A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

PubMed

Han, Renmin; Wang, Liansan; Liu, Zhiyong; Sun, Fei; Zhang, Fa

2015-12-01

Although the topic of fiducial marker-based alignment in electron tomography (ET) has been widely discussed for decades, alignment without human intervention remains a difficult problem. Specifically, the emergence of subtomogram averaging has increased the demand for batch processing during tomographic reconstruction; fully automatic fiducial marker-based alignment is the main technique in this process. However, the lack of an accurate method for detecting and tracking fiducial markers precludes fully automatic alignment. In this paper, we present a novel, fully automatic alignment scheme for ET. Our scheme has two main contributions: First, we present a series of algorithms to ensure a high recognition rate and precise localization during the detection of fiducial markers. Our proposed solution reduces fiducial marker detection to a sampling and classification problem and further introduces an algorithm to solve the parameter dependence of marker diameter and marker number. Second, we propose a novel algorithm to solve the tracking of fiducial markers by reducing the tracking problem to an incomplete point set registration problem. Because a global optimization of a point set registration occurs, the result of our tracking is independent of the initial image position in the tilt series, allowing for the robust tracking of fiducial markers without pre-alignment. The experimental results indicate that our method can achieve an accurate tracking, almost identical to the current best one in IMOD with half automatic scheme. Furthermore, our scheme is fully automatic, depends on fewer parameters (only requires a gross value of the marker diameter) and does not require any manual interaction, providing the possibility of automatic batch processing of electron tomographic reconstruction. Copyright © 2015 Elsevier Inc. All rights reserved.

A Biocompatible Near-Infrared 3D Tracking System*

PubMed Central

Decker, Ryan S.; Shademan, Azad; Opfermann, Justin D.; Leonard, Simon; Kim, Peter C. W.; Krieger, Axel

2017-01-01

A fundamental challenge in soft-tissue surgery is that target tissue moves and deforms, becomes occluded by blood or other tissue, and is difficult to differentiate from surrounding tissue. We developed small biocompatible near-infrared fluorescent (NIRF) markers with a novel fused plenoptic and NIR camera tracking system, enabling 3D tracking of tools and target tissue while overcoming blood and tissue occlusion in the uncontrolled, rapidly changing surgical environment. In this work, we present the tracking system and marker design and compare tracking accuracies to standard optical tracking methods using robotic experiments. At speeds of 1 mm/s, we observe tracking accuracies of 1.61 mm, degrading only to 1.71 mm when the markers are covered in blood and tissue. PMID:28129145

Biocompatible Near-Infrared Three-Dimensional Tracking System.

PubMed

Decker, Ryan S; Shademan, Azad; Opfermann, Justin D; Leonard, Simon; Kim, Peter C W; Krieger, Axel

2017-03-01

A fundamental challenge in soft-tissue surgery is that target tissue moves and deforms, becomes occluded by blood or other tissue, and is difficult to differentiate from surrounding tissue. We developed small biocompatible near-infrared fluorescent (NIRF) markers with a novel fused plenoptic and NIR camera tracking system, enabling three-dimensional tracking of tools and target tissue while overcoming blood and tissue occlusion in the uncontrolled, rapidly changing surgical environment. In this work, we present the tracking system and marker design and compare tracking accuracies to standard optical tracking methods using robotic experiments. At speeds of 1 mm/s, we observe tracking accuracies of 1.61 mm, degrading only to 1.71 mm when the markers are covered in blood and tissue.

Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean

PubMed Central

Patil, Gunvant; Do, Tuyen; Vuong, Tri D.; Valliyodan, Babu; Lee, Jeong-Dong; Chaudhary, Juhi; Shannon, J. Grover; Nguyen, Henry T.

2016-01-01

Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars. PMID:26781337

SU-G-BRA-06: Quantification of Tracking Performance of a Multi-Layer Electronic Portal Imaging Device

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

Hu, Y; Rottmann, J; Myronakis, M

2016-06-15

Purpose: The purpose of this study was to quantify the improvement in tumor tracking, with and without fiducial markers, afforded by employing a multi-layer (MLI) electronic portal imaging device (EPID) over the current state-of-the-art, single-layer, digital megavolt imager (DMI) architecture. Methods: An ideal observer signal-to-noise ratio (d’) approach was used to quantify the ability of an MLI EPID and a current, state-of-the-art DMI EPID to track lung tumors from the treatment beam’s-eye-view. Using each detector modulation transfer function (MTF) and noise power spectrum (NPS) as inputs, a detection task was employed with object functions describing simple three-dimensional Cartesian shapes (spheresmore » and cylinders). Marker-less tumor tracking algorithms often use texture discrimination to differentiate benign and malignant tissue. The performance of such algorithms is simulated by employing a discrimination task for the ideal observer, which measures the ability of a system to differentiate two image quantities. These were defined as the measured textures for benign and malignant lung tissue. Results: The NNPS of the MLI ∼25% of that of the DMI at the expense of decreased MTF at intermediate frequencies (0.25≤« less

Novel Technique for Hepatic Fiducial Marker Placement for Stereotactic Body Radiation Therapy

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

Jarraya, Hajer, E-mail: h-jarraya@o-lambret.fr; Chalayer, Chloé; Tresch, Emmanuelle

2014-09-01

Purpose: To report experience with fiducial marker insertion and describe an advantageous, novel technique for fiducial placement in the liver for stereotactic body radiation therapy with respiratory tracking. Methods and Materials: We implanted 1444 fiducials (single: 834; linked: 610) in 328 patients with 424 hepatic lesions. Two methods of implantation were compared: the standard method (631 single fiducials) performed on 153 patients from May 2007 to May 2010, and the cube method (813 fiducials: 610 linked/203 single) applied to 175 patients from April 2010 to March 2013. The standard method involved implanting a single marker at a time. The novel techniquemore » entailed implanting 2 pairs of linked markers when possible in a way to occupy the perpendicular edges of a cube containing the tumor inside. Results: Mean duration of the cube method was shorter than the standard method (46 vs 61 minutes; P<.0001). Median numbers of skin and subcapsular entries were significantly smaller with the cube method (2 vs 4, P<.0001, and 2 vs 4, P<.0001, respectively). The rate of overall complications (total, major, and minor) was significantly lower in the cube method group compared with the standard method group (5.7% vs 13.7%; P=.013). Major complications occurred while using single markers only. The success rate was 98.9% for the cube method and 99.3% for the standard method. Conclusions: We propose a new technique of hepatic fiducial implantation that makes use of linked fiducials and involves fewer skin entries and shorter time of implantation. The technique is less complication-prone and is migration-resistant.« less

Development and testing of passive tracking markers for different field strengths and tracking speeds.

PubMed

Peeters, J M; Seppenwoolde, J-H; Bartels, L W; Bakker, C J G

2006-03-21

Susceptibility markers for passive tracking need to be small in order to maintain the shape and mechanical properties of the endovascular device. Nevertheless, they also must have a high magnetic moment to induce an adequate artefact at a variety of scan techniques, tracking speeds and, preferably, field strengths. Paramagnetic markers do not satisfy all of these requirements. Ferro- and ferrimagnetic materials were therefore investigated with a vibrating sample magnetometer and compared with the strongly paramagnetic dysprosium oxide. Results indicated that the magnetic behaviour of stainless steel type AISI 410 corresponds the best with ideal marker properties. Markers with different magnetic moments were constructed and tested in in vitro and in vivo experiments. The appearance of the corresponding artefacts was field strength independent above magnetic saturation of 1.5 T. Generally, the contrast-to-noise ratio decreased at increasing tracking speed and decreasing magnetic moment. Device depiction was most consistent at a frame rate of 20 frames per second.

Real time markerless motion tracking using linked kinematic chains

DOEpatents

Luck, Jason P [Arvada, CO; Small, Daniel E [Albuquerque, NM

2007-08-14

A markerless method is described for tracking the motion of subjects in a three dimensional environment using a model based on linked kinematic chains. The invention is suitable for tracking robotic, animal or human subjects in real-time using a single computer with inexpensive video equipment, and does not require the use of markers or specialized clothing. A simple model of rigid linked segments is constructed of the subject and tracked using three dimensional volumetric data collected by a multiple camera video imaging system. A physics based method is then used to compute forces to align the model with subsequent volumetric data sets in real-time. The method is able to handle occlusion of segments and accommodates joint limits, velocity constraints, and collision constraints and provides for error recovery. The method further provides for elimination of singularities in Jacobian based calculations, which has been problematic in alternative methods.

Semi-quantitative evaluation of fecal contamination potential by human and ruminant sources using multiple lines of evidence.

PubMed

Stoeckel, Donald M; Stelzer, Erin A; Stogner, Robert W; Mau, David P

2011-05-01

Protocols for microbial source tracking of fecal contamination generally are able to identify when a source of contamination is present, but thus far have been unable to evaluate what portion of fecal-indicator bacteria (FIB) came from various sources. A mathematical approach to estimate relative amounts of FIB, such as Escherichia coli, from various sources based on the concentration and distribution of microbial source tracking markers in feces was developed. The approach was tested using dilute fecal suspensions, then applied as part of an analytical suite to a contaminated headwater stream in the Rocky Mountains (Upper Fountain Creek, Colorado). In one single-source fecal suspension, a source that was not present could not be excluded because of incomplete marker specificity; however, human and ruminant sources were detected whenever they were present. In the mixed-feces suspension (pet and human), the minority contributor (human) was detected at a concentration low enough to preclude human contamination as the dominant source of E. coli to the sample. Without the semi-quantitative approach described, simple detects of human-associated marker in stream samples would have provided inaccurate evidence that human contamination was a major source of E. coli to the stream. In samples from Upper Fountain Creek the pattern of E. coli, general and host-associated microbial source tracking markers, nutrients, and wastewater-associated chemical detections--augmented with local observations and land-use patterns--indicated that, contrary to expectations, birds rather than humans or ruminants were the predominant source of fecal contamination to Upper Fountain Creek. This new approach to E. coli allocation, validated by a controlled study and tested by application in a relatively simple setting, represents a widely applicable step forward in the field of microbial source tracking of fecal contamination. Copyright © 2011 Elsevier Ltd. 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

Tracking the Sources of Fecal Contaminations: an Interdisciplinary Toolbox

NASA Astrophysics Data System (ADS)

Jeanneau, L.; Jarde, E.; Derrien, M.; Gruau, G.; Solecki, O.; Pourcher, A.; Marti, R.; Wéry, N.; Caprais, M.; Gourmelon, M.; Mieszkin, S.; Jadas-Hécart, A.; Communal, P.

2011-12-01

Fecal contaminations of inland and coastal waters induce risks to human health and economic losses. In order to improve water management, it is necessary to identify the sources of contamination, which implies the development of specific markers. In order to be considered as a valuable host-specific marker, one must (1) be source specific, (2) occur in high concentration in polluting matrices, (3) exhibit extra-intestinal persistence similar to fecal indicator bacteria (FIB) and (4) not grow out of the host. However, up to day no single marker has fulfilled all those criteria. Thus, it has been suggested to use a combination of markers in order to generate more reliable data. This has lead to the development of a Microbial Source Tracking (MST) toolbox including FIB and microbial and chemical specific markers in order to differentiate between human, bovine and porcine fecal contaminations. Those specific markers are, (1) genotypes of F-specific RNA bacteriophages, (2) bacterial markers belonging to the Bacteroidales (human-specific HF183, ruminant-specific Rum-2-Bac and pig-specific Pig-2-Bac markers), to the Bifidobacterium (Bifidobacterium adolescentis) and pig-specific Lactobacillus amylovorus, (3) fecal stanols and (4) caffeine. The development of this MST toolbox was composed of four steps, from the molecular scale to the watershed scale. At the molecular scale, the specificity and the concentration of those markers were studied in cattle and pig manures and in waste water treatment plant (WWTP) effluents and influents. At the microcosm scale, the transfer of bovine and porcine specific markers was investigated by rainfall simulations on agricultural plots amended with cattle or pig manure. Moreover, the relative persistence of FIB and human, porcine and bovine specific markers was investigated in freshwater and seawater microcosms inoculated with a WWTP influent, pig manure and cow manure. Finally, the aforementioned MST toolbox has been validated at the catchment scale by analysing three rivers impacted by fecal contaminations. The development and the application of this MST toolbox have highlighted (1) the specificity of the aforementioned markers, (2) their conservative transfer from soils to rivers and (3) their difference of persistence in seawater and in freshwater. Those results provide useful data in order to identify and manage fecal contaminations of superficial waters. In the case of single source contaminations, the markers provide coherent information: (1) the bovine or porcine markers were not detected in a river impacted by a WWTP effluent; (2) the occurrence of Rum-2-Bac and the distribution of stanols indicated a bovine contamination in a river flowing through cattle pasture. In the case of multiple source contaminations, the combination of markers is necessary to identify the main sources and the statistical treatment of the distribution of stanols could provide an approximation of their proportion.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

PubMed

Janssen, Xander J A; Lipfert, Jan; Jager, Tessa; Daudey, Renier; Beekman, Jaap; Dekker, Nynke H

2012-07-11

The well-established single-molecule force-spectroscopy techniques have recently been complemented by methods that can measure torque and twist directly, notably magnetic torque tweezers and the optical torque wrench. A limitation of the current torque measurement schemes is the intrinsic coupling between the force and torque degrees of freedom. Here we present electromagnetic torque tweezers (eMTT) that combine permanent and electromagnets to enable independent control of the force and torsional trap stiffness for sensitive measurements of single molecule torque and twist. Using the eMTT, we demonstrate sensitive torque measurements on tethered DNA molecules from simple tracking of the beads' (x,y)-position, obviating the need for any angular tracking algorithms or markers. Employing the eMTT for high-resolution torque measurements, we experimentally confirm the theoretically predicted torque overshoot at the DNA buckling transition in high salt conditions. We envision that the flexibility and control afforded by the eMTT will enable a range of new torque and twist measurement schemes from single-molecules to living cells.

Implications of comorbidity for genetic studies of bipolar disorder: P300 and eye tracking as biological markers for illness.

PubMed

Blackwood, D H; Sharp, C W; Walker, M T; Doody, G A; Glabus, M F; Muir, W J

1996-06-01

In large families with affective illness, identification of a biological variable is needed that reflects brain dysfunction at an earlier point than symptom development. Eye movement disorder, a possible vulnerability marker in schizophrenia, is less clearly associated with affective illness, although a subgroup of affective disorders shows smooth-pursuit eye movement disorder. The auditory P300 event-related potential may be a useful marker for risk to schizophrenia, but a role in bipolar illness is less certain. The distribution of these two biological variables and their association with symptoms in two multiply affected bipolar families is described. In a single, five-generation family identified for linkage studies through two bipolar I (BPI) probands, 128 members (including 20 spouses) were interviewed. The 108 related individuals had diagnoses of BPI (7), bipolar II (2), cyclothymia (3), or major depressive disorder (19). Eight others had generalised anxiety (1), minor depression (5), intermittent depression (1), or alcoholism (1). Sixty-nine subjects had no psychiatric diagnosis. P300 latency (81) and eye tracking (71) were recorded from a subgroup of relatives within the pedigree. Eye tracking was abnormal in 11 of 71 relatives (15.5%) and was bimodally distributed. In these 11 relatives, clinical diagnoses included minor depression (1), alcoholism (1) and generalised anxiety disorder (1). P300 latency was normally distributed and did not differ from controls. In a second family in which five of seven siblings have BPI illness, P300 latency and eye movement disorder were found in affected relatives and in some unaffected offspring. In these large families, clinical diagnoses of general anxiety, alcoholism and minor depression, when associated with eye tracking abnormality, may be considered alternative clinical manifestations of the same trait that in other relatives is expressed as bipolar illness.

Decay of Fecal Indicator Bacteria and Microbial Source Tracking Markers in Cattle Feces

EPA Science Inventory

The survival of fecal indicator bacteria (FIB) and microbial source tracking (MST) markers in water microcosms and manure amended soils has been well documented; however, little is known about the survival of MST markers in bovine feces deposited on pastures. We conducted a study...

Technical aspects of real time positron emission tracking for gated radiotherapy

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

Chamberland, Marc; Xu, Tong, E-mail: txu@physics.carleton.ca; McEwen, Malcolm R.

2016-02-15

Purpose: Respiratory motion can lead to treatment errors in the delivery of radiotherapy treatments. Respiratory gating can assist in better conforming the beam delivery to the target volume. We present a study of the technical aspects of a real time positron emission tracking system for potential use in gated radiotherapy. Methods: The tracking system, called PeTrack, uses implanted positron emission markers and position sensitive gamma ray detectors to track breathing motion in real time. PeTrack uses an expectation–maximization algorithm to track the motion of fiducial markers. A normalized least mean squares adaptive filter predicts the location of the markers amore » short time ahead to account for system response latency. The precision and data collection efficiency of a prototype PeTrack system were measured under conditions simulating gated radiotherapy. The lung insert of a thorax phantom was translated in the inferior–superior direction with regular sinusoidal motion and simulated patient breathing motion (maximum amplitude of motion ±10 mm, period 4 s). The system tracked the motion of a {sup 22}Na fiducial marker (0.34 MBq) embedded in the lung insert every 0.2 s. The position of the was marker was predicted 0.2 s ahead. For sinusoidal motion, the equation used to model the motion was fitted to the data. The precision of the tracking was estimated as the standard deviation of the residuals. Software was also developed to communicate with a Linac and toggle beam delivery. In a separate experiment involving a Linac, 500 monitor units of radiation were delivered to the phantom with a 3 × 3 cm photon beam and with 6 and 10 MV accelerating potential. Radiochromic films were inserted in the phantom to measure spatial dose distribution. In this experiment, the period of motion was set to 60 s to account for beam turn-on latency. The beam was turned off when the marker moved outside of a 5-mm gating window. Results: The precision of the tracking in the IS direction was 0.53 mm for a sinusoidally moving target, with an average count rate ∼250 cps. The average prediction error was 1.1 ± 0.6 mm when the marker moved according to irregular patient breathing motion. Across all beam deliveries during the radiochromic film measurements, the average prediction error was 0.8 ± 0.5 mm. The maximum error was 2.5 mm and the 95th percentile error was 1.5 mm. Clear improvement of the dose distribution was observed between gated and nongated deliveries. The full-width at halfmaximum of the dose profiles of gated deliveries differed by 3 mm or less than the static reference dose distribution. Monitoring of the beam on/off times showed synchronization with the location of the marker within the latency of the system. Conclusions: PeTrack can track the motion of internal fiducial positron emission markers with submillimeter precision. The system can be used to gate the delivery of a Linac beam based on the position of a moving fiducial marker. This highlights the potential of the system for use in respiratory-gated radiotherapy.« less

A method to track rotational motion for use in single-molecule biophysics.

PubMed

Lipfert, Jan; Kerssemakers, Jacob J W; Rojer, Maylon; Dekker, Nynke H

2011-10-01

The double helical nature of DNA links many cellular processes such as DNA replication, transcription, and repair to rotational motion and the accumulation of torsional strain. Magnetic tweezers (MTs) are a single-molecule technique that enables the application of precisely calibrated stretching forces to nucleic acid tethers and to control their rotational motion. However, conventional magnetic tweezers do not directly monitor rotation or measure torque. Here, we describe a method to directly measure rotational motion of particles in MT. The method relies on attaching small, non-magnetic beads to the magnetic beads to act as fiducial markers for rotational tracking. CCD images of the beads are analyzed with a tracking algorithm specifically designed to minimize crosstalk between translational and rotational motion: first, the in-plane center position of the magnetic bead is determined with a kernel-based tracker, while subsequently the height and rotation angle of the bead are determined via correlation-based algorithms. Evaluation of the tracking algorithm using both simulated images and recorded images of surface-immobilized beads demonstrates a rotational resolution of 0.1°, while maintaining a translational resolution of 1-2 nm. Example traces of the rotational fluctuations exhibited by DNA-tethered beads confined in magnetic potentials of varying stiffness demonstrate the robustness of the method and the potential for simultaneous tracking of multiple beads. Our rotation tracking algorithm enables the extension of MTs to magnetic torque tweezers (MTT) to directly measure the torque in single molecules. In addition, we envision uses of the algorithm in a range of biophysical measurements, including further extensions of MT, tethered particle motion, and optical trapping measurements.

Interactive, computer-assisted tracking of speckle trajectories in fluorescence microscopy: application to actin polymerization and membrane fusion.

PubMed

Smith, Matthew B; Karatekin, Erdem; Gohlke, Andrea; Mizuno, Hiroaki; Watanabe, Naoki; Vavylonis, Dimitrios

2011-10-05

Analysis of particle trajectories in images obtained by fluorescence microscopy reveals biophysical properties such as diffusion coefficient or rates of association and dissociation. Particle tracking and lifetime measurement is often limited by noise, large mobilities, image inhomogeneities, and path crossings. We present Speckle TrackerJ, a tool that addresses some of these challenges using computer-assisted techniques for finding positions and tracking particles in different situations. A dynamic user interface assists in the creation, editing, and refining of particle tracks. The following are results from application of this program: 1), Tracking single molecule diffusion in simulated images. The shape of the diffusing marker on the image changes from speckle to cloud, depending on the relationship of the diffusion coefficient to the camera exposure time. We use these images to illustrate the range of diffusion coefficients that can be measured. 2), We used the program to measure the diffusion coefficient of capping proteins in the lamellipodium. We found values ∼0.5 μm(2)/s, suggesting capping protein association with protein complexes or the membrane. 3), We demonstrate efficient measuring of appearance and disappearance of EGFP-actin speckles within the lamellipodium of motile cells that indicate actin monomer incorporation into the actin filament network. 4), We marked appearance and disappearance events of fluorescently labeled vesicles to supported lipid bilayers and tracked single lipids from the fused vesicle on the bilayer. This is the first time, to our knowledge, that vesicle fusion has been detected with single molecule sensitivity and the program allowed us to perform a quantitative analysis. 5), By discriminating between undocking and fusion events, dwell times for vesicle fusion after vesicle docking to membranes can be measured. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Prospective motion correction using inductively coupled wireless RF coils.

PubMed

Ooi, Melvyn B; Aksoy, Murat; Maclaren, Julian; Watkins, Ronald D; Bammer, Roland

2013-09-01

A novel prospective motion correction technique for brain MRI is presented that uses miniature wireless radio-frequency coils, or "wireless markers," for position tracking. Each marker is free of traditional cable connections to the scanner. Instead, its signal is wirelessly linked to the MR receiver via inductive coupling with the head coil. Real-time tracking of rigid head motion is performed using a pair of glasses integrated with three wireless markers. A tracking pulse-sequence, combined with knowledge of the markers' unique geometrical arrangement, is used to measure their positions. Tracking data from the glasses is then used to prospectively update the orientation and position of the image-volume so that it follows the motion of the head. Wireless-marker position measurements were comparable to measurements using traditional wired radio-frequency tracking coils, with the standard deviation of the difference < 0.01 mm over the range of positions measured inside the head coil. Wireless-marker safety was verified with B1 maps and temperature measurements. Prospective motion correction was demonstrated in a 2D spin-echo scan while the subject performed a series of deliberate head rotations. Prospective motion correction using wireless markers enables high quality images to be acquired even during bulk motions. Wireless markers are small, avoid radio-frequency safety risks from electrical cables, are not hampered by mechanical connections to the scanner, and require minimal setup times. These advantages may help to facilitate adoption in the clinic. Copyright © 2013 Wiley Periodicals, Inc.

Effectiveness of an automatic tracking software in underwater motion analysis.

PubMed

Magalhaes, Fabrício A; Sawacha, Zimi; Di Michele, Rocco; Cortesi, Matteo; Gatta, Giorgio; Fantozzi, Silvia

2013-01-01

Tracking of markers placed on anatomical landmarks is a common practice in sports science to perform the kinematic analysis that interests both athletes and coaches. Although different software programs have been developed to automatically track markers and/or features, none of them was specifically designed to analyze underwater motion. Hence, this study aimed to evaluate the effectiveness of a software developed for automatic tracking of underwater movements (DVP), based on the Kanade-Lucas-Tomasi feature tracker. Twenty-one video recordings of different aquatic exercises (n = 2940 markers' positions) were manually tracked to determine the markers' center coordinates. Then, the videos were automatically tracked using DVP and a commercially available software (COM). Since tracking techniques may produce false targets, an operator was instructed to stop the automatic procedure and to correct the position of the cursor when the distance between the calculated marker's coordinate and the reference one was higher than 4 pixels. The proportion of manual interventions required by the software was used as a measure of the degree of automation. Overall, manual interventions were 10.4% lower for DVP (7.4%) than for COM (17.8%). Moreover, when examining the different exercise modes separately, the percentage of manual interventions was 5.6% to 29.3% lower for DVP than for COM. Similar results were observed when analyzing the type of marker rather than the type of exercise, with 9.9% less manual interventions for DVP than for COM. In conclusion, based on these results, the developed automatic tracking software presented can be used as a valid and useful tool for underwater motion analysis. Key PointsThe availability of effective software for automatic tracking would represent a significant advance for the practical use of kinematic analysis in swimming and other aquatic sports.An important feature of automatic tracking software is to require limited human interventions and supervision, thus allowing short processing time.When tracking underwater movements, the degree of automation of the tracking procedure is influenced by the capability of the algorithm to overcome difficulties linked to the small target size, the low image quality and the presence of background clutters.The newly developed feature-tracking algorithm has shown a good automatic tracking effectiveness in underwater motion analysis with significantly smaller percentage of required manual interventions when compared to a commercial software.

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

Compact tracking of surgical instruments through structured markers.

PubMed

Alberto Borghese, N; Frosio, I

2013-07-01

Virtual and augmented reality surgery calls for reliable and efficient tracking of the surgical instruments in the virtual or real operating theatre. The most diffused approach uses three or more not aligned markers, attached to each instrument and surveyed by a set of cameras. However, the structure required to carry the markers does modify the instrument's mass distribution and can interfere with surgeon movements. To overcome these problems, we propose here a new methodology, based on structured markers, to compute the six degrees of freedom of a surgical instrument. Two markers are attached on the instrument axis and one of them has a stripe painted over its surface. We also introduce a procedure to compute with high accuracy the markers center on the cameras image, even when partially occluded by the instrument's axis or by other structures. Experimental results demonstrate the reliability and accuracy of the proposed approach. The introduction of structured passive markers can open new possibilities to accurate tracking, combining markers detection with real-time image processing.

Marker-less multi-frame motion tracking and compensation in PET-brain imaging

NASA Astrophysics Data System (ADS)

Lindsay, C.; Mukherjee, J. M.; Johnson, K.; Olivier, P.; Song, X.; Shao, L.; King, M. A.

2015-03-01

In PET brain imaging, patient motion can contribute significantly to the degradation of image quality potentially leading to diagnostic and therapeutic problems. To mitigate the image artifacts resulting from patient motion, motion must be detected and tracked then provided to a motion correction algorithm. Existing techniques to track patient motion fall into one of two categories: 1) image-derived approaches and 2) external motion tracking (EMT). Typical EMT requires patients to have markers in a known pattern on a rigid too attached to their head, which are then tracked by expensive and bulky motion tracking camera systems or stereo cameras. This has made marker-based EMT unattractive for routine clinical application. Our main contributions are the development of a marker-less motion tracking system that uses lowcost, small depth-sensing cameras which can be installed in the bore of the imaging system. Our motion tracking system does not require anything to be attached to the patient and can track the rigid transformation (6-degrees of freedom) of the patient's head at a rate 60 Hz. We show that our method can not only be used in with Multi-frame Acquisition (MAF) PET motion correction, but precise timing can be employed to determine only the necessary frames needed for correction. This can speeds up reconstruction by eliminating the unnecessary subdivision of frames.

Abandoning peracetic acid-based dialyzer reuse is associated with improved survival.

PubMed

Lacson, Eduardo; Wang, Weiling; Mooney, Ann; Ofsthun, Norma; Lazarus, J Michael; Hakim, Raymond M

2011-02-01

Higher mortality risk reported with reuse versus single use of dialyzers is potentially related to reuse reagents that modify membrane surface characteristics and the blood-membrane interface. A key mechanism may involve stimulation of an inflammatory response. In a prospective crossover design, laboratory markers and mortality from 23 hemodialysis facilities abandoning reuse with peracetic acid mixture were tracked. C-reactive protein (CRP), white blood cell (WBC) count, albumin, and prealbumin were measured for 2 consecutive months before abandoning reuse and subsequently within 3 and 6 months on single use. Survival models were utilized to compare the 6-month period before abandoning reuse (baseline) and the 6-month period on single use of dialyzers after a 3-month "washout period." Patients from baseline and single-use periods had a mean age of approximately 63 years; 44% were female, 54% were diabetic, 60% were white, and the mean vintage was approximately 3.2 years. The unadjusted hazard ratio for death was 0.70 and after case-mix adjustment was 0.74 for single use compared with reuse. Patients with CRP≥5 mg/L during reuse (mean CRP=26.6 mg/ml in April) declined on single use to 20.2 mg/L by August and 20.4 mg/L by November. WBC count declined slightly during single use, but nutritional markers were unchanged. Abandonment of peracetic-acid-based reuse was associated with improved survival and lower levels of inflammatory but not nutritional markers. Further study is needed to evaluate a potential link between dialyzer reuse, inflammation, and mortality.

Simultaneous Monitoring of Ballistocardiogram and Photoplethysmogram Using Camera

PubMed Central

Shao, Dangdang; Tsow, Francis; Liu, Chenbin; Yang, Yuting; Tao, Nongjian

2017-01-01

We present a noncontact method to measure Ballistocardiogram (BCG) and Photoplethysmogram (PPG) simultaneously using a single camera. The method tracks the motion of facial features to determine displacement BCG, and extracts the corresponding velocity and acceleration BCGs by taking first and second temporal derivatives from the displacement BCG, respectively. The measured BCG waveforms are consistent with those reported in literature and also with those recorded with an accelerometer-based reference method. The method also tracks PPG based on the reflected light from the same facial region, which makes it possible to track both BCG and PPG with the same optics. We verify the robustness and reproducibility of the noncontact method with a small pilot study with 23 subjects. The presented method is the first demonstration of simultaneous BCG and PPG monitoring without wearing any extra equipment or marker by the subject. PMID:27362754

Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

USGS Publications Warehouse

Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

2013-01-01

Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

Development of a real-time internal and external marker tracking system for particle therapy: a phantom study using patient tumor trajectory data

PubMed Central

Cho, Junsang; Cheon, Wonjoong; Ahn, Sanghee; Jung, Hyunuk; Sheen, Heesoon; Park, Hee Chul

2017-01-01

Abstract Target motion–induced uncertainty in particle therapy is more complicated than that in X-ray therapy, requiring more accurate motion management. Therefore, a hybrid motion-tracking system that can track internal tumor motion and as well as an external surrogate of tumor motion was developed. Recently, many correlation tests between internal and external markers in X-ray therapy have been developed; however, the accuracy of such internal/external marker tracking systems, especially in particle therapy, has not yet been sufficiently tested. In this article, the process of installing an in-house hybrid internal/external motion-tracking system is described and the accuracy level of tracking system was acquired. Our results demonstrated that the developed in-house external/internal combined tracking system has submillimeter accuracy, and can be clinically used as a particle therapy system as well as a simulation system for moving tumor treatment. PMID:28201522

Comparison of Two Alternative Methods for Tracking Toe Trajectory

NASA Technical Reports Server (NTRS)

Miller, Chris; Peters, Brian; Brady, Rachel; Mulavara, Ajitkumar; Warren, Liz; Feiveson, Al; Bloomberg, Jacob

2007-01-01

Toe trajectory during the swing phase of locomotion has been identified as a precise motor control task (Karst, et al., 1999). The standard method for tracking toe trajectory is to place a marker on the superior aspect of the distal end of the 2nd toe itself (Karst, et al., 1999; Winter, 1992). However, others have based their toe trajectory results either on a marker positioned on the lateral aspect of the 5th metatarsal head (Dingwell, et al., 1999; Osaki, et al., 2007), or on a virtual toe marker computed at the anterior tip of the second toe based on the positions of other real foot markers (Miller, et al., 2006). While these methods for tracking the toe may seem similar, their results may not be directly comparable. The purpose of this study was to compute toe trajectory parameters using a 5th metatarsal marker and a virtual toe marker, and compare their results with those of the standard toe marker.

Passive Markers for Tracking Surgical Instruments in Real-Time 3-D Ultrasound Imaging

PubMed Central

Stoll, Jeffrey; Ren, Hongliang; Dupont, Pierre E.

2013-01-01

A family of passive echogenic markers is presented by which the position and orientation of a surgical instrument can be determined in a 3-D ultrasound volume, using simple image processing. Markers are attached near the distal end of the instrument so that they appear in the ultrasound volume along with the instrument tip. They are detected and measured within the ultrasound image, thus requiring no external tracking device. This approach facilitates imaging instruments and tissue simultaneously in ultrasound-guided interventions. Marker-based estimates of instrument pose can be used in augmented reality displays or for image-based servoing. Design principles for marker shapes are presented that ensure imaging system and measurement uniqueness constraints are met. An error analysis is included that can be used to guide marker design and which also establishes a lower bound on measurement uncertainty. Finally, examples of marker measurement and tracking algorithms are presented along with experimental validation of the concepts. PMID:22042148

Tracking Single Cells in Live Animals Using a Photoconvertible Near-Infrared Cell Membrane Label

PubMed Central

Wu, Juwell; Runnels, Judith M.; Turcotte, Raphaël; Celso, Cristina Lo; Scadden, David T.; Strom, Terry B.; Lin, Charles P.

2013-01-01

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4+ T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution. PMID:23990881

Tracking single cells in live animals using a photoconvertible near-infrared cell membrane label.

PubMed

Carlson, Alicia L; Fujisaki, Joji; Wu, Juwell; Runnels, Judith M; Turcotte, Raphaël; Spencer, Joel A; Celso, Cristina Lo; Scadden, David T; Strom, Terry B; Lin, Charles P

2013-01-01

We describe a novel photoconversion technique to track individual cells in vivo using a commercial lipophilic membrane dye, DiR. We show that DiR exhibits a permanent fluorescence emission shift (photoconversion) after light exposure and does not reacquire the original color over time. Ratiometric imaging can be used to distinguish photoconverted from non-converted cells with high sensitivity. Combining the use of this photoconvertible dye with intravital microscopy, we tracked the division of individual hematopoietic stem/progenitor cells within the calvarium bone marrow of live mice. We also studied the peripheral differentiation of individual T cells by tracking the gain or loss of FoxP3-GFP expression, a marker of the immune suppressive function of CD4(+) T cells. With the near-infrared photoconvertible membrane dye, the entire visible spectral range is available for simultaneous use with other fluorescent proteins to monitor gene expression or to trace cell lineage commitment in vivo with high spatial and temporal resolution.

Tracking accuracy of a real-time fiducial tracking system for patient positioning and monitoring in radiation therapy.

PubMed

Shchory, Tal; Schifter, Dan; Lichtman, Rinat; Neustadter, David; Corn, Benjamin W

2010-11-15

In radiation therapy there is a need to accurately know the location of the target in real time. A novel radioactive tracking technology has been developed to answer this need. The technology consists of a radioactive implanted fiducial marker designed to minimize migration and a linac mounted tracking device. This study measured the static and dynamic accuracy of the new tracking technology in a clinical radiation therapy environment. The tracking device was installed on the linac gantry. The radioactive marker was located in a tissue equivalent phantom. Marker location was measured simultaneously by the radioactive tracking system and by a Microscribe G2 coordinate measuring machine (certified spatial accuracy of 0.38 mm). Localization consistency throughout a volume and absolute accuracy in the Fixed coordinate system were measured at multiple gantry angles over volumes of at least 10 cm in diameter centered at isocenter. Dynamic accuracy was measured with the marker located inside a breathing phantom. The mean consistency for the static source was 0.58 mm throughout the tested region at all measured gantry angles. The mean absolute position error in the Fixed coordinate system for all gantry angles was 0.97 mm. The mean real-time tracking error for the dynamic source within the breathing phantom was less than 1 mm. This novel radioactive tracking technology has the potential to be useful in accurate target localization and real-time monitoring for radiation therapy. Copyright © 2010 Elsevier Inc. All rights reserved.

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool.

PubMed

Winfield, Mark O; Allen, Alexandra M; Burridge, Amanda J; Barker, Gary L A; Benbow, Harriet R; Wilkinson, Paul A; Coghill, Jane; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa; Brew, Fiona; Bloor, Claire; King, Julie; West, Claire; Griffiths, Simon; King, Ian; Bentley, Alison R; Edwards, Keith J

2016-05-01

In wheat, a lack of genetic diversity between breeding lines has been recognized as a significant block to future yield increases. Species belonging to bread wheat's secondary and tertiary gene pools harbour a much greater level of genetic variability, and are an important source of genes to broaden its genetic base. Introgression of novel genes from progenitors and related species has been widely employed to improve the agronomic characteristics of hexaploid wheat, but this approach has been hampered by a lack of markers that can be used to track introduced chromosome segments. Here, we describe the identification of a large number of single nucleotide polymorphisms that can be used to genotype hexaploid wheat and to identify and track introgressions from a variety of sources. We have validated these markers using an ultra-high-density Axiom(®) genotyping array to characterize a range of diploid, tetraploid and hexaploid wheat accessions and wheat relatives. To facilitate the use of these, both the markers and the associated sequence and genotype information have been made available through an interactive web site. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Orthographic and Phonological Contributions to Reading Development: Tracking Developmental Trajectories Using Masked Priming

ERIC Educational Resources Information Center

Ziegler, Johannes C.; Bertrand, Daisy; Lété, Bernard; Grainger, Jonathan

2014-01-01

The present study used a variant of masked priming to track the development of 2 marker effects of orthographic and phonological processing from Grade 1 through Grade 5 in a cross-sectional study. Pseudohomophone (PsH) priming served as a marker for phonological processing, whereas transposed-letter (TL) priming was a marker for coarse-grained…

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

Ishii, H.; Fujino, H.; Bian, Z.

In this study, two types of marker-based tracking methods for Augmented Reality have been developed. One is a method which employs line-shaped markers and the other is a method which employs circular-shaped markers. These two methods recognize the markers by means of image processing and calculate the relative position and orientation between the markers and the camera in real time. The line-shaped markers are suitable to be pasted in the buildings such as NPPs where many pipes and tanks exist. The circular-shaped markers are suitable for the case that there are many obstacles and it is difficult to use line-shapedmore » markers because the obstacles hide the part of the line-shaped markers. Both methods can extend the maximum distance between the markers and the camera compared to the legacy marker-based tracking methods. (authors)« less

Evaluation of Hands-On Clinical Exam Performance Using Marker-less Video Tracking.

PubMed

Azari, David; Pugh, Carla; Laufer, Shlomi; Cohen, Elaine; Kwan, Calvin; Chen, Chia-Hsiung Eric; Yen, Thomas Y; Hu, Yu Hen; Radwin, Robert

2014-09-01

This study investigates the potential of using marker-less video tracking of the hands for evaluating hands-on clinical skills. Experienced family practitioners attending a national conference were recruited and asked to conduct a breast examination on a simulator that simulates different clinical presentations. Videos were made of the clinician's hands during the exam and video processing software for tracking hand motion to quantify hand motion kinematics was used. Practitioner motion patterns indicated consistent behavior of participants across multiple pathologies. Different pathologies exhibited characteristic motion patterns in the aggregate at specific parts of an exam, indicating consistent inter-participant behavior. Marker-less video kinematic tracking therefore shows promise in discriminating between different examination procedures, clinicians, and pathologies.

Abandoning Peracetic Acid-Based Dialyzer Reuse Is Associated with Improved Survival

PubMed Central

Wang, Weiling; Mooney, Ann; Ofsthun, Norma; Lazarus, J. Michael; Hakim, Raymond M.

2011-01-01

Summary Background and objectives Higher mortality risk reported with reuse versus single use of dialyzers is potentially related to reuse reagents that modify membrane surface characteristics and the blood-membrane interface. A key mechanism may involve stimulation of an inflammatory response. Design, setting, participants, & measurements In a prospective crossover design, laboratory markers and mortality from 23 hemodialysis facilities abandoning reuse with peracetic acid mixture were tracked. C-reactive protein (CRP), white blood cell (WBC) count, albumin, and prealbumin were measured for 2 consecutive months before abandoning reuse and subsequently within 3 and 6 months on single use. Survival models were utilized to compare the 6-month period before abandoning reuse (baseline) and the 6-month period on single use of dialyzers after a 3-month “washout period.” Results Patients from baseline and single-use periods had a mean age of approximately 63 years; 44% were female, 54% were diabetic, 60% were white, and the mean vintage was approximately 3.2 years. The unadjusted hazard ratio for death was 0.70 and after case-mix adjustment was 0.74 for single use compared with reuse. Patients with CRP ≥ 5 mg/L during reuse (mean CRP = 26.6 mg/ml in April) declined on single use to 20.2 mg/L by August and 20.4 mg/L by November. WBC count declined slightly during single use, but nutritional markers were unchanged. Conclusions Abandonment of peracetic-acid-based reuse was associated with improved survival and lower levels of inflammatory but not nutritional markers. Further study is needed to evaluate a potential link between dialyzer reuse, inflammation, and mortality. PMID:20947788

Development of a real-time internal and external marker tracking system for particle therapy: a phantom study using patient tumor trajectory data.

PubMed

Cho, Junsang; Cheon, Wonjoong; Ahn, Sanghee; Jung, Hyunuk; Sheen, Heesoon; Park, Hee Chul; Han, Youngyih

2017-09-01

Target motion-induced uncertainty in particle therapy is more complicated than that in X-ray therapy, requiring more accurate motion management. Therefore, a hybrid motion-tracking system that can track internal tumor motion and as well as an external surrogate of tumor motion was developed. Recently, many correlation tests between internal and external markers in X-ray therapy have been developed; however, the accuracy of such internal/external marker tracking systems, especially in particle therapy, has not yet been sufficiently tested. In this article, the process of installing an in-house hybrid internal/external motion-tracking system is described and the accuracy level of tracking system was acquired. Our results demonstrated that the developed in-house external/internal combined tracking system has submillimeter accuracy, and can be clinically used as a particle therapy system as well as a simulation system for moving tumor treatment. © The Author 2017. Published by Oxford University Press on behalf of The Japan Radiation Research Society and Japanese Society for Radiation Oncology.

Tracking multiple surgical instruments in a near-infrared optical system.

PubMed

Cai, Ken; Yang, Rongqian; Lin, Qinyong; Wang, Zhigang

2016-12-01

Surgical navigation systems can assist doctors in performing more precise and more efficient surgical procedures to avoid various accidents. The near-infrared optical system (NOS) is an important component of surgical navigation systems. However, several surgical instruments are used during surgery, and effectively tracking all of them is challenging. A stereo matching algorithm using two intersecting lines and surgical instrument codes is proposed in this paper. In our NOS, the markers on the surgical instruments can be captured by two near-infrared cameras. After automatically searching and extracting their subpixel coordinates in the left and right images, the coordinates of the real and pseudo markers are determined by the two intersecting lines. Finally, the pseudo markers are removed to achieve accurate stereo matching by summing the codes for the distances between a specific marker with the other two markers on the surgical instrument. Experimental results show that the markers on the different surgical instruments can be automatically and accurately recognized. The NOS can accurately track multiple surgical instruments.

Tracking Accuracy of a Real-Time Fiducial Tracking System for Patient Positioning and Monitoring in Radiation Therapy

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

Shchory, Tal; Schifter, Dan; Lichtman, Rinat

Purpose: In radiation therapy there is a need to accurately know the location of the target in real time. A novel radioactive tracking technology has been developed to answer this need. The technology consists of a radioactive implanted fiducial marker designed to minimize migration and a linac mounted tracking device. This study measured the static and dynamic accuracy of the new tracking technology in a clinical radiation therapy environment. Methods and Materials: The tracking device was installed on the linac gantry. The radioactive marker was located in a tissue equivalent phantom. Marker location was measured simultaneously by the radioactive trackingmore » system and by a Microscribe G2 coordinate measuring machine (certified spatial accuracy of 0.38 mm). Localization consistency throughout a volume and absolute accuracy in the Fixed coordinate system were measured at multiple gantry angles over volumes of at least 10 cm in diameter centered at isocenter. Dynamic accuracy was measured with the marker located inside a breathing phantom. Results: The mean consistency for the static source was 0.58 mm throughout the tested region at all measured gantry angles. The mean absolute position error in the Fixed coordinate system for all gantry angles was 0.97 mm. The mean real-time tracking error for the dynamic source within the breathing phantom was less than 1 mm. Conclusions: This novel radioactive tracking technology has the potential to be useful in accurate target localization and real-time monitoring for radiation therapy.« less

Markerless motion estimation for motion-compensated clinical brain imaging

NASA Astrophysics Data System (ADS)

Kyme, Andre Z.; Se, Stephen; Meikle, Steven R.; Fulton, Roger R.

2018-05-01

Motion-compensated brain imaging can dramatically reduce the artifacts and quantitative degradation associated with voluntary and involuntary subject head motion during positron emission tomography (PET), single photon emission computed tomography (SPECT) and computed tomography (CT). However, motion-compensated imaging protocols are not in widespread clinical use for these modalities. A key reason for this seems to be the lack of a practical motion tracking technology that allows for smooth and reliable integration of motion-compensated imaging protocols in the clinical setting. We seek to address this problem by investigating the feasibility of a highly versatile optical motion tracking method for PET, SPECT and CT geometries. The method requires no attached markers, relying exclusively on the detection and matching of distinctive facial features. We studied the accuracy of this method in 16 volunteers in a mock imaging scenario by comparing the estimated motion with an accurate marker-based method used in applications such as image guided surgery. A range of techniques to optimize performance of the method were also studied. Our results show that the markerless motion tracking method is highly accurate (<2 mm discrepancy against a benchmarking system) on an ethnically diverse range of subjects and, moreover, exhibits lower jitter and estimation of motion over a greater range than some marker-based methods. Our optimization tests indicate that the basic pose estimation algorithm is very robust but generally benefits from rudimentary background masking. Further marginal gains in accuracy can be achieved by accounting for non-rigid motion of features. Efficiency gains can be achieved by capping the number of features used for pose estimation provided that these features adequately sample the range of head motion encountered in the study. These proof-of-principle data suggest that markerless motion tracking is amenable to motion-compensated brain imaging and holds good promise for a practical implementation in clinical PET, SPECT and CT systems.

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

SU-D-207-05: Real-Time Intrafractional Motion Tracking During VMAT Delivery Using a Conventional Elekta CBCT System

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

Park, Yang-Kyun; Sharp, Gregory C.; Gierga, David P.

2015-06-15

Purpose: Real-time kV projection streaming capability has become recently available for Elekta XVI version 5.0. This study aims to investigate the feasibility and accuracy of real-time fiducial marker tracking during CBCT acquisition with or without simultaneous VMAT delivery using a conventional Elekta linear accelerator. Methods: A client computer was connected to an on-board kV imaging system computer, and receives and processes projection images immediately after image acquisition. In-house marker tracking software based on FFT normalized cross-correlation was developed and installed in the client computer. Three gold fiducial markers with 3 mm length were implanted in a pelvis-shaped phantom with 36more » cm width. The phantom was placed on a programmable motion platform oscillating in anterior-posterior and superior-inferior directions simultaneously. The marker motion was tracked in real-time for (1) a kV-only CBCT scan with treatment beam off and (2) a kV CBCT scan during a 6-MV VMAT delivery. The exposure parameters per projection were 120 kVp and 1.6 mAs. Tracking accuracy was assessed by comparing superior-inferior positions between the programmed and tracked trajectories. Results: The projection images were successfully transferred to the client computer at a frequency of about 5 Hz. In the kV-only scan, highly accurate marker tracking was achieved over the entire range of cone-beam projection angles (detection rate / tracking error were 100.0% / 0.6±0.5 mm). In the kV-VMAT scan, MV-scatter degraded image quality, particularly for lateral projections passing through the thickest part of the phantom (kV source angle ranging 70°-110° and 250°-290°), resulting in a reduced detection rate (90.5%). If the lateral projections are excluded, tracking performance was comparable to the kV-only case (detection rate / tracking error were 100.0% / 0.8±0.5 mm). Conclusion: Our phantom study demonstrated a promising Result for real-time motion tracking using a conventional Elekta linear accelerator. MV-scatter suppression is needed to improve tracking accuracy during MV delivery. This research is funded by Motion Management Research Grant from Elekta.« less

Evaluation of tracking accuracy of the CyberKnife system using a webcam and printed calibrated grid.

PubMed

Sumida, Iori; Shiomi, Hiroya; Higashinaka, Naokazu; Murashima, Yoshikazu; Miyamoto, Youichi; Yamazaki, Hideya; Mabuchi, Nobuhisa; Tsuda, Eimei; Ogawa, Kazuhiko

2016-03-08

Tracking accuracy for the CyberKnife's Synchrony system is commonly evaluated using a film-based verification method. We have evaluated a verification system that uses a webcam and a printed calibrated grid to verify tracking accuracy over three different motion patterns. A box with an attached printed calibrated grid and four fiducial markers was attached to the motion phantom. A target marker was positioned at the grid's center. The box was set up using the other three markers. Target tracking accuracy was evaluated under three conditions: 1) stationary; 2) sinusoidal motion with different amplitudes of 5, 10, 15, and 20 mm for the same cycle of 4 s and different cycles of 2, 4, 6, and 8 s with the same amplitude of 15 mm; and 3) irregular breathing patterns in six human volunteers breathing normally. Infrared markers were placed on the volunteers' abdomens, and their trajectories were used to simulate the target motion. All tests were performed with one-dimensional motion in craniocaudal direction. The webcam captured the grid's motion and a laser beam was used to simulate the CyberKnife's beam. Tracking error was defined as the difference between the grid's center and the laser beam. With a stationary target, mean tracking error was measured at 0.4 mm. For sinusoidal motion, tracking error was less than 2 mm for any amplitude and breathing cycle. For the volunteers' breathing patterns, the mean tracking error range was 0.78-1.67 mm. Therefore, accurate lesion targeting requires individual quality assurance for each patient.

Decay of Fecal Indicator Bacterial Populations and Bovine-Associated Source-Tracking Markers in Freshly Deposited Cow Pats

EPA Science Inventory

Understanding the survival of fecal indicator bacteria (FIB) and microbial source-tracking (MST) markers is critical to developing pathogen fate and transport models. Although pathogen survival in water microcosms and manure-amended soils is well documented, little is known about...

Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater.

PubMed

Tran, Ngoc Han; Gin, Karina Yew-Hoong; Ngo, Huu Hao

2015-12-15

The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater. Copyright © 2015 Elsevier B.V. All rights reserved.

Application of leftover sample material from waterborne protozoa monitoring for the molecular detection of Bacteroidales and fecal source tracking markers

EPA Science Inventory

In this study, we examined the potential for detecting fecal bacteria and microbial source tracking markers in samples discarded during the concentration of Cryptosporidium and Giardia using USEPA Method 1623. Recovery rates for different fecal bacteria were determined using sp...

Prospective Motion Correction using Inductively-Coupled Wireless RF Coils

PubMed Central

Ooi, Melvyn B.; Aksoy, Murat; Maclaren, Julian; Watkins, Ronald D.; Bammer, Roland

2013-01-01

Purpose A novel prospective motion correction technique for brain MRI is presented that uses miniature wireless radio-frequency (RF) coils, or “wireless markers”, for position tracking. Methods Each marker is free of traditional cable connections to the scanner. Instead, its signal is wirelessly linked to the MR receiver via inductive coupling with the head coil. Real-time tracking of rigid head motion is performed using a pair of glasses integrated with three wireless markers. A tracking pulse-sequence, combined with knowledge of the markers’ unique geometrical arrangement, is used to measure their positions. Tracking data from the glasses is then used to prospectively update the orientation and position of the image-volume so that it follows the motion of the head. Results Wireless-marker position measurements were comparable to measurements using traditional wired RF tracking coils, with the standard deviation of the difference < 0.01 mm over the range of positions measured inside the head coil. RF safety was verified with B1 maps and temperature measurements. Prospective motion correction was demonstrated in a 2D spin-echo scan while the subject performed a series of deliberate head rotations. Conclusion Prospective motion correction using wireless markers enables high quality images to be acquired even during bulk motions. Wireless markers are small, avoid RF safety risks from electrical cables, are not hampered by mechanical connections to the scanner, and require minimal setup times. These advantages may help to facilitate adoption in the clinic. PMID:23813444

Collection methods and quality assessment for Esche-richia coli, water quality, and microbial source tracking data within Tumacácori National Historical Park and the upper Santa Cruz River, Arizona, 2015-16

USGS Publications Warehouse

Paretti, Nicholas; Coes, Alissa L.; Kephart, Christopher M.; Mayo, Justine

2018-03-05

Tumacácori National Historical Park protects the culturally important Mission, San José de Tumacácori, while also managing a portion of the ecologically diverse riparian corridor of the Santa Cruz River. This report describes the methods and quality assurance procedures used in the collection of water samples for the analysis of Escherichia coli (E. coli), microbial source tracking markers, suspended sediment, water-quality parameters, turbidity, and the data collection for discharge and stage; the process for data review and approval is also described. Finally, this report provides a quantitative assessment of the quality of the E. coli, microbial source tracking, and suspended sediment data.The data-quality assessment revealed that bias attributed to field and laboratory contamination was minimal, with E. coli detections in only 3 out of 33 field blank samples analyzed. Concentrations in the field blanks were several orders of magnitude lower than environmental concentrations. The microbial source tracking (MST) field blank was below the detection limit for all MST markers analyzed. Laboratory blanks for E. coli at the USGS Arizona Water Science Center and laboratory blanks for MST markers at the USGS Ohio Water Microbiology Laboratory were all below the detection limit. Irreplicate data for E. coli and suspended sediment indicated that bias was not introduced to the data by combining samples collected using discrete sampling methods with samples collected using automatic sampling methods.The split and sequential E. coli replicate data showed consistent analytical variability and a single equation was developed to explain the variability of E. coli concentrations. An additional analysis of analytical variability for E. coli indicated analytical variability around 18 percent relative standard deviation and no trend was observed in the concentration during the processing and analysis of multiple split-replicates. Two replicate samples were collected for MST and individual markers were compared for a base flow and flood sample. For the markers found in common between the two types of samples, the relative standard deviation for the base flow sample was more than 3 times greater than the markers in the flood sample. Sequential suspended sediment replicates had a relative standard deviation of about 1.3 percent, indicating that environmental and analytical variability was minimal.A holding time review and laboratory study analysis supported the extended holding times required for this investigation. Most concentrations for flood and base-flow samples were within the theoretical variability specified in the most probable number approach suggesting that extended hold times did not overly influence the final concentrations reported.

Dedicated ultrasound speckle tracking to study tendon displacement

NASA Astrophysics Data System (ADS)

Korstanje, Jan-Wiebe H.; Selles, Ruud W.; Stam, Henk J.; Hovius, Steven E. R.; Bosch, Johan G.

2009-02-01

Ultrasound can be used to study tendon and muscle movement. However, quantization is mostly based on manual tracking of anatomical landmarks such as the musculotendinous junction, limiting the applicability to a small number of muscle-tendon units. The aim of this study is to quantify tendon displacement without employing anatomical landmarks, using dedicated speckle tracking in long B-mode image sequences. We devised a dedicated two-dimensional multikernel block-matching scheme with subpixel accuracy to handle large displacements over long sequences. Images were acquired with a Philips iE33 with a 7 MHz linear array and a VisualSonics Vevo 770 using a 40 MHz mechanical probe. We displaced the flexor digitorum superficialis of two pig cadaver forelegs with three different velocities (4,10 and 16 mm/s) over 3 distances (5, 10, 15 mm). As a reference, we manually determined the total displacement of an injected hyperechogenic bullet in the tendons. We automatically tracked tendon parts with and without markers and compared results to the true displacement. Using the iE33, mean tissue displacement underestimations for the three different velocities were 2.5 +/- 1.0%, 1.7 +/- 1.1% and 0.7 +/- 0.4%. Using the Vevo770, mean tissue displacement underestimations were 0.8 +/- 1.3%, 0.6 +/- 0.3% and 0.6 +/- 0.3%. Marker tracking displacement underestimations were only slightly smaller, showing limited tracking drift for non-marker tendon tissue as well as for markers. This study showed that our dedicated speckle tracking can quantify extensive tendon displacement with physiological velocities without anatomical landmarks with good accuracy for different types of ultrasound configurations. This technique allows tracking of a much larger range of muscle-tendon units than by using anatomical landmarks.

Evaluation of tracking accuracy of the CyberKnife system using a webcam and printed calibrated grid

PubMed Central

Shiomi, Hiroya; Higashinaka, Naokazu; Murashima, Yoshikazu; Miyamoto, Youichi; Yamazaki, Hideya; Mabuchi, Nobuhisa; Tsuda, Eimei; Ogawa, Kazuhiko

2016-01-01

Tracking accuracy for the CyberKnife's Synchrony system is commonly evaluated using a film‐based verification method. We have evaluated a verification system that uses a webcam and a printed calibrated grid to verify tracking accuracy over three different motion patterns. A box with an attached printed calibrated grid and four fiducial markers was attached to the motion phantom. A target marker was positioned at the grid's center. The box was set up using the other three markers. Target tracking accuracy was evaluated under three conditions: 1) stationary; 2) sinusoidal motion with different amplitudes of 5, 10, 15, and 20 mm for the same cycle of 4 s and different cycles of 2, 4, 6, and 8 s with the same amplitude of 15 mm; and 3) irregular breathing patterns in six human volunteers breathing normally. Infrared markers were placed on the volunteers’ abdomens, and their trajectories were used to simulate the target motion. All tests were performed with one‐dimensional motion in craniocaudal direction. The webcam captured the grid's motion and a laser beam was used to simulate the CyberKnife's beam. Tracking error was defined as the difference between the grid's center and the laser beam. With a stationary target, mean tracking error was measured at 0.4 mm. For sinusoidal motion, tracking error was less than 2 mm for any amplitude and breathing cycle. For the volunteers’ breathing patterns, the mean tracking error range was 0.78‐1.67 mm. Therefore, accurate lesion targeting requires individual quality assurance for each patient. PACS number(s): 87.55.D‐, 87.55.km, 87.55.Qr, 87.56.Fc PMID:27074474

Can hip and knee kinematics be improved by eliminating thigh markers?

PubMed Central

Schulz, Brian W.; Kimmel, Wendy L.

2017-01-01

Background Marker sets developed for gait analysis are often applied to more dynamic tasks with little or no validation, despite known complications of soft tissue artifact. Methods This study presents a comparison of hip and knee kinematics as calculated by five concurrently-worn tracking marker sets during eight different tasks. The first three marker sets were based on Helen Hayes but used 1) proximal thigh wands, 2) distal thigh wands, and 3) patellar markers instead of thigh wands. The remaining two marker sets used rigid clusters on the 4) thighs and shanks and 5) only shanks. Pelvis and foot segments were shared by all marker sets. The first three tasks were maximal femoral rotations using different knee and hip positions to quantify the ability of each marker set to capture this motion. The remaining five tasks were walking, walking a 1m radius circle, running, jumping, and lunging. Findings In general, few and small differences in knee and hip flexion-extension were observed between marker sets, while many and large differences in adduction-abduction and external-internal rotations were observed. The shank-only tracking marker set was capable of detecting the greatest hip external-internal rotation, yet only did so during dynamic tasks where greater hip axial motions would be expected. All data are available as supplementary material. Interpretation Marker set selection is critical to non-sagittal hip and knee motions. The shank-only tracking marker set presented here is a viable alternative that may improve knee and hip kinematics by eliminating errors from thigh soft tissue artifact. PMID:20493599

External radioactive markers for PET data-driven respiratory gating in positron emission tomography.

PubMed

Büther, Florian; Ernst, Iris; Hamill, James; Eich, Hans T; Schober, Otmar; Schäfers, Michael; Schäfers, Klaus P

2013-04-01

Respiratory gating is an established approach to overcoming respiration-induced image artefacts in PET. Of special interest in this respect are raw PET data-driven gating methods which do not require additional hardware to acquire respiratory signals during the scan. However, these methods rely heavily on the quality of the acquired PET data (statistical properties, data contrast, etc.). We therefore combined external radioactive markers with data-driven respiratory gating in PET/CT. The feasibility and accuracy of this approach was studied for [(18)F]FDG PET/CT imaging in patients with malignant liver and lung lesions. PET data from 30 patients with abdominal or thoracic [(18)F]FDG-positive lesions (primary tumours or metastases) were included in this prospective study. The patients underwent a 10-min list-mode PET scan with a single bed position following a standard clinical whole-body [(18)F]FDG PET/CT scan. During this scan, one to three radioactive point sources (either (22)Na or (18)F, 50-100 kBq) in a dedicated holder were attached the patient's abdomen. The list mode data acquired were retrospectively analysed for respiratory signals using established data-driven gating approaches and additionally by tracking the motion of the point sources in sinogram space. Gated reconstructions were examined qualitatively, in terms of the amount of respiratory displacement and in respect of changes in local image intensity in the gated images. The presence of the external markers did not affect whole-body PET/CT image quality. Tracking of the markers led to characteristic respiratory curves in all patients. Applying these curves for gated reconstructions resulted in images in which motion was well resolved. Quantitatively, the performance of the external marker-based approach was similar to that of the best intrinsic data-driven methods. Overall, the gain in measured tumour uptake from the nongated to the gated images indicating successful removal of respiratory motion was correlated with the magnitude of the respiratory displacement of the respective tumour lesion, but not with lesion size. Respiratory information can be assessed from list-mode PET/CT through PET data-derived tracking of external radioactive markers. This information can be successfully applied to respiratory gating to reduce motion-related image blurring. In contrast to other previously described PET data-driven approaches, the external marker approach is independent of tumour uptake and thereby applicable even in patients with poor uptake and small tumours.

Validation of XMALab software for marker-based XROMM.

PubMed

Knörlein, Benjamin J; Baier, David B; Gatesy, Stephen M; Laurence-Chasen, J D; Brainerd, Elizabeth L

2016-12-01

Marker-based XROMM requires software tools for: (1) correcting fluoroscope distortion; (2) calibrating X-ray cameras; (3) tracking radio-opaque markers; and (4) calculating rigid body motion. In this paper we describe and validate XMALab, a new open-source software package for marker-based XROMM (C++ source and compiled versions on Bitbucket). Most marker-based XROMM studies to date have used XrayProject in MATLAB. XrayProject can produce results with excellent accuracy and precision, but it is somewhat cumbersome to use and requires a MATLAB license. We have designed XMALab to accelerate the XROMM process and to make it more accessible to new users. Features include the four XROMM steps (listed above) in one cohesive user interface, real-time plot windows for detecting errors, and integration with an online data management system, XMAPortal. Accuracy and precision of XMALab when tracking markers in a machined object are ±0.010 and ±0.043 mm, respectively. Mean precision for nine users tracking markers in a tutorial dataset of minipig feeding was ±0.062 mm in XMALab and ±0.14 mm in XrayProject. Reproducibility of 3D point locations across nine users was 10-fold greater in XMALab than in XrayProject, and six degree-of-freedom bone motions calculated with a joint coordinate system were 3- to 6-fold more reproducible in XMALab. XMALab is also suitable for tracking white or black markers in standard light videos with optional checkerboard calibration. We expect XMALab to increase both the quality and quantity of animal motion data available for comparative biomechanics research. © 2016. Published by The Company of Biologists Ltd.

Surgical navigation in urology: European perspective.

PubMed

Rassweiler, Jens; Rassweiler, Marie-Claire; Müller, Michael; Kenngott, Hannes; Meinzer, Hans-Peter; Teber, Dogu

2014-01-01

Use of virtual reality to navigate open and endoscopic surgery has significantly evolved during the last decade. Current status of seven most interesting projects inside the European Association of Urology section of uro-technology is summarized with review of literature. Marker-based endoscopic tracking during laparoscopic radical prostatectomy using high-definition technology reduces positive margins. Marker-based endoscopic tracking during laparoscopic partial nephrectomy by mechanical overlay of three-dimensional-segmented virtual anatomy is helpful during planning of trocar placement and dissection of renal hilum. Marker-based, iPAD-assisted puncture of renal collecting system shows more benefit for trainees with reduction of radiation exposure. Three-dimensional laser-assisted puncture of renal collecting system using Uro-Dyna-CT realized in an ex-vivo model enables minimal radiation time. Electromagnetic tracking for puncture of renal collecting system using a sensor at the tip of ureteral catheter worked in an in-vivo model of porcine ureter and kidney. Attitude tracking for ultrasound-guided puncture of renal tumours by accelerometer reduces the puncture error from 4.7 to 1.8 mm. Feasibility of electromagnetic and optical tracking with the da Vinci telemanipulator was shown in vitro as well as using in-vivo model of oesophagectomy. Target registration error was 11.2 mm because of soft-tissue deformation. Intraoperative navigation is helpful during percutaneous puncture collecting system and biopsy of renal tumour using various tracking techniques. Early clinical studies demonstrate advantages of marker-based navigation during laparoscopic radical prostatectomy and partial nephrectomy. Combination of different tracking techniques may further improve this interesting addition to video-assisted surgery.

Integrated site-specific quantification of faecal bacteria and detection of DNA markers in faecal contamination source tracking as a microbial risk tracking tool in urban Lake ecosystems

NASA Astrophysics Data System (ADS)

Donde, Oscar Omondi; Tian, Cuicui; Xiao, Bangding

2017-11-01

The presence of feacal-derived pathogens in water is responsible for several infectious diseases and deaths worldwide. As a solution, sources of fecal pollution in waters must be accurately assessed, properly determined and strictly controlled. However, the exercise has remained challenging due to the existing overlapping characteristics by different members of faecal coliform bacteria and the inadequacy of information pertaining to the contribution of seasonality and weather condition on tracking the possible sources of pollution. There are continued efforts to improve the Faecal Contamination Source Tracking (FCST) techniques such as Microbial Source Tracking (MST). This study aimed to make contribution to MST by evaluating the efficacy of combining site specific quantification of faecal contamination indicator bacteria and detection of DNA markers while accounting for seasonality and weather conditions' effects in tracking the major sources of faecal contamination in a freshwater system (Donghu Lake, China). The results showed that the use of cyd gene in addition to lacZ and uidA genes differentiates E. coli from other closely related faecal bacteria. The use of selective media increases the pollution source tracking accuracy. BSA addition boosts PCR detection and increases FCST efficiency. Seasonality and weather variability also influence the detection limit for DNA markers.

Numerical study of the vortex tube reconnection using vortex particle method on many graphics cards

NASA Astrophysics Data System (ADS)

Kudela, Henryk; Kosior, Andrzej

2014-08-01

Vortex Particle Methods are one of the most convenient ways of tracking the vorticity evolution. In the article we presented numerical recreation of the real life experiment concerning head-on collision of two vortex rings. In the experiment the evolution and reconnection of the vortex structures is tracked with passive markers (paint particles) which in viscous fluid does not follow the evolution of vorticity field. In numerical computations we showed the difference between vorticity evolution and movement of passive markers. The agreement with the experiment was very good. Due to problems with very long time of computations on a single processor the Vortex-in-Cell method was implemented on the multicore architecture of the graphics cards (GPUs). Vortex Particle Methods are very well suited for parallel computations. As there are myriads of particles in the flow and for each of them the same equations of motion have to be solved the SIMD architecture used in GPUs seems to be perfect. The main disadvantage in this case is the small amount of the RAM memory. To overcome this problem we created a multiGPU implementation of the VIC method. Some remarks on parallel computing are given in the article.

Transgenic mice that accept Luciferase- or GFP-expressing syngeneic tumor cells at high efficiencies.

PubMed

Aoyama, Naoki; Miyoshi, Hiroyuki; Miyachi, Hitoshi; Sonoshita, Masahiro; Okabe, Masaru; Taketo, Makoto Mark

2018-05-11

Jellyfish green fluorescent protein (GFP) and firefly luciferase can serve as versatile tracking markers for identification and quantification of transplanted cancer cells in vivo. However, immune reactions against these markers can hamper the formation of syngraft tumors and metastasis that follows. Here, we report two transgenic (Tg) mouse lines that express nonfunctional mutant marker proteins, namely modified firefly luciferase (Luc2) or enhanced GFP (EGFP). These mice, named as Tg-mLuc2 and Tg-mEGFP, turned out to be immunologically tolerant to the respective tracking markers and thus efficiently accepted syngeneic cancer cells expressing the active forms of the markers. We then injected intrarectally the F 1 hybrid Tg mice (BALB/c × C57BL/6J) with Colon-26 (C26) colon cancer cells that originated from a BALB/c mouse. Even when C26 cells expressed active Luc2 or EGFP, they formed primary tumors in the Tg mice with only 10 4 cells per mouse compared with more than 10 6 cells required in the nontransgenic BALB/c hosts. Furthermore, we detected metastatic foci of C26 cells in the liver and lungs of the Tg mice by tracking the specific reporter activities. These results show the usefulness of the Tg mouse lines as recipients for transplantation experiments with the non-self tracking marker-expressing cells. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

Investigation of tracking systems properties in CAVE-type virtual reality systems

NASA Astrophysics Data System (ADS)

Szymaniak, Magda; Mazikowski, Adam; Meironke, Michał

2017-08-01

In recent years, many scientific and industrial centers in the world developed a virtual reality systems or laboratories. One of the most advanced solutions are Immersive 3D Visualization Lab (I3DVL), a CAVE-type (Cave Automatic Virtual Environment) laboratory. It contains two CAVE-type installations: six-screen installation arranged in a form of a cube, and four-screen installation, a simplified version of the previous one. The user feeling of "immersion" and interaction with virtual world depend on many factors, in particular on the accuracy of the tracking system of the user. In this paper properties of the tracking systems applied in I3DVL was investigated. For analysis two parameters were selected: the accuracy of the tracking system and the range of detection of markers by the tracking system in space of the CAVE. Measurements of system accuracy were performed for six-screen installation, equipped with four tracking cameras for three axes: X, Y, Z. Rotation around the Y axis was also analyzed. Measured tracking system shows good linear and rotating accuracy. The biggest issue was the range of the monitoring of markers inside the CAVE. It turned out, that the tracking system lose sight of the markers in the corners of the installation. For comparison, for a simplified version of CAVE (four-screen installation), equipped with eight tracking cameras, this problem was not occur. Obtained results will allow for improvement of cave quality.

Nearly automatic motion capture system for tracking octopus arm movements in 3D space.

PubMed

Zelman, Ido; Galun, Meirav; Akselrod-Ballin, Ayelet; Yekutieli, Yoram; Hochner, Binyamin; Flash, Tamar

2009-08-30

Tracking animal movements in 3D space is an essential part of many biomechanical studies. The most popular technique for human motion capture uses markers placed on the skin which are tracked by a dedicated system. However, this technique may be inadequate for tracking animal movements, especially when it is impossible to attach markers to the animal's body either because of its size or shape or because of the environment in which the animal performs its movements. Attaching markers to an animal's body may also alter its behavior. Here we present a nearly automatic markerless motion capture system that overcomes these problems and successfully tracks octopus arm movements in 3D space. The system is based on three successive tracking and processing stages. The first stage uses a recently presented segmentation algorithm to detect the movement in a pair of video sequences recorded by two calibrated cameras. In the second stage, the results of the first stage are processed to produce 2D skeletal representations of the moving arm. Finally, the 2D skeletons are used to reconstruct the octopus arm movement as a sequence of 3D curves varying in time. Motion tracking, segmentation and reconstruction are especially difficult problems in the case of octopus arm movements because of the deformable, non-rigid structure of the octopus arm and the underwater environment in which it moves. Our successful results suggest that the motion-tracking system presented here may be used for tracking other elongated objects.

Microbial source tracking markers at three inland recreational lakes in Ohio, 2011

USGS Publications Warehouse

Francy, Donna S.; Stelzer, Erin A.

2012-01-01

During the 2011 recreational season, samples were collected for E. coli and microbial source tracking (MST) marker concentrations to begin to understand potential sources of fecal contamination at three inland recreational lakes in Ohio - Buckeye, Atwood, and Tappan Lakes. The results from 32 regular samples, 4 field blanks, and 7 field replicates collected at 5 sites are presented in this report. At the three lakes, the ruminant-associated marker was found most often (57-73 percent of samples) but at estimated quantities, followed by the dog-associated marker (30-43 percent of samples). The human-associated marker was found in 14 and 50 percent of samples from Atwood and Tappan Lakes, respectively, but was not found in any samples from the two Buckeye Lake sites. The gull-associated marker was detected in only two samples, both from Tappan Lake.

Digital stereophotogrammetry based on circular markers and zooming cameras: evaluation of a method for 3D analysis of small motions in orthopaedic research

PubMed Central

2011-01-01

Background Orthopaedic research projects focusing on small displacements in a small measurement volume require a radiation free, three dimensional motion analysis system. A stereophotogrammetrical motion analysis system can track wireless, small, light-weight markers attached to the objects. Thereby the disturbance of the measured objects through the marker tracking can be kept at minimum. The purpose of this study was to develop and evaluate a non-position fixed compact motion analysis system configured for a small measurement volume and able to zoom while tracking small round flat markers in respect to a fiducial marker which was used for the camera pose estimation. Methods The system consisted of two web cameras and the fiducial marker placed in front of them. The markers to track were black circles on a white background. The algorithm to detect a centre of the projected circle on the image plane was described and applied. In order to evaluate the accuracy (mean measurement error) and precision (standard deviation of the measurement error) of the optical measurement system, two experiments were performed: 1) inter-marker distance measurement and 2) marker displacement measurement. Results The first experiment of the 10 mm distances measurement showed a total accuracy of 0.0086 mm and precision of ± 0.1002 mm. In the second experiment, translations from 0.5 mm to 5 mm were measured with total accuracy of 0.0038 mm and precision of ± 0.0461 mm. The rotations of 2.25° amount were measured with the entire accuracy of 0.058° and the precision was of ± 0.172°. Conclusions The description of the non-proprietary measurement device with very good levels of accuracy and precision may provide opportunities for new, cost effective applications of stereophotogrammetrical analysis in musculoskeletal research projects, focusing on kinematics of small displacements in a small measurement volume. PMID:21284867

Manual Dexterity in Schizophrenia—A Neglected Clinical Marker?

PubMed Central

Térémetz, Maxime; Carment, Loïc; Brénugat-Herne, Lindsay; Croca, Marta; Bleton, Jean-Pierre; Krebs, Marie-Odile; Maier, Marc A.; Amado, Isabelle; Lindberg, Påvel G.

2017-01-01

Impaired manual dexterity is commonly observed in schizophrenia. However, a quantitative description of key sensorimotor components contributing to impaired dexterity is lacking. Whether the key components of dexterity are differentially affected and how they relate to clinical characteristics also remains unclear. We quantified the degree of dexterity in 35 stabilized patients with schizophrenia and in 20 age-matched control subjects using four visuomotor tasks: (i) force tracking to quantify visuomotor precision, (ii) sequential finger tapping to measure motor sequence recall, (iii) single-finger tapping to assess temporal regularity, and (iv) multi-finger tapping to measure independence of finger movements. Diverse clinical and neuropsychological tests were also applied. A patient subgroup (N = 15) participated in a 14-week cognitive remediation protocol and was assessed before and after remediation. Compared to control subjects, patients with schizophrenia showed greater error in force tracking, poorer recall of tapping sequences, decreased tapping regularity, and reduced degree of finger individuation. A composite performance measure discriminated patients from controls with sensitivity = 0.79 and specificity = 0.9. Aside from force-tracking error, no other dexterity components correlated with antipsychotic medication. In patients, some dexterity components correlated with neurological soft signs, Positive and Negative Syndrome Scale (PANSS), or neuropsychological scores. This suggests differential cognitive contributions to these components. Cognitive remediation lead to significant improvement in PANSS, tracking error, and sequence recall (without change in medication). These findings show that multiple aspects of sensorimotor control contribute to impaired manual dexterity in schizophrenia. Only visuomotor precision was related to antipsychotic medication. Good diagnostic accuracy and responsiveness to treatment suggest that manual dexterity may represent a useful clinical marker in schizophrenia. PMID:28740470

Quantitative Cell Cycle Analysis Based on an Endogenous All-in-One Reporter for Cell Tracking and Classification.

PubMed

Zerjatke, Thomas; Gak, Igor A; Kirova, Dilyana; Fuhrmann, Markus; Daniel, Katrin; Gonciarz, Magdalena; Müller, Doris; Glauche, Ingmar; Mansfeld, Jörg

2017-05-30

Cell cycle kinetics are crucial to cell fate decisions. Although live imaging has provided extensive insights into this relationship at the single-cell level, the limited number of fluorescent markers that can be used in a single experiment has hindered efforts to link the dynamics of individual proteins responsible for decision making directly to cell cycle progression. Here, we present fluorescently tagged endogenous proliferating cell nuclear antigen (PCNA) as an all-in-one cell cycle reporter that allows simultaneous analysis of cell cycle progression, including the transition into quiescence, and the dynamics of individual fate determinants. We also provide an image analysis pipeline for automated segmentation, tracking, and classification of all cell cycle phases. Combining the all-in-one reporter with labeled endogenous cyclin D1 and p21 as prime examples of cell-cycle-regulated fate determinants, we show how cell cycle and quantitative protein dynamics can be simultaneously extracted to gain insights into G1 phase regulation and responses to perturbations. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Transesophageal Echocardiography, 3-Dimensional and Speckle Tracking Together as Sensitive Markers for Early Outcome in Patients With Left Ventricular Dysfunction Undergoing Cardiac Surgery.

PubMed

Kumar, Alok; Puri, Goverdhan Dutt; Bahl, Ajay

2017-10-01

Speckle tracking, when combined with 3-dimensional (3D) left ventricular ejection fraction, might prove to be a more sensitive marker for postoperative ventricular dysfunction. This study investigated early outcomes in a cohort of patients with left ventricular dysfunction undergoing cardiac surgery. Prospective, blinded, observational study. University hospital; single institution. The study comprised 73 adult patients with left ventricular ejection fraction <50% undergoing cardiac surgery using cardiopulmonary bypass. Routine transesophageal echocardiography before and after bypass. Global longitudinal strain using speckle tracking and 3D left ventricular ejection fraction were computed using transesophageal echocardiography. Mean prebypass global longitudinal strain and 3D left ventricle ejection fraction were significantly lower in patients with postoperative low-cardiac-output syndrome compared with patients who did not develop low cardiac output (global longitudinal strain -7.5% v -10.7% and 3D left ventricular ejection fraction 29% v 39%, respectively; p < 0.0001). The cut-off value of global longitudinal strain predicting postoperative low-cardiac-output syndrome was -6%, with 95% sensitivity and 68% specificity; and 3D left ventricular ejection fraction was 19% with 98% sensitivity and 81% specificity. Preoperative left ventricular global longitudinal strain (-6%) and 3D left ventricular ejection fraction (19%) together could act as predictor of postoperative low-cardiac-output states with high sensitivity (99.9%) in patients undergoing cardiac surgery. Copyright © 2017 Elsevier Inc. All rights reserved.

SU-E-J-42: Evaluation of Fiducial Markers for Ultrasound and X-Ray Images Used for Motion Tracking in Pancreas SBRT

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

Ng, SK; Armour, E; Su, L

Purpose Ultrasound tracking of target motion relies on visibility of vascular and/or anatomical landmark. However this is challenging when the target is located far from vascular structures or in organs that lack ultrasound landmark structure, such as in the case of pancreas cancer. The purpose of this study is to evaluate visibility, artifacts and distortions of fusion coils and solid gold markers in ultrasound, CT, CBCT and kV images to identify markers suitable for real-time ultrasound tracking of tumor motion in SBRT pancreas treatment. Methods Two fusion coils (1mm × 5mm and 1mm × 10 mm) and a solid goldmore » marker (0.8mm × 10mm) were embedded in a tissue–like ultrasound phantom. The phantom (5cm × 12cm × 20cm) was prepared using water, gelatin and psyllium-hydrophilic-mucilloid fiber. Psylliumhydrophilic mucilloid acts as scattering medium to produce echo texture that simulates sonographic appearance of human tissue in ultrasound images while maintaining electron density close to that of water in CT images. Ultrasound images were acquired using 3D-ultrasound system with markers embedded at 5, 10 and 15mm depth from phantom surface. CT images were acquired using Philips Big Bore CT while CBCT and kV images were acquired with XVI-system (Elexta). Visual analysis was performed to compare visibility of the markers and visibility score (1 to 3) were assigned. Results All markers embedded at various depths are clearly visible (score of 3) in ultrasound images. Good visibility of all markers is observed in CT, CBCT and kV images. The degree of artifact produced by the markers in CT and CBCT images are indistinguishable. No distortion is observed in images from any modalities. Conclusion All markers are visible in images across all modalities in this homogenous tissue-like phantom. Human subject data is necessary to confirm the marker type suitable for real-time ultrasound tracking of tumor motion in SBRT pancreas treatment.« less

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

PubMed Central

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

2015-01-01

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

Dosimetric impact of gold markers implanted closely to lung tumors: a Monte Carlo simulation.

PubMed

Shiinoki, Takehiro; Sawada, Akira; Ishihara, Yoshitomo; Miyabe, Yuki; Matsuo, Yukinori; Mizowaki, Takashi; Kokubo, Masaki; Hiraoka, Masahiro

2014-05-08

We are developing an innovative dynamic tumor tracking irradiation technique using gold markers implanted around a tumor as a surrogate signal, a real-time marker detection system, and a gimbaled X-ray head in the Vero4DRT. The gold markers implanted in a normal organ will produce uncertainty in the dose calculation during treatment planning because the photon mass attenuation coefficient of a gold marker is much larger than that of normal tissue. The purpose of this study was to simulate the dose variation near the gold markers in a lung irradiated by a photon beam using the Monte Carlo method. First, the single-beam and the opposing-beam geometries were simulated using both water and lung phantoms. Subsequently, the relative dose profiles were calculated using a stereotactic body radiotherapy (SBRT) treatment plan for a lung cancer patient having gold markers along the anterior-posterior (AP) and right-left (RL) directions. For the single beam, the dose at the gold marker-phantom interface laterally along the perpendicular to the beam axis increased by a factor of 1.35 in the water phantom and 1.58 in the lung phantom, respectively. Furthermore, the entrance dose at the interface along the beam axis increased by a factor of 1.63 in the water phantom and 1.91 in the lung phantom, while the exit dose increased by a factor of 1.00 in the water phantom and 1.12 in the lung phantom, respectively. On the other hand, both dose escalations and dose de-escalations were canceled by each beam for opposing portal beams with the same beam weight. For SBRT patient data, the dose at the gold marker edge located in the tumor increased by a factor of 1.30 in both AP and RL directions. In clinical cases, dose escalations were observed at the small area where the distance between a gold marker and the lung tumor was ≤ 5 mm, and it would be clinically negligible in multibeam treatments, although further investigation may be required.

SU-E-J-191: Motion Prediction Using Extreme Learning Machine in Image Guided Radiotherapy

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

Jia, J; Cao, R; Pei, X

Purpose: Real-time motion tracking is a critical issue in image guided radiotherapy due to the time latency caused by image processing and system response. It is of great necessity to fast and accurately predict the future position of the respiratory motion and the tumor location. Methods: The prediction of respiratory position was done based on the positioning and tracking module in ARTS-IGRT system which was developed by FDS Team (www.fds.org.cn). An approach involving with the extreme learning machine (ELM) was adopted to predict the future respiratory position as well as the tumor’s location by training the past trajectories. For themore » training process, a feed-forward neural network with one single hidden layer was used for the learning. First, the number of hidden nodes was figured out for the single layered feed forward network (SLFN). Then the input weights and hidden layer biases of the SLFN were randomly assigned to calculate the hidden neuron output matrix. Finally, the predicted movement were obtained by applying the output weights and compared with the actual movement. Breathing movement acquired from the external infrared markers was used to test the prediction accuracy. And the implanted marker movement for the prostate cancer was used to test the implementation of the tumor motion prediction. Results: The accuracy of the predicted motion and the actual motion was tested. Five volunteers with different breathing patterns were tested. The average prediction time was 0.281s. And the standard deviation of prediction accuracy was 0.002 for the respiratory motion and 0.001 for the tumor motion. Conclusion: The extreme learning machine method can provide an accurate and fast prediction of the respiratory motion and the tumor location and therefore can meet the requirements of real-time tumor-tracking in image guided radiotherapy.« less

Human silhouette matching based on moment invariants

NASA Astrophysics Data System (ADS)

Sun, Yong-Chao; Qiu, Xian-Jie; Xia, Shi-Hong; Wang, Zhao-Qi

2005-07-01

This paper aims to apply the method of silhouette matching based on moment invariants to infer the human motion parameters from video sequences of single monocular uncalibrated camera. Currently, there are two ways of tracking human motion: Marker and Markerless. While a hybrid framework is introduced in this paper to recover the input video contents. A standard 3D motion database is built up by marker technique in advance. Given a video sequences, human silhouettes are extracted as well as the viewpoint information of the camera which would be utilized to project the standard 3D motion database onto the 2D one. Therefore, the video recovery problem is formulated as a matching issue of finding the most similar body pose in standard 2D library with the one in video image. The framework is applied to the special trampoline sport where we can obtain the complicated human motion parameters in the single camera video sequences, and a lot of experiments are demonstrated that this approach is feasible in the field of monocular video-based 3D motion reconstruction.

A Delay Vector Variance based Marker for an Output-Only Assessment of Structural Changes in Tension Leg Platforms

NASA Astrophysics Data System (ADS)

Jaksic, V.; Wright, C.; Mandic, D. P.; Murphy, J.; Pakrashi, V.

2015-07-01

Although aspects of power generation of many offshore renewable devices are well understood, their dynamic responses under high wind and wave conditions are still to be investigated to a great detail. Output only statistical markers are important for these offshore devices, since access to the device is limited and information about the exposure conditions and the true behaviour of the devices are generally partial, limited, and vague or even absent. The markers can summarise and characterise the behaviour of these devices from their dynamic response available as time series data. The behaviour may be linear or nonlinear and consequently a marker that can track the changes in structural situations can be quite important. These markers can then be helpful in assessing the current condition of the structure and can indicate possible intervention, monitoring or assessment. This paper considers a Delay Vector Variance based marker for changes in a tension leg platform tested in an ocean wave basin for structural changes brought about by single column dampers. The approach is based on dynamic outputs of the device alone and is based on the estimation of the nonlinearity of the output signal. The advantages of the selected marker and its response with changing structural properties are discussed. The marker is observed to be important for monitoring the as- deployed structural condition and is sensitive to changes in such conditions. Influence of exposure conditions of wave loading is also discussed in this study based only on experimental data.

Plugin-docking system for autonomous charging using particle filter

NASA Astrophysics Data System (ADS)

Koyasu, Hiroshi; Wada, Masayoshi

2017-03-01

Autonomous charging of the robot battery is one of the key functions for the sake of expanding working areas of the robots. To realize it, most of existing systems use custom docking stations or artificial markers. By the other words, they can only charge on a few specific outlets. If the limit can be removed, working areas of the robots significantly expands. In this paper, we describe a plugin-docking system for the autonomous charging, which does not require any custom docking stations or artificial markers. A single camera is used for recognizing the 3D position of an outlet socket. A particle filter-based image tracking algorithm which is robust to the illumination change is applied. The algorithm is implemented on a robot with an omnidirectional moving system. The experimental results show the effectiveness of our system.

Catheter tracking in an interventional photoacoustic surgical system

NASA Astrophysics Data System (ADS)

Cheng, Alexis; Itsarachaiyot, Yuttana; Kim, Younsu; Zhang, Haichong K.; Taylor, Russell H.; Boctor, Emad M.

2017-03-01

In laparoscopic medical procedures, accurate tracking of interventional tools such as catheters are necessary. Current practice for tracking catheters often involve using fluoroscopy, which is best avoided to minimize radiation dose to the patient and the surgical team. Photoacoustic imaging is an emerging imaging modality that can be used for this purpose and does not currently have a general tool tracking solution. Photoacoustic-based catheter tracking would increase its attractiveness, by providing both an imaging and tracking solution. We present a catheter tracking method based on the photoacoustic effect. Photoacoustic markers are simultaneously observed by a stereo camera as well as a piezoelectric element attached to the tip of a catheter. The signals received by the piezoelectric element can be used to compute its position relative to the photoacoustic markers using multilateration. This combined information can be processed to localize the position of the piezoelectric element with respect to the stereo camera system. We presented the methods to enable this work and demonstrated precisions of 1-3mm and a relative accuracy of less than 4% in four independent locations, which are comparable to conventional systems. In addition, we also showed in another experiment a reconstruction precision up to 0.4mm and an estimated accuracy up to 0.5mm. Future work will include simulations to better evaluate this method and its challenges and the development of concurrent photoacoustic marker projection and its associated methods.

Two-dimensional right ventricular strain by speckle tracking for assessment of longitudinal right ventricular function after paediatric congenital heart disease surgery.

PubMed

Karsenty, Clement; Hadeed, Khaled; Dulac, Yves; Semet, Florent; Alacoque, Xavier; Breinig, Sophie; Leobon, Bertrand; Acar, Philippe; Hascoet, Sebastien

2017-03-01

Right ventricular (RV) function is a prognostic marker of cardiac disease in children. Speckle tracking has been developed to assess RV longitudinal shortening, the dominant deformation during systole; little is known about its feasibility in children with congenital heart disease (CHD). To evaluate the feasibility and reproducibility of RV two-dimensional (2D) strain assessed by speckle tracking in infants undergoing CHD surgery compared with conventional markers. In this prospective single-centre study, RV peak systolic strain (RV-PSS) was measured using 2D speckle tracking in 37 consecutive children undergoing CHD surgery. Examinations were performed the day before surgery, a few hours after surgery and before discharge. Relationships with the z score of tricuspid annular plane systolic excursion (TAPSE) and tricuspid annular systolic velocity (TA Sa) were assessed. Median (interquartile range) age was 19 months (5-63); median weight was 9.2 kg (5.3-18.0). RV-PSS analysis was feasible in 92.9% (95% confidence interval [CI]: 86.0-97.1) of examinations. The coefficient of variation was 9.7% (95% CI: 7.4-11.9) for intraobserver variability and 15.1% (95% CI: 12.7-17.6) for interobserver variability. Correlations between RV-PSS and z score of TAPSE and TA Sa were strong (r=0.71, P<0.0001 and r=0.70, P<0.0001, respectively). RV-PSS was significantly reduced after surgery compared with baseline (-10.5±2.9% vs. -19.5±4.8%; P<0.0001) and at discharge (-13.5±4.0% vs. -19.5±4.8%; P<0.0001). Similar evolutions were observed with TAPSE and TA Sa (both P<0.0001). RV longitudinal strain by speckle tracking is a feasible and reproducible method of assessing perioperative evolution of RV function in children with CHD. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

TH-AB-202-05: BEST IN PHYSICS (JOINT IMAGING-THERAPY): First Online Ultrasound-Guided MLC Tracking for Real-Time Motion Compensation in Radiotherapy

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

Ipsen, S; Bruder, R; Schweikard, A

Purpose: While MLC tracking has been successfully used for motion compensation of moving targets, current real-time target localization methods rely on correlation models with x-ray imaging or implanted electromagnetic transponders rather than direct target visualization. In contrast, ultrasound imaging yields volumetric data in real-time (4D) without ionizing radiation. We report the first results of online 4D ultrasound-guided MLC tracking in a phantom. Methods: A real-time tracking framework was installed on a 4D ultrasound station (Vivid7 dimension, GE) and used to detect a 2mm spherical lead marker inside a water tank. The volumetric frame rate was 21.3Hz (47ms). The marker wasmore » rigidly attached to a motion stage programmed to reproduce nine tumor trajectories (five prostate, four lung). The 3D marker position from ultrasound was used for real-time MLC aperture adaption. The tracking system latency was measured and compensated by prediction for lung trajectories. To measure geometric accuracy, anterior and lateral conformal fields with 10cm circular aperture were delivered for each trajectory. The tracking error was measured as the difference between marker position and MLC aperture in continuous portal imaging. For dosimetric evaluation, 358° VMAT fields were delivered to a biplanar diode array dosimeter using the same trajectories. Dose measurements with and without MLC tracking were compared to a static reference dose using a 3%/3 mm γ-test. Results: The tracking system latency was 170ms. The mean root-mean-square tracking error was 1.01mm (0.75mm prostate, 1.33mm lung). Tracking reduced the mean γ-failure rate from 13.9% to 4.6% for prostate and from 21.8% to 0.6% for lung with high-modulation VMAT plans and from 5% (prostate) and 18% (lung) to 0% with low modulation. Conclusion: Real-time ultrasound tracking was successfully integrated with MLC tracking for the first time and showed similar accuracy and latency as other methods while holding the potential to measure target motion non-invasively. SI was supported by the Graduate School for Computing in Medicine and Life Science, German Excellence Initiative [grant DFG GSC 235/1].« less

Optimal marker placement in hadrontherapy: intelligent optimization strategies with augmented Lagrangian pattern search.

PubMed

Altomare, Cristina; Guglielmann, Raffaella; Riboldi, Marco; Bellazzi, Riccardo; Baroni, Guido

2015-02-01

In high precision photon radiotherapy and in hadrontherapy, it is crucial to minimize the occurrence of geometrical deviations with respect to the treatment plan in each treatment session. To this end, point-based infrared (IR) optical tracking for patient set-up quality assessment is performed. Such tracking depends on external fiducial points placement. The main purpose of our work is to propose a new algorithm based on simulated annealing and augmented Lagrangian pattern search (SAPS), which is able to take into account prior knowledge, such as spatial constraints, during the optimization process. The SAPS algorithm was tested on data related to head and neck and pelvic cancer patients, and that were fitted with external surface markers for IR optical tracking applied for patient set-up preliminary correction. The integrated algorithm was tested considering optimality measures obtained with Computed Tomography (CT) images (i.e. the ratio between the so-called target registration error and fiducial registration error, TRE/FRE) and assessing the marker spatial distribution. Comparison has been performed with randomly selected marker configuration and with the GETS algorithm (Genetic Evolutionary Taboo Search), also taking into account the presence of organs at risk. The results obtained with SAPS highlight improvements with respect to the other approaches: (i) TRE/FRE ratio decreases; (ii) marker distribution satisfies both marker visibility and spatial constraints. We have also investigated how the TRE/FRE ratio is influenced by the number of markers, obtaining significant TRE/FRE reduction with respect to the random configurations, when a high number of markers is used. The SAPS algorithm is a valuable strategy for fiducial configuration optimization in IR optical tracking applied for patient set-up error detection and correction in radiation therapy, showing that taking into account prior knowledge is valuable in this optimization process. Further work will be focused on the computational optimization of the SAPS algorithm toward fast point-of-care applications. Copyright © 2014 Elsevier Inc. All rights reserved.

SU-G-BRA-05: Application of a Feature-Based Tracking Algorithm to KV X-Ray Fluoroscopic Images Toward Marker-Less Real-Time Tumor Tracking

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

Nakamura, M; Matsuo, Y; Mukumoto, N

Purpose: To detect target position on kV X-ray fluoroscopic images using a feature-based tracking algorithm, Accelerated-KAZE (AKAZE), for markerless real-time tumor tracking (RTTT). Methods: Twelve lung cancer patients treated with RTTT on the Vero4DRT (Mitsubishi Heavy Industries, Japan, and Brainlab AG, Feldkirchen, Germany) were enrolled in this study. Respiratory tumor movement was greater than 10 mm. Three to five fiducial markers were implanted around the lung tumor transbronchially for each patient. Before beam delivery, external infrared (IR) markers and the fiducial markers were monitored for 20 to 40 s with the IR camera every 16.7 ms and with an orthogonalmore » kV x-ray imaging subsystem every 80 or 160 ms, respectively. Target positions derived from the fiducial markers were determined on the orthogonal kV x-ray images, which were used as the ground truth in this study. Meanwhile, tracking positions were identified by AKAZE. Among a lot of feature points, AKAZE found high-quality feature points through sequential cross-check and distance-check between two consecutive images. Then, these 2D positional data were converted to the 3D positional data by a transformation matrix with a predefined calibration parameter. Root mean square error (RMSE) was calculated to evaluate the difference between 3D tracking and target positions. A total of 393 frames was analyzed. The experiment was conducted on a personal computer with 16 GB RAM, Intel Core i7-2600, 3.4 GHz processor. Results: Reproducibility of the target position during the same respiratory phase was 0.6 +/− 0.6 mm (range, 0.1–3.3 mm). Mean +/− SD of the RMSEs was 0.3 +/− 0.2 mm (range, 0.0–1.0 mm). Median computation time per frame was 179 msec (range, 154–247 msec). Conclusion: AKAZE successfully and quickly detected the target position on kV X-ray fluoroscopic images. Initial results indicate that the differences between 3D tracking and target position would be clinically acceptable.« less

State of the art molecular markers for fecal pollution source tracking in water.

PubMed

Roslev, Peter; Bukh, Annette S

2011-03-01

Most environmental waters are susceptible to fecal contamination from animal and/or human pollution sources. To attenuate or eliminate such contamination, it is often critical that the pollution sources are rapidly and correctly identified. Fecal pollution source tracking (FST) is a promising research area that aims to identify the origin(s) of fecal pollution in water. This mini-review focuses on the potentials and limitations of library independent molecular markers that are exclusively or strongly associated with fecal pollution from humans and different animals. Fecal-source-associated molecular markers include nucleic acid sequences from prokaryotes and viruses associated with specific biological hosts, but also sequences such as mitochondrial DNA retrieved directly from humans and animals. However, some fecal-source-associated markers may not be absolutely specific for a given source type, and apparent specificity and frequency established in early studies are sometimes compromised by new studies suggesting variation in specificity and abundance on a regional, global and/or temporal scale. It is therefore recommended that FST studies are based on carefully selected arrays of markers, and that identification of human and animal contributions are based on a multi-marker toolkit with several markers for each source category. Furthermore, future FST studies should benefit from increased knowledge regarding sampling strategies and temporal and spatial variability of marker ratios. It will also be important to obtain a better understanding of marker persistence and the quantitative relationship between marker abundance and the relative contribution from individual fecal pollution source types. A combination of enhanced pathogen screening methods, and validated quantitative source tracking techniques could then contribute significantly to future management of environmental water quality including improved microbial risk assessment.

Characterization of polymorphic microsatellites for Tripterygium (Celastraceae), a monospecific genus of medicinal importance.

PubMed

Novy, Ari; Jones, Kenneth C

2011-10-01

Microsatellite markers were developed for the medicinal plant Tripterygium (Celastraceae) to assess its population structure and to facilitate source tracking of plant materials used for medicinal extracts. Ten microsatellite markers were isolated and characterized in T. wilfordii using an enriched genomic library. The number of alleles per locus ranged from five to 12. Observed and expected heterozygosity ranged from 0.166 to 0.630 and 0.392 to 0.562, respectively. These markers will be useful for a variety of applications including source tracking of plant materials, resolution of taxonomic issues, and population genetics studies.

Simultaneous 3D localization of multiple MR-visible markers in fully reconstructed MR images: proof-of-concept for subsecond position tracking.

PubMed

Thörmer, Gregor; Garnov, Nikita; Moche, Michael; Haase, Jürgen; Kahn, Thomas; Busse, Harald

2012-04-01

To determine whether a greatly reduced spatial resolution of fully reconstructed projection MR images can be used for the simultaneous 3D localization of multiple MR-visible markers and to assess the feasibility of a subsecond position tracking for clinical purposes. Miniature, inductively coupled RF coils were imaged in three orthogonal planes with a balanced steady-state free precession (SSFP) sequence and automatically localized using a two-dimensional template fitting and a subsequent three-dimensional (3D) matching of the coordinates. Precision, accuracy, speed and robustness of 3D localization were assessed for decreasing in-plane resolutions (0.6-4.7 mm). The feasibility of marker tracking was evaluated at the lowest resolution by following a robotically driven needle on a complex 3D trajectory. Average 3D precision and accuracy, sensitivity and specificity of localization ranged between 0.1 and 0.4 mm, 0.5 and 1.0 mm, 100% and 95%, and 100% and 96%, respectively. At the lowest resolution, imaging and localization took ≈350 ms and provided an accuracy of ≈1.0 mm. In the tracking experiment, the needle was clearly depicted on the oblique scan planes defined by the markers. Image-based marker localization at a greatly reduced spatial resolution is considered a feasible approach to monitor reference points or rigid instruments at subsecond update rates. Copyright © 2012 Elsevier Inc. All rights reserved.

Quantifying skin motion artifact error of the hindfoot and forefoot marker clusters with the optical tracking of a multi-segment foot model using single-plane fluoroscopy.

PubMed

Shultz, R; Kedgley, A E; Jenkyn, T R

2011-05-01

The trajectories of skin-mounted markers tracked with optical motion capture are assumed to be an adequate representation of the underlying bone motions. However, it is well known that soft tissue artifact (STA) exists between marker and bone. This study quantifies the STA associated with the hindfoot and midfoot marker clusters of a multi-segment foot model. To quantify STA of the hindfoot and midfoot marker clusters with respect to the calcaneus and navicular respectively, fluoroscopic images were collected on 27 subjects during four quasi-static positions, (1) quiet standing (non-weight bearing), (2) at heel strike (weight-bearing), (3) at midstance (weight-bearing) and (4) at toe-off (weight-bearing). The translation and rotation components of STA were calculated in the sagittal plane. Translational STA at the calcaneus varied from 5.9±7.3mm at heel-strike to 12.1±0.3mm at toe-off. For the navicular the translational STA ranged from 7.6±7.6mm at heel strike to 16.4±16.7mm at toe-off. Rotational STA was relatively smaller for both bones at all foot positions. For the calcaneus they varied between 0.1±2.2° at heel-strike to 0.2±0.6° at toe-off. For the navicular, the rotational STA ranged from 0.6±0.9° at heel-strike to 0.7±0.7° at toe-off. The largest translational STA found in this study (16mm for the navicular) was smaller than those reported in the literature for the thigh and the lower leg, but was larger than the STA of individual spherical markers affixed to the foot. The largest errors occurred at toe-off position for all subjects for both the hindfoot and midfoot clusters. Future studies are recommended to quantify true three-dimensional STA of the entire foot during gait. Copyright © 2011. Published by Elsevier B.V.

A proto-type design of a real-tissue phantom for the validation of deformation algorithms and 4D dose calculations

NASA Astrophysics Data System (ADS)

Szegedi, M.; Rassiah-Szegedi, P.; Fullerton, G.; Wang, B.; Salter, B.

2010-07-01

The purpose of this study is to design a real-tissue phantom for use in the validation of deformation algorithms. A phantom motion controller that runs sinusoidal and non-regular patient-based breathing pattern, via a piston, was applied to porcine liver tissue. It was regulated to simulate movement ranges similar to recorded implanted liver markers from patients. 4D CT was applied to analyze deformation. The suitability of various markers in the liver and the position reproducibility of markers and of reference points were studied. The similarity of marker motion pattern in the liver phantom and in real patients was evaluated. The viability of the phantom over time and its use with electro-magnetic tracking devices were also assessed. High contrast markers, such as carbon markers, implanted in the porcine liver produced less image artifacts on CT and were well visualized compared to metallic ones. The repositionability of markers was within a measurement accuracy of ±2 mm. Similar anatomical patient motions were reproducible up to elongations of 3 cm for a time period of at least 90 min. The phantom is compatible with electro-magnetic tracking devices and 4D CT. The phantom motion is reproducible and simulates realistic patient motion and deformation. The ability to carry out voxel-based tracking allows for the evaluation of deformation algorithms in a controlled environment with recorded patient traces. The phantom is compatible with all therapy devices clinically encountered in our department.

Single wheel testers, single track testers, and instrumented tractors

USDA-ARS?s Scientific Manuscript database

Single wheel testers and single track testers are used for determining tractive performance characteristics of tires and tracks. Instrumented tractors are useful in determining the tractive performance of tractors. These machines are also used for determining soil-tire and soil-track interactions,...

SU-G-JeP1-11: Feasibility Study of Markerless Tracking Using Dual Energy Fluoroscopic Images for Real-Time Tumor-Tracking Radiotherapy System

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

Shiinoki, T; Shibuya, K; Sawada, A

Purpose: The new real-time tumor-tracking radiotherapy (RTRT) system was installed in our institution. This system consists of two x-ray tubes and color image intensifiers (I.I.s). The fiducial marker which was implanted near the tumor was tracked using color fluoroscopic images. However, the implantation of the fiducial marker is very invasive. Color fluoroscopic images enable to increase the recognition of the tumor. However, these images were not suitable to track the tumor without fiducial marker. The purpose of this study was to investigate the feasibility of markerless tracking using dual energy colored fluoroscopic images for real-time tumor-tracking radiotherapy system. Methods: Themore » colored fluoroscopic images of static and moving phantom that had the simulated tumor (30 mm diameter sphere) were experimentally acquired using the RTRT system. The programmable respiratory motion phantom was driven using the sinusoidal pattern in cranio-caudal direction (Amplitude: 20 mm, Time: 4 s). The x-ray condition was set to 55 kV, 50 mA and 105 kV, 50 mA for low energy and high energy, respectively. Dual energy images were calculated based on the weighted logarithmic subtraction of high and low energy images of RGB images. The usefulness of dual energy imaging for real-time tracking with an automated template image matching algorithm was investigated. Results: Our proposed dual energy subtraction improve the contrast between tumor and background to suppress the bone structure. For static phantom, our results showed that high tracking accuracy using dual energy subtraction images. For moving phantom, our results showed that good tracking accuracy using dual energy subtraction images. However, tracking accuracy was dependent on tumor position, tumor size and x-ray conditions. Conclusion: We indicated that feasibility of markerless tracking using dual energy fluoroscopic images for real-time tumor-tracking radiotherapy system. Furthermore, it is needed to investigate the tracking accuracy using proposed dual energy subtraction images for clinical cases.« less

Biomechanical comparison of locked versus non-locked symphyseal plating of unstable pelvic ring injuries.

PubMed

Godinsky, R J; Vrabec, G A; Guseila, L M; Filipkowski, D E; Elias, J J

2018-04-01

Locked symphyseal plates are utilized to provide higher levels of construct stiffness than non-locked plates. The current biomechanical study was performed to compare stiffness at the pubic symphysis between locked and non-locked plating systems. Synthetic models were utilized to represent injury to the pelvis and symphyseal plating combined with a sacro-iliac screw. Seven models were evaluated with plates and locking screws, and seven were evaluated with non-locking screws. Single limb stance was simulated, with all models loaded for 1000 cycles with 350 N applied at the sacrum. Two pairs of markers crossing the symphysis were tracked with a video-based tracking system. A coordinate system was developed to quantify motion between the pairs in three directions: medial-lateral gap, anterior-posterior shear translation, and superior-inferior shear translation. Significant differences between the plating systems were identified with t tests (p < 0.05). Anterior-posterior shear translation varied significantly between the two plating systems. From cycles 100 to 1000, average shear translation for the non-locked and locked systems was ~0.7 and 0.3 mm, respectively, at the markers closest to the plate and 2.2 and 1.4 mm, respectively, at the markers further from the plate. Motion in the other two directions did not differ significantly between locked and non-locked models. Locked symphyseal plating systems can provide better stability than non-locked systems for anterior-posterior shear translation. More stability could potentially reduce the risk of failure of the plate or screws.

Evaluation of an image-based tracking workflow with Kalman filtering for automatic image plane alignment in interventional MRI.

PubMed

Neumann, M; Cuvillon, L; Breton, E; de Matheli, M

2013-01-01

Recently, a workflow for magnetic resonance (MR) image plane alignment based on tracking in real-time MR images was introduced. The workflow is based on a tracking device composed of 2 resonant micro-coils and a passive marker, and allows for tracking of the passive marker in clinical real-time images and automatic (re-)initialization using the microcoils. As the Kalman filter has proven its benefit as an estimator and predictor, it is well suited for use in tracking applications. In this paper, a Kalman filter is integrated in the previously developed workflow in order to predict position and orientation of the tracking device. Measurement noise covariances of the Kalman filter are dynamically changed in order to take into account that, according to the image plane orientation, only a subset of the 3D pose components is available. The improved tracking performance of the Kalman extended workflow could be quantified in simulation results. Also, a first experiment in the MRI scanner was performed but without quantitative results yet.

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

PubMed

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

2012-06-01

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

An Inertial and Optical Sensor Fusion Approach for Six Degree-of-Freedom Pose Estimation

PubMed Central

He, Changyu; Kazanzides, Peter; Sen, Hasan Tutkun; Kim, Sungmin; Liu, Yue

2015-01-01

Optical tracking provides relatively high accuracy over a large workspace but requires line-of-sight between the camera and the markers, which may be difficult to maintain in actual applications. In contrast, inertial sensing does not require line-of-sight but is subject to drift, which may cause large cumulative errors, especially during the measurement of position. To handle cases where some or all of the markers are occluded, this paper proposes an inertial and optical sensor fusion approach in which the bias of the inertial sensors is estimated when the optical tracker provides full six degree-of-freedom (6-DOF) pose information. As long as the position of at least one marker can be tracked by the optical system, the 3-DOF position can be combined with the orientation estimated from the inertial measurements to recover the full 6-DOF pose information. When all the markers are occluded, the position tracking relies on the inertial sensors that are bias-corrected by the optical tracking system. Experiments are performed with an augmented reality head-mounted display (ARHMD) that integrates an optical tracking system (OTS) and inertial measurement unit (IMU). Experimental results show that under partial occlusion conditions, the root mean square errors (RMSE) of orientation and position are 0.04° and 0.134 mm, and under total occlusion conditions for 1 s, the orientation and position RMSE are 0.022° and 0.22 mm, respectively. Thus, the proposed sensor fusion approach can provide reliable 6-DOF pose under long-term partial occlusion and short-term total occlusion conditions. PMID:26184191

An Inertial and Optical Sensor Fusion Approach for Six Degree-of-Freedom Pose Estimation.

PubMed

He, Changyu; Kazanzides, Peter; Sen, Hasan Tutkun; Kim, Sungmin; Liu, Yue

2015-07-08

Optical tracking provides relatively high accuracy over a large workspace but requires line-of-sight between the camera and the markers, which may be difficult to maintain in actual applications. In contrast, inertial sensing does not require line-of-sight but is subject to drift, which may cause large cumulative errors, especially during the measurement of position. To handle cases where some or all of the markers are occluded, this paper proposes an inertial and optical sensor fusion approach in which the bias of the inertial sensors is estimated when the optical tracker provides full six degree-of-freedom (6-DOF) pose information. As long as the position of at least one marker can be tracked by the optical system, the 3-DOF position can be combined with the orientation estimated from the inertial measurements to recover the full 6-DOF pose information. When all the markers are occluded, the position tracking relies on the inertial sensors that are bias-corrected by the optical tracking system. Experiments are performed with an augmented reality head-mounted display (ARHMD) that integrates an optical tracking system (OTS) and inertial measurement unit (IMU). Experimental results show that under partial occlusion conditions, the root mean square errors (RMSE) of orientation and position are 0.04° and 0.134 mm, and under total occlusion conditions for 1 s, the orientation and position RMSE are 0.022° and 0.22 mm, respectively. Thus, the proposed sensor fusion approach can provide reliable 6-DOF pose under long-term partial occlusion and short-term total occlusion conditions.

Automatic Indexing for Content Analysis of Whale Recordings and XML Representation

NASA Astrophysics Data System (ADS)

Bénard, Frédéric; Glotin, Hervé

2010-12-01

This paper focuses on the robust indexing of sperm whale hydrophone recordings based on a set of features extracted from a real-time passive underwater acoustic tracking algorithm for multiple whales using four hydrophones. Acoustic localization permits the study of whale behavior in deep water without interfering with the environment. Given the position coordinates, we are able to generate different features such as the speed, energy of the clicks, Inter-Click-Interval (ICI), and so on. These features allow to construct different markers which allow us to index and structure the audio files. Thus, the behavior study is facilitated by choosing and accessing the corresponding index in the audio file. The complete indexing algorithm is processed on real data from the NUWC (Naval Undersea Warfare Center of the US Navy) and the AUTEC (Atlantic Undersea Test & Evaluation Center-Bahamas). Our model is validated by similar results from the US Navy (NUWC) and SOEST (School of Ocean and Earth Science and Technology) Hawaii university labs in a single whale case. Finally, as an illustration, we index a single whale sound file using the extracted whale's features provided by the tracking, and we present an example of an XML script structuring it.

Feasibility of two-dimensional speckle tracking in evaluation of arterial stiffness: Comparison with pulse wave velocity and conventional sonographic markers of atherosclerosis.

PubMed

Podgórski, Michał; Grzelak, Piotr; Kaczmarska, Magdalena; Polguj, Michał; Łukaszewski, Maciej; Stefańczyk, Ludomir

2018-02-01

Objective Arterial stiffening is an early marker of atherosclerosis that has a prognostic value for cardiovascular morbidity and mortality. Although many markers of arterial hardening have been proposed, the search is on for newer, more user-friendly and reliable surrogates. One such potential candidate has emerged from cardiology, the speckle-tracking technique. The aim of this study was to evaluate the feasibility of the two-dimensional speckle tracking for the evaluation of arterial wall stiffness in comparison with standard stiffness parameters. Methods Carotid ultrasound and applanation tonometry were performed in 188 patients with no cardiovascular risk factors. The following parameters were then evaluated: the intima-media complex thickness, distensibility coefficient, β-stiffness index, circumferential strain/strain rate, and pulse wave velocity and augmentation index. These variables were compared with each other and with patient age, and their reliability was assessed with Bland-Altman plots. Results Strain parameters derived from two-dimensional speckle tracking and intima-media complex thickness correlated better with age and pulse wave velocity than standard makers of arterial stiffness. Moreover, the reliability of these measurements was significantly higher than conventional surrogates. Conclusions Two-dimensional speckle tracing is a reliable method for the evaluation of arterial stiffness. Therefore, together with intima-media complex thickness measurement, it offers great potential in clinical practice as an early marker of atherosclerosis.

Sewage pollution in urban stormwater runoff as evident from the widespread presence of multiple microbial and chemical source tracking markers.

PubMed

Sidhu, J P S; Ahmed, W; Gernjak, W; Aryal, R; McCarthy, D; Palmer, A; Kolotelo, P; Toze, S

2013-10-01

The concurrence of human sewage contamination in urban stormwater runoff (n=23) from six urban catchments across Australia was assessed by using both microbial source tracking (MST) and chemical source tracking (CST) markers. Out of 23 stormwater samples human adenovirus (HAv), human polyomavirus (HPv) and the sewage-associated markers; Methanobrevibacter smithii nifH and Bacteroides HF183 were detected in 91%, 56%, 43% and 96% of samples, respectively. Similarly, CST markers paracetamol (87%), salicylic acid (78%) acesulfame (96%) and caffeine (91%) were frequently detected. Twenty one samples (91%) were positive for six to eight sewage related MST and CST markers and remaining two samples were positive for five and four markers, respectively. A very good consensus (>91%) observed between the concurrence of the HF183, HAv, acesulfame and caffeine suggests good predictability of the presence of HAv in samples positive for one of the three markers. High prevalence of HAv (91%) also suggests that other enteric viruses may also be present in the stormwater samples which may pose significant health risks. This study underscores the benefits of employing a set of MST and CST markers which could include monitoring for HF183, adenovirus, caffeine and paracetamol to accurately detect human sewage contamination along with credible information on the presence of human enteric viruses, which could be used for more reliable public health risk assessments. Based on the results obtained in this study, it is recommended that some degree of treatment of captured stormwater would be required if it were to be used for non-potable purposes. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

A Real-Time Localization System for an Endoscopic Capsule Using Magnetic Sensors †

PubMed Central

Pham, Duc Minh; Aziz, Syed Mahfuzul

2014-01-01

Magnetic sensing technology offers an attractive alternative for in vivo tracking with much better performance than RF and ultrasound technologies. In this paper, an efficient in vivo magnetic tracking system is presented. The proposed system is intended to localize an endoscopic capsule which delivers biomarkers around specific locations of the gastrointestinal (GI) tract. For efficiently localizing a magnetic marker inside the capsule, a mathematical model has been developed for the magnetic field around a cylindrical magnet and used with a localization algorithm that provides minimum error and fast computation. The proposed tracking system has much reduced complexity compared to the ones reported in the literature to date. Laboratory tests and in vivo animal trials have demonstrated the suitability of the proposed system for tracking a magnetic marker with expected accuracy. PMID:25379813

Evaluation of the accuracy of the CyberKnife Synchrony™ Respiratory Tracking System using a plastic scintillator.

PubMed

Akino, Yuichi; Sumida, Iori; Shiomi, Hiroya; Higashinaka, Naokazu; Murashima, Yoshiichi; Hayashida, Miori; Mabuchi, Nobuhisa; Ogawa, Kazuhiko

2018-06-01

The Synchrony ™ Respiratory Tracking System of the CyberKnife ® Robotic Radiosurgery System (Accuray, Inc., Sunnyvale CA) enables real-time tracking of moving targets such as lung and liver tumors during radiotherapy. Although film measurements have been used for quality assurance of the tracking system, they cannot evaluate the temporal tracking accuracy. We have developed a verification system using a plastic scintillator that can evaluate the temporal accuracy of the CyberKnife Synchrony. A phantom consisting of a U-shaped plastic frame with three fiducial markers was used. The phantom was moved on a plastic scintillator plate. To identify the phantom position on the recording video in darkness, four pieces of fluorescent tape representing the corners of a 10 cm × 10 cm square around an 8 cm × 8 cm window were attached to the phantom. For a stable respiration model, the phantom was moved with the fourth power of a sinusoidal wave with breathing cycles of 4, 3, and 2 s and an amplitude of 1 cm. To simulate irregular breathing, the respiratory cycle was varied with Gaussian random numbers. A virtual target was generated at the center of the fluorescent markers using the MultiPlan ™ treatment planning system. Photon beams were irradiated using a fiducial tracking technique. In a dark room, the fluorescent light of the markers and the scintillation light of the beam position were recorded using a camera. For each video frame, a homography matrix was calculated from the four fluorescent marker positions, and the beam position derived from the scintillation light was corrected. To correct the displacement of the beam position due to oblique irradiation angles and other systematic measurement errors, offset values were derived from measurements with the phantom held stationary. The average SDs of beam position measured without phantom motion were 0.16 mm and 0.20 mm for lateral and longitudinal directions, respectively. For the stable respiration model, the tracking errors (mean ± SD) were 0.40 ± 0.64 mm, -0.07 ± 0.79 mm, and 0.45 ± 1.14 mm for breathing cycles of 4, 3, and 2 s, respectively. The tracking errors showed significant linear correlation with the phantom velocity. The correlation coefficients were 0.897, 0.913, and 0.957 for breathing cycles of 4, 3, and 2 s, respectively. The unstable respiration model also showed linear correlation between tracking errors and phantom velocity. The probability of tracking error incidents increased with decreasing length of the respiratory cycles. Although the tracking error incidents increased with larger variations in respiratory cycle, the effect on the cumulative probability was insignificant. For a respiratory cycle of 4 s, the maximum tracking error was 1.10 mm and 1.43 mm at the probability of 10% and 5%, respectively. Large tracking errors were observed when there was phase shift between the tumor and the LED marker. This technique allows evaluation of the motion tracking accuracy of the Synchrony ™ system over time by measurement of the photon beam. The velocity of the target and phase shift have significant effects on accuracy. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Pathogenic bacteria and microbial-source tracking markers in Brandywine Creek Basin, Pennsylvania and Delaware, 2009-10

USGS Publications Warehouse

Duris, Joseph W.; Reif, Andrew G.; Olson, Leif E.; Johnson, Heather E.

2011-01-01

The City of Wilmington, Delaware, is in the downstream part of the Brandywine Creek Basin, on the main stem of Brandywine Creek. Wilmington uses this stream, which drains a mixed-land-use area upstream, for its main drinking-water supply. Because the stream is used for drinking water, Wilmington is in need of information about the occurrence and distribution of specific fecally derived pathogenic bacteria (disease-causing bacteria) and their relations to commonly measured fecal-indicator bacteria (FIB), as well as information regarding the potential sources of the fecal pollution and pathogens in the basin. This study focused on five routinely sampled sites within the basin, one each on the West Branch and the East Branch of Brandywine Creek and at three on the main stem below the confluence of the West and East Branches. These sites were sampled monthly for 1 year. Targeted event samples were collected on two occasions during high flow and two occasions during normal flow. On the basis of this study, high flows in the Brandywine Creek Basin were related to increases in FIB densities, and in the frequency of selected pathogen and source markers, in the West Branch and main stem of Brandywine Creek, but not in the East Branch. Water exceeding the moderate fullbody-contact single-sample recreational water-quality criteria (RWQC) for Escherichia coli (E. coli) was more likely to contain selected markers for pathogenic E. coli (eaeA,stx1, and rfbO157 gene markers) and bovine fecal sources (E. hirae and LTIIa gene markers), whereas samples exceeding the enterococci RWQC were more likely to contain the same pathogenic markers but also were more likely to carry a marker indicative of human source (esp gene marker). On four sample dates, during high flow between October and March, the West Branch was the only observed potential contributor of selected pathogen and bovine source markers to the main stem of Brandywine Creek. Indeed, the stx2 marker, which indicates a highly virulent type of pathogenic E. coli, was found only in the West Branch and main stem at high flow but was not found in the East Branch under similar conditions. However, it must be noted that throughout the entire year of sampling there were occasions, during both high and normal flows, when both the East and West Branches were potential contributors of pathogen and microbial-source tracking markers to the main stem. Therefore, this study indicates that under selected conditions (high flow, October through March), West Branch Brandywine Creek Basin was the most likely source of elevated FIB densities in the main stem. These elevated densities are associated with more frequent detection of selected pathogenic E. coli markers (rfbO157 stx1) and are associated with MST markers of bovine source. However, during other times of the year, both the West Branch and East Branch Basins are acting as potential sources of FIB and fecally derived pathogens.

Identifying fecal sources in a selected catchment reach using multiple source-tracking tools

USGS Publications Warehouse

Vogel, J.R.; Stoeckel, D.M.; Lamendella, R.; Zelt, R.B.; Santo, Domingo J.W.; Walker, S.R.; Oerther, D.B.

2007-01-01

Given known limitations of current microbial source-tracking (MST) tools, emphasis on small, simple study areas may enhance interpretations of fecal contamination sources in streams. In this study, three MST tools - Escherichia coli repetitive element polymerase chain reaction (rep-PCR), coliphage typing, and Bacteroidales 16S rDNA host-associated markers - were evaluated in a selected reach of Plum Creek in sooth-central Nebraska. Water-quality samples were collected from six sites. One reach was selected for MST evaluation based on observed patterns of E. coli contamination. Despite high E. coli concentrations, coliphages were detected only once among water samples, precluding their use as a MST tool in this setting. Rep-PCR classification of E. coli isolates from both water and sediment samples supported the hypothesis that cattle and wildlife were dominant sources of fecal contamination, with minor contributions by horses and humans. Conversely, neither ruminant nor human sources were detected by Bacteroidales markers in most water samples. In bed sediment, ruminant- and human-associated Bacteroidales markers were detected throughout the interval from 0 to 0.3 m, with detections independent of E. coli concentrations in the sediment. Although results by E. coli-based and Bacteroidales-based MST methods led to similar interpretations, detection of Bacteroidales markers in sediment more commonly than in water indicates that different tools to track fecal contamination (in this case, tools based on Bacteroidales DNA and E. coli isolates) may have varying relevance to the more specific goal of tracking the sources of E. coli in watersheds. This is the first report of simultaneous, toolbox approach application of a library-based and marker-based MST analyses to lowing surface water. ?? ASA, CSSA, SSSA.

Concept and simulation study of a novel localization method for robotic endoscopic capsules using multiple positron emission markers

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

Than, Trung Duc, E-mail: dtt581@uowmail.edu.au; Alici, Gursel, E-mail: gursel@uow.edu.au; Zhou, Hao, E-mail: hz467@uowmail.edu.au

2014-07-15

Purpose: Over the last decade, wireless capsule endoscope has been the tool of choice for noninvasive inspection of the gastrointestinal tract, especially in the small intestine. However, the latest clinical products have not been equipped with a sufficiently accurate localization system which makes it difficult to determine the location of intestinal abnormalities, and to apply follow-up interventions such as biopsy or drug delivery. In this paper, the authors present a novel localization method based on tracking three positron emission markers embedded inside an endoscopic capsule. Methods: Three spherical {sup 22}Na markers with diameters of less than 1 mm are embeddedmore » in the cover of the capsule. Gamma ray detectors are arranged around a patient body to detect coincidence gamma rays emitted from the three markers. The position of each marker can then be estimated using the collected data by the authors’ tracking algorithm which consists of four consecutive steps: a method to remove corrupted data, an initialization method, a clustering method based on the Fuzzy C-means clustering algorithm, and a failure prediction method. Results: The tracking algorithm has been implemented inMATLAB utilizing simulation data generated from the Geant4 Application for Emission Tomography toolkit. The results show that this localization method can achieve real-time tracking with an average position error of less than 0.4 mm and an average orientation error of less than 2°. Conclusions: The authors conclude that this study has proven the feasibility and potential of the proposed technique in effectively determining the position and orientation of a robotic endoscopic capsule.« less

Markers and mapping revisited: finding your gene.

PubMed

Jones, Neil; Ougham, Helen; Thomas, Howard; Pasakinskiene, Izolda

2009-01-01

This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.

New markers for tracking endoderm induction and hepatocyte differentiation from human pluripotent stem cells

PubMed Central

Holtzinger, Audrey; Streeter, Philip R.; Sarangi, Farida; Hillborn, Scott; Niapour, Maryam; Ogawa, Shinichiro; Keller, Gordon

2015-01-01

The efficient generation of hepatocytes from human pluripotent stem cells (hPSCs) requires the induction of a proper endoderm population, broadly characterized by the expression of the cell surface marker CXCR4. Strategies to identify and isolate endoderm subpopulations predisposed to the liver fate do not exist. In this study, we generated mouse monoclonal antibodies against human embryonic stem cell-derived definitive endoderm with the goal of identifying cell surface markers that can be used to track the development of this germ layer and its specification to a hepatic fate. Through this approach, we identified two endoderm-specific antibodies, HDE1 and HDE2, which stain different stages of endoderm development and distinct derivative cell types. HDE1 marks a definitive endoderm population with high hepatic potential, whereas staining of HDE2 tracks with developing hepatocyte progenitors and hepatocytes. When used in combination, the staining patterns of these antibodies enable one to optimize endoderm induction and hepatic specification from any hPSC line. PMID:26493401

SU-G-JeP4-13: Continuous Intra-Fractional Monitoring of the Prostate Using Dynamic KV Collimation and Tube Current Modulation

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

Parsons, D; Robar, J; Nova Scotia Health Authority, Halifax, NS

Purpose: The focus of this work is to improve the available kV image quality for continuous intra-fraction monitoring of the prostate. This is investigated using a novel blade collimation system enabling modulated volume-of-interest (VOI) imaging of prostate fiducial markers. Methods: A four-blade dynamic kV collimator was used to track a VOI during gantry rotation. Planar image quality was investigated as a function of collimator dimension, while maintaining the same dose to isocenter, for a 22.2 cm diameter cylindrical water phantom with a 9 mm diameter bone insert. A sample prostate anatomy was defined in the planning system, including three fiducialmore » markers within the CTV. The VOI margin around each marker was set to be 2σ of the population covariance matrix characterizing prostate motion. DRRs were used to calculate the kV attenuation for each VOI as a function of angle. The optimal marker and tube current were determined using kV attenuation. Monte Carlo simulations were used to calculate the imaging dose to the phantom and MV scatter dose to the imaging panel. Results: Preliminary measurements show an increase in CNR by a factor of 1.3 with the VOI method, when decreasing from an 6×6 to 2×2 cm{sup 2} field. Attenuation calculations show a change in kV fluence at the detector by a factor of 21.6 with fiducial optimization; resultant tube current modulation increases maximum dose by a factor of 1.4 compared to no modulation. MV scatter contribution to the kV detector changes by approximately a factor of two over a complete gantry rotation. Conclusion: The dynamic collimation system allows single fiducial marker tracking at a very low dose, with reduction of scatter and improvement of image quality, compared to imaging the entire prostate. The approach is compatible with tube current modulation, which enables consistent image quality throughout the range of gantry rotation. This project was funded by Varian Medical Systems.« less

Clinical assessment of coiled fiducial markers as internal surrogates for hepatocellular carcinomas during gated stereotactic body radiotherapy with a real-time tumor-tracking system.

PubMed

Hanazawa, Hideki; Takahashi, Shotaro; Shiinoki, Takehiro; Park, Sung Chul; Yuasa, Yuki; Koike, Masahiro; Kawamura, Shinji; Shibuya, Keiko

2017-04-01

To report the clinical usefulness of coiled fiducial markers as an internal surrogate in gated stereotactic body radiotherapy (SBRT) for hepatocellular carcinoma (HCC) using a real-time tumor-tracking radiotherapy (RTRT) system. Seventeen HCC patients with Child-Pugh (CP) scores of A or B received gated SBRT (45-50Gy in 5-10 fractions) using an RTRT system and Visicoil markers. Local control (LC), progression-free (PFS), and overall survival (OS) rates were assessed using the Kaplan-Meier method. Toxicities were assessed using the Common Terminology Criteria for Adverse Events, Version 4.0. Of the 17 patients, 14 had a CP score A. The mean planning target volume was 54.6cc. Only 1 patient developed pneumothorax after marker implantation. Visicoil tracking during SBRT was possible in all cases. With a median follow-up of 16months, 1-year LC, PFS, and OS rates were 100%, 53%, and 82%, respectively. Grade≥2 late toxicity was observed in 2 patients (grade 2 duodenal ulcer and grade 3 temporary transaminase elevation). Using an RTRT system and Visicoil markers, gated SBRT was well tolerated in patients with HCC. This can be considered a safe treatment strategy with potential for delivering favorable outcomes. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluation of Bovine Feces-Associated Microbial Source Tracking Markers and Their Correlations with Fecal Indicators and Zoonotic Pathogens in a Brisbane, Australia, Reservoir

PubMed Central

Sritharan, T.; Palmer, A.; Sidhu, J. P. S.; Toze, S.

2013-01-01

This study was aimed at evaluating the host specificity and host sensitivity of two bovine feces-associated bacterial (BacCow-UCD and cowM3) and one viral [bovine adenovirus (B-AVs)] microbial source tracking (MST) markers by screening 130 fecal and wastewater samples from 10 target and nontarget host groups in southeast Queensland, Australia. In addition, 36 water samples were collected from a reservoir and tested for the occurrence of all three bovine feces-associated markers along with fecal indicator bacteria (FIB), Campylobacter spp., Escherichia coli O157, and Salmonella spp. The overall host specificity values of the BacCow-UCD, cowM3, and B-AVs markers to differentiate between bovine and other nontarget host groups were 0.66, 0.88, and 1.00, respectively (maximum value of 1.00). The overall host sensitivity values of these markers, however, in composite bovine wastewater and individual bovine fecal DNA samples were 0.93, 0.90, and 0.60, respectively (maximum value of 1.00). Among the 36 water samples tested, 56%, 22%, and 6% samples were PCR positive for the BacCow-UCD, cowM3, and B-AVs markers, respectively. Among the 36 samples tested, 50% and 14% samples were PCR positive for the Campylobacter 16S rRNA and E. coli O157 rfbE genes, respectively. Based on the results, we recommend that multiple bovine feces-associated markers be used if possible for bovine fecal pollution tracking. Nonetheless, the presence of the multiple bovine feces-associated markers along with the presence of potential zoonotic pathogens indicates bovine fecal pollution in the reservoir water samples. Further research is required to understand the decay rates of these markers in relation to FIB and zoonotic pathogens. PMID:23417003

Utility of Microbial Source-Tracking Markers for Assessing Fecal Contamination in the Portage River Watershed, Northwestern Ohio, 2008

USGS Publications Warehouse

Kephart, Christopher M.; Bushon, Rebecca N.

2010-01-01

An influx of concentrated animal feeding operations in northwest Ohio has prompted local agencies to examine the effects of these industrial farms on water quality in the upper Portage River watershed. The utility of microbial source-tracking (MST) tools as a means of characterizing sources of fecal contamination in the watershed was evaluated. From 2007 to 2008, scientists with the U.S. Geological Survey, Bowling Green State University, and the Wood County Health Department collected and analyzed 17 environmental samples and 13 fecal source samples for Bacteroides-based host-associated DNA markers. At many of the environmental sites tested, MST marker results corroborated the presumptive fecal contamination sources. Results from this demonstration study support the utility of using MST with host-specific molecular markers to characterize the sources of fecal contamination in the Portage River watershed.

Enhancement of a 2D front-tracking algorithm with a non-uniform distribution of Lagrangian markers

NASA Astrophysics Data System (ADS)

Febres, Mijail; Legendre, Dominique

2018-04-01

The 2D front tracking method is enhanced to control the development of spurious velocities for non-uniform distributions of markers. The hybrid formulation of Shin et al. (2005) [7] is considered. A new tangent calculation is proposed for the calculation of the tension force at markers. A new reconstruction method is also proposed to manage non-uniform distributions of markers. We show that for both the static and the translating spherical drop test case the spurious currents are reduced to the machine precision. We also show that the ratio of the Lagrangian grid size Δs over the Eulerian grid size Δx has to satisfy Δs / Δx > 0.2 for ensuring such low level of spurious velocity. The method is found to provide very good agreement with benchmark test cases from the literature.

Coarse-to-fine markerless gait analysis based on PCA and Gauss-Laguerre decomposition

NASA Astrophysics Data System (ADS)

Goffredo, Michela; Schmid, Maurizio; Conforto, Silvia; Carli, Marco; Neri, Alessandro; D'Alessio, Tommaso

2005-04-01

Human movement analysis is generally performed through the utilization of marker-based systems, which allow reconstructing, with high levels of accuracy, the trajectories of markers allocated on specific points of the human body. Marker based systems, however, show some drawbacks that can be overcome by the use of video systems applying markerless techniques. In this paper, a specifically designed computer vision technique for the detection and tracking of relevant body points is presented. It is based on the Gauss-Laguerre Decomposition, and a Principal Component Analysis Technique (PCA) is used to circumscribe the region of interest. Results obtained on both synthetic and experimental tests provide significant reduction of the computational costs, with no significant reduction of the tracking accuracy.

A combined vision-inertial fusion approach for 6-DoF object pose estimation

NASA Astrophysics Data System (ADS)

Li, Juan; Bernardos, Ana M.; Tarrío, Paula; Casar, José R.

2015-02-01

The estimation of the 3D position and orientation of moving objects (`pose' estimation) is a critical process for many applications in robotics, computer vision or mobile services. Although major research efforts have been carried out to design accurate, fast and robust indoor pose estimation systems, it remains as an open challenge to provide a low-cost, easy to deploy and reliable solution. Addressing this issue, this paper describes a hybrid approach for 6 degrees of freedom (6-DoF) pose estimation that fuses acceleration data and stereo vision to overcome the respective weaknesses of single technology approaches. The system relies on COTS technologies (standard webcams, accelerometers) and printable colored markers. It uses a set of infrastructure cameras, located to have the object to be tracked visible most of the operation time; the target object has to include an embedded accelerometer and be tagged with a fiducial marker. This simple marker has been designed for easy detection and segmentation and it may be adapted to different service scenarios (in shape and colors). Experimental results show that the proposed system provides high accuracy, while satisfactorily dealing with the real-time constraints.

LightDenseYOLO: A Fast and Accurate Marker Tracker for Autonomous UAV Landing by Visible Light Camera Sensor on Drone.

PubMed

Nguyen, Phong Ha; Arsalan, Muhammad; Koo, Ja Hyung; Naqvi, Rizwan Ali; Truong, Noi Quang; Park, Kang Ryoung

2018-05-24

Autonomous landing of an unmanned aerial vehicle or a drone is a challenging problem for the robotics research community. Previous researchers have attempted to solve this problem by combining multiple sensors such as global positioning system (GPS) receivers, inertial measurement unit, and multiple camera systems. Although these approaches successfully estimate an unmanned aerial vehicle location during landing, many calibration processes are required to achieve good detection accuracy. In addition, cases where drones operate in heterogeneous areas with no GPS signal should be considered. To overcome these problems, we determined how to safely land a drone in a GPS-denied environment using our remote-marker-based tracking algorithm based on a single visible-light-camera sensor. Instead of using hand-crafted features, our algorithm includes a convolutional neural network named lightDenseYOLO to extract trained features from an input image to predict a marker's location by visible light camera sensor on drone. Experimental results show that our method significantly outperforms state-of-the-art object trackers both using and not using convolutional neural network in terms of both accuracy and processing time.

Tracking ongoing cognition in individuals using brief, whole-brain functional connectivity patterns

PubMed Central

Gonzalez-Castillo, Javier; Hoy, Colin W.; Handwerker, Daniel A.; Robinson, Meghan E.; Buchanan, Laura C.; Saad, Ziad S.; Bandettini, Peter A.

2015-01-01

Functional connectivity (FC) patterns in functional MRI exhibit dynamic behavior on the scale of seconds, with rich spatiotemporal structure and limited sets of whole-brain, quasi-stable FC configurations (FC states) recurring across time and subjects. Based on previous evidence linking various aspects of cognition to group-level, minute-to-minute FC changes in localized connections, we hypothesized that whole-brain FC states may reflect the global, orchestrated dynamics of cognitive processing on the scale of seconds. To test this hypothesis, subjects were continuously scanned as they engaged in and transitioned between mental states dictated by tasks. FC states computed within windows as short as 22.5 s permitted robust tracking of cognition in single subjects with near perfect accuracy. Accuracy dropped markedly for subjects with the lowest task performance. Spatially restricting FC information decreased accuracy at short time scales, emphasizing the distributed nature of whole-brain FC dynamics, beyond univariate magnitude changes, as valuable markers of cognition. PMID:26124112

Characterization of polymorphic microsatellites for the invasive grass Microstegium vimineum (Poaceae).

PubMed

Novy, Ari; Flory, S Luke; Honig, Joshua A; Bonos, Stacy; Hartman, Jean Marie

2012-02-01

Microsatellite markers were developed for the invasive plant Microstegium vimineum (Poaceae) to assess its population structure and to facilitate tracking of invasion expansion. Using 454 sequencing, 11 polymorphic and six monomorphic microsatellite primer sets were developed for M. vimineum. The primer sets were tested on individuals sampled from six populations in the United States and China. The polymorphic primers amplified di-, tri-, and tetranucleotide repeats with three to 10 alleles per locus. These markers will be useful for a variety of applications including tracking of invasion dynamics and population genetics studies.

Fluoroscopic tumor tracking for image-guided lung cancer radiotherapy

NASA Astrophysics Data System (ADS)

Lin, Tong; Cerviño, Laura I.; Tang, Xiaoli; Vasconcelos, Nuno; Jiang, Steve B.

2009-02-01

Accurate lung tumor tracking in real time is a keystone to image-guided radiotherapy of lung cancers. Existing lung tumor tracking approaches can be roughly grouped into three categories: (1) deriving tumor position from external surrogates; (2) tracking implanted fiducial markers fluoroscopically or electromagnetically; (3) fluoroscopically tracking lung tumor without implanted fiducial markers. The first approach suffers from insufficient accuracy, while the second may not be widely accepted due to the risk of pneumothorax. Previous studies in fluoroscopic markerless tracking are mainly based on template matching methods, which may fail when the tumor boundary is unclear in fluoroscopic images. In this paper we propose a novel markerless tumor tracking algorithm, which employs the correlation between the tumor position and surrogate anatomic features in the image. The positions of the surrogate features are not directly tracked; instead, we use principal component analysis of regions of interest containing them to obtain parametric representations of their motion patterns. Then, the tumor position can be predicted from the parametric representations of surrogates through regression. Four regression methods were tested in this study: linear and two-degree polynomial regression, artificial neural network (ANN) and support vector machine (SVM). The experimental results based on fluoroscopic sequences of ten lung cancer patients demonstrate a mean tracking error of 2.1 pixels and a maximum error at a 95% confidence level of 4.6 pixels (pixel size is about 0.5 mm) for the proposed tracking algorithm.

Improving z-tracking accuracy in the two-photon single-particle tracking microscope.

PubMed

Liu, C; Liu, Y-L; Perillo, E P; Jiang, N; Dunn, A K; Yeh, H-C

2015-10-12

Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we have precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico . Our method can be generally applied to other 3D single-particle tracking techniques.

Improving z-tracking accuracy in the two-photon single-particle tracking microscope

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

Liu, C.; Liu, Y.-L.; Perillo, E. P.

Here, we present a method that can improve the z-tracking accuracy of the recently invented TSUNAMI (Tracking of Single particles Using Nonlinear And Multiplexed Illumination) microscope. This method utilizes a maximum likelihood estimator (MLE) to determine the particle's 3D position that maximizes the likelihood of the observed time-correlated photon count distribution. Our Monte Carlo simulations show that the MLE-based tracking scheme can improve the z-tracking accuracy of TSUNAMI microscope by 1.7 fold. In addition, MLE is also found to reduce the temporal correlation of the z-tracking error. Taking advantage of the smaller and less temporally correlated z-tracking error, we havemore » precisely recovered the hybridization-melting kinetics of a DNA model system from thousands of short single-particle trajectories in silico. Our method can be generally applied to other 3D single-particle tracking techniques.« less

Virtual rigid body: a new optical tracking paradigm in image-guided interventions

NASA Astrophysics Data System (ADS)

Cheng, Alexis; Lee, David S.; Deshmukh, Nishikant; Boctor, Emad M.

2015-03-01

Tracking technology is often necessary for image-guided surgical interventions. Optical tracking is one the options, but it suffers from line of sight and workspace limitations. Optical tracking is accomplished by attaching a rigid body marker, having a pattern for pose detection, onto a tool or device. A larger rigid body results in more accurate tracking, but at the same time large size limits its usage in a crowded surgical workspace. This work presents a prototype of a novel optical tracking method using a virtual rigid body (VRB). We define the VRB as a 3D rigid body marker in the form of pattern on a surface generated from a light source. Its pose can be recovered by observing the projected pattern with a stereo-camera system. The rigid body's size is no longer physically limited as we can manufacture small size light sources. Conventional optical tracking also requires line of sight to the rigid body. VRB overcomes these limitations by detecting a pattern projected onto the surface. We can project the pattern onto a region of interest, allowing the pattern to always be in the view of the optical tracker. This helps to decrease the occurrence of occlusions. This manuscript describes the method and results compared with conventional optical tracking in an experiment setup using known motions. The experiments are done using an optical tracker and a linear-stage, resulting in targeting errors of 0.38mm+/-0.28mm with our method compared to 0.23mm+/-0.22mm with conventional optical markers. Another experiment that replaced the linear stage with a robot arm resulted in rotational errors of 0.50+/-0.31° and 2.68+/-2.20° and the translation errors of 0.18+/-0.10 mm and 0.03+/-0.02 mm respectively.

Bronchoscopic Implantation of a Novel Wireless Electromagnetic Transponder in the Canine Lung: A Feasibility Study

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

Mayse, Martin L.; Parikh, Parag J.; Lechleiter, Kristen M.

2008-09-01

Purpose: The success of targeted radiation therapy for lung cancer treatment is limited by tumor motion during breathing. A real-time, objective, nonionizing, electromagnetic localization system using implanted electromagnetic transponders has been developed (Beacon electromagnetic transponder, Calypso Medical Technologies, Inc., Seattle, WA). We evaluated the feasibility and fixation of electromagnetic transponders bronchoscopically implanted in small airways of canine lungs and compared to results using gold markers. Methods and Materials: After approval of the Animal Studies Committee, five mongrel dogs were anesthetized, intubated, and ventilated. Three transponders were inserted into the tip of a plastic catheter, passed through the working channel ofmore » a flexible bronchoscope, and implanted into small airways of a single lobe using fluoroscopic guidance. This procedure was repeated for three spherical gold markers in the opposite lung. One, 7, 14, 28, and 60 days postimplantation imaging was used to assess implant fixation. Results: Successful bronchoscopic implantation was possible for 15 of 15 transponders and 12 of 15 gold markers; 3 markers were deposited in the pleural space. Fixation at 1 day was 15 of 15 for transponders and 12 of 12 for gold markers. Fixation at 60 days was 6 of 15 for transponders and 7 of 12 for gold markers, p value = 0.45. Conclusions: Bronchoscopic implantation of both transponders and gold markers into the canine lung is feasible, but fixation rates are low. If fixation rates can be improved, implantable electromagnetic transponders may allow improved radiation therapy for lung cancer by providing real-time continuous target tracking. Developmental work is under way to improve the fixation rates and to reduce sensitivity to implantation technique.« less

TIP maker and TIP marker; EB1 as a master controller of microtubule plus ends.

PubMed

Vaughan, Kevin T

2005-10-24

The EB1 protein is a member of the exciting and enigmatic family of microtubule (MT) tip-tracking proteins. EB1 acts as an exquisite marker of dynamic MT plus ends in some cases, whereas in others EB1 is thought to directly dictate the behavior of the plus ends. How EB1 differentiates between these two roles remains unclear; however, a growing list of interactions between EB1 and other MT binding proteins suggests there may be a single mechanism. Adding another layer of complexity to these interactions, two studies published in this issue implicate EB1 in cross-talk between mitotic MTs and between MTs and actin filaments (Goshima et al., p. 229; Wu et al., p. 201). These results raise the possibility that EB1 is a central player in MT-based transport, and that the activity of MT-binding proteins depends on their ability or inability to interact with EB1.

Multimodality and nanoparticles in medical imaging

PubMed Central

Huang, Wen-Yen; Davis, Jason J.

2015-01-01

A number of medical imaging techniques are used heavily in the provision of spatially resolved information on disease and physiological status and accordingly play a critical role in clinical diagnostics and subsequent treatment. Though, for most imaging modes, contrast is potentially enhanced through the use of contrast agents or improved hardware or imaging protocols, no single methodology provides, in isolation, a detailed mapping of anatomy, disease markers or physiological status. In recent years, the concept of complementing the strengths of one imaging modality with those of another has come to the fore and been further bolstered by the development of fused instruments such as PET/CT and PET/MRI stations. Coupled with the continual development in imaging hardware has been a surge in reports of contrast agents bearing multiple functionality, potentially providing not only a powerful and highly sensitised means of co-localising physiological/disease status and anatomy, but also the tracking and delineation of multiple markers and indeed subsequent or simultaneous highly localized therapy (“theragnostics”). PMID:21409202

Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory

PubMed Central

Puchner, Elias M.; Walter, Jessica M.; Kasper, Robert; Huang, Bo; Lim, Wendell A.

2013-01-01

Cells tightly regulate trafficking of intracellular organelles, but a deeper understanding of this process is technically limited by our inability to track the molecular composition of individual organelles below the diffraction limit in size. Here we develop a technique for intracellularly calibrated superresolution microscopy that can measure the size of individual organelles as well as accurately count absolute numbers of molecules, by correcting for undercounting owing to immature fluorescent proteins and overcounting owing to fluorophore blinking. Using this technique, we characterized the size of individual vesicles in the yeast endocytic pathway and the number of accessible phosphatidylinositol 3-phosphate binding sites they contain. This analysis reveals a characteristic vesicle maturation trajectory of composition and size with both stochastic and regulated components. The trajectory displays some cell-to-cell variability, with smaller variation between organelles within the same cell. This approach also reveals mechanistic information on the order of events in this trajectory: Colocalization analysis with known markers of different vesicle maturation stages shows that phosphatidylinositol 3-phosphate production precedes fusion into larger endosomes. This single-organelle analysis can potentially be applied to a range of small organelles to shed light on their precise composition/structure relationships, the dynamics of their regulation, and the noise in these processes. PMID:24043832

Localized strain measurements of the intervertebral disc annulus during biaxial tensile testing.

PubMed

Karakolis, Thomas; Callaghan, Jack P

2015-01-01

Both inter-lamellar and intra-lamellar failures of the annulus have been described as potential modes of disc herniation. Attempts to characterize initial lamellar failure of the annulus have involved tensile testing of small tissue samples. The purpose of this study was to evaluate a method of measuring local surface strains through image analysis of a tensile test conducted on an isolated sample of annular tissue in order to enhance future studies of intervertebral disc failure. An annulus tissue sample was biaxial strained to 10%. High-resolution images captured the tissue surface throughout testing. Three test conditions were evaluated: submerged, non-submerged and marker. Surface strains were calculated for the two non-marker conditions based on motion of virtual tracking points. Tracking algorithm parameters (grid resolution and template size) were varied to determine the effect on estimated strains. Accuracy of point tracking was assessed through a comparison of the non-marker conditions to a condition involving markers placed on tissue surface. Grid resolution had a larger effect on local strain than template size. Average local strain error ranged from 3% to 9.25% and 0.1% to 2.0%, for the non-submerged and submerged conditions, respectively. Local strain estimation has a relatively high potential for error. Submerging the tissue provided superior strain estimates.

SU-F-I-11: Software Development for 4D-CBCT Research of Real-Time-Image Gated Spot Scanning Proton Therapy

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

Fujii, T; Fujii, Y; Shimizu, S

Purpose: To acquire correct information for inside the body in patient positioning of Real-time-image Gated spot scanning Proton Therapy (RGPT), utilization of tomographic image at exhale phase of patient respiration obtained from 4-dimensional Cone beam CT (4D-CBCT) has been desired. We developed software named “Image Analysis Platform” for 4D-CBCT researches which has technique to segment projection-images based on 3D marker position in the body. The 3D marker position can be obtained by using two axes CBCT system at Hokkaido University Hospital Proton Therapy Center. Performance verification of the software was implemented. Methods: The software calculates 3D marker position retrospectively bymore » using matching positions on pair projection-images obtained by two axes fluoroscopy mode of CBCT system. Log data of 3D marker tracking are outputted after the tracking. By linking the Log data and gantry-angle file of projection-image, all projection-images are equally segmented to spatial five-phases according to marker 3D position of SI direction and saved to specified phase folder. Segmented projection-images are used for CBCT reconstruction of each phase. As performance verification of the software, test of segmented projection-images was implemented for sample CT phantom (Catphan) image acquired by two axes fluoroscopy mode of CBCT. Dummy marker was added on the images. Motion of the marker was modeled to move in 3D space. Motion type of marker is sin4 wave function has amplitude 10.0 mm/5.0 mm/0 mm, cycle 4 s/4 s/0 s for SI/AP/RL direction. Results: The marker was tracked within 0.58 mm accuracy in 3D for all images, and it was confirmed that all projection-images were segmented and saved to each phase folder correctly. Conclusion: We developed software for 4D-CBCT research which can segment projection-image based on 3D marker position. It will be helpful to create high quality of 4D-CBCT reconstruction image for RGPT.« less

WE-AB-BRA-12: Virtual Endoscope Tracking for Endoscopy-CT Image Registration

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

Ingram, W; Rao, A; Wendt, R

Purpose: The use of endoscopy in radiotherapy will remain limited until we can register endoscopic video to CT using standard clinical equipment. In this phantom study we tested a registration method using virtual endoscopy to measure CT-space positions from endoscopic video. Methods: Our phantom is a contorted clay cylinder with 2-mm-diameter markers in the luminal surface. These markers are visible on both CT and endoscopic video. Virtual endoscope images were rendered from a polygonal mesh created by segmenting the phantom’s luminal surface on CT. We tested registration accuracy by tracking the endoscope’s 6-degree-of-freedom coordinates frame-to-frame in a video recorded asmore » it moved through the phantom, and using these coordinates to measure CT-space positions of markers visible in the final frame. To track the endoscope we used the Nelder-Mead method to search for coordinates that render the virtual frame most similar to the next recorded frame. We measured the endoscope’s initial-frame coordinates using a set of visible markers, and for image similarity we used a combination of mutual information and gradient alignment. CT-space marker positions were measured by projecting their final-frame pixel addresses through the virtual endoscope to intersect with the mesh. Registration error was quantified as the distance between this intersection and the marker’s manually-selected CT-space position. Results: Tracking succeeded for 6 of 8 videos, for which the mean registration error was 4.8±3.5mm (24 measurements total). The mean error in the axial direction (3.1±3.3mm) was larger than in the sagittal or coronal directions (2.0±2.3mm, 1.7±1.6mm). In the other 2 videos, the virtual endoscope got stuck in a false minimum. Conclusion: Our method can successfully track the position and orientation of an endoscope, and it provides accurate spatial mapping from endoscopic video to CT. This method will serve as a foundation for an endoscopy-CT registration framework that is clinically valuable and requires no specialized equipment.« less

Tackling Production Techniques: Professional Studio Sound at Amateur Prices: the Power of the Portable Four-Track Audio Recorder.

ERIC Educational Resources Information Center

Robinson, David E.

1997-01-01

One solution to poor quality sound in student video projects is a four-track audio cassette recorder. This article discusses the advantages of four-track over single-track recorders and compares two student productions, one using a single-track and the other a four-track recorder. (PEN)

An Interactive Augmented Reality Implementation of Hijaiyah Alphabet for Children Education

NASA Astrophysics Data System (ADS)

Rahmat, R. F.; Akbar, F.; Syahputra, M. F.; Budiman, M. A.; Hizriadi, A.

2018-03-01

Hijaiyah alphabet is letters used in the Qur’an. An attractive and exciting learning process of Hijaiyah alphabet is necessary for the children. One of the alternatives to create attractive and interesting learning process of Hijaiyah alphabet is to develop it into a mobile application using augmented reality technology. Augmented reality is a technology that combines two-dimensional or three-dimensional virtual objects into actual three-dimensional circles and projects them in real time. The purpose of application aims to foster the children interest in learning Hijaiyah alphabet. This application is using Smartphone and marker as the medium. It was built using Unity and augmented reality library, namely Vuforia, then using Blender as the 3D object modeling software. The output generated from this research is the learning application of Hijaiyah letters using augmented reality. How to use it is as follows: first, place marker that has been registered and printed; second, the smartphone camera will track the marker. If the marker is invalid, the user should repeat the tracking process. If the marker is valid and identified, the marker will have projected the objects of Hijaiyah alphabet in three-dimensional form. Lastly, the user can learn and understand the shape and pronunciation of Hijaiyah alphabet by touching the virtual button on the marker

Global Inter-Laboratory Fecal Source Identification Methods Comparison Study

EPA Science Inventory

Source tracking is key to identifying sources of fecal contamination for remediation as well as risk assessment. Previous intra- and inter-lab studies have investigated the performance of human and cow-associated source tracking markers, as well as library-dependent fecal source ...

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

Poels, Kenneth, E-mail: kenneth.poels@uzbrussel.be; Verellen, Dirk; Van de Vondel, Iwein

Purpose: Because frame rates on current clinical available electronic portal imaging devices (EPID’s) are limited to 7.5 Hz, a new commercially available PerkinElmer EPID (XRD 1642 AP19) with a maximum frame rate of 30 Hz and a new scintillator (Kyokko PI200) with improved sensitivity (light output) for megavolt (MV) irradiation was evaluated. In this work, the influence of MV pulse artifacts and pulsing artifact suppression techniques on fiducial marker and marker-less detection of a lung lesion was investigated, because target localization is an important component of uncertainty in geometrical verification of real-time tumor tracking. Methods: Visicoil™ markers with a diametermore » of 0.05 and 0.075 cm were used for MV marker tracking with a frame rate of, respectively, 7.5, 15, and 30 Hz. A 30 Hz readout of the detector was obtained by a 2 × 2 pixel binning, reducing spatial resolution. Static marker detection was conducted in function of increasing phantom thickness. Additionally, marker-less tracking was conducted and compared with the ground-truth fiducial marker motion. Performance of MV target detection was investigated by comparing the least-square sine wave fit of the detected marker positions with the predefined sine wave motion. For fiducial marker detection, a Laplacian-of-Gaussian enhancement was applied after which normalized cross correlation was used to find the most probable marker position. Marker-less detection was performed by using the scale and orientation adaptive mean shift tracking algorithm. For each MV fluoroscopy, a free running (FR-nF) (ignoring MV pulsing during readout) acquisition mode was compared with two acquisition modes intending to reduce MV pulsing artifacts, i.e., combined wavelet-FFT filtering (FR-wF) and electronic readout synchronized with respect to MV pulses. Results: A 0.05 cm Visicoil marker resulted in an unacceptable root-mean square error (RMSE) > 0.2 cm with a maximum frame rate of 30 Hz during FR-nF readout. With a 30 Hz synchronized readout (S-nF) and during 15 Hz readout (independent of readout mode), RMSE was submillimeter for a static 0.05 cm Visicoil. A dynamic 0.05 cm Visicoil was not detectable on the XRD 1642 AP19, despite a fast synchronized readout. For a 0.075 cm Visicoil, deviations of sine wave motion were submillimeter (RMSE < 0.08 cm), independent of the acquisition mode (FR, S). For marker-less tumor detection, FR-nF images resulted in RMSE > 0.3 cm, while for MV fluoroscopy in S-mode RMSE < 0.1 cm for 15 Hz and RMSE < 0.16 cm for 30 Hz. Largest consistency in target localization was experienced during 15 Hz S-nF readout. Conclusions: In general, marker contrast decreased in function of higher frame rates, which was detrimental for marker detection success. In this work, Visicoils with a thickness of 0.075 cm were showing best results for a 15 Hz frame rate, while non-MV compatible 0.05 cm Visicoil markers were not visible on the new EPID with improved sensitivity compared to EPID models based on a Kodak Lanex Fast scintillator. No noticeable influence of pulsing artifacts on the detection of a 0.075 cm Visicoil was observed, while a synchronized readout provided most reliable detection of a marker-less soft-tissue structure.« less

Measurement of the translation and rotation of a sphere in fluid flow

NASA Astrophysics Data System (ADS)

Barros, Diogo; Hiltbrand, Ben; Longmire, Ellen K.

2018-06-01

The problem of determining the translation and rotation of a spherical particle moving in fluid flow is considered. Lagrangian tracking of markers printed over the surface of a sphere is employed to compute the center motion and the angular velocity of the solid body. The method initially calculates the sphere center from the 3D coordinates of the reconstructed markers, then finds the optimal rotation matrix that aligns a set of markers tracked at sequential time steps. The parameters involved in the experimental implementation of this procedure are discussed, and the associated uncertainty is estimated from numerical analysis. Finally, the proposed methodology is applied to characterize the motion of a large spherical particle released in a turbulent boundary layer developing in a water channel.

Simulation approach for the evaluation of tracking accuracy in radiotherapy: a preliminary study.

PubMed

Tanaka, Rie; Ichikawa, Katsuhiro; Mori, Shinichiro; Sanada, Sigeru

2013-01-01

Real-time tumor tracking in external radiotherapy can be achieved by diagnostic (kV) X-ray imaging with a dynamic flat-panel detector (FPD). It is important to keep the patient dose as low as possible while maintaining tracking accuracy. A simulation approach would be helpful to optimize the imaging conditions. This study was performed to develop a computer simulation platform based on a noise property of the imaging system for the evaluation of tracking accuracy at any noise level. Flat-field images were obtained using a direct-type dynamic FPD, and noise power spectrum (NPS) analysis was performed. The relationship between incident quantum number and pixel value was addressed, and a conversion function was created. The pixel values were converted into a map of quantum number using the conversion function, and the map was then input into the random number generator to simulate image noise. Simulation images were provided at different noise levels by changing the incident quantum numbers. Subsequently, an implanted marker was tracked automatically and the maximum tracking errors were calculated at different noise levels. The results indicated that the maximum tracking error increased with decreasing incident quantum number in flat-field images with an implanted marker. In addition, the range of errors increased with decreasing incident quantum number. The present method could be used to determine the relationship between image noise and tracking accuracy. The results indicated that the simulation approach would aid in determining exposure dose conditions according to the necessary tracking accuracy.

Fast internal marker tracking algorithm for onboard MV and kV imaging systems

PubMed Central

Mao, W.; Wiersma, R. D.; Xing, L.

2008-01-01

Intrafraction organ motion can limit the advantage of highly conformal dose techniques such as intensity modulated radiation therapy (IMRT) due to target position uncertainty. To ensure high accuracy in beam targeting, real-time knowledge of the target location is highly desired throughout the beam delivery process. This knowledge can be gained through imaging of internally implanted radio-opaque markers with fluoroscopic or electronic portal imaging devices (EPID). In the case of MV based images, marker detection can be problematic due to the significantly lower contrast between different materials in comparison to their kV-based counterparts. This work presents a fully automated algorithm capable of detecting implanted metallic markers in both kV and MV images with high consistency. Using prior CT information, the algorithm predefines the volumetric search space without manual region-of-interest (ROI) selection by the user. Depending on the template selected, both spherical and cylindrical markers can be detected. Multiple markers can be simultaneously tracked without indexing confusion. Phantom studies show detection success rates of 100% for both kV and MV image data. In addition, application of the algorithm to real patient image data results in successful detection of all implanted markers for MV images. Near real-time operational speeds of ∼10 frames∕sec for the detection of five markers in a 1024×768 image are accomplished using an ordinary PC workstation. PMID:18561670

Stability of Markers Used for Real-Time Tumor Tracking After Percutaneous Intrapulmonary Placement

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

Voort van Zyp, Noelle C. van der, E-mail: n.vandervoortvanzyp@erasmusmc.nl; Hoogeman, Mischa S.; Water, Steven van de

2011-11-01

Purpose: To determine the stability of markers used for real-time tumor tracking after percutaneous intrapulmonary placement. Methods and Materials: A total of 42 patients with 44 lesions, 111 markers, and {>=}2 repeat computed tomography (CT) scans were studied. The tumor on the repeat CT scans was registered with the tumor on the planning CT scan. Next, the three-dimensional marker coordinates were determined on the planning CT scan and repeat CT scans. Marker stability was analyzed by the displacement of the markers and the displacement of the center of mass (COM) of the marker configurations. In addition, we assessed the reliabilitymore » of using the intermarker distance as a check for displacements in the COM of the marker configurations. Results: The median marker displacement was 1.3 mm (range, 0.1-53.6). The marker displacement was >5 mm in 12% of the markers and >10 mm in 5% of the markers. The causes of marker displacement >5 mm included marker migration (2 of 13) and target volume changes (5 of 13). Nonsynchronous tumor and marker movement during breathing might have been responsible for the displacements >5 mm in the other 6 of 13 markers. The median displacement in the COM of the marker configurations was 1.0 mm (range, 0.1-23.3). Displacements in the COM of the marker configurations of {>=}2.0 mm were detected by changes in the intermarker distance of >1.5 mm in 96% of the treatment fractions. Conclusion: The median marker displacement was small (1.3 mm). Nevertheless, displacements >5 mm occurred in 12% of the markers. Therefore, we recommend the implantation of multiple markers because multiple markers will enable a quick and reliable check of marker displacement by determining the change in the intermarker distance. A displacement in the COM of the marker configuration of {>=}2.0 mm was almost always detected (96%) by a change in the distance between the markers of >1.5 mm. This enabled the displaced marker to be disabled, such that tumor localization was not compromised.« less

Development of a robust and cost-effective 3D respiratory motion monitoring system using the kinect device: Accuracy comparison with the conventional stereovision navigation system.

PubMed

Bae, Myungsoo; Lee, Sangmin; Kim, Namkug

2018-07-01

To develop and validate a robust and cost-effective 3D respiratory monitoring system based on a Kinect device with a custom-made simple marker. A 3D respiratory monitoring system comprising the simple marker and the Microsoft Kinect v2 device was developed. The marker was designed for simple and robust detection, and the tracking algorithm was developed using the depth, RGB, and infra-red images acquired from the Kinect sensor. A Kalman filter was used to suppress movement noises. The major movements of the marker attached to the four different locations of body surface were determined from the initially collected tracking points of the marker while breathing. The signal level of respiratory motion with the tracking point was estimated along the major direction vector. The accuracy of the results was evaluated through a comparison with those of the conventional stereovision navigation system (NDI Polaris Spectra). Sixteen normal volunteers were enrolled to evaluate the accuracy of this system. The correlation coefficients between the respiratory motion signal from the Kinect device and conventional navigation system ranged from 0.970 to 0.999 and from 0.837 to 0.995 at the abdominal and thoracic surfaces, respectively. The respiratory motion signal from this system was obtained at 27-30 frames/s. This system with the Kinect v2 device and simple marker could be used for cost-effective, robust and accurate 3D respiratory motion monitoring. In addition, this system is as reliable for respiratory motion signal generation and as practically useful as the conventional stereovision navigation system and is less sensitive to patient posture. Copyright © 2018 Elsevier B.V. All rights reserved.

Using Microbial Source Tracking Markers to Predict Occurrence of Waterborne Pathogens in Urban and Agricultural Watershed

EPA Science Inventory

Runoff from agricultural fields and urban landscapes may carry a variety of microbial contaminants that compromises water quality and increases the possibility of human exposure to pathogenic microorganisms. Establishing the relationship between microbial source tracking (MST) ma...

Accuracy and efficiency of an infrared based positioning and tracking system for patient set-up and monitoring in image guided radiotherapy

NASA Astrophysics Data System (ADS)

Jia, Jing; Xu, Gongming; Pei, Xi; Cao, Ruifen; Hu, Liqin; Wu, Yican

2015-03-01

An infrared based positioning and tracking (IPT) system was introduced and its accuracy and efficiency for patient setup and monitoring were tested for daily radiotherapy treatment. The IPT system consists of a pair of floor mounted infrared stereoscopic cameras, passive infrared markers and tools used for acquiring localization information as well as a custom controlled software which can perform the positioning and tracking functions. The evaluation of IPT system characteristics was conducted based on the AAPM 147 task report. Experiments on spatial drift and reproducibility as well as static and dynamic localization accuracy were carried out to test the efficiency of the IPT system. Measurements of known translational (up to 55.0 mm) set-up errors in three dimensions have been performed on a calibration phantom. The accuracy of positioning was evaluated on an anthropomorphic phantom with five markers attached to the surface; the precision of the tracking ability was investigated through a sinusoidal motion platform. For the monitoring of the respiration, three volunteers contributed to the breathing testing in real time. The spatial drift of the IPT system was 0.65 mm within 60 min to be stable. The reproducibility of position variations were between 0.01 and 0.04 mm. The standard deviation of static marker localization was 0.26 mm. The repositioning accuracy was 0.19 mm, 0.29 mm, and 0.53 mm in the left/right (L/R), superior/inferior (S/I) and anterior/posterior (A/P) directions, respectively. The measured dynamic accuracy was 0.57 mm and discrepancies measured for the respiratory motion tracking was better than 1 mm. The overall positioning accuracy of the IPT system was within 2 mm. In conclusion, the IPT system is an accurate and effective tool for assisting patient positioning in the treatment room. The characteristics of the IPT system can successfully meet the needs for real time external marker tracking and patient positioning as well as respiration monitoring during image guided radiotherapy treatments.

Molecular Imaging Markers to Track Huntington's Disease Pathology.

PubMed

Wilson, Heather; De Micco, Rosa; Niccolini, Flavia; Politis, Marios

2017-01-01

Huntington's disease (HD) is a progressive, monogenic dominant neurodegenerative disorder caused by repeat expansion mutation in the huntingtin gene. The accumulation of mutant huntingtin protein, forming intranuclear inclusions, subsequently leads to degeneration of medium spiny neurons in the striatum and cortical areas. Genetic testing can identify HD gene carriers before individuals develop overt cognitive, psychiatric, and chorea symptoms. Thus, HD gene carriers can be studied in premanifest stages to understand and track the evolution of HD pathology. While advances have been made, the precise pathophysiological mechanisms underlying HD are unclear. Magnetic resonance imaging (MRI) and positron emission tomography (PET) have been employed to understand HD pathology in presymptomatic and symptomatic disease stages. PET imaging uses radioactive tracers to detect specific changes, at a molecular level, which could be used as markers of HD progression and to monitor response to therapeutic treatments for HD gene expansion carriers (HDGECs). This review focuses on available PET techniques, employed in cross-sectional and longitudinal human studies, as biomarkers for HD, and highlights future potential PET targets. PET studies have assessed changes in postsynaptic dopaminergic receptors, brain metabolism, microglial activation, and recently phosphodiesterase 10A (PDE10A) as markers to track HD progression. Alterations in PDE10A expression are the earliest biochemical change identified in HD gene carriers up to 43 years before predicted symptomatic onset. Thus, PDE10A expression could be a promising marker to track HD progression from early premanifest disease stages. Other PET targets which have been less well investigated as biomarkers include cannabinoid, adenosine, and GABA receptors. Future longitudinal studies are required to fully validate these PET biomarkers for use to track disease progression from far-onset premanifest to manifest HD stages. PET imaging is a crucial neuroimaging tool, with the potential to detect early changes and validate sensitivity of biomarkers for tracking HD pathology. Moreover, continued development of novel PET tracers provides exciting opportunities to investigate new molecular targets, such as histamine and serotonin receptors, to further understand the mechanisms underlying HD pathology.

CD24 tracks divergent pluripotent states in mouse and human cells

PubMed Central

Shakiba, Nika; White, Carl A.; Lipsitz, Yonatan Y.; Yachie-Kinoshita, Ayako; Tonge, Peter D; Hussein, Samer M. I.; Puri, Mira C.; Elbaz, Judith; Morrissey-Scoot, James; Li, Mira; Munoz, Javier; Benevento, Marco; Rogers, Ian M.; Hanna, Jacob H.; Heck, Albert J. R.; Wollscheid, Bernd; Nagy, Andras; Zandstra, Peter W

2015-01-01

Reprogramming is a dynamic process that can result in multiple pluripotent cell types emerging from divergent paths. Cell surface protein expression is a particularly desirable tool to categorize reprogramming and pluripotency as it enables robust quantification and enrichment of live cells. Here we use cell surface proteomics to interrogate mouse cell reprogramming dynamics and discover CD24 as a marker that tracks the emergence of reprogramming-responsive cells, while enabling the analysis and enrichment of transgene-dependent (F-class) and -independent (traditional) induced pluripotent stem cells (iPSCs) at later stages. Furthermore, CD24 can be used to delineate epiblast stem cells (EpiSCs) from embryonic stem cells (ESCs) in mouse pluripotent culture. Importantly, regulated CD24 expression is conserved in human pluripotent stem cells (PSCs), tracking the conversion of human ESCs to more naive-like PSC states. Thus, CD24 is a conserved marker for tracking divergent states in both reprogramming and standard pluripotent culture. PMID:26076835

Evaluation of five microbial and four mitochondrial DNA markers for tracking human and pig fecal pollution in freshwater

PubMed Central

He, Xiwei; Liu, Peng; Zheng, Guolu; Chen, Huimei; Shi, Wei; Cui, Yibin; Ren, Hongqiang; Zhang, Xu-Xiang

2016-01-01

This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84.0–88.8%) except Pig-2-Bac (100%). Specificities of the human mtDNA markers (99.1 and 98.1%) were higher than those of the human-associated microbial ones (57.0–88.8%). But this pattern was not observed in the pig-associated markers where Pig-2-Bac had 100% specificity. The reliability of H-ND6 and H-ND5 was further evidenced to identify locations of the most polluted within the Taihu Lake watershed of China. In general, the microbial DNA markers demonstrated a higher fecal concentration than the mtDNA ones; increasing temperature and sunlight exposure accelerated significantly the decay of all the DNA markers. Results of this study suggest that DNA markers H-ND6, H-ND5, and Pig-2-Bac may be among the best for fecal source tracking in water. PMID:27734941

Evaluation of five microbial and four mitochondrial DNA markers for tracking human and pig fecal pollution in freshwater

NASA Astrophysics Data System (ADS)

He, Xiwei; Liu, Peng; Zheng, Guolu; Chen, Huimei; Shi, Wei; Cui, Yibin; Ren, Hongqiang; Zhang, Xu-Xiang

2016-10-01

This study systematically evaluated five microbial and four mitochondrial DNA (mtDNA) markers, including sensitivities and specificities under PCR method, and fecal concentrations and decay rates in water under qPCR method. The microbial DNA markers were the three human-associated (BacH, HF183 and B.adolescentis) and two pig-associated (Pig-2-Bac and L.amylovorus), while the mtDNA ones were two human- (H-ND6 and H-ND5) and two pig-associated (P-CytB and P-ND5). All the mtDNA markers showed higher sensitivity (100%) than the microbial ones (84.0-88.8%) except Pig-2-Bac (100%). Specificities of the human mtDNA markers (99.1 and 98.1%) were higher than those of the human-associated microbial ones (57.0-88.8%). But this pattern was not observed in the pig-associated markers where Pig-2-Bac had 100% specificity. The reliability of H-ND6 and H-ND5 was further evidenced to identify locations of the most polluted within the Taihu Lake watershed of China. In general, the microbial DNA markers demonstrated a higher fecal concentration than the mtDNA ones; increasing temperature and sunlight exposure accelerated significantly the decay of all the DNA markers. Results of this study suggest that DNA markers H-ND6, H-ND5, and Pig-2-Bac may be among the best for fecal source tracking in water.

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.

Hollow-Fiber Ultrafiltration and PCR Detection of Human-Associated Genetic Markers from Various Types of Surface Water in Florida ▿

PubMed Central

Leskinen, Stephaney D.; Brownell, Miriam; Lim, Daniel V.; Harwood, Valerie J.

2010-01-01

Hollow-fiber ultrafiltration (HFUF) and PCR were combined to detect human-associated microbial source tracking marker genes in large volumes of fresh and estuarine Florida water. HFUF allowed marker detection when membrane filtration did not, demonstrating HFUF's ability to facilitate detection of diluted targets by PCR in a variety of water types. PMID:20435774

In-vivo measurement of dynamic joint motion using high speed biplane radiography and CT: application to canine ACL deficiency.

PubMed

Tashman, Scott; Anderst, William

2003-04-01

Dynamic assessment of three-dimensional (3D) skeletal kinematics is essential for understanding normal joint function as well as the effects of injury or disease. This paper presents a novel technique for measuring in-vivo skeletal kinematics that combines data collected from high-speed biplane radiography and static computed tomography (CT). The goals of the present study were to demonstrate that highly precise measurements can be obtained during dynamic movement studies employing high frame-rate biplane video-radiography, to develop a method for expressing joint kinematics in an anatomically relevant coordinate system and to demonstrate the application of this technique by calculating canine tibio-femoral kinematics during dynamic motion. The method consists of four components: the generation and acquisition of high frame rate biplane radiographs, identification and 3D tracking of implanted bone markers, CT-based coordinate system determination, and kinematic analysis routines for determining joint motion in anatomically based coordinates. Results from dynamic tracking of markers inserted in a phantom object showed the system bias was insignificant (-0.02 mm). The average precision in tracking implanted markers in-vivo was 0.064 mm for the distance between markers and 0.31 degree for the angles between markers. Across-trial standard deviations for tibio-femoral translations were similar for all three motion directions, averaging 0.14 mm (range 0.08 to 0.20 mm). Variability in tibio-femoral rotations was more dependent on rotation axis, with across-trial standard deviations averaging 1.71 degrees for flexion/extension, 0.90 degree for internal/external rotation, and 0.40 degree for varus/valgus rotation. Advantages of this technique over traditional motion analysis methods include the elimination of skin motion artifacts, improved tracking precision and the ability to present results in a consistent anatomical reference frame.

Microbial source tracking in highly vulnerable karst drinking water resources.

PubMed

Diston, D; Robbi, R; Baumgartner, A; Felleisen, R

2018-02-01

Water resources situated in areas with underlying karst geology are particularly vulnerable to fecal pollution. In such vulnerable systems, microbial source tracking (MST) methods are useful tools to elucidate the pathways of both animal and human fecal pollution, leading to more accurate water use risk assessments. Here, we describe the application of a MST toolbox using both culture-dependent bacteriophage and molecular-dependent 16S rRNA assays at spring and well sites in the karstic St Imier Valley, Switzerland. Culture-dependent and molecular-dependent marker performance varied significantly, with the 16S rRNA assays displaying greater sensitivity than their phage counterpart; HF183 was the best performing human wastewater-associated marker while Rum2Bac was the best performing ruminant marker. Differences were observed in pollution regimes between the well and spring sampling sites, with the spring water being more degraded than the well site. Our results inform the choice of marker selection for MST studies and highlight differences in microbial water quality between well and spring karst sites.

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.

Long-Term Monitoring of Waterborne Pathogens and Microbial Source Tracking Markers in Paired Agricultural Watersheds under Controlled and Conventional Tile Drainage Management

PubMed Central

Wilkes, Graham; Brassard, Julie; Edge, Thomas A.; Gannon, Victor; Gottschall, Natalie; Jokinen, Cassandra C.; Jones, Tineke H.; Khan, Izhar U. H.; Marti, Romain; Sunohara, Mark D.; Topp, Edward

2014-01-01

Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization. PMID:24727274

Insect cyborgs: a new frontier in flight control systems

NASA Astrophysics Data System (ADS)

Reissman, Timothy; Crawford, Jackie H.; Garcia, Ephrahim

2007-04-01

The development of a micro-UAV via a cybernetic organism, primarily the Manduca sexta moth, is presented. An observer to gather output data of the system response of the moth is given by means of an image following system. The visual tracking was implemented to gather the required information about the time history of the moth's six degrees of freedom. This was performed with three cameras tracking a white line as a marker on the moth's thorax to maximize contrast between the moth and the marker. Evaluation of the implemented six degree of freedom visual tracking system finds precision greater than 0.1 mm within three standard deviations and accuracy on the order of 1 mm. Acoustic and visual response systems are presented to lay the groundwork for creating a stochastic response catalog of the organisms to varied stimuli.

Three-dimensional, automated, real-time video system for tracking limb motion in brain-machine interface studies.

PubMed

Peikon, Ian D; Fitzsimmons, Nathan A; Lebedev, Mikhail A; Nicolelis, Miguel A L

2009-06-15

Collection and analysis of limb kinematic data are essential components of the study of biological motion, including research into biomechanics, kinesiology, neurophysiology and brain-machine interfaces (BMIs). In particular, BMI research requires advanced, real-time systems capable of sampling limb kinematics with minimal contact to the subject's body. To answer this demand, we have developed an automated video tracking system for real-time tracking of multiple body parts in freely behaving primates. The system employs high-contrast markers painted on the animal's joints to continuously track the three-dimensional positions of their limbs during activity. Two-dimensional coordinates captured by each video camera are combined and converted to three-dimensional coordinates using a quadratic fitting algorithm. Real-time operation of the system is accomplished using direct memory access (DMA). The system tracks the markers at a rate of 52 frames per second (fps) in real-time and up to 100fps if video recordings are captured to be later analyzed off-line. The system has been tested in several BMI primate experiments, in which limb position was sampled simultaneously with chronic recordings of the extracellular activity of hundreds of cortical cells. During these recordings, multiple computational models were employed to extract a series of kinematic parameters from neuronal ensemble activity in real-time. The system operated reliably under these experimental conditions and was able to compensate for marker occlusions that occurred during natural movements. We propose that this system could also be extended to applications that include other classes of biological motion.

Collecting Kinematic Data on a Ski Track with Optoelectronic Stereophotogrammetry: A Methodological Study Assessing the Feasibility of Bringing the Biomechanics Lab to the Field.

PubMed

Spörri, Jörg; Schiefermüller, Christian; Müller, Erich

2016-01-01

In the laboratory, optoelectronic stereophotogrammetry is one of the most commonly used motion capture systems; particularly, when position- or orientation-related analyses of human movements are intended. However, for many applied research questions, field experiments are indispensable, and it is not a priori clear whether optoelectronic stereophotogrammetric systems can be expected to perform similarly to in-lab experiments. This study aimed to assess the instrumental errors of kinematic data collected on a ski track using optoelectronic stereophotogrammetry, and to investigate the magnitudes of additional skiing-specific errors and soft tissue/suit artifacts. During a field experiment, the kinematic data of different static and dynamic tasks were captured by the use of 24 infrared-cameras. The distances between three passive markers attached to a rigid bar were stereophotogrammetrically reconstructed and, subsequently, were compared to the manufacturer-specified exact values. While at rest or skiing at low speed, the optoelectronic stereophotogrammetric system's accuracy and precision for determining inter-marker distances were found to be comparable to those known for in-lab experiments (< 1 mm). However, when measuring a skier's kinematics under "typical" skiing conditions (i.e., high speeds, inclined/angulated postures and moderate snow spraying), additional errors were found to occur for distances between equipment-fixed markers (total measurement errors: 2.3 ± 2.2 mm). Moreover, for distances between skin-fixed markers, such as the anterior hip markers, additional artifacts were observed (total measurement errors: 8.3 ± 7.1 mm). In summary, these values can be considered sufficient for the detection of meaningful position- or orientation-related differences in alpine skiing. However, it must be emphasized that the use of optoelectronic stereophotogrammetry on a ski track is seriously constrained by limited practical usability, small-sized capture volumes and the occurrence of extensive snow spraying (which results in marker obscuration). The latter limitation possibly might be overcome by the use of more sophisticated cluster-based marker sets.

Distributions of Fecal Markers in Wastewater from Different Climatic Zones for Human Fecal Pollution Tracking in Australian Surface Waters

PubMed Central

Sidhu, J. P. S.; Smith, K.; Beale, D. J.; Gyawali, P.; Toze, S.

2015-01-01

Recreational and potable water supplies polluted with human wastewater can pose a direct health risk to humans. Therefore, sensitive detection of human fecal pollution in environmental waters is very important to water quality authorities around the globe. Microbial source tracking (MST) utilizes human fecal markers (HFMs) to detect human wastewater pollution in environmental waters. The concentrations of these markers in raw wastewater are considered important because it is likely that a marker whose concentration is high in wastewater will be more frequently detected in polluted waters. In this study, quantitative PCR (qPCR) assays were used to determine the concentrations of fecal indicator bacteria (FIB) Escherichia coli and Enterococcus spp., HFMs Bacteroides HF183, human adenoviruses (HAdVs), and polyomaviruses (HPyVs) in raw municipal wastewater influent from various climatic zones in Australia. E. coli mean concentrations in pooled human wastewater data sets (from various climatic zones) were the highest (3.2 × 106 gene copies per ml), followed by those of HF183 (8.0 × 105 gene copies per ml) and Enterococcus spp. (3.6 × 105 gene copies per ml). HAdV and HPyV concentrations were 2 to 3 orders of magnitude lower than those of FIB and HF183. Strong positive and negative correlations were observed between the FIB and HFM concentrations within and across wastewater treatment plants (WWTPs). To identify the most sensitive marker of human fecal pollution, environmental water samples were seeded with raw human wastewater. The results from the seeding experiments indicated that Bacteroides HF183 was more sensitive for detecting human fecal pollution than HAdVs and HPyVs. Since the HF183 marker can occasionally be present in nontarget animal fecal samples, it is recommended that HF183 along with a viral marker (HAdVs or HPyVs) be used for tracking human fecal pollution in Australian environmental waters. PMID:26682850

Visual Tracking of Plant Virus Infection and Movement Using a Reporter MYB Transcription Factor That Activates Anthocyanin Biosynthesis1[W

PubMed Central

Bedoya, Leonor C.; Martínez, Fernando; Orzáez, Diego; Daròs, José-Antonio

2012-01-01

Insertion of reporter genes into plant virus genomes is a common experimental strategy to research many aspects of the viral infection dynamics. Their numerous advantages make fluorescent proteins the markers of choice in most studies. However, the use of fluorescent proteins still has some limitations, such as the need of specialized material and facilities to detect the fluorescence. Here, we demonstrate a visual reporter marker system to track virus infection and movement through the plant. The reporter system is based on expression of Antirrhinum majus MYB-related Rosea1 (Ros1) transcription factor (220 amino acids; 25.7 kD) that activates a series of biosynthetic genes leading to accumulation of colored anthocyanins. Using two different tobacco etch potyvirus recombinant clones tagged with Ros1, we show that infected tobacco (Nicotiana tabacum) tissues turn bright red, demonstrating that in this context, the sole expression of Ros1 is sufficient to induce pigment accumulation to a level readily detectable to the naked eye. This marker system also reports viral load qualitatively and quantitatively by means of a very simple extraction process. The Ros1 marker remained stable within the potyvirus genome through successive infectious passages from plant to plant. The main limitation of this marker system is that color output will depend on each particular plant host-virus combination and must be previously tested. However, our experiments demonstrate accurate tracking of turnip mosaic potyvirus infecting Arabidopsis (Arabidopsis thaliana) and either tobacco mosaic virus or potato X virus infecting Nicotiana benthamiana, stressing the general applicability of the method. PMID:22238422

Features of single tracks in coaxial laser cladding of a NIbased self-fluxing alloy

NASA Astrophysics Data System (ADS)

Feldshtein, Eugene; Devojno, Oleg; Kardapolava, Marharyta; Lutsko, Nikolaj

2017-10-01

In the present paper, the influence of coaxial laser cladding conditions on the dimensions, microstructure, phases and microhardness of Ni-based self-fluxing alloy single tracks is studied. The height and width of single tracks depend on the speed and distance of the laser cladding: increasing the nozzle distance from the deposited surface 1.4 times reduces the width of the track 1.2 - 1.3 times and increases its height 1.2 times. The increase of the laser spot speed 3 times reduces the track width 1.2 - 1.4 times and the height in 1.5 - 1.6 times. At the same time, the increase of the laser spot speed 3 times reduces the track width 1.2 - 1.4 times and the height 1.5 - 1.6 times. Regularities in the formation of single tracks microstructure with different cladding conditions are defined, as well as regularity of distribution of elements over the track depth and in the transient zone. The patterns of microhardness distribution over the track depth for different cladding conditions are found.

Single-tube tetradecaplex panel of highly polymorphic microsatellite markers < 1 Mb from F8 for simplified preimplantation genetic diagnosis of hemophilia A.

PubMed

Zhao, M; Chen, M; Tan, A S C; Cheah, F S H; Mathew, J; Wong, P C; Chong, S S

2017-07-01

Essentials Preimplantation genetic diagnosis (PGD) of severe hemophilia A relies on linkage analysis. Simultaneous multi-marker screening can simplify selection of informative markers in a couple. We developed a single-tube tetradecaplex panel of polymorphic markers for hemophilia A PGD use. Informative markers can be used for linkage analysis alone or combined with mutation detection. Background It is currently not possible to perform single-cell preimplantation genetic diagnosis (PGD) to directly detect the common inversion mutations of the factor VIII (F8) gene responsible for severe hemophilia A (HEMA). As such, PGD for such inversion carriers relies on indirect analysis of linked polymorphic markers. Objectives To simplify linkage-based PGD of HEMA, we aimed to develop a panel of highly polymorphic microsatellite markers located near the F8 gene that could be simultaneously genotyped in a multiplex-PCR reaction. Methods We assessed the polymorphism of various microsatellite markers located ≤ 1 Mb from F8 in 177 female subjects. Highly polymorphic markers were selected for co-amplification with the AMELX/Y indel dimorphism in a single-tube reaction. Results Thirteen microsatellite markers located within 0.6 Mb of F8 were successfully co-amplified with AMELX/Y in a single-tube reaction. Observed heterozygosities of component markers ranged from 0.43 to 0.84, and ∼70-80% of individuals were heterozygous for ≥ 5 markers. The tetradecaplex panel successfully identified fully informative markers in a couple interested in PGD for HEMA because of an intragenic F8 point mutation, with haplotype phasing established through a carrier daughter. In-vitro fertilization (IVF)-PGD involved single-tube co-amplification of fully informative markers with AMELX/Y and the mutation-containing F8 amplicon, followed by microsatellite analysis and amplicon mutation-site minisequencing analysis. Conclusions The single-tube multiplex-PCR format of this highly polymorphic microsatellite marker panel simplifies identification and selection of informative markers for linkage-based PGD of HEMA. Informative markers can also be easily co-amplified with mutation-containing F8 amplicons for combined mutation detection and linkage analysis. © 2017 International Society on Thrombosis and Haemostasis.

Application of TrackEye in equine locomotion research.

PubMed

Drevemo, S; Roepstorff, L; Kallings, P; Johnston, C J

1993-01-01

TrackEye is an analysis system, which is applicable for equine biokinematic studies. It covers the whole process from digitizing of images, automatic target tracking and analysis. Key components in the system are an image work station for processing of video images and a high-resolution film-to-video scanner for 16-mm film. A recording module controls the input device and handles the capture of image sequences into a videodisc system, and a tracking module is able to follow reference markers automatically. The system offers a flexible analysis including calculations of markers displacements, distances and joint angles, velocities and accelerations. TrackEye was used to study effects of phenylbutazone on the fetlock and carpal joint angle movements in a horse with a mild lameness caused by osteo-arthritis in the fetlock joint of a forelimb. Significant differences, most evident before treatment, were observed in the minimum fetlock and carpal joint angles when contralateral limbs were compared (p < 0.001). The minimum fetlock angle and the minimum carpal joint angle were significantly greater in the lame limb before treatment compared to those 6, 37 and 49 h after the last treatment (p < 0.001).

The strategy of fusion genes construction determines efficient expression of introduced transcription factors.

PubMed

Adamus, Tomasz; Konieczny, Paweł; Sekuła, Małgorzata; Sułkowski, Maciej; Majka, Marcin

2014-01-01

The main goal in gene therapy and biomedical research is an efficient transcription factors (TFs) delivery system. SNAIL, a zinc finger transcription factor, is strongly involved in tumor, what makes its signaling pathways an interesting research subject. The necessity of tracking activation of intracellular pathways has prompted fluorescent proteins usage as localization markers. Advanced molecular cloning techniques allow to generate fusion proteins from fluorescent markers and transcription factors. Depending on fusion strategy, the protein expression levels and nuclear transport ability are significantly different. The P2A self-cleavage motif through its cleavage ability allows two single proteins to be simultaneously expressed. The aim of this study was to compare two strategies for introducing a pair of genes using expression vector system. We have examined GFP and SNAI1 gene fusions by comprising common nucleotide polylinker (multiple cloning site) or P2A motif in between them, resulting in one fusion or two independent protein expressions respectively. In each case transgene expression levels and translation efficiency as well as nuclear localization of expressed protein have been analyzed. Our data showed that usage of P2A motif provides more effective nuclear transport of SNAIL transcription factor than conventional genes linker. At the same time the fluorescent marker spreads evenly in subcellular space.

The Effects of Water Matrix on Decay of Human Fecal Molecular Markers and Campylobacter spp.

EPA Science Inventory

Although molecular source tracking for human fecal contamination is used on a wide range of sample types, little is known about comparative decay of proposed molecular markers under different conditions, or correlation with pathogen decay. Our purpose was to measure correlations ...

TRACKING FECAL CONTAMINATION WITH BACTEROIDALES MOLECULAR MARKERS: AN ANALYSIS OF THE DYNAMICS OF FECAL CONTAMINATION IN THE TILLAMOOK BASIN, OREGON

EPA Science Inventory

Although amplification of source-specific molecular markers from Bacteroidales fecal bacteria can identify several different kinds of fecal contamination in water, it remains unclear how this technique relates to fecal indicator measurements in natural waters. The objectives of t...

Validation of Microbial Source Tracking Markers and Detection Protocols: Considerations for Effective Interpretation

EPA Science Inventory

The goal of this chapter is to provide an overview of MST marker characteristics, to describe performance criteria of detection protocols used and to offer guidelines for the effective interpretation of the results. Since the trend in the research community has shifted towards (q...

Spatial and rotational quality assurance of 6DOF patient tracking systems

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

Belcher, Andrew H.; Liu, Xinmin; Grelewicz, Zachary

Purpose: External tracking systems used for patient positioning and motion monitoring during radiotherapy are now capable of detecting both translations and rotations. In this work, the authors develop a novel technique to evaluate the 6 degree of freedom 6(DOF) (translations and rotations) performance of external motion tracking systems. The authors apply this methodology to an infrared marker tracking system and two 3D optical surface mapping systems in a common tumor 6DOF workspace. Methods: An in-house designed and built 6DOF parallel kinematics robotic motion phantom was used to perform motions with sub-millimeter and subdegree accuracy in a 6DOF workspace. An infraredmore » marker tracking system was first used to validate a calibration algorithm which associates the motion phantom coordinate frame to the camera frame. The 6DOF positions of the mobile robotic system in this space were then tracked and recorded independently by an optical surface tracking system after a cranial phantom was rigidly fixed to the moveable platform of the robotic stage. The calibration methodology was first employed, followed by a comprehensive 6DOF trajectory evaluation, which spanned a full range of positions and orientations in a 20 × 20 × 16 mm and 5° × 5° × 5° workspace. The intended input motions were compared to the calibrated 6DOF measured points. Results: The technique found the accuracy of the infrared (IR) marker tracking system to have maximal root-mean square error (RMSE) values of 0.18, 0.25, 0.07 mm, 0.05°, 0.05°, and 0.09° in left–right (LR), superior–inferior (SI), anterior–posterior (AP), pitch, roll, and yaw, respectively, comparing the intended 6DOF position and the measured position by the IR camera. Similarly, the 6DOF RSME discrepancy for the HD optical surface tracker yielded maximal values of 0.46, 0.60, 0.54 mm, 0.06°, 0.11°, and 0.08° in LR, SI, AP, pitch, roll, and yaw, respectively, over the same 6DOF evaluative workspace. An earlier generation 3D optical surface tracking unit was observed to have worse tracking capabilities than both the IR camera unit and the newer 3D surface tracking system with maximal RMSE of 0.69, 0.74, 0.47 mm, 0.28°, 0.19°, and 0.18°, in LR, SI, AP, pitch, roll, and yaw, respectively, in the same 6DOF evaluation space. Conclusions: The proposed technique was found to be effective at evaluating the performance of 6DOF patient tracking systems. All observed optical tracking systems were found to exhibit tracking capabilities at the sub-millimeter and subdegree level within a 6DOF workspace.« less

Inertial Motion Tracking for Inserting Humans into a Networked Synthetic Environment

DTIC Science & Technology

2007-08-31

tracking methods. One method requires markers on the tracked buman body, and other method does not use nmkers. OPTOTRAK from Northem Digital Inc. is a...of using multicasting protocols. Unfortunately, most routers on the Internet are not configured for multicasting. A technique called tunneling is...used to overcome this problem. Tunneling is a software solution that m s on the end point routerslcomputers and allows multicast packets to traverse

Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries▿

PubMed Central

Gourmelon, Michèle; Caprais, Marie Paule; Ségura, Raphaël; Le Mennec, Cécile; Lozach, Solen; Piriou, Jean Yves; Rincé, Alain

2007-01-01

In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers. PMID:17557850

Markers for the identification of tendon-derived stem cells in vitro and tendon stem cells in situ - update and future development.

PubMed

Lui, Pauline Po Yee

2015-06-02

The efficacy of tendon-derived stem cells (TDSCs) for the promotion of tendon and tendon-bone junction repair has been reported in animal studies. Modulation of the tendon stem cell niche in vivo has also been reported to influence tendon structure. There is a need to have specific and reliable markers that can define TDSCs in vitro and tendon stem cells in situ for several reasons: to understand the basic biology of TDSCs and their subpopulations in vitro; to understand the identity, niches and functions of tendon/progenitor stem cells in vivo; to meet the governmental regulatory requirements for quality of TDSCs when translating the exciting preclinical findings into clinical trial/practice; and to develop new treatment strategies for mobilizing endogenous stem/progenitor cells in tendon. TDSCs were reported to express the common mesenchymal stem cell (MSC) markers and some embryonic stem cell (ESC) markers, and there were attempts to use these markers to label tendon stem cells in situ. Are these stem cell markers useful for the identification of TDSCs in vitro and tracking of tendon stem cells in situ? This review aims to discuss the values of the panel of MSC, ESC and tendon-related markers for the identification of TDSCs in vitro. Important factors influencing marker expression by TDSCs are discussed. The usefulness and limitations of the panel of MSC, ESC and tendon-related markers for tracking stem cells in tendon, especially tendon stem cells, in situ are then reviewed. Future research directions are proposed.

A fiducial detection algorithm for real-time image guided IMRT based on simultaneous MV and kV imaging

PubMed Central

Mao, Weihua; Riaz, Nadeem; Lee, Louis; Wiersma, Rodney; Xing, Lei

2008-01-01

The advantage of highly conformal dose techniques such as 3DCRT and IMRT is limited by intrafraction organ motion. A new approach to gain near real-time 3D positions of internally implanted fiducial markers is to analyze simultaneous onboard kV beam and treatment MV beam images (from fluoroscopic or electronic portal image devices). Before we can use this real-time image guidance for clinical 3DCRT and IMRT treatments, four outstanding issues need to be addressed. (1) How will fiducial motion blur the image and hinder tracking fiducials? kV and MV images are acquired while the tumor is moving at various speeds. We find that a fiducial can be successfully detected at a maximum linear speed of 1.6 cm∕s. (2) How does MV beam scattering affect kV imaging? We investigate this by varying MV field size and kV source to imager distance, and find that common treatment MV beams do not hinder fiducial detection in simultaneous kV images. (3) How can one detect fiducials on images from 3DCRT and IMRT treatment beams when the MV fields are modified by a multileaf collimator (MLC)? The presented analysis is capable of segmenting a MV field from the blocking MLC and detecting visible fiducials. This enables the calculation of nearly real-time 3D positions of markers during a real treatment. (4) Is the analysis fast enough to track fiducials in nearly real time? Multiple methods are adopted to predict marker positions and reduce search regions. The average detection time per frame for three markers in a 1024×768 image was reduced to 0.1 s or less. Solving these four issues paves the way to tracking moving fiducial markers throughout a 3DCRT or IMRT treatment. Altogether, these four studies demonstrate that our algorithm can track fiducials in real time, on degraded kV images (MV scatter), in rapidly moving tumors (fiducial blurring), and even provide useful information in the case when some fiducials are blocked from view by the MLC. This technique can provide a gating signal or be used for intra-fractional tumor tracking on a Linac equipped with a kV imaging system. Any motion exceeding a preset threshold can warn the therapist to suspend a treatment session and reposition the patient. PMID:18777916

Spiked GBS: A unified, open platform for single marker genotyping and whole-genome profiling

USDA-ARS?s Scientific Manuscript database

In plant breeding, there are two primary applications for DNA markers in selection: 1) selection of known genes using a single marker assay (marker-assisted selection; MAS); and 2) whole-genome profiling and prediction (genomic selection; GS). Typically, marker platforms have addressed only one of t...

Canine scent detection and microbial source tracking of human waste contamination in storm drains.

PubMed

Van De Werfhorst, Laurie C; Murray, Jill L S; Reynolds, Scott; Reynolds, Karen; Holden, Patricia A

2014-06-01

Human fecal contamination of surface waters and drains is difficult to diagnose. DNA-based and chemical analyses of water samples can be used to specifically quantify human waste contamination, but their expense precludes routine use. We evaluated canine scent tracking, using two dogs trained to respond to the scent of municipal wastewater, as a field approach for surveying human fecal contamination. Fecal indicator bacteria, as well as DNA-based and chemical markers of human waste, were analyzed in waters sampled from canine scent-evaluated sites (urban storm drains and creeks). In the field, the dogs responded positively (70% and 100%) at sites for which sampled waters were then confirmed as contaminated with human waste. When both dogs indicated a negative response, human waste markers were absent. Overall, canine scent tracking appears useful for prioritizing sampling sites for which DNA-based and similarly expensive assays can confirm and quantify human waste contamination.

Model-based registration of multi-rigid-body for augmented reality

NASA Astrophysics Data System (ADS)

Ikeda, Sei; Hori, Hajime; Imura, Masataka; Manabe, Yoshitsugu; Chihara, Kunihiro

2009-02-01

Geometric registration between a virtual object and the real space is the most basic problem in augmented reality. Model-based tracking methods allow us to estimate three-dimensional (3-D) position and orientation of a real object by using a textured 3-D model instead of visual marker. However, it is difficult to apply existing model-based tracking methods to the objects that have movable parts such as a display of a mobile phone, because these methods suppose a single, rigid-body model. In this research, we propose a novel model-based registration method for multi rigid-body objects. For each frame, the 3-D models of each rigid part of the object are first rendered according to estimated motion and transformation from the previous frame. Second, control points are determined by detecting the edges of the rendered image and sampling pixels on these edges. Motion and transformation are then simultaneously calculated from distances between the edges and the control points. The validity of the proposed method is demonstrated through experiments using synthetic videos.

Multi-year microbial source tracking study characterizing fecal contamination in an urban watershed

USGS Publications Warehouse

Bushon, Rebecca N.; Brady, Amie M. G.; Christensen, Eric D.; Stelzer, Erin A.

2017-01-01

Microbiological and hydrological data were used to rank tributary stream contributions of bacteria to the Little Blue River in Independence, Missouri. Concentrations, loadings and yields of E. coli and microbial source tracking (MST) markers, were characterized during base flow and storm events in five subbasins within Independence, as well as sources entering and leaving the city through the river. The E. coli water quality threshold was exceeded in 29% of base-flow and 89% of storm-event samples. The total contribution of E. coli and MST markers from tributaries within Independence to the Little Blue River, regardless of streamflow, did not significantly increase the median concentrations leaving the city. Daily loads and yields of E. coli and MST markers were used to rank the subbasins according to their contribution of each constituent to the river. The ranking methodology used in this study may prove useful in prioritizing remediation in the different subbasins.

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

Yan, Guanghua, E-mail: yan@ufl.edu; Li, Jonathan; Huang, Yin

Purpose: To propose a simple model to explain the origin of ghost markers in marker-based optical tracking systems (OTS) and to develop retrospective strategies to detect and eliminate ghost markers. Methods: In marker-based OTS, ghost markers are virtual markers created due to the cross-talk between the two camera sensors, which can lead to system execution failure or inaccuracy in patient tracking. As a result, the users have to limit the number of markers and avoid certain marker configurations to reduce the chances of ghost markers. In this work, the authors propose retrospective strategies to detect and eliminate ghost markers. Themore » two camera sensors were treated as mathematical points in space. The authors identified the coplanar within limit (CWL) condition as the necessary condition for ghost marker occurrence. A simple ghost marker detection method was proposed based on the model. Ghost marker elimination was achieved through pattern matching: a ghost marker-free reference set was matched with the optical marker set observed by the OTS; unmatched optical markers were eliminated as either ghost markers or misplaced markers. The pattern matching problem was formulated as a constraint satisfaction problem (using pairwise distances as constraints) and solved with an iterative backtracking algorithm. Wildcard markers were introduced to address missing or misplaced markers. An experiment was designed to measure the sensor positions and the limit for the CWL condition. The ghost marker detection and elimination algorithms were verified with samples collected from a five-marker jig and a nine-marker anthropomorphic phantom, rotated with the treatment couch from −60° to +60°. The accuracy of the pattern matching algorithm was further validated with marker patterns from 40 patients who underwent stereotactic body radiotherapy (SBRT). For this purpose, a synthetic optical marker pattern was created for each patient by introducing ghost markers, marker position uncertainties, and marker displacement. Results: The sensor positions and the limit for the CWL condition were measured with excellent reproducibility (standard deviation ≤ 0.39 mm). The ghost marker detection algorithm had perfect detection accuracy for both the jig (1544 samples) and the anthropomorphic phantom (2045 samples). Pattern matching was successful for all samples from both phantoms as well as the 40 patient marker patterns. Conclusions: The authors proposed a simple model to explain the origin of ghost markers and identified the CWL condition as the necessary condition for ghost marker occurrence. The retrospective ghost marker detection and elimination algorithms guarantee complete ghost marker elimination while providing the users with maximum flexibility in selecting the number of markers and their configuration to meet their clinic needs.« less

Microbial Source Tracking Markers for Detection of Fecal Contamination in Environmental Waters: Relationships Between Pathogens and Human Health Outcomes

EPA Science Inventory

Microbial source tracking (MST) describes a suite of methods and an investigative strategy designed to identify the dominant sources of fecal pollution in environmental waters. The methods rely on the close association of certain fecal microorganisms with a particular host speci...

36. View of preset counter (PC) console and tracking console ...

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

36. View of preset counter (PC) console and tracking console on right, located in MWOC facility in transmitter building no. 102. - Clear Air Force Station, Ballistic Missile Early Warning System Site II, One mile west of mile marker 293.5 on Parks Highway, 5 miles southwest of Anderson, Anderson, Denali Borough, AK

PD-L1 is an activation-independent marker of brown adipocytes.

PubMed

Ingram, Jessica R; Dougan, Michael; Rashidian, Mohammad; Knoll, Marko; Keliher, Edmund J; Garrett, Sarah; Garforth, Scott; Blomberg, Olga S; Espinosa, Camilo; Bhan, Atul; Almo, Steven C; Weissleder, Ralph; Lodish, Harvey; Dougan, Stephanie K; Ploegh, Hidde L

2017-09-21

Programmed death ligand 1 (PD-L1) is expressed on a number of immune and cancer cells, where it can downregulate antitumor immune responses. Its expression has been linked to metabolic changes in these cells. Here we develop a radiolabeled camelid single-domain antibody (anti-PD-L1 VHH) to track PD-L1 expression by immuno-positron emission tomography (PET). PET-CT imaging shows a robust and specific PD-L1 signal in brown adipose tissue (BAT). We confirm expression of PD-L1 on brown adipocytes and demonstrate that signal intensity does not change in response to cold exposure or β-adrenergic activation. This is the first robust method of visualizing murine brown fat independent of its activation state.Current approaches to visualise brown adipose tissue (BAT) rely primarily on markers that reflect its metabolic activity. Here, the authors show that PD-L1 is expressed on brown adipocytes, does not change upon BAT activation, and that BAT volume in mice can be measured by PET-CT with a radiolabeled anti-PD-L1 antibody.

A preclinical murine model for the early detection of radiation-induced brain injury using magnetic resonance imaging and behavioral tests for learning and memory: with applications for the evaluation of possible stem cell imaging agents and therapies.

PubMed

Ngen, Ethel J; Wang, Lee; Gandhi, Nishant; Kato, Yoshinori; Armour, Michael; Zhu, Wenlian; Wong, John; Gabrielson, Kathleen L; Artemov, Dmitri

2016-06-01

Stem cell therapies are being developed for radiotherapy-induced brain injuries (RIBI). Magnetic resonance imaging (MRI) offers advantages for imaging transplanted stem cells. However, most MRI cell-tracking techniques employ superparamagnetic iron oxide particles (SPIOs), which are difficult to distinguish from hemorrhage. In current preclinical RIBI models, hemorrhage occurs concurrently with other injury markers. This makes the evaluation of the recruitment of transplanted SPIO-labeled stem cells to injury sites difficult. Here, we developed a RIBI model, with early injury markers reflective of hippocampal dysfunction, which can be detected noninvasively with MRI and behavioral tests. Lesions were generated by sub-hemispheric irradiation of mouse hippocampi with single X-ray beams of 80 Gy. Lesion formation was monitored with anatomical and contrast-enhanced MRI and changes in memory and learning were assessed with fear-conditioning tests. Early injury markers were detected 2 weeks after irradiation. These included an increase in the permeability of the blood-brain barrier, demonstrated by a 92 ± 20 % contrast enhancement of the irradiated versus the non-irradiated brain hemispheres, within 15 min of the administration of an MRI contrast agent. A change in short-term memory was also detected, as demonstrated by a 40.88 ± 5.03 % decrease in the freezing time measured during the short-term memory context test at this time point, compared to that before irradiation. SPIO-labeled stem cells transplanted contralateral to the lesion migrated toward the lesion at this time point. No hemorrhage was detected up to 10 weeks after irradiation. This model can be used to evaluate SPIO-based stem cell-tracking agents, short-term.

A simple and rapid method for high-resolution visualization of single-ion tracks

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

Omichi, Masaaki; Center for Collaborative Research, Anan National College of Technology, Anan, Tokushima 774-0017; Choi, Wookjin

2014-11-15

Prompt determination of spatial points of single-ion tracks plays a key role in high-energy particle induced-cancer therapy and gene/plant mutations. In this study, a simple method for the high-resolution visualization of single-ion tracks without etching was developed through the use of polyacrylic acid (PAA)-N, N’-methylene bisacrylamide (MBAAm) blend films. One of the steps of the proposed method includes exposure of the irradiated films to water vapor for several minutes. Water vapor was found to promote the cross-linking reaction of PAA and MBAAm to form a bulky cross-linked structure; the ion-track scars were detectable at a nanometer scale by atomic forcemore » microscopy. This study demonstrated that each scar is easily distinguishable, and the amount of generated radicals of the ion tracks can be estimated by measuring the height of the scars, even in highly dense ion tracks. This method is suitable for the visualization of the penumbra region in a single-ion track with a high spatial resolution of 50 nm, which is sufficiently small to confirm that a single ion hits a cell nucleus with a size ranging between 5 and 20 μm.« less

Visual tracking for multi-modality computer-assisted image guidance

NASA Astrophysics Data System (ADS)

Basafa, Ehsan; Foroughi, Pezhman; Hossbach, Martin; Bhanushali, Jasmine; Stolka, Philipp

2017-03-01

With optical cameras, many interventional navigation tasks previously relying on EM, optical, or mechanical guidance can be performed robustly, quickly, and conveniently. We developed a family of novel guidance systems based on wide-spectrum cameras and vision algorithms for real-time tracking of interventional instruments and multi-modality markers. These navigation systems support the localization of anatomical targets, support placement of imaging probe and instruments, and provide fusion imaging. The unique architecture - low-cost, miniature, in-hand stereo vision cameras fitted directly to imaging probes - allows for an intuitive workflow that fits a wide variety of specialties such as anesthesiology, interventional radiology, interventional oncology, emergency medicine, urology, and others, many of which see increasing pressure to utilize medical imaging and especially ultrasound, but have yet to develop the requisite skills for reliable success. We developed a modular system, consisting of hardware (the Optical Head containing the mini cameras) and software (components for visual instrument tracking with or without specialized visual features, fully automated marker segmentation from a variety of 3D imaging modalities, visual observation of meshes of widely separated markers, instant automatic registration, and target tracking and guidance on real-time multi-modality fusion views). From these components, we implemented a family of distinct clinical and pre-clinical systems (for combinations of ultrasound, CT, CBCT, and MRI), most of which have international regulatory clearance for clinical use. We present technical and clinical results on phantoms, ex- and in-vivo animals, and patients.

A reductionist approach to extract robust molecular markers from microarray data series - Isolating markers to track osseointegration.

PubMed

Barik, Anwesha; Banerjee, Satarupa; Dhara, Santanu; Chakravorty, Nishant

2017-04-01

Complexities in the full genome expression studies hinder the extraction of tracker genes to analyze the course of biological events. In this study, we demonstrate the applications of supervised machine learning methods to reduce the irrelevance in microarray data series and thereby extract robust molecular markers to track biological processes. The methodology has been illustrated by analyzing whole genome expression studies on bone-implant integration (ossointegration). Being a biological process, osseointegration is known to leave a trail of genetic footprint during the course. In spite of existence of enormous amount of raw data in public repositories, researchers still do not have access to a panel of genes that can definitively track osseointegration. The results from our study revealed panels comprising of matrix metalloproteinases and collagen genes were able to track osseointegration on implant surfaces (MMP9 and COL1A2 on micro-textured; MMP12 and COL6A3 on superimposed nano-textured surfaces) with 100% classification accuracy, specificity and sensitivity. Further, our analysis showed the importance of the progression of the duration in establishment of the mechanical connection at bone-implant surface. The findings from this study are expected to be useful to researchers investigating osseointegration of novel implant materials especially at the early stage. The methodology demonstrated can be easily adapted by scientists in different fields to analyze large databases for other biological processes. Copyright © 2017 Elsevier Inc. All rights reserved.

Use of MV and kV imager correlation for maintaining continuous real-time 3D internal marker tracking during beam interruptions

NASA Astrophysics Data System (ADS)

Wiersma, R. D.; Riaz, N.; Dieterich, Sonja; Suh, Yelin; Xing, L.

2009-01-01

The integration of onboard kV imaging together with a MV electronic portal imaging device (EPID) on linear accelerators (LINAC) can provide an easy to implement real-time 3D organ position monitoring solution for treatment delivery. Currently, real-time MV-kV tracking has only been demonstrated by simultaneous imagining by both MV and kV imaging devices. However, modalities such as step-and-shoot IMRT (SS-IMRT), which inherently contain MV beam interruptions, can lead to loss of target information necessary for 3D localization. Additionally, continuous kV imaging throughout the treatment delivery can lead to high levels of imaging dose to the patient. This work demonstrates for the first time how full 3D target tracking can be maintained even in the presence of such beam interruption, or MV/kV beam interleave, by use of a relatively simple correlation model together with MV-kV tracking. A moving correlation model was constructed using both present and prior positions of the marker in the available MV or kV image to compute the position of the marker on the interrupted imager. A commercially available radiotherapy system, equipped with both MV and kV imaging devices, was used to deliver typical SS-IMRT lung treatment plans to a 4D phantom containing internally embedded metallic markers. To simulate actual lung tumor motion, previous recorded 4D lung patient motion data were used. Lung tumor motion data of five separate patients were inputted into the 4D phantom, and typical SS-IMRT lung plans were delivered to simulate actual clinical deliveries. Application of the correlation model to SS-IMRT lung treatment deliveries was found to be an effective solution for maintaining continuous 3D tracking during 'step' beam interruptions. For deliveries involving five or more gantry angles with 50 or more fields per plan, the positional errors were found to have <=1 mm root mean squared error (RMSE) in all three spatial directions. In addition to increasing the robustness of MV-kV tracking against beam interruption, it was also found that use of correlation can be an effective way of lowering kV dose to the patient and for increasing kV image quality by reduction of MV scatter interference.

Molecular Investigations of Bacteroides as Microbial Source Tracking Tools in Southeast Louisiana Watersheds

NASA Astrophysics Data System (ADS)

Schulz, C. J.; Childers, G. W.; Engel, A. S.

2006-12-01

Microbial Source Tracking (MST) is a developing field that is gaining increased attention. MST refers to a host of techniques that discriminates among the origins of fecal material found in natural waters from different sources (e.g. human, livestock, and wildlife) by using microbial indicator species with specificity to only certain host organisms. The development of species-specific molecular markers would allow for better evaluation of public health risks and tracking of nutrient sources impacting a watershed. Although several MST methods have been reported with varying levels of success, few offer general applicability for natural waters due to spatial and temporal constraints associated with these methods. One group of molecular MST markers that show promise for broad environmental applications are molecular 16S rDNA probes for Bacteroides. This method is based on 16S rDNA detection directly from environmental samples without the need for a preliminary cultivation step. In this study we have expanded previous sampling efforts to compile a database of over 1000 partial 16S rRNA Bacteroides genes retrieved from the fecal material of 15 different host species (human, cat, dog, pig, kangaroo). To characterize survival of Bacteroides outside of the host, survival time of the Bacteroides marker was compared to that of E.coli under varying natural environmental conditions (temperature and salinity). Bacteroides displayed a survival curve with shouldering and tailing similar to that of E.coli, but log reduction times differed with treatment. In summary, MST marker stability was identified within host species and the overall Bacteroides community structure correlated to host diet, suggesting that detection of a Bacteroides community could confidently identify fecal contamination point sources. Natural water samples from southeast Louisiana were collected for MST including the Tangipahoa River watershed where the source of fecal contamination has been hotly debated. The Bacteroides tool repeatedly demonstrated the presence of cattle related Bacteroides markers and the absence of human markers.This study is now being expanded to include the entire Lake Pontchartrain Basin.

SU-G-BRA-12: Development of An Intra-Fractional Motion Tracking and Dose Reconstruction System for Adaptive Stereotactic Body Radiation Therapy in High-Risk Prostate Cancer

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

Rezaeian, N Hassan; Chi, Y; Tian, Z

Purpose: A clinical trial on stereotactic body radiation therapy (SBRT) for high-risk prostate cancer is undergoing at our institution. In addition to escalating dose to the prostate, we have increased dose to intra-prostatic lesions. Intra-fractional prostate motion deteriorates well planned radiation dose, especially for the small intra-prostatic lesions. To solve this problem, we have developed a motion tracking and 4D dose-reconstruction system to facilitate adaptive re-planning. Methods: Patients in the clinical trial were treated with VMAT using four arcs and 10 FFF beam. KV triggered x-ray projections were taken every 3 sec during delivery to acquire 2D projections of 3Dmore » anatomy at the direction orthogonal to the therapeutic beam. Each patient had three implanted prostate markers. Our developed system first determined 2D projection locations of these markers and then 3D prostate translation and rotation via 2D/3D registration of the markers. Using delivery log files, our GPU-based Monte Carlo tool (goMC) reconstructed dose corresponding to each triggered image. The calculated 4D dose distributions were further aggregated to yield the delivered dose. Results: We first tested each module in our system. MC dose engine were commissioned to our treatment planning system with dose difference of <0.5%. For motion tracking, 1789 kV projections from 7 patients were acquired. The 2D marker location error was <1 mm. For 3D motion tracking, root mean square (RMS) errors along LR, AP, and CC directions were 0.26mm, 0.36mm, and 0.01mm respectively in simulation studies and 1.99mm, 1.37mm, and 0.22mm in phantom studies. We also tested the entire system workflow. Our system was able to reconstruct delivered dose. Conclusion: We have developed a functional intra-fractional motion tracking and 4D dose re-construction system to support our clinical trial on adaptive high-risk prostate cancer SBRT. Comprehensive evaluations have shown the capability and accuracy of our system.« less

Real-time automatic registration in optical surgical navigation

NASA Astrophysics Data System (ADS)

Lin, Qinyong; Yang, Rongqian; Cai, Ken; Si, Xuan; Chen, Xiuwen; Wu, Xiaoming

2016-05-01

An image-guided surgical navigation system requires the improvement of the patient-to-image registration time to enhance the convenience of the registration procedure. A critical step in achieving this aim is performing a fully automatic patient-to-image registration. This study reports on a design of custom fiducial markers and the performance of a real-time automatic patient-to-image registration method using these markers on the basis of an optical tracking system for rigid anatomy. The custom fiducial markers are designed to be automatically localized in both patient and image spaces. An automatic localization method is performed by registering a point cloud sampled from the three dimensional (3D) pedestal model surface of a fiducial marker to each pedestal of fiducial markers searched in image space. A head phantom is constructed to estimate the performance of the real-time automatic registration method under four fiducial configurations. The head phantom experimental results demonstrate that the real-time automatic registration method is more convenient, rapid, and accurate than the manual method. The time required for each registration is approximately 0.1 s. The automatic localization method precisely localizes the fiducial markers in image space. The averaged target registration error for the four configurations is approximately 0.7 mm. The automatic registration performance is independent of the positions relative to the tracking system and the movement of the patient during the operation.

Mitochondrial Genome Sequencing and Development of Genetic Markers for the Detection of DNA of Invasive Bighead and Silver Carp (Hypophthalmichthys nobilis and H. molitrix) in Environmental Water Samples from the United States

PubMed Central

Farrington, Heather L.; Edwards, Christine E.; Guan, Xin; Carr, Matthew R.; Baerwaldt, Kelly; Lance, Richard F.

2015-01-01

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species. PMID:25706532

Mitochondrial genome sequencing and development of genetic markers for the detection of DNA of invasive bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) in environmental water samples from the United States.

PubMed

Farrington, Heather L; Edwards, Christine E; Guan, Xin; Carr, Matthew R; Baerwaldt, Kelly; Lance, Richard F

2015-01-01

Invasive Asian bighead and silver carp (Hypophthalmichthys nobilis and H. molitrix) pose a substantial threat to North American aquatic ecosystems. Recently, environmental DNA (eDNA), genetic material shed by organisms into their environment that can be detected by non-invasive sampling strategies and genetic assays, has gained recognition as a tool for tracking the invasion front of these species toward the Great Lakes. The goal of this study was to develop new species-specific conventional PCR (cPCR) and quantitative (qPCR) markers for detection of these species in North American surface waters. We first generated complete mitochondrial genome sequences from 33 bighead and 29 silver carp individuals collected throughout their introduced range. These sequences were aligned with those from other common and closely related fish species from the Illinois River watershed to identify and design new species-specific markers for the detection of bighead and silver carp DNA in environmental water samples. We then tested these genetic markers in the laboratory for species-specificity and sensitivity. Newly developed markers performed well in field trials, did not have any false positive detections, and many markers had much higher detection rates and sensitivity compared to the markers currently used in eDNA surveillance programs. We also explored the use of multiple genetic markers to determine whether it would improve detection rates, results of which showed that using multiple highly sensitive markers should maximize detection rates in environmental samples. The new markers developed in this study greatly expand the number of species-specific genetic markers available to track the invasion front of bighead and silver carp and will improve the resolution of these assays. Additionally, the use of the qPCR markers developed in this study may reduce sample processing time and cost of eDNA monitoring for these species.

Long-term monitoring of waterborne pathogens and microbial source tracking markers in paired agricultural watersheds under controlled and conventional tile drainage management.

PubMed

Wilkes, Graham; Brassard, Julie; Edge, Thomas A; Gannon, Victor; Gottschall, Natalie; Jokinen, Cassandra C; Jones, Tineke H; Khan, Izhar U H; Marti, Romain; Sunohara, Mark D; Topp, Edward; Lapen, David R

2014-06-01

Surface waters from paired agricultural watersheds under controlled tile drainage (CTD) and uncontrolled tile drainage (UCTD) were monitored over 7 years in order to determine if there was an effect of CTD (imposed during the growing season) on occurrences and loadings of bacterial and viral pathogens, coliphages, and microbial source tracking markers. There were significantly lower occurrences of human, ruminant, and livestock (ruminant plus pig) Bacteroidales markers in the CTD watershed in relation to the UCTD watershed. As for pathogens, there were significantly lower occurrences of Salmonella spp. and Arcobacter spp. in the CTD watershed. There were no instances where there were significantly higher quantitative loadings of any microbial target in the CTD watershed, except for F-specific DNA (F-DNA) and F-RNA coliphages, perhaps as a result of fecal inputs from a hobby farm independent of the drainage practice treatments. There was lower loading of the ruminant marker in the CTD watershed in relation to the UCTD system, and results were significant at the level P = 0.06. The odds of Salmonella spp. occurring increased when a ruminant marker was present relative to when the ruminant marker was absent, yet for Arcobacter spp., the odds of this pathogen occurring significantly decreased when a ruminant marker was present relative to when the ruminant marker was absent (but increased when a wildlife marker was present relative to when the wildlife marker was absent). Interestingly, the odds of norovirus GII (associated with human and swine) occurring in water increased significantly when a ruminant marker was present relative to when a ruminant marker was absent. Overall, this study suggests that fecal pollution from tile-drained fields to stream could be reduced by CTD utilization. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

SU-G-JeP1-08: Dual Modality Verification for Respiratory Gating Using New Real- Time Tumor Tracking Radiotherapy System

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

Shiinoki, T; Hanazawa, H; Shibuya, K

Purpose: The respirato ry gating system combined the TrueBeam and a new real-time tumor-tracking radiotherapy system (RTRT) was installed. The RTRT system consists of two x-ray tubes and color image intensifiers. Using fluoroscopic images, the fiducial marker which was implanted near the tumor was tracked and was used as the internal surrogate for respiratory gating. The purposes of this study was to develop the verification technique of the respiratory gating with the new RTRT using cine electronic portal image device images (EPIDs) of TrueBeam and log files of the RTRT. Methods: A patient who underwent respiratory gated SBRT of themore » lung using the RTRT were enrolled in this study. For a patient, the log files of three-dimensional coordinate of fiducial marker used as an internal surrogate were acquired using the RTRT. Simultaneously, the cine EPIDs were acquired during respiratory gated radiotherapy. The data acquisition was performed for one field at five sessions during the course of SBRT. The residual motion errors were calculated using the log files (E{sub log}). The fiducial marker used as an internal surrogate into the cine EPIDs was automatically extracted by in-house software based on the template-matching algorithm. The differences between the the marker positions of cine EPIDs and digitally reconstructed radiograph were calculated (E{sub EPID}). Results: Marker detection on EPID using in-house software was influenced by low image contrast. For one field during the course of SBRT, the respiratory gating using the RTRT showed the mean ± S.D. of 95{sup th} percentile E{sub EPID} were 1.3 ± 0.3 mm,1.1 ± 0.5 mm,and those of E{sub log} were 1.5 ± 0.2 mm, 1.1 ± 0.2 mm in LR and SI directions, respectively. Conclusion: We have developed the verification method of respiratory gating combined TrueBeam and new real-time tumor-tracking radiotherapy system using EPIDs and log files.« less

Performance of two quantitative PCR methods for microbial source tracking of human sewage and implications for microbial risk assessment in recreational waters

EPA Science Inventory

Before new, rapid quantitative PCR (qPCR) methods for recreational water quality assessment and microbial source tracking (MST) can be useful in a regulatory context, an understanding of the ability of the method to detect a DNA target (marker) when the contaminant soure has been...

105. View of tracking radome replacement project, progress photograph, official ...

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

105. View of tracking radome replacement project, progress photograph, official photograph BMEWS Project by unknown photographer, 11 August 1981, clear as negative no. A-18562. - Clear Air Force Station, Ballistic Missile Early Warning System Site II, One mile west of mile marker 293.5 on Parks Highway, 5 miles southwest of Anderson, Anderson, Denali Borough, AK

CCL3L1-CCR5 genotype improves the assessment of AIDS Risk in HIV-1-infected individuals.

PubMed

Kulkarni, Hemant; Agan, Brian K; Marconi, Vincent C; O'Connell, Robert J; Camargo, Jose F; He, Weijing; Delmar, Judith; Phelps, Kenneth R; Crawford, George; Clark, Robert A; Dolan, Matthew J; Ahuja, Sunil K

2008-09-08

Whether vexing clinical decision-making dilemmas can be partly addressed by recent advances in genomics is unclear. For example, when to initiate highly active antiretroviral therapy (HAART) during HIV-1 infection remains a clinical dilemma. This decision relies heavily on assessing AIDS risk based on the CD4+ T cell count and plasma viral load. However, the trajectories of these two laboratory markers are influenced, in part, by polymorphisms in CCR5, the major HIV coreceptor, and the gene copy number of CCL3L1, a potent CCR5 ligand and HIV-suppressive chemokine. Therefore, we determined whether accounting for both genetic and laboratory markers provided an improved means of assessing AIDS risk. In a prospective, single-site, ethnically-mixed cohort of 1,132 HIV-positive subjects, we determined the AIDS risk conveyed by the laboratory and genetic markers separately and in combination. Subjects were assigned to a low, moderate or high genetic risk group (GRG) based on variations in CCL3L1 and CCR5. The predictive value of the CCL3L1-CCR5 GRGs, as estimated by likelihood ratios, was equivalent to that of the laboratory markers. GRG status also predicted AIDS development when the laboratory markers conveyed a contrary risk. Additionally, in two separate and large groups of HIV+ subjects from a natural history cohort, the results from additive risk-scoring systems and classification and regression tree (CART) analysis revealed that the laboratory and CCL3L1-CCR5 genetic markers together provided more prognostic information than either marker alone. Furthermore, GRGs independently predicted the time interval from seroconversion to CD4+ cell count thresholds used to guide HAART initiation. The combination of the laboratory and genetic markers captures a broader spectrum of AIDS risk than either marker alone. By tracking a unique aspect of AIDS risk distinct from that captured by the laboratory parameters, CCL3L1-CCR5 genotypes may have utility in HIV clinical management. These findings illustrate how genomic information might be applied to achieve practical benefits of personalized medicine.

Tracking single particle rotation: Probing dynamics in four dimensions

DOE PAGES

Anthony, Stephen Michael; Yu, Yan

2015-04-29

Direct visualization and tracking of small particles at high spatial and temporal resolution provides a powerful approach to probing complex dynamics and interactions in chemical and biological processes. Analysis of the rotational dynamics of particles adds a new dimension of information that is otherwise impossible to obtain with conventional 3-D particle tracking. In this review, we survey recent advances in single-particle rotational tracking, with highlights on the rotational tracking of optically anisotropic Janus particles. Furthermore, strengths and weaknesses of the various particle tracking methods, and their applications are discussed.

Lateral charge transport from heavy-ion tracks in integrated circuit chips

NASA Technical Reports Server (NTRS)

Zoutendyk, J. A.; Schwartz, H. R.; Nevill, L. R.

1988-01-01

A 256K DRAM has been used to study the lateral transport of charge (electron-hole pairs) induced by direct ionization from heavy-ion tracks in an IC. The qualitative charge transport has been simulated using a two-dimensional numerical code in cylindrical coordinates. The experimental bit-map data clearly show the manifestation of lateral charge transport in the creation of adjacent multiple-bit errors from a single heavy-ion track. The heavy-ion data further demonstrate the occurrence of multiple-bit errors from single ion tracks with sufficient stopping power. The qualitative numerical simulation results suggest that electric-field-funnel-aided (drift) collection accounts for single error generated by an ion passing through a charge-collecting junction, while multiple errors from a single ion track are due to lateral diffusion of ion-generated charge.

Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. Part I. Numerical model-based optimization.

PubMed

Choi, Jang-Hwan; Fahrig, Rebecca; Keil, Andreas; Besier, Thor F; Pal, Saikat; McWalter, Emily J; Beaupré, Gary S; Maier, Andreas

2013-09-01

Human subjects in standing positions are apt to show much more involuntary motion than in supine positions. The authors aimed to simulate a complicated realistic lower body movement using the four-dimensional (4D) digital extended cardiac-torso (XCAT) phantom. The authors also investigated fiducial marker-based motion compensation methods in two-dimensional (2D) and three-dimensional (3D) space. The level of involuntary movement-induced artifacts and image quality improvement were investigated after applying each method. An optical tracking system with eight cameras and seven retroreflective markers enabled us to track involuntary motion of the lower body of nine healthy subjects holding a squat position at 60° of flexion. The XCAT-based knee model was developed using the 4D XCAT phantom and the optical tracking data acquired at 120 Hz. The authors divided the lower body in the XCAT into six parts and applied unique affine transforms to each so that the motion (6 degrees of freedom) could be synchronized with the optical markers' location at each time frame. The control points of the XCAT were tessellated into triangles and 248 projection images were created based on intersections of each ray and monochromatic absorption. The tracking data sets with the largest motion (Subject 2) and the smallest motion (Subject 5) among the nine data sets were used to animate the XCAT knee model. The authors defined eight skin control points well distributed around the knees as pseudo-fiducial markers which functioned as a reference in motion correction. Motion compensation was done in the following ways: (1) simple projection shifting in 2D, (2) deformable projection warping in 2D, and (3) rigid body warping in 3D. Graphics hardware accelerated filtered backprojection was implemented and combined with the three correction methods in order to speed up the simulation process. Correction fidelity was evaluated as a function of number of markers used (4-12) and marker distribution in three scenarios. Average optical-based translational motion for the nine subjects was 2.14 mm (± 0.69 mm) and 2.29 mm (± 0.63 mm) for the right and left knee, respectively. In the representative central slices of Subject 2, the authors observed 20.30%, 18.30%, and 22.02% improvements in the structural similarity (SSIM) index with 2D shifting, 2D warping, and 3D warping, respectively. The performance of 2D warping improved as the number of markers increased up to 12 while 2D shifting and 3D warping were insensitive to the number of markers used. The minimum required number of markers for 2D shifting, 2D warping, and 3D warping was 4-6, 12, and 8, respectively. An even distribution of markers over the entire field of view provided robust performance for all three correction methods. The authors were able to simulate subject-specific realistic knee movement in weight-bearing positions. This study indicates that involuntary motion can seriously degrade the image quality. The proposed three methods were evaluated with the numerical knee model; 3D warping was shown to outperform the 2D methods. The methods are shown to significantly reduce motion artifacts if an appropriate marker setup is chosen.

Collecting Kinematic Data on a Ski Track with Optoelectronic Stereophotogrammetry: A Methodological Study Assessing the Feasibility of Bringing the Biomechanics Lab to the Field

PubMed Central

Müller, Erich

2016-01-01

In the laboratory, optoelectronic stereophotogrammetry is one of the most commonly used motion capture systems; particularly, when position- or orientation-related analyses of human movements are intended. However, for many applied research questions, field experiments are indispensable, and it is not a priori clear whether optoelectronic stereophotogrammetric systems can be expected to perform similarly to in-lab experiments. This study aimed to assess the instrumental errors of kinematic data collected on a ski track using optoelectronic stereophotogrammetry, and to investigate the magnitudes of additional skiing-specific errors and soft tissue/suit artifacts. During a field experiment, the kinematic data of different static and dynamic tasks were captured by the use of 24 infrared-cameras. The distances between three passive markers attached to a rigid bar were stereophotogrammetrically reconstructed and, subsequently, were compared to the manufacturer-specified exact values. While at rest or skiing at low speed, the optoelectronic stereophotogrammetric system’s accuracy and precision for determining inter-marker distances were found to be comparable to those known for in-lab experiments (< 1 mm). However, when measuring a skier’s kinematics under “typical” skiing conditions (i.e., high speeds, inclined/angulated postures and moderate snow spraying), additional errors were found to occur for distances between equipment-fixed markers (total measurement errors: 2.3 ± 2.2 mm). Moreover, for distances between skin-fixed markers, such as the anterior hip markers, additional artifacts were observed (total measurement errors: 8.3 ± 7.1 mm). In summary, these values can be considered sufficient for the detection of meaningful position- or orientation-related differences in alpine skiing. However, it must be emphasized that the use of optoelectronic stereophotogrammetry on a ski track is seriously constrained by limited practical usability, small-sized capture volumes and the occurrence of extensive snow spraying (which results in marker obscuration). The latter limitation possibly might be overcome by the use of more sophisticated cluster-based marker sets. PMID:27560498

Human and Animal Fecal Contamination of Community Water Sources, Stored Drinking Water and Hands in Rural India Measured with Validated Microbial Source Tracking Assays

PubMed Central

Schriewer, Alexander; Odagiri, Mitsunori; Wuertz, Stefan; Misra, Pravas R.; Panigrahi, Pinaki; Clasen, Thomas; Jenkins, Marion W.

2015-01-01

We examined pathways of exposure to fecal contamination of human and animal origin in 24 villages in Odisha, India. In a cross-sectional study during the monsoon season, fecal exposure via community water sources (N = 123) and in the home (N = 137) was assessed using human- and nonhuman-associated Bacteroidales microbial source tracking (MST) markers and fecal coliforms (FCs). Detection rates and marker concentrations were examined to pinpoint pathways of human fecal exposure in the public and domestic domains of disease transmission in study communities. Human fecal markers were detected much more frequently in the domestic domain (45% of households) than in public domain sources (8% of ponds; 4% of groundwater drinking sources). Animal fecal markers were widely detected in both domains (74% of ponds, 96% of households, 10% of groundwater drinking sources), indicating ubiquitous risks of exposure to animal feces and zoonotic pathogens. This study confirms an often suggested contamination link from hands to stored water in the home in developing countries separately for mothers' and children's hands and both human and animal fecal contamination. In contrast to MST markers, FCs provided a poor metric to assess risks of exposure to fecal contamination of human origin in this rural setting. PMID:26149868

An efficient fluorescent single-particle position tracking system for long-term pulsed measurements of nitrogen-vacancy centers in diamond

NASA Astrophysics Data System (ADS)

Kim, Kiho; Yun, Jiwon; Lee, Donghyuck; Kim, Dohun

2018-02-01

A simple and convenient design enables real-time three-dimensional position tracking of nitrogen-vacancy (NV) centers in diamond. The system consists entirely of commercially available components (a single-photon counter, a high-speed digital-to-analog converter, a phase-sensitive detector-based feedback device, and a piezo stage), eliminating the need for custom programming or rigorous optimization processes. With a large input range of counters and trackers combined with high sensitivity of single-photon counting, high-speed position tracking (upper bound recovery time of 0.9 s upon 250 nm of step-like positional shift) not only of bright ensembles, but also of low-photon-collection-efficiency single to few NV centers (down to 103 s-1) is possible. The tracking requires position modulation of only 10 nm, which allows simultaneous position tracking and pulsed measurements in the long term. Therefore, this tracking system enables measuring a single-spin magnetic resonance and Rabi oscillations at a very high resolution even without photon collection optimization. The system is widely applicable to various fields related to NV center quantum manipulation research such as NV optical trapping, NV tracking in fluid dynamics, and biological sensing using NV centers inside a biological cell.

A Protocol for Real-time 3D Single Particle Tracking.

PubMed

Hou, Shangguo; Welsher, Kevin

2018-01-03

Real-time three-dimensional single particle tracking (RT-3D-SPT) has the potential to shed light on fast, 3D processes in cellular systems. Although various RT-3D-SPT methods have been put forward in recent years, tracking high speed 3D diffusing particles at low photon count rates remains a challenge. Moreover, RT-3D-SPT setups are generally complex and difficult to implement, limiting their widespread application to biological problems. This protocol presents a RT-3D-SPT system named 3D Dynamic Photon Localization Tracking (3D-DyPLoT), which can track particles with high diffusive speed (up to 20 µm 2 /s) at low photon count rates (down to 10 kHz). 3D-DyPLoT employs a 2D electro-optic deflector (2D-EOD) and a tunable acoustic gradient (TAG) lens to drive a single focused laser spot dynamically in 3D. Combined with an optimized position estimation algorithm, 3D-DyPLoT can lock onto single particles with high tracking speed and high localization precision. Owing to the single excitation and single detection path layout, 3D-DyPLoT is robust and easy to set up. This protocol discusses how to build 3D-DyPLoT step by step. First, the optical layout is described. Next, the system is calibrated and optimized by raster scanning a 190 nm fluorescent bead with the piezoelectric nanopositioner. Finally, to demonstrate real-time 3D tracking ability, 110 nm fluorescent beads are tracked in water.

Photostable bipolar fluorescent probe for video tracking plasma membranes related cellular processes.

PubMed

Zhang, Xinfu; Wang, Chao; Jin, Liji; Han, Zhuo; Xiao, Yi

2014-08-13

Plasma membranes can sense the stimulations and transmit the signals from extracellular environment and then make further responses through changes in locations, shapes or morphologies. Common fluorescent membrane markers are not well suited for long time tracking due to their shorter retention time inside plasma membranes and/or their lower photostability. To this end, we develop a new bipolar marker, Mem-SQAC, which can stably insert into plasma membranes of different cells and exhibits a long retention time over 30 min. Mem-SQAC also inherits excellent photostability from the BODIPY dye family. Large two-photon absorption cross sections and long wavelength fluorescence emissions further enhance the competitiveness of Mem-SQAC as a membrane marker. By using Mem-SQAC, significant morphological changes of plasma membranes have been monitored during heavy metal poisoning and drug induced apoptosis of MCF-7 cells; the change tendencies are so distinctly different from each other that they can be used as indicators to distinguish different cell injuries. Further on, the complete processes of endocytosis toward Staphylococcus aureus and Escherichia coli by RAW 264.7 cells have been dynamically tracked. It is discovered that plasma membranes take quite different actions in response to the two bacteria, information unavailable in previous research reports.

Technical Note: A respiratory monitoring and processing system based on computer vision: prototype and proof of principle

PubMed Central

Atallah, Vincent; Escarmant, Patrick; Vinh‐Hung, Vincent

2016-01-01

Monitoring and controlling respiratory motion is a challenge for the accuracy and safety of therapeutic irradiation of thoracic tumors. Various commercial systems based on the monitoring of internal or external surrogates have been developed but remain costly. In this article we describe and validate Madibreast, an in‐house‐made respiratory monitoring and processing device based on optical tracking of external markers. We designed an optical apparatus to ensure real‐time submillimetric image resolution at 4 m. Using OpenCv libraries, we optically tracked high‐contrast markers set on patients' breasts. Validation of spatial and time accuracy was performed on a mechanical phantom and on human breast. Madibreast was able to track motion of markers up to a 5 cm/s speed, at a frame rate of 30 fps, with submillimetric accuracy on mechanical phantom and human breasts. Latency was below 100 ms. Concomitant monitoring of three different locations on the breast showed discrepancies in axial motion up to 4 mm for deep‐breathing patterns. This low‐cost, computer‐vision system for real‐time motion monitoring of the irradiation of breast cancer patients showed submillimetric accuracy and acceptable latency. It allowed the authors to highlight differences in surface motion that may be correlated to tumor motion. PACS number(s): 87.55.km PMID:27685116

Technical Note: A respiratory monitoring and processing system based on computer vision: prototype and proof of principle.

PubMed

Leduc, Nicolas; Atallah, Vincent; Escarmant, Patrick; Vinh-Hung, Vincent

2016-09-08

Monitoring and controlling respiratory motion is a challenge for the accuracy and safety of therapeutic irradiation of thoracic tumors. Various commercial systems based on the monitoring of internal or external surrogates have been developed but remain costly. In this article we describe and validate Madibreast, an in-house-made respiratory monitoring and processing device based on optical tracking of external markers. We designed an optical apparatus to ensure real-time submillimetric image resolution at 4 m. Using OpenCv libraries, we optically tracked high-contrast markers set on patients' breasts. Validation of spatial and time accuracy was performed on a mechanical phantom and on human breast. Madibreast was able to track motion of markers up to a 5 cm/s speed, at a frame rate of 30 fps, with submillimetric accuracy on mechanical phantom and human breasts. Latency was below 100 ms. Concomitant monitoring of three different locations on the breast showed discrepancies in axial motion up to 4 mm for deep-breathing patterns. This low-cost, computer-vision system for real-time motion monitoring of the irradiation of breast cancer patients showed submillimetric accuracy and acceptable latency. It allowed the authors to highlight differences in surface motion that may be correlated to tumor motion.v. © 2016 The Authors.

Dynamic Projection Mapping onto Deforming Non-Rigid Surface Using Deformable Dot Cluster Marker.

PubMed

Narita, Gaku; Watanabe, Yoshihiro; Ishikawa, Masatoshi

2017-03-01

Dynamic projection mapping for moving objects has attracted much attention in recent years. However, conventional approaches have faced some issues, such as the target objects being limited to rigid objects, and the limited moving speed of the targets. In this paper, we focus on dynamic projection mapping onto rapidly deforming non-rigid surfaces with a speed sufficiently high that a human does not perceive any misalignment between the target object and the projected images. In order to achieve such projection mapping, we need a high-speed technique for tracking non-rigid surfaces, which is still a challenging problem in the field of computer vision. We propose the Deformable Dot Cluster Marker (DDCM), a novel fiducial marker for high-speed tracking of non-rigid surfaces using a high-frame-rate camera. The DDCM has three performance advantages. First, it can be detected even when it is strongly deformed. Second, it realizes robust tracking even in the presence of external and self occlusions. Third, it allows millisecond-order computational speed. Using DDCM and a high-speed projector, we realized dynamic projection mapping onto a deformed sheet of paper and a T-shirt with a speed sufficiently high that the projected images appeared to be printed on the objects.

Using commodity accelerometers and gyroscopes to improve speed and accuracy of JanusVF

NASA Astrophysics Data System (ADS)

Hutson, Malcolm; Reiners, Dirk

2010-01-01

Several critical limitations exist in the currently available commercial tracking technologies for fully-enclosed virtual reality (VR) systems. While several 6DOF solutions can be adapted to work in fully-enclosed spaces, they still include elements of hardware that can interfere with the user's visual experience. JanusVF introduced a tracking solution for fully-enclosed VR displays that achieves comparable performance to available commercial solutions but without artifacts that can obscure the user's view. JanusVF employs a small, high-resolution camera that is worn on the user's head, but faces backwards. The VR rendering software draws specific fiducial markers with known size and absolute position inside the VR scene behind the user but in view of the camera. These fiducials are tracked by ARToolkitPlus and integrated by a single-constraint-at-a-time (SCAAT) filter to update the head pose. In this paper we investigate the addition of low-cost accelerometers and gyroscopes such as those in Nintendo Wii remotes, the Wii Motion Plus, and the Sony Sixaxis controller to improve the precision and accuracy of JanusVF. Several enthusiast projects have implemented these units as basic trackers or for gesture recognition, but none so far have created true 6DOF trackers using only the accelerometers and gyroscopes. Our original experiments were repeated after adding the low-cost inertial sensors, showing considerable improvements and noise reduction.

Visualization of complex DNA damage along accelerated ions tracks

NASA Astrophysics Data System (ADS)

Kulikova, Elena; Boreyko, Alla; Bulanova, Tatiana; Ježková, Lucie; Zadneprianetc, Mariia; Smirnova, Elena

2018-04-01

The most deleterious DNA lesions induced by ionizing radiation are clustered DNA double-strand breaks (DSB). Clustered or complex DNA damage is a combination of a few simple lesions (single-strand breaks, base damage etc.) within one or two DNA helix turns. It is known that yield of complex DNA lesions increases with increasing linear energy transfer (LET) of radiation. For investigation of the induction and repair of complex DNA lesions, human fibroblasts were irradiated with high-LET 15N ions (LET = 183.3 keV/μm, E = 13MeV/n) and low-LET 60Co γ-rays (LET ≈ 0.3 keV/μm) radiation. DNA DSBs (γH2AX and 53BP1) and base damage (OGG1) markers were visualized by immunofluorecence staining and high-resolution microscopy. The obtained results showed slower repair kinetics of induced DSBs in cells irradiated with accelerated ions compared to 60Co γ-rays, indicating induction of more complex DNA damage. Confirming previous assumptions, detailed 3D analysis of γH2AX/53BP1 foci in 15N ions tracks revealed more complicated structure of the foci in contrast to γ-rays. It was shown that proteins 53BP1 and OGG1 involved in repair of DNA DSBs and modified bases, respectively, were colocalized in tracks of 15N ions and thus represented clustered DNA DSBs.

A novel approach to tracking antigen-experienced CD4 T cells into functional compartments via tandem deep and shallow TCR clonotyping.

PubMed

Estorninho, Megan; Gibson, Vivienne B; Kronenberg-Versteeg, Deborah; Liu, Yuk-Fun; Ni, Chester; Cerosaletti, Karen; Peakman, Mark

2013-12-01

Extensive diversity in the human repertoire of TCRs for Ag is both a cornerstone of effective adaptive immunity that enables host protection against a multiplicity of pathogens and a weakness that gives rise to potential pathological self-reactivity. The complexity arising from diversity makes detection and tracking of single Ag-specific CD4 T cells (ASTs) involved in these immune responses challenging. We report a tandem, multistep process to quantify rare TCRβ-chain variable sequences of ASTs in large polyclonal populations. The approach combines deep high-throughput sequencing (HTS) within functional CD4 T cell compartments, such as naive/memory cells, with shallow, multiple identifier-based HTS of ASTs identified by activation marker upregulation after short-term Ag stimulation in vitro. We find that clonotypes recognizing HLA class II-restricted epitopes of both pathogen-derived Ags and self-Ags are oligoclonal and typically private. Clonotype tracking within an individual reveals private AST clonotypes resident in the memory population, as would be expected, representing clonal expansions (identical nucleotide sequence; "ultraprivate"). Other AST clonotypes share CDR3β amino acid sequences through convergent recombination and are found in memory populations of multiple individuals. Tandem HTS-based clonotyping will facilitate studying AST dynamics, epitope spreading, and repertoire changes that arise postvaccination and following Ag-specific immunotherapies for cancer and autoimmune disease.

Survey of Motion Tracking Methods Based on Inertial Sensors: A Focus on Upper Limb Human Motion

PubMed Central

Filippeschi, Alessandro; Schmitz, Norbert; Miezal, Markus; Bleser, Gabriele; Ruffaldi, Emanuele; Stricker, Didier

2017-01-01

Motion tracking based on commercial inertial measurements units (IMUs) has been widely studied in the latter years as it is a cost-effective enabling technology for those applications in which motion tracking based on optical technologies is unsuitable. This measurement method has a high impact in human performance assessment and human-robot interaction. IMU motion tracking systems are indeed self-contained and wearable, allowing for long-lasting tracking of the user motion in situated environments. After a survey on IMU-based human tracking, five techniques for motion reconstruction were selected and compared to reconstruct a human arm motion. IMU based estimation was matched against motion tracking based on the Vicon marker-based motion tracking system considered as ground truth. Results show that all but one of the selected models perform similarly (about 35 mm average position estimation error). PMID:28587178

Simple quality assurance method of dynamic tumor tracking with the gimbaled linac system using a light field.

PubMed

Miura, Hideharu; Ozawa, Shuichi; Hayata, Masahiro; Tsuda, Shintaro; Yamada, Kiyoshi; Nagata, Yasushi

2016-09-08

We proposed a simple visual method for evaluating the dynamic tumor tracking (DTT) accuracy of a gimbal mechanism using a light field. A single photon beam was set with a field size of 30 × 30 mm2 at a gantry angle of 90°. The center of a cube phantom was set up at the isocenter of a motion table, and 4D modeling was performed based on the tumor and infrared (IR) marker motion. After 4D modeling, the cube phantom was replaced with a sheet of paper, which was placed perpen-dicularly, and a light field was projected on the sheet of paper. The light field was recorded using a web camera in a treatment room that was as dark as possible. Calculated images from each image obtained using the camera were summed to compose a total summation image. Sinusoidal motion sequences were produced by moving the phantom with a fixed amplitude of 20 mm and different breathing periods of 2, 4, 6, and 8 s. The light field was projected on the sheet of paper under three conditions: with the moving phantom and DTT based on the motion of the phantom, with the moving phantom and non-DTT, and with a stationary phantom for comparison. The values of tracking errors using the light field were 1.12 ± 0.72, 0.31 ± 0.19, 0.27 ± 0.12, and 0.15 ± 0.09 mm for breathing periods of 2, 4, 6, and 8s, respectively. The tracking accuracy showed dependence on the breath-ing period. We proposed a simple quality assurance (QA) process for the tracking accuracy of a gimbal mechanism system using a light field and web camera. Our method can assess the tracking accuracy using a light field without irradiation and clearly visualize distributions like film dosimetry. © 2016 The Authors.

77 FR 25781 - Environmental Impact Statement; Washington, DC

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-01

... do not meet the needs of modern freight rail infrastructure due to its single track arrangement and the inability to accommodate double-stack intermodal container freight trains. The single-track... network that encompasses about 21,000 route miles of track in 23 states, the District of Columbia and the...

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map.

PubMed

N'Diaye, Amidou; Haile, Jemanesh K; Cory, Aron T; Clarke, Fran R; Clarke, John M; Knox, Ron E; Pozniak, Curtis J

2017-01-01

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.

Video capture virtual reality as a flexible and effective rehabilitation tool

PubMed Central

Weiss, Patrice L; Rand, Debbie; Katz, Noomi; Kizony, Rachel

2004-01-01

Video capture virtual reality (VR) uses a video camera and software to track movement in a single plane without the need to place markers on specific bodily locations. The user's image is thereby embedded within a simulated environment such that it is possible to interact with animated graphics in a completely natural manner. Although this technology first became available more than 25 years ago, it is only within the past five years that it has been applied in rehabilitation. The objective of this article is to describe the way this technology works, to review its assets relative to other VR platforms, and to provide an overview of some of the major studies that have evaluated the use of video capture technologies for rehabilitation. PMID:15679949

Sub-pixel localisation of passive micro-coil fiducial markers in interventional MRI.

PubMed

Rea, Marc; McRobbie, Donald; Elhawary, Haytham; Tse, Zion T H; Lamperth, Michael; Young, Ian

2009-04-01

Electromechanical devices enable increased accuracy in surgical procedures, and the recent development of MRI-compatible mechatronics permits the use of MRI for real-time image guidance. Integrated imaging of resonant micro-coil fiducials provides an accurate method of tracking devices in a scanner with increased flexibility compared to gradient tracking. Here we report on the ability of ten different image-processing algorithms to track micro-coil fiducials with sub-pixel accuracy. Five algorithms: maximum pixel, barycentric weighting, linear interpolation, quadratic fitting and Gaussian fitting were applied both directly to the pixel intensity matrix and to the cross-correlation matrix obtained by 2D convolution with a reference image. Using images of a 3 mm fiducial marker and a pixel size of 1.1 mm, intensity linear interpolation, which calculates the position of the fiducial centre by interpolating the pixel data to find the fiducial edges, was found to give the best performance for minimal computing power; a maximum error of 0.22 mm was observed in fiducial localisation for displacements up to 40 mm. The inherent standard deviation of fiducial localisation was 0.04 mm. This work enables greater accuracy to be achieved in passive fiducial tracking.

A new method for motion capture of the scapula using an optoelectronic tracking device: a feasibility study.

PubMed

Šenk, Miroslav; Chèze, Laurence

2010-06-01

Optoelectronic tracking systems are rarely used in 3D studies examining shoulder movements including the scapula. Among the reasons is the important slippage of skin markers with respect to scapula. Methods using electromagnetic tracking devices are validated and frequently applied. Thus, the aim of this study was to develop a new method for in vivo optoelectronic scapular capture dealing with the accepted accuracy issues of validated methods. Eleven arm positions in three anatomical planes were examined using five subjects in static mode. The method was based on local optimisation, and recalculation procedures were made using a set of five scapular surface markers. The scapular rotations derived from the recalculation-based method yielded RMS errors comparable with the frequently used electromagnetic scapular methods (RMS up to 12.6° for 150° arm elevation). The results indicate that the present method can be used under careful considerations for 3D kinematical studies examining different shoulder movements.

Automated tilt series alignment and tomographic reconstruction in IMOD.

PubMed

Mastronarde, David N; Held, Susannah R

2017-02-01

Automated tomographic reconstruction is now possible in the IMOD software package, including the merging of tomograms taken around two orthogonal axes. Several developments enable the production of high-quality tomograms. When using fiducial markers for alignment, the markers to be tracked through the series are chosen automatically; if there is an excess of markers available, a well-distributed subset is selected that is most likely to track well. Marker positions are refined by applying an edge-enhancing Sobel filter, which results in a 20% improvement in alignment error for plastic-embedded samples and 10% for frozen-hydrated samples. Robust fitting, in which outlying points are given less or no weight in computing the fitting error, is used to obtain an alignment solution, so that aberrant points from the automated tracking can have little effect on the alignment. When merging two dual-axis tomograms, the alignment between them is refined from correlations between local patches; a measure of structure was developed so that patches with insufficient structure to give accurate correlations can now be excluded automatically. We have also developed a script for running all steps in the reconstruction process with a flexible mechanism for setting parameters, and we have added a user interface for batch processing of tilt series to the Etomo program in IMOD. Batch processing is fully compatible with interactive processing and can increase efficiency even when the automation is not fully successful, because users can focus their effort on the steps that require manual intervention. Copyright © 2016 Elsevier Inc. All rights reserved.

PhotoGate microscopy: tracking single molecules in a cytoplasm (Conference Presentation)

NASA Astrophysics Data System (ADS)

Yildiz, Ahmet

2016-02-01

Tracking single molecules inside cells reveals the dynamics of biological processes, including receptor trafficking, signaling and cargo transport. However, individual molecules often cannot be resolved inside cells due to their high density in the cellular environment. We developed a photobleaching gate assay, which controls the number of fluorescent particles in a region of interest by repeatedly photobleaching its boundary. Using this method, we tracked single particles at surface densities two orders of magnitude higher than the single-molecule detection limit. We observed ligand-induced dimerization of epidermal growth factor receptors (EGFR) on a live cell membrane. In addition, we tracked individual intraflagellar transport (IFT) trains along the length of a cilium and observed their remodeling at the ciliary tip.

Fiducial marker-based correction for involuntary motion in weight-bearing C-arm CT scanning of knees. Part I. Numerical model-based optimization

PubMed Central

Choi, Jang-Hwan; Fahrig, Rebecca; Keil, Andreas; Besier, Thor F.; Pal, Saikat; McWalter, Emily J.; Beaupré, Gary S.; Maier, Andreas

2013-01-01

Purpose: Human subjects in standing positions are apt to show much more involuntary motion than in supine positions. The authors aimed to simulate a complicated realistic lower body movement using the four-dimensional (4D) digital extended cardiac-torso (XCAT) phantom. The authors also investigated fiducial marker-based motion compensation methods in two-dimensional (2D) and three-dimensional (3D) space. The level of involuntary movement-induced artifacts and image quality improvement were investigated after applying each method. Methods: An optical tracking system with eight cameras and seven retroreflective markers enabled us to track involuntary motion of the lower body of nine healthy subjects holding a squat position at 60° of flexion. The XCAT-based knee model was developed using the 4D XCAT phantom and the optical tracking data acquired at 120 Hz. The authors divided the lower body in the XCAT into six parts and applied unique affine transforms to each so that the motion (6 degrees of freedom) could be synchronized with the optical markers’ location at each time frame. The control points of the XCAT were tessellated into triangles and 248 projection images were created based on intersections of each ray and monochromatic absorption. The tracking data sets with the largest motion (Subject 2) and the smallest motion (Subject 5) among the nine data sets were used to animate the XCAT knee model. The authors defined eight skin control points well distributed around the knees as pseudo-fiducial markers which functioned as a reference in motion correction. Motion compensation was done in the following ways: (1) simple projection shifting in 2D, (2) deformable projection warping in 2D, and (3) rigid body warping in 3D. Graphics hardware accelerated filtered backprojection was implemented and combined with the three correction methods in order to speed up the simulation process. Correction fidelity was evaluated as a function of number of markers used (4–12) and marker distribution in three scenarios. Results: Average optical-based translational motion for the nine subjects was 2.14 mm (±0.69 mm) and 2.29 mm (±0.63 mm) for the right and left knee, respectively. In the representative central slices of Subject 2, the authors observed 20.30%, 18.30%, and 22.02% improvements in the structural similarity (SSIM) index with 2D shifting, 2D warping, and 3D warping, respectively. The performance of 2D warping improved as the number of markers increased up to 12 while 2D shifting and 3D warping were insensitive to the number of markers used. The minimum required number of markers for 2D shifting, 2D warping, and 3D warping was 4–6, 12, and 8, respectively. An even distribution of markers over the entire field of view provided robust performance for all three correction methods. Conclusions: The authors were able to simulate subject-specific realistic knee movement in weight-bearing positions. This study indicates that involuntary motion can seriously degrade the image quality. The proposed three methods were evaluated with the numerical knee model; 3D warping was shown to outperform the 2D methods. The methods are shown to significantly reduce motion artifacts if an appropriate marker setup is chosen. PMID:24007156

Results From a Microbial Source-Tracking Study at Villa Angela Beach, Cleveland, Ohio, 2007

USGS Publications Warehouse

Bushon, Rebecca N.; Stelzer, Erin A.; Stoeckel, Donald M.

2009-01-01

During the 2007 recreational season at Villa Angela Beach in Cleveland, Ohio, scientists with the U.S. Geological Survey (USGS) and the Northeast Ohio Regional Sewer District (NEORSD) found high Escherichia coli (E. coli) concentrations that were not easily explained by results obtained to date in ongoing investigations of recreational water quality at the beach. To help understand the sources behind these elevated E. coli concentrations, the USGS and NEORSD sampled beach-area water for Bacteroides DNA markers. Bacteroides are a group of enteric bacteria that are being used in microbial source tracking, in hope that host-associated DNA markers could be used to indicate potential sources of E. coli in the Villa Angela environment. The USGS Ohio Water Microbiology Laboratory analyzed a total of 13 source samples (sewage and waterfowl feces) and 33 beach-area water and sand samples for three Bacteroides DNA markers. This report lists the results of those analyses, along with environmental conditions at Villa Angela on the dates that samples were collected.

Characterizing relationships among fecal indicator bacteria, microbial source tracking markers, and associated waterborne pathogen occurrence in stream water and sediments in a mixed land use watershed

USDA-ARS?s Scientific Manuscript database

Bed sediments of streams and rivers may store high concentrations of fecal indicator bacteria (FIB) and pathogens. These contaminants can be mobilized into the water column due to resuspension events, thus affecting overall water quality. Along with the contaminants, other markers such as microbia...

Probability density function of a puff dispersing from the wall of a turbulent channel

NASA Astrophysics Data System (ADS)

Nguyen, Quoc; Papavassiliou, Dimitrios

2015-11-01

Study of dispersion of passive contaminants in turbulence has proved to be helpful in understanding fundamental heat and mass transfer phenomena. Many simulation and experimental works have been carried out to locate and track motions of scalar markers in a flow. One method is to combine Direct Numerical Simulation (DNS) and Lagrangian Scalar Tracking (LST) to record locations of markers. While this has proved to be useful, high computational cost remains a concern. In this study, we develop a model that could reproduce results obtained by DNS and LST for turbulent flow. Puffs of markers with different Schmidt numbers were released into a flow field at a frictional Reynolds number of 150. The point of release was at the channel wall, so that both diffusion and convection contribute to the puff dispersion pattern, defining different stages of dispersion. Based on outputs from DNS and LST, we seek the most suitable and feasible probability density function (PDF) that represents distribution of markers in the flow field. The PDF would play a significant role in predicting heat and mass transfer in wall turbulence, and would prove to be helpful where DNS and LST are not always available.

Genomewide predictions from maize single-cross data.

PubMed

Massman, Jon M; Gordillo, Andres; Lorenzana, Robenzon E; Bernardo, Rex

2013-01-01

Maize (Zea mays L.) breeders evaluate many single-cross hybrids each year in multiple environments. Our objective was to determine the usefulness of genomewide predictions, based on marker effects from maize single-cross data, for identifying the best untested single crosses and the best inbreds within a biparental cross. We considered 479 experimental maize single crosses between 59 Iowa Stiff Stalk Synthetic (BSSS) inbreds and 44 non-BSSS inbreds. The single crosses were evaluated in multilocation experiments from 2001 to 2009 and the BSSS and non-BSSS inbreds had genotypic data for 669 single nucleotide polymorphism (SNP) markers. Single-cross performance was predicted by a previous best linear unbiased prediction (BLUP) approach that utilized marker-based relatedness and information on relatives, and from genomewide marker effects calculated by ridge-regression BLUP (RR-BLUP). With BLUP, the mean prediction accuracy (r(MG)) of single-cross performance was 0.87 for grain yield, 0.90 for grain moisture, 0.69 for stalk lodging, and 0.84 for root lodging. The BLUP and RR-BLUP models did not lead to r(MG) values that differed significantly. We then used the RR-BLUP model, developed from single-cross data, to predict the performance of testcrosses within 14 biparental populations. The r(MG) values within each testcross population were generally low and were often negative. These results were obtained despite the above-average level of linkage disequilibrium, i.e., r(2) between adjacent markers of 0.35 in the BSSS inbreds and 0.26 in the non-BSSS inbreds. Overall, our results suggested that genomewide marker effects estimated from maize single crosses are not advantageous (cofmpared with BLUP) for predicting single-cross performance and have erratic usefulness for predicting testcross performance within a biparental cross.

Stable isotope analyses of feather amino acids identify penguin migration strategies at ocean basin scales.

PubMed

Polito, Michael J; Hinke, Jefferson T; Hart, Tom; Santos, Mercedes; Houghton, Leah A; Thorrold, Simon R

2017-08-01

Identifying the at-sea distribution of wide-ranging marine predators is critical to understanding their ecology. Advances in electronic tracking devices and intrinsic biogeochemical markers have greatly improved our ability to track animal movements on ocean-wide scales. Here, we show that, in combination with direct tracking, stable carbon isotope analysis of essential amino acids in tail feathers provides the ability to track the movement patterns of two, wide-ranging penguin species over ocean basin scales. In addition, we use this isotopic approach across multiple breeding colonies in the Scotia Arc to evaluate migration trends at a regional scale that would be logistically challenging using direct tracking alone. © 2017 The Author(s).

Accuracy and precision of a custom camera-based system for 2D and 3D motion tracking during speech and nonspeech motor tasks

PubMed Central

Feng, Yongqiang; Max, Ludo

2014-01-01

Purpose Studying normal or disordered motor control requires accurate motion tracking of the effectors (e.g., orofacial structures). The cost of electromagnetic, optoelectronic, and ultrasound systems is prohibitive for many laboratories, and limits clinical applications. For external movements (lips, jaw), video-based systems may be a viable alternative, provided that they offer high temporal resolution and sub-millimeter accuracy. Method We examined the accuracy and precision of 2D and 3D data recorded with a system that combines consumer-grade digital cameras capturing 60, 120, or 240 frames per second (fps), retro-reflective markers, commercially-available computer software (APAS, Ariel Dynamics), and a custom calibration device. Results Overall mean error (RMSE) across tests was 0.15 mm for static tracking and 0.26 mm for dynamic tracking, with corresponding precision (SD) values of 0.11 and 0.19 mm, respectively. The effect of frame rate varied across conditions, but, generally, accuracy was reduced at 240 fps. The effect of marker size (3 vs. 6 mm diameter) was negligible at all frame rates for both 2D and 3D data. Conclusion Motion tracking with consumer-grade digital cameras and the APAS software can achieve sub-millimeter accuracy at frame rates that are appropriate for kinematic analyses of lip/jaw movements for both research and clinical purposes. PMID:24686484

Compatibility of pedigree-based and marker-based relationship matrices for single-step genetic evaluation.

PubMed

Christensen, Ole F

2012-12-03

Single-step methods provide a coherent and conceptually simple approach to incorporate genomic information into genetic evaluations. An issue with single-step methods is compatibility between the marker-based relationship matrix for genotyped animals and the pedigree-based relationship matrix. Therefore, it is necessary to adjust the marker-based relationship matrix to the pedigree-based relationship matrix. Moreover, with data from routine evaluations, this adjustment should in principle be based on both observed marker genotypes and observed phenotypes, but until now this has been overlooked. In this paper, I propose a new method to address this issue by 1) adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix instead of the reverse and 2) extending the single-step genetic evaluation using a joint likelihood of observed phenotypes and observed marker genotypes. The performance of this method is then evaluated using two simulated datasets. The method derived here is a single-step method in which the marker-based relationship matrix is constructed assuming all allele frequencies equal to 0.5 and the pedigree-based relationship matrix is constructed using the unusual assumption that animals in the base population are related and inbred with a relationship coefficient γ and an inbreeding coefficient γ / 2. Taken together, this γ parameter and a parameter that scales the marker-based relationship matrix can handle the issue of compatibility between marker-based and pedigree-based relationship matrices. The full log-likelihood function used for parameter inference contains two terms. The first term is the REML-log-likelihood for the phenotypes conditional on the observed marker genotypes, whereas the second term is the log-likelihood for the observed marker genotypes. Analyses of the two simulated datasets with this new method showed that 1) the parameters involved in adjusting marker-based and pedigree-based relationship matrices can depend on both observed phenotypes and observed marker genotypes and 2) a strong association between these two parameters exists. Finally, this method performed at least as well as a method based on adjusting the marker-based relationship matrix. Using the full log-likelihood and adjusting the pedigree-based relationship matrix to be compatible with the marker-based relationship matrix provides a new and interesting approach to handle the issue of compatibility between the two matrices in single-step genetic evaluation.

Maximization of Markers Linked in Coupling for Tetraploid Potatoes via Monoparental Haploids

PubMed Central

Bartkiewicz, Annette M.; Chilla, Friederike; Terefe-Ayana, Diro; Lübeck, Jens; Strahwald, Josef; Tacke, Eckhard; Hofferbert, Hans-Reinhard; Linde, Marcus; Debener, Thomas

2018-01-01

Haploid potato populations derived from a single tetraploid donor constitute an efficient strategy to analyze markers segregating from a single donor genotype. Analysis of marker segregation in populations derived from crosses between polysomic tetraploids is complicated by a maximum of eight segregating alleles, multiple dosages of the markers and problems related to linkage analysis of marker segregation in repulsion. Here, we present data on two monoparental haploid populations generated by prickle pollination of two tetraploid cultivars with Solanum phureja and genotyped with the 12.8 k SolCAP single nucleotide polymorphism (SNP) array. We show that in a population of monoparental haploids, the number of biallelic SNP markers segregating in linkage to loci from the tetraploid donor genotype is much larger than in putative crosses of this genotype to a diverse selection of 125 tetraploid cultivars. Although this strategy is more laborious than conventional breeding, the generation of haploid progeny for efficient marker analysis is straightforward if morphological markers and flow cytometry are utilized to select true haploid progeny. The level of introgressed fragments from S. phureja, the haploid inducer, is very low, supporting its suitability for genetic analysis. Mapping with single-dose markers allowed the analysis of quantitative trait loci (QTL) for four phenotypic traits. PMID:29868076

Tracking single mRNA molecules in live cells

NASA Astrophysics Data System (ADS)

Moon, Hyungseok C.; Lee, Byung Hun; Lim, Kiseong; Son, Jae Seok; Song, Minho S.; Park, Hye Yoon

2016-06-01

mRNAs inside cells interact with numerous RNA-binding proteins, microRNAs, and ribosomes that together compose a highly heterogeneous population of messenger ribonucleoprotein (mRNP) particles. Perhaps one of the best ways to investigate the complex regulation of mRNA is to observe individual molecules. Single molecule imaging allows the collection of quantitative and statistical data on subpopulations and transient states that are otherwise obscured by ensemble averaging. In addition, single particle tracking reveals the sequence of events that occur in the formation and remodeling of mRNPs in real time. Here, we review the current state-of-the-art techniques in tagging, delivery, and imaging to track single mRNAs in live cells. We also discuss how these techniques are applied to extract dynamic information on the transcription, transport, localization, and translation of mRNAs. These studies demonstrate how single molecule tracking is transforming the understanding of mRNA regulation in live cells.

Single-organelle tracking by two-photon conversion

NASA Astrophysics Data System (ADS)

Watanabe, Wataru; Shimada, Tomoko; Matsunaga, Sachihiro; Kurihara, Daisuke; Fukui, Kiichi; Shin-Ichi Arimura, Shin-Ichi; Tsutsumi, Nobuhiro; Isobe, Keisuke; Itoh, Kazuyoshi

2007-03-01

Spatial and temporal information about intracellular objects and their dynamics within a living cell are essential for dynamic analysis of such objects in cell biology. A specific intracellular object can be discriminated by photoactivatable fluorescent proteins that exhibit pronounced light-induced spectral changes. Here, we report on selective labeling and tracking of a single organelle by using two-photon conversion of a photoconvertible fluorescent protein with near-infrared femtosecond laser pulses. We performed selective labeling of a single mitochondrion in a living tobacco BY-2 cell using two-photon photoconversion of Kaede. Using this technique, we demonstrated that, in plants, the directed movement of individual mitochondria along the cytoskeletons was mediated by actin filaments, whereas microtubules were not required for the movement of mitochondria. This single-organelle labeling technique enabled us to track the dynamics of a single organelle, revealing the mechanisms involved in organelle dynamics. The technique has potential application in direct tracking of selective cellular and intracellular structures.

Selectively active markers for solving of the partial occlusion problem in matchmoving and chromakeying workflow

NASA Astrophysics Data System (ADS)

Mazurek, Przemysław

2013-09-01

Matchmoving (Match Moving) is the process used for the estimation of camera movements for further integration of acquired video image with computer graphics. The estimation of movements is possible using pattern recognition, 2D and 3D tracking algorithms. The main problem for the workflow is the partial occlusion of markers by the actor, because manual rotoscoping is necessary for fixing of the chroma-keyed footage. In the paper, the partial occlusion problem is solved using the invented, selectively active electronic markers. The sensor network with multiple infrared links detects occlusion state (no-occlusion, partial, full) and switch LED's based markers.

Human and Animal Fecal Contamination of Community Water Sources, Stored Drinking Water and Hands in Rural India Measured with Validated Microbial Source Tracking Assays.

PubMed

Schriewer, Alexander; Odagiri, Mitsunori; Wuertz, Stefan; Misra, Pravas R; Panigrahi, Pinaki; Clasen, Thomas; Jenkins, Marion W

2015-09-01

We examined pathways of exposure to fecal contamination of human and animal origin in 24 villages in Odisha, India. In a cross-sectional study during the monsoon season, fecal exposure via community water sources (N = 123) and in the home (N = 137) was assessed using human- and nonhuman-associated Bacteroidales microbial source tracking (MST) markers and fecal coliforms (FCs). Detection rates and marker concentrations were examined to pinpoint pathways of human fecal exposure in the public and domestic domains of disease transmission in study communities. Human fecal markers were detected much more frequently in the domestic domain (45% of households) than in public domain sources (8% of ponds; 4% of groundwater drinking sources). Animal fecal markers were widely detected in both domains (74% of ponds, 96% of households, 10% of groundwater drinking sources), indicating ubiquitous risks of exposure to animal feces and zoonotic pathogens. This study confirms an often suggested contamination link from hands to stored water in the home in developing countries separately for mothers' and children's hands and both human and animal fecal contamination. In contrast to MST markers, FCs provided a poor metric to assess risks of exposure to fecal contamination of human origin in this rural setting. © The American Society of Tropical Medicine and Hygiene.

Image to physical space registration of supine breast MRI for image guided breast surgery

NASA Astrophysics Data System (ADS)

Conley, Rebekah H.; Meszoely, Ingrid M.; Pheiffer, Thomas S.; Weis, Jared A.; Yankeelov, Thomas E.; Miga, Michael I.

2014-03-01

Breast conservation therapy (BCT) is a desirable option for many women diagnosed with early stage breast cancer and involves a lumpectomy followed by radiotherapy. However, approximately 50% of eligible women will elect for mastectomy over BCT despite equal survival benefit (provided margins of excised tissue are cancer free) due to uncertainty in outcome with regards to complete excision of cancerous cells, risk of local recurrence, and cosmesis. Determining surgical margins intraoperatively is difficult and achieving negative margins is not as robust as it needs to be, resulting in high re-operation rates and often mastectomy. Magnetic resonance images (MRI) can provide detailed information about tumor margin extents, however diagnostic images are acquired in a fundamentally different patient presentation than that used in surgery. Therefore, the high quality diagnostic MRIs taken in the prone position with pendant breast are not optimal for use in surgical planning/guidance due to the drastic shape change between preoperative images and the common supine surgical position. This work proposes to investigate the value of supine MRI in an effort to localize tumors intraoperatively using image-guidance. Mock intraoperative setups (realistic patient positioning in non-sterile environment) and preoperative imaging data were collected from a patient scheduled for a lumpectomy. The mock intraoperative data included a tracked laser range scan of the patient's breast surface, tracked center points of MR visible fiducials on the patient's breast, and tracked B-mode ultrasound and strain images. The preoperative data included a supine MRI with visible fiducial markers. Fiducial markers localized in the MRI were rigidly registered to their mock intraoperative counterparts using an optically tracked stylus. The root mean square (RMS) fiducial registration error using the tracked markers was 3.4mm. Following registration, the average closest point distance between the MR generated surface nodes and the LRS point cloud was 1.76±0.502 mm.

WE-AB-303-11: Verification of a Deformable 4DCT Motion Model for Lung Tumor Tracking Using Different Driving Surrogates

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

Woelfelschneider, J; Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, DE; Seregni, M

2015-06-15

Purpose: Tumor tracking is an advanced technique to treat intra-fractionally moving tumors. The aim of this study is to validate a surrogate-driven model based on four-dimensional computed tomography (4DCT) that is able to predict CT volumes corresponding to arbitrary respiratory states. Further, the comparison of three different driving surrogates is evaluated. Methods: This study is based on multiple 4DCTs of two patients treated for bronchial carcinoma and metastasis. Analyses for 18 additional patients are currently ongoing. The motion model was estimated from the planning 4DCT through deformable image registration. To predict a certain phase of a follow-up 4DCT, the modelmore » considers for inter-fractional variations (baseline correction) and intra-fractional respiratory parameters (amplitude and phase) derived from surrogates. In this evaluation, three different approaches were used to extract the motion surrogate: for each 4DCT phase, the 3D thoraco-abdominal surface motion, the body volume and the anterior-posterior motion of a virtual single external marker defined on the sternum were investigated. The estimated volumes resulting from the model were compared to the ground-truth clinical 4DCTs using absolute HU differences in the lung volume and landmarks localized using the Scale Invariant Feature Transform (SIFT). Results: The results show absolute HU differences between estimated and ground-truth images with median values limited to 55 HU and inter-quartile ranges (IQR) lower than 100 HU. Median 3D distances between about 1500 matching landmarks are below 2 mm for 3D surface motion and body volume methods. The single marker surrogates Result in increased median distances up to 0.6 mm. Analyses for the extended database incl. 20 patients are currently in progress. Conclusion: The results depend mainly on the image quality of the initial 4DCTs and the deformable image registration. All investigated surrogates can be used to estimate follow-up 4DCT phases, however uncertainties decrease for three-dimensional approaches. This work was funded in parts by the German Research Council (DFG) - KFO 214/2.« less

Lung tumor tracking in fluoroscopic video based on optical flow

PubMed Central

Xu, Qianyi; Hamilton, Russell J.; Schowengerdt, Robert A.; Alexander, Brian; Jiang, Steve B.

2008-01-01

Respiratory gating and tumor tracking for dynamic multileaf collimator delivery require accurate and real-time localization of the lung tumor position during treatment. Deriving tumor position from external surrogates such as abdominal surface motion may have large uncertainties due to the intra- and interfraction variations of the correlation between the external surrogates and internal tumor motion. Implanted fiducial markers can be used to track tumors fluoroscopically in real time with sufficient accuracy. However, it may not be a practical procedure when implanting fiducials bronchoscopically. In this work, a method is presented to track the lung tumor mass or relevant anatomic features projected in fluoroscopic images without implanted fiducial markers based on an optical flow algorithm. The algorithm generates the centroid position of the tracked target and ignores shape changes of the tumor mass shadow. The tracking starts with a segmented tumor projection in an initial image frame. Then, the optical flow between this and all incoming frames acquired during treatment delivery is computed as initial estimations of tumor centroid displacements. The tumor contour in the initial frame is transferred to the incoming frames based on the average of the motion vectors, and its positions in the incoming frames are determined by fine-tuning the contour positions using a template matching algorithm with a small search range. The tracking results were validated by comparing with clinician determined contours on each frame. The position difference in 95% of the frames was found to be less than 1.4 pixels (∼0.7 mm) in the best case and 2.8 pixels (∼1.4 mm) in the worst case for the five patients studied. PMID:19175094

Lung tumor tracking in fluoroscopic video based on optical flow.

PubMed

Xu, Qianyi; Hamilton, Russell J; Schowengerdt, Robert A; Alexander, Brian; Jiang, Steve B

2008-12-01

Respiratory gating and tumor tracking for dynamic multileaf collimator delivery require accurate and real-time localization of the lung tumor position during treatment. Deriving tumor position from external surrogates such as abdominal surface motion may have large uncertainties due to the intra- and interfraction variations of the correlation between the external surrogates and internal tumor motion. Implanted fiducial markers can be used to track tumors fluoroscopically in real time with sufficient accuracy. However, it may not be a practical procedure when implanting fiducials bronchoscopically. In this work, a method is presented to track the lung tumor mass or relevant anatomic features projected in fluoroscopic images without implanted fiducial markers based on an optical flow algorithm. The algorithm generates the centroid position of the tracked target and ignores shape changes of the tumor mass shadow. The tracking starts with a segmented tumor projection in an initial image frame. Then, the optical flow between this and all incoming frames acquired during treatment delivery is computed as initial estimations of tumor centroid displacements. The tumor contour in the initial frame is transferred to the incoming frames based on the average of the motion vectors, and its positions in the incoming frames are determined by fine-tuning the contour positions using a template matching algorithm with a small search range. The tracking results were validated by comparing with clinician determined contours on each frame. The position difference in 95% of the frames was found to be less than 1.4 pixels (approximately 0.7 mm) in the best case and 2.8 pixels (approximately 1.4 mm) in the worst case for the five patients studied.

Magic cards: a new augmented-reality approach.

PubMed

Demuynck, Olivier; Menendez, José Manuel

2013-01-01

Augmented reality (AR) commonly uses markers for detection and tracking. Such multimedia applications associate each marker with a virtual 3D model stored in the memory of the camera-equipped device running the application. Application users are limited in their interactions, which require knowing how to design and program 3D objects. This generally prevents them from developing their own entertainment AR applications. The Magic Cards application solves this problem by offering an easy way to create and manage an unlimited number of virtual objects that are encoded on special markers.

Techniques for 3D tracking of single molecules with nanometer accuracy in living cells

NASA Astrophysics Data System (ADS)

Gardini, Lucia; Capitanio, Marco; Pavone, Francesco S.

2013-06-01

We describe a microscopy technique that, combining wide-field single molecule microscopy, bifocal imaging and Highly Inclined and Laminated Optical sheet (HILO) microscopy, allows a 3D tracking with nanometer accuracy of single fluorescent molecules in vitro and in living cells.

Genotyping of Toxoplasma gondii isolates with 15 microsatellite markers in a single multiplex PCR assay.

PubMed

Ajzenberg, Daniel; Collinet, Frédéric; Mercier, Aurélien; Vignoles, Philippe; Dardé, Marie-Laure

2010-12-01

We developed an easy-to-use method for genotyping Toxoplasma gondii isolates in a single multiplex PCR assay with 15 microsatellite markers. This method was validated by testing 26 reference isolates that had been characterized with other sets of markers.

Genetic barcoding with fluorescent proteins for multiplexed applications.

PubMed

Smurthwaite, Cameron A; Williams, Wesley; Fetsko, Alexandra; Abbadessa, Darin; Stolp, Zachary D; Reed, Connor W; Dharmawan, Andre; Wolkowicz, Roland

2015-04-14

Fluorescent proteins, fluorescent dyes and fluorophores in general have revolutionized the field of molecular cell biology. In particular, the discovery of fluorescent proteins and their genes have enabled the engineering of protein fusions for localization, the analysis of transcriptional activation and translation of proteins of interest, or the general tracking of individual cells and cell populations. The use of fluorescent protein genes in combination with retroviral technology has further allowed the expression of these proteins in mammalian cells in a stable and reliable manner. Shown here is how one can utilize these genes to give cells within a population of cells their own biosignature. As the biosignature is achieved with retroviral technology, cells are barcoded 'indefinitely'. As such, they can be individually tracked within a mixture of barcoded cells and utilized in more complex biological applications. The tracking of distinct populations in a mixture of cells is ideal for multiplexed applications such as discovery of drugs against a multitude of targets or the activation profile of different promoters. The protocol describes how to elegantly develop and amplify barcoded mammalian cells with distinct genetic fluorescent markers, and how to use several markers at once or one marker at different intensities. Finally, the protocol describes how the cells can be further utilized in combination with cell-based assays to increase the power of analysis through multiplexing.

TH-AB-202-11: Spatial and Rotational Quality Assurance of 6DOF Patient Tracking Systems

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

Belcher, AH; Liu, X; Grelewicz, Z

2016-06-15

Purpose: External tracking systems used for patient positioning and motion monitoring during radiotherapy are now capable of detecting both translations and rotations (6DOF). In this work, we develop a novel technique to evaluate the 6DOF performance of external motion tracking systems. We apply this methodology to an infrared (IR) marker tracking system and two 3D optical surface mapping systems in a common tumor 6DOF workspace. Methods: An in-house designed and built 6DOF parallel kinematics robotic motion phantom was used to follow input trajectories with sub-millimeter and sub-degree accuracy. The 6DOF positions of the robotic system were then tracked and recordedmore » independently by three optical camera systems. A calibration methodology which associates the motion phantom and camera coordinate frames was first employed, followed by a comprehensive 6DOF trajectory evaluation, which spanned a full range of positions and orientations in a 20×20×16 mm and 5×5×5 degree workspace. The intended input motions were compared to the calibrated 6DOF measured points. Results: The technique found the accuracy of the IR marker tracking system to have maximal root mean square error (RMSE) values of 0.25 mm translationally and 0.09 degrees rotationally, in any one axis, comparing intended 6DOF positions to positions measured by the IR camera. The 6DOF RSME discrepancy for the first 3D optical surface tracking unit yielded maximal values of 0.60 mm and 0.11 degrees over the same 6DOF volume. An earlier generation 3D optical surface tracker was observed to have worse tracking capabilities than both the IR camera unit and the newer 3D surface tracking system with maximal RMSE of 0.74 mm and 0.28 degrees within the same 6DOF evaluation space. Conclusion: The proposed technique was effective at evaluating the performance of 6DOF patient tracking systems. All systems examined exhibited tracking capabilities at the sub-millimeter and sub-degree level within a 6DOF workspace.« less

Multileaf collimator tracking integrated with a novel x-ray imaging system and external surrogate monitoring

NASA Astrophysics Data System (ADS)

Krauss, Andreas; Fast, Martin F.; Nill, Simeon; Oelfke, Uwe

2012-04-01

We have previously developed a tumour tracking system, which adapts the aperture of a Siemens 160 MLC to electromagnetically monitored target motion. In this study, we exploit the use of a novel linac-mounted kilovoltage x-ray imaging system for MLC tracking. The unique in-line geometry of the imaging system allows the detection of target motion perpendicular to the treatment beam (i.e. the directions usually featuring steep dose gradients). We utilized the imaging system either alone or in combination with an external surrogate monitoring system. We equipped a Siemens ARTISTE linac with two flat panel detectors, one directly underneath the linac head for motion monitoring and the other underneath the patient couch for geometric tracking accuracy assessments. A programmable phantom with an embedded metal marker reproduced three patient breathing traces. For MLC tracking based on x-ray imaging alone, marker position was detected at a frame rate of 7.1 Hz. For the combined external and internal motion monitoring system, a total of only 85 x-ray images were acquired prior to or in between the delivery of ten segments of an IMRT beam. External motion was monitored with a potentiometer. A correlation model between external and internal motion was established. The real-time component of the MLC tracking procedure then relied solely on the correlation model estimations of internal motion based on the external signal. Geometric tracking accuracies were 0.6 mm (1.1 mm) and 1.8 mm (1.6 mm) in directions perpendicular and parallel to the leaf travel direction for the x-ray-only (the combined external and internal) motion monitoring system in spite of a total system latency of ˜0.62 s (˜0.51 s). Dosimetric accuracy for a highly modulated IMRT beam-assessed through radiographic film dosimetry-improved substantially when tracking was applied, but depended strongly on the respective geometric tracking accuracy. In conclusion, we have for the first time integrated MLC tracking with x-ray imaging in the in-line geometry and demonstrated highly accurate respiratory motion tracking.

Exploring dynamics in living cells by tracking single particles.

PubMed

Levi, Valeria; Gratton, Enrico

2007-01-01

In the last years, significant advances in microscopy techniques and the introduction of a novel technology to label living cells with genetically encoded fluorescent proteins revolutionized the field of Cell Biology. Our understanding on cell dynamics built from snapshots on fixed specimens has evolved thanks to our actual capability to monitor in real time the evolution of processes in living cells. Among these new tools, single particle tracking techniques were developed to observe and follow individual particles. Hence, we are starting to unravel the mechanisms driving the motion of a wide variety of cellular components ranging from organelles to protein molecules by following their way through the cell. In this review, we introduce the single particle tracking technology to new users. We briefly describe the instrumentation and explain some of the algorithms commonly used to locate and track particles. Also, we present some common tools used to analyze trajectories and illustrate with some examples the applications of single particle tracking to study dynamics in living cells.

64Cu-ATSM Reflects pO2 Levels in Human Head and Neck Cancer Xenografts but Not in Colorectal Cancer Xenografts: Comparison with 64CuCl2.

PubMed

Li, Fan; Jørgensen, Jesper T; Forman, Julie; Hansen, Anders E; Kjaer, Andreas

2016-03-01

The hypoxia PET tracer (64)Cu-diacetyl-bis(N(4)-methylthiosemicarbazonate) ((64)Cu-ATSM) has shown promising results in clinical studies. However, concerns have been raised with regard to the possible effect of copper metabolism and free copper on tumor uptake and thereby the robustness of (64)Cu-ATSM as a hypoxia marker. In this study, accumulation and distribution of (64)Cu-ATSM and (64)CuCl2 in tumor tissue were compared with partial pressure of oxygen (pO2) probe measurements. One-hour dynamic PET scans were performed on nude mice bearing subcutaneous human head and neck tumors (FaDu) and human colorectal tumors (HT29) after administration of either (64)Cu-ATSM or (64)CuCl2. Subsequently, tracks were generated and track markers were positioned in tumors to allow for registration of their exact location on the high-resolution CT scan. After completion of the CT scan, pO2 probe measurements were performed along each track. PET and CT images were coregistered and ROIs drawn on the basis of the location of track markers and pO2 probe measurement depth. A linear mixed model for repeated measures was applied for the comparison of PET tracer uptake to corresponding pO2 values. Comparable uptake of (64)Cu-ATSM and (64)CuCl2 was found in the kidney, muscle, and liver of all animals, but (64)CuCl2 showed a higher uptake 10-60 min after injection in both tumor models. Significant differences were also found for both tumor-to-muscle and tumor-to-liver ratios. The intratumoral distribution of (64)Cu-ATSM, but not (64)CuCl2, showed a significant negative relationship with pO2 measurements in FaDu tumors. However, this relationship was not found in HT29 tumors. (64)Cu-ATSM and (64)CuCl2 displayed different uptake in tumors. In human head and neck xenografts, (64)Cu-ATSM but not (64)CuCl2 reflected pO2 measurements, indicating that (64)Cu-ATSM is a hypoxia-specific marker in this tumor type. However, data from colorectal cancer xenografts indicated that (64)Cu-ATSM may not be a hypoxia marker in all tumor types. © 2016 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

WE-G-BRD-03: Development of a Real-Time Optical Tracking Goggle System (OTGS) for Intracranial Stereotactic Radiotherapy

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

Mittauer, K; Yan, G; Lu, B

2014-06-15

Purpose: Optical tracking systems (OTS) are an acceptable alternative to frame-based stereotactic radiotherapy (SRT). However, current surface-based OTS lack the ability to target exclusively rigid/bony anatomical features. We propose a novel marker-based optical tracking goggle system (OTGS) that provides real-time guidance based on the nose/facial bony anatomy. This ongoing study involves the development and characterization of the OTGS for clinical implementation in intracranial stereotactic radiotherapy. Methods: The OTGS consists of eye goggles, a custom thermoplastic nosepiece, and 6 infrared markers pre-attached to the goggles. A phantom and four healthy volunteers were used to evaluate the calibration/registration accuracy, intrafraction accuracy, interfractionmore » reproducibility, and end-to-end accuracy of the OTGS. The performance of the OTGS was compared with that of the frameless SonArray system and cone-beam computed tomography (CBCT) for volunteer and phantom cases, respectively. The performance of the OTGS with commercial immobilization devices and under treatment conditions (i.e., couch rotation and translation range) was also evaluated. Results: The difference in the calibration/registration accuracy of 24 translations or rotation combinations between CBCT and in-house OTS software was within 0.5 mm/0.4°. The mean intrafraction and interfraction accuracy among the volunteers was 0.004+/−0.4mm with −0.09+/−0.5° (n=6,170) and −0.26+/−0.8mm with 0.15+/0.8° (n=11), respectively. The difference in end-to-end accuracy between the OTGS and CBCT was within 1.3 mm/1.1°. The predetermined marker pattern (1) minimized marker occlusions, (2) allowed for continuous tracking for couch angles +/− 90°, (3) and eliminated individual marker misplacement. The device was feasible with open and half masks for immobilization. Conclusion: Bony anatomical localization eliminated potential errors due to facial hair changes and/or soft tissue deformation. The OTGS offers a workflow-friendly, patient-friendly solution for intracranial SRT, while being comparable to other real-time options. The minimum rotation uncertainty of the OTGS can be combined with CBCT to ensure maximum accuracy for high-precision SRT.« less

Multidirectional four-dimensional shape measurement system

NASA Astrophysics Data System (ADS)

Lenar, Janusz; Sitnik, Robert; Witkowski, Marcin

2012-03-01

Currently, a lot of different scanning techniques are used for 3D imaging of human body. Most of existing systems are based on static registration of internal structures using MRI or CT techniques as well as 3D scanning of outer surface of human body by laser triangulation or structured light methods. On the other hand there is an existing mature 4D method based on tracking in time the position of retro-reflective markers attached to human body. There are two main drawbacks of this solution: markers are attached to skin (no real skeleton movement is registered) and it gives (x, y, z, t) coordinates only in those points (not for the whole surface). In this paper we present a novel multidirectional structured light measurement system that is capable of measuring 3D shape of human body surface with frequency reaching 60Hz. The developed system consists of two spectrally separated and hardware-synchronized 4D measurement heads. The principle of the measurement is based on single frame analysis. Projected frame is composed from sine-modulated intensity pattern and a special stripe allowing absolute phase measurement. Several different geometrical set-ups will be proposed depending on type of movements that are to be registered.

Kelp genes reveal effects of subantarctic sea ice during the Last Glacial Maximum

PubMed Central

Fraser, Ceridwen I.; Nikula, Raisa; Spencer, Hamish G.; Waters, Jonathan M.

2009-01-01

The end of the Last Glacial Maximum (LGM) dramatically reshaped temperate ecosystems, with many species moving poleward as temperatures rose and ice receded. Whereas reinvading terrestrial taxa tracked melting glaciers, marine biota recolonized ocean habitats freed by retreating sea ice. The extent of sea ice in the Southern Hemisphere during the LGM has, however, yet to be fully resolved, with most palaeogeographic studies suggesting only minimal or patchy ice cover in subantarctic waters. Here, through population genetic analyses of the widespread Southern Bull Kelp (Durvillaea antarctica), we present evidence for persistent ice scour affecting subantarctic islands during the LGM. Using mitochondrial and chloroplast genetic markers (COI; rbcL) to genetically characterize some 300 kelp samples from 45 Southern Ocean localities, we reveal a remarkable pattern of recent recolonization in the subantarctic. Specifically, in contrast to the marked phylogeographic structure observed across coastal New Zealand and Chile (10- to 100-km scales), subantarctic samples show striking genetic homogeneity over vast distances (10,000-km scales), with a single widespread haplotype observed for each marker. From these results, we suggest that sea ice expanded further and ice scour during the LGM impacted shallow-water subantarctic marine ecosystems more extensively than previously suggested. PMID:19204277

Long-term monitoring of molecular markers can distinguish different seasonal patterns of fecal indicating bacteria sources.

PubMed

Riedel, Timothy E; Thulsiraj, Vanessa; Zimmer-Faust, Amity G; Dagit, Rosi; Krug, Jenna; Hanley, Kaitlyn T; Adamek, Krista; Ebentier, Darcy L; Torres, Robert; Cobian, Uriel; Peterson, Sophie; Jay, Jennifer A

2015-03-15

Elevated levels of fecal indicator bacteria (FIB) have been observed at Topanga Beach, CA, USA. To identify the FIB sources, a microbial source tracking study using a dog-, a gull- and two human-associated molecular markers was conducted at 10 sites over 21 months. Historical data suggest that episodic discharge from the lagoon at the mouth of Topanga Creek is the main source of bacteria to the beach. A decline in creek FIB/markers downstream from upper watershed development and a sharp increase in FIB/markers at the lagoon sites suggest sources are local to the lagoon. At the lagoon and beach, human markers are detected sporadically, dog marker peaks in abundance mid-winter, and gull marker is chronically elevated. Varied seasonal patterns of FIB and source markers were identified showing the importance of applying a suite of markers over long-term spatial and temporal sampling to identify a complex combination of sources of contamination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Development of SSR Markers Linked to Low Hydrocyanic Acid Content in Sorghum-Sudan Grass Hybrid Based on BSA Method.

PubMed

Xiao-Xia, Yu; Zhi-Hua, Liu; Zhuo, Yu; Yue, Shi; Xiao-Yu, Li

2016-01-01

Sorghum-Sudan grass hybrid containing high hydrocyanic acid content can cause hydrocyanic acid poisoning to the livestock and limit the popularization of this forage crop. Molecular markers associated with low hydrocyanic acid content can speed up the process of identification of genotypes with low hydrocyanic acid content. In the present study, 11 polymorphic SSR primers were screened and used for bulked segregant analysis and single marker analysis. Three SSR markers Xtxp7230, Xtxp7375 and Bnlg667960 associated with low hydrocyanic acid content were rapidly identified by BSA. In single marker analysis, six markers Xtxp7230, Xtxp7375, Bnlg667960, Xtxp67-11, Xtxp295-7 and Xtxp12-9 were linked to low hydrocyanic acid content, which explained the proportion of phenotypic variation from 7.6 % to 41.2 %. The markers identified by BSA were also verified by single marker analysis. The three SSR marker bands were then cloned and sequenced for sequence homology analysis in NCBI. It is the first report on the development of molecular markers associated with low hydrocyanic acid content in sorghum- Sudan grass hybrid. These markers will be useful for genetic improvement of low hydrocyanic acid sorghum-Sudan grass hybrid by marker-assisted breeding.

Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map

PubMed Central

Haile, Jemanesh K.; Cory, Aron T.; Clarke, Fran R.; Clarke, John M.; Knox, Ron E.; Pozniak, Curtis J.

2017-01-01

Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat. PMID:28135299

Genotyping of Toxoplasma gondii Isolates with 15 Microsatellite Markers in a Single Multiplex PCR Assay ▿

PubMed Central

Ajzenberg, Daniel; Collinet, Frédéric; Mercier, Aurélien; Vignoles, Philippe; Dardé, Marie-Laure

2010-01-01

We developed an easy-to-use method for genotyping Toxoplasma gondii isolates in a single multiplex PCR assay with 15 microsatellite markers. This method was validated by testing 26 reference isolates that had been characterized with other sets of markers. PMID:20881166

MetaTracker: integration and abstraction of 3D motion tracking data from multiple hardware systems

NASA Astrophysics Data System (ADS)

Kopecky, Ken; Winer, Eliot

2014-06-01

Motion tracking has long been one of the primary challenges in mixed reality (MR), augmented reality (AR), and virtual reality (VR). Military and defense training can provide particularly difficult challenges for motion tracking, such as in the case of Military Operations in Urban Terrain (MOUT) and other dismounted, close quarters simulations. These simulations can take place across multiple rooms, with many fast-moving objects that need to be tracked with a high degree of accuracy and low latency. Many tracking technologies exist, such as optical, inertial, ultrasonic, and magnetic. Some tracking systems even combine these technologies to complement each other. However, there are no systems that provide a high-resolution, flexible, wide-area solution that is resistant to occlusion. While frameworks exist that simplify the use of tracking systems and other input devices, none allow data from multiple tracking systems to be combined, as if from a single system. In this paper, we introduce a method for compensating for the weaknesses of individual tracking systems by combining data from multiple sources and presenting it as a single tracking system. Individual tracked objects are identified by name, and their data is provided to simulation applications through a server program. This allows tracked objects to transition seamlessly from the area of one tracking system to another. Furthermore, it abstracts away the individual drivers, APIs, and data formats for each system, providing a simplified API that can be used to receive data from any of the available tracking systems. Finally, when single-piece tracking systems are used, those systems can themselves be tracked, allowing for real-time adjustment of the trackable area. This allows simulation operators to leverage limited resources in more effective ways, improving the quality of training.

Deep divergence and apparent sex-biased dispersal revealed by a Y-linked marker in rainbow trout

PubMed Central

Brunelli, Joseph P.; Steele, Craig A.; Thorgaard, Gary H.

2010-01-01

Y-chromosome and mitochondrial DNA markers can reveal phylogenetic patterns by allowing tracking of male and female lineages, respectively. We used sequence data from a recently discovered Y-linked marker and a mitochondrial marker to examine phylogeographic structure in the widespread and economically important rainbow trout (Oncorhynchus mykiss). Two distinct geographic groupings that generally correspond to coastal and inland subspecies were evident within the Y marker network while the mtDNA haplotype network showed little geographic structure. Our results suggest that male-specific behavior has prevented widespread admixture of Y haplotypes and that gene flow between the coastal and inland subspecies has largely occurred through females. This new Y marker may also aid conservation efforts by genetically identifying inland populations that have not hybridized with widely stocked coastal-derived hatchery fish. PMID:20546904

Power optimal single-axis articulating strategies

NASA Technical Reports Server (NTRS)

Kumar, Renjith R.; Heck, Michael L.

1991-01-01

Power optimal single axis articulating PV array motion for Space Station Freedom is investigated. The motivation is to eliminate one of the articular joints to reduce Station costs. Optimal (maximum power) Beta tracking is addressed for local vertical local horizontal (LVLH) and non-LVLH attitudes. Effects of intra-array shadowing are also presented. Maximum power availability while Beta tracking is compared to full sun tracking and optimal alpha tracking. The results are quantified in orbital and yearly minimum, maximum, and average values of power availability.

Influence of Laser Power on the Shape of Single Tracks in Scanner Based Laser Wire Cladding

NASA Astrophysics Data System (ADS)

Barroi, A.; Gonçalves, D. Albertazzi; Hermsdorf, J.; Kaierle, S.; Overmeyer, L.

The shape of the cladding tracks is extremely important for producing layers or structures by adding them sequently. This paper shows the influence of the laser power of a diode laser in the range of 500 to 1000 W on the shapes of single tracks in scanner based laser wire cladding. The scanner was used to oscillate the beam perpendiculary to the welding direction. Stainless steel (ER 318 Si) wire with a 0.6 mm diameter was used as deposition material. Height, width, penetration, molten area and weld seam angles of single tracks were obtained from cross-sections at three different positions of each track. The influence of these different positions on the results depends on the traverse speed. The paper discusses this influence in respect to the heat dissipation in the substrate material.

Extracellular NGFR Spacers Allow Efficient Tracking and Enrichment of Fully Functional CAR-T Cells Co-Expressing a Suicide Gene

PubMed Central

Casucci, Monica; Falcone, Laura; Camisa, Barbara; Norelli, Margherita; Porcellini, Simona; Stornaiuolo, Anna; Ciceri, Fabio; Traversari, Catia; Bordignon, Claudio; Bonini, Chiara; Bondanza, Attilio

2018-01-01

Chimeric antigen receptor (CAR)-T cell immunotherapy is at the forefront of innovative cancer therapeutics. However, lack of standardization of cellular products within the same clinical trial and lack of harmonization between different trials have hindered the clear identification of efficacy and safety determinants that should be unveiled in order to advance the field. With the aim of facilitating the isolation and in vivo tracking of CAR-T cells, we here propose the inclusion within the CAR molecule of a novel extracellular spacer based on the low-affinity nerve-growth-factor receptor (NGFR). We screened four different spacer designs using as target antigen the CD44 isoform variant 6 (CD44v6). We successfully generated NGFR-spaced CD44v6 CAR-T cells that could be efficiently enriched with clinical-grade immuno-magnetic beads without negative consequences on subsequent expansion, immuno-phenotype, in vitro antitumor reactivity, and conditional ablation when co-expressing a suicide gene. Most importantly, these cells could be tracked with anti-NGFR monoclonal antibodies in NSG mice, where they expanded, persisted, and exerted potent antitumor effects against both high leukemia and myeloma burdens. Similar results were obtained with NGFR-enriched CAR-T cells specific for CD19 or CEA, suggesting the universality of this strategy. In conclusion, we have demonstrated that the incorporation of the NGFR marker gene within the CAR sequence allows for a single molecule to simultaneously work as a therapeutic and selection/tracking gene. Looking ahead, NGFR spacer enrichment might allow good manufacturing procedures-manufacturing of standardized CAR-T cell products with high therapeutic potential, which could be harmonized in different clinical trials and used in combination with a suicide gene for future application in the allogeneic setting. PMID:29619024

Performance of Single Nucleotide Polymorphisms versus Haplotypes for Genome-Wide Association Analysis in Barley

PubMed Central

Jannink, Jean-Luc

2010-01-01

Genome-wide association studies (GWAS) may benefit from utilizing haplotype information for making marker-phenotype associations. Several rationales for grouping single nucleotide polymorphisms (SNPs) into haplotype blocks exist, but any advantage may depend on such factors as genetic architecture of traits, patterns of linkage disequilibrium in the study population, and marker density. The objective of this study was to explore the utility of haplotypes for GWAS in barley (Hordeum vulgare) to offer a first detailed look at this approach for identifying agronomically important genes in crops. To accomplish this, we used genotype and phenotype data from the Barley Coordinated Agricultural Project and constructed haplotypes using three different methods. Marker-trait associations were tested by the efficient mixed-model association algorithm (EMMA). When QTL were simulated using single SNPs dropped from the marker dataset, a simple sliding window performed as well or better than single SNPs or the more sophisticated methods of blocking SNPs into haplotypes. Moreover, the haplotype analyses performed better 1) when QTL were simulated as polymorphisms that arose subsequent to marker variants, and 2) in analysis of empirical heading date data. These results demonstrate that the information content of haplotypes is dependent on the particular mutational and recombinational history of the QTL and nearby markers. Analysis of the empirical data also confirmed our intuition that the distribution of QTL alleles in nature is often unlike the distribution of marker variants, and hence utilizing haplotype information could capture associations that would elude single SNPs. We recommend routine use of both single SNP and haplotype markers for GWAS to take advantage of the full information content of the genotype data. PMID:21124933

Microbial source tracking as a tool for TMDL development, Little Blue River in Independence, Missouri

USGS Publications Warehouse

Christensen, Eric D.; Bushon, Rebecca N.; Brady, Amie M.G.

2013-01-01

The Little Blue River in Jackson County, Missouri has been listed by the Missouri Department of Natural Resources as impaired by bacteria for the protection of aquatic life and contact recreation from urban point and nonpoint sources. The Clean Water Act requires that a total maximum daily load (TMDL) for Escherichia coli (E. coli) be developed. Over a 5-year period, 108 base-flow, 87 stormflow, 48 fecal source, and 12 sewage influent samples were collected and analyzed for E. coli and Bacteroides general and host-associated microbial source tracking (MST) genetic markers. Less than half of the main-stem base-flow samples exceeded the E. coli state standard, whereas, all of the stormflow samples exceeded the standard during the recreation season (April through October). Both E. coli and MST markers were detected more frequently and at higher concentrations in stormflow samples. Only 14 percent of samples with E. coli detections greater than the Missouri state standard of 206 colonies per 100 milliliters had the human-associated Bacteroides marker as the only identified marker; therefore, Little Blue River TMDL development may require a broader scope beyond the municipal separate storm sewer system if bacteria sources are to be identified and addressed. Fecal samples showed a greater specificity with the human-associated marker than the dog- or ruminant-associated Bacteroides markers; however, false positives were at least one order of magnitude lower than true positives. MST data may be a useful tool for identifying probable sources of contamination and directing TMDL strategies.

Association of Fecal Indicator Bacteria with Human Viruses and Microbial Source Tracking Markers at Coastal Beaches Impacted by Nonpoint Source Pollution

PubMed Central

McQuaig, Shannon; Griffith, John

2012-01-01

Water quality was assessed at two marine beaches in California by measuring the concentrations of culturable fecal indicator bacteria (FIB) and by library-independent microbial source tracking (MST) methods targeting markers of human-associated microbes (human polyomavirus [HPyV] PCR and quantitative PCR, Methanobrevibacter smithii PCR, and Bacteroides sp. strain HF183 PCR) and a human pathogen (adenovirus by nested PCR). FIB levels periodically exceeded regulatory thresholds at Doheny and Avalon Beaches for enterococci (28.5% and 31.7% of samples, respectively) and fecal coliforms (20% and 5.8%, respectively). Adenoviruses were detected at four of five sites at Doheny Beach and were correlated with detection of HPyVs and human Bacteroides HF183; however, adenoviruses were not detected at Avalon Beach. The most frequently detected human source marker at both beaches was Bacteroides HF183, which was detected in 27% of samples. Correlations between FIBs and human markers were much more frequent at Doheny Beach than at Avalon Beach; e.g., adenovirus was correlated with HPyVs and HF183. Human sewage markers and adenoviruses were routinely detected in samples meeting FIB regulatory standards. The toolbox approach of FIB measurement coupled with analysis of several MST markers targeting human pathogens used here demonstrated that human sewage is at least partly responsible for the degradation of water quality, particularly at Doheny Beach, and resulted in a more definitive assessment of recreational water quality and human health risk than reliance on FIB concentrations alone could have provided. PMID:22773625

The Accuracy of Conventional 2D Video for Quantifying Upper Limb Kinematics in Repetitive Motion Occupational Tasks

PubMed Central

Chen, Chia-Hsiung; Azari, David; Hu, Yu Hen; Lindstrom, Mary J.; Thelen, Darryl; Yen, Thomas Y.; Radwin, Robert G.

2015-01-01

Objective Marker-less 2D video tracking was studied as a practical means to measure upper limb kinematics for ergonomics evaluations. Background Hand activity level (HAL) can be estimated from speed and duty cycle. Accuracy was measured using a cross correlation template-matching algorithm for tracking a region of interest on the upper extremities. Methods Ten participants performed a paced load transfer task while varying HAL (2, 4, and 5) and load (2.2 N, 8.9 N and 17.8 N). Speed and acceleration measured from 2D video were compared against ground truth measurements using 3D infrared motion capture. Results The median absolute difference between 2D video and 3D motion capture was 86.5 mm/s for speed, and 591 mm/s2 for acceleration, and less than 93 mm/s for speed and 656 mm/s2 for acceleration when camera pan and tilt were within ±30 degrees. Conclusion Single-camera 2D video had sufficient accuracy (< 100 mm/s) for evaluating HAL. Practitioner Summary This study demonstrated that 2D video tracking had sufficient accuracy to measure HAL for ascertaining the American Conference of Government Industrial Hygienists Threshold Limit Value® for repetitive motion when the camera is located within ±30 degrees off the plane of motion when compared against 3D motion capture for a simulated repetitive motion task. PMID:25978764

Single-Molecule Tracking and Its Application in Biomolecular Binding Detection.

PubMed

Liu, Cong; Liu, Yen-Liang; Perillo, Evan P; Dunn, Andrew K; Yeh, Hsin-Chih

2016-01-01

In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges.

Single-Molecule Tracking and Its Application in Biomolecular Binding Detection

PubMed Central

Liu, Cong; Liu, Yen-Liang; Perillo, Evan P.; Dunn, Andrew K.; Yeh, Hsin-Chih

2016-01-01

In the past two decades significant advances have been made in single-molecule detection, which enables the direct observation of single biomolecules at work in real time and under physiological conditions. In particular, the development of single-molecule tracking (SMT) microscopy allows us to monitor the motion paths of individual biomolecules in living systems, unveiling the localization dynamics and transport modalities of the biomolecules that support the development of life. Beyond the capabilities of traditional camera-based tracking techniques, state-of-the-art SMT microscopies developed in recent years can record fluorescence lifetime while tracking a single molecule in the 3D space. This multiparameter detection capability can open the door to a wide range of investigations at the cellular or tissue level, including identification of molecular interaction hotspots and characterization of association/dissociation kinetics between molecules. In this review, we discuss various SMT techniques developed to date, with an emphasis on our recent development of the next generation 3D tracking system that not only achieves ultrahigh spatiotemporal resolution but also provides sufficient working depth suitable for live animal imaging. We also discuss the challenges that current SMT techniques are facing and the potential strategies to tackle those challenges. PMID:27660404

Track-A-Worm, An Open-Source System for Quantitative Assessment of C. elegans Locomotory and Bending Behavior

PubMed Central

Wang, Sijie Jason; Wang, Zhao-Wen

2013-01-01

A major challenge of neuroscience is to understand the circuit and gene bases of behavior. C. elegans is commonly used as a model system to investigate how various gene products function at specific tissue, cellular, and synaptic foci to produce complicated locomotory and bending behavior. The investigation generally requires quantitative behavioral analyses using an automated single-worm tracker, which constantly records and analyzes the position and body shape of a freely moving worm at a high magnification. Many single-worm trackers have been developed to meet lab-specific needs, but none has been widely implemented for various reasons, such as hardware difficult to assemble, and software lacking sufficient functionality, having closed source code, or using a programming language that is not broadly accessible. The lack of a versatile system convenient for wide implementation makes data comparisons difficult and compels other labs to develop new worm trackers. Here we describe Track-A-Worm, a system rich in functionality, open in source code, and easy to use. The system includes plug-and-play hardware (a stereomicroscope, a digital camera and a motorized stage), custom software written to run with Matlab in Windows 7, and a detailed user manual. Grayscale images are automatically converted to binary images followed by head identification and placement of 13 markers along a deduced spline. The software can extract and quantify a variety of parameters, including distance traveled, average speed, distance/time/speed of forward and backward locomotion, frequency and amplitude of dominant bends, overall bending activities measured as root mean square, and sum of all bends. It also plots worm travel path, bend trace, and bend frequency spectrum. All functionality is performed through graphical user interfaces and data is exported to clearly-annotated and documented Excel files. These features make Track-A-Worm a good candidate for implementation in other labs. PMID:23922769

Dependence in Alzheimer's disease and service use costs, quality of life, and caregiver burden: the DADE study.

PubMed

Jones, Roy W; Romeo, Renee; Trigg, Richard; Knapp, Martin; Sato, Azusa; King, Derek; Niecko, Timothy; Lacey, Loretto

2015-03-01

Most models determining how patient and caregiver characteristics and costs change with Alzheimer's disease (AD) progression focus on one aspect, for example, cognition. AD is inadequately defined by a single domain; tracking progression by focusing on a single aspect may mean other important aspects are insufficiently addressed. Dependence has been proposed as a better marker for following disease progression. This was a cross-sectional observational study (18 UK sites). Two hundred forty-nine community or institutionalized patients, with possible/probable AD, Mini-Mental State Examination (3-26), and a knowledgeable informant participated. Significant associations noted between dependence (Dependence Scale [DS]) and clinical measures of severity (cognition, function, and behavior). Bivariate and multivariate models demonstrated significant associations between DS and service use cost, patient quality of life, and caregiver perceived burden. The construct of dependence may help to translate the combined impact of changes in cognition, function, and behavior into a more readily interpretable form. The DS is useful for assessing patients with AD in clinical trials/research. Copyright © 2015 The Alzheimer's Association. Published by Elsevier Inc. All rights reserved.

Orthographic and phonological contributions to reading development: tracking developmental trajectories using masked priming.

PubMed

Ziegler, Johannes C; Bertrand, Daisy; Lété, Bernard; Grainger, Jonathan

2014-04-01

The present study used a variant of masked priming to track the development of 2 marker effects of orthographic and phonological processing from Grade 1 through Grade 5 in a cross-sectional study. Pseudohomophone (PsH) priming served as a marker for phonological processing, whereas transposed-letter (TL) priming was a marker for coarse-grained orthographic processing. The results revealed a clear developmental picture. First, the PsH priming effect was significant and remained stable across development, suggesting that phonology not only plays an important role in early reading development but continues to exert a robust influence throughout reading development. This finding challenges the view that more advanced readers should rely less on phonological information than younger readers. Second, the TL priming effect increased monotonically with grade level and reading age, which suggests greater reliance on coarse-grained orthographic coding as children become better readers. Thus, TL priming effects seem to be a good marker effect for children's ability to use coarse-grained orthographic coding to speed up direct lexical access in alphabetic languages. The results were predicted by the dual-route model of orthographic processing, which suggests that direct orthographic access is achieved through coarse-grained orthographic coding that tolerates some degree of flexibility in letter order. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Comparative analysis of respiratory motion tracking using Microsoft Kinect v2 sensor.

PubMed

Silverstein, Evan; Snyder, Michael

2018-05-01

To present and evaluate a straightforward implementation of a marker-less, respiratory motion-tracking process utilizing Kinect v2 camera as a gating tool during 4DCT or during radiotherapy treatments. Utilizing the depth sensor on the Kinect as well as author written C# code, respiratory motion of a subject was tracked by recording depth values obtained at user selected points on the subject, with each point representing one pixel on the depth image. As a patient breathes, specific anatomical points on the chest/abdomen will move slightly within the depth image across pixels. By tracking how depth values change for a specific pixel, instead of how the anatomical point moves throughout the image, a respiratory trace can be obtained based on changing depth values of the selected pixel. Tracking these values was implemented via marker-less setup. Varian's RPM system and the Anzai belt system were used in tandem with the Kinect to compare respiratory traces obtained by each using two different subjects. Analysis of the depth information from the Kinect for purposes of phase- and amplitude-based binning correlated well with the RPM and Anzai systems. Interquartile Range (IQR) values were obtained comparing times correlated with specific amplitude and phase percentages against each product. The IQR time spans indicated the Kinect would measure specific percentage values within 0.077 s for Subject 1 and 0.164 s for Subject 2 when compared to values obtained with RPM or Anzai. For 4DCT scans, these times correlate to less than 1 mm of couch movement and would create an offset of 1/2 an acquired slice. By tracking depth values of user selected pixels within the depth image, rather than tracking specific anatomical locations, respiratory motion can be tracked and visualized utilizing the Kinect with results comparable to that of the Varian RPM and Anzai belt. © 2018 The Authors. Journal of Applied Clinical Medical Physics published by Wiley Periodicals, Inc. on behalf of American Association of Physicists in Medicine.

Remote Marker-Based Tracking for UAV Landing Using Visible-Light Camera Sensor.

PubMed

Nguyen, Phong Ha; Kim, Ki Wan; Lee, Young Won; Park, Kang Ryoung

2017-08-30

Unmanned aerial vehicles (UAVs), which are commonly known as drones, have proved to be useful not only on the battlefields where manned flight is considered too risky or difficult, but also in everyday life purposes such as surveillance, monitoring, rescue, unmanned cargo, aerial video, and photography. More advanced drones make use of global positioning system (GPS) receivers during the navigation and control loop which allows for smart GPS features of drone navigation. However, there are problems if the drones operate in heterogeneous areas with no GPS signal, so it is important to perform research into the development of UAVs with autonomous navigation and landing guidance using computer vision. In this research, we determined how to safely land a drone in the absence of GPS signals using our remote maker-based tracking algorithm based on the visible light camera sensor. The proposed method uses a unique marker designed as a tracking target during landing procedures. Experimental results show that our method significantly outperforms state-of-the-art object trackers in terms of both accuracy and processing time, and we perform test on an embedded system in various environments.

Freehand three-dimensional ultrasound imaging of carotid artery using motion tracking technology.

PubMed

Chung, Shao-Wen; Shih, Cho-Chiang; Huang, Chih-Chung

2017-02-01

Ultrasound imaging has been extensively used for determining the severity of carotid atherosclerotic stenosis. In particular, the morphological characterization of carotid plaques can be performed for risk stratification of patients. However, using 2D ultrasound imaging for detecting morphological changes in plaques has several limitations. Due to the scan was performed on a single longitudinal cross-section, the selected 2D image is difficult to represent the entire morphology and volume of plaque and vessel lumen. In addition, the precise positions of 2D ultrasound images highly depend on the radiologists' experience, it makes the serial long-term exams of anti-atherosclerotic therapies are difficult to relocate the same corresponding planes by using 2D B-mode images. This has led to the recent development of three-dimensional (3D) ultrasound imaging, which offers improved visualization and quantification of complex morphologies of carotid plaques. In the present study, a freehand 3D ultrasound imaging technique based on optical motion tracking technology is proposed. Unlike other optical tracking systems, the marker is a small rigid body that is attached to the ultrasound probe and is tracked by eight high-performance digital cameras. The probe positions in 3D space coordinates are then calibrated at spatial and temporal resolutions of 10μm and 0.01s, respectively. The image segmentation procedure involves Otsu's and the active contour model algorithms and accurately detects the contours of the carotid arteries. The proposed imaging technique was verified using normal artery and atherosclerotic stenosis phantoms. Human experiments involving freehand scanning of the carotid artery of a volunteer were also performed. The results indicated that compared with manual segmentation, the lowest percentage errors of the proposed segmentation procedure were 7.8% and 9.1% for the external and internal carotid arteries, respectively. Finally, the effect of handshaking was calibrated using the optical tracking system for reconstructing a 3D image. Copyright © 2016 Elsevier B.V. All rights reserved.

Patient training in respiratory-gated radiotherapy

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

Kini, Vijay R.; Vedam, Subrahmanya S.; Keall, Paul J.

2003-03-31

Respiratory gating is used to counter the effects of organ motion during radiotherapy for chest tumors. The effects of variations in patient breathing patterns during a single treatment and from day to day are unknown. We evaluated the feasibility of using patient training tools and their effect on the breathing cycle regularity and reproducibility during respiratory-gated radiotherapy. To monitor respiratory patterns, we used a component of a commercially available respiratory-gated radiotherapy system (Real Time Position Management (RPM) System, Varian Oncology Systems, Palo Alto, CA 94304). This passive marker video tracking system consists of reflective markers placed on the patient's chestmore » or abdomen, which are detected by a wall-mounted video camera. Software installed on a PC interfaced to this camera detects the marker motion digitally and records it. The marker position as a function of time serves as the motion signal that may be used to trigger imaging or treatment. The training tools used were audio prompting and visual feedback, with free breathing as a control. The audio prompting method used instructions to 'breathe in' or 'breathe out' at periodic intervals deduced from patients' own breathing patterns. In the visual feedback method, patients were shown a real-time trace of their abdominal wall motion due to breathing. Using this, they were asked to maintain a constant amplitude of motion. Motion traces of the abdominal wall were recorded for each patient for various maneuvers. Free breathing showed a variable amplitude and frequency. Audio prompting resulted in a reproducible frequency; however, the variability and the magnitude of amplitude increased. Visual feedback gave a better control over the amplitude but showed minor variations in frequency. We concluded that training improves the reproducibility of amplitude and frequency of patient breathing cycles. This may increase the accuracy of respiratory-gated radiation therapy.« less

TrackMate: An open and extensible platform for single-particle tracking.

PubMed

Tinevez, Jean-Yves; Perry, Nick; Schindelin, Johannes; Hoopes, Genevieve M; Reynolds, Gregory D; Laplantine, Emmanuel; Bednarek, Sebastian Y; Shorte, Spencer L; Eliceiri, Kevin W

2017-02-15

We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools. The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Microfluidic platform for detection and quantification of magnetic markers

NASA Astrophysics Data System (ADS)

Kokkinis, Georgios; Cardoso, Susana; Giouroudi, Ioanna

2017-05-01

This paper reports on a microfluidic platform with an integrated spin valve giant magneto-resistance (GMR) sensor used for the detection and quantification of single magnetic micromarkers. A microfluidic channel containing the magnetic fluid, microconductors (MCs) for collection of the magnetic markers and a spin valve GMR sensor for detecting the presence of their magnetic stray field were integrated on a single chip. The results show that the sensor is capable of detecting a single magnetic marker with 2.8 μm diameter.

Optimum location of external markers using feature selection algorithms for real‐time tumor tracking in external‐beam radiotherapy: a virtual phantom study

PubMed Central

Nankali, Saber; Miandoab, Payam Samadi; Baghizadeh, Amin

2016-01-01

In external‐beam radiotherapy, using external markers is one of the most reliable tools to predict tumor position, in clinical applications. The main challenge in this approach is tumor motion tracking with highest accuracy that depends heavily on external markers location, and this issue is the objective of this study. Four commercially available feature selection algorithms entitled 1) Correlation‐based Feature Selection, 2) Classifier, 3) Principal Components, and 4) Relief were proposed to find optimum location of external markers in combination with two “Genetic” and “Ranker” searching procedures. The performance of these algorithms has been evaluated using four‐dimensional extended cardiac‐torso anthropomorphic phantom. Six tumors in lung, three tumors in liver, and 49 points on the thorax surface were taken into account to simulate internal and external motions, respectively. The root mean square error of an adaptive neuro‐fuzzy inference system (ANFIS) as prediction model was considered as metric for quantitatively evaluating the performance of proposed feature selection algorithms. To do this, the thorax surface region was divided into nine smaller segments and predefined tumors motion was predicted by ANFIS using external motion data of given markers at each small segment, separately. Our comparative results showed that all feature selection algorithms can reasonably select specific external markers from those segments where the root mean square error of the ANFIS model is minimum. Moreover, the performance accuracy of proposed feature selection algorithms was compared, separately. For this, each tumor motion was predicted using motion data of those external markers selected by each feature selection algorithm. Duncan statistical test, followed by F‐test, on final results reflected that all proposed feature selection algorithms have the same performance accuracy for lung tumors. But for liver tumors, a correlation‐based feature selection algorithm, in combination with a genetic search algorithm, proved to yield best performance accuracy for selecting optimum markers. PACS numbers: 87.55.km, 87.56.Fc PMID:26894358

Optimum location of external markers using feature selection algorithms for real-time tumor tracking in external-beam radiotherapy: a virtual phantom study.

PubMed

Nankali, Saber; Torshabi, Ahmad Esmaili; Miandoab, Payam Samadi; Baghizadeh, Amin

2016-01-08

In external-beam radiotherapy, using external markers is one of the most reliable tools to predict tumor position, in clinical applications. The main challenge in this approach is tumor motion tracking with highest accuracy that depends heavily on external markers location, and this issue is the objective of this study. Four commercially available feature selection algorithms entitled 1) Correlation-based Feature Selection, 2) Classifier, 3) Principal Components, and 4) Relief were proposed to find optimum location of external markers in combination with two "Genetic" and "Ranker" searching procedures. The performance of these algorithms has been evaluated using four-dimensional extended cardiac-torso anthropomorphic phantom. Six tumors in lung, three tumors in liver, and 49 points on the thorax surface were taken into account to simulate internal and external motions, respectively. The root mean square error of an adaptive neuro-fuzzy inference system (ANFIS) as prediction model was considered as metric for quantitatively evaluating the performance of proposed feature selection algorithms. To do this, the thorax surface region was divided into nine smaller segments and predefined tumors motion was predicted by ANFIS using external motion data of given markers at each small segment, separately. Our comparative results showed that all feature selection algorithms can reasonably select specific external markers from those segments where the root mean square error of the ANFIS model is minimum. Moreover, the performance accuracy of proposed feature selection algorithms was compared, separately. For this, each tumor motion was predicted using motion data of those external markers selected by each feature selection algorithm. Duncan statistical test, followed by F-test, on final results reflected that all proposed feature selection algorithms have the same performance accuracy for lung tumors. But for liver tumors, a correlation-based feature selection algorithm, in combination with a genetic search algorithm, proved to yield best performance accuracy for selecting optimum markers.

Design of quantum dot-conjugated lipids for long-term, high-speed tracking experiments on cell surfaces.

PubMed

Murcia, Michael J; Minner, Daniel E; Mustata, Gina-Mirela; Ritchie, Kenneth; Naumann, Christoph A

2008-11-12

The current study reports the facile design of quantum dot (QD)-conjugated lipids and their application to high-speed tracking experiments on cell surfaces. CdSe/ZnS core/shell QDs with two types of hydrophilic coatings, 2-(2-aminoethoxy)ethanol (AEE) and a 60:40 molar mixture of 1,2-dipalmitoyl- sn-glycero-3-phosphocholine and 1,2-dipalmitoyl- sn-glycero-3-phosphoethanolamine- N-[methoxy(polyethylene glycol-2000], are conjugated to sulfhydryl lipids via maleimide reactive groups on the QD surface. Prior to lipid conjugation, the colloidal stability of both types of coated QDs in aqueous solution is confirmed using fluorescence correlation spectroscopy. A sensitive assay based on single lipid tracking experiments on a planar solid-supported phospholipid bilayer is presented that establishes conditions of monovalent conjugation of QDs to lipids. The QD-lipids are then employed as single-molecule tracking probes in plasma membranes of several cell types. Initial tracking experiments at a frame rate of 30 frames/s corroborate that QD-lipids diffuse like dye-labeled lipids in the plasma membrane of COS-7, HEK-293, 3T3, and NRK cells, thus confirming monovalent labeling. Finally, QD-lipids are applied for the first time to high-speed single-molecule imaging by tracking their lateral mobility in the plasma membrane of NRK fibroblasts with up to 1000 frames/s. Our high-speed tracking data, which are in excellent agreement with previous tracking experiments that used larger (40 nm) Au labels, not only push the time resolution in long-time, continuous fluorescence-based single-molecule tracking but also show that highly photostable, photoluminescent nanoprobes of 10 nm size can be employed (AEE-coated QDs). These probes are also attractive because, unlike Au nanoparticles, they facilitate complex multicolor experiments.

Insights to Genetic Characterization Tools for Epidemiological Tracking of Francisella tularensis in Sweden

PubMed Central

Wahab, Tara; Birdsell, Dawn N.; Hjertqvist, Marika; Mitchell, Cedar L.; Wagner, David M.; Keim, Paul S.; Hedenström, Ingela; Löfdahl, Sven

2014-01-01

Tularaemia, caused by the bacterium Francisella tularensis, is endemic in Sweden and is poorly understood. The aim of this study was to evaluate the effectiveness of three different genetic typing systems to link a genetic type to the source and place of tularemia infection in Sweden. Canonical single nucleotide polymorphisms (canSNPs), MLVA including five variable number of tandem repeat loci and PmeI-PFGE were tested on 127 F. tularensis positive specimens collected from Swedish case-patients. All three typing methods identified two major genetic groups with near-perfect agreement. Higher genetic resolution was obtained with canSNP and MLVA compared to PFGE; F. tularensis samples were first assigned into ten phylogroups based on canSNPs followed by 33 unique MLVA types. Phylogroups were geographically analysed to reveal complex phylogeographic patterns in Sweden. The extensive phylogenetic diversity found within individual counties posed a challenge to linking specific genetic types with specific geographic locations. Despite this, a single phylogroup (B.22), defined by a SNP marker specific to a lone Swedish sequenced strain, did link genetic type with a likely geographic place. This result suggests that SNP markers, highly specific to a particular reference genome, may be found most frequently among samples recovered from the same location where the reference genome originated. This insight compels us to consider whole-genome sequencing (WGS) as the appropriate tool for effectively linking specific genetic type to geography. Comparing the WGS of an unknown sample to WGS databases of archived Swedish strains maximizes the likelihood of revealing those rare geographically informative SNPs. PMID:25401326

3. NORTHEAST SIDE, WITH A SINGLE BULLET GLASS WINDOW AND ...

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

3. NORTHEAST SIDE, WITH A SINGLE BULLET GLASS WINDOW AND SOUTHEAST REAR WITH ENTRY DOOR. - Edwards Air Force Base, South Base Sled Track, Observation Block House, Station "O" area, east end of Sled Track, Lancaster, Los Angeles County, CA

Single-Track Melt-Pool Measurements and Microstructures in Inconel 625

NASA Astrophysics Data System (ADS)

Ghosh, Supriyo; Ma, Li; Levine, Lyle E.; Ricker, Richard E.; Stoudt, Mark R.; Heigel, Jarred C.; Guyer, Jonathan E.

2018-06-01

We use single-track laser melting experiments and simulations on Inconel 625 to estimate the dimensions and microstructure of the resulting melt pool. Our work is based on a design-of-experiments approach which uses multiple laser power and scan speed combinations. Single-track experiments generated melt pools of certain dimensions that showed reasonable agreement with our finite-element calculations. Phase-field simulations were used to predict the size and segregation of the cellular microstructure that formed along the melt-pool boundaries for the solidification conditions that changed as a function of melt-pool dimensions.

Single-Track Melt-Pool Measurements and Microstructures in Inconel 625

NASA Astrophysics Data System (ADS)

Ghosh, Supriyo; Ma, Li; Levine, Lyle E.; Ricker, Richard E.; Stoudt, Mark R.; Heigel, Jarred C.; Guyer, Jonathan E.

2018-02-01

We use single-track laser melting experiments and simulations on Inconel 625 to estimate the dimensions and microstructure of the resulting melt pool. Our work is based on a design-of-experiments approach which uses multiple laser power and scan speed combinations. Single-track experiments generated melt pools of certain dimensions that showed reasonable agreement with our finite-element calculations. Phase-field simulations were used to predict the size and segregation of the cellular microstructure that formed along the melt-pool boundaries for the solidification conditions that changed as a function of melt-pool dimensions.

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii

PubMed Central

Caffaro-Filho, Roberto A.; Wong, Mayee; Harwood, Valerie J.; Moravcik, Philip; Fujioka, Roger S.

2016-01-01

ABSTRACT Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. IMPORTANCE This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. PMID:27613686

I’ll Be Back: On the Multiple Lives of Users of a Mobile Activity Tracking Application

PubMed Central

Lin, Zhiyuan; Althoff, Tim; Leskovec, Jure

2018-01-01

Mobile health applications that track activities, such as exercise, sleep, and diet, are becoming widely used. While these activity tracking applications have the potential to improve our health, user engagement and retention are critical factors for their success. However, long-term user engagement patterns in real-world activity tracking applications are not yet well understood. Here we study user engagement patterns within a mobile physical activity tracking application consisting of 115 million logged activities taken by over a million users over 31 months. Specifically, we show that over 75% of users return and re-engage with the application after prolonged periods of inactivity, no matter the duration of the inactivity. We find a surprising result that the re-engagement usage patterns resemble those of the start of the initial engagement period, rather than being a simple continuation of the end of the initial engagement period. This evidence points to a conceptual model of multiple lives of user engagement, extending the prevalent single life view of user activity. We demonstrate that these multiple lives occur because the users have a variety of different primary intents or goals for using the app. These primary intents are associated with how long each life lasts and how likely the user is to re-engage for a new life. We find evidence for users being more likely to stop using the app once they achieved their primary intent or goal (e.g., weight loss). However, these users might return once their original intent resurfaces (e.g., wanting to lose newly gained weight). We discuss implications of the multiple life paradigm and propose a novel prediction task of predicting the number of lives of a user. Based on insights developed in this work, including a marker of improved primary intent performance, our prediction models achieve 71% ROC AUC. Overall, our research has implications for modeling user re-engagement in health activity tracking applications and has consequences for how notifications, recommendations as well as gamification can be used to increase engagement. PMID:29780978

Oxygen Nanobubble Tracking by Light Scattering in Single Cells and Tissues.

PubMed

Bhandari, Pushpak; Wang, Xiaolei; Irudayaraj, Joseph

2017-03-28

Oxygen nanobubbles (ONBs) have significant potential in targeted imaging and treatment in cancer diagnosis and therapy. Precise localization and tracking of single ONBs is demonstrated based on hyperspectral dark-field microscope (HSDFM) to image and track single oxygen nanobubbles in single cells. ONBs were proposed as promising contrast-generating imaging agents due to their strong light scattering generated from nonuniformity of refractive index at the interface. With this powerful platform, we have revealed the trajectories and quantities of ONBs in cells, and demonstrated the relation between the size and diffusion coefficient. We have also evaluated the presence of ONBs in the nucleus with respect to an increase in incubation time and have quantified the uptake in single cells in ex vivo tumor tissues. Our results demonstrate that HSDFM can be a versatile platform to detect and measure cellulosic nanoparticles at the single-cell level and to assess the dynamics and trajectories of this delivery system.

Analysis of four microsatellite markers on the long arm of chromosome 9 by meiotic recombination in flow-sorted single sperm

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

Furlong, R.A.; Goudie, D.R.; Carter, N.P.

1993-06-01

Meiotic recombination in flow-sorted single sperm was used to analyze four highly polymorphic microsatellite markers on the long arm of chromosome 9. The microsatellites comprised three tightly linked markers: 9CMP1 (D9S109), 9CMP2 (D9S127), and D9S53, which map to 9q31, and a reference marker, ASS, which is located in 9q34.1. Haplotypes of single sperm were assessed by using PCR in a single-step multiplex reaction to amplify each locus. Recombinant haplotypes were identified by their relative infrequency and were analyzed using THREELOC, a maximum-likelihood-analysis program, and an adaptation of CRI-MAP. The most likely order of these markers was cen-D9S109-D9S127-D9S53-ASS-tel with D9S109, D9S127,more » and D9S53 being separated by a genetic distance of approximately 3%. The order of the latter three markers did not however achieve statistical significance using the THREELOC program. 21 refs., 2 figs., 4 tabs.« less

Characterization of single α-tracks by photoresist detection and AFM analysis-focus on biomedical science and technology

NASA Astrophysics Data System (ADS)

Falzone, Nadia; Myhra, Sverre; Chakalova, Radka; Hill, Mark A.; Thomson, James; Vallis, Katherine A.

2013-11-01

The interactions between energetic ions and biological and/or organic target materials have recently attracted theoretical and experimental attention, due to their implications for detector and device technologies, and for therapeutic applications. Most of the attention has focused on detection of the primary ionization tracks, and their effects, while recoil target atom tracks remain largely unexplored. Detection of tracks by a negative tone photoresist (SU-8), followed by standard development, in combination with analysis by atomic force microscopy, shows that both primary and recoil tracks are revealed as conical spikes, and can be characterized at high spatial resolution. The methodology has the potential to provide detailed information about single impact events, which may lead to more effective and informative detector technologies and advanced therapeutic procedures. In comparison with current characterization methods the advantageous features include: greater spatial resolution by an order of magnitude (20 nm) detection of single primary and associated recoil tracks; increased range of fluence (to 2.5 × 109 cm-2) sensitivity to impacts at grazing angle incidence; and better definition of the lateral interaction volume in target materials.

Microbial Source Tracking in Adjacent Karst Springs.

PubMed

Ohad, Shoshanit; Vaizel-Ohayon, Dalit; Rom, Meir; Guttman, Joseph; Berger, Diego; Kravitz, Valeria; Pilo, Shlomo; Huberman, Zohar; Kashi, Yechezkel; Rorman, Efrat

2015-08-01

Modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. Microbial source tracking (MST) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. This study was intended to assess karst spring susceptibilities to different fecal sources using MST quantitative PCR (qPCR) assays targeting human, bovine, and swine markers. It involved a dual-time monitoring frame: (i) monthly throughout the calendar year and (ii) daily during a rainfall event. Data integration was taken from both monthly and daily MST profile monitoring and improved identification of spring susceptibility to host fecal contamination; three springs located in close geographic proximity revealed different MST profiles. The Giach spring showed moderate fluctuations of MST marker quantities amid wet and dry samplings, while the Zuf spring had the highest rise of the GenBac3 marker during the wet event, which was mirrored in other markers as well. The revelation of human fecal contamination during the dry season not connected to incidents of raining leachates suggests a continuous and direct exposure to septic systems. Pigpens were identified in the watersheds of Zuf, Shefa, and Giach springs and on the border of the Gaaton spring watershed. Their impact was correlated with partial detection of the Pig-2-Bac marker in Gaaton spring, which was lower than detection levels in all three of the other springs. Ruminant and swine markers were detected intermittently, and their contamination potential during the wet samplings was exposed. These results emphasized the importance of sampling design to utilize the MST approach to delineate subtleties of fecal contamination in the environment. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Using the Image Analysis Method for Describing Soil Detachment by a Single Water Drop Impact

PubMed Central

Ryżak, Magdalena; Bieganowski, Andrzej

2012-01-01

The aim of the present work was to develop a method based on image analysis for describing soil detachment caused by the impact of a single water drop. The method consisted of recording tracks made by splashed particles on blotting paper under an optical microscope. The analysis facilitated division of the recorded particle tracks on the paper into drops, “comets” and single particles. Additionally, the following relationships were determined: (i) the distances of splash; (ii) the surface areas of splash tracks into relation to distance; (iii) the surface areas of the solid phase transported over a given distance; and (iv) the ratio of the solid phase to the splash track area in relation to distance. Furthermore, the proposed method allowed estimation of the weight of soil transported by a single water drop splash in relation to the distance of the water drop impact. It was concluded that the method of image analysis of splashed particles facilitated analysing the results at very low water drop energy and generated by single water drops.

7. 'Tunnel No 14, Concrete Lining,' Southern Pacific Standard SingleTrack ...

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

7. 'Tunnel No 14, Concrete Lining,' Southern Pacific Standard Single-Track Tunnel, ca. 1909. Under current numbering, this is now Tunnel 29 (HAER No. CA-205). - Central Pacific Transcontinental Railroad, Sacramento to Nevada state line, Sacramento, Sacramento County, CA

Spacing and length of passing sidings and the incremental capacity of single track.

DOT National Transportation Integrated Search

2016-02-18

The objective of this study is to evaluate the effect of initial siding spacing and distribution of siding length on the incremental capacity of infrastructure investments on single-track railway lines. Previous research has shown a linear reduction ...

Intra-operative prostate motion tracking using surface markers for robot-assisted laparoscopic radical prostatectomy

NASA Astrophysics Data System (ADS)

Esteghamatian, Mehdi; Sarkar, Kripasindhu; Pautler, Stephen E.; Chen, Elvis C. S.; Peters, Terry M.

2012-02-01

Radical prostatectomy surgery (RP) is the gold standard for treatment of localized prostate cancer (PCa). Recently, emergence of minimally invasive techniques such as Laparoscopic Radical Prostatectomy (LRP) and Robot-Assisted Laparoscopic Radical Prostatectomy (RARP) has improved the outcomes for prostatectomy. However, it remains difficult for the surgeons to make informed decisions regarding resection margins and nerve sparing since the location of the tumor within the organ is not usually visible in a laparoscopic view. While MRI enables visualization of the salient structures and cancer foci, its efficacy in LRP is reduced unless it is fused into a stereoscopic view such that homologous structures overlap. Registration of the MRI image and peri-operative ultrasound image using a tracked probe can potentially be exploited to bring the pre-operative information into alignment with the patient coordinate system during the procedure. While doing so, prostate motion needs to be compensated in real-time to synchronize the stereoscopic view with the pre-operative MRI during the prostatectomy procedure. In this study, a point-based stereoscopic tracking technique is investigated to compensate for rigid prostate motion so that the same motion can be applied to the pre-operative images. This method benefits from stereoscopic tracking of the surface markers implanted over the surface of the prostate phantom. The average target registration error using this approach was 3.25+/-1.43mm.

Automation and apps for clinical dental biomechanics.

PubMed

Adams, Bruce W

2016-09-01

The aim of this research summary is to introduce the current and ongoing work using smartphone video, tracking markers to measure musculoskeletal disorders of cranial and mandibular origin, and the potential significance of the technology to doctors and therapists. The MPA™ biomechanical measuring apps are in beta trials with various doctors and therapists. The technique requires substantial image processing and statistical analysis, best suited to server-side processing. A smartphone environment has enabled a virtual laboratory, which provides automated generation of graphics and in some cases automated interpretation. The system enables highly accurate real-time biomechanics studies using only a smartphone and tracking markers. Despite the technical challenges in setting up and testing of the virtual environment and with interpretation of clinical relevance, the trials have enabled a demonstration of real-time biomechanics studies. The technology has prompted a lot of discussion about the relevance of rapid assessment tools in clinical practice. It seems that a prior bias against motion tracking and its relevance is very strong with occlusion related use cases, yet there has been a general agreement about the use case for cranial movement tracking in managing complex issues related to the head, neck, and TMJ. Measurement of cranial and mandibular functions using a smartphone video as the input have been investigated. Ongoing research will depend upon doctors and therapists to provide feedback as to which uses are considered clinically relevant.

An analysis of particle track effects on solid mammalian tissues

NASA Technical Reports Server (NTRS)

Todd, P.; Clarkson, T. W. (Principal Investigator)

1992-01-01

Relative biological effectiveness (RBE) and quality factor (Q) at extreme values of linear energy transfer (LET) have been determined on the basis of experiments with single-cell systems and specific tissue responses. In typical single-cell systems, each heavy particle (Ar or Fe) passes through a single cell or no cell. In experiments on animal tissues, however, each heavy particle passes through several cells, and the LET can exceed 200 keV micrometers-1 in every cell. In most laboratory animal tissue systems, however, only a small portion of the hit cells are capable of expressing the end-point being measured, such as cell killing, mutation or carcinogenesis. The following question was therefore addressed: do RBEs and Q factors derived from single-cell experiments properly account for the damage at high LET when multiple cells are hit by HZE tracks? A review is offered in which measured radiation effects and known tissue properties are combined to estimate on the one hand, the number of cells at risk, p3n, per track, where n is the number of cells per track based on tissue and organ geometry, and p3 is the probability that a cell in the track is capable of expressing the experimental end-point. On the other hand, the tissue and single-cell responses are compared by determining the ratio RBE in tissue/RBE in corresponding single cells. Experimental data from the literature indicate that tissue RBEs at very high LET (Fe and Ar ions) are higher than corresponding single-cell RBEs, especially in tissues in which p3n is high.

Application of unscented Kalman filter for robust pose estimation in image-guided surgery

NASA Astrophysics Data System (ADS)

Vaccarella, Alberto; De Momi, Elena; Valenti, Marta; Ferrigno, Giancarlo; Enquobahrie, Andinet

2012-02-01

Image-guided surgery (IGS) allows clinicians to view current, intra-operative scenes superimposed on preoperative images (typically MRI or CT scans). IGS systems use localization systems to track and visualize surgical tools overlaid on top of preoperative images of the patient during surgery. The most commonly used localization systems in the Operating Rooms (OR) are optical tracking systems (OTS) due to their ease of use and cost effectiveness. However, OTS' suffer from the major drawback of line-of-sight requirements. State space approaches based on different implementations of the Kalman filter have recently been investigated in order to compensate for short line-of-sight occlusion. However, the proposed parameterizations for the rigid body orientation suffer from singularities at certain values of rotation angles. The purpose of this work is to develop a quaternion-based Unscented Kalman Filter (UKF) for robust optical tracking of both position and orientation of surgical tools in order to compensate marker occlusion issues. This paper presents preliminary results towards a Kalman-based Sensor Management Engine (SME). The engine will filter and fuse multimodal tracking streams of data. This work was motivated by our experience working in robot-based applications for keyhole neurosurgery (ROBOCAST project). The algorithm was evaluated using real data from NDI Polaris tracker. The results show that our estimation technique is able to compensate for marker occlusion with a maximum error of 2.5° for orientation and 2.36 mm for position. The proposed approach will be useful in over-crowded state-of-the-art ORs where achieving continuous visibility of all tracked objects will be difficult.

Hybrid MV-kV 3D respiratory motion tracking during radiation therapy with low imaging dose

NASA Astrophysics Data System (ADS)

Yan, Huagang; Li, Haiyun; Liu, Zhixiang; Nath, Ravinder; Liu, Wu

2012-12-01

A novel real-time adaptive MV-kV imaging framework for image-guided radiation therapy is developed to reduce the thoracic and abdominal tumor targeting uncertainty caused by respiration-induced intrafraction motion with ultra-low patient imaging dose. In our method, continuous stereoscopic MV-kV imaging is used at the beginning of a radiation therapy delivery for several seconds to measure the implanted marker positions. After this stereoscopic imaging period, the kV imager is switched off except for the times when no fiducial marker is detected in the cine-MV images. The 3D time-varying marker positions are estimated by combining the MV 2D projection data and the motion correlations between directional components of marker motion established from the stereoscopic imaging period and updated afterwards; in particular, the most likely position is assumed to be the position on the projection line that has the shortest distance to the first principal component line segment constructed from previous trajectory points. An adaptive windowed auto-regressive prediction is utilized to predict the marker position a short time later (310 ms and 460 ms in this study) to allow for tracking system latency. To demonstrate the feasibility and evaluate the accuracy of the proposed method, computer simulations were performed for both arc and fixed-gantry deliveries using 66 h of retrospective tumor motion data from 42 patients treated for thoracic or abdominal cancers. The simulations reveal that using our hybrid approach, a smaller than 1.2 mm or 1.5 mm root-mean-square tracking error can be achieved at a system latency of 310 ms or 460 ms, respectively. Because the kV imaging is only used for a short period of time in our method, extra patient imaging dose can be reduced by an order of magnitude compared to continuous MV-kV imaging, while the clinical tumor targeting accuracy for thoracic or abdominal cancers is maintained. Furthermore, no additional hardware is required with the proposed method.

Non-invasive timing of gas gun projectiles with light detection and ranging

NASA Astrophysics Data System (ADS)

Goodwin, P. M.; Bartram, B. D.; Gibson, L. L.; Wu, M.; Dattelbaum, D. M.

2014-05-01

We have developed a Light Detection and Ranging (LIDAR) diagnostic to track the position of a projectile inside of a gas gun launch tube in real-time. This capability permits the generation of precisely timed trigger pulses useful for triggering high-latency diagnostics such as a flash lamp-pumped laser. An initial feasibility test was performed using a 72 mm bore diameter single-stage gas gun routinely used for dynamic research at Los Alamos. A 655 nm pulsed diode laser operating at a pulse repetition rate of 100 kHz was used to interrogate the position of the moving projectile in real-time. The position of the projectile in the gun barrel was tracked over a distance of ~ 3 meters prior to impact. The position record showed that the projectile moved at a velocity of 489 m/s prior to impacting the target. This velocity was in good agreement with independent measurements of the projectile velocity by photon Doppler velocimetry and timing of the passage of the projectile through optical marker beams positioned at the muzzle of the gun. The time-to-amplitude conversion electronics used enable the LIDAR data to be processed in real-time to generate trigger pulses at preset separations between the projectile and target.

Identification of genetic variants associated with Huntington's disease progression: a genome-wide association study.

PubMed

Hensman Moss, Davina J; Pardiñas, Antonio F; Langbehn, Douglas; Lo, Kitty; Leavitt, Blair R; Roos, Raymund; Durr, Alexandra; Mead, Simon; Holmans, Peter; Jones, Lesley; Tabrizi, Sarah J

2017-09-01

Huntington's disease is caused by a CAG repeat expansion in the huntingtin gene, HTT. Age at onset has been used as a quantitative phenotype in genetic analysis looking for Huntington's disease modifiers, but is hard to define and not always available. Therefore, we aimed to generate a novel measure of disease progression and to identify genetic markers associated with this progression measure. We generated a progression score on the basis of principal component analysis of prospectively acquired longitudinal changes in motor, cognitive, and imaging measures in the 218 indivduals in the TRACK-HD cohort of Huntington's disease gene mutation carriers (data collected 2008-11). We generated a parallel progression score using data from 1773 previously genotyped participants from the European Huntington's Disease Network REGISTRY study of Huntington's disease mutation carriers (data collected 2003-13). We did a genome-wide association analyses in terms of progression for 216 TRACK-HD participants and 1773 REGISTRY participants, then a meta-analysis of these results was undertaken. Longitudinal motor, cognitive, and imaging scores were correlated with each other in TRACK-HD participants, justifying use of a single, cross-domain measure of disease progression in both studies. The TRACK-HD and REGISTRY progression measures were correlated with each other (r=0·674), and with age at onset (TRACK-HD, r=0·315; REGISTRY, r=0·234). The meta-analysis of progression in TRACK-HD and REGISTRY gave a genome-wide significant signal (p=1·12 × 10 -10 ) on chromosome 5 spanning three genes: MSH3, DHFR, and MTRNR2L2. The genes in this locus were associated with progression in TRACK-HD (MSH3 p=2·94 × 10 -8 DHFR p=8·37 × 10 -7 MTRNR2L2 p=2·15 × 10 -9 ) and to a lesser extent in REGISTRY (MSH3 p=9·36 × 10 -4 DHFR p=8·45 × 10 -4 MTRNR2L2 p=1·20 × 10 -3 ). The lead single nucleotide polymorphism (SNP) in TRACK-HD (rs557874766) was genome-wide significant in the meta-analysis (p=1·58 × 10 -8 ), and encodes an aminoacid change (Pro67Ala) in MSH3. In TRACK-HD, each copy of the minor allele at this SNP was associated with a 0·4 units per year (95% CI 0·16-0·66) reduction in the rate of change of the Unified Huntington's Disease Rating Scale (UHDRS) Total Motor Score, and a reduction of 0·12 units per year (95% CI 0·06-0·18) in the rate of change of UHDRS Total Functional Capacity score. These associations remained significant after adjusting for age of onset. The multidomain progression measure in TRACK-HD was associated with a functional variant that was genome-wide significant in our meta-analysis. The association in only 216 participants implies that the progression measure is a sensitive reflection of disease burden, that the effect size at this locus is large, or both. Knockout of Msh3 reduces somatic expansion in Huntington's disease mouse models, suggesting this mechanism as an area for future therapeutic investigation. The European Commission FP7 NeurOmics project; CHDI Foundation; the Medical Research Council UK; the Brain Research Trust; and the Guarantors of Brain. Copyright © 2017 Elsevier Ltd. All rights reserved.

Radiation modelling and performance evaluations of fixed, single- and double-axis tracking surfaces: a case study for Dhahran city, Saudi Arabia

NASA Astrophysics Data System (ADS)

Abdulsalam, Alrowashed; Idris, Azni Bin; Ahmad, Thamer; Ahsan, Amimul

2017-01-01

This work overviews the solar radiation basics and insolation of different surfaces is presented. A complete solar radiation modelling and investigation on the effect of horizontal plate, yearly tilt, monthly tilt, and single-axis and double-axis tracking surface on the insolation are carried out to conduct performance evaluation using the case study in Dhahran city of Saudi Arabia. The increments received by insolation for the yearly tilt, monthly tilt, and single-axis and dual-axis tracking surface with respect to traditional flat-plate collector is estimated. The results show that the yearly optimal tilt angle due to the south is close to the 0.913 time latitude of Dhahran. It is found that the yearly irradiation gains using yearly and monthly optimal tilts relative to flat panel installation are 7% and 14%, respectively. The yearly insulation gains made by single-axis and dual-axis continuous tracking surfaces are 33% and 48%, respectively.

A population 'consensus', partial linkage map of Picea abies Karst. based on RAPD markers

Treesearch

G. Bucci; Thomas L. Kubisiak; W.L. Nance; P. Menozzi

1997-01-01

The authors built a "consensus" partial linkage map based on RAPD markers using 48 sibships of eight megagametophytes each from a natural population of Norway spruce. A RAPD linkage map for a single individual from the same population had previously been constructed. Using 30 random decamers that had yielded 83 RAPD markers in the single-tree map, eight...

Comparison of Maximum Likelihood Estimation Approach and Regression Approach in Detecting Quantitative Trait Lco Using RAPD Markers

Treesearch

Changren Weng; Thomas L. Kubisiak; C. Dana Nelson; James P. Geaghan; Michael Stine

1999-01-01

Single marker regression and single marker maximum likelihood estimation were tied to detect quantitative trait loci (QTLs) controlling the early height growth of longleaf pine and slash pine using a ((longleaf pine x slash pine) x slash pine) BC, population consisting of 83 progeny. Maximum likelihood estimation was found to be more power than regression and could...

Performance Characteristics of qPCR Assays Targeting Human- and Ruminant-Associated Bacteroidetes for Microbial Source Tracking across Sixteen Countries on Six Continents

PubMed Central

2013-01-01

Numerous quantitative PCR assays for microbial fecal source tracking (MST) have been developed and evaluated in recent years. Widespread application has been hindered by a lack of knowledge regarding the geographical stability and hence applicability of such methods beyond the regional level. This study assessed the performance of five previously reported quantitative PCR assays targeting human-, cattle-, or ruminant-associated Bacteroidetes populations on 280 human and animal fecal samples from 16 countries across six continents. The tested cattle-associated markers were shown to be ruminant-associated. The quantitative distributions of marker concentrations in target and nontarget samples proved to be essential for the assessment of assay performance and were used to establish a new metric for quantitative source-specificity. In general, this study demonstrates that stable target populations required for marker-based MST occur around the globe. Ruminant-associated marker concentrations were strongly correlated with total intestinal Bacteroidetes populations and with each other, indicating that the detected ruminant-associated populations seem to be part of the intestinal core microbiome of ruminants worldwide. Consequently tested ruminant-targeted assays appear to be suitable quantitative MST tools beyond the regional level while the targeted human-associated populations seem to be less prevalent and stable, suggesting potential for improvements in human-targeted methods. PMID:23755882

Performance analysis of visual tracking algorithms for motion-based user interfaces on mobile devices

NASA Astrophysics Data System (ADS)

Winkler, Stefan; Rangaswamy, Karthik; Tedjokusumo, Jefry; Zhou, ZhiYing

2008-02-01

Determining the self-motion of a camera is useful for many applications. A number of visual motion-tracking algorithms have been developed till date, each with their own advantages and restrictions. Some of them have also made their foray into the mobile world, powering augmented reality-based applications on phones with inbuilt cameras. In this paper, we compare the performances of three feature or landmark-guided motion tracking algorithms, namely marker-based tracking with MXRToolkit, face tracking based on CamShift, and MonoSLAM. We analyze and compare the complexity, accuracy, sensitivity, robustness and restrictions of each of the above methods. Our performance tests are conducted over two stages: The first stage of testing uses video sequences created with simulated camera movements along the six degrees of freedom in order to compare accuracy in tracking, while the second stage analyzes the robustness of the algorithms by testing for manipulative factors like image scaling and frame-skipping.

Suture spanning augmentation of single-row rotator cuff repair: a biomechanical analysis.

PubMed

Early, Nicholas A; Elias, John J; Lippitt, Steven B; Filipkowski, Danielle E; Pedowitz, Robert A; Ciccone, William J

2017-02-01

This in vitro study evaluated the biomechanical benefit of adding spanning sutures to single-row rotator cuff repair. Mechanical testing was performed to evaluate 9 pairs of cadaveric shoulders with complete rotator cuff repairs, with a single-row technique used on one side and the suture spanning technique on the other. The spanning technique included sutures from 2 lateral anchors securing tendon near the musculotendinous junction, spanning the same anchor placement from single-row repair. The supraspinatus muscle was loaded to 100 N at 0.25 Hz for 100 cycles, followed by a ramp to failure. Markers and a video tracking system measured anterior and posterior gap formation across the repair at 25-cycle intervals. The force at which the stiffness decreased by 50% and 75% was determined. Data were compared using paired t-tests. One single-row repair failed at <25 cycles. Both anterior and posterior gap distances tended to be 1 to 2 mm larger for the single-row repairs than for the suture spanning technique. The difference was statistically significant at all cycles for the posterior gap formation (P ≤ .02). The trends were not significant for the anterior gap (P ≥ .13). The loads at which the stiffness decreased by 50% and 75% did not differ significantly between the 2 types of repair (P ≥ .10). The suture spanning technique primarily improved posterior gap formation. Decreased posterior gap formation could reduce failure rates for rotator cuff repair. Copyright © 2017 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies.

PubMed

Li, Chenhong; Riethoven, Jean-Jack M; Naylor, Gavin J P

2012-09-01

Recent innovations in next-generation sequencing have lowered the cost of genome projects. Nevertheless, sequencing entire genomes for all representatives in a study remains expensive and unnecessary for most studies in ecology, evolution and conservation. It is still more cost-effective and efficient to target and sequence single-copy nuclear gene markers for such studies. Many tools have been developed for identifying nuclear markers, but most of these have focused on particular taxonomic groups. We have built a searchable database, EvolMarkers, for developing single-copy coding sequence (CDS) and exon-primed-intron-crossing (EPIC) markers that is designed to work across a broad range of phylogenetic divergences. The database is made up of single-copy CDS derived from BLAST searches of a variety of metazoan genomes. Users can search the database for different types of markers (CDS or EPIC) that are common to different sets of input species with different divergence characteristics. EvolMarkers can be applied to any taxonomic group for which genome data are available for two or more species. We included 82 genomes in the first version of EvolMarkers and have found the methods to be effective across Placozoa, Cnidaria, Arthropod, Nematoda, Annelida, Mollusca, Echinodermata, Hemichordata, Chordata and plants. We demonstrate the effectiveness of searching for CDS markers within annelids and show how to find potentially useful intronic markers within the lizard Anolis. © 2012 Blackwell Publishing Ltd.

Single nanoparticle tracking spectroscopic microscope

DOEpatents

Yang, Haw [Moraga, CA; Cang, Hu [Berkeley, CA; Xu, Cangshan [Berkeley, CA; Wong, Chung M [San Gabriel, CA

2011-07-19

A system that can maintain and track the position of a single nanoparticle in three dimensions for a prolonged period has been disclosed. The system allows for continuously imaging the particle to observe any interactions it may have. The system also enables the acquisition of real-time sequential spectroscopic information from the particle. The apparatus holds great promise in performing single molecule spectroscopy and imaging on a non-stationary target.

The ultimate picture-the combination of live cell superresolution microscopy and single molecule tracking yields highest spatio-temporal resolution.

PubMed

Dersch, Simon; Graumann, Peter L

2018-06-01

We are witnessing a breathtaking development in light (fluorescence) microscopy, where structures can be resolved down to the size of a ribosome within cells. This has already yielded surprising insight into the subcellular structure of cells, including the smallest cells, bacteria. Moreover, it has become possible to visualize and track single fluorescent protein fusions in real time, and quantify molecule numbers within individual cells. Combined, super resolution and single molecule tracking are pushing the limits of our understanding of the spatio-temporal organization even of the smallest cells to an unprecedented depth. Copyright © 2017 Elsevier Ltd. All rights reserved.

Device localization and dynamic scan plane selection using a wireless magnetic resonance imaging detector array.

PubMed

Riffe, Matthew J; Yutzy, Stephen R; Jiang, Yun; Twieg, Michael D; Blumenthal, Colin J; Hsu, Daniel P; Pan, Li; Gilson, Wesley D; Sunshine, Jeffrey L; Flask, Christopher A; Duerk, Jeffrey L; Nakamoto, Dean; Gulani, Vikas; Griswold, Mark A

2014-06-01

A prototype wireless guidance device using single sideband amplitude modulation (SSB) is presented for a 1.5T magnetic resonance imaging system. The device contained three fiducial markers each mounted to an independent receiver coil equipped with wireless SSB technology. Acquiring orthogonal projections of these markers determined the position and orientation of the device, which was used to define the scan plane for a subsequent image acquisition. Device localization and scan plane update required approximately 30 ms, so it could be interleaved with high temporal resolution imaging. Since the wireless device is used for localization and does not require full imaging capability, the design of the SSB wireless system was simplified by allowing an asynchronous clock between the transmitter and receiver. When coupled to a high readout bandwidth, the error caused by the lack of a shared frequency reference was quantified to be less than one pixel (0.78 mm) in the projection acquisitions. Image guidance with the prototype was demonstrated with a phantom where a needle was successfully guided to a target and contrast was delivered. The feasibility of active tracking with a wireless detector array is demonstrated. Wireless arrays could be incorporated into devices to assist in image-guided procedures. Copyright © 2013 Wiley Periodicals, Inc.

Device localization and dynamic scan plane selection using a wireless MRI detector array

PubMed Central

Riffe, Matthew J.; Yutzy, Stephen R.; Jiang, Yun; Twieg, Michael D.; Blumenthal, Colin J.; Hsu, Daniel P.; Pan, Li; Gilson, Wesley D.; Sunshine, Jeffrey L.; Flask, Christopher A.; Duerk, Jeffrey L.; Nakamoto, Dean; Gulani, Vikas; Griswold, Mark A.

2013-01-01

Purpose A prototype wireless guidance device using single sideband amplitude modulation (SSB) is presented for a 1.5T MRI system. Methods The device contained three fiducial markers each mounted to an independent receiver coil equipped with wireless SSB technology. Acquiring orthogonal projections of these markers determined the position and orientation of the device, which was used to define the scan plane for a subsequent image acquisition. Device localization and scan plane update required approximately 30 ms, so it could be interleaved with high temporal resolution imaging. Since the wireless device is used for localization and doesn’t require full imaging capability, the design of the SSB wireless system was simplified by allowing an asynchronous clock between the transmitter and receiver. Results When coupled to a high readout bandwidth, the error caused by the lack of a shared frequency reference was quantified to be less than one pixel (0.78 mm) in the projection acquisitions. Image-guidance with the prototype was demonstrated with a phantom where a needle was successfully guided to a target and contrast was delivered. Conclusion The feasibility of active tracking with a wireless detector array is demonstrated. Wireless arrays could be incorporated into devices to assist in image-guided procedures. PMID:23900921

A low cost PSD-based monocular motion capture system

NASA Astrophysics Data System (ADS)

Ryu, Young Kee; Oh, Choonsuk

2007-10-01

This paper describes a monocular PSD-based motion capture sensor to employ with commercial video game systems such as Microsoft's XBOX and Sony's Playstation II. The system is compact, low-cost, and only requires a one-time calibration at the factory. The system includes a PSD(Position Sensitive Detector) and active infrared (IR) LED markers that are placed on the object to be tracked. The PSD sensor is placed in the focal plane of a wide-angle lens. The micro-controller calculates the 3D position of the markers using only the measured intensity and the 2D position on the PSD. A series of experiments were performed to evaluate the performance of our prototype system. From the experimental results we see that the proposed system has the advantages of the compact size, the low cost, the easy installation, and the high frame rates to be suitable for high speed motion tracking in games.

Optical Indoor Positioning System Based on TFT Technology.

PubMed

Gőzse, István

2015-12-24

A novel indoor positioning system is presented in the paper. Similarly to the camera-based solutions, it is based on visual detection, but it conceptually differs from the classical approaches. First, the objects are marked by LEDs, and second, a special sensing unit is applied, instead of a camera, to track the motion of the markers. This sensing unit realizes a modified pinhole camera model, where the light-sensing area is fixed and consists of a small number of sensing elements (photodiodes), and it is the hole that can be moved. The markers are tracked by controlling the motion of the hole, such that the light of the LEDs always hits the photodiodes. The proposed concept has several advantages: Apart from its low computational demands, it is insensitive to the disturbing ambient light. Moreover, as every component of the system can be realized by simple and inexpensive elements, the overall cost of the system can be kept low.

Characterization of sources and loadings of fecal pollutants using microbial source tracking assays in urban and rural areas of the Grand River Watershed, Southwestern Ontario.

PubMed

Lee, Dae-Young; Lee, Hung; Trevors, Jack T; Weir, Susan C; Thomas, Janis L; Habash, Marc

2014-04-15

Sources of fecal water pollution were assessed in the Grand River and two of its tributaries (Ontario, Canada) using total and host-specific (human and bovine) Bacteroidales genetic markers in conjunction with reference information, such as land use and weather. In-stream levels of the markers and culturable Escherichia coli were also monitored during multiple rain events to gain information on fecal loadings to catchment from diffuse sources. Elevated human-specific marker levels were accurately identified in river water impacted by a municipal wastewater treatment plant (WWTP) effluent and at a downstream site in the Grand River. In contrast, the bovine-specific marker showed high levels of cattle fecal pollution in two tributaries, both of which are characterized as intensely farmed areas. The bovine-specific Bacteroidales marker increased with rainfall in the agricultural tributaries, indicating enhanced loading of cattle-derived fecal pollutants to river from non-point sources following rain events. However, rain-triggered fecal loading was not substantiated in urban settings, indicating continuous inputs of human-originated fecal pollutants from point sources, such as WWTP effluent. This study demonstrated that the Bacteroidales source tracking assays, in combination with land use information and hydrological data, may provide additional insight into the spatial and temporal distribution of source-specific fecal contamination in streams impacted by varying land uses. Using the approach described in this study may help to characterize impacted water sources and to design targeted land use management plans in other watersheds in the future. Copyright © 2014 Elsevier Ltd. All rights reserved.

NucliTrack: an integrated nuclei tracking application.

PubMed

Cooper, Sam; Barr, Alexis R; Glen, Robert; Bakal, Chris

2017-10-15

Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack's interactive, graphical interface makes it significantly more user friendly. NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. sam@socooper.com. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species.

PubMed

Moolhuijzen, P; Cakir, M; Hunter, A; Schibeci, D; Macgregor, A; Smith, C; Francki, M; Jones, M G K; Appels, R; Bellgard, M

2006-06-01

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin.

Remote Marker-Based Tracking for UAV Landing Using Visible-Light Camera Sensor

PubMed Central

Nguyen, Phong Ha; Kim, Ki Wan; Lee, Young Won; Park, Kang Ryoung

2017-01-01

Unmanned aerial vehicles (UAVs), which are commonly known as drones, have proved to be useful not only on the battlefields where manned flight is considered too risky or difficult, but also in everyday life purposes such as surveillance, monitoring, rescue, unmanned cargo, aerial video, and photography. More advanced drones make use of global positioning system (GPS) receivers during the navigation and control loop which allows for smart GPS features of drone navigation. However, there are problems if the drones operate in heterogeneous areas with no GPS signal, so it is important to perform research into the development of UAVs with autonomous navigation and landing guidance using computer vision. In this research, we determined how to safely land a drone in the absence of GPS signals using our remote maker-based tracking algorithm based on the visible light camera sensor. The proposed method uses a unique marker designed as a tracking target during landing procedures. Experimental results show that our method significantly outperforms state-of-the-art object trackers in terms of both accuracy and processing time, and we perform test on an embedded system in various environments. PMID:28867775

Evaluating the Promise of Single-Track Year-Round Schools.

ERIC Educational Resources Information Center

Haenn, Joseph F.

1996-01-01

Describes two single-track year-round elementary schools in Durham, North Carolina, established in discrete attendance zones. Remediation and enrichment activities were provided during intersession. Low-SES students were overrepresented in remediation sessions. Student outcomes data (end-of-grade reading and math test scores) suggest that…

Nonrigid motion compensation in B-mode and contrast enhanced ultrasound image sequences of the carotid artery

NASA Astrophysics Data System (ADS)

Carvalho, Diego D. B.; Akkus, Zeynettin; Bosch, Johan G.; van den Oord, Stijn C. H.; Niessen, Wiro J.; Klein, Stefan

2014-03-01

In this work, we investigate nonrigid motion compensation in simultaneously acquired (side-by-side) B-mode ultrasound (BMUS) and contrast enhanced ultrasound (CEUS) image sequences of the carotid artery. These images are acquired to study the presence of intraplaque neovascularization (IPN), which is a marker of plaque vulnerability. IPN quantification is visualized by performing the maximum intensity projection (MIP) on the CEUS image sequence over time. As carotid images contain considerable motion, accurate global nonrigid motion compensation (GNMC) is required prior to the MIP. Moreover, we demonstrate that an improved lumen and plaque differentiation can be obtained by averaging the motion compensated BMUS images over time. We propose to use a previously published 2D+t nonrigid registration method, which is based on minimization of pixel intensity variance over time, using a spatially and temporally smooth B-spline deformation model. The validation compares displacements of plaque points with manual trackings by 3 experts in 11 carotids. The average (+/- standard deviation) root mean square error (RMSE) was 99+/-74μm for longitudinal and 47+/-18μm for radial displacements. These results were comparable with the interobserver variability, and with results of a local rigid registration technique based on speckle tracking, which estimates motion in a single point, whereas our approach applies motion compensation to the entire image. In conclusion, we evaluated that the GNMC technique produces reliable results. Since this technique tracks global deformations, it can aid in the quantification of IPN and the delineation of lumen and plaque contours.

Multicolor Three-Dimensional Tracking for Single-Molecule Fluorescence Resonance Energy Transfer Measurements

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

Keller, Aaron M.; DeVore, Matthew S.; Stich, Dominik G.

Single-molecule fluorescence resonance energy transfer (smFRET) remains a widely utilized and powerful tool for quantifying heterogeneous interactions and conformational dynamics of biomolecules. However, traditional smFRET experiments either are limited to short observation times (typically less than 1 ms) in the case of “burst” confocal measurements or require surface immobilization which usually has a temporal resolution limited by the camera framing rate. We developed a smFRET 3D tracking microscope that is capable of observing single particles for extended periods of time with high temporal resolution. The confocal tracking microscope utilizes closed-loop feedback to follow the particle in solution by recentering itmore » within two overlapping tetrahedral detection elements, corresponding to donor and acceptor channels. We demonstrated the microscope’s multicolor tracking capability via random walk simulations and experimental tracking of 200 nm fluorescent beads in water with a range of apparent smFRET efficiency values, 0.45-0.69. We also demonstrated the microscope’s capability to track and quantify double-stranded DNA undergoing intramolecular smFRET in a viscous glycerol solution. In future experiments, the smFRET 3D tracking system will be used to study protein conformational dynamics while diffusing in solution and native biological environments with high temporal resolution.« less

Multicolor Three-Dimensional Tracking for Single-Molecule Fluorescence Resonance Energy Transfer Measurements

DOE PAGES

Keller, Aaron M.; DeVore, Matthew S.; Stich, Dominik G.; ...

2018-04-19

Single-molecule fluorescence resonance energy transfer (smFRET) remains a widely utilized and powerful tool for quantifying heterogeneous interactions and conformational dynamics of biomolecules. However, traditional smFRET experiments either are limited to short observation times (typically less than 1 ms) in the case of “burst” confocal measurements or require surface immobilization which usually has a temporal resolution limited by the camera framing rate. We developed a smFRET 3D tracking microscope that is capable of observing single particles for extended periods of time with high temporal resolution. The confocal tracking microscope utilizes closed-loop feedback to follow the particle in solution by recentering itmore » within two overlapping tetrahedral detection elements, corresponding to donor and acceptor channels. We demonstrated the microscope’s multicolor tracking capability via random walk simulations and experimental tracking of 200 nm fluorescent beads in water with a range of apparent smFRET efficiency values, 0.45-0.69. We also demonstrated the microscope’s capability to track and quantify double-stranded DNA undergoing intramolecular smFRET in a viscous glycerol solution. In future experiments, the smFRET 3D tracking system will be used to study protein conformational dynamics while diffusing in solution and native biological environments with high temporal resolution.« less

Optical Mapping of Membrane Potential and Epicardial Deformation in Beating Hearts.

PubMed

Zhang, Hanyu; Iijima, Kenichi; Huang, Jian; Walcott, Gregory P; Rogers, Jack M

2016-07-26

Cardiac optical mapping uses potentiometric fluorescent dyes to image membrane potential (Vm). An important limitation of conventional optical mapping is that contraction is usually arrested pharmacologically to prevent motion artifacts from obscuring Vm signals. However, these agents may alter electrophysiology, and by abolishing contraction, also prevent optical mapping from being used to study coupling between electrical and mechanical function. Here, we present a method to simultaneously map Vm and epicardial contraction in the beating heart. Isolated perfused swine hearts were stained with di-4-ANEPPS and fiducial markers were glued to the epicardium for motion tracking. The heart was imaged at 750 Hz with a video camera. Fluorescence was excited with cyan or blue LEDs on alternating camera frames, thus providing a 375-Hz effective sampling rate. Marker tracking enabled the pixel(s) imaging any epicardial site within the marked region to be identified in each camera frame. Cyan- and blue-elicited fluorescence have different sensitivities to Vm, but other signal features, primarily motion artifacts, are common. Thus, taking the ratio of fluorescence emitted by a motion-tracked epicardial site in adjacent frames removes artifacts, leaving Vm (excitation ratiometry). Reconstructed Vm signals were validated by comparison to monophasic action potentials and to conventional optical mapping signals. Binocular imaging with additional video cameras enabled marker motion to be tracked in three dimensions. From these data, epicardial deformation during the cardiac cycle was quantified by computing finite strain fields. We show that the method can simultaneously map Vm and strain in a left-sided working heart preparation and can image changes in both electrical and mechanical function 5 min after the induction of regional ischemia. By allowing high-resolution optical mapping in the absence of electromechanical uncoupling agents, the method relieves a long-standing limitation of optical mapping and has potential to enhance new studies in coupled cardiac electromechanics. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Screening for malnutrition in nursing home residents: comparison of different risk markers and their association to functional impairment.

PubMed

Stange, I; Poeschl, K; Stehle, P; Sieber, C C; Volkert, D

2013-04-01

To identify nursing home residents with malnutrition or at risk of malnutrition by using different markers, determine if the Mini Nutritional Assessment (MNA®) is able to identify all residents at risk according to single risk markers and explore the relation between risk markers and functional impairment. Cross-sectional study. Six German nursing homes. 286 residents (86±7y, 89% female). Screening for malnutrition or its risk included low BMI (≤22 kg/m²), recent weight loss (WL), low food intake (LI) as single risk markers and MNA (<24 points, p.) as composite marker. Prevalence of single nutritional risk markers in different MNA categories was compared by cross-tables. Mental (cognition, mood) and physical function (mobility) were assessed by interviewing nursing staff and association of impaired status to nutritional risk markers determined by Chi² test. 32.9% of residents had a low BMI, 11.9% WL and 21.3% LI. 60.2% were categorized malnourished (18.2%) or at risk of malnutrition (42.0%) by MNA. 64% presented at least one of these nutritional risk markers. Of those classified malnourished by MNA, 96.2% also showed low BMI, WL or LI. In contrast, eleven residents (9.6%) considered well-nourished by MNA presented single risk markers (9 low BMI, 2 WL). Cognitive impairment, depressive symptoms and immobility was present in 59.0%, 20.8% and 25.5%, respectively. Functional impairment, and in particular severe impairment, was to a higher proportion present in residents at nutritional risk independent of the chosen marker (MNA<24 p., low BMI, WL, LI). The high prevalence of nutritional risk highlights the importance of regular screening of nursing home residents. The MNA identified nearly all residents with low BMI, WL and LI. The close association between nutritional risk and functional impairment requires increased awareness for nutritional problems especially in functionally impaired residents, to early initiate nutritional measures and thus, prevent further nutritional and functional deterioration.

Targeting neurotransmitter receptors with nanoparticles in vivo allows single-molecule tracking in acute brain slices

NASA Astrophysics Data System (ADS)

Varela, Juan A.; Dupuis, Julien P.; Etchepare, Laetitia; Espana, Agnès; Cognet, Laurent; Groc, Laurent

2016-03-01

Single-molecule imaging has changed the way we understand many biological mechanisms, particularly in neurobiology, by shedding light on intricate molecular events down to the nanoscale. However, current single-molecule studies in neuroscience have been limited to cultured neurons or organotypic slices, leaving as an open question the existence of fast receptor diffusion in intact brain tissue. Here, for the first time, we targeted dopamine receptors in vivo with functionalized quantum dots and were able to perform single-molecule tracking in acute rat brain slices. We propose a novel delocalized and non-inflammatory way of delivering nanoparticles (NPs) in vivo to the brain, which allowed us to label and track genetically engineered surface dopamine receptors in neocortical neurons, revealing inherent behaviour and receptor activity regulations. We thus propose a NP-based platform for single-molecule studies in the living brain, opening new avenues of research in physiological and pathological animal models.

How far could energy transport within a single crystal

NASA Astrophysics Data System (ADS)

Zhang, Yifan; Che, Yanke; Zhao, Jincai; Steve, Granick

Efficient transport of excitation energy over long distance is a vital process in light-harvesting systems and molecular electronics. The energy transfer distance is largely restricted by the probability decay of the exciton when hopping within a single crystal. Here, we fabricated an organic single crystal within which the energy could transfer more than 100 μm, a distance only limited by its crystal size. Our system could be regarded as a ``Sprint relay game'' performing on different surface of tracks. Photoinduced ``athletes'' (excitons) triggered intermolecular ``domino'' reaction to propagate energy for a long distance. In addition, athletes with the same ability runs much farther on smooth ideal track (single crystal assembled from merely van der Waals interaction) than bumpy mud track (crystal assembled from combination of pi-stacking, hydrogen bond and van der Waals interactions). Our finding presents new physics on enhancing energy transfer length within a single crystal. Current Affiliation: Institute for Basic Science, South Korea.

Single quantum dot tracking reveals the impact of nanoparticle surface on intracellular state.

PubMed

Zahid, Mohammad U; Ma, Liang; Lim, Sung Jun; Smith, Andrew M

2018-05-08

Inefficient delivery of macromolecules and nanoparticles to intracellular targets is a major bottleneck in drug delivery, genetic engineering, and molecular imaging. Here we apply live-cell single-quantum-dot imaging and tracking to analyze and classify nanoparticle states after intracellular delivery. By merging trajectory diffusion parameters with brightness measurements, multidimensional analysis reveals distinct and heterogeneous populations that are indistinguishable using single parameters alone. We derive new quantitative metrics of particle loading, cluster distribution, and vesicular release in single cells, and evaluate intracellular nanoparticles with diverse surfaces following osmotic delivery. Surface properties have a major impact on cell uptake, but little impact on the absolute cytoplasmic numbers. A key outcome is that stable zwitterionic surfaces yield uniform cytosolic behavior, ideal for imaging agents. We anticipate that this combination of quantum dots and single-particle tracking can be widely applied to design and optimize next-generation imaging probes, nanoparticle therapeutics, and biologics.

Impact of agglomeration state of nano- and submicron sized gold particles on pulmonary inflammation

PubMed Central

2010-01-01

Background Nanoparticle (NP) toxicity testing comes with many challenges. Characterization of the test substance is of crucial importance and in the case of NPs, agglomeration/aggregation state in physiological media needs to be considered. In this study, we have addressed the effect of agglomerated versus single particle suspensions of nano- and submicron sized gold on the inflammatory response in the lung. Rats were exposed to a single dose of 1.6 mg/kg body weight (bw) of spherical gold particles with geometric diameters of 50 nm or 250 nm diluted either by ultrapure water or by adding phosphate buffered saline (PBS). A single dose of 1.6 mg/kg bw DQ12 quartz was used as a positive control for pulmonary inflammation. Extensive characterization of the particle suspensions has been performed by determining the zetapotential, pH, gold concentration and particle size distribution. Primary particle size and particle purity has been verified using transmission electron microscopy (TEM) techniques. Pulmonary inflammation (total cell number, differential cell count and pro-inflammatory cytokines), cell damage (total protein and albumin) and cytotoxicity (alkaline phosphatase and lactate dehydrogenase) were determined in bronchoalveolar lavage fluid (BALF) and acute systemic effects in blood (total cell number, differential cell counts, fibrinogen and C-reactive protein) 3 and 24 hours post exposure. Uptake of gold particles in alveolar macrophages has been determined by TEM. Results Particles diluted in ultrapure water are well dispersed, while agglomerates are formed when diluting in PBS. The particle size of the 50 nm particles was confirmed, while the 250 nm particles appear to be 200 nm using tracking analysis and 210 nm using TEM. No major differences in pulmonary and systemic toxicity markers were observed after instillation of agglomerated versus single gold particles of different sizes. Both agglomerated as well as single nanoparticles were taken up by macrophages. Conclusion Primary particle size, gold concentration and particle purity are important features to check, since these characteristics may deviate from the manufacturer's description. Suspensions of well dispersed 50 nm and 250 nm particles as well as their agglomerates produced very mild pulmonary inflammation at the same mass based dose. We conclude that single 50 nm gold particles do not pose a greater acute hazard than their agglomerates or slightly larger gold particles when using pulmonary inflammation as a marker for toxicity. PMID:21126342

Chimpanzees (Pan troglodytes) use markers to monitor the movement of a hidden item.

PubMed

Beran, Michael J; Beran, Mary M; Menzel, Charles R

2005-10-01

Four chimpanzees (Pan troglodytes) monitored the movement of hidden items in arrays of opaque cups. A chocolate candy was hidden in an array of four cups and temporarily presented paper markers indicated the location of the candy (which otherwise was not visible). These markers were either non-symbolic or symbolic (lexigram) stimuli that in other contexts acted as a label for the hidden candy, and the array was either rotated 180 degrees after the marker was removed or the array remained in the same location. For three of four chimpanzees, performance was better than chance in all conditions and there was no effect of the type of marker. These experiments indicate that chimpanzees can track the movement of a hidden item in an array of identical cups even when they never see the item itself, but only see a temporarily presented marker for the location of that item. However, there was no benefit to the use of symbolic as opposed to non-symbolic stimuli in this performance.

Genomic Selection in Multi-environment Crop Trials.

PubMed

Oakey, Helena; Cullis, Brian; Thompson, Robin; Comadran, Jordi; Halpin, Claire; Waugh, Robbie

2016-05-03

Genomic selection in crop breeding introduces modeling challenges not found in animal studies. These include the need to accommodate replicate plants for each line, consider spatial variation in field trials, address line by environment interactions, and capture nonadditive effects. Here, we propose a flexible single-stage genomic selection approach that resolves these issues. Our linear mixed model incorporates spatial variation through environment-specific terms, and also randomization-based design terms. It considers marker, and marker by environment interactions using ridge regression best linear unbiased prediction to extend genomic selection to multiple environments. Since the approach uses the raw data from line replicates, the line genetic variation is partitioned into marker and nonmarker residual genetic variation (i.e., additive and nonadditive effects). This results in a more precise estimate of marker genetic effects. Using barley height data from trials, in 2 different years, of up to 477 cultivars, we demonstrate that our new genomic selection model improves predictions compared to current models. Analyzing single trials revealed improvements in predictive ability of up to 5.7%. For the multiple environment trial (MET) model, combining both year trials improved predictive ability up to 11.4% compared to a single environment analysis. Benefits were significant even when fewer markers were used. Compared to a single-year standard model run with 3490 markers, our partitioned MET model achieved the same predictive ability using between 500 and 1000 markers depending on the trial. Our approach can be used to increase accuracy and confidence in the selection of the best lines for breeding and/or, to reduce costs by using fewer markers. Copyright © 2016 Oakey et al.

Investigating RFID for Roadside Identification Involving Freight Commercial Vehicle Operators

DOT National Transportation Integrated Search

2010-01-01

Radio Frequency Identification (RFID) is an emerging technology to track commercial vehicles. This transcript describes research that investigates the ability for RFID technologies to work in license plates. Mile markers are common fixtures on the ro...

A Survey of Recent Advances in Particle Filters and Remaining Challenges for Multitarget Tracking

PubMed Central

Wang, Xuedong; Sun, Shudong; Corchado, Juan M.

2017-01-01

We review some advances of the particle filtering (PF) algorithm that have been achieved in the last decade in the context of target tracking, with regard to either a single target or multiple targets in the presence of false or missing data. The first part of our review is on remarkable achievements that have been made for the single-target PF from several aspects including importance proposal, computing efficiency, particle degeneracy/impoverishment and constrained/multi-modal systems. The second part of our review is on analyzing the intractable challenges raised within the general multitarget (multi-sensor) tracking due to random target birth and termination, false alarm, misdetection, measurement-to-track (M2T) uncertainty and track uncertainty. The mainstream multitarget PF approaches consist of two main classes, one based on M2T association approaches and the other not such as the finite set statistics-based PF. In either case, significant challenges remain due to unknown tracking scenarios and integrated tracking management. PMID:29168772

Human-Associated Bacteroides spp. and Human Polyomaviruses as Microbial Source Tracking Markers in Hawaii.

PubMed

Kirs, Marek; Caffaro-Filho, Roberto A; Wong, Mayee; Harwood, Valerie J; Moravcik, Philip; Fujioka, Roger S

2016-11-15

Identification of sources of fecal contaminants is needed to (i) determine the health risk associated with recreational water use and (ii) implement appropriate management practices to mitigate this risk and protect the environment. This study evaluated human-associated Bacteroides spp. (HF183TaqMan) and human polyomavirus (HPyV) markers for host sensitivity and specificity using human and animal fecal samples collected in Hawaii. The decay rates of those markers and indicator bacteria were identified in marine and freshwater microcosms exposed and not exposed to sunlight, followed by field testing of the usability of the molecular markers. Both markers were strongly associated with sewage, although the cross-reactivity of the HF183TaqMan (also present in 82% of canine [n = 11], 30% of mongoose [n = 10], and 10% of feline [n = 10] samples) needs to be considered. Concentrations of HF183TaqMan in human fecal samples exceeded those in cross-reactive animals at least 1,000-fold. In the absence of sunlight, the decay rates of both markers were comparable to the die-off rates of enterococci in experimental freshwater and marine water microcosms. However, in sunlight, the decay rates of both markers were significantly lower than the decay rate of enterococci. While both markers have their individual limitations in terms of sensitivity and specificity, these limitations can be mitigated by using both markers simultaneously; ergo, this study supports the concurrent use of HF183TaqMan and HPyV markers for the detection of sewage contamination in coastal and inland waters in Hawaii. This study represents an in-depth characterization of microbial source tracking (MST) markers in Hawaii. The distribution and concentrations of HF183TaqMan and HPyV markers in human and animal fecal samples and in wastewater, coupled with decay data obtained from sunlight-exposed and unexposed microcosms, support the concurrent application of HF183TaqMan and HPyV markers for sewage contamination detection in Hawaii waters. Both markers are more conservative and more specific markers of sewage than fecal indicator bacteria (enterococci and Escherichia coli). Analysis of HF183TaqMan (or newer derivatives) is recommended for inclusion in future epidemiological studies concerned with beach water quality, while better concentration techniques are needed for HPyV. Such epidemiological studies can be used to develop new recreational water quality criteria, which will provide direct information on the absence or presence of sewage contamination in water samples as well as reliable measurements of the risk of waterborne disease transmission to swimmers. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Apparatus and method for tracking a molecule or particle in three dimensions

DOEpatents

Werner, James H [Los Alamos, NM; Goodwin, Peter M [Los Alamos, NM; Lessard, Guillaume [Santa Fe, NM

2009-03-03

An apparatus and method were used to track the movement of fluorescent particles in three dimensions. Control software was used with the apparatus to implement a tracking algorithm for tracking the motion of the individual particles in glycerol/water mixtures. Monte Carlo simulations suggest that the tracking algorithms in combination with the apparatus may be used for tracking the motion of single fluorescent or fluorescently labeled biomolecules in three dimensions.

NM-Scale Anatomy of an Entire Stardust Carrot Track

NASA Technical Reports Server (NTRS)

Nakamura-Messenger, K.; Keller, L. P.; Clemett, S. J.; Messenger, S.

2009-01-01

Comet Wild-2 samples collected by NASA s Stardust mission are extremely complex, heterogeneous, and have experienced wide ranges of alteration during the capture process. There are two major types of track morphologies: "carrot" and "bulbous," that reflect different structural/compositional properties of the impactors. Carrot type tracks are typically produced by compact or single mineral grains which survive essentially intact as a single large terminal particle. Bulbous tracks are likely produced by fine-grained or organic-rich impactors [1]. Owing to their challenging nature and especially high value of Stardust samples, we have invested considerable effort in developing both sample preparation and analytical techniques tailored for Stardust sample analyses. Our report focuses on our systematic disassembly and coordinated analysis of Stardust carrot track #112 from the mm to nm-scale.

Positron emission particle tracking and its application to granular media

NASA Astrophysics Data System (ADS)

Parker, D. J.

2017-05-01

Positron emission particle tracking (PEPT) is a technique for tracking a single radioactively labelled particle. Accurate 3D tracking is possible even when the particle is moving at high speed inside a dense opaque system. In many cases, tracking a single particle within a granular system provides sufficient information to determine the time-averaged behaviour of the entire granular system. After a general introduction, this paper describes the detector systems (PET scanners and positron cameras) used to record PEPT data, the techniques used to label particles, and the algorithms used to process the data. This paper concentrates on the use of PEPT for studying granular systems: the focus is mainly on work at Birmingham, but reference is also made to work from other centres, and options for wider diversification are suggested.

Multiple-hypothesis multiple-model line tracking

NASA Astrophysics Data System (ADS)

Pace, Donald W.; Owen, Mark W.; Cox, Henry

2000-07-01

Passive sonar signal processing generally includes tracking of narrowband and/or broadband signature components observed on a Lofargram or on a Bearing-Time-Record (BTR) display. Fielded line tracking approaches to date have been recursive and single-hypthesis-oriented Kalman- or alpha-beta filters, with no mechanism for considering tracking alternatives beyond the most recent scan of measurements. While adaptivity is often built into the filter to handle changing track dynamics, these approaches are still extensions of single target tracking solutions to multiple target tracking environment. This paper describes an application of multiple-hypothesis, multiple target tracking technology to the sonar line tracking problem. A Multiple Hypothesis Line Tracker (MHLT) is developed which retains the recursive minimum-mean-square-error tracking behavior of a Kalman Filter in a maximum-a-posteriori delayed-decision multiple hypothesis context. Multiple line track filter states are developed and maintained using the interacting multiple model (IMM) state representation. Further, the data association and assignment problem is enhanced by considering line attribute information (line bandwidth and SNR) in addition to beam/bearing and frequency fit. MHLT results on real sonar data are presented to demonstrate the benefits of the multiple hypothesis approach. The utility of the system in cluttered environments and particularly in crossing line situations is shown.

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.

A single mutation in the GSTe2 gene allows tracking of metabolically based insecticide resistance in a major malaria vector

PubMed Central

2014-01-01

Background Metabolic resistance to insecticides is the biggest threat to the continued effectiveness of malaria vector control. However, its underlying molecular basis, crucial for successful resistance management, remains poorly characterized. Results Here, we demonstrate that the single amino acid change L119F in an upregulated glutathione S-transferase gene, GSTe2, confers high levels of metabolic resistance to DDT in the malaria vector Anopheles funestus. Genome-wide transcription analysis revealed that GSTe2 was the most over-expressed detoxification gene in DDT and permethrin-resistant mosquitoes from Benin. Transgenic expression of GSTe2 in Drosophila melanogaster demonstrated that over-transcription of this gene alone confers DDT resistance and cross-resistance to pyrethroids. Analysis of GSTe2 polymorphism established that the point mutation is tightly associated with metabolic resistance to DDT and its geographical distribution strongly correlates with DDT resistance patterns across Africa. Functional characterization of recombinant GSTe2 further supports the role of the L119F mutation, with the resistant allele being more efficient at metabolizing DDT than the susceptible one. Importantly, we also show that GSTe2 directly metabolizes the pyrethroid permethrin. Structural analysis reveals that the mutation confers resistance by enlarging the GSTe2 DDT-binding cavity, leading to increased DDT access and metabolism. Furthermore, we show that GSTe2 is under strong directional selection in resistant populations, and a restriction of gene flow is observed between African regions, enabling the prediction of the future spread of this resistance. Conclusions This first DNA-based metabolic resistance marker in mosquitoes provides an essential tool to track the evolution of resistance and to design suitable resistance management strategies. PMID:24565444

Tracking Image Correlation: Combining Single-Particle Tracking and Image Correlation

PubMed Central

Dupont, A.; Stirnnagel, K.; Lindemann, D.; Lamb, D.C.

2013-01-01

The interactions and coordination of biomolecules are crucial for most cellular functions. The observation of protein interactions in live cells may provide a better understanding of the underlying mechanisms. After fluorescent labeling of the interacting partners and live-cell microscopy, the colocalization is generally analyzed by quantitative global methods. Recent studies have addressed questions regarding the individual colocalization of moving biomolecules, usually by using single-particle tracking (SPT) and comparing the fluorescent intensities in both color channels. Here, we introduce a new method that combines SPT and correlation methods to obtain a dynamical 3D colocalization analysis along single trajectories of dual-colored particles. After 3D tracking, the colocalization is computed at each particle’s position via the local 3D image cross correlation of the two detection channels. For every particle analyzed, the output consists of the 3D trajectory, the time-resolved 3D colocalization information, and the fluorescence intensity in both channels. In addition, the cross-correlation analysis shows the 3D relative movement of the two fluorescent labels with an accuracy of 30 nm. We apply this method to the tracking of viral fusion events in live cells and demonstrate its capacity to obtain the time-resolved colocalization status of single particles in dense and noisy environments. PMID:23746509

Single and multiple object tracking using log-euclidean Riemannian subspace and block-division appearance model.

PubMed

Hu, Weiming; Li, Xi; Luo, Wenhan; Zhang, Xiaoqin; Maybank, Stephen; Zhang, Zhongfei

2012-12-01

Object appearance modeling is crucial for tracking objects, especially in videos captured by nonstationary cameras and for reasoning about occlusions between multiple moving objects. Based on the log-euclidean Riemannian metric on symmetric positive definite matrices, we propose an incremental log-euclidean Riemannian subspace learning algorithm in which covariance matrices of image features are mapped into a vector space with the log-euclidean Riemannian metric. Based on the subspace learning algorithm, we develop a log-euclidean block-division appearance model which captures both the global and local spatial layout information about object appearances. Single object tracking and multi-object tracking with occlusion reasoning are then achieved by particle filtering-based Bayesian state inference. During tracking, incremental updating of the log-euclidean block-division appearance model captures changes in object appearance. For multi-object tracking, the appearance models of the objects can be updated even in the presence of occlusions. Experimental results demonstrate that the proposed tracking algorithm obtains more accurate results than six state-of-the-art tracking algorithms.

NucliTrack: an integrated nuclei tracking application

PubMed Central

Cooper, Sam; Barr, Alexis R.; Glen, Robert; Bakal, Chris

2017-01-01

Abstract Summary Live imaging studies give unparalleled insight into dynamic single cell behaviours and fate decisions. However, the challenge of reliably tracking single cells over long periods of time limits both the throughput and ease with which such studies can be performed. Here, we present NucliTrack, a cross platform solution for automatically segmenting, tracking and extracting features from fluorescently labelled nuclei. NucliTrack performs similarly to other state-of-the-art cell tracking algorithms, but NucliTrack’s interactive, graphical interface makes it significantly more user friendly. Availability and implementation NucliTrack is available as a free, cross platform application and open source Python package. Installation details and documentation are at: http://nuclitrack.readthedocs.io/en/latest/ A video guide can be viewed online: https://www.youtube.com/watch?v=J6e0D9F-qSU Source code is available through Github: https://github.com/samocooper/nuclitrack. A Matlab toolbox is also available at: https://uk.mathworks.com/matlabcentral/fileexchange/61479-samocooper-nuclitrack-matlab. Contact sam@socooper.com Supplementary information Supplementary data are available at Bioinformatics online. PMID:28637183

Photothermal confocal multicolor microscopy of nanoparticles and nanodrugs in live cells

PubMed Central

Nedosekin, Dmitry A.; Foster, Stephen; Nima, Zeid A.; Biris, Alexandru S.; Galanzha, Ekaterina I.; Zharov, Vladimir P.

2018-01-01

Growing biomedical applications of non-fluorescent nanoparticles (NPs) for molecular imaging, disease diagnosis, drug delivery, and theranostics require new tools for real-time detection of nanomaterials, drug nano-carriers and NP-drug conjugates (nanodrugs) in complex biological environments without additional labeling. Photothermal (PT) microscopy (PTM) has an enormous potential for absorption-based identification and quantification of non-fluorescent molecules and NPs at a single molecule and 1.4 nm gold NP level. Recently, we have developed confocal PTM providing three-dimensional (3-D) mapping and spectral identification of multiple chromophores and fluorophores in live cells. Here, we summarize recent advances in the application of confocal multicolor PTM for 3-D visualization of single and clustered NPs, alone and in individual cells. In particular, we demonstrate identification of functionalized magnetic and gold-silver NPs, as well as graphene and carbon nanotubes in cancer cells and among blood cells. The potentials to use PTM for super-resolution imaging (down to 50nm), real-time NP tracking, guidance of PT nanotherapy and multiplex cancer markers targeting, as well as analysis of nonlinear PT phenomena and amplification of nanodrug efficacy through NP clustering and nanobubble formation are also discussed. PMID:26133539

Peptide immunotherapy in allergic asthma generates IL-10–dependent immunological tolerance associated with linked epitope suppression

PubMed Central

Campbell, John D.; Buckland, Karen F.; McMillan, Sarah J.; Kearley, Jennifer; Oldfield, William L.G.; Stern, Lawrence J.; Grönlund, Hans; van Hage, Marianne; Reynolds, Catherine J.; Boyton, Rosemary J.; Cobbold, Stephen P.; Kay, A. Barry; Altmann, Daniel M.; Larché, Mark

2009-01-01

Treatment of patients with allergic asthma using low doses of peptides containing T cell epitopes from Fel d 1, the major cat allergen, reduces allergic sensitization and improves surrogate markers of disease. Here, we demonstrate a key immunological mechanism, linked epitope suppression, associated with this therapeutic effect. Treatment with selected epitopes from a single allergen resulted in suppression of responses to other (“linked”) epitopes within the same molecule. This phenomenon was induced after peptide immunotherapy in human asthmatic subjects and in a novel HLA-DR1 transgenic mouse model of asthma. Tracking of allergen-specific T cells using DR1 tetramers determined that suppression was associated with the induction of interleukin (IL)-10+ T cells that were more abundant than T cells specific for the single-treatment peptide and was reversed by anti–IL-10 receptor administration. Resolution of airway pathophysiology in this model was associated with reduced recruitment, proliferation, and effector function of allergen-specific Th2 cells. Our results provide, for the first time, in vivo evidence of linked epitope suppression and IL-10 induction in both human allergic disease and a mouse model designed to closely mimic peptide therapy in humans. PMID:19528258

Close-Range Tracking of Underwater Vehicles Using Light Beacons

PubMed Central

Bosch, Josep; Gracias, Nuno; Ridao, Pere; Istenič, Klemen; Ribas, David

2016-01-01

This paper presents a new tracking system for autonomous underwater vehicles (AUVs) navigating in a close formation, based on computer vision and the use of active light markers. While acoustic localization can be very effective from medium to long distances, it is not so advantageous in short distances when the safety of the vehicles requires higher accuracy and update rates. The proposed system allows the estimation of the pose of a target vehicle at short ranges, with high accuracy and execution speed. To extend the field of view, an omnidirectional camera is used. This camera provides a full coverage of the lower hemisphere and enables the concurrent tracking of multiple vehicles in different positions. The system was evaluated in real sea conditions by tracking vehicles in mapping missions, where it demonstrated robust operation during extended periods of time. PMID:27023547

Close-Range Tracking of Underwater Vehicles Using Light Beacons.

PubMed

Bosch, Josep; Gracias, Nuno; Ridao, Pere; Istenič, Klemen; Ribas, David

2016-03-25

This paper presents a new tracking system for autonomous underwater vehicles (AUVs) navigating in a close formation, based on computer vision and the use of active light markers. While acoustic localization can be very effective from medium to long distances, it is not so advantageous in short distances when the safety of the vehicles requires higher accuracy and update rates. The proposed system allows the estimation of the pose of a target vehicle at short ranges, with high accuracy and execution speed. To extend the field of view, an omnidirectional camera is used. This camera provides a full coverage of the lower hemisphere and enables the concurrent tracking of multiple vehicles in different positions. The system was evaluated in real sea conditions by tracking vehicles in mapping missions, where it demonstrated robust operation during extended periods of time.

C(G)-Band and X(I)-Band Noncoherent Radar Transponder Performance Specification Standard

DTIC Science & Technology

2014-06-01

transmitter with an integral power supply. The transponder must accept interrogation signals from single or multiple radar sets and provide a...the transponder receives a coded pulse interrogation from the ground radar and transmits a single pulse reply in the same frequency band. The...obtained by using either a single tracking station or several tracking stations along the flight path of the target vehicle. The accuracy gained by use

Optically tracked, single-coil, scanning magnetic induction tomography

NASA Astrophysics Data System (ADS)

Feldkamp, Joe R.; Quirk, Stephen

2017-03-01

Recent work has shown the feasibility of single-coil, magnetic induction tomography, for visualizing a 3D distribution of electrical conductivity in portions of the human body. Loss is measured in a single, planar coil consisting of concentric circular loops while the coil is relocated to various non-redundant positions and orientations in the vicinity of the target. These loss values, together with measured coil position and orientation, are processed by a quantitative mapping equation that enables reconstruction of an electrical conductivity image. Up until now, the position of the coil had to be established by a template, which required assignment of locations for the coil to visit without necessarily giving any prior consideration to target geometry. We have now added optical tracking to our existing single-coil device so that position and orientation are tracked automatically, allowing collection of coil loss data at arbitrary positions or orientations as needed. Optical tracking is accomplished via a set of IR reflective spheres mounted on the same enclosure that supports the coil. Position for a select sphere within the set, together with the four quaternions specifying optical body orientation, is fed to a laptop at the same time coil loss data is streamed to the same laptop via Bluetooth. The coil center can be tracked with sub-millimeter accuracy while orientation angle is known to a fraction of a degree. This work illustrates the use of single-coil MIT in full, position-orientation-tracked scan mode while imaging laboratory phantoms. Phantoms are based upon simple materials having biologic conductivity (< 5 S/m), including a cut of bone-in steak. The goal is not just to reconstruct an image that contains the features of the actual target, but also return correct conductivity values for the various features within the image.

A comparative study between the imaging system and the optical tracking system in proton therapy at CNAO

PubMed Central

Desplanques, Maxime; Tagaste, Barbara; Fontana, Giulia; Pella, Andrea; Riboldi, Marco; Fattori, Giovanni; Donno, Andrea; Baroni, Guido; Orecchia, Roberto

2013-01-01

The synergy between in-room imaging and optical tracking, in co-operation with highly accurate robotic patient handling represents a concept for patient-set-up which has been implemented at CNAO (Centro Nazionale di Adroterapia Oncologica). In-room imaging is based on a double oblique X-ray projection system; optical tracking consists of the detection of the position of spherical markers placed directly on the patient's skin or on the immobilization devices. These markers are used as external fiducials during patient positioning and dose delivery. This study reports the results of a comparative analysis between in-room imaging and optical tracking data for patient positioning within the framework of high-precision particle therapy. Differences between the optical tracking system (OTS) and the imaging system (IS) were on average within the expected localization accuracy. On the first 633 fractions for head and neck (H&N) set-up procedures, the corrections applied by the IS, after patient positioning using the OTS only, were for the mostly sub-millimetric regarding the translations (0.4±1.1 mm) and sub-gradual regarding the rotations (0.0°±0.8°). On the first 236 fractions for pelvis localizations the amplitude of the corrections applied by the IS after preliminary optical set-up correction were moderately higher and more dispersed (translations: 1.3±2.9 mm, rotations 0.1±0.9°). Although the indication of the OTS cannot replace information provided by in-room imaging devices and 2D-3D image registration, the reported data show that OTS preliminary correction might greatly support image-based patient set-up refinement and also provide a secondary, independent verification system for patient positioning. PMID:23824116

Automatic Intra-Operative Stitching of Non-Overlapping Cone-Beam CT Acquisitions

PubMed Central

Fotouhi, Javad; Fuerst, Bernhard; Unberath, Mathias; Reichenstein, Stefan; Lee, Sing Chun; Johnson, Alex A.; Osgood, Greg M.; Armand, Mehran; Navab, Nassir

2018-01-01

Purpose Cone-Beam Computed Tomography (CBCT) is one of the primary imaging modalities in radiation therapy, dentistry, and orthopedic interventions. While CBCT provides crucial intraoperative information, it is bounded by a limited imaging volume, resulting in reduced effectiveness. This paper introduces an approach allowing real-time intraoperative stitching of overlapping and non-overlapping CBCT volumes to enable 3D measurements on large anatomical structures. Methods A CBCT-capable mobile C-arm is augmented with a Red-Green-Blue-Depth (RGBD) camera. An off-line co-calibration of the two imaging modalities results in co-registered video, infrared, and X-ray views of the surgical scene. Then, automatic stitching of multiple small, non-overlapping CBCT volumes is possible by recovering the relative motion of the C-arm with respect to the patient based on the camera observations. We propose three methods to recover the relative pose: RGB-based tracking of visual markers that are placed near the surgical site, RGBD-based simultaneous localization and mapping (SLAM) of the surgical scene which incorporates both color and depth information for pose estimation, and surface tracking of the patient using only depth data provided by the RGBD sensor. Results On an animal cadaver, we show stitching errors as low as 0.33 mm, 0.91 mm, and 1.72mm when the visual marker, RGBD SLAM, and surface data are used for tracking, respectively. Conclusions The proposed method overcomes one of the major limitations of CBCT C-arm systems by integrating vision-based tracking and expanding the imaging volume without any intraoperative use of calibration grids or external tracking systems. We believe this solution to be most appropriate for 3D intraoperative verification of several orthopedic procedures. PMID:29569728

Genotypes are useful for more than genomic evaluation

USDA-ARS?s Scientific Manuscript database

New services that provide pedigree discovery, breed composition, mating programs, genomic inbreeding, fertility defects, and inheritance tracking all are possible from low-cost genotyping in addition to genomic evaluation. Genetic markers let breeders select among sibs before their phenotypes became...

Weighing Scale-Based Pulse Transit Time is a Superior Marker of Blood Pressure than Conventional Pulse Arrival Time

NASA Astrophysics Data System (ADS)

Martin, Stephanie L.-O.; Carek, Andrew M.; Kim, Chang-Sei; Ashouri, Hazar; Inan, Omer T.; Hahn, Jin-Oh; Mukkamala, Ramakrishna

2016-12-01

Pulse transit time (PTT) is being widely pursued for cuff-less blood pressure (BP) monitoring. Most efforts have employed the time delay between ECG and finger photoplethysmography (PPG) waveforms as a convenient surrogate of PTT. However, these conventional pulse arrival time (PAT) measurements include the pre-ejection period (PEP) and the time delay through small, muscular arteries and may thus be an unreliable marker of BP. We assessed a bathroom weighing scale-like system for convenient measurement of ballistocardiography and foot PPG waveforms - and thus PTT through larger, more elastic arteries - in terms of its ability to improve tracking of BP in individual subjects. We measured “scale PTT”, conventional PAT, and cuff BP in humans during interventions that increased BP but changed PEP and smooth muscle contraction differently. Scale PTT tracked the diastolic BP changes well, with correlation coefficient of -0.80 ± 0.02 (mean ± SE) and root-mean-squared-error of 7.6 ± 0.5 mmHg after a best-case calibration. Conventional PAT was significantly inferior in tracking these changes, with correlation coefficient of -0.60 ± 0.04 and root-mean-squared-error of 14.6 ± 1.5 mmHg (p < 0.05). Scale PTT also tracked the systolic BP changes better than conventional PAT but not to an acceptable level. With further development, scale PTT may permit reliable, convenient measurement of BP.

Weighing Scale-Based Pulse Transit Time is a Superior Marker of Blood Pressure than Conventional Pulse Arrival Time.

PubMed

Martin, Stephanie L-O; Carek, Andrew M; Kim, Chang-Sei; Ashouri, Hazar; Inan, Omer T; Hahn, Jin-Oh; Mukkamala, Ramakrishna

2016-12-15

Pulse transit time (PTT) is being widely pursued for cuff-less blood pressure (BP) monitoring. Most efforts have employed the time delay between ECG and finger photoplethysmography (PPG) waveforms as a convenient surrogate of PTT. However, these conventional pulse arrival time (PAT) measurements include the pre-ejection period (PEP) and the time delay through small, muscular arteries and may thus be an unreliable marker of BP. We assessed a bathroom weighing scale-like system for convenient measurement of ballistocardiography and foot PPG waveforms - and thus PTT through larger, more elastic arteries - in terms of its ability to improve tracking of BP in individual subjects. We measured "scale PTT", conventional PAT, and cuff BP in humans during interventions that increased BP but changed PEP and smooth muscle contraction differently. Scale PTT tracked the diastolic BP changes well, with correlation coefficient of -0.80 ± 0.02 (mean ± SE) and root-mean-squared-error of 7.6 ± 0.5 mmHg after a best-case calibration. Conventional PAT was significantly inferior in tracking these changes, with correlation coefficient of -0.60 ± 0.04 and root-mean-squared-error of 14.6 ± 1.5 mmHg (p < 0.05). Scale PTT also tracked the systolic BP changes better than conventional PAT but not to an acceptable level. With further development, scale PTT may permit reliable, convenient measurement of BP.

High-Order Discontinuous Galerkin Level Set Method for Interface Tracking and Re-Distancing on Unstructured Meshes

NASA Astrophysics Data System (ADS)

Greene, Patrick; Nourgaliev, Robert; Schofield, Sam

2015-11-01

A new sharp high-order interface tracking method for multi-material flow problems on unstructured meshes is presented. The method combines the marker-tracking algorithm with a discontinuous Galerkin (DG) level set method to implicitly track interfaces. DG projection is used to provide a mapping from the Lagrangian marker field to the Eulerian level set field. For the level set re-distancing, we developed a novel marching method that takes advantage of the unique features of the DG representation of the level set. The method efficiently marches outward from the zero level set with values in the new cells being computed solely from cell neighbors. Results are presented for a number of different interface geometries including ones with sharp corners and multiple hierarchical level sets. The method can robustly handle the level set discontinuities without explicit utilization of solution limiters. Results show that the expected high order (3rd and higher) of convergence for the DG representation of the level set is obtained for smooth solutions on unstructured meshes. High-order re-distancing on irregular meshes is a must for applications were the interfacial curvature is important for underlying physics, such as surface tension, wetting and detonation shock dynamics. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Information management release number LLNL-ABS-675636.

Reliability and concurrent validity of the Microsoft Xbox One Kinect for assessment of standing balance and postural control.

PubMed

Clark, Ross A; Pua, Yong-Hao; Oliveira, Cristino C; Bower, Kelly J; Thilarajah, Shamala; McGaw, Rebekah; Hasanki, Ksaniel; Mentiplay, Benjamin F

2015-07-01

The Microsoft Kinect V2 for Windows, also known as the Xbox One Kinect, includes new and potentially far improved depth and image sensors which may increase its accuracy for assessing postural control and balance. The aim of this study was to assess the concurrent validity and reliability of kinematic data recorded using a marker-based three dimensional motion analysis (3DMA) system and the Kinect V2 during a variety of static and dynamic balance assessments. Thirty healthy adults performed two sessions, separated by one week, consisting of static standing balance tests under different visual (eyes open vs. closed) and supportive (single limb vs. double limb) conditions, and dynamic balance tests consisting of forward and lateral reach and an assessment of limits of stability. Marker coordinate and joint angle data were concurrently recorded using the Kinect V2 skeletal tracking algorithm and the 3DMA system. Task-specific outcome measures from each system on Day 1 and 2 were compared. Concurrent validity of trunk angle data during the dynamic tasks and anterior-posterior range and path length in the static balance tasks was excellent (Pearson's r>0.75). In contrast, concurrent validity for medial-lateral range and path length was poor to modest for all trials except single leg eyes closed balance. Within device test-retest reliability was variable; however, the results were generally comparable between devices. In conclusion, the Kinect V2 has the potential to be used as a reliable and valid tool for the assessment of some aspects of balance performance. Copyright © 2015 Elsevier B.V. All rights reserved.

Development of genomic microsatellite multiplex PCR using dye-labeled universal primer and its validation in pedigree analysis of Pacific oyster ( Crassostrea gigas)

NASA Astrophysics Data System (ADS)

Liu, Ting; Li, Qi; Song, Junlin; Yu, Hong

2017-02-01

There is an increasing requirement for traceability of aquaculture products, both for consumer protection and for food safety. There are high error rates in the conventional traceability systems depending on physical labels. Genetic traceability technique depending on DNA-based tracking system can overcome this problem. Genealogy information is essential for genetic traceability, and microsatellite DNA marker is a good choice for pedigree analysis. As increasing genotyping throughput of microsatellites, microsatellite multiplex PCR has become a fast and cost-effective technique. As a commercially important cultured aquatic species, Pacific oyster Crassostrea gigas has the highest global production. The objective of this study was to develop microsatellite multiplex PCR panels with dye-labeled universal primer for pedigree analysis in C. gigas, and these multiplex PCRs were validated using 12 full-sib families with known pedigrees. Here we developed six informative multiplex PCRs using 18 genomic microsatellites in C. gigas. Each multiplex panel contained a single universal primer M13(-21) used as a tail on each locus-specific forward primer and a single universal primer M13(-21) labeled with fluorophores. The polymorphisms of the markers were moderate, with an average of 10.3 alleles per locus and average polymorphic information content of 0.740. The observed heterozygosity per locus ranged from 0.492 to 0.822. Cervus simulations revealed that the six panels would still be of great value when massive families were analysed. Pedigree analysis of real offspring demonstrated that 100% of the offspring were unambiguously allocated to their parents when two multiplex PCRs were used. The six sets of multiplex PCRs can be an important tool for tracing cultured individuals, population genetic analysis, and selective breeding program in C. gigas.

Tracking Marsupial Evolution Using Archaic Genomic Retroposon Insertions

PubMed Central

Nilsson, Maria A.; Churakov, Gennady; Sommer, Mirjam; Tran, Ngoc Van; Zemann, Anja; Brosius, Jürgen; Schmitz, Jürgen

2010-01-01

The Australasian and South American marsupial mammals, such as kangaroos and opossums, are the closest living relatives to placental mammals, having shared a common ancestor around 130 million years ago. The evolutionary relationships among the seven marsupial orders have, however, so far eluded resolution. In particular, the relationships between the four Australasian and three South American marsupial orders have been intensively debated since the South American order Microbiotheria was taxonomically moved into the group Australidelphia. Australidelphia is significantly supported by both molecular and morphological data and comprises the four Australasian marsupial orders and the South American order Microbiotheria, indicating a complex, ancient, biogeographic history of marsupials. However, the exact phylogenetic position of Microbiotheria within Australidelphia has yet to be resolved using either sequence or morphological data analysis. Here, we provide evidence from newly established and virtually homoplasy-free retroposon insertion markers for the basal relationships among marsupial orders. Fifty-three phylogenetically informative markers were retrieved after in silico and experimental screening of ∼217,000 retroposon-containing loci from opossum and kangaroo. The four Australasian orders share a single origin with Microbiotheria as their closest sister group, supporting a clear divergence between South American and Australasian marsupials. In addition, the new data place the South American opossums (Didelphimorphia) as the first branch of the marsupial tree. The exhaustive computational and experimental evidence provides important insight into the evolution of retroposable elements in the marsupial genome. Placing the retroposon insertion pattern in a paleobiogeographic context indicates a single marsupial migration from South America to Australia. The now firmly established phylogeny can be used to determine the direction of genomic changes and morphological transitions within marsupials. PMID:20668664

Common Origin and Fixation of Plasmodium falciparum dhfr and dhps Mutations Associated with Sulfadoxine-Pyrimethamine Resistance in a Low-Transmission Area in South America▿ †

PubMed Central

McCollum, Andrea M.; Mueller, Kristen; Villegas, Leopoldo; Udhayakumar, Venkatachalam; Escalante, Ananias A.

2007-01-01

Recent studies indicated that sensitive parasites could increase in frequency in a population when drugs are removed, suggesting that the life span of affordable antimalarial drugs could be expanded. We studied 97 samples from Bolivar State, Venezuela, an area where sulfadoxine-pyrimethamine (SP) has not been used for 8 years due to its ineffectiveness. We characterized point mutations in two genes that have been implicated in resistance to SP, dihydrofolate reductase (dhfr) and dihydropteroate synthase (dhps). We also assayed neutral microsatellite markers around the dhfr (chromosome 4) and dhps (chromosome 8) genes and on chromosomes 2 and 3 to track the origin and spread of resistant alleles. We found that drug-resistant SP mutants are fixed in the population. Two genotypes were present in the samples, dhfr(50R/51I/108N) dhps(437G/540E/581G) (90.7%) and dhfr(51I/108N) dhps(437G/581G) (9.3%). We show a single microsatellite haplotype for all of the dhfr and dhps alleles, and the alleles at the microsatellite loci are different from those present in Africa. Thus, in these samples from Venezuela, there is a single origin for both dhfr and dhps SP-resistant alleles, and these alleles originated independently of those characterized from Africa. Furthermore, this is the first report of a “hitchhiking effect” on the genetic variation around dhps due to selection by SP using an extensive set of microsatellite markers. Our results indicate that, in areas where there is limited gene flow, the fixation of drug-resistant parasites in the population is stable, even after drug selection is relaxed. PMID:17283199

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

Yewondwossen, M; Robar, J; Parsons, D

Purpose: During radiotherapy treatment, lung tumors can display substantial respiratory motion. This motion usually necessitates enlarged treatment margins to provide full tumour coverage. Unfortunately, these margins limit the dose that can be prescribed for tumour control and cause complications to normal tissue. Options for real-time methods of direct detection of tumour position, and particularly those that obviate the need for inserted fiducial markers, are limited. We propose a method of tumor tracking without implanted fiducial markers using a novel fast switching-target that toggles between a FFF copper/tungsten therapy mode and a FFF low-Z target mode for imaging. In this workmore » we demonstrate proof-of-concept of this new technology. Methods: The prototype includes two targets: i) a FFF copper/tungsten target equivalent to that in the Varian 2100 EX 6 MV, and ii) a low-Z (carbon) target with a thickness of 110% of continuous slowing down approximation range (CSDA) at 7 MeV. The two targets can be exchanged with a custom made linear slide and motor-driven actuator. The usefulness of the switching-target concept is demonstrated through experimental BEV Planar images acquired with continual treatment and imaging at a user-defined period. Results: The prototype switching-target demonstrates that two recent advances in linac technology (FFF target for therapy and low-Z target) can be combined with synergy. The switching-target approach offers the capacity for rapid switching between treatment and high-contrast imaging modes, allowing intrafractional tracking, as demonstrated in this work with dynamic breathing phantom. By using a single beam-line, the design is streamlined and may obviate the need for an auxiliary imaging system (e.g., kV OBI.) Conclusion: This switching-target approach is a feasible combination of two current advances in linac technology (FFF target for therapy and a FFF low-Z target) allowing new options in on-line IGRT.« less

Accurate and ergonomic method of registration for image-guided neurosurgery

NASA Astrophysics Data System (ADS)

Henderson, Jaimie M.; Bucholz, Richard D.

1994-05-01

There has been considerable interest in the development of frameless stereotaxy based upon scalp mounted fiducials. In practice we have experienced difficulty in relating markers to the image data sets in our series of 25 frameless cases, as well as inaccuracy due to scalp movement and the size of the markers. We have developed an alternative system for accurately and conveniently achieving surgical registration for image-guided neurosurgery based on alignment and matching of patient forehead contours. The system consists of a laser contour digitizer which is used in the operating room to acquire forehead contours, editing software for extracting contours from patient image data sets, and a contour-match algorithm for aligning the two contours and performing data set registration. The contour digitizer is tracked by a camera array which relates its position with respect to light emitting diodes placed on the head clamp. Once registered, surgical instrument can be tracked throughout the procedure. Contours can be extracted from either CT or MRI image datasets. The system has proven to be robust in the laboratory setting. Overall error of registration is 1 - 2 millimeters in routine use. Image to patient registration can therefore be achieved quite easily and accurately, without the need for fixation of external markers to the skull, or manually finding markers on the scalp and image datasets. The system is unobtrusive and imposes little additional effort on the neurosurgeon, broadening the appeal of image-guided surgery.

Biotic Interactions and Sunlight Affect Persistence of Fecal Indicator Bacteria and Microbial Source Tracking Genetic Markers in the Upper Mississippi River

PubMed Central

McMinn, Brian R.; Shanks, Orin C.; Sivaganesan, Mano; Fout, G. Shay; Ashbolt, Nicholas J.

2014-01-01

The sanitary quality of recreational waters that may be impacted by sewage is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); these organisms are found in the gastrointestinal tracts of humans and many other animals, and hence their presence provides no information about the pollution source. Microbial source tracking (MST) methods can discriminate between different pollution sources, providing critical information to water quality managers, but relatively little is known about factors influencing the decay of FIB and MST genetic markers following release into aquatic environments. An in situ mesocosm was deployed at a temperate recreational beach in the Mississippi River to evaluate the effects of ambient sunlight and biotic interactions (predation, competition, and viral lysis) on the decay of culture-based FIB, as well as molecularly based FIB (Entero1a and GenBac3) and human-associated MST genetic markers (HF183 and HumM2) measured by quantitative real-time PCR (qPCR). In general, culturable FIB decayed the fastest, while molecularly based FIB and human-associated genetic markers decayed more slowly. There was a strong correlation between the decay of molecularly based FIB and that of human-associated genetic markers (r2, 0.96 to 0.98; P < 0.0001) but not between culturable FIB and any qPCR measurement. Overall, exposure to ambient sunlight may be an important factor in the early-stage decay dynamics but generally was not after continued exposure (i.e., after 120 h), when biotic interactions tended to be the only/major influential determinant of persistence. PMID:24747902

Bone orientation and position estimation errors using Cosserat point elements and least squares methods: Application to gait.

PubMed

Solav, Dana; Camomilla, Valentina; Cereatti, Andrea; Barré, Arnaud; Aminian, Kamiar; Wolf, Alon

2017-09-06

The aim of this study was to analyze the accuracy of bone pose estimation based on sub-clusters of three skin-markers characterized by triangular Cosserat point elements (TCPEs) and to evaluate the capability of four instantaneous physical parameters, which can be measured non-invasively in vivo, to identify the most accurate TCPEs. Moreover, TCPE pose estimations were compared with the estimations of two least squares minimization methods applied to the cluster of all markers, using rigid body (RBLS) and homogeneous deformation (HDLS) assumptions. Analysis was performed on previously collected in vivo treadmill gait data composed of simultaneous measurements of the gold-standard bone pose by bi-plane fluoroscopy tracking the subjects' knee prosthesis and a stereophotogrammetric system tracking skin-markers affected by soft tissue artifact. Femur orientation and position errors estimated from skin-marker clusters were computed for 18 subjects using clusters of up to 35 markers. Results based on gold-standard data revealed that instantaneous subsets of TCPEs exist which estimate the femur pose with reasonable accuracy (median root mean square error during stance/swing: 1.4/2.8deg for orientation, 1.5/4.2mm for position). A non-invasive and instantaneous criteria to select accurate TCPEs for pose estimation (4.8/7.3deg, 5.8/12.3mm), was compared with RBLS (4.3/6.6deg, 6.9/16.6mm) and HDLS (4.6/7.6deg, 6.7/12.5mm). Accounting for homogeneous deformation, using HDLS or selected TCPEs, yielded more accurate position estimations than RBLS method, which, conversely, yielded more accurate orientation estimations. Further investigation is required to devise effective criteria for cluster selection that could represent a significant improvement in bone pose estimation accuracy. Copyright © 2017 Elsevier Ltd. All rights reserved.

Joint kinematics estimation using a multi-body kinematics optimisation and an extended Kalman filter, and embedding a soft tissue artefact model.

PubMed

Bonnet, Vincent; Richard, Vincent; Camomilla, Valentina; Venture, Gentiane; Cappozzo, Aurelio; Dumas, Raphaël

2017-09-06

To reduce the impact of the soft tissue artefact (STA) on the estimate of skeletal movement using stereophotogrammetric and skin-marker data, multi-body kinematics optimisation (MKO) and extended Kalman filters (EKF) have been proposed. This paper assessed the feasibility and efficiency of these methods when they embed a mathematical model of the STA and simultaneously estimate the ankle, knee and hip joint kinematics and the model parameters. A STA model was used that provides an estimate of the STA affecting the marker-cluster located on a body segment as a function of the kinematics of the adjacent joints. The MKO and the EKF were implemented with and without the STA model. To assess these methods, intra-cortical pin and skin markers located on the thigh, shank, and foot of three subjects and tracked during the stance phase of running were used. Embedding the STA model in MKO and EKF reduced the average RMS of marker tracking from 12.6 to 1.6mm and from 4.3 to 1.9mm, respectively, showing that a STA model trial-specific calibration is feasible. Nevertheless, with the STA model embedded in MKO, the RMS difference between the estimated and the reference joint kinematics determined from the pin markers slightly increased (from 2.0 to 2.1deg) On the contrary, when the STA model was embedded in the EKF, this RMS difference was slightly reduced (from 2.0 to 1.7deg) thus showing a better potentiality of this method to attenuate STA effects and improve the accuracy of joint kinematics estimate. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cluster-based upper body marker models for three-dimensional kinematic analysis: Comparison with an anatomical model and reliability analysis.

PubMed

Boser, Quinn A; Valevicius, Aïda M; Lavoie, Ewen B; Chapman, Craig S; Pilarski, Patrick M; Hebert, Jacqueline S; Vette, Albert H

2018-04-27

Quantifying angular joint kinematics of the upper body is a useful method for assessing upper limb function. Joint angles are commonly obtained via motion capture, tracking markers placed on anatomical landmarks. This method is associated with limitations including administrative burden, soft tissue artifacts, and intra- and inter-tester variability. An alternative method involves the tracking of rigid marker clusters affixed to body segments, calibrated relative to anatomical landmarks or known joint angles. The accuracy and reliability of applying this cluster method to the upper body has, however, not been comprehensively explored. Our objective was to compare three different upper body cluster models with an anatomical model, with respect to joint angles and reliability. Non-disabled participants performed two standardized functional upper limb tasks with anatomical and cluster markers applied concurrently. Joint angle curves obtained via the marker clusters with three different calibration methods were compared to those from an anatomical model, and between-session reliability was assessed for all models. The cluster models produced joint angle curves which were comparable to and highly correlated with those from the anatomical model, but exhibited notable offsets and differences in sensitivity for some degrees of freedom. Between-session reliability was comparable between all models, and good for most degrees of freedom. Overall, the cluster models produced reliable joint angles that, however, cannot be used interchangeably with anatomical model outputs to calculate kinematic metrics. Cluster models appear to be an adequate, and possibly advantageous alternative to anatomical models when the objective is to assess trends in movement behavior. Copyright © 2018 Elsevier Ltd. All rights reserved.

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers

PubMed Central

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains. PMID:27035434

Population Structure in Naegleria fowleri as Revealed by Microsatellite Markers.

PubMed

Coupat-Goutaland, Bénédicte; Régoudis, Estelle; Besseyrias, Matthieu; Mularoni, Angélique; Binet, Marie; Herbelin, Pascaline; Pélandakis, Michel

2016-01-01

Naegleria sp. is a free living amoeba belonging to the Heterolobosea class. Over 40 species of Naegleria were identified and recovered worldwide in different habitats such as swimming pools, freshwater lakes, soil or dust. Among them, N. fowleri, is a human pathogen responsible for primary amoeboic meningoencephalitis (PAM). Around 300 cases were reported in 40 years worldwide but PAM is a fatal disease of the central nervous system with only 5% survival of infected patients. Since both pathogenic and non pathogenic species were encountered in the environment, detection and dispersal mode are crucial points in the fight against this pathogenic agent. Previous studies on identification and genotyping of N. fowleri strains were focused on RAPD analysis and on ITS sequencing and identified 5 variants: euro-american, south pacific, widespread, cattenom and chooz. Microsatellites are powerful markers in population genetics with broad spectrum of applications (such as paternity test, fingerprinting, genetic mapping or genetic structure analysis). They are characterized by a high degree of length polymorphism. The aim of this study was to genotype N. fowleri strains using microsatellites markers in order to track this population and to better understand its evolution. Six microsatellite loci and 47 strains from different geographical origins were used for this analysis. The microsatellite markers revealed a level of discrimination higher than any other marker used until now, enabling the identification of seven genetic groups, included in the five main genetic groups based on the previous RAPD and ITS analyses. This analysis also allowed us to go further in identifying private alleles highlighting intra-group variability. A better identification of the N. fowleri isolates could be done with this type of analysis and could allow a better tracking of the clinical and environmental N. fowleri strains.

Association mapping of seed and disease resistance traits in Theobroma cacao L.

PubMed

Motilal, Lambert A; Zhang, Dapeng; Mischke, Sue; Meinhardt, Lyndel W; Boccara, Michel; Fouet, Olivier; Lanaud, Claire; Umaharan, Pathmanathan

2016-12-01

Microsatellite and single nucleotide polymorphism markers that could be used in marker assisted breeding of cacao were identified for number of filled seeds, black pod resistance and witches' broom disease resistance. An association mapping approach was employed to identify markers for seed number and resistance to black pod and witches' broom disease (WBD) in cacao (Theobroma cacao L.). Ninety-five microsatellites (SSRs) and 775 single nucleotide polymorphisms (SNPs) were assessed on 483 unique trees in the International Cocoa Genebank Trinidad (ICGT). Linkage disequilibrium (LD) and association mapping studies were conducted to identify markers to tag the phenotypic traits. Decay of LD occurred over an average 9.3 cM for chromosomes 1-9 and 2.5 cM for chromosome 10. Marker/trait associations were generally identified based on general linear models (GLMs) that incorporated principal components from molecular information on relatedness factor. Seven markers (mTcCIR 8, 66, 126, 212; TcSNP368, 697, 1370) on chromosomes 1 and 9 were identified for number of filled seeds (NSEED). A single marker was found for black pod resistance (mTcCIR280) on chromosome 3, whereas six markers on chromosomes 4, 5, 6, 8, and 10 were detected for WBD (mTcCIR91, 183; TcSNP375, 720, 1230 and 1374). It is expected that this association mapping study in cacao would contribute to the knowledge of the genetic determinism of cocoa traits and that the markers identified herein would prove useful in marker assisted breeding of cacao.

Magnetic tracking for TomoTherapy systems: gradiometer based methods to filter eddy-current magnetic fields.

PubMed

McGary, John E; Xiong, Zubiao; Chen, Ji

2013-07-01

TomoTherapy systems lack real-time, tumor tracking. A possible solution is to use electromagnetic markers; however, eddy-current magnetic fields generated in response to a magnetic source can be comparable to the signal, thus degrading the localization accuracy. Therefore, the tracking system must be designed to account for the eddy fields created along the inner bore conducting surfaces. The aim of this work is to investigate localization accuracy using magnetic field gradients to determine feasibility toward TomoTherapy applications. Electromagnetic models are used to simulate magnetic fields created by a source and its simultaneous generation of eddy currents within a conducting cylinder. The source position is calculated using a least-squares fit of simulated sensor data using the dipole equation as the model equation. To account for field gradients across the sensor area (≈ 25 cm(2)), an iterative method is used to estimate the magnetic field at the sensor center. Spatial gradients are calculated with two arrays of uniaxial, paired sensors that form a gradiometer array, where the sensors are considered ideal. Experimental measurements of magnetic fields within the TomoTherapy bore are shown to be 1%-10% less than calculated with the electromagnetic model. Localization results using a 5 × 5 array of gradiometers are, in general, 2-4 times more accurate than a planar array of sensors, depending on the solenoid orientation and position. Simulation results show that the localization accuracy using a gradiometer array is within 1.3 mm over a distance of 20 cm from the array plane. In comparison, localization errors using single array are within 5 mm. The results indicate that the gradiometer method merits further studies and work due to the accuracy achieved with ideal sensors. Future studies should include realistic sensor models and extensive numerical studies to estimate the expected magnetic tracking accuracy within a TomoTherapy system before proceeding with prototype development.

Prototype Test Results for the Single Photon Detection SLR2000 Satellite Laser Ranging System

NASA Technical Reports Server (NTRS)

Zagwodzki, Thomas W.; McGarry, Jan F.; Degnan, John J.; Cheek, Jack W.; Dunn, Peter J.; Patterson, Don; Donovan, Howard

2004-01-01

NASA's aging Satellite Laser Ranging (SLR) network is scheduled to be replaced over the next few years with a fully automated single photon detection system. A prototype of this new system, called SLR2000, is currently undergoing field trials at the Goddard Space Flight Center in Greenbelt, Maryland to evaluate photon counting techniques and determine system hardware, software, and control algorithm performance levels and limitations. Newly developed diode pumped microchip lasers and quadrant microchannel plate-based photomultiplier tubes have enabled the development of this high repetition rate single photon detection SLR system. The SLR2000 receiver threshold is set at the single photoelectron (pe) level but tracks satellites with an average signal level typically much less than 1 pe. The 2 kHz laser fire rate aids in satellite acquisition and tracking and will enable closed loop tracking by accumulating single photon count statistics in a quadrant detector and using this information to correct for pointing errors. Laser transmitter beamwidths of 10 arcseconds (FWHM) or less are currently being used to maintain an adequate signal level for tracking while the receiver field of view (FOV) has been opened to 40 arcseconds to accommodate point ahead/look behind angular offsets. In the near future, the laser transmitter point ahead will be controlled by a pair of Risley prisms. This will allow the telescope to point behind and enable closure of the receiver FOV to roughly match the transmitter beam divergence. Bandpass filters (BPF) are removed for night tracking operations while 0.2 nm or 1 nm filters are used during daylight operation. Both day and night laser tracking of Low Earth Orbit (LEO) satellites has been achieved with a laser transmitter energy of only 65 microjoules per pulse. Satellite tracking is presently limited to LEO satellites until the brassboard laser transmitter can be upgraded or replaced. Simultaneous tracks have also been observed with NASA s SLR standard, MOBLAS 7, for the purposes of data comparison and identification of biases. Work continues to optimize the receive optics; upgrade or replace the laser transmitter; calibrate the quadrant detector, the point ahead Risley prisms, and event timer verniers; and test normal point generation with SLR2000 data. This paper will report on the satellite tracking results to date, issues yet to be resolved, and future plans for the SLR2000 system.

Genetic diversity of Plasmodium Vivax revealed by the merozoite surface protein-1 icb5-6 fragment.

PubMed

Ruan, Wei; Zhang, Ling-Ling; Feng, Yan; Zhang, Xuan; Chen, Hua-Liang; Lu, Qiao-Yi; Yao, Li-Nong; Hu, Wei

2017-06-05

Plasmodium vivax remains a potential cause of morbidity and mortality for people living in its endemic areas. Understanding the genetic diversity of P. vivax from different regions is valuable for studying population dynamics and tracing the origins of parasites. The PvMSP-1 gene is highly polymorphic and has been used as a marker in many P. vivax population studies. The aim of this study was to investigate the genetic diversity of the PvMSP-1 gene icb5-6 fragment and to provide more genetic polymorphism data for further studies on P. vivax population structure and tracking of the origin of clinical cases. Nested PCR and sequencing of the PvMSP-1 icb5-6 marker were performed to obtain the nucleotide sequences of 95 P. vivax isolates collected from Zhejiang province, China. To investigate the genetic diversity of PvMSP-1, the 95 nucleotide sequences of the PvMSP-1 icb5-6 fragment were genotyped and analyzed using DnaSP v5, MEGA software. The 95 P. vivax isolates collected from Zhejiang province were either indigenous cases or imported cases from different regions around the world. A total of 95 sequences ranging from 390 to 460 bp were obtained. The 95 sequences were genotyped into four allele-types (Sal I, Belem, R-III and R-IV) and 17 unique haplotypes. R-III and Sal I were the predominant allele-types. The haplotype diversity (Hd) and nucleotide diversity (Pi) were estimated to be 0.729 and 0.062, indicating that the PvMSP-1 icb5-6 fragment had the highest level of polymorphism due to frequent recombination processes and single nucleotide polymorphism. The values of dN/dS and Tajima's D both suggested neutral selection for the PvMSP-1icb5-6 fragment. In addition, a rare recombinant style of R-IV type was identified. This study presented high genetic diversity in the PvMSP-1 marker among P. vivax strains from around the world. The genetic data is valuable for expanding the polymorphism information on P. vivax, which could be helpful for further study on population dynamics and tracking the origin of P. vivax.

Development of single-copy nuclear intron markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae).

PubMed

Chery, Joyce G; Sass, Chodon; Specht, Chelsea D

2017-09-01

We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae. This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls.

PubMed

Staley, Zachery R; Grabuski, Josey; Sverko, Ed; Edge, Thomas A

2016-11-01

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log 10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log 10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log 10 CFU/100 ml, and 7.65 log 10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination. © Crown copyright 2016.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

PubMed Central

Grabuski, Josey; Sverko, Ed; Edge, Thomas A.

2016-01-01

ABSTRACT Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log10 CFU/100 ml, and 7.65 log10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. IMPORTANCE Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can potentially degrade water quality and pose risks to human and ecosystem health. Therefore, identifying fecal contamination in storm water runoff and outfalls is essential for remediation efforts to reduce risks to public health. This study employed multiple methods of identifying levels and sources of fecal contamination in both river and storm water outfall sites, evaluating the efficacy of using culture-based enumeration of E. coli, molecular methods of determining the source(s) of contamination, and CST markers as indicators of fecal contamination. The results identified pervasive human sewage contamination in storm water outfalls and throughout an urban watershed and highlight the utility of using both MST and CST to identify raw sewage contamination. PMID:27542934

Automatic colonic lesion detection and tracking in endoscopic videos

NASA Astrophysics Data System (ADS)

Li, Wenjing; Gustafsson, Ulf; A-Rahim, Yoursif

2011-03-01

The biology of colorectal cancer offers an opportunity for both early detection and prevention. Compared with other imaging modalities, optical colonoscopy is the procedure of choice for simultaneous detection and removal of colonic polyps. Computer assisted screening makes it possible to assist physicians and potentially improve the accuracy of the diagnostic decision during the exam. This paper presents an unsupervised method to detect and track colonic lesions in endoscopic videos. The aim of the lesion screening and tracking is to facilitate detection of polyps and abnormal mucosa in real time as the physician is performing the procedure. For colonic lesion detection, the conventional marker controlled watershed based segmentation is used to segment the colonic lesions, followed by an adaptive ellipse fitting strategy to further validate the shape. For colonic lesion tracking, a mean shift tracker with background modeling is used to track the target region from the detection phase. The approach has been tested on colonoscopy videos acquired during regular colonoscopic procedures and demonstrated promising results.

A Novel Eye-Tracking Method to Assess Attention Allocation in Individuals with and without Aphasia Using a Dual-Task Paradigm

PubMed Central

Heuer, Sabine; Hallowell, Brooke

2015-01-01

Numerous authors report that people with aphasia have greater difficulty allocating attention than people without neurological disorders. Studying how attention deficits contribute to language deficits is important. However, existing methods for indexing attention allocation in people with aphasia pose serious methodological challenges. Eye-tracking methods have great potential to address such challenges. We developed and assessed the validity of a new dual-task method incorporating eye tracking to assess attention allocation. Twenty-six adults with aphasia and 33 control participants completed auditory sentence comprehension and visual search tasks. To test whether the new method validly indexes well-documented patterns in attention allocation, demands were manipulated by varying task complexity in single- and dual-task conditions. Differences in attention allocation were indexed via eye-tracking measures. For all participants significant increases in attention allocation demands were observed from single- to dual-task conditions and from simple to complex stimuli. Individuals with aphasia had greater difficulty allocating attention with greater task demands. Relationships between eye-tracking indices of comprehension during single and dual tasks and standardized testing were examined. Results support the validity of the novel eye-tracking method for assessing attention allocation in people with and without aphasia. Clinical and research implications are discussed. PMID:25913549

Towards establishing a human fecal contamination index in microbial source tracking

EPA Science Inventory

There have been significant advances in development of PCR-based methods to detect source associated DNA sequences (markers), but method evaluation has focused on performance with individual challenge samples. Little attention has been given to integration of multiple samples fro...

Super-resolution imaging applied to moving object tracking

NASA Astrophysics Data System (ADS)

Swalaganata, Galandaru; Ratna Sulistyaningrum, Dwi; Setiyono, Budi

2017-10-01

Moving object tracking in a video is a method used to detect and analyze changes that occur in an object that being observed. Visual quality and the precision of the tracked target are highly wished in modern tracking system. The fact that the tracked object does not always seem clear causes the tracking result less precise. The reasons are low quality video, system noise, small object, and other factors. In order to improve the precision of the tracked object especially for small object, we propose a two step solution that integrates a super-resolution technique into tracking approach. First step is super-resolution imaging applied into frame sequences. This step was done by cropping the frame in several frame or all of frame. Second step is tracking the result of super-resolution images. Super-resolution image is a technique to obtain high-resolution images from low-resolution images. In this research single frame super-resolution technique is proposed for tracking approach. Single frame super-resolution was a kind of super-resolution that it has the advantage of fast computation time. The method used for tracking is Camshift. The advantages of Camshift was simple calculation based on HSV color that use its histogram for some condition and color of the object varies. The computational complexity and large memory requirements required for the implementation of super-resolution and tracking were reduced and the precision of the tracked target was good. Experiment showed that integrate a super-resolution imaging into tracking technique can track the object precisely with various background, shape changes of the object, and in a good light conditions.

Identification of the Viscous Superlayer on the Low-Speed Side of a Single-Stream Shear Layer

NASA Astrophysics Data System (ADS)

Foss, John; Peabody, Jason

2010-11-01

Image pairs (elevation/plan views) have been acquired of a smoke streakline originating in the irrotational region on the low-speed side of a high Re single-stream shear layer of Morris and Foss (2003). The viscous superlayer (VSL) is identified as the terminus of the streak; 1800 such images provide VSL position statistics. Hot-wire data acquired concurrently at the shear layer edge and interior are used to investigate the relationship between these velocity magnitudes and the large-scale motions. Distinctive features (plumes) along the streakline are tracked between images to provide discrete irrotational region velocity magnitudes and material trajectories. A non-diffusive marker, introduced in the separating (high speed) boundary layer and imaged at x/θo=352, has revealed an unexpected bias in the streak-defined VSL locations. The interpretation of this bias clarifies the induced flow patterns in the entrainment region. The observations are consistent with a conception of the large-scale shear layer motions as "billows" of vortical fluid separated by re-entrant "wedges" of irrotational fluid, per Phillips (1972). Morris, S.C. and Foss, J.F. (2003). "Turbulent Boundary Layer to Single Stream Shear Layer: The Transition Region." Journal of Fluid Mechanics. Vol. 494, pp. 187-221. Phillips, O. M. (1972). "The Entrainment Interface." Journal of Fluid Mechanics. Vol. 51, pp. 97-118.

Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm

USDA-ARS?s Scientific Manuscript database

Longan (Dimocarpus longan Lour.) is an important tropical fruit tree crop. Accurate varietal identification is essential for germplasm management and breeding. Using longan transcriptome sequences from public databases, we developed single nucleotide polymorphism (SNP) markers; validated 60 SNPs in...

Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies

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

Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.

The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.

Performance comparison of single axis tracking and 40° solar panels for sunny weather

NASA Astrophysics Data System (ADS)

Chua, Yaw Long; Yong, Yoon Kuang; Koh, Yit Yan

2017-09-01

The rapid increment in human population and economy growth had led to the rise of the energy demand globally. With the rapid diminishing fossil fuels based energy sources, renewable energy sources had been introduced due to its unlimited availability especially solar energy which is a sustainable and reliable energy. This research was conducted to study and compare the efficiency of the single axis tracking solar panel with a 40° inclined angle solar panel in sunny weather condition. The results indicated that the output generated by the solar panel was directly affected by the angle which the solar panel facing the sun. In terms of performance the single axis tracking solar panel emerged to be more efficient with greater energy generated.

[Cloning goat producing human lactoferrin with genetically modified donor cells selected by single or dual markers].

PubMed

An, Liyou; Yuan, Yuguo; Yu, Baoli; Yang, Tingjia; Cheng, Yong

2012-12-01

We compared the efficiency of cloning goat using human lactoferrin (hLF) with genetically modified donor cells marked by single (Neo(r)) or double (Neo(r)/GFP) markers. Single marker expression vector (pBLC14) or dual markers expression vector (pAPLM) was delivered to goat fetal fibroblasts (GFF), and then the transgenic GFF was used as donor cells to produce transgenic goats. Respectively, 58.8% (20/34) and 86.7% (26/30) resistant cell lines confirmed the transgenic integration by PCR. Moreover, pAPLM cells lines were subcultured with several passages, only 20% (6/30) cell lines was observed fluorescence from each cell during the cell passage. Somatic cell nuclear transfer using the donor cells harbouring pBLC14 or pAPLM construct, resulting in a total of 806 reconstructed embryos, a pregnancy rate at 35 d (53.8%, 39.1%) and 60 d (26.9%, 21.7%), and an offspring birth rate (1.9%, 1.4%) with 5 and 7 newborn cloned goats, respectively. Transgene was confirmed by PCR and southern-blot in all cloned offspring. There were no significant differences at the reconstructed embryo fusion rates, pregnancy rates and the birth rate (P > 0.05) between single and double markers groups. The Neo(r)/GFP double markers could improve the reliability for accurately and efficiently selecting the genetically modified donor cells. No adverse effect was observed on the efficiency of transgenic goat production by SCNT using somatic cells transfected with double (Neo(r)/GFP) markers vector.

Scaling and automation of a high-throughput single-cell-derived tumor sphere assay chip.

PubMed

Cheng, Yu-Heng; Chen, Yu-Chih; Brien, Riley; Yoon, Euisik

2016-10-07

Recent research suggests that cancer stem-like cells (CSCs) are the key subpopulation for tumor relapse and metastasis. Due to cancer plasticity in surface antigen and enzymatic activity markers, functional tumorsphere assays are promising alternatives for CSC identification. To reliably quantify rare CSCs (1-5%), thousands of single-cell suspension cultures are required. While microfluidics is a powerful tool in handling single cells, previous works provide limited throughput and lack automatic data analysis capability required for high-throughput studies. In this study, we present the scaling and automation of high-throughput single-cell-derived tumor sphere assay chips, facilitating the tracking of up to ∼10 000 cells on a chip with ∼76.5% capture rate. The presented cell capture scheme guarantees sampling a representative population from the bulk cells. To analyze thousands of single-cells with a variety of fluorescent intensities, a highly adaptable analysis program was developed for cell/sphere counting and size measurement. Using a Pluronic® F108 (poly(ethylene glycol)-block-poly(propylene glycol)-block-poly(ethylene glycol)) coating on polydimethylsiloxane (PDMS), a suspension culture environment was created to test a controversial hypothesis: whether larger or smaller cells are more stem-like defined by the capability to form single-cell-derived spheres. Different cell lines showed different correlations between sphere formation rate and initial cell size, suggesting heterogeneity in pathway regulation among breast cancer cell lines. More interestingly, by monitoring hundreds of spheres, we identified heterogeneity in sphere growth dynamics, indicating the cellular heterogeneity even within CSCs. These preliminary results highlight the power of unprecedented high-throughput and automation in CSC studies.

Interfacing sensory input with motor output: does the control architecture converge to a serial process along a single channel?

PubMed Central

van de Kamp, Cornelis; Gawthrop, Peter J.; Gollee, Henrik; Lakie, Martin; Loram, Ian D.

2013-01-01

Modular organization in control architecture may underlie the versatility of human motor control; but the nature of the interface relating sensory input through task-selection in the space of performance variables to control actions in the space of the elemental variables is currently unknown. Our central question is whether the control architecture converges to a serial process along a single channel? In discrete reaction time experiments, psychologists have firmly associated a serial single channel hypothesis with refractoriness and response selection [psychological refractory period (PRP)]. Recently, we developed a methodology and evidence identifying refractoriness in sustained control of an external single degree-of-freedom system. We hypothesize that multi-segmental whole-body control also shows refractoriness. Eight participants controlled their whole body to ensure a head marker tracked a target as fast and accurately as possible. Analysis showed enhanced delays in response to stimuli with close temporal proximity to the preceding stimulus. Consistent with our preceding work, this evidence is incompatible with control as a linear time invariant process. This evidence is consistent with a single-channel serial ballistic process within the intermittent control paradigm with an intermittent interval of around 0.5 s. A control architecture reproducing intentional human movement control must reproduce refractoriness. Intermittent control is designed to provide computational time for an online optimization process and is appropriate for flexible adaptive control. For human motor control we suggest that parallel sensory input converges to a serial, single channel process involving planning, selection, and temporal inhibition of alternative responses prior to low dimensional motor output. Such design could aid robots to reproduce the flexibility of human control. PMID:23675342

Real-time 3D internal marker tracking during arc radiotherapy by the use of combined MV kV imaging

NASA Astrophysics Data System (ADS)

Liu, W.; Wiersma, R. D.; Mao, W.; Luxton, G.; Xing, L.

2008-12-01

To minimize the adverse dosimetric effect caused by tumor motion, it is desirable to have real-time knowledge of the tumor position throughout the beam delivery process. A promising technique to realize the real-time image guided scheme in external beam radiation therapy is through the combined use of MV and onboard kV beam imaging. The success of this MV-kV triangulation approach for fixed-gantry radiation therapy has been demonstrated. With the increasing acceptance of modern arc radiotherapy in the clinics, a timely and clinically important question is whether the image guidance strategy can be extended to arc therapy to provide the urgently needed real-time tumor motion information. While conceptually feasible, there are a number of theoretical and practical issues specific to the arc delivery that need to be resolved before clinical implementation. The purpose of this work is to establish a robust procedure of system calibration for combined MV and kV imaging for internal marker tracking during arc delivery and to demonstrate the feasibility and accuracy of the technique. A commercially available LINAC equipped with an onboard kV imager and electronic portal imaging device (EPID) was used for the study. A custom built phantom with multiple ball bearings was used to calibrate the stereoscopic MV-kV imaging system to provide the transformation parameters from imaging pixels to 3D world coordinates. The accuracy of the fiducial tracking system was examined using a 4D motion phantom capable of moving in accordance with a pre-programmed trajectory. Overall, spatial accuracy of MV-kV fiducial tracking during the arc delivery process for normal adult breathing amplitude and period was found to be better than 1 mm. For fast motion, the results depended on the imaging frame rates. The RMS error ranged from ~0.5 mm for the normal adult breathing pattern to ~1.5 mm for more extreme cases with a low imaging frame rate of 3.4 Hz. In general, highly accurate real-time tracking of implanted markers using hybrid MV-kV imaging is achievable and the technique should be useful to improve the beam targeting accuracy of arc therapy.

Real-time 3D internal marker tracking during arc radiotherapy by the use of combined MV-kV imaging.

PubMed

Liu, W; Wiersma, R D; Mao, W; Luxton, G; Xing, L

2008-12-21

To minimize the adverse dosimetric effect caused by tumor motion, it is desirable to have real-time knowledge of the tumor position throughout the beam delivery process. A promising technique to realize the real-time image guided scheme in external beam radiation therapy is through the combined use of MV and onboard kV beam imaging. The success of this MV-kV triangulation approach for fixed-gantry radiation therapy has been demonstrated. With the increasing acceptance of modern arc radiotherapy in the clinics, a timely and clinically important question is whether the image guidance strategy can be extended to arc therapy to provide the urgently needed real-time tumor motion information. While conceptually feasible, there are a number of theoretical and practical issues specific to the arc delivery that need to be resolved before clinical implementation. The purpose of this work is to establish a robust procedure of system calibration for combined MV and kV imaging for internal marker tracking during arc delivery and to demonstrate the feasibility and accuracy of the technique. A commercially available LINAC equipped with an onboard kV imager and electronic portal imaging device (EPID) was used for the study. A custom built phantom with multiple ball bearings was used to calibrate the stereoscopic MV-kV imaging system to provide the transformation parameters from imaging pixels to 3D world coordinates. The accuracy of the fiducial tracking system was examined using a 4D motion phantom capable of moving in accordance with a pre-programmed trajectory. Overall, spatial accuracy of MV-kV fiducial tracking during the arc delivery process for normal adult breathing amplitude and period was found to be better than 1 mm. For fast motion, the results depended on the imaging frame rates. The RMS error ranged from approximately 0.5 mm for the normal adult breathing pattern to approximately 1.5 mm for more extreme cases with a low imaging frame rate of 3.4 Hz. In general, highly accurate real-time tracking of implanted markers using hybrid MV-kV imaging is achievable and the technique should be useful to improve the beam targeting accuracy of arc therapy.

Loop shaping design for tracking performance in machine axes.

PubMed

Schinstock, Dale E; Wei, Zhouhong; Yang, Tao

2006-01-01

A modern interpretation of classical loop shaping control design methods is presented in the context of tracking control for linear motor stages. Target applications include noncontacting machines such as laser cutters and markers, water jet cutters, and adhesive applicators. The methods are directly applicable to the common PID controller and are pertinent to many electromechanical servo actuators other than linear motors. In addition to explicit design techniques a PID tuning algorithm stressing the importance of tracking is described. While the theory behind these techniques is not new, the analysis of their application to modern systems is unique in the research literature. The techniques and results should be important to control practitioners optimizing PID controller designs for tracking and in comparing results from classical designs to modern techniques. The methods stress high-gain controller design and interpret what this means for PID. Nothing in the methods presented precludes the addition of feedforward control methods for added improvements in tracking. Laboratory results from a linear motor stage demonstrate that with large open-loop gain very good tracking performance can be achieved. The resultant tracking errors compare very favorably to results from similar motions on similar systems that utilize much more complicated controllers.

Optimal Geometrical Set for Automated Marker Placement to Virtualized Real-Time Facial Emotions

PubMed Central

Maruthapillai, Vasanthan; Murugappan, Murugappan

2016-01-01

In recent years, real-time face recognition has been a major topic of interest in developing intelligent human-machine interaction systems. Over the past several decades, researchers have proposed different algorithms for facial expression recognition, but there has been little focus on detection in real-time scenarios. The present work proposes a new algorithmic method of automated marker placement used to classify six facial expressions: happiness, sadness, anger, fear, disgust, and surprise. Emotional facial expressions were captured using a webcam, while the proposed algorithm placed a set of eight virtual markers on each subject’s face. Facial feature extraction methods, including marker distance (distance between each marker to the center of the face) and change in marker distance (change in distance between the original and new marker positions), were used to extract three statistical features (mean, variance, and root mean square) from the real-time video sequence. The initial position of each marker was subjected to the optical flow algorithm for marker tracking with each emotional facial expression. Finally, the extracted statistical features were mapped into corresponding emotional facial expressions using two simple non-linear classifiers, K-nearest neighbor and probabilistic neural network. The results indicate that the proposed automated marker placement algorithm effectively placed eight virtual markers on each subject’s face and gave a maximum mean emotion classification rate of 96.94% using the probabilistic neural network. PMID:26859884

Optimal Geometrical Set for Automated Marker Placement to Virtualized Real-Time Facial Emotions.

PubMed

Maruthapillai, Vasanthan; Murugappan, Murugappan

2016-01-01

In recent years, real-time face recognition has been a major topic of interest in developing intelligent human-machine interaction systems. Over the past several decades, researchers have proposed different algorithms for facial expression recognition, but there has been little focus on detection in real-time scenarios. The present work proposes a new algorithmic method of automated marker placement used to classify six facial expressions: happiness, sadness, anger, fear, disgust, and surprise. Emotional facial expressions were captured using a webcam, while the proposed algorithm placed a set of eight virtual markers on each subject's face. Facial feature extraction methods, including marker distance (distance between each marker to the center of the face) and change in marker distance (change in distance between the original and new marker positions), were used to extract three statistical features (mean, variance, and root mean square) from the real-time video sequence. The initial position of each marker was subjected to the optical flow algorithm for marker tracking with each emotional facial expression. Finally, the extracted statistical features were mapped into corresponding emotional facial expressions using two simple non-linear classifiers, K-nearest neighbor and probabilistic neural network. The results indicate that the proposed automated marker placement algorithm effectively placed eight virtual markers on each subject's face and gave a maximum mean emotion classification rate of 96.94% using the probabilistic neural network.

Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

PubMed

Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

2014-05-15

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of dose to patient, spouse/caretaker, and staff, from an implanted trackable radioactive fiducial for use in the radiation treatment of prostate cancer

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

Neustadter, David; Barnea, Gideon; Stokar, Saul

Purpose: A fiducial tracking system based on a novel radioactive tracking technology is being developed for real-time target tracking in radiation therapy. In this study, the authors calculate the radiation dose to the patient, the spouse/caretaker, and the medical staff that would result from a 100 {mu}Ci Ir192 radioactive fiducial marker permanently implanted in the prostate of a radiation therapy patient. Methods: Local tissue dose was calculated by Monte Carlo simulation. The patient's whole body effective dose equivalent was calculated by summing the doses to the sensitive organs. Exposure of the spouse/caretaker was calculated from the NRC guidelines. Exposure ofmore » the medical staff was based on estimates of proximity to and time spent with the patient. Results: The local dose is below 40 Gy at 5 mm from the marker and below 10 Gy at 10 mm from the marker. The whole body effective dose equivalent to the patient is 64 mSv. The dose to the spouse/caretaker is 0.25 mSv. The annual exposures of the medical staff are 0.2 mSv for a doctor performing implantations and 0.34 mSv for a radiation therapist positioning patients for therapy. Conclusions: The local dose is not expected to have any clinically significant effect on the surrounding tissue which is irradiated during therapy. The dose to the patient is small in comparison to the whole body dose received from the therapy itself. The exposure of all other people is well below the recommended limits. The authors conclude that there is no radiation exposure related contraindication for use of this technology in the radiation treatment of prostate cancer.« less

Validation of the Leap Motion Controller using markered motion capture technology.

PubMed

Smeragliuolo, Anna H; Hill, N Jeremy; Disla, Luis; Putrino, David

2016-06-14

The Leap Motion Controller (LMC) is a low-cost, markerless motion capture device that tracks hand, wrist and forearm position. Integration of this technology into healthcare applications has begun to occur rapidly, making validation of the LMC׳s data output an important research goal. Here, we perform a detailed evaluation of the kinematic data output from the LMC, and validate this output against gold-standard, markered motion capture technology. We instructed subjects to perform three clinically-relevant wrist (flexion/extension, radial/ulnar deviation) and forearm (pronation/supination) movements. The movements were simultaneously tracked using both the LMC and a marker-based motion capture system from Motion Analysis Corporation (MAC). Adjusting for known inconsistencies in the LMC sampling frequency, we compared simultaneously acquired LMC and MAC data by performing Pearson׳s correlation (r) and root mean square error (RMSE). Wrist flexion/extension and radial/ulnar deviation showed good overall agreement (r=0.95; RMSE=11.6°, and r=0.92; RMSE=12.4°, respectively) with the MAC system. However, when tracking forearm pronation/supination, there were serious inconsistencies in reported joint angles (r=0.79; RMSE=38.4°). Hand posture significantly influenced the quality of wrist deviation (P<0.005) and forearm supination/pronation (P<0.001), but not wrist flexion/extension (P=0.29). We conclude that the LMC is capable of providing data that are clinically meaningful for wrist flexion/extension, and perhaps wrist deviation. It cannot yet return clinically meaningful data for measuring forearm pronation/supination. Future studies should continue to validate the LMC as updated versions of their software are developed. Copyright © 2016 Elsevier Ltd. All rights reserved.

INFLIGHT (MISSION CONTROL CENTER) - STS-2 - JSC

NASA Image and Video Library

1981-11-13

S81-39494 (12 Nov. 1981) --- An overall view of activity in the mission operations control room (MOCR) in Houston?s Mission Control Center (MCC) as viewed from the second front row of consoles during the STS-2 mission. The remote manipulator system (RMS) console is in the immediate foreground. Note TV transmission on the Eidophor screen at front of MOCR and shuttle orbiter marker on tracking map at left indicating the vehicle?s location over the Hawaiian Islands. The downlink was through the Hawaii tracking station. Photo credit: NASA

A virtual reality system for arm and hand rehabilitation

NASA Astrophysics Data System (ADS)

Luo, Zhiqiang; Lim, Chee Kian; Chen, I.-Ming; Yeo, Song Huat

2011-03-01

This paper presents a virtual reality (VR) system for upper limb rehabilitation. The system incorporates two motion track components, the Arm Suit and the Smart Glove which are composed of a range of the optical linear encoders (OLE) and the inertial measurement units (IMU), and two interactive practice applications designed for driving users to perform the required functional and non-functional motor recovery tasks. We describe the technique details about the two motion track components and the rational to design two practice applications. The experiment results show that, compared with the marker-based tracking system, the Arm Suit can accurately track the elbow and wrist positions. The repeatability of the Smart Glove on measuring the five fingers' movement can be satisfied. Given the low cost, high accuracy and easy installation, the system thus promises to be a valuable complement to conventional therapeutic programs offered in rehabilitation clinics and at home.

Design and preliminary accuracy studies of an MRI-guided transrectal prostate intervention system.

PubMed

Krieger, Axel; Csoma, Csaba; Iordachital, Iulian I; Guion, Peter; Singh, Anurag K; Fichtinger, Gabor; Whitcomb, Louis L

2007-01-01

This paper reports a novel system for magnetic resonance imaging (MRI) guided transrectal prostate interventions, such as needle biopsy, fiducial marker placement, and therapy delivery. The system utilizes a hybrid tracking method, comprised of passive fiducial tracking for initial registration and subsequent incremental motion measurement along the degrees of freedom using fiber-optical encoders and mechanical scales. Targeting accuracy of the system is evaluated in prostate phantom experiments. Achieved targeting accuracy and procedure times were found to compare favorably with existing systems using passive and active tracking methods. Moreover, the portable design of the system using only standard MRI image sequences and minimal custom scanner interfacing allows the system to be easily used on different MRI scanners.

Reliability of Urinary Dehydration Markers in Elite Youth Boxers.

PubMed

Zubac, Damir; Cular, Drazen; Marusic, Uros

2018-03-01

To determine the reliability and diagnostic accuracy of noninvasive urinary dehydration markers in field-based settings on a day-to-day basis in elite adolescent amateur boxers. Sixty-nine urine samples were collected daily from 23 athletes (17.3 ± 1.9 y) during their weight-stable phase and analyzed by field and laboratory measures of hydration status. Urine osmolality (U OSM ), urine specific gravity (U SG ), total protein content (T PC ), and body-mass stability were evaluated to determine fluid balance and hydration status. Overall macronutrient and water intake were determined using dietary records. According to their anthropometric characteristics, athletes were assigned into 2 groups: lightweight (L WB ) and heavyweight (H WB ) boxers. Data presented on U OSM demonstrated a uniform increment by 11.2% ± 12.8% (L WB ) and 19.9% ± 22.7% (H WB ) (P < .001) over the course of the study, even during the weight-stable phase (body mass, ICC = .99) and ad libitum fluid intake (42 ± 4 mL · kg -1  · d -1 ). The intraclass correlation coefficients (ICCs) ranged from .52 to .55 for U SG and .38 to .52 for U OSM , further indicating inconsistency of the urinary dehydration markers. Poor correlations were found between U SG and T PC metabolites (r = .27, P = .211). Urinary dehydration markers (both U SG and U OSM ) exhibit high variability and seem to be unreliable diagnostic tools to track actual body-weight loss in real-life settings. The ad libitum fluid intake was apparently inadequate to match acute fluid loss during and after intense preparation. The applicability of a single-time-point hydration-status assessment concept may preclude accurate assessment of actual body-weight deficits in youth boxers.

SU-E-J-23: An Accurate Algorithm to Match Imperfectly Matched Images for Lung Tumor Detection Without Markers

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

Rozario, T; Bereg, S; Chiu, T

Purpose: In order to locate lung tumors on projection images without internal markers, digitally reconstructed radiograph (DRR) is created and compared with projection images. Since lung tumors always move and their locations change on projection images while they are static on DRRs, a special DRR (background DRR) is generated based on modified anatomy from which lung tumors are removed. In addition, global discrepancies exist between DRRs and projections due to their different image originations, scattering, and noises. This adversely affects comparison accuracy. A simple but efficient comparison algorithm is reported. Methods: This method divides global images into a matrix ofmore » small tiles and similarities will be evaluated by calculating normalized cross correlation (NCC) between corresponding tiles on projections and DRRs. The tile configuration (tile locations) will be automatically optimized to keep the tumor within a single tile which has bad matching with the corresponding DRR tile. A pixel based linear transformation will be determined by linear interpolations of tile transformation results obtained during tile matching. The DRR will be transformed to the projection image level and subtracted from it. The resulting subtracted image now contains only the tumor. A DRR of the tumor is registered to the subtracted image to locate the tumor. Results: This method has been successfully applied to kV fluoro images (about 1000 images) acquired on a Vero (Brainlab) for dynamic tumor tracking on phantom studies. Radiation opaque markers are implanted and used as ground truth for tumor positions. Although, other organs and bony structures introduce strong signals superimposed on tumors at some angles, this method accurately locates tumors on every projection over 12 gantry angles. The maximum error is less than 2.6 mm while the total average error is 1.0 mm. Conclusion: This algorithm is capable of detecting tumor without markers despite strong background signals.« less

A Diagnostic Marker to Discriminate Childhood Apraxia of Speech from Speech Delay: Introduction

ERIC Educational Resources Information Center

Shriberg, Lawrence D.; Strand, Edythe A.; Fourakis, Marios; Jakielski, Kathy J.; Hall, Sheryl D.; Karlsson, Heather B.; Mabie, Heather L.; McSweeny, Jane L.; Tilkens, Christie M.; Wilson, David L.

2017-01-01

Purpose: The goal of this article is to introduce the pause marker (PM), a single-sign diagnostic marker proposed to discriminate early or persistent childhood apraxia of speech (CAS) from speech delay.

Multiple objects tracking in fluorescence microscopy.

PubMed

Kalaidzidis, Yannis

2009-01-01

Many processes in cell biology are connected to the movement of compact entities: intracellular vesicles and even single molecules. The tracking of individual objects is important for understanding cellular dynamics. Here we describe the tracking algorithms which have been developed in the non-biological fields and successfully applied to object detection and tracking in biological applications. The characteristics features of the different algorithms are compared.

Self-paced model learning for robust visual tracking

NASA Astrophysics Data System (ADS)

Huang, Wenhui; Gu, Jason; Ma, Xin; Li, Yibin

2017-01-01

In visual tracking, learning a robust and efficient appearance model is a challenging task. Model learning determines both the strategy and the frequency of model updating, which contains many details that could affect the tracking results. Self-paced learning (SPL) has recently been attracting considerable interest in the fields of machine learning and computer vision. SPL is inspired by the learning principle underlying the cognitive process of humans, whose learning process is generally from easier samples to more complex aspects of a task. We propose a tracking method that integrates the learning paradigm of SPL into visual tracking, so reliable samples can be automatically selected for model learning. In contrast to many existing model learning strategies in visual tracking, we discover the missing link between sample selection and model learning, which are combined into a single objective function in our approach. Sample weights and model parameters can be learned by minimizing this single objective function. Additionally, to solve the real-valued learning weight of samples, an error-tolerant self-paced function that considers the characteristics of visual tracking is proposed. We demonstrate the robustness and efficiency of our tracker on a recent tracking benchmark data set with 50 video sequences.

Real-Time Tracking of Implanted Markers During Radiation Treatment by Use of Simultaneous kV and MV Imaging

DTIC Science & Technology

2009-03-01

the MV–kV correlation method by sinusoidally moving a block of solid water (measuring 5 × 5× 10 cm3) containing three embedded BB metallic markers (3 mm...in diameter). A 4D motion platform (Washington University, St Louis, MO) holding the block of solid water (figure 1) was programmed to produce the...Varian Medical Systems, Palo Alto, CA). The SS-IMRT plans were delivered to either the moving pelvic phantom or the cube of solid water attached to the

Non-Invasive Timing of Gas Gun Projectiles with Light Detection and Ranging

NASA Astrophysics Data System (ADS)

Goodwin, Peter; Wu, Ming; Dattelbaum, Dana

2013-06-01

We have developed a Light Detection and Ranging (LIDAR) diagnostic to track the position of a projectile inside of the gas gun barrel in real-time. This capability permits the generation of precisely timed trigger pulses useful for pre-triggering high-latency diagnostics such as a flash lamp-pumped laser. An initial feasibility test was performed using a 72 mm bore single-stage gas gun routinely used for dynamic research at Los Alamos National Laboratory. A 655-nm pulsed (~100 ps) diode laser operating at a pulse repetition rate of ~100 kHz was used to interrogate the position of the moving projectile in real-time. The position of the projectile in the gun barrel was tracked over a distance of ~3 meters prior to impact. The position record showed that the projectile moved at a constant velocity (483 m/s) prior to impacting the target. This velocity was in good agreement with independent measurements of the projectile velocity by photon Doppler velocimetry, and timing of the passage of the projectile through optical marker beams positioned at the muzzle of the gun. The LIDAR return can be processed in real-time to generate pre-trigger pulses at preset separations between the projectile and target. Work funded by LANL Laboratory Directed Research Project 2011012DR. LA-UR-13-21121, approved for public release.

Time-resolved measurements of coherent structures in the turbulent boundary layer

NASA Astrophysics Data System (ADS)

LeHew, J. A.; Guala, M.; McKeon, B. J.

2013-04-01

Time-resolved particle image velocimetry was used to examine the structure and evolution of swirling coherent structure (SCS), one interpretation of which is a marker for a three-dimensional coherent vortex structure, in wall-parallel planes of a turbulent boundary layer with a large field of view, 4.3 δ × 2.2 δ. Measurements were taken at four different wall-normal locations ranging from y/ δ = 0.08-0.48 at a friction Reynolds number, Re τ = 410. The data set yielded statistically converged results over a larger field of view than typically observed in the literature. The method for identifying and tracking swirling coherent structure is discussed, and the resulting trajectories, convection velocities, and lifespan of these structures are analyzed at each wall-normal location. The ability of a model in which the entirety of an individual SCS travels at a single convection velocity, consistent with the attached eddy hypothesis of Townsend (The structure of turbulent shear flows. Cambridge University Press, Cambridge, 1976), to describe the data is investigated. A methodology for determining whether such structures are "attached" or "detached" from the wall is also proposed and used to measure the lifespan and convection velocity distributions of these different structures. SCS were found to persist for longer periods of time further from the wall, particularly those inferred to be "detached" from the wall, which could be tracked for longer than 5 eddy turnover times.

Single-chip microcomputer for image processing in the photonic measuring system

NASA Astrophysics Data System (ADS)

Smoleva, Olga S.; Ljul, Natalia Y.

2002-04-01

The non-contact measuring system has been designed for rail- track parameters control on the Moscow Metro. It detects some significant parameters: rail-track width, rail-track height, gage, rail-slums, crosslevel, pickets, and car speed. The system consists of three subsystems: non-contact system of rail-track width, height, and gage inspection, non-contact system of rail-slums inspection and subsystem for crosslevel, speed, and pickets detection. Data from subsystems is transferred to pre-processing unit. In order to process data received from subsystems, the single-chip signal processor ADSP-2185 must be used due to providing required processing speed. After data will be processed, it is send to PC, which processes it and outputs it in the readable form.

Symplectic multi-particle tracking on GPUs

NASA Astrophysics Data System (ADS)

Liu, Zhicong; Qiang, Ji

2018-05-01

A symplectic multi-particle tracking model is implemented on the Graphic Processing Units (GPUs) using the Compute Unified Device Architecture (CUDA) language. The symplectic tracking model can preserve phase space structure and reduce non-physical effects in long term simulation, which is important for beam property evaluation in particle accelerators. Though this model is computationally expensive, it is very suitable for parallelization and can be accelerated significantly by using GPUs. In this paper, we optimized the implementation of the symplectic tracking model on both single GPU and multiple GPUs. Using a single GPU processor, the code achieves a factor of 2-10 speedup for a range of problem sizes compared with the time on a single state-of-the-art Central Processing Unit (CPU) node with similar power consumption and semiconductor technology. It also shows good scalability on a multi-GPU cluster at Oak Ridge Leadership Computing Facility. In an application to beam dynamics simulation, the GPU implementation helps save more than a factor of two total computing time in comparison to the CPU implementation.

Identifying Mechanisms of Interfacial Dynamics Using Single-Molecule Tracking

PubMed Central

Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

2012-01-01

The “soft” (i.e. non-covalent) interactions between molecules and surfaces are complex and highly-varied (e.g. hydrophobic, hydrogen bonding, ionic) often leading to heterogeneous interfacial behavior. Heterogeneity can arise either from spatial variation of the surface/interface itself or from molecular configurations (i.e. conformation, orientation, aggregation state, etc.). By observing adsorption, diffusion, and desorption of individual fluorescent molecules, single-molecule tracking can characterize these types of heterogeneous interfacial behavior in ways that are inaccessible to traditional ensemble-averaged methods. Moreover, the fluorescence intensity or emission wavelength (in resonance energy transfer experiments) can be used to simultaneously track molecular configuration and directly relate this to the resulting interfacial mobility or affinity. In this feature article, we review recent advances involving the use of single-molecule tracking to characterize heterogeneous molecule-surface interactions including: multiple modes of diffusion and desorption associated with both internal and external molecular configuration, Arrhenius activated interfacial transport, spatially dependent interactions, and many more. PMID:22716995

A Polymorphism in Mitochondrial DNA Associated with IQ?

ERIC Educational Resources Information Center

Skuder, Patricia; And Others

1995-01-01

Of 100 DNA markers examined in an allelic association study, only 1 showed a replicated association with IQ in samples totaling 107 children. How the gene marked by the particular restriction fragment length polymorphism was tracked and its mitochondrial origin identified is described. (SLD)

Microbial Source Tracking of Avian Sources

EPA Science Inventory

What Have We Learned After 10 Years of MST Research: Its Importance in the Developments of New Markers and Future Directions. Feces Production in the U.S.: Human - 07%; Chickens - 22%; Pigs - 20%; Dairy - 10%; and Beef Cattle 44%. Evaluation of Swine Assays - PF163 targeting...

Beyond fitness tracking: The use of consumer-grade wearable data from normal volunteers in cardiovascular and lipidomics research

PubMed Central

Teo, Jing Xian; Yang, Chengxi; Pua, Chee Jian; Blöcker, Christopher; Lim, Jing Quan; Ching, Jianhong; Yap, Jonathan Jiunn Liang; Tan, Swee Yaw; Sahlén, Anders; Chin, Calvin Woon-Loong; Teh, Bin Tean; Rozen, Steven G.; Cook, Stuart Alexander; Yeo, Khung Keong; Tan, Patrick

2018-01-01

The use of consumer-grade wearables for purposes beyond fitness tracking has not been comprehensively explored. We generated and analyzed multidimensional data from 233 normal volunteers, integrating wearable data, lifestyle questionnaires, cardiac imaging, sphingolipid profiling, and multiple clinical-grade cardiovascular and metabolic disease markers. We show that subjects can be stratified into distinct clusters based on daily activity patterns and that these clusters are marked by distinct demographic and behavioral patterns. While resting heart rates (RHRs) performed better than step counts in being associated with cardiovascular and metabolic disease markers, step counts identified relationships between physical activity and cardiac remodeling, suggesting that wearable data may play a role in reducing overdiagnosis of cardiac hypertrophy or dilatation in active individuals. Wearable-derived activity levels can be used to identify known and novel activity-modulated sphingolipids that are in turn associated with insulin sensitivity. Our findings demonstrate the potential for wearables in biomedical research and personalized health. PMID:29485983

Low-cost three-dimensional gait analysis system for mice with an infrared depth sensor.

PubMed

Nakamura, Akihiro; Funaya, Hiroyuki; Uezono, Naohiro; Nakashima, Kinichi; Ishida, Yasumasa; Suzuki, Tomohiro; Wakana, Shigeharu; Shibata, Tomohiro

2015-11-01

Three-dimensional (3D) open-field gait analysis of mice is an essential procedure in genetic and nerve regeneration research. Existing gait analysis systems are generally expensive and may interfere with the natural behaviors of mice because of optical markers and transparent floors. In contrast, the proposed system captures the subjects shape from beneath using a low-cost infrared depth sensor (Microsoft Kinect) and an opaque infrared pass filter. This means that we can track footprints and 3D paw-tip positions without optical markers or a transparent floor, thereby preventing any behavioral changes. Our experimental results suggest with healthy mice that they are more active on opaque floors and spend more time in the center of the open-field, when compared with transparent floors. The proposed system detected footprints with a comparable performance to existing systems, and precisely tracked the 3D paw-tip positions in the depth image coordinates. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Optical Indoor Positioning System Based on TFT Technology

PubMed Central

Gőzse, István

2015-01-01

A novel indoor positioning system is presented in the paper. Similarly to the camera-based solutions, it is based on visual detection, but it conceptually differs from the classical approaches. First, the objects are marked by LEDs, and second, a special sensing unit is applied, instead of a camera, to track the motion of the markers. This sensing unit realizes a modified pinhole camera model, where the light-sensing area is fixed and consists of a small number of sensing elements (photodiodes), and it is the hole that can be moved. The markers are tracked by controlling the motion of the hole, such that the light of the LEDs always hits the photodiodes. The proposed concept has several advantages: Apart from its low computational demands, it is insensitive to the disturbing ambient light. Moreover, as every component of the system can be realized by simple and inexpensive elements, the overall cost of the system can be kept low. PMID:26712753

Design and implementation of a remote UAV-based mobile health monitoring system

NASA Astrophysics Data System (ADS)

Li, Songwei; Wan, Yan; Fu, Shengli; Liu, Mushuang; Wu, H. Felix

2017-04-01

Unmanned aerial vehicles (UAVs) play increasing roles in structure health monitoring. With growing mobility in modern Internet-of-Things (IoT) applications, the health monitoring of mobile structures becomes an emerging application. In this paper, we develop a UAV-carried vision-based monitoring system that allows a UAV to continuously track and monitor a mobile infrastructure and transmit back the monitoring information in real- time from a remote location. The monitoring system uses a simple UAV-mounted camera and requires only a single feature located on the mobile infrastructure for target detection and tracking. The computation-effective vision-based tracking solution based on a single feature is an improvement over existing vision-based lead-follower tracking systems that either have poor tracking performance due to the use of a single feature, or have improved tracking performance at a cost of the usage of multiple features. In addition, a UAV-carried aerial networking infrastructure using directional antennas is used to enable robust real-time transmission of monitoring video streams over a long distance. Automatic heading control is used to self-align headings of directional antennas to enable robust communication in mobility. Compared to existing omni-communication systems, the directional communication solution significantly increases the operation range of remote monitoring systems. In this paper, we develop the integrated modeling framework of camera and mobile platforms, design the tracking algorithm, develop a testbed of UAVs and mobile platforms, and evaluate system performance through both simulation studies and field tests.

Precise Orbit Determination for LEO Spacecraft Using GNSS Tracking Data from Multiple Antennas

NASA Technical Reports Server (NTRS)

Kuang, Da; Bertiger, William; Desai, Shailen; Haines, Bruce

2010-01-01

To support various applications, certain Earth-orbiting spacecrafts (e.g., SRTM, COSMIC) use multiple GNSS antennas to provide tracking data for precise orbit determination (POD). POD using GNSS tracking data from multiple antennas poses some special technical issues compared to the typical single-antenna approach. In this paper, we investigate some of these issues using both real and simulated data. Recommendations are provided for POD with multiple GNSS antennas and for antenna configuration design. The observability of satellite position with multiple antennas data is compared against single antenna case. The impact of differential clock (line biases) and line-of-sight (up, along-track, and cross-track) on kinematic and reduced-dynamic POD is evaluated. The accuracy of monitoring the stability of the spacecraft structure by simultaneously performing POD of the spacecraft and relative positioning of the multiple antennas is also investigated.

Single-camera three-dimensional tracking of natural particulate and zooplankton

NASA Astrophysics Data System (ADS)

Troutman, Valerie A.; Dabiri, John O.

2018-07-01

We develop and characterize an image processing algorithm to adapt single-camera defocusing digital particle image velocimetry (DDPIV) for three-dimensional (3D) particle tracking velocimetry (PTV) of natural particulates, such as those present in the ocean. The conventional DDPIV technique is extended to facilitate tracking of non-uniform, non-spherical particles within a volume depth an order of magnitude larger than current single-camera applications (i.e. 10 cm  ×  10 cm  ×  24 cm depth) by a dynamic template matching method. This 2D cross-correlation method does not rely on precise determination of the centroid of the tracked objects. To accommodate the broad range of particle number densities found in natural marine environments, the performance of the measurement technique at higher particle densities has been improved by utilizing the time-history of tracked objects to inform 3D reconstruction. The developed processing algorithms were analyzed using synthetically generated images of flow induced by Hill’s spherical vortex, and the capabilities of the measurement technique were demonstrated empirically through volumetric reconstructions of the 3D trajectories of particles and highly non-spherical, 5 mm zooplankton.

49 CFR 220.5 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... equipment, or track motor car, singly or in combination with other equipment, on the track of a railroad... systems, electric traction systems, roadway facilities or roadway maintenance machinery on or near track... one or more locomotives coupled with or without cars, requiring an air brake test in accordance with...

Experimental Study of Lightweight Tracked Vehicle Performance on Dry Granular Materials

DTIC Science & Technology

2013-09-12

agricultural tractor and found that the length of the ground contact area is the most important factor affecting tractive performance, while track...authors are grateful to Ce- cilia Cantu and to Meccanotecnica Riesi SRL for collaborating on designing and manufacturing the single track device

Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

PubMed Central

Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

2016-01-01

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

Nicotine as a Marker for Environmental Tobacco Smoke: Implications of Sorption on Indoor Surface Materials.

PubMed

Van Loy, Michael D; Nazaroff, William W; Daisey, Joan M

1998-10-01

Recently developed models and data describing the interactions of gas-phase semi-volatile organic compounds with indoor surfaces are employed to examine the effects of sorption on nicotine's suitability as an environmental tobacco smoke (ETS) marker. Using parameters from our studies of nicotine sorption on carpet, painted wallboard, and stainless steel and previously published data on ETS particle deposition, the dynamic behavior of nicotine was modeled in two different indoor environments: a house and a stainless steel chamber. The results show that apparently contradictory observations of nicotine's behavior in indoor air can be understood by considering the effects of sorption under different experimental conditions. In indoor environments in which smoking has occurred regularly for an extended period, the sorbed mass of nicotine is very large relative to the mass emitted by a single cigarette. The importance of nicotine adsorption relative to ventilation as a gas-phase removal mechanism is reduced. Where smoking occurs less regularly or the indoor surfaces are cleaned prior to smoking (as in a laboratory chamber), nicotine deposition is more significant. Nicotine concentrations closely track the levels of other ETS constituents in environments with habitual smoking if the data are averaged over a period significantly longer than the period between cigarette combustion episodes. However, nicotine is not a suitable tracer for predicting ETS exposures at fine time scales or in settings where smoking occurs infrequently and irregularly.

EINVis: a visualization tool for analyzing and exploring genetic interactions in large-scale association studies.

PubMed

Wu, Yubao; Zhu, Xiaofeng; Chen, Jian; Zhang, Xiang

2013-11-01

Epistasis (gene-gene interaction) detection in large-scale genetic association studies has recently drawn extensive research interests as many complex traits are likely caused by the joint effect of multiple genetic factors. The large number of possible interactions poses both statistical and computational challenges. A variety of approaches have been developed to address the analytical challenges in epistatic interaction detection. These methods usually output the identified genetic interactions and store them in flat file formats. It is highly desirable to develop an effective visualization tool to further investigate the detected interactions and unravel hidden interaction patterns. We have developed EINVis, a novel visualization tool that is specifically designed to analyze and explore genetic interactions. EINVis displays interactions among genetic markers as a network. It utilizes a circular layout (specially, a tree ring view) to simultaneously visualize the hierarchical interactions between single nucleotide polymorphisms (SNPs), genes, and chromosomes, and the network structure formed by these interactions. Using EINVis, the user can distinguish marginal effects from interactions, track interactions involving more than two markers, visualize interactions at different levels, and detect proxy SNPs based on linkage disequilibrium. EINVis is an effective and user-friendly free visualization tool for analyzing and exploring genetic interactions. It is publicly available with detailed documentation and online tutorial on the web at http://filer.case.edu/yxw407/einvis/. © 2013 WILEY PERIODICALS, INC.

Polymorphic chloroplast microsatellite markers in the octoploid Lepidium meyenii (Brassicaceae) and cross-species amplification in Lepidium.

PubMed

Hasan, Nabeeh A; Mummenhoff, Klaus; Quiros, Carlos F; Tay, C David; Bailey, C Donovan

2010-10-01

As a crop and medicinal plant, the octoploid Andean endemic Lepidium meyenii suffers from taxonomic uncertainty. Few molecular markers are available to genotype individuals or track gene flow in wild and cultivated material. • Using available sequence data, eight cpSSR primer pairs were developed for L. meyenii. Levels of polymorphism checked in 56 individual L. meyenii, including cultivated and wild material, revealed that the number of alleles per locus ranged from three to five, and intrapopulation allele frequencies ranged from 0.071 to 1.0. Polymerase-chain-reaction screens using our cpSSR primers in 27 other Lepidium species and three Coronopus species suggested a high degree of interspecific amplification. • These polymorphic cpSSR markers should prove useful in characterizing genetic variation among cultivated and wild L. meyenii. Additionally, interspecific amplifications suggest that these markers will be useful for the study of related taxa.

SYTO probes: markers of apoptotic cell demise.

PubMed

Wlodkowic, Donald; Skommer, Joanna

2007-10-01

As mechanistic studies on tumor cell death advance towards their ultimate translational goal, there is a need for specific, rapid, and high-throughput analytical tools to detect diverse cell demise modes. Patented DNA-binding SYTO probes, for example, are gaining increasing interest as easy-to-use markers of caspase-dependent apoptotic cell death. They are proving convenient for tracking apoptosis in diverse hematopoietic cell lines and primary tumor samples, and, due to their spectral characteristics, appear to be useful for the development of multiparameter flow cytometry assays. Herein, several protocols for multiparametric assessment of apoptotic events using SYTO probes are provided. There are protocols describing the use of green fluorescent SYTO 16 and red fluorescent SYTO 17 dyes in combination with plasma membrane permeability markers. Another protocol highlights the multiparametric use of SYTO 16 dye in conjunction with the mitochondrial membrane potential sensitive probe, tetramethylrhodamine methyl ester (TMRM), and the plasma membrane permeability marker, 7-aminoactinomycin D (7-AAD).

Automatic respiration tracking for radiotherapy using optical 3D camera

NASA Astrophysics Data System (ADS)

Li, Tuotuo; Geng, Jason; Li, Shidong

2013-03-01

Rapid optical three-dimensional (O3D) imaging systems provide accurate digitized 3D surface data in real-time, with no patient contact nor radiation. The accurate 3D surface images offer crucial information in image-guided radiation therapy (IGRT) treatments for accurate patient repositioning and respiration management. However, applications of O3D imaging techniques to image-guided radiotherapy have been clinically challenged by body deformation, pathological and anatomical variations among individual patients, extremely high dimensionality of the 3D surface data, and irregular respiration motion. In existing clinical radiation therapy (RT) procedures target displacements are caused by (1) inter-fractional anatomy changes due to weight, swell, food/water intake; (2) intra-fractional variations from anatomy changes within any treatment session due to voluntary/involuntary physiologic processes (e.g. respiration, muscle relaxation); (3) patient setup misalignment in daily reposition due to user errors; and (4) changes of marker or positioning device, etc. Presently, viable solution is lacking for in-vivo tracking of target motion and anatomy changes during the beam-on time without exposing patient with additional ionized radiation or high magnet field. Current O3D-guided radiotherapy systems relay on selected points or areas in the 3D surface to track surface motion. The configuration of the marks or areas may change with time that makes it inconsistent in quantifying and interpreting the respiration patterns. To meet the challenge of performing real-time respiration tracking using O3D imaging technology in IGRT, we propose a new approach to automatic respiration motion analysis based on linear dimensionality reduction technique based on PCA (principle component analysis). Optical 3D image sequence is decomposed with principle component analysis into a limited number of independent (orthogonal) motion patterns (a low dimension eigen-space span by eigen-vectors). New images can be accurately represented as weighted summation of those eigen-vectors, which can be easily discriminated with a trained classifier. We developed algorithms, software and integrated with an O3D imaging system to perform the respiration tracking automatically. The resulting respiration tracking system requires no human intervene during it tracking operation. Experimental results show that our approach to respiration tracking is more accurate and robust than the methods using manual selected markers, even in the presence of incomplete imaging data.

Evaluation of a video-based head motion tracking system for dedicated brain PET

NASA Astrophysics Data System (ADS)

Anishchenko, S.; Beylin, D.; Stepanov, P.; Stepanov, A.; Weinberg, I. N.; Schaeffer, S.; Zavarzin, V.; Shaposhnikov, D.; Smith, M. F.

2015-03-01

Unintentional head motion during Positron Emission Tomography (PET) data acquisition can degrade PET image quality and lead to artifacts. Poor patient compliance, head tremor, and coughing are examples of movement sources. Head motion due to patient non-compliance can be an issue with the rise of amyloid brain PET in dementia patients. To preserve PET image resolution and quantitative accuracy, head motion can be tracked and corrected in the image reconstruction algorithm. While fiducial markers can be used, a contactless approach is preferable. A video-based head motion tracking system for a dedicated portable brain PET scanner was developed. Four wide-angle cameras organized in two stereo pairs are used for capturing video of the patient's head during the PET data acquisition. Facial points are automatically tracked and used to determine the six degree of freedom head pose as a function of time. The presented work evaluated the newly designed tracking system using a head phantom and a moving American College of Radiology (ACR) phantom. The mean video-tracking error was 0.99±0.90 mm relative to the magnetic tracking device used as ground truth. Qualitative evaluation with the ACR phantom shows the advantage of the motion tracking application. The developed system is able to perform tracking with accuracy close to millimeter and can help to preserve resolution of brain PET images in presence of movements.

Search for lightly ionizing particles with the MACRO detector

NASA Astrophysics Data System (ADS)

Ambrosio, M.; Antolini, R.; Auriemma, G.; Bakari, D.; Baldini, A.; Barbarino, G. C.; Barish, B. C.; Battistoni, G.; Bellotti, R.; Bemporad, C.; Bernardini, P.; Bilokon, H.; Bisi, V.; Bloise, C.; Bower, C.; Brigida, M.; Bussino, S.; Cafagna, F.; Calicchio, M.; Campana, D.; Carboni, M.; Cecchini, S.; Cei, F.; Chiarella, V.; Choudhary, B. C.; Coutu, S.; de Cataldo, G.; Dekhissi, H.; de Marzo, C.; de Mitri, I.; Derkaoui, J.; de Vincenzi, M.; di Credico, A.; Erriquez, O.; Favuzzi, C.; Forti, C.; Fusco, P.; Giacomelli, G.; Giannini, G.; Giglietto, N.; Giorgini, M.; Grassi, M.; Gray, L.; Grillo, A.; Guarino, F.; Gustavino, C.; Habig, A.; Hanson, K.; Heinz, R.; Iarocci, E.; Katsavounidis, E.; Katsavounidis, I.; Kearns, E.; Kim, H.; Kyriazopoulou, S.; Lamanna, E.; Lane, C.; Levin, D. S.; Lipari, P.; Longley, N. P.; Longo, M. J.; Loparco, F.; Maaroufi, F.; Mancarella, G.; Mandrioli, G.; Margiotta, A.; Marini, A.; Martello, D.; Marzari-Chiesa, A.; Mazziotta, M. N.; Michael, D. G.; Mikheyev, S.; Miller, L.; Monacelli, P.; Montaruli, T.; Monteno, M.; Mufson, S.; Musser, J.; Nicolò, D.; Nolty, R.; Orth, C.; Okada, C.; Osteria, G.; Ouchrif, M.; Palamara, O.; Patera, V.; Patrizii, L.; Pazzi, R.; Peck, C. W.; Perrone, L.; Petrera, S.; Pistilli, P.; Popa, V.; Rainò, A.; Reynoldson, J.; Ronga, F.; Satriano, C.; Satta, L.; Scapparone, E.; Scholberg, K.; Sciubba, A.; Serra, P.; Sioli, M.; Sitta, M.; Spinelli, P.; Spinetti, M.; Spurio, M.; Steinberg, R.; Stone, J. L.; Sulak, L. R.; Surdo, A.; Tarlè, G.; Togo, V.; Vakili, M.; Vilela, E.; Walter, C. W.; Webb, R.

2000-09-01

A search for lightly ionizing particles has been performed with the MACRO detector. This search was sensitive to particles with charges between 15 e and close to the charge of an electron, with β between approximately 0.25 and 1.0. Unlike previous searches both single track events and tracks buried within high multiplicity muon showers were examined. In a period of approximately one year no candidates were observed. Assuming an isotropic flux, for the single track sample this corresponds to a 90% C.L. upper flux limit Φ<=9.2×10-15 cm-2 s-1 sr-1.

Nano-scale measurement of biomolecules by optical microscopy and semiconductor nanoparticles

PubMed Central

Ichimura, Taro; Jin, Takashi; Fujita, Hideaki; Higuchi, Hideo; Watanabe, Tomonobu M.

2014-01-01

Over the past decade, great developments in optical microscopy have made this technology increasingly compatible with biological studies. Fluorescence microscopy has especially contributed to investigating the dynamic behaviors of live specimens and can now resolve objects with nanometer precision and resolution due to super-resolution imaging. Additionally, single particle tracking provides information on the dynamics of individual proteins at the nanometer scale both in vitro and in cells. Complementing advances in microscopy technologies has been the development of fluorescent probes. The quantum dot, a semi-conductor fluorescent nanoparticle, is particularly suitable for single particle tracking and super-resolution imaging. This article overviews the principles of single particle tracking and super resolution along with describing their application to the nanometer measurement/observation of biological systems when combined with quantum dot technologies. PMID:25120488

Single Particle Orientation and Rotational Tracking (SPORT) in biophysical studies

NASA Astrophysics Data System (ADS)

Gu, Yan; Ha, Ji Won; Augspurger, Ashley E.; Chen, Kuangcai; Zhu, Shaobin; Fang, Ning

2013-10-01

The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport.The single particle orientation and rotational tracking (SPORT) techniques have seen rapid development in the past 5 years. Recent technical advances have greatly expanded the applicability of SPORT in biophysical studies. In this feature article, we survey the current development of SPORT and discuss its potential applications in biophysics, including cellular membrane processes and intracellular transport. Electronic supplementary information (ESI) available: Three supplementary movies and an experimental section. See DOI: 10.1039/c3nr02254d

A novel method for quantification of beam's-eye-view tumor tracking performance.

PubMed

Hu, Yue-Houng; Myronakis, Marios; Rottmann, Joerg; Wang, Adam; Morf, Daniel; Shedlock, Daniel; Baturin, Paul; Star-Lack, Josh; Berbeco, Ross

2017-11-01

In-treatment imaging using an electronic portal imaging device (EPID) can be used to confirm patient and tumor positioning. Real-time tumor tracking performance using current digital megavolt (MV) imagers is hindered by poor image quality. Novel EPID designs may help to improve quantum noise response, while also preserving the high spatial resolution of the current clinical detector. Recently investigated EPID design improvements include but are not limited to multi-layer imager (MLI) architecture, thick crystalline and amorphous scintillators, and phosphor pixilation and focusing. The goal of the present study was to provide a method of quantitating improvement in tracking performance as well as to reveal the physical underpinnings of detector design that impact tracking quality. The study employs a generalizable ideal observer methodology for the quantification of tumor tracking performance. The analysis is applied to study both the effect of increasing scintillator thickness on a standard, single-layer imager (SLI) design as well as the effect of MLI architecture on tracking performance. The present study uses the ideal observer signal-to-noise ratio (d') as a surrogate for tracking performance. We employ functions which model clinically relevant tasks and generalized frequency-domain imaging metrics to connect image quality with tumor tracking. A detection task for relevant Cartesian shapes (i.e., spheres and cylinders) was used to quantitate trackability of cases employing fiducial markers. Automated lung tumor tracking algorithms often leverage the differences in benign and malignant lung tissue textures. These types of algorithms (e.g., soft-tissue localization - STiL) were simulated by designing a discrimination task, which quantifies the differentiation of tissue textures, measured experimentally and fit as a power-law in trend (with exponent β) using a cohort of MV images of patient lungs. The modeled MTF and NPS were used to investigate the effect of scintillator thickness and MLI architecture on tumor tracking performance. Quantification of MV images of lung tissue as an inverse power-law with respect to frequency yields exponent values of β = 3.11 and 3.29 for benign and malignant tissues, respectively. Tracking performance with and without fiducials was found to be generally limited by quantum noise, a factor dominated by quantum detective efficiency (QDE). For generic SLI construction, increasing the scintillator thickness (gadolinium oxysulfide - GOS) from a standard 290 μm to 1720 μm reduces noise to about 10%. However, 81% of this reduction is appreciated between 290 and 1000 μm. In comparing MLI and SLI detectors of equivalent individual GOS layer thickness, the improvement in noise is equal to the number of layers in the detector (i.e., 4) with almost no difference in MTF. Further, improvement in tracking performance was slightly less than the square-root of the reduction in noise, approximately 84-90%. In comparing an MLI detector with an SLI with a GOS scintillator of equivalent total thickness, improvement in object detectability is approximately 34-39%. We have presented a novel method for quantification of tumor tracking quality and have applied this model to evaluate the performance of SLI and MLI EPID designs. We showed that improved tracking quality is primarily limited by improvements in NPS. When compared to very thick scintillator SLI, employing MLI architecture exhibits the same gains in QDE, but by mitigating the effect of optical Swank noise, results in more dramatic improvements in tracking performance. © 2017 American Association of Physicists in Medicine.

Covert enaction at work: Recording the continuous movements of visuospatial attention to visible or imagined targets by means of Steady-State Visual Evoked Potentials (SSVEPs).

PubMed

Gregori Grgič, Regina; Calore, Enrico; de'Sperati, Claudio

2016-01-01

Whereas overt visuospatial attention is customarily measured with eye tracking, covert attention is assessed by various methods. Here we exploited Steady-State Visual Evoked Potentials (SSVEPs) - the oscillatory responses of the visual cortex to incoming flickering stimuli - to record the movements of covert visuospatial attention in a way operatively similar to eye tracking (attention tracking), which allowed us to compare motion observation and motion extrapolation with and without eye movements. Observers fixated a central dot and covertly tracked a target oscillating horizontally and sinusoidally. In the background, the left and the right halves of the screen flickered at two different frequencies, generating two SSVEPs in occipital regions whose size varied reciprocally as observers attended to the moving target. The two signals were combined into a single quantity that was modulated at the target frequency in a quasi-sinusoidal way, often clearly visible in single trials. The modulation continued almost unchanged when the target was switched off and observers mentally extrapolated its motion in imagery, and also when observers pointed their finger at the moving target during covert tracking, or imagined doing so. The amplitude of modulation during covert tracking was ∼25-30% of that measured when observers followed the target with their eyes. We used 4 electrodes in parieto-occipital areas, but similar results were achieved with a single electrode in Oz. In a second experiment we tested ramp and step motion. During overt tracking, SSVEPs were remarkably accurate, showing both saccadic-like and smooth pursuit-like modulations of cortical responsiveness, although during covert tracking the modulation deteriorated. Covert tracking was better with sinusoidal motion than ramp motion, and better with moving targets than stationary ones. The clear modulation of cortical responsiveness recorded during both overt and covert tracking, identical for motion observation and motion extrapolation, suggests to include covert attention movements in enactive theories of mental imagery. Copyright © 2015 Elsevier Ltd. All rights reserved.

Weighing Scale-Based Pulse Transit Time is a Superior Marker of Blood Pressure than Conventional Pulse Arrival Time

PubMed Central

Martin, Stephanie L.-O.; Carek, Andrew M.; Kim, Chang-Sei; Ashouri, Hazar; Inan, Omer T.; Hahn, Jin-Oh; Mukkamala, Ramakrishna

2016-01-01

Pulse transit time (PTT) is being widely pursued for cuff-less blood pressure (BP) monitoring. Most efforts have employed the time delay between ECG and finger photoplethysmography (PPG) waveforms as a convenient surrogate of PTT. However, these conventional pulse arrival time (PAT) measurements include the pre-ejection period (PEP) and the time delay through small, muscular arteries and may thus be an unreliable marker of BP. We assessed a bathroom weighing scale-like system for convenient measurement of ballistocardiography and foot PPG waveforms – and thus PTT through larger, more elastic arteries – in terms of its ability to improve tracking of BP in individual subjects. We measured “scale PTT”, conventional PAT, and cuff BP in humans during interventions that increased BP but changed PEP and smooth muscle contraction differently. Scale PTT tracked the diastolic BP changes well, with correlation coefficient of −0.80 ± 0.02 (mean ± SE) and root-mean-squared-error of 7.6 ± 0.5 mmHg after a best-case calibration. Conventional PAT was significantly inferior in tracking these changes, with correlation coefficient of −0.60 ± 0.04 and root-mean-squared-error of 14.6 ± 1.5 mmHg (p < 0.05). Scale PTT also tracked the systolic BP changes better than conventional PAT but not to an acceptable level. With further development, scale PTT may permit reliable, convenient measurement of BP. PMID:27976741

TrackArt: the user friendly interface for single molecule tracking data analysis and simulation applied to complex diffusion in mica supported lipid bilayers.

PubMed

Matysik, Artur; Kraut, Rachel S

2014-05-01

Single molecule tracking (SMT) analysis of fluorescently tagged lipid and protein probes is an attractive alternative to ensemble averaged methods such as fluorescence correlation spectroscopy (FCS) or fluorescence recovery after photobleaching (FRAP) for measuring diffusion in artificial and plasma membranes. The meaningful estimation of diffusion coefficients and their errors is however not straightforward, and is heavily dependent on sample type, acquisition method, and equipment used. Many approaches require advanced computing and programming skills for their implementation. Here we present TrackArt software, an accessible graphic interface for simulation and complex analysis of multiple particle paths. Imported trajectories can be filtered to eliminate spurious or corrupted tracks, and are then analyzed using several previously described methodologies, to yield single or multiple diffusion coefficients, their population fractions, and estimated errors. We use TrackArt to analyze the single-molecule diffusion behavior of a sphingolipid analog SM-Atto647N, in mica supported DOPC (1,2-dioleoyl-sn-glycero-3-phosphocholine) bilayers. Fitting with a two-component diffusion model confirms the existence of two separate populations of diffusing particles in these bilayers on mica. As a demonstration of the TrackArt workflow, we characterize and discuss the effective activation energies required to increase the diffusion rates of these populations, obtained from Arrhenius plots of temperature-dependent diffusion. Finally, TrackArt provides a simulation module, allowing the user to generate models with multiple particle trajectories, diffusing with different characteristics. Maps of domains, acting as impermeable or permeable obstacles for particles diffusing with given rate constants and diffusion coefficients, can be simulated or imported from an image. Importantly, this allows one to use simulated data with a known diffusion behavior as a comparison for results acquired using particular algorithms on actual, "natural" samples whose diffusion behavior is to be extracted. It can also serve as a tool for demonstrating diffusion principles. TrackArt is an open source, platform-independent, Matlab-based graphical user interface, and is easy to use even for those unfamiliar with the Matlab programming environment. TrackArt can be used for accurate simulation and analysis of complex diffusion data, such as diffusion in lipid bilayers, providing publication-quality formatted results.

The Effects of Interval Duration on Temporal Tracking and Alternation Learning

ERIC Educational Resources Information Center

Ludvig, Elliot A.; Staddon, John E. R.

2005-01-01

On cyclic-interval reinforcement schedules, animals typically show a postreinforcement pause that is a function of the immediately preceding time interval ("temporal tracking"). Animals, however, do not track single-alternation schedules--when two different intervals are presented in strict alternation on successive trials. In this experiment,…

Relationships and trends of E. Coli, human-associated Bacteroides, and pathogens in the Proctor Creek Watershed

EPA Science Inventory

Urban surface waters can be impacted by anthropogenic sources such as impervious surfaces, sanitary and storm sewers, and failing infrastructure. Fecal indicator bacteria (FIB) and microbial source tracking (MST) markers are common gauges of stream water quality, however, little...

Actionable Intelligence about Early Childhood Risks in Philadelphia

ERIC Educational Resources Information Center

LeBoeuf, Whitney A.; Barghaus, Katherine; Fantuzzo, John; Coe, Kristen; Brumley, Benjamin

2016-01-01

"Early childhood risks" are markers of early childhood experiences that extensive research has shown to be detrimental to later academic and behavioral outcomes. In Philadelphia, evidence indicates that seven early childhood risks tracked by public agencies have negative effects on early school outcomes. These risks include low…

Enterococcus and Escherichia coli fecal source apportionment with microbial source tracking genetic markers - is it feasible?

EPA Science Inventory

Fecal pollution is measured in surface waters using culture-based measurements of enterococci and Escherichia coli bacteria. Source apportionment of these two fecal indicator bacteria is an urgent need for prioritizing remediation efforts and quantifying health risks associated...

Time-Lapse Monitoring of DNA Damage Colocalized With Particle Tracks in Single Living Cells

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

McFadden, Conor H.; Hallacy, Timothy M.; Department of Physics and Astronomy, Rice University, Houston, Texas

2016-09-01

Purpose: Understanding the DNA damage and repair induced by hadron therapy (HT) beams is crucial for developing novel strategies to maximize the use of HT beams to treat cancer patients. However, spatiotemporal studies of DNA damage and repair for beam energies relevant to HT have been challenging. We report a technique that enables spatiotemporal measurement of radiation-induced damage in live cells and colocalization of this damage with charged particle tracks over a broad range of clinically relevant beam energies. The technique uses novel fluorescence nuclear track detectors with fluorescence confocal laser scanning microscopy in the beam line to visualize particlemore » track traversals within the subcellular compartments of live cells within seconds after injury. Methods and Materials: We designed and built a portable fluorescence confocal laser scanning microscope for use in the beam path, coated fluorescence nuclear track detectors with fluorescent-tagged live cells (HT1080 expressing enhanced green fluorescent protein tagged to XRCC1, a single-strand break repair protein), placed the entire assembly into a proton therapy beam line, and irradiated the cells with a fluence of ∼1 × 10{sup 6} protons/cm{sup 2}. Results: We successfully obtained confocal images of proton tracks and foci of DNA single-strand breaks immediately after irradiation. Conclusions: This technique represents an innovative method for analyzing biological responses in any HT beam line at energies and dose rates relevant to therapy. It allows precise determination of the number of tracks traversing a subcellular compartment and monitoring the cellular damage therein, and has the potential to measure the linear energy transfer of each track from therapeutic beams.« less

Measurement and Modeling of Fugitive Dust from Off Road DoD Activities

DTIC Science & Technology

2017-12-08

each soil and vehicle type (see Table 2). Note, no tracked vehicles were run at YTC. CT is the curve track sampling location, CR is the curve ridge...Soil is SL = sandy loam. ...................... 116 Figure 35. Single-event Wind Erosion Evaluation Program (SWEEP) Run example results. ... 121...Figure 36. Single-event Wind Erosion Evaluation Program (SWEEP) Threshold Run example results screen

Hiking shared-use single-track trails: a look at hikers and hunters along the Falls Lake Trail

Treesearch

Christopher M. Snow; Roger L. Moore

2007-01-01

The Falls Lake Trail, a 26.8-mile, single-track pedestrian trail located near the Research Triangle Region of North Carolina, traverses lands managed by the United States Army Corps of Engineers; North Carolina Division of Parks and Recreation; North Carolina Division of Wildlife Resources; and Wake County Parks, Recreation and Open Space. The non-profit trail advocacy...

Cacao single-nucleotide polymorphism (SNP) markers: A discovery strategy to identify SNPs for genotyping, genetic mapping and genome wide association studies (GWAS)

USDA-ARS?s Scientific Manuscript database

Single-nucleotide polymorphisms (SNPs) are the most common genetic markers in Theobroma cacao, occurring approximately once in every 200 nucleotides. SNPs, like microsatellites, are co-dominant and PCR-based, but they have several advantages over microsatellites. They are unambiguous, so that a SN...

An integrated genetic linkage map of watermelon and genetic diversity based on single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers

USDA-ARS?s Scientific Manuscript database

Watermelon (Citrullus lanatus var. lanatus) is an important vegetable fruit throughout the world. A high number of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers should provide large coverage of the watermelon genome and high phylogenetic resolution of germplasm acces...

Fast-tracking determination of homozygous transgenic lines and transgene stacking using a reliable quantitative real-time PCR assay.

PubMed

Wang, Xianghong; Jiang, Daiming; Yang, Daichang

2015-01-01

The selection of homozygous lines is a crucial step in the characterization of newly generated transgenic plants. This is particularly time- and labor-consuming when transgenic stacking is required. Here, we report a fast and accurate method based on quantitative real-time PCR with a rice gene RBE4 as a reference gene for selection of homozygous lines when using multiple transgenic stacking in rice. Use of this method allowed can be used to determine the stacking of up to three transgenes within four generations. Selection accuracy reached 100 % for a single locus and 92.3 % for two loci. This method confers distinct advantages over current transgenic research methodologies, as it is more accurate, rapid, and reliable. Therefore, this protocol could be used to efficiently select homozygous plants and to expedite time- and labor-consuming processes normally required for multiple transgene stacking. This protocol was standardized for determination of multiple gene stacking in molecular breeding via marker-assisted selection.

Structural basis for plant plasma membrane protein dynamics and organization into functional nanodomains.

PubMed

Gronnier, Julien; Crowet, Jean-Marc; Habenstein, Birgit; Nasir, Mehmet Nail; Bayle, Vincent; Hosy, Eric; Platre, Matthieu Pierre; Gouguet, Paul; Raffaele, Sylvain; Martinez, Denis; Grelard, Axelle; Loquet, Antoine; Simon-Plas, Françoise; Gerbeau-Pissot, Patricia; Der, Christophe; Bayer, Emmanuelle M; Jaillais, Yvon; Deleu, Magali; Germain, Véronique; Lins, Laurence; Mongrand, Sébastien

2017-07-31

Plasma Membrane is the primary structure for adjusting to ever changing conditions. PM sub-compartmentalization in domains is thought to orchestrate signaling. Yet, mechanisms governing membrane organization are mostly uncharacterized. The plant-specific REMORINs are proteins regulating hormonal crosstalk and host invasion. REMs are the best-characterized nanodomain markers via an uncharacterized moiety called REMORIN C-terminal Anchor. By coupling biophysical methods, super-resolution microscopy and physiology, we decipher an original mechanism regulating the dynamic and organization of nanodomains. We showed that targeting of REMORIN is independent of the COP-II-dependent secretory pathway and mediated by PI4P and sterol. REM-CA is an unconventional lipid-binding motif that confers nanodomain organization. Analyses of REM-CA mutants by single particle tracking demonstrate that mobility and supramolecular organization are critical for immunity. This study provides a unique mechanistic insight into how the tight control of spatial segregation is critical in the definition of PM domain necessary to support biological function.

Parallel computation of level set method for 500 Hz visual servo control

NASA Astrophysics Data System (ADS)

Fei, Xianfeng; Igarashi, Yasunobu; Hashimoto, Koichi

2008-11-01

We propose a 2D microorganism tracking system using a parallel level set method and a column parallel vision system (CPV). This system keeps a single microorganism in the middle of the visual field under a microscope by visual servoing an automated stage. We propose a new energy function for the level set method. This function constrains an amount of light intensity inside the detected object contour to control the number of the detected objects. This algorithm is implemented in CPV system and computational time for each frame is 2 [ms], approximately. A tracking experiment for about 25 s is demonstrated. Also we demonstrate a single paramecium can be kept tracking even if other paramecia appear in the visual field and contact with the tracked paramecium.

Single-particle tracking of endocytosis and exocytosis of single-walled carbon nanotubes in NIH-3T3 cells.

PubMed

Jin, Hong; Heller, Daniel A; Strano, Michael S

2008-06-01

Over 10000 individual trajectories of nonphotobleaching single-walled carbon nanotubes (SWNT) were tracked as they are incorporated into and expelled from NIH-3T3 cells in real time on a perfusion microscope stage. An analysis of mean square displacement allows the complete construction of the mechanistic steps involved from single duration experiments. We observe the first conclusive evidence of SWNT exocytosis and show that the rate closely matches the endocytosis rate with negligible temporal offset. We identify and study the endocytosis and exocytosis pathway that leads to the previously observed aggregation and accumulation of SWNT within the cells.

Interactive projection for aerial dance using depth sensing camera

NASA Astrophysics Data System (ADS)

Dubnov, Tammuz; Seldess, Zachary; Dubnov, Shlomo

2014-02-01

This paper describes an interactive performance system for oor and Aerial Dance that controls visual and sonic aspects of the presentation via a depth sensing camera (MS Kinect). In order to detect, measure and track free movement in space, 3 degree of freedom (3-DOF) tracking in space (on the ground and in the air) is performed using IR markers. Gesture tracking and recognition is performed using a simpli ed HMM model that allows robust mapping of the actor's actions to graphics and sound. Additional visual e ects are achieved by segmentation of the actor body based on depth information, allowing projection of separate imagery on the performer and the backdrop. Artistic use of augmented reality performance relative to more traditional concepts of stage design and dramaturgy are discussed.

Labeled RFS-Based Track-Before-Detect for Multiple Maneuvering Targets in the Infrared Focal Plane Array.

PubMed

Li, Miao; Li, Jun; Zhou, Yiyu

2015-12-08

The problem of jointly detecting and tracking multiple targets from the raw observations of an infrared focal plane array is a challenging task, especially for the case with uncertain target dynamics. In this paper a multi-model labeled multi-Bernoulli (MM-LMB) track-before-detect method is proposed within the labeled random finite sets (RFS) framework. The proposed track-before-detect method consists of two parts-MM-LMB filter and MM-LMB smoother. For the MM-LMB filter, original LMB filter is applied to track-before-detect based on target and measurement models, and is integrated with the interacting multiple models (IMM) approach to accommodate the uncertainty of target dynamics. For the MM-LMB smoother, taking advantage of the track labels and posterior model transition probability, the single-model single-target smoother is extended to a multi-model multi-target smoother. A Sequential Monte Carlo approach is also presented to implement the proposed method. Simulation results show the proposed method can effectively achieve tracking continuity for multiple maneuvering targets. In addition, compared with the forward filtering alone, our method is more robust due to its combination of forward filtering and backward smoothing.

Labeled RFS-Based Track-Before-Detect for Multiple Maneuvering Targets in the Infrared Focal Plane Array

PubMed Central

Li, Miao; Li, Jun; Zhou, Yiyu

2015-01-01

The problem of jointly detecting and tracking multiple targets from the raw observations of an infrared focal plane array is a challenging task, especially for the case with uncertain target dynamics. In this paper a multi-model labeled multi-Bernoulli (MM-LMB) track-before-detect method is proposed within the labeled random finite sets (RFS) framework. The proposed track-before-detect method consists of two parts—MM-LMB filter and MM-LMB smoother. For the MM-LMB filter, original LMB filter is applied to track-before-detect based on target and measurement models, and is integrated with the interacting multiple models (IMM) approach to accommodate the uncertainty of target dynamics. For the MM-LMB smoother, taking advantage of the track labels and posterior model transition probability, the single-model single-target smoother is extended to a multi-model multi-target smoother. A Sequential Monte Carlo approach is also presented to implement the proposed method. Simulation results show the proposed method can effectively achieve tracking continuity for multiple maneuvering targets. In addition, compared with the forward filtering alone, our method is more robust due to its combination of forward filtering and backward smoothing. PMID:26670234

Monocular Stereo Measurement Using High-Speed Catadioptric Tracking

PubMed Central

Hu, Shaopeng; Matsumoto, Yuji; Takaki, Takeshi; Ishii, Idaku

2017-01-01

This paper presents a novel concept of real-time catadioptric stereo tracking using a single ultrafast mirror-drive pan-tilt active vision system that can simultaneously switch between hundreds of different views in a second. By accelerating video-shooting, computation, and actuation at the millisecond-granularity level for time-division multithreaded processing in ultrafast gaze control, the active vision system can function virtually as two or more tracking cameras with different views. It enables a single active vision system to act as virtual left and right pan-tilt cameras that can simultaneously shoot a pair of stereo images for the same object to be observed at arbitrary viewpoints by switching the direction of the mirrors of the active vision system frame by frame. We developed a monocular galvano-mirror-based stereo tracking system that can switch between 500 different views in a second, and it functions as a catadioptric active stereo with left and right pan-tilt tracking cameras that can virtually capture 8-bit color 512×512 images each operating at 250 fps to mechanically track a fast-moving object with a sufficient parallax for accurate 3D measurement. Several tracking experiments for moving objects in 3D space are described to demonstrate the performance of our monocular stereo tracking system. PMID:28792483

DIAGNOSTIC MODEL EVALUATION FOR CARBONACEOUS PM 2.5 USING ORGANIC MARKERS MEASURED IN THE SOUTHEASTERN U.S.

EPA Science Inventory

Summertime concentrations of fine particulate carbon in the southeastern United States are consistently underestimated by air quality models. In an effort to understand the cause of this error, the Community Multiscale Air Quality (CMAQ) model is instrumented to track primary org...

Relationships and trends of E. Coli, human-associated bacteroides, and pathogens in the Proctor Creek watershed (GWRC 2017)

EPA Science Inventory

Urban surface waters can be impacted by anthropogenic sources such as impervious surfaces, sani-tary and storm sewers, and failing infrastructure. Fecal indicator bacteria (FIB) and microbial source tracking (MST) markers are common gauges of stream water qual-ity, however, litt...

Tracking the genetic stability of a honeybee breeding program with genetic markers

USDA-ARS?s Scientific Manuscript database

A genetic stock identification (GSI) assay was developed in 2008 to distinguish Russian honey bees from other honey bee stocks that are commercially produced in the United States. Probability of assignment (POA) values have been collected and maintained since the stock release in 2008 to the Russian...

Biotic interactions and sunlight affect persistence of fecal indicator bacteria and microbial source tracking genetic markers in the Upper Mississippi River

EPA Science Inventory

Sanitary quality of recreational waters is assessed by enumerating fecal indicator bacteria (FIB) (Escherichia coli and enterococci); organisms present in the gastrointestinal tract of humans and many other animals, hence providing no information about the pollution source. Micro...

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

Kuo, Li-Jung; Lee, Chon-Lin; Louchouarn, Patrick

A 100-year history of human and natural disturbances in southwestern Taiwan was reconstructed using a suite of molecular markers in four dated sediment cores from the upper slope region off the Gaoping River mouth. Trends in polycyclic aromatic hydrocarbons (PAHs) tracked Taiwan's industrialization/urbanization starting in the 1970s, and the enactment of environmental regulatory policies thereafter.

DEVELOPMENT OF HOST-SPECIFIC METAGENOMIC MARKERS FOR MICROBIAL SOURCE TRACKING USING A NOVEL METAGENOMIC APPROACH

EPA Science Inventory

Fecal contamination of source waters is an important issue to the drinking water industry. Improper disposal of animal waste, leaky septic tanks, storm runoff, and wildlife can all be responsible for spreading enteric pathogens into source waters. As a result, methods that can pi...

Temporal Assessment of the Impact of Exposure to Cow Feces in Two Watersheds by Multiple Host-Specific PCR Assays

EPA Science Inventory

Exposure to feces in two watersheds with different management histories was assessed by tracking cattle feces bacterial populations using multiple host-specific PCR assays. In addition, environmental factors affecting the occurrence of these markers were identified. Each assay wa...

Temporal Assessment of the Impact of Exposure to Cow Feces inTwo Watersheds by Multiple Host-Specific PCR Assays

EPA Science Inventory

Fecal exposure in two watersheds with different management histories was assessed by tracking cattle fecal bacterial populations using multiple host-specific PCR assays. In addition, environmental factors affecting the occurrence of these markers were identified. Each assay was t...

Role of Receptor Sialylation in the Ovarian Tumor Cell Phenotype

DTIC Science & Technology

2014-08-01

Chemical Society meeting, Baton Rouge, LA, Nov 2012; (3) 19th World Congress on Advances in Oncology conference, Athens, Greece, scheduled for Oct, 2014...dehydrogenase 1 is a marker for normal and malignant human colonic stem cells (SC) and tracks SC overpopulation during colon tumorigenesis. Cancer Res 2009;69

Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

USDA-ARS?s Scientific Manuscript database

Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

A Site-Specific Recombinase-Based Method to Produce Antibiotic Selectable Marker Free Transgenic Cattle

PubMed Central

Tong, Qi; Liu, Xu; Su, Feng; Quan, Fusheng; Guo, Zekun; Zhang, Yong

2013-01-01

Antibiotic selectable marker genes have been widely used to generate transgenic animals. Once transgenic animals have been obtained, the selectable marker is no longer necessary but raises public concerns regarding biological safety. The aim of this study was to prepare competent antibiotic selectable marker free transgenic cells for somatic cell nuclear transfer (SCNT). PhiC31 intergrase was used to insert a transgene cassette into a “safe harbor” in the bovine genome. Then, Cre recombinase was employed to excise the selectable marker under the monitoring of a fluorescent double reporter. By visually tracking the phenotypic switch from red to green fluorescence, antibiotic selectable marker free cells were easily detected and sorted by fluorescence-activated cell sorting. For safety, we used phiC31 mRNA and cell-permeant Cre protein in this study. When used as donor nuclei for SCNT, these safe harbor integrated marker-free transgenic cells supported a similar developmental competence of SCNT embryos compared with that of non-transgenic cells. After embryo transfer, antibiotic selectable marker free transgenic cattle were generated and anti-bacterial recombinant human β-defensin-3 in milk was detected during their lactation period. Thus, this approach offers a rapid and safe alternative to produce antibiotic selectable marker free transgenic farm animals, thereby making it a valuable tool to promote the healthy development and welfare of transgenic farm animals. PMID:23658729

Rethinking Tracking Practices: What Teachers Say

ERIC Educational Resources Information Center

Özelçi, Serap Yilmaz; Çengel, Meltem; Vural, Ruken Akar; Gömleksiz, Müfit

2016-01-01

Under the different sides of discussion on the tracking, we attempted to understand how teachers and administrators evaluate tracking system in their school. We gathered data from teachers who employed in one of the government mandated schools in west part of Turkey. In this single case study, we collected data from 16 teachers, 1 administrator…

Oculomotor Behavior Metrics Change According to Circadian Phase and Time Awake

NASA Technical Reports Server (NTRS)

Flynn-Evans, Erin E.; Tyson, Terence L.; Cravalho, Patrick; Feick, Nathan; Stone, Leland S.

2017-01-01

There is a need for non-invasive, objective measures to forecast performance impairment arising from sleep loss and circadian misalignment, particularly in safety-sensitive occupations. Eye-tracking devices have been used in some operational scenarios, but such devices typically focus on eyelid closures and slow rolling eye movements and are susceptible to the intrusion of head movement artifacts. We hypothesized that an expanded suite of oculomotor behavior metrics, collected during a visual tracking task, would change according to circadian phase and time awake, and could be used as a marker of performance impairment.

Q-adjusting technique applied to vertical deflections estimation in a single-axis rotation INS/GPS integrated system

NASA Astrophysics Data System (ADS)

Zhu, Jing; Wang, Xingshu; Wang, Jun; Dai, Dongkai; Xiong, Hao

2016-10-01

Former studies have proved that the attitude error in a single-axis rotation INS/GPS integrated system tracks the high frequency component of the deflections of the vertical (DOV) with a fixed delay and tracking error. This paper analyses the influence of the nominal process noise covariance matrix Q on the tracking error as well as the response delay, and proposed a Q-adjusting technique to obtain the attitude error which can track the DOV better. Simulation results show that different settings of Q lead to different response delay and tracking error; there exists optimal Q which leads to a minimum tracking error and a comparatively short response delay; for systems with different accuracy, different Q-adjusting strategy should be adopted. In this way, the DOV estimation accuracy of using the attitude error as the observation can be improved. According to the simulation results, the DOV estimation accuracy after using the Q-adjusting technique is improved by approximate 23% and 33% respectively compared to that of the Earth Model EGM2008 and the direct attitude difference method.

Terminal sliding mode tracking control for a class of SISO uncertain nonlinear systems.

PubMed

Chen, Mou; Wu, Qing-Xian; Cui, Rong-Xin

2013-03-01

In this paper, the terminal sliding mode tracking control is proposed for the uncertain single-input and single-output (SISO) nonlinear system with unknown external disturbance. For the unmeasured disturbance of nonlinear systems, terminal sliding mode disturbance observer is presented. The developed disturbance observer can guarantee the disturbance approximation error to converge to zero in the finite time. Based on the output of designed disturbance observer, the terminal sliding mode tracking control is presented for uncertain SISO nonlinear systems. Subsequently, terminal sliding mode tracking control is developed using disturbance observer technique for the uncertain SISO nonlinear system with control singularity and unknown non-symmetric input saturation. The effects of the control singularity and unknown input saturation are combined with the external disturbance which is approximated using the disturbance observer. Under the proposed terminal sliding mode tracking control techniques, the finite time convergence of all closed-loop signals are guaranteed via Lyapunov analysis. Numerical simulation results are given to illustrate the effectiveness of the proposed terminal sliding mode tracking control. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

Unsupervised markerless 3-DOF motion tracking in real time using a single low-budget camera.

PubMed

Quesada, Luis; León, Alejandro J

2012-10-01

Motion tracking is a critical task in many computer vision applications. Existing motion tracking techniques require either a great amount of knowledge on the target object or specific hardware. These requirements discourage the wide spread of commercial applications based on motion tracking. In this paper, we present a novel three degrees of freedom motion tracking system that needs no knowledge on the target object and that only requires a single low-budget camera that can be found installed in most computers and smartphones. Our system estimates, in real time, the three-dimensional position of a nonmodeled unmarked object that may be nonrigid, nonconvex, partially occluded, self-occluded, or motion blurred, given that it is opaque, evenly colored, enough contrasting with the background in each frame, and that it does not rotate. Our system is also able to determine the most relevant object to track in the screen. Our proposal does not impose additional constraints, therefore it allows a market-wide implementation of applications that require the estimation of the three position degrees of freedom of an object.

Multimode intravascular RF coil for MRI-guided interventions.

PubMed

Kurpad, Krishna N; Unal, Orhan

2011-04-01

To demonstrate the feasibility of using a single intravascular radiofrequency (RF) probe connected to the external magnetic resonance imaging (MRI) system via a single coaxial cable to perform active tip tracking and catheter visualization and high signal-to-noise ratio (SNR) intravascular imaging. A multimode intravascular RF coil was constructed on a 6F balloon catheter and interfaced to a 1.5T MRI scanner via a decoupling circuit. Bench measurements of coil impedances were followed by imaging experiments in saline and phantoms. The multimode coil behaves as an inductively coupled transmit coil. The forward-looking capability of 6 mm was measured. A greater than 3-fold increase in SNR compared to conventional imaging using optimized external coil was demonstrated. Simultaneous active tip tracking and catheter visualization was demonstrated. It is feasible to perform 1) active tip tracking, 2) catheter visualization, and 3) high SNR imaging using a single multimode intravascular RF coil that is connected to the external system via a single coaxial cable. Copyright © 2011 Wiley-Liss, Inc.

Multi-mode Intravascular RF Coil for MRI-guided Interventions

PubMed Central

Kurpad, Krishna N.; Unal, Orhan

2011-01-01

Purpose To demonstrate the feasibility of using a single intravascular RF probe connected to the external MRI system via a single coaxial cable to perform active tip tracking and catheter visualization, and high SNR intravascular imaging. Materials and Methods A multi-mode intravascular RF coil was constructed on a 6F balloon catheter and interfaced to a 1.5T MRI scanner via a decoupling circuit. Bench measurements of coil impedances were followed by imaging experiments in saline and phantoms. Results The multi-mode coil behaves as an inductively-coupled transmit coil. Forward looking capability of 6mm is measured. Greater than 3-fold increase in SNR compared to conventional imaging using optimized external coil is demonstrated. Simultaneous active tip tracking and catheter visualization is demonstrated. Conclusions It is feasible to perform 1) active tip tracking, 2) catheter visualization, and 3) high SNR imaging using a single multi-mode intravascular RF coil that is connected to the external system via a single coaxial cable. PMID:21448969

Controlling Brownian motion of single protein molecules and single fluorophores in aqueous buffer.

PubMed

Cohen, Adam E; Moerner, W E

2008-05-12

We present an Anti-Brownian Electrokinetic trap (ABEL trap) capable of trapping individual fluorescently labeled protein molecules in aqueous buffer. The ABEL trap operates by tracking the Brownian motion of a single fluorescent particle in solution, and applying a time-dependent electric field designed to induce an electrokinetic drift that cancels the Brownian motion. The trapping strength of the ABEL trap is limited by the latency of the feedback loop. In previous versions of the trap, this latency was set by the finite frame rate of the camera used for video-tracking. In the present system, the motion of the particle is tracked entirely in hardware (without a camera or image-processing software) using a rapidly rotating laser focus and lock-in detection. The feedback latency is set by the finite rate of arrival of photons. We demonstrate trapping of individual molecules of the protein GroEL in buffer, and we show confinement of single fluorophores of the dye Cy3 in water.

Is a multivariate consensus representation of genetic relationships among populations always meaningful?

PubMed Central

Moazami-Goudarzi, K; Laloë, D

2002-01-01

To determine the relationships among closely related populations or species, two methods are commonly used in the literature: phylogenetic reconstruction or multivariate analysis. The aim of this article is to assess the reliability of multivariate analysis. We describe a method that is based on principal component analysis and Mantel correlations, using a two-step process: The first step consists of a single-marker analysis and the second step tests if each marker reveals the same typology concerning population differentiation. We conclude that if single markers are not congruent, the compromise structure is not meaningful. Our model is not based on any particular mutation process and it can be applied to most of the commonly used genetic markers. This method is also useful to determine the contribution of each marker to the typology of populations. We test whether our method is efficient with two real data sets based on microsatellite markers. Our analysis suggests that for closely related populations, it is not always possible to accept the hypothesis that an increase in the number of markers will increase the reliability of the typology analysis. PMID:12242255

Single file diffusion into a semi-infinite tube.

PubMed

Farrell, Spencer G; Brown, Aidan I; Rutenberg, Andrew D

2015-11-23

We investigate single file diffusion (SFD) of large particles entering a semi-infinite tube, such as luminal diffusion of proteins into microtubules or flagella. While single-file effects have no impact on the evolution of particle density, we report significant single-file effects for individually tracked tracer particle motion. Both exact and approximate ordering statistics of particles entering semi-infinite tubes agree well with our stochastic simulations. Considering initially empty semi-infinite tubes, with particles entering at one end starting from an initial time t = 0, tracked particles are initially super-diffusive after entering the system, but asymptotically diffusive at later times. For finite time intervals, the ratio of the net displacement of individual single-file particles to the average displacement of untracked particles is reduced at early times and enhanced at later times. When each particle is numbered, from the first to enter (n = 1) to the most recent (n = N), we find good scaling collapse of this distance ratio for all n. Experimental techniques that track individual particles, or local groups of particles, such as photo-activation or photobleaching of fluorescently tagged proteins, should be able to observe these single-file effects. However, biological phenomena that depend on local concentration, such as flagellar extension or luminal enzymatic activity, should not exhibit single-file effects.

Faint Debris Detection by Particle Based Track-Before-Detect Method

NASA Astrophysics Data System (ADS)

Uetsuhara, M.; Ikoma, N.

2014-09-01

This study proposes a particle method to detect faint debris, which is hardly seen in single frame, from an image sequence based on the concept of track-before-detect (TBD). The most widely used detection method is detect-before-track (DBT), which firstly detects signals of targets from single frame by distinguishing difference of intensity between foreground and background then associate the signals for each target between frames. DBT is capable of tracking bright targets but limited. DBT is necessary to consider presence of false signals and is difficult to recover from false association. On the other hand, TBD methods try to track targets without explicitly detecting the signals followed by evaluation of goodness of each track and obtaining detection results. TBD has an advantage over DBT in detecting weak signals around background level in single frame. However, conventional TBD methods for debris detection apply brute-force search over candidate tracks then manually select true one from the candidates. To reduce those significant drawbacks of brute-force search and not-fully automated process, this study proposes a faint debris detection algorithm by a particle based TBD method consisting of sequential update of target state and heuristic search of initial state. The state consists of position, velocity direction and magnitude, and size of debris over the image at a single frame. The sequential update process is implemented by a particle filter (PF). PF is an optimal filtering technique that requires initial distribution of target state as a prior knowledge. An evolutional algorithm (EA) is utilized to search the initial distribution. The EA iteratively applies propagation and likelihood evaluation of particles for the same image sequences and resulting set of particles is used as an initial distribution of PF. This paper describes the algorithm of the proposed faint debris detection method. The algorithm demonstrates performance on image sequences acquired during observation campaigns dedicated to GEO breakup fragments, which would contain a sufficient number of faint debris images. The results indicate the proposed method is capable of tracking faint debris with moderate computational costs at operational level.

Identification of 29 Rat Genetic Markers by Arbitrarily Primed Polymerase Chain Reaction

PubMed Central

Canzian, Federico; Toyota, Minoru; Hosoya, Yoko; Sugimura, Takashi; Nagao, Minako

1996-01-01

The number of genetic markers for the rat is still limited, in spite of its wide use in cancer research. To facilitate accurate mapping of both established and novel rat genetic markers, we constructed a linkage map by genotyping 105 F2 rats from ACI/N (ACI) and BUF/Nac (BUF) crosses. This map consists of 120 genetic markers that had been previously reported, mainly by two research groups, but had not been integrated. To find new genetic markers, the arbitrarily primed polymerase chain reaction (AP‐PCR) was applied to detect polymorphic bands between ACI and BUF rats. After testing 56 single primers and 12 combinations of primers, we found 36 bands produced by 16 single primers and two combinations to be reliably polymorphic between ACI and BUF rats. The 36 bands were typed in the 105 F2 rats, and 29 of them could be linkage‐mapped. AP‐PCR is thus useful to detect new genetic markers in laboratory strains of rats. PMID:8698613

Rapid Solidification in Bulk Ti-Nb Alloys by Single-Track Laser Melting

NASA Astrophysics Data System (ADS)

Roehling, John D.; Perron, Aurélien; Fattebert, Jean-Luc; Haxhimali, Tomorr; Guss, Gabe; Li, Tian T.; Bober, David; Stokes, Adam W.; Clarke, Amy J.; Turchi, Patrice E. A.; Matthews, Manyalibo J.; McKeown, Joseph T.

2018-05-01

Single-track laser melting experiments were performed on bulk Ti-Nb alloys to explore process parameters and the resultant macroscopic structure and microstructure. The microstructures in Ti-20Nb and Ti-50Nb (at.%) alloys exhibited cellular growth during rapid solidification, with average cell size of approximately 0.5 µm. Solidification velocities during cellular growth were calculated from images of melt tracks. Measurements of the composition in the cellular and intercellular regions revealed nonequilibrium partitioning and its dependence on velocity during rapid solidification. Experimental results were used to benchmark a phase-field model to describe rapid solidification under conditions relevant to additive manufacturing.

Simple Perfusion Apparatus (SPA) for Manipulation, Tracking and Study of Oocytes and Embryos

PubMed Central

Angione, Stephanie L.; Oulhen, Nathalie; Brayboy, Lynae M.; Tripathi, Anubhav; Wessel, Gary M.

2016-01-01

Objective To develop and implement a device and protocol for oocyte analysis at a single cell level. The device must be capable of high resolution imaging, temperature control, perfusion of media, drugs, sperm, and immunolabeling reagents all at defined flow-rates. Each oocyte and resultant embryo must remain spatially separated and defined. Design Experimental laboratory study Setting University and Academic Center for reproductive medicine. Patients/Animals Women with eggs retrieved for ICSI cycles, adult female FVBN and B6C3F1 mouse strains, sea stars. Intervention Real-time, longitudinal imaging of oocytes following fluorescent labeling, insemination, and viability tests. Main outcome measure(s) Cell and embryo viability, immunolabeling efficiency, live cell endocytosis quantitation, precise metrics of fertilization and embryonic development. Results Single oocytes were longitudinally imaged following significant changes in media, markers, endocytosis quantitation, and development, all with supreme control by microfluidics. Cells remained viable, enclosed, and separate for precision measurements, repeatability, and imaging. Conclusions We engineered a simple device to load, visualize, experiment, and effectively record individual oocytes and embryos, without loss of cells. Prolonged incubation capabilities provide longitudinal studies without need for transfer and potential loss of cells. This simple perfusion apparatus (SPA) provides for careful, precise, and flexible handling of precious samples facilitating clinical in vitro fertilization approaches. PMID:25450296

Swift heavy ion irradiation of CaF2 - from grooves to hillocks in a single ion track

NASA Astrophysics Data System (ADS)

Gruber, Elisabeth; Salou, Pierre; Bergen, Lorenz; El Kharrazi, Mourad; Lattouf, Elie; Grygiel, Clara; Wang, Yuyu; Benyagoub, Abdenacer; Levavasseur, Delphine; Rangama, Jimmy; Lebius, Henning; Ban-d'Etat, Brigitte; Schleberger, Marika; Aumayr, Friedrich

2016-10-01

A novel form of ion-tracks, namely nanogrooves and hillocks, are observed on CaF2 after irradiation with xenon and lead ions of about 100 MeV kinetic energy. The irradiation is performed under grazing incidence (0.3°-3°) which forces the track to a region in close vicinity to the surface. Atomic force microscopy imaging of the impact sites with high spatial resolution reveals that the surface track consists in fact of three distinct parts: each swift heavy ion impacting on the CaF2 surface first opens a several 100 nm long groove bordered by a series of nanohillocks on both sides. The end of the groove is marked by a huge single hillock and the further penetration of the swift projectile into deeper layers of the target is accompanied by a single protrusion of several 100 nm in length slowly fading until the track vanishes. By comparing experimental data for various impact angles with results of a simulation, based on a three-dimensional version of the two-temperature-model (TTM), we are able to link the crater and hillock formation to sublimation and melting processes of CaF2 due to the local energy deposition by swift heavy ions.

Single Tracking Location Acoustic Radiation Force Impulse Viscoelasticity Estimation (STL-VE): A Method for Measuring Tissue Viscoelastic Parameters

PubMed Central

Langdon, Jonathan H; Elegbe, Etana; McAleavey, Stephen A

2015-01-01

Single Tracking Location (STL) Shear wave Elasticity Imaging (SWEI) is a method for detecting elastic differences between tissues. It has the advantage of intrinsic speckle bias suppression compared to Multiple Tracking Location (MTL) variants of SWEI. However, the assumption of a linear model leads to an overestimation of the shear modulus in viscoelastic media. A new reconstruction technique denoted Single Tracking Location Viscosity Estimation (STL-VE) is introduced to correct for this overestimation. This technique utilizes the same raw data generated in STL-SWEI imaging. Here, the STL-VE technique is developed by way of a Maximum Likelihood Estimation (MLE) for general viscoelastic materials. The method is then implemented for the particular case of the Kelvin-Voigt Model. Using simulation data, the STL-VE technique is demonstrated and the performance of the estimator is characterized. Finally, the STL-VE method is used to estimate the viscoelastic parameters of ex-vivo bovine liver. We find good agreement between the STL-VE results and the simulation parameters as well as between the liver shear wave data and the modeled data fit. PMID:26168170

Robot-assisted endoscope guidance versus manual endoscope guidance in functional endonasal sinus surgery (FESS).

PubMed

Eichhorn, Klaus Wolfgang; Westphal, Ralf; Rilk, Markus; Last, Carsten; Bootz, Friedrich; Wahl, Friedrich; Jakob, Mark; Send, Thorsten

2017-10-01

Having one hand occupied with the endoscope is the major disadvantage for the surgeon when it comes to functional endoscopic sinus surgery (FESS). Only the other hand is free to use the surgical instruments. Tiredness or frequent instrument changes can thus lead to shaky endoscopic images. We collected the pose data (position and orientation) of the rigid 0° endoscope and all the instruments used in 16 FESS procedures with manual endoscope guidance as well as robot-assisted endoscope guidance. In combination with the DICOM CT data, we tracked the endoscope poses and workspaces using self-developed tracking markers. All surgeries were performed once with the robot and once with the surgeon holding the endoscope. Looking at the durations required, we observed a decrease in the operating time because one surgeon doing all the procedures and so a learning curve occurred what we expected. The visual inspection of the specimens showed no damages to any of the structures outside the paranasal sinuses. Robot-assisted endoscope guidance in sinus surgery is possible. Further CT data, however, are desirable for the surgical analysis of a tracker-based navigation within the anatomic borders. Our marker-based tracking of the endoscope as well as the instruments makes an automated endoscope guidance feasible. On the subjective side, we see that RASS brings a relief for the surgeon.

Determining residual reduction algorithm kinematic tracking weights for a sidestep cut via numerical optimization.

PubMed

Samaan, Michael A; Weinhandl, Joshua T; Bawab, Sebastian Y; Ringleb, Stacie I

2016-12-01

Musculoskeletal modeling allows for the determination of various parameters during dynamic maneuvers by using in vivo kinematic and ground reaction force (GRF) data as inputs. Differences between experimental and model marker data and inconsistencies in the GRFs applied to these musculoskeletal models may not produce accurate simulations. Therefore, residual forces and moments are applied to these models in order to reduce these differences. Numerical optimization techniques can be used to determine optimal tracking weights of each degree of freedom of a musculoskeletal model in order to reduce differences between the experimental and model marker data as well as residual forces and moments. In this study, the particle swarm optimization (PSO) and simplex simulated annealing (SIMPSA) algorithms were used to determine optimal tracking weights for the simulation of a sidestep cut. The PSO and SIMPSA algorithms were able to produce model kinematics that were within 1.4° of experimental kinematics with residual forces and moments of less than 10 N and 18 Nm, respectively. The PSO algorithm was able to replicate the experimental kinematic data more closely and produce more dynamically consistent kinematic data for a sidestep cut compared to the SIMPSA algorithm. Future studies should use external optimization routines to determine dynamically consistent kinematic data and report the differences between experimental and model data for these musculoskeletal simulations.

A Biomarker Combining Imaging and Neuropsychological Assessment for Tracking Early Alzheimer's Disease in Clinical Trials.

PubMed

Verma, Nishant; Beretvas, S Natasha; Pascual, Belen; Masdeu, Joseph C; Markey, Mia K

2018-03-14

Combining optimized cognitive (Alzheimer's Disease Assessment Scale- Cognitive subscale, ADAS-Cog) and atrophy markers of Alzheimer's disease for tracking progression in clinical trials may provide greater sensitivity than currently used methods, which have yielded negative results in multiple recent trials. Furthermore, it is critical to clarify the relationship among the subcomponents yielded by cognitive and imaging testing, to address the symptomatic and anatomical variability of Alzheimer's disease. Using latent variable analysis, we thoroughly investigated the relationship between cognitive impairment, as assessed on the ADAS-Cog, and cerebral atrophy. A biomarker was developed for Alzheimer's clinical trials that combines cognitive and atrophy markers. Atrophy within specific brain regions was found to be closely related with impairment in cognitive domains of memory, language, and praxis. The proposed biomarker showed significantly better sensitivity in tracking progression of cognitive impairment than the ADAS-Cog in simulated trials and a real world problem. The biomarker also improved the selection of MCI patients (78.8±4.9% specificity at 80% sensitivity) that will evolve to Alzheimer's disease for clinical trials. The proposed biomarker provides a boost to the efficacy of clinical trials focused in the mild cognitive impairment (MCI) stage by significantly improving the sensitivity to detect treatment effects and improving the selection of MCI patients that will evolve to Alzheimer's disease. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Online Activity Levels Are Related to Caffeine Dependency.

PubMed

Phillips, James G; Landhuis, C Erik; Shepherd, Daniel; Ogeil, Rowan P

2016-05-01

Online activity could serve in the future as behavioral markers of emotional states for computer systems (i.e., affective computing). Hence, this study considered relationships between self-reported stimulant use and online study patterns. Sixty-two undergraduate psychology students estimated their daily caffeine use, and this was related to study patterns as tracked by their use of a Learning Management System (Blackboard). Caffeine dependency was associated with less time spent online, lower rates of file access, and fewer online activities completed. Reduced breadth or depth of processing during work/study could be used as a behavioral marker of stimulant use.

Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking

PubMed Central

von Diezmann, Alex; Shechtman, Yoav; Moerner, W. E.

2017-01-01

Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers, or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information of single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field-dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems. PMID:28151646

Development of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae.

PubMed

Liu, Hailan; Guo, Xiaoqin; Wu, Jiasheng; Chen, Guo-Bo; Ying, Yeqing

2013-03-01

KEY MESSAGE : We develop a set of universal genetic markers based on single-copy orthologous (COSII) genes in Poaceae. Being evolutionary conserved, single-copy orthologous (COSII) genes are particularly useful in comparative mapping and phylogenetic investigation among species. In this study, we identified 2,684 COSII genes based on five sequenced Poaceae genomes including rice, maize, sorghum, foxtail millet, and brachypodium, and then developed 1,072 COSII markers whose transferability and polymorphism among five bamboo species were further evaluated with 46 pairs of randomly selected primers. 91.3 % of the 46 primers obtained clear amplification in at least one bamboo species, and 65.2 % of them produced polymorphism in more than one species. We also used 42 of them to construct the phylogeny for the five bamboo species, and it might reflect more precise evolutionary relationship than the one based on the vegetative morphology. The results indicated a promising prospect of applying these markers to the investigation of genetic diversity and the classification of Poaceae. To ease and facilitate access of the information of common interest to readers, a web-based database of the COSII markers is provided ( http://www.sicau.edu.cn/web/yms/PCOSWeb/PCOS.html ).

An accurate algorithm to match imperfectly matched images for lung tumor detection without markers

PubMed Central

Rozario, Timothy; Bereg, Sergey; Yan, Yulong; Chiu, Tsuicheng; Liu, Honghuan; Kearney, Vasant; Jiang, Lan

2015-01-01

In order to locate lung tumors on kV projection images without internal markers, digitally reconstructed radiographs (DRRs) are created and compared with projection images. However, lung tumors always move due to respiration and their locations change on projection images while they are static on DRRs. In addition, global image intensity discrepancies exist between DRRs and projections due to their different image orientations, scattering, and noises. This adversely affects comparison accuracy. A simple but efficient comparison algorithm is reported to match imperfectly matched projection images and DRRs. The kV projection images were matched with different DRRs in two steps. Preprocessing was performed in advance to generate two sets of DRRs. The tumors were removed from the planning 3D CT for a single phase of planning 4D CT images using planning contours of tumors. DRRs of background and DRRs of tumors were generated separately for every projection angle. The first step was to match projection images with DRRs of background signals. This method divided global images into a matrix of small tiles and similarities were evaluated by calculating normalized cross‐correlation (NCC) between corresponding tiles on projections and DRRs. The tile configuration (tile locations) was automatically optimized to keep the tumor within a single projection tile that had a bad matching with the corresponding DRR tile. A pixel‐based linear transformation was determined by linear interpolations of tile transformation results obtained during tile matching. The background DRRs were transformed to the projection image level and subtracted from it. The resulting subtracted image now contained only the tumor. The second step was to register DRRs of tumors to the subtracted image to locate the tumor. This method was successfully applied to kV fluoro images (about 1000 images) acquired on a Vero (BrainLAB) for dynamic tumor tracking on phantom studies. Radiation opaque markers were implanted and used as ground truth for tumor positions. Although other organs and bony structures introduced strong signals superimposed on tumors at some angles, this method accurately located tumors on every projection over 12 gantry angles. The maximum error was less than 2.2 mm, while the total average error was less than 0.9 mm. This algorithm was capable of detecting tumors without markers, despite strong background signals. PACS numbers: 87.57.cj, 87.57.cp87.57.nj, 87.57.np, 87.57.Q‐, 87.59.bf, 87.63.lm

Evaluation of the Intel RealSense SR300 camera for image-guided interventions and application in vertebral level localization

NASA Astrophysics Data System (ADS)

House, Rachael; Lasso, Andras; Harish, Vinyas; Baum, Zachary; Fichtinger, Gabor

2017-03-01

PURPOSE: Optical pose tracking of medical instruments is often used in image-guided interventions. Unfortunately, compared to commonly used computing devices, optical trackers tend to be large, heavy, and expensive devices. Compact 3D vision systems, such as Intel RealSense cameras can capture 3D pose information at several magnitudes lower cost, size, and weight. We propose to use Intel SR300 device for applications where it is not practical or feasible to use conventional trackers and limited range and tracking accuracy is acceptable. We also put forward a vertebral level localization application utilizing the SR300 to reduce risk of wrong-level surgery. METHODS: The SR300 was utilized as an object tracker by extending the PLUS toolkit to support data collection from RealSense cameras. Accuracy of the camera was tested by comparing to a high-accuracy optical tracker. CT images of a lumbar spine phantom were obtained and used to create a 3D model in 3D Slicer. The SR300 was used to obtain a surface model of the phantom. Markers were attached to the phantom and a pointer and tracked using Intel RealSense SDK's built-in object tracking feature. 3D Slicer was used to align CT image with phantom using landmark registration and display the CT image overlaid on the optical image. RESULTS: Accuracy of the camera yielded a median position error of 3.3mm (95th percentile 6.7mm) and orientation error of 1.6° (95th percentile 4.3°) in a 20x16x10cm workspace, constantly maintaining proper marker orientation. The model and surface correctly aligned demonstrating the vertebral level localization application. CONCLUSION: The SR300 may be usable for pose tracking in medical procedures where limited accuracy is acceptable. Initial results suggest the SR300 is suitable for vertebral level localization.

A Direct Method for Mapping the Center of Pressure Measured by an Insole Pressure Sensor System to the Shoe's Local Coordinate System.

PubMed

Weaver, Brian T; Braman, Jerrod E; Haut, Roger C

2016-06-01

A direct method to express the center of pressure (CoP) measured by an insole pressure sensor system (IPSS) into a known coordinate system measured by motion tracking equipment is presented. A custom probe was constructed with reflective markers to allow its tip to be precisely tracked with motion tracking equipment. This probe was utilized to activate individual sensors on an IPSS that was placed in a shoe fitted with reflective markers used to establish a local shoe coordinate system. When pressed onto the IPSS the location of the probe's tip was coincident with the CoP measured by the IPSS (IPSS-CoP). Two separate pushes (i.e., data points) were used to develop vectors in each respective coordinate system. Simple vector mathematics determined the rotational and translational components of the transformation matrix needed to express the IPSS-CoP into the local shoe coordinate system. Validation was performed by comparing IPSS-CoP with an embedded force plate measured CoP (FP-CoP) from data gathered during kinematic trials. Six male subjects stood on an embedded FP and performed anterior/posterior (AP) sway, internal rotation, and external rotation of the body relative to a firmly planted foot. The IPSS-CoP was highly correlated with the FP-CoP for all motions, root mean square errors (RMSRRs) were comparable to other research, and there were no statistical differences between the displacement of the IPSS-CoP and FP-CoP for both the AP and medial/lateral (ML) axes, respectively. The results demonstrated that this methodology could be utilized to determine the transformation variables need to express IPSS-CoP into a known coordinate system measured by motion tracking equipment and that these variables can be determined outside the laboratory anywhere motion tracking equipment is available.

The History of Tree and Shrub Taxa on Bol’shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data

PubMed Central

Raschke, Elena; Epp, Laura S.; Stoof-Leichsenring, Kathleen R.; Schwamborn, Georg; Herzschuh, Ulrike

2017-01-01

Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol’shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns. PMID:29027988

Approach for gait analysis in persons with limb loss including residuum and prosthesis socket dynamics.

PubMed

LaPrè, A K; Price, M A; Wedge, R D; Umberger, B R; Sup, Frank C

2018-04-01

Musculoskeletal modeling and marker-based motion capture techniques are commonly used to quantify the motions of body segments, and the forces acting on them during human gait. However, when these techniques are applied to analyze the gait of people with lower limb loss, the clinically relevant interaction between the residual limb and prosthesis socket is typically overlooked. It is known that there is considerable motion and loading at the residuum-socket interface, yet traditional gait analysis techniques do not account for these factors due to the inability to place tracking markers on the residual limb inside of the socket. In the present work, we used a global optimization technique and anatomical constraints to estimate the motion and loading at the residuum-socket interface as part of standard gait analysis procedures. We systematically evaluated a range of parameters related to the residuum-socket interface, such as the number of degrees of freedom, and determined the configuration that yields the best compromise between faithfully tracking experimental marker positions while yielding anatomically realistic residuum-socket kinematics and loads that agree with data from the literature. Application of the present model to gait analysis for people with lower limb loss will deepen our understanding of the biomechanics of walking with a prosthesis, which should facilitate the development of enhanced rehabilitation protocols and improved assistive devices. Copyright © 2017 John Wiley & Sons, Ltd.

Incorporating expert judgments in utility evaluation of bacteroidales qPCR assays for microbial source tracking in a drinking water source.

PubMed

Åström, Johan; Pettersson, Thomas J R; Reischer, Georg H; Norberg, Tommy; Hermansson, Malte

2015-02-03

Several assays for the detection of host-specific genetic markers of the order Bacteroidales have been developed and used for microbial source tracking (MST) in environmental waters. It is recognized that the source-sensitivity and source-specificity are unknown and variable when introducing these assays in new geographic regions, which reduces their reliability and use. A Bayesian approach was developed to incorporate expert judgments with regional assay sensitivity and specificity assessments in a utility evaluation of a human and a ruminant-specific qPCR assay for MST in a drinking water source. Water samples from Lake Rådasjön were analyzed for E. coli, intestinal enterococci and somatic coliphages through cultivation and for human (BacH) and ruminant-specific (BacR) markers through qPCR assays. Expert judgments were collected regarding the probability of human and ruminant fecal contamination based on fecal indicator organism data and subjective information. Using Bayes formula, the conditional probability of a true human or ruminant fecal contamination given the presence of BacH or BacR was determined stochastically from expert judgments and regional qPCR assay performance, using Beta distributions to represent uncertainties. A web-based computational tool was developed for the procedure, which provides a measure of confidence to findings of host-specific markers and demonstrates the information value from these assays.

Incorporating Expert Judgments in Utility Evaluation of Bacteroidales qPCR Assays for Microbial Source Tracking in a Drinking Water Source

PubMed Central

Åström, Johan; Pettersson, Thomas J. R.; Reischer, Georg H.; Norberg, Tommy; Hermansson, Malte

2017-01-01

Several assays for the detection of host-specific genetic markers of the order Bacteroidales have been developed and used for microbial source tracking (MST) in environmental waters. It is recognized that the source-sensitivity and source-specificity are unknown and variable when introducing these assays in new geographic regions, which reduces their reliability and use. A Bayesian approach was developed to incorporate expert judgments with regional assay sensitivity and specificity assessments in a utility evaluation of a human and a ruminant-specific qPCR assay for MST in a drinking water source. Water samples from Lake Rådasjön were analyzed for E. coli, intestinal enterococci and somatic coliphages through cultivation and for human (BacH) and ruminant-specific (BacR) markers through qPCR assays. Expert judgments were collected regarding the probability of human and ruminant fecal contamination based on fecal indicator organism data and subjective information. Using Bayes formula, the conditional probability of a true human or ruminant fecal contamination given the presence of BacH or BacR was determined stochastically from expert judgments and regional qPCR assay performance, using Beta distributions to represent uncertainties. A web-based computational tool was developed for the procedure, which provides a measure of confidence to findings of host-specific markers and demonstrates the information value from these assays. PMID:25545113

On the formation features, microstructure and microhardness of single laser tracks formed by laser cladding of a NiCrBSi self-fluxing alloy

NASA Astrophysics Data System (ADS)

Devojno, O. G.; Feldshtein, E.; Kardapolava, M. A.; Lutsko, N. I.

2018-07-01

In the present paper, the influence of laser cladding conditions on the powder flow conditions, as well as the microstructure, phases and microhardness of an Ni-based self-fluxing alloy coating are described. The optimal granulations of a self-fluxing alloy powder and the relationship between the flow of powder of various fractions and the flow rate and pressure of the transporting gas have been determined. The laser beam speed, track pitch and the distance from the nozzle to the coated surface influence the height and width of single tracks. Regularities in the formation of microstructure under different cladding conditions are defined, as well as regularity of distribution of elements over the track depth and in the transient zone. The patterns of microhardness distribution over the track depth for different cladding conditions are found. These patterns as well as the optimal laser spot pitch allowed obtaining a uniform cladding layer.

Design of state-feedback controllers including sensitivity reduction, with applications to precision pointing

NASA Technical Reports Server (NTRS)

Hadass, Z.

1974-01-01

The design procedure of feedback controllers was described and the considerations for the selection of the design parameters were given. The frequency domain properties of single-input single-output systems using state feedback controllers are analyzed, and desirable phase and gain margin properties are demonstrated. Special consideration is given to the design of controllers for tracking systems, especially those designed to track polynomial commands. As an example, a controller was designed for a tracking telescope with a polynomial tracking requirement and some special features such as actuator saturation and multiple measurements, one of which is sampled. The resulting system has a tracking performance comparing favorably with a much more complicated digital aided tracker. The parameter sensitivity reduction was treated by considering the variable parameters as random variables. A performance index is defined as a weighted sum of the state and control convariances that sum from both the random system disturbances and the parameter uncertainties, and is minimized numerically by adjusting a set of free parameters.

Predicting the language proficiency of Chinese student pilots within American airspace: Single-task versus dual-task English-language assessment

NASA Astrophysics Data System (ADS)

Noble, Clifford Elliott, II

2002-09-01

The problem. The purpose of this study was to investigate the ability of three single-task instruments---(a) the Test of English as a Foreign Language, (b) the Aviation Test of Spoken English, and (c) the Single Manual-Tracking Test---and three dual-task instruments---(a) the Concurrent Manual-Tracking and Communication Test, (b) the Certified Flight Instructor's Test, and (c) the Simulation-Based English Test---to predict the language performance of 10 Chinese student pilots speaking English as a second language when operating single-engine and multiengine aircraft within American airspace. Method. This research implemented a correlational design to investigate the ability of the six described instruments to predict the mean score of the criterion evaluation, which was the Examiner's Test. This test assessed the oral communication skill of student pilots on the flight portion of the terminal checkride in the Piper Cadet, Piper Seminole, and Beechcraft King Air airplanes. Results. Data from the Single Manual-Tracking Test, as well as the Concurrent Manual-Tracking and Communication Test, were discarded due to performance ceiling effects. Hypothesis 1, which stated that the average correlation between the mean scores of the dual-task evaluations and that of the Examiner's Test would predict the mean score of the criterion evaluation with a greater degree of accuracy than that of single-task evaluations, was not supported. Hypothesis 2, which stated that the correlation between the mean scores of the participants on the Simulation-Based English Test and the Examiner's Test would predict the mean score of the criterion evaluation with a greater degree of accuracy than that of all single- and dual-task evaluations, was also not supported. The findings suggest that single- and dual-task assessments administered after initial flight training are equivalent predictors of language performance when piloting single-engine and multiengine aircraft.

Textual and shape-based feature extraction and neuro-fuzzy classifier for nuclear track recognition

NASA Astrophysics Data System (ADS)

Khayat, Omid; Afarideh, Hossein

2013-04-01

Track counting algorithms as one of the fundamental principles of nuclear science have been emphasized in the recent years. Accurate measurement of nuclear tracks on solid-state nuclear track detectors is the aim of track counting systems. Commonly track counting systems comprise a hardware system for the task of imaging and software for analysing the track images. In this paper, a track recognition algorithm based on 12 defined textual and shape-based features and a neuro-fuzzy classifier is proposed. Features are defined so as to discern the tracks from the background and small objects. Then, according to the defined features, tracks are detected using a trained neuro-fuzzy system. Features and the classifier are finally validated via 100 Alpha track images and 40 training samples. It is shown that principle textual and shape-based features concomitantly yield a high rate of track detection compared with the single-feature based methods.

Single-Cell, Multiplexed Protein Detection of Rare Tumor Cells Based on a Beads-on-Barcode Antibody Microarray.

PubMed

Yang, Liu; Wang, Zhihua; Deng, Yuliang; Li, Yan; Wei, Wei; Shi, Qihui

2016-11-15

Circulating tumor cells (CTCs) shed from tumor sites and represent the molecular characteristics of the tumor. Besides genetic and transcriptional characterization, it is important to profile a panel of proteins with single-cell precision for resolving CTCs' phenotype, organ-of-origin, and drug targets. We describe a new technology that enables profiling multiple protein markers of extraordinarily rare tumor cells at the single-cell level. This technology integrates a microchip consisting of 15000 60 pL-sized microwells and a novel beads-on-barcode antibody microarray (BOBarray). The BOBarray allows for multiplexed protein detection by assigning two independent identifiers (bead size and fluorescent color) of the beads to each protein. Four bead sizes (1.75, 3, 4.5, and 6 μm) and three colors (blue, green, and yellow) are utilized to encode up to 12 different proteins. The miniaturized BOBarray can fit an array of 60 pL-sized microwells that isolate single cells for cell lysis and the subsequent detection of protein markers. An enclosed 60 pL-sized microchamber defines a high concentration of proteins released from lysed single cells, leading to single-cell resolution of protein detection. The protein markers assayed in this study include organ-specific markers and drug targets that help to characterize the organ-of-origin and drug targets of isolated rare tumor cells from blood samples. This new approach enables handling a very small number of cells and achieves single-cell, multiplexed protein detection without loss of rare but clinically important tumor cells.

Intraoperative visualization and assessment of electromagnetic tracking error

NASA Astrophysics Data System (ADS)

Harish, Vinyas; Ungi, Tamas; Lasso, Andras; MacDonald, Andrew; Nanji, Sulaiman; Fichtinger, Gabor

2015-03-01

Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

Single particle tracking through highly scattering media with multiplexed two-photon excitation

NASA Astrophysics Data System (ADS)

Perillo, Evan; Liu, Yen-Liang; Liu, Cong; Yeh, Hsin-Chih; Dunn, Andrew K.

2015-03-01

3D single-particle tracking (SPT) has been a pivotal tool to furthering our understanding of dynamic cellular processes in complex biological systems, with a molecular localization accuracy (10-100 nm) often better than the diffraction limit of light. However, current SPT techniques utilize either CCDs or a confocal detection scheme which not only suffer from poor temporal resolution but also limit tracking to a depth less than one scattering mean free path in the sample (typically <15μm). In this report we highlight our novel design for a spatiotemporally multiplexed two-photon microscope which is able to reach sub-diffraction-limit tracking accuracy and sub-millisecond temporal resolution, but with a dramatically extended SPT range of up to 200 μm through dense cell samples. We have validated our microscope by tracking (1) fluorescent nanoparticles in a prescribed motion inside gelatin gel (with 1% intralipid) and (2) labeled single EGFR complexes inside skin cancer spheroids (at least 8 layers of cells thick) for ~10 minutes. Furthermore we discuss future capabilities of our multiplexed two-photon microscope design, specifically to the extension of (1) simultaneous multicolor tracking (i.e. spatiotemporal co-localization analysis) and (2) FRET studies (i.e. lifetime analysis). The high resolution, high depth penetration, and multicolor features of this microscope make it well poised to study a variety of molecular scale dynamics in the cell, especially related to cellular trafficking studies with in vitro tumor models and in vivo.

Label-free cell-cycle analysis by high-throughput quantitative phase time-stretch imaging flow cytometry

NASA Astrophysics Data System (ADS)

Mok, Aaron T. Y.; Lee, Kelvin C. M.; Wong, Kenneth K. Y.; Tsia, Kevin K.

2018-02-01

Biophysical properties of cells could complement and correlate biochemical markers to characterize a multitude of cellular states. Changes in cell size, dry mass and subcellular morphology, for instance, are relevant to cell-cycle progression which is prevalently evaluated by DNA-targeted fluorescence measurements. Quantitative-phase microscopy (QPM) is among the effective biophysical phenotyping tools that can quantify cell sizes and sub-cellular dry mass density distribution of single cells at high spatial resolution. However, limited camera frame rate and thus imaging throughput makes QPM incompatible with high-throughput flow cytometry - a gold standard in multiparametric cell-based assay. Here we present a high-throughput approach for label-free analysis of cell cycle based on quantitative-phase time-stretch imaging flow cytometry at a throughput of > 10,000 cells/s. Our time-stretch QPM system enables sub-cellular resolution even at high speed, allowing us to extract a multitude (at least 24) of single-cell biophysical phenotypes (from both amplitude and phase images). Those phenotypes can be combined to track cell-cycle progression based on a t-distributed stochastic neighbor embedding (t-SNE) algorithm. Using multivariate analysis of variance (MANOVA) discriminant analysis, cell-cycle phases can also be predicted label-free with high accuracy at >90% in G1 and G2 phase, and >80% in S phase. We anticipate that high throughput label-free cell cycle characterization could open new approaches for large-scale single-cell analysis, bringing new mechanistic insights into complex biological processes including diseases pathogenesis.

A customized vision system for tracking humans wearing reflective safety clothing from industrial vehicles and machinery.

PubMed

Mosberger, Rafael; Andreasson, Henrik; Lilienthal, Achim J

2014-09-26

This article presents a novel approach for vision-based detection and tracking of humans wearing high-visibility clothing with retro-reflective markers. Addressing industrial applications where heavy vehicles operate in the vicinity of humans, we deploy a customized stereo camera setup with active illumination that allows for efficient detection of the reflective patterns created by the worker's safety garments. After segmenting reflective objects from the image background, the interest regions are described with local image feature descriptors and classified in order to discriminate safety garments from other reflective objects in the scene. In a final step, the trajectories of the detected humans are estimated in 3D space relative to the camera. We evaluate our tracking system in two industrial real-world work environments on several challenging video sequences. The experimental results indicate accurate tracking performance and good robustness towards partial occlusions, body pose variation, and a wide range of different illumination conditions.

Refraction-compensated motion tracking of unrestrained small animals in positron emission tomography.

PubMed

Kyme, Andre; Meikle, Steven; Baldock, Clive; Fulton, Roger

2012-08-01

Motion-compensated radiotracer imaging of fully conscious rodents represents an important paradigm shift for preclinical investigations. In such studies, if motion tracking is performed through a transparent enclosure containing the awake animal, light refraction at the interface will introduce errors in stereo pose estimation. We have performed a thorough investigation of how this impacts the accuracy of pose estimates and the resulting motion correction, and developed an efficient method to predict and correct for refraction-based error. The refraction model underlying this study was validated using a state-of-the-art motion tracking system. Refraction-based error was shown to be dependent on tracking marker size, working distance, and interface thickness and tilt. Correcting for refraction error improved the spatial resolution and quantitative accuracy of motion-corrected positron emission tomography images. Since the methods are general, they may also be useful in other contexts where data are corrupted by refraction effects. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

A Customized Vision System for Tracking Humans Wearing Reflective Safety Clothing from Industrial Vehicles and Machinery

PubMed Central

Mosberger, Rafael; Andreasson, Henrik; Lilienthal, Achim J.

2014-01-01

This article presents a novel approach for vision-based detection and tracking of humans wearing high-visibility clothing with retro-reflective markers. Addressing industrial applications where heavy vehicles operate in the vicinity of humans, we deploy a customized stereo camera setup with active illumination that allows for efficient detection of the reflective patterns created by the worker's safety garments. After segmenting reflective objects from the image background, the interest regions are described with local image feature descriptors and classified in order to discriminate safety garments from other reflective objects in the scene. In a final step, the trajectories of the detected humans are estimated in 3D space relative to the camera. We evaluate our tracking system in two industrial real-world work environments on several challenging video sequences. The experimental results indicate accurate tracking performance and good robustness towards partial occlusions, body pose variation, and a wide range of different illumination conditions. PMID:25264956

Matching Real and Synthetic Panoramic Images Using a Variant of Geometric Hashing

NASA Astrophysics Data System (ADS)

Li-Chee-Ming, J.; Armenakis, C.

2017-05-01

This work demonstrates an approach to automatically initialize a visual model-based tracker, and recover from lost tracking, without prior camera pose information. These approaches are commonly referred to as tracking-by-detection. Previous tracking-by-detection techniques used either fiducials (i.e. landmarks or markers) or the object's texture. The main contribution of this work is the development of a tracking-by-detection algorithm that is based solely on natural geometric features. A variant of geometric hashing, a model-to-image registration algorithm, is proposed that searches for a matching panoramic image from a database of synthetic panoramic images captured in a 3D virtual environment. The approach identifies corresponding features between the matched panoramic images. The corresponding features are to be used in a photogrammetric space resection to estimate the camera pose. The experiments apply this algorithm to initialize a model-based tracker in an indoor environment using the 3D CAD model of the building.

High-accuracy and real-time 3D positioning, tracking system for medical imaging applications based on 3D digital image correlation

NASA Astrophysics Data System (ADS)

Xue, Yuan; Cheng, Teng; Xu, Xiaohai; Gao, Zeren; Li, Qianqian; Liu, Xiaojing; Wang, Xing; Song, Rui; Ju, Xiangyang; Zhang, Qingchuan

2017-01-01

This paper presents a system for positioning markers and tracking the pose of a rigid object with 6 degrees of freedom in real-time using 3D digital image correlation, with two examples for medical imaging applications. Traditional DIC method was improved to meet the requirements of the real-time by simplifying the computations of integral pixel search. Experiments were carried out and the results indicated that the new method improved the computational efficiency by about 4-10 times in comparison with the traditional DIC method. The system was aimed for orthognathic surgery navigation in order to track the maxilla segment after LeFort I osteotomy. Experiments showed noise for the static point was at the level of 10-3 mm and the measurement accuracy was 0.009 mm. The system was demonstrated on skin surface shape evaluation of a hand for finger stretching exercises, which indicated a great potential on tracking muscle and skin movements.

Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads

PubMed Central

2013-01-01

Background Brachiaria ruziziensis is one of the most important forage species planted in the tropics. The application of genomic tools to aid the selection of superior genotypes can provide support to B. ruziziensis breeding programs. However, there is a complete lack of information about the B. ruziziensis genome. Also, the availability of genomic tools, such as molecular markers, to support B. ruziziensis breeding programs is rather limited. Recently, next-generation sequencing technologies have been applied to generate sequence data for the identification of microsatellite regions and primer design. In this study, we present a first validated set of SSR markers for Brachiaria ruziziensis, selected from a de novo partial genome assembly of single-end Illumina reads. Results A total of 85,567 perfect microsatellite loci were detected in contigs with a minimum 10X coverage. We selected a set of 500 microsatellite loci identified in contigs with minimum 100X coverage for primer design and synthesis, and tested a subset of 269 primer pairs, 198 of which were polymorphic on 11 representative B. ruziziensis accessions. Descriptive statistics for these primer pairs are presented, as well as estimates of marker transferability to other relevant brachiaria species. Finally, a set of 11 multiplex panels containing the 30 most informative markers was validated and proposed for B. ruziziensis genetic analysis. Conclusions We show that the detection and development of microsatellite markers from genome assembled Illumina single-end DNA sequences is highly efficient. The developed markers are readily suitable for genetic analysis and marker assisted selection of Brachiaria ruziziensis. The use of this approach for microsatellite marker development is promising for species with limited genomic information, whose breeding programs would benefit from the use of genomic tools. To our knowledge, this is the first set of microsatellite markers developed for this important species. PMID:23324172

Single-particle tracking of quantum dot-conjugated prion proteins inside yeast cells

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

Tsuji, Toshikazu; Kawai-Noma, Shigeko; Pack, Chan-Gi

2011-02-25

Research highlights: {yields} We develop a method to track a quantum dot-conjugated protein in yeast cells. {yields} We incorporate the conjugated quantum dot proteins into yeast spheroplasts. {yields} We track the motions by conventional or 3D tracking microscopy. -- Abstract: Yeast is a model eukaryote with a variety of biological resources. Here we developed a method to track a quantum dot (QD)-conjugated protein in the budding yeast Saccharomyces cerevisiae. We chemically conjugated QDs with the yeast prion Sup35, incorporated them into yeast spheroplasts, and tracked the motions by conventional two-dimensional or three-dimensional tracking microscopy. The method paves the way towardmore » the individual tracking of proteins of interest inside living yeast cells.« less