enrico; Kilner, John A.

2015-02-01

Highly textured thin films with small grain boundary regions can be used as model systems to directly measure the bulk conductivity of oxygen ion conducting oxides. Ionic conducting thin films and epitaxial heterostructures are also widely used to probe the effect of strain on the oxygen ion migration in oxide materials. For the purpose of these investigations a good lattice matching between the film and the substrate is required to promote the ordered film growth. Moreover, the substrate should be a good electrical insulator at high temperature to allow a reliable electrical characterization of the deposited film. Here we report the fabrication of an epitaxial heterostructure made with a double buffer layer of BaZrO3 and SrTiO3 grown on MgO substrates that fulfills both requirements. Based on such template platform, highly ordered (001) epitaxially oriented thin films of 15% Sm-doped CeO2 and 8 mol% Y2O3 stabilized ZrO2 are grown. Bulk conductivities as well as activation energies are measured for both materials, confirming the success of the approach. The reported insulating template platform promises potential application also for the electrical characterization of other novel electrolyte materials that still need a thorough understanding of their ionic conductivity.

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.

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.

Three Dimensional Object Recognition Using a Complex Autoregressive Model

DTIC Science & Technology

1993-12-01

3.4.2 Template Matching Algorithm ...................... 3-16 3.4.3 K-Nearest-Neighbor ( KNN ) Techniques ................. 3-25 3.4.4 Hidden Markov Model...Neighbor ( KNN ) Test Results ...................... 4-13 4.2.1 Single-Look 1-NN Testing .......................... 4-14 4.2.2 Multiple-Look 1-NN Testing...4-15 4.2.3 Discussion of KNN Test Results ...................... 4-15 4.3 Hidden Markov Model (HMM) Test Results

Seismicity rate increases associated with slow slip episodes prior to the 2012 Mw 7.4 Ometepec earthquake

NASA Astrophysics Data System (ADS)

Colella, Harmony V.; Sit, Stefany M.; Brudzinski, Michael R.; Graham, Shannon E.; DeMets, Charles; Holtkamp, Stephen G.; Skoumal, Robert J.; Ghouse, Noorulann; Cabral-Cano, Enrique; Kostoglodov, Vladimir; Arciniega-Ceballos, Alejandra

2017-04-01

The March 20, 2012 Mw 7.4 Ometepec earthquake in the Oaxaca region of Southern Mexico provides a unique opportunity to examine whether subtle changes in seismicity, tectonic tremor, or slow slip can be observed prior to a large earthquake that may illuminate changes in stress or background slip rate. Continuous Global Positioning System (cGPS) data reveal a 5-month-long slow slip event (SSE) between ∼20 and 35 km depth that migrated toward and reached the vicinity of the mainshock a few weeks prior to the earthquake. Seismicity in Oaxaca is examined using single station tectonic tremor detection and multi-station waveform template matching of earthquake families. An increase in seismic activity, detected with template matching using aftershock waveforms, is only observed in the weeks prior to the mainshock in the region between the SSE and mainshock. In contrast, a SSE ∼15 months earlier occurred at ∼25-40 km depth and was primarily associated with an increase in tectonic tremor. Together, these observations indicate that in the Oaxaca region of Mexico shallower slow slip promotes elevated seismicity rates, and deeper slow slip promotes tectonic tremor. Results from this study add to a growing number of published accounts that indicate slow slip may be a common pre-earthquake signature.

Characterizing the SEMG patterns with myofascial pain using a multi-scale wavelet model through machine learning approaches.

PubMed

Lin, Yu-Ching; Yu, Nan-Ying; Jiang, Ching-Fen; Chang, Shao-Hsia

2018-06-02

In this paper, we introduce a newly developed multi-scale wavelet model for the interpretation of surface electromyography (SEMG) signals and validate the model's capability to characterize changes in neuromuscular activation in cases with myofascial pain syndrome (MPS) via machine learning methods. The SEMG data collected from normal (N = 30; 27 women, 3 men) and MPS subjects (N = 26; 22 women, 4 men) were adopted for this retrospective analysis. SMEGs were measured from the taut-band loci on both sides of the trapezius muscle on the upper back while he/she conducted a cyclic bilateral backward shoulder extension movement within 1 min. Classification accuracy of the SEMG model to differentiate MPS patients from normal subjects was 77% using template matching and 60% using K-means clustering. Classification consistency between the two machine learning methods was 87% in the normal group and 93% in the MPS group. The 2D feature graphs derived from the proposed multi-scale model revealed distinct patterns between normal subjects and MPS patients. The classification consistency using template matching and K-means clustering suggests the potential of using the proposed model to characterize interference pattern changes induced by MPS. Copyright © 2018. Published by Elsevier Ltd.

High Quality Bioreplication of Intricate Nanostructures from a Fragile Gecko Skin Surface with Bactericidal Properties

NASA Astrophysics Data System (ADS)

Green, David William; Lee, Kenneth Ka-Ho; Watson, Jolanta Anna; Kim, Hyun-Yi; Yoon, Kyung-Sik; Kim, Eun-Jung; Lee, Jong-Min; Watson, Gregory Shaun; Jung, Han-Sung

2017-01-01

The external epithelial surfaces of plants and animals are frequently carpeted with small micro- and nanostructures, which broadens their adaptive capabilities in challenging physical habitats. Hairs and other shaped protuberances manage with excessive water, light contaminants, predators or parasites in innovative ways. We are interested in transferring these intricate architectures onto biomedical devices and daily-life surfaces. Such a project requires a very rapid and accurate small-scale fabrication process not involving lithography. In this study, we describe a simple benchtop biotemplating method using shed gecko lizard skin that generates duplicates that closely replicate the small nanotipped hairs (spinules) that cover the original skin. Synthetic replication of the spinule arrays in popular biomaterials closely matched the natural spinules in length. More significantly, the shape, curvature and nanotips of the synthetic arrays are virtually identical to the natural ones. Despite some small differences, the synthetic gecko skin surface resisted wetting and bacterial contamination at the same level as natural shed skin templates. Such synthetic gecko skin surfaces are excellent platforms to test for bacterial control in clinical settings. We envision testing the biocidal properties of the well-matched templates for fungal spores and viral resistance in biomedicine as well as co/multi-cultures.

Development of a two wheeled self balancing robot with speech recognition and navigation algorithm

NASA Astrophysics Data System (ADS)

Rahman, Md. Muhaimin; Ashik-E-Rasul, Haq, Nowab. Md. Aminul; Hassan, Mehedi; Hasib, Irfan Mohammad Al; Hassan, K. M. Rafidh

2016-07-01

This paper is aimed to discuss modeling, construction and development of navigation algorithm of a two wheeled self balancing mobile robot in an enclosure. In this paper, we have discussed the design of two of the main controller algorithms, namely PID algorithms, on the robot model. Simulation is performed in the SIMULINK environment. The controller is developed primarily for self-balancing of the robot and also it's positioning. As for the navigation in an enclosure, template matching algorithm is proposed for precise measurement of the robot position. The navigation system needs to be calibrated before navigation process starts. Almost all of the earlier template matching algorithms that can be found in the open literature can only trace the robot. But the proposed algorithm here can also locate the position of other objects in an enclosure, like furniture, tables etc. This will enable the robot to know the exact location of every stationary object in the enclosure. Moreover, some additional features, such as Speech Recognition and Object Detection, are added. For Object Detection, the single board Computer Raspberry Pi is used. The system is programmed to analyze images captured via the camera, which are then processed through background subtraction, followed by active noise reduction.

Multiscale Reconstruction for Magnetic Resonance Fingerprinting

PubMed Central

Pierre, Eric Y.; Ma, Dan; Chen, Yong; Badve, Chaitra; Griswold, Mark A.

2015-01-01

Purpose To reduce acquisition time needed to obtain reliable parametric maps with Magnetic Resonance Fingerprinting. Methods An iterative-denoising algorithm is initialized by reconstructing the MRF image series at low image resolution. For subsequent iterations, the method enforces pixel-wise fidelity to the best-matching dictionary template then enforces fidelity to the acquired data at slightly higher spatial resolution. After convergence, parametric maps with desirable spatial resolution are obtained through template matching of the final image series. The proposed method was evaluated on phantom and in-vivo data using the highly-undersampled, variable-density spiral trajectory and compared with the original MRF method. The benefits of additional sparsity constraints were also evaluated. When available, gold standard parameter maps were used to quantify the performance of each method. Results The proposed approach allowed convergence to accurate parametric maps with as few as 300 time points of acquisition, as compared to 1000 in the original MRF work. Simultaneous quantification of T1, T2, proton density (PD) and B0 field variations in the brain was achieved in vivo for a 256×256 matrix for a total acquisition time of 10.2s, representing a 3-fold reduction in acquisition time. Conclusions The proposed iterative multiscale reconstruction reliably increases MRF acquisition speed and accuracy. PMID:26132462

SNSEDextend: SuperNova Spectral Energy Distributions extrapolation toolkit

NASA Astrophysics Data System (ADS)

Pierel, Justin D. R.; Rodney, Steven A.; Avelino, Arturo; Bianco, Federica; Foley, Ryan J.; Friedman, Andrew; Hicken, Malcolm; Hounsell, Rebekah; Jha, Saurabh W.; Kessler, Richard; Kirshner, Robert; Mandel, Kaisey; Narayan, Gautham; Filippenko, Alexei V.; Scolnic, Daniel; Strolger, Louis-Gregory

2018-05-01

SNSEDextend extrapolates core-collapse and Type Ia Spectral Energy Distributions (SEDs) into the UV and IR for use in simulations and photometric classifications. The user provides a library of existing SED templates (such as those in the authors' SN SED Repository) along with new photometric constraints in the UV and/or NIR wavelength ranges. The software then extends the existing template SEDs so their colors match the input data at all phases. SNSEDextend can also extend the SALT2 spectral time-series model for Type Ia SN for a "first-order" extrapolation of the SALT2 model components, suitable for use in survey simulations and photometric classification tools; as the code does not do a rigorous re-training of the SALT2 model, the results should not be relied on for precision applications such as light curve fitting for cosmology.

Coupling effects in 3D plasmonic structures templated by Morpho butterfly wings.

PubMed

He, Jiaqing; Shen, Qingchen; Yang, Shuai; He, Gufeng; Tao, Peng; Song, Chengyi; Wu, Jianbo; Deng, Tao; Shang, Wen

2018-01-03

This paper presents the study of the coupling effects of three dimensional (3D) plasmonic nanostructures templated by Morpho butterfly wings. Different from the random deposition of metallic nanoparticles (NPs) or conformal coating of metallic layers on butterfly wings reported previously, the 3D plasmonic nanostructures studied in this work consist of gold (Au) nanostrips quasi-periodically arranged in 3D, which allows us to investigate the plasmonic coupling effects. Through refractive index (RI) matching, the plasmonic coupling can be differentiated from the optical contribution of butterfly wings. By tuning the deposition thickness of Au from 30 to 90 nm, the plasmonic coupling effects between the 3D Au nanostrips are gradually enhanced. In particular, the near-field coupling results in two resonant modes and enhances the surface-enhanced Raman scattering (SERS) signals.

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

Computer-assisted template-guided custom-designed 3D-printed implant placement with custom-designed 3D-printed surgical tooling: an in-vitro proof of a novel concept.

PubMed

Anssari Moin, David; Derksen, Wiebe; Waars, Hugo; Hassan, Bassam; Wismeijer, Daniel

2017-05-01

The aim of this study was to introduce a new concept for computer-assisted template-guided placement of a custom 3D-designed/3D-printed implant with congruent custom 3D-designed/3D-printed surgical tooling and to test the feasibility and accuracy of this method in-vitro. One partially edentulous human mandibular cadaver was scanned with a cone-beam computed tomography (CBCT) system and intra-oral scan system. The 3D data of this cadaver were imported in specialized software and used to analyse the region of a missing tooth. Based on the functional and anatomical parameters, an individual implant with congruent surgical tooling and surgical guided template was designed and 3D-printed. The guided osteotomy was performed, and the custom implant inserted. To evaluate the planned implant position in comparison with the placed implant position, the mandible with implant was scanned again with the CBCT system and software matching was applied to measure the accuracy of the procedure. The angular deflection with the planned implant position was 0.40°. When comparing the 3D positions of the shoulder, there is a deviation of 0.72 mm resulting in an apical deviation of 0.72 mm. With the use of currently available technology, it is very well feasible to create in a virtual simulation a custom implant with congruent custom surgical tooling and to transfer this to a clinical setting. However, further research on multiple levels is needed to explore this novel approach. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Best chirplet chain: Near-optimal detection of gravitational wave chirps

NASA Astrophysics Data System (ADS)

Chassande-Mottin, Éric; Pai, Archana

2006-02-01

The list of putative sources of gravitational waves possibly detected by the ongoing worldwide network of large scale interferometers has been continuously growing in the last years. For some of them, the detection is made difficult by the lack of a complete information about the expected signal. We concentrate on the case where the expected gravitational wave (GW) is a quasiperiodic frequency modulated signal i.e., a chirp. In this article, we address the question of detecting an a priori unknown GW chirp. We introduce a general chirp model and claim that it includes all physically realistic GW chirps. We produce a finite grid of template waveforms which samples the resulting set of possible chirps. If we follow the classical approach (used for the detection of inspiralling binary chirps, for instance), we would build a bank of quadrature matched filters comparing the data to each of the templates of this grid. The detection would then be achieved by thresholding the output, the maximum giving the individual which best fits the data. In the present case, this exhaustive search is not tractable because of the very large number of templates in the grid. We show that the exhaustive search can be reformulated (using approximations) as a pattern search in the time-frequency plane. This motivates an approximate but feasible alternative solution which is clearly linked to the optimal one. The time-frequency representation and pattern search algorithm are fully determined by the reformulation. This contrasts with the other time-frequency based methods presented in the literature for the same problem, where these choices are justified by “ad hoc” arguments. In particular, the time-frequency representation has to be unitary. Finally, we assess the performance, robustness and computational cost of the proposed method with several benchmarks using simulated data.

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.

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…

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 .

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.

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.

Image velocimetry for clouds with relaxation labeling based on deformation consistency

NASA Astrophysics Data System (ADS)

Horinouchi, Takeshi; Murakami, Shin-ya; Kouyama, Toru; Ogohara, Kazunori; Yamazaki, Atsushi; Yamada, Manabu; Watanabe, Shigeto

2017-08-01

Correlation-based cloud tracking has been extensively used to measure atmospheric winds, but still difficulty remains. In this study, aiming at developing a cloud tracking system for Akatsuki, an artificial satellite orbiting Venus, a formulation is developed for improving the relaxation labeling technique to select appropriate peaks of cross-correlation surfaces which tend to have multiple peaks. The formulation makes an explicit use of consistency inherent in the type of cross-correlation method where template sub-images are slid without deformation; if the resultant motion vectors indicate a too-large deformation, it is contradictory to the assumption of the method. The deformation consistency is exploited further to develop two post processes; one clusters the motion vectors into groups within each of which the consistency is perfect, and the other extends the groups using the original candidate lists. These processes are useful to eliminate erroneous vectors, distinguish motion vectors at different altitudes, and detect phase velocities of waves in fluids such as atmospheric gravity waves. As a basis of the relaxation labeling and the post processes as well as uncertainty estimation, the necessity to find isolated (well-separated) peaks of cross-correlation surfaces is argued, and an algorithm to realize it is presented. All the methods are implemented, and their effectiveness is demonstrated with initial images obtained by the ultraviolet imager onboard Akatsuki. Since the deformation consistency regards the logical consistency inherent in template matching methods, it should have broad application beyond cloud tracking.

Computational design of d-peptide inhibitors of hepatitis delta antigen dimerization

NASA Astrophysics Data System (ADS)

Elkin, Carl D.; Zuccola, Harmon J.; Hogle, James M.; Joseph-McCarthy, Diane

2000-11-01

Hepatitis delta virus (HDV) encodes a single polypeptide called hepatitis delta antigen (DAg). Dimerization of DAg is required for viral replication. The structure of the dimerization region, residues 12 to 60, consists of an anti-parallel coiled coil [Zuccola et al., Structure, 6 (1998) 821]. Multiple Copy Simultaneous Searches (MCSS) of the hydrophobic core region formed by the bend in the helix of one monomer of this structure were carried out for many diverse functional groups. Six critical interaction sites were identified. The Protein Data Bank was searched for backbone templates to use in the subsequent design process by matching to these sites. A 14 residue helix expected to bind to the d-isomer of the target structure was selected as the template. Over 200 000 mutant sequences of this peptide were generated based on the MCSS results. A secondary structure prediction algorithm was used to screen all sequences, and in general only those that were predicted to be highly helical were retained. Approximately 100 of these 14-mers were model built as d-peptides and docked with the l-isomer of the target monomer. Based on calculated interaction energies, predicted helicity, and intrahelical salt bridge patterns, a small number of peptides were selected as the most promising candidates. The ligand design approach presented here is the computational analogue of mirror image phage display. The results have been used to characterize the interactions responsible for formation of this model anti-parallel coiled coil and to suggest potential ligands to disrupt it.

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.

Photoluminescence emission from GaAs nanodisks in GaAs/AlGaAs nanopillar arrays fabricated by neutral beam etching

NASA Astrophysics Data System (ADS)

Ohori, Daisuke; Fukuyama, Atsuhiko; Sakai, Kentaro; Higo, Akio; Thomas, Cedric; Samukawa, Seiji; Ikari, Tetsuo

2017-05-01

GaAs quantum nanodisks (QNDs) in nanopillar (NP) arrays are considered to be an attractive candidate for photonic device applications. We report a damageless fabrication technique that can be used to produce large-area lattice-matched GaAs/AlGaAs heterostructure NP arrays through the use of a bio-template and neutral beam etching. We have successfully realized GaAs QNDs in NPs owing to nanoscale iron oxide masks included in poly(ethylene glycol)-decorated ferritin protein shells. We observed for first time the photoluminescence emission from as-etched GaAs QNDs and confirmed quantum confinement by quantum mechanical calculation. Our methodology is vital for high-efficiency pillar-based optoelectronic devices such as NP laser diodes.

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.

Composite multi-lobe descriptor for cross spectral face recognition: matching active IR to visible light images

NASA Astrophysics Data System (ADS)

Cao, Zhicheng; Schmid, Natalia A.

2015-05-01

Matching facial images across electromagnetic spectrum presents a challenging problem in the field of biometrics and identity management. An example of this problem includes cross spectral matching of active infrared (IR) face images or thermal IR face images against a dataset of visible light images. This paper describes a new operator named Composite Multi-Lobe Descriptor (CMLD) for facial feature extraction in cross spectral matching of near-infrared (NIR) or short-wave infrared (SWIR) against visible light images. The new operator is inspired by the design of ordinal measures. The operator combines Gaussian-based multi-lobe kernel functions, Local Binary Pattern (LBP), generalized LBP (GLBP) and Weber Local Descriptor (WLD) and modifies them into multi-lobe functions with smoothed neighborhoods. The new operator encodes both the magnitude and phase responses of Gabor filters. The combining of LBP and WLD utilizes both the orientation and intensity information of edges. Introduction of multi-lobe functions with smoothed neighborhoods further makes the proposed operator robust against noise and poor image quality. Output templates are transformed into histograms and then compared by means of a symmetric Kullback-Leibler metric resulting in a matching score. The performance of the multi-lobe descriptor is compared with that of other operators such as LBP, Histogram of Oriented Gradients (HOG), ordinal measures, and their combinations. The experimental results show that in many cases the proposed method, CMLD, outperforms the other operators and their combinations. In addition to different infrared spectra, various standoff distances from close-up (1.5 m) to intermediate (50 m) and long (106 m) are also investigated in this paper. Performance of CMLD is evaluated for of each of the three cases of distances.

Systematic Biases in Parameter Estimation of Binary Black-Hole Mergers

NASA Technical Reports Server (NTRS)

Littenberg, Tyson B.; Baker, John G.; Buonanno, Alessandra; Kelly, Bernard J.

2012-01-01

Parameter estimation of binary-black-hole merger events in gravitational-wave data relies on matched filtering techniques, which, in turn, depend on accurate model waveforms. Here we characterize the systematic biases introduced in measuring astrophysical parameters of binary black holes by applying the currently most accurate effective-one-body templates to simulated data containing non-spinning numerical-relativity waveforms. For advanced ground-based detectors, we find that the systematic biases are well within the statistical error for realistic signal-to-noise ratios (SNR). These biases grow to be comparable to the statistical errors at high signal-to-noise ratios for ground-based instruments (SNR approximately 50) but never dominate the error budget. At the much larger signal-to-noise ratios expected for space-based detectors, these biases will become large compared to the statistical errors but are small enough (at most a few percent in the black-hole masses) that we expect they should not affect broad astrophysical conclusions that may be drawn from the data.

Comparison between Frame-Constrained Fix-Pixel-Value and Frame-Free Spiking-Dynamic-Pixel ConvNets for Visual Processing

PubMed Central

Farabet, Clément; Paz, Rafael; Pérez-Carrasco, Jose; Zamarreño-Ramos, Carlos; Linares-Barranco, Alejandro; LeCun, Yann; Culurciello, Eugenio; Serrano-Gotarredona, Teresa; Linares-Barranco, Bernabe

2012-01-01

Most scene segmentation and categorization architectures for the extraction of features in images and patches make exhaustive use of 2D convolution operations for template matching, template search, and denoising. Convolutional Neural Networks (ConvNets) are one example of such architectures that can implement general-purpose bio-inspired vision systems. In standard digital computers 2D convolutions are usually expensive in terms of resource consumption and impose severe limitations for efficient real-time applications. Nevertheless, neuro-cortex inspired solutions, like dedicated Frame-Based or Frame-Free Spiking ConvNet Convolution Processors, are advancing real-time visual processing. These two approaches share the neural inspiration, but each of them solves the problem in different ways. Frame-Based ConvNets process frame by frame video information in a very robust and fast way that requires to use and share the available hardware resources (such as: multipliers, adders). Hardware resources are fixed- and time-multiplexed by fetching data in and out. Thus memory bandwidth and size is important for good performance. On the other hand, spike-based convolution processors are a frame-free alternative that is able to perform convolution of a spike-based source of visual information with very low latency, which makes ideal for very high-speed applications. However, hardware resources need to be available all the time and cannot be time-multiplexed. Thus, hardware should be modular, reconfigurable, and expansible. Hardware implementations in both VLSI custom integrated circuits (digital and analog) and FPGA have been already used to demonstrate the performance of these systems. In this paper we present a comparison study of these two neuro-inspired solutions. A brief description of both systems is presented and also discussions about their differences, pros and cons. PMID:22518097

Comparison between Frame-Constrained Fix-Pixel-Value and Frame-Free Spiking-Dynamic-Pixel ConvNets for Visual Processing.

PubMed

Farabet, Clément; Paz, Rafael; Pérez-Carrasco, Jose; Zamarreño-Ramos, Carlos; Linares-Barranco, Alejandro; Lecun, Yann; Culurciello, Eugenio; Serrano-Gotarredona, Teresa; Linares-Barranco, Bernabe

2012-01-01

Most scene segmentation and categorization architectures for the extraction of features in images and patches make exhaustive use of 2D convolution operations for template matching, template search, and denoising. Convolutional Neural Networks (ConvNets) are one example of such architectures that can implement general-purpose bio-inspired vision systems. In standard digital computers 2D convolutions are usually expensive in terms of resource consumption and impose severe limitations for efficient real-time applications. Nevertheless, neuro-cortex inspired solutions, like dedicated Frame-Based or Frame-Free Spiking ConvNet Convolution Processors, are advancing real-time visual processing. These two approaches share the neural inspiration, but each of them solves the problem in different ways. Frame-Based ConvNets process frame by frame video information in a very robust and fast way that requires to use and share the available hardware resources (such as: multipliers, adders). Hardware resources are fixed- and time-multiplexed by fetching data in and out. Thus memory bandwidth and size is important for good performance. On the other hand, spike-based convolution processors are a frame-free alternative that is able to perform convolution of a spike-based source of visual information with very low latency, which makes ideal for very high-speed applications. However, hardware resources need to be available all the time and cannot be time-multiplexed. Thus, hardware should be modular, reconfigurable, and expansible. Hardware implementations in both VLSI custom integrated circuits (digital and analog) and FPGA have been already used to demonstrate the performance of these systems. In this paper we present a comparison study of these two neuro-inspired solutions. A brief description of both systems is presented and also discussions about their differences, pros and cons.

On the precision of automated activation time estimation

NASA Technical Reports Server (NTRS)

Kaplan, D. T.; Smith, J. M.; Rosenbaum, D. S.; Cohen, R. J.

1988-01-01

We examined how the assignment of local activation times in epicardial and endocardial electrograms is affected by sampling rate, ambient signal-to-noise ratio, and sinx/x waveform interpolation. Algorithms used for the estimation of fiducial point locations included dV/dtmax, and a matched filter detection algorithm. Test signals included epicardial and endocardial electrograms overlying both normal and infarcted regions of dog myocardium. Signal-to-noise levels were adjusted by combining known data sets with white noise "colored" to match the spectral characteristics of experimentally recorded noise. For typical signal-to-noise ratios and sampling rates, the template-matching algorithm provided the greatest precision in reproducibly estimating fiducial point location, and sinx/x interpolation allowed for an additional significant improvement. With few restrictions, combining these two techniques may allow for use of digitization rates below the Nyquist rate without significant loss of precision.

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.

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.

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.

Model-based morphological segmentation and labeling of coronary angiograms.

PubMed

Haris, K; Efstratiadis, S N; Maglaveras, N; Pappas, C; Gourassas, J; Louridas, G

1999-10-01

A method for extraction and labeling of the coronary arterial tree (CAT) using minimal user supervision in single-view angiograms is proposed. The CAT structural description (skeleton and borders) is produced, along with quantitative information for the artery dimensions and assignment of coded labels, based on a given coronary artery model represented by a graph. The stages of the method are: 1) CAT tracking and detection; 2) artery skeleton and border estimation; 3) feature graph creation; and iv) artery labeling by graph matching. The approximate CAT centerline and borders are extracted by recursive tracking based on circular template analysis. The accurate skeleton and borders of each CAT segment are computed, based on morphological homotopy modification and watershed transform. The approximate centerline and borders are used for constructing the artery segment enclosing area (ASEA), where the defined skeleton and border curves are considered as markers. Using the marked ASEA, an artery gradient image is constructed where all the ASEA pixels (except the skeleton ones) are assigned the gradient magnitude of the original image. The artery gradient image markers are imposed as its unique regional minima by the homotopy modification method, the watershed transform is used for extracting the artery segment borders, and the feature graph is updated. Finally, given the created feature graph and the known model graph, a graph matching algorithm assigns the appropriate labels to the extracted CAT using weighted maximal cliques on the association graph corresponding to the two given graphs. Experimental results using clinical digitized coronary angiograms are presented.

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.

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.

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.

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.

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.

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.

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

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

Altered white matter integrity and development in children with autism: a combined voxel-based morphometry and diffusion imaging study.

PubMed

Mengotti, Paola; D'Agostini, Serena; Terlevic, Robert; De Colle, Cristina; Biasizzo, Elsa; Londero, Danielle; Ferro, Adele; Rambaldelli, Gianluca; Balestrieri, Matteo; Zanini, Sergio; Fabbro, Franco; Molteni, Massimo; Brambilla, Paolo

2011-02-01

A combined protocol of voxel-based morphometry (VBM) and diffusion-weighted imaging (DWI) was applied to investigate the neurodevelopment of gray and white matter in autism. Twenty children with autism (mean age= 7 ± 2.75 years old; age range: 4-14; 2 girls) and 22 matched normally developing children (mean age = 7.68 ± 2.03 years old; age range: 4-11; 2 girls) underwent magnetic resonance imaging (MRI). VBM was employed by applying the Template-o-Matic toolbox (TOM), a new approach which constructs the age-matched customized template for tissue segmentation. Also, the apparent diffusion coefficients (ADC) of water molecules were obtained from the analysis of DWI. Regions of interests (ROIs), standardized at 5 pixels, were placed in cortical lobes and corpus callosum on the non-diffusion weighted echo-planar images (b = 0) and were then automatically transferred to the corresponding maps to obtain the ADC values. Compared to normal children, individuals with autism had significantly: (1) increased white matter volumes in the right inferior frontal gyrus, the right fusiform gyrus, the left precentral and supplementary motor area and the left hippocampus, (2) increased gray matter volumes in the inferior temporal gyri bilaterally, the right inferior parietal cortex, the right superior occipital lobe and the left superior parietal lobule, and (3) decreased gray matter volumes in the right inferior frontal gyrus and the left supplementary motor area. Abnormally increased ADC values in the bilateral frontal cortex and in the left side of the genu of the corpus callosum were also reported in autism. Finally, age correlated negatively with lobar and callosal ADC measurements in individuals with autism, but not in children with normal development. These findings suggest cerebral dysconnectivity in the early phases of autism coupled with an altered white matter maturation trajectory during childhood potentially taking place in the frontal and parietal lobes, which may represent a neurodevelopmental marker of the disorder, possibly accounting for the cognitive and social deficits. Copyright © 2010 Elsevier Inc. All rights reserved.

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.

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.

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,…

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.

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.

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.

Assessing the calorific significance of episodes of human cannibalism in the Palaeolithic

PubMed Central

Cole, James

2017-01-01

Episodes of Palaeolithic cannibalism have frequently been defined as ‘nutritional’ in nature, but with little empirical evidence to assess their dietary significance. This paper presents a nutritional template that offers a proxy calorie value for the human body. When applied to the Palaeolithic record, the template provides a framework for assessing the dietary value of prehistoric cannibalistic episodes compared to the faunal record. Results show that humans have a comparable nutritional value to those faunal species that match our typical body weight, but significantly lower than a range of fauna often found in association with anthropogenically modified hominin remains. This could suggest that the motivations behind hominin anthropophagy may not have been purely nutritionally motivated. It is proposed here that the comparatively low nutritional value of hominin cannibalism episodes support more socially or culturally driven narratives in the interpretation of Palaeolithic cannibalism. PMID:28383521