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Sample records for rapid image sequences

  1. Rapid 3D Reconstruction for Image Sequence Acquired from UAV Camera

    Directory of Open Access Journals (Sweden)

    Yufu Qu

    2018-01-01

    Full Text Available In order to reconstruct three-dimensional (3D structures from an image sequence captured by unmanned aerial vehicles’ camera (UAVs and improve the processing speed, we propose a rapid 3D reconstruction method that is based on an image queue, considering the continuity and relevance of UAV camera images. The proposed approach first compresses the feature points of each image into three principal component points by using the principal component analysis method. In order to select the key images suitable for 3D reconstruction, the principal component points are used to estimate the interrelationships between images. Second, these key images are inserted into a fixed-length image queue. The positions and orientations of the images are calculated, and the 3D coordinates of the feature points are estimated using weighted bundle adjustment. With this structural information, the depth maps of these images can be calculated. Next, we update the image queue by deleting some of the old images and inserting some new images into the queue, and a structural calculation of all the images can be performed by repeating the previous steps. Finally, a dense 3D point cloud can be obtained using the depth–map fusion method. The experimental results indicate that when the texture of the images is complex and the number of images exceeds 100, the proposed method can improve the calculation speed by more than a factor of four with almost no loss of precision. Furthermore, as the number of images increases, the improvement in the calculation speed will become more noticeable.

  2. Rapid 3D Reconstruction for Image Sequence Acquired from UAV Camera.

    Science.gov (United States)

    Qu, Yufu; Huang, Jianyu; Zhang, Xuan

    2018-01-14

    In order to reconstruct three-dimensional (3D) structures from an image sequence captured by unmanned aerial vehicles' camera (UAVs) and improve the processing speed, we propose a rapid 3D reconstruction method that is based on an image queue, considering the continuity and relevance of UAV camera images. The proposed approach first compresses the feature points of each image into three principal component points by using the principal component analysis method. In order to select the key images suitable for 3D reconstruction, the principal component points are used to estimate the interrelationships between images. Second, these key images are inserted into a fixed-length image queue. The positions and orientations of the images are calculated, and the 3D coordinates of the feature points are estimated using weighted bundle adjustment. With this structural information, the depth maps of these images can be calculated. Next, we update the image queue by deleting some of the old images and inserting some new images into the queue, and a structural calculation of all the images can be performed by repeating the previous steps. Finally, a dense 3D point cloud can be obtained using the depth-map fusion method. The experimental results indicate that when the texture of the images is complex and the number of images exceeds 100, the proposed method can improve the calculation speed by more than a factor of four with almost no loss of precision. Furthermore, as the number of images increases, the improvement in the calculation speed will become more noticeable.

  3. A rapid Look-Locker imaging sequence for quantitative tissue oximetry

    Science.gov (United States)

    Vidya Shankar, Rohini; Kodibagkar, Vikram D.

    2015-03-01

    Tissue oximetry studies using magnetic resonance imaging are increasingly contributing to advances in the imaging and treatment of cancer. The non-invasive measurement of tissue oxygenation (pO2) may facilitate a better understanding of the pathophysiology and prognosis of diseases, particularly in the assessment of the extensive hypoxic regions associated with cancerous lesions. The availability of tumor hypoxia maps could help quantify and predict tumor response to intervention and therapy. The PISTOL (Proton Imaging of Siloxanes to map Tissue Oxygenation Levels) oximetry technique maps the T1 of administered hexamethyldisiloxane (HMDSO), an 1H NMR pO2 reporter molecule in about 3 ½ min. This allows us to subsequently monitor static and dynamic changes in the tissue pO2 (in response to intervention) at various locations due to the linear relationship between 1/T1 and pO2. In this work, an HMDSO-selective Look-Locker imaging sequence with EPI readout has been developed to enable faster PISTOL acquisitions. The new sequence incorporates the fast Look-Locker measurement method to enable T1, and hence, pO2 mapping of HMDSO in under one minute. To demonstrate the application of this pulse sequence in vivo, 50 μL of neat HMDSO was administered to the thigh muscle of a healthy rat (Fischer F344, n=4). Dynamic changes in the mean pO2 of the thigh muscle were measured using both PISTOL and the developed LL oximetry sequence in response to oxygen challenge and compared. Results demonstrate the efficacy of the new sequence in rapidly mapping the pO2 changes, leading to advances in fast quantitative 1H MR oximetry.

  4. Rapid Measurements of Intensities for Safety Assessment of Advanced Imaging Sequences

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Stuart, Matthias Bo

    2014-01-01

    FDA requires that intensity and safety parameters are measured for all imaging schemes for clinical imaging. This is often cumbersome, since the scan sequence has to broken apart, measurements conducted for the individually emitted beams, and the nal intensity levels calculated by combining the i...

  5. Rapid Polymer Sequencer

    Science.gov (United States)

    Stolc, Viktor (Inventor); Brock, Matthew W (Inventor)

    2013-01-01

    Method and system for rapid and accurate determination of each of a sequence of unknown polymer components, such as nucleic acid components. A self-assembling monolayer of a selected substance is optionally provided on an interior surface of a pipette tip, and the interior surface is immersed in a selected liquid. A selected electrical field is impressed in a longitudinal direction, or in a transverse direction, in the tip region, a polymer sequence is passed through the tip region, and a change in an electrical current signal is measured as each polymer component passes through the tip region. Each of the measured changes in electrical current signals is compared with a database of reference electrical change signals, with each reference signal corresponding to an identified polymer component, to identify the unknown polymer component with a reference polymer component. The nanopore preferably has a pore inner diameter of no more than about 40 nm and is prepared by heating and pulling a very small section of a glass tubing.

  6. Hepatic adenomatosis: rapid sequence MR imaging following gadolinium enhancement: a case report

    Energy Technology Data Exchange (ETDEWEB)

    Brummett, D. [Dept. of Radiology, Medical College of Georgia, Augusta (United States); Burton, E.M. [Dept. of Radiology, Medical College of Georgia, Augusta (United States)]|[Dept. of Pediatrics, Medical College of Georgia, Augusta (United States); Sabio, H. [Dept. of Pediatrics, Medical College of Georgia, Augusta (United States)

    1999-04-01

    Hepatic adenomas are primary liver tumors usually associated with underlying metabolic disease or with anabolic steroid or oral contraceptive use. Hepatic adenomatosis (HA) is defined as the presence of more than four adenomas. Only 13 cases of HA have been reported in patients without glycogen storage disease or steroid use. We report a case of HA imaged by postcontrast T1-weighted images obtained during a breath-holding series. The lesions were most conspicuous 3-4 min after contrast administration; 4 of the 5 tumors were not identified on T2-weighted images. Unlike previous reports of HA in which the lesions remained hyperintense during sequential postcontrast imaging, the smaller lesions in this case demonstrated contrast washout, thereby distinguishing them from hemangiomata. (orig.) With 3 figs., 10 refs.

  7. Image sequence analysis

    CERN Document Server

    1981-01-01

    The processing of image sequences has a broad spectrum of important applica­ tions including target tracking, robot navigation, bandwidth compression of TV conferencing video signals, studying the motion of biological cells using microcinematography, cloud tracking, and highway traffic monitoring. Image sequence processing involves a large amount of data. However, because of the progress in computer, LSI, and VLSI technologies, we have now reached a stage when many useful processing tasks can be done in a reasonable amount of time. As a result, research and development activities in image sequence analysis have recently been growing at a rapid pace. An IEEE Computer Society Workshop on Computer Analysis of Time-Varying Imagery was held in Philadelphia, April 5-6, 1979. A related special issue of the IEEE Transactions on Pattern Anal­ ysis and Machine Intelligence was published in November 1980. The IEEE Com­ puter magazine has also published a special issue on the subject in 1981. The purpose of this book ...

  8. Wideband arrhythmia-Insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by an implantable-cardioverter-defibrillator.

    Science.gov (United States)

    Hong, KyungPyo; Jeong, Eun-Kee; Wall, T Scott; Drakos, Stavros G; Kim, Daniel

    2015-08-01

    To develop and evaluate a wideband arrhythmia-insensitive-rapid (AIR) pulse sequence for cardiac T1 mapping without image artifacts induced by implantable-cardioverter-defibrillator (ICD). We developed a wideband AIR pulse sequence by incorporating a saturation pulse with wide frequency bandwidth (8.9 kHz) to achieve uniform T1 weighting in the heart with ICD. We tested the performance of original and "wideband" AIR cardiac T1 mapping pulse sequences in phantom and human experiments at 1.5 Tesla. In five phantoms representing native myocardium and blood and postcontrast blood/tissue T1 values, compared with the control T1 values measured with an inversion-recovery pulse sequence without ICD, T1 values measured with original AIR with ICD were considerably lower (absolute percent error > 29%), whereas T1 values measured with wideband AIR with ICD were similar (absolute percent error T1 values measured with original AIR without ICD, T1 measured with original AIR with ICD was significantly lower (absolute percent error > 10.1%), whereas T1 measured with wideband AIR with ICD was similar (absolute percent error T1 mapping without significant image artifacts induced by ICD. © 2015 Wiley Periodicals, Inc.

  9. Region segmentation along image sequence

    Energy Technology Data Exchange (ETDEWEB)

    Monchal, L.; Aubry, P.

    1995-12-31

    A method to extract regions in sequence of images is proposed. Regions are not matched from one image to the following one. The result of a region segmentation is used as an initialization to segment the following and image to track the region along the sequence. The image sequence is exploited as a spatio-temporal event. (authors). 12 refs., 8 figs.

  10. MR sequences and rapid acquisition for MR guided interventions

    Science.gov (United States)

    Campbell-Washburn, Adrienne E; Faranesh, Anthony Z; Lederman, Robert J; Hansen, Michael S

    2015-01-01

    Synopsis Interventional MR uses rapid imaging to guide diagnostic and therapeutic procedures. One of the attractions of MR-guidance is the abundance of inherent contrast mechanisms available. Dynamic procedural guidance with real-time imaging has pushed the limits of MR technology, demanding rapid acquisition and reconstruction paired with interactive control and device visualization. This article reviews the technical aspects of real-time MR sequences that enable MR-guided interventions. PMID:26499283

  11. TOPPE: A framework for rapid prototyping of MR pulse sequences.

    Science.gov (United States)

    Nielsen, Jon-Fredrik; Noll, Douglas C

    2017-11-02

    To introduce a framework for rapid prototyping of MR pulse sequences. We propose a simple file format, called "TOPPE", for specifying all details of an MR imaging experiment, such as gradient and radiofrequency waveforms and the complete scan loop. In addition, we provide a TOPPE file "interpreter" for GE scanners, which is a binary executable that loads TOPPE files and executes the sequence on the scanner. We also provide MATLAB scripts for reading and writing TOPPE files and previewing the sequence prior to hardware execution. With this setup, the task of the pulse sequence programmer is reduced to creating TOPPE files, eliminating the need for hardware-specific programming. No sequence-specific compilation is necessary; the interpreter only needs to be compiled once (for every scanner software upgrade). We demonstrate TOPPE in three different applications: k-space mapping, non-Cartesian PRESTO whole-brain dynamic imaging, and myelin mapping in the brain using inhomogeneous magnetization transfer. We successfully implemented and executed the three example sequences. By simply changing the various TOPPE sequence files, a single binary executable (interpreter) was used to execute several different sequences. The TOPPE file format is a complete specification of an MR imaging experiment, based on arbitrary sequences of a (typically small) number of unique modules. Along with the GE interpreter, TOPPE comprises a modular and flexible platform for rapid prototyping of new pulse sequences. Magn Reson Med, 2017. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  12. Rapid resistome mapping using nanopore sequencing

    DEFF Research Database (Denmark)

    van der Helm, Eric; Imamovic, Lejla; Ellabaan, Mostafa M Hashim

    2017-01-01

    of bacterial infections. Yet, rapid workflows for resistome characterization are lacking. To address this challenge we developed the poreFUME workflow that deploys functional metagenomic selections and nanopore sequencing to resistome mapping. We demonstrate the approach by functionally characterizing the gut...

  13. First results in rapid MR imaging of focal liver and spleen lesions using field echos and small angle excitation (gradient echo sequences)

    Energy Technology Data Exchange (ETDEWEB)

    Griebel, J.; Hess, C.F.; Kurtz, B.; Klose, U.; Kueper, K.

    1987-01-01

    15 healthy subjects and 39 patients with focal liver and spleen lesions were examined via MR tomography at 1.5 tesla. Gradient field echos at small angle excitation (< 90/sup 0/) were employed. The imaging time per layer was 10 seconds so that rapid imaging could be carried out at respiratory standstill. This enabled visualisation of liver and spleen without interference by breathing artifacts and with accurate localisation. Focal lesions can be imaged best at low flip-angle pulses (liver) or low to medium-angle pulses (spleen). The primary liver cell carcinoma is visualised as an inhomogeneous structure with similar signal intensity as the surrounding tissue. All other examined liver lesions (metastases, haemangiomas, lymphatic infiltrates, echinococcus cysts, FNH, gummae) showed greater signal intensity than the remaining organ at small angle excitation. Furthermore, contrast reversals were seen at medium-angle pulses. Contrariwise, with the exception of the light-coloured spleen infarcts, spleen lesions (lymphatic infiltrate, Boeck's disease or sarcoidosis) appeared darker at all excitation angles than the surrounding tissue.

  14. A multi-plane scout sequence using flash imaging.

    Science.gov (United States)

    Wright, S M; Wright, R M

    1988-01-01

    A new pulse sequence is presented for multi-plane imaging which simultaneously acquires images in the axial, coronal, and sagittal planes. Combined with FLASH imaging or other similar techniques, T1- and T2-weighted images in all three planes can be acquired in approximately 12 and 30 seconds, respectively. The sequence is easily implemented by modifying a multi-slice sequence to provide a rotation of gradient assignments between slice excitations. This sequence has been used extensively as a rapid "scout" scan. Several clinical examples are included.

  15. SSh versus TSE sequence protocol in rapid MR examination of pediatric patients with programmable drainage system.

    Science.gov (United States)

    Brichtová, Eva; Šenkyřík, J

    2017-05-01

    A low radiation burden is essential during diagnostic procedures in pediatric patients due to their high tissue sensitivity. Using MR examination instead of the routinely used CT reduces the radiation exposure and the risk of adverse stochastic effects. Our retrospective study evaluated the possibility of using ultrafast single-shot (SSh) sequences and turbo spin echo (TSE) sequences in rapid MR brain imaging in pediatric patients with hydrocephalus and a programmable ventriculoperitoneal drainage system. SSh sequences seem to be suitable for examining pediatric patients due to the speed of using this technique, but significant susceptibility artifacts due to the programmable drainage valve degrade the image quality. Therefore, a rapid MR examination protocol based on TSE sequences, less sensitive to artifacts due to ferromagnetic components, has been developed. Of 61 pediatric patients who were examined using MR and the SSh sequence protocol, a group of 15 patients with hydrocephalus and a programmable drainage system also underwent TSE sequence MR imaging. The susceptibility artifact volume in both rapid MR protocols was evaluated using a semiautomatic volumetry system. A statistically significant decrease in the susceptibility artifact volume has been demonstrated in TSE sequence imaging in comparison with SSh sequences. Using TSE sequences reduced the influence of artifacts from the programmable valve, and the image quality in all cases was rated as excellent. In all patients, rapid MR examinations were performed without any need for intravenous sedation or general anesthesia. Our study results strongly suggest the superiority of the TSE sequence MR protocol compared to the SSh sequence protocol in pediatric patients with a programmable ventriculoperitoneal drainage system due to a significant reduction of susceptibility artifact volume. Both rapid sequence MR protocols provide quick and satisfactory brain imaging with no ionizing radiation and a reduced need

  16. Safety Assessment of Advanced Imaging Sequences I: Measurements

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Pihl, Michael Johannes

    2016-01-01

    A method for rapid measurement of intensities (Ispta), mechanical index (MI), and probe surface temperature for any ultrasound scanning sequence is presented. It uses the scanner’s sampling capability to give an accurate measurement of the whole imaging sequence for all emissions to yield the tru...

  17. Image enhancement and moving target detection in IR image sequences

    NARCIS (Netherlands)

    Beck, W.

    1993-01-01

    Results are presented of noise reduction by motion compensated temporal filtering in a noisy IR image sequence and of moving target detection in an air-to-ground IR image sequence. In the case of motion compensated temporal filtering our approach consists of estimating the optical flow between

  18. Failed rapid sequence induction in an achondroplastic dwarf

    Directory of Open Access Journals (Sweden)

    Jasleen Kaur

    2011-01-01

    Full Text Available Achondroplasia, a common cause of short limbed type of dwarfism is due to quantitative decrease in rate of endochondral ossification. This abnormal bone growth leads to disproportionate body and head structure, thus placing them under high risk for anaesthetic management. There is paucity in literatures, regarding appropriate drug dosage selection in these patients. Use of drugs as per standard dosage recommendations based on body weight or body surface area, may not be adequate in these patients owing to discrepancies in overall body weight and lean body weight, especially during rapid sequence induction. Here, we report a case of failed rapid sequence induction due to abnormal response to administered drugs in an adult achondroplastic dwarf. Standard doses of thiopentone and rocuronium had to be repeated thrice to achieve adequate conditions for intubation.

  19. Multilocus DNA Sequence Comparisons Rapidly Identify Pathogenic Molds

    Science.gov (United States)

    Rakeman, Jennifer L.; Bui, Uyen; LaFe, Karen; Chen, Yi-Ching; Honeycutt, Rhonda J.; Cookson, Brad T.

    2005-01-01

    The increasing incidence of opportunistic fungal infections necessitates rapid and accurate identification of the associated fungi to facilitate optimal patient treatment. Traditional phenotype-based identification methods utilized in clinical laboratories rely on the production and recognition of reproductive structures, making identification difficult or impossible when these structures are not observed. We hypothesized that DNA sequence analysis of multiple loci is useful for rapidly identifying medically important molds. Our study included the analysis of the D1/D2 hypervariable region of the 28S ribosomal gene and the internal transcribed spacer (ITS) regions 1 and 2 of the rRNA operon. Two hundred one strains, including 143 clinical isolates and 58 reference and type strains, representing 43 recognized species and one possible new species, were examined. We generated a phenotypically validated database of 118 diagnostic alleles. DNA length polymorphisms detected among ITS1 and ITS2 PCR products can differentiate 20 of 33 species of molds tested, and ITS DNA sequence analysis permits identification of all species tested. For 42 of 44 species tested, conspecific strains displayed >99% sequence identity at ITS1 and ITS2; sequevars were detected in two species. For all 44 species, identifications by genotypic and traditional phenotypic methods were 100% concordant. Because dendrograms based on ITS sequence analysis are similar in topology to 28S-based trees, we conclude that ITS sequences provide phylogenetically valid information and can be utilized to identify clinically important molds. Additionally, this phenotypically validated database of ITS sequences will be useful for identifying new species of pathogenic molds. PMID:16000456

  20. Ion Torren Semiconductor Sequencing Allows Rapid, Low Cost Sequencing of the Human Exome ( 7th Annual SFAF Meeting, 2012)

    Energy Technology Data Exchange (ETDEWEB)

    Jenkins, David [EdgeBio

    2012-06-01

    David Jenkins on "Ion Torrent semiconductor sequencing allows rapid, low-cost sequencing of the human exome" at the 2012 Sequencing, Finishing, Analysis in the Future Meeting held June 5-7, 2012 in Santa Fe, New Mexico.

  1. Rapid imaging of free radicals in vivo using field cycled PEDRI.

    Science.gov (United States)

    Puwanich, P; Lurie, D J; Foster, M A

    1999-12-01

    Imaging of free radicals in vivo using an interleaved field-cycled proton-electron double-resonance imaging (FC-PEDRI) pulse sequence has recently been investigated. In this work, in order to reduce the EPR (electron paramagnetic resonance) irradiation power required and the imaging time, a centric reordered snapshot FC-PEDRI pulse sequence has been implemented. This is based on the FLASH pulse sequence with a very short repetition time and the use of centric reordering of the phase-encoding gradient, allowing the most significant free induction decay (FID) signals to be collected before the signal enhancement decays significantly. A new technique of signal phaseshift correction was required to eliminate ghost artefacts caused by the instability of the main magnetic field after field cycling. An FID amplitude correction scheme has also been implemented to reduce edge enhancement artefacts caused by the rapid change of magnetization population before reaching the steady state. Using the rapid pulse sequence, the time required for acquisition of a 64 x 64 pixel FC-PEDRI image was reduced to 6 s per image compared with about 2.5 min with the conventional pulse sequence. The EPR irradiation power applied to the sample was reduced by a factor of approximately 64. Although the resulting images obtained by the rapid pulse sequence have a lower signal to noise than those obtained by a normal interleaved FC-PEDRI pulse sequence, the results show that rapid imaging of free radicals in vivo using snapshot FC-PEDRI is possible.

  2. Fractal-based image sequence compression scheme

    Science.gov (United States)

    Li, Haibo; Novak, Mirek; Forchheimer, Robert

    1993-07-01

    The dominant image transformation used in the existing fractal coding schemes is the affine function. Although an affine transformation is easy to compute and understand, its linear approximation ability limits the employment of larger range blocks, that is, it limits further improvement in compression efficiency. We generalize the image transformation from the usual affine form to the more general quadratic form, and provide theoretical requirements for the generalized transformation to be contractive. Based on the self-transformation system (STS) model, an image sequence coding scheme--fractal-based image sequence coding--is proposed. In this coding scheme, our generalized transformation is used to model the self- transformation is used to model the self-transformation from the domain block to its range blocks. Experimental results on a real image sequence show that for the same size of blocks, the SNR can be improved by 10 dB, or, for the same SNR of the decoded image sequence, the compression ratio is raised twofold when the new generalized transformation is used to replace the usual affine transformation. In addition, due to the utilization of the STS model, the computational complexity is only linearly related to the size of the 3-D blocks. This provides for fast encoding and decoding.

  3. Image correlation method for DNA sequence alignment.

    Directory of Open Access Journals (Sweden)

    Millaray Curilem Saldías

    Full Text Available The complexity of searches and the volume of genomic data make sequence alignment one of bioinformatics most active research areas. New alignment approaches have incorporated digital signal processing techniques. Among these, correlation methods are highly sensitive. This paper proposes a novel sequence alignment method based on 2-dimensional images, where each nucleic acid base is represented as a fixed gray intensity pixel. Query and known database sequences are coded to their pixel representation and sequence alignment is handled as object recognition in a scene problem. Query and database become object and scene, respectively. An image correlation process is carried out in order to search for the best match between them. Given that this procedure can be implemented in an optical correlator, the correlation could eventually be accomplished at light speed. This paper shows an initial research stage where results were "digitally" obtained by simulating an optical correlation of DNA sequences represented as images. A total of 303 queries (variable lengths from 50 to 4500 base pairs and 100 scenes represented by 100 x 100 images each (in total, one million base pair database were considered for the image correlation analysis. The results showed that correlations reached very high sensitivity (99.01%, specificity (98.99% and outperformed BLAST when mutation numbers increased. However, digital correlation processes were hundred times slower than BLAST. We are currently starting an initiative to evaluate the correlation speed process of a real experimental optical correlator. By doing this, we expect to fully exploit optical correlation light properties. As the optical correlator works jointly with the computer, digital algorithms should also be optimized. The results presented in this paper are encouraging and support the study of image correlation methods on sequence alignment.

  4. Digital image sequence processing, compression, and analysis

    CERN Document Server

    Reed, Todd R

    2004-01-01

    IntroductionTodd R. ReedCONTENT-BASED IMAGE SEQUENCE REPRESENTATIONPedro M. Q. Aguiar, Radu S. Jasinschi, José M. F. Moura, andCharnchai PluempitiwiriyawejTHE COMPUTATION OF MOTIONChristoph Stiller, Sören Kammel, Jan Horn, and Thao DangMOTION ANALYSIS AND DISPLACEMENT ESTIMATION IN THE FREQUENCY DOMAINLuca Lucchese and Guido Maria CortelazzoQUALITY OF SERVICE ASSESSMENT IN NEW GENERATION WIRELESS VIDEO COMMUNICATIONSGaetano GiuntaERROR CONCEALMENT IN DIGITAL VIDEOFrancesco G.B. De NataleIMAGE SEQUENCE RESTORATION: A WIDER PERSPECTIVEAnil KokaramVIDEO SUMMARIZATIONCuneyt M. Taskiran and Edward

  5. Feasibility of Rapid-Sequence {sup 31}P Magnetic Resonance Spectroscopy in Cardiac Patients

    Energy Technology Data Exchange (ETDEWEB)

    Chida, K.; Otani, H.; Saito, H.; Nagasaka, T.; Kagaya, Y.; Kohzuki, M.; Zuguchi, M.; Shirato, K. [Tohoku Univ., School of Health Sciences, Sendai (Japan). Dept. of Radiological Technology

    2005-07-01

    Purpose: To determine the clinical feasibility of rapid-sequence phosphorus-31 magnetic resonance spectroscopy ({sup 31}P -MRS) of the heart with cardiac patients using a 5T clinical MR system. Material and Methods: Twenty cardiac patients, i.e. dilated cardiomyopathy (DCM)3 cases, hypertrophic cardiomyopathy (HCM) 3 cases, hypertensive heart diseases (HHD) 3 cases, and aortic regurgitation (AR) case were examined using rapid cardiac {sup 31}P-MRS. Complete three-dimensional localization was performed using a two-dimensional phosphorus chemical-shift imaging sequence in combination with 30-mm axial slice-selective excitation. The rapid-sequence {sup 31}P-MRS procedure was phase encoded in arrays of 8x8 steps with an average of 4 acquisitions. The total examination time, including proton imaging and shimming, for the rapid cardiac {sup 31}P-MRS procedure, ranged from 0 to 5 min, depending on the heart rate. Student's t test was used to compare creatine phosphate (PCr)/adenosine triphosphate (ATP) ratios from the cardiac patients with those of the control subjects (n{approx_equal}13). Results: The myocardial PCr/ATP ratio obtained by rapid {sup 31}P-MRS was significantly lower (P <0.001) in DCM patients (1.82{+-}0.33, mean{+-}SD), and in patients with global myocardial dysfunction (combined data for 20 patients:.89{+-}0.32) than in normal volunteers (2.96{+-}0.59). These results are similar to previous studies. Conclusion: Rapid-sequence {sup 31}P-MRS may be a valid diagnostic tool for patients with cardiac disease.

  6. Safety Assessment of Advanced Imaging Sequences I: Measurements.

    Science.gov (United States)

    Jensen, Jorgen Arendt; Rasmussen, Morten Fischer; Pihl, Michael Johannes; Holbek, Simon; Hoyos, Carlos Armando Villagómez; Bradway, David P; Stuart, Matthias Bo; Tomov, Borislav Gueorguiev

    2016-01-01

    A method for rapid measurement of intensities (I(spta)), mechanical index (MI), and probe surface temperature for any ultrasound scanning sequence is presented. It uses the scanner's sampling capability to give an accurate measurement of the whole imaging sequence for all emissions to yield the true distributions. The method is several orders of magnitude faster than approaches using an oscilloscope, and it also facilitates validating the emitted pressure field and the scanner's emission sequence software. It has been implemented using the experimental synthetic aperture real-time ultrasound system (SARUS) scanner and the Onda AIMS III intensity measurement system (Onda Corporation, Sunnyvale, CA, USA). Four different sequences have been measured: a fixed focus emission, a duplex sequence containing B-mode and flow emissions, a vector flow sequence with B-mode and flow emissions in 17 directions, and finally a SA duplex flow sequence. A BK8820e (BK Medical, Herlev, Denmark) convex array probe is used for the first three sequences and a BK8670 linear array probe for the SA sequence. The method is shown to give the same intensity values within 0.24% of the AIMS III Soniq 5.0 (Onda Corporation, Sunnyvale, CA, USA) commercial intensity measurement program. The approach can measure and store data for a full imaging sequence in 3.8-8.2 s per spatial position. Based on I(spta), MI, and probe surface temperature, the method gives the ability to determine whether a sequence is within U.S. FDA limits, or alternatively indicate how to scale it to be within limits.

  7. Coronary magnetic resonance vein imaging: imaging contrast, sequence, and timing.

    Science.gov (United States)

    Nezafat, Reza; Han, Yuchi; Peters, Dana C; Herzka, Daniel A; Wylie, John V; Goddu, Beth; Kissinger, Kraig K; Yeon, Susan B; Zimetbaum, Peter J; Manning, Warren J

    2007-12-01

    Recently, there has been increased interest in imaging the coronary vein anatomy to guide interventional cardiovascular procedures such as cardiac resynchronization therapy (CRT), a device therapy for congestive heart failure (CHF). With CRT the lateral wall of the left ventricle is electrically paced using a transvenous coronary sinus lead or surgically placed epicardial lead. Proper transvenous lead placement is facilitated by the knowledge of the coronary vein anatomy. Cardiovascular MR (CMR) has the potential to image the coronary veins. In this study we propose and test CMR techniques and protocols for imaging the coronary venous anatomy. Three aspects of design of imaging sequence were studied: magnetization preparation schemes (T(2) preparation and magnetization transfer), imaging sequences (gradient-echo (GRE) and steady-state free precession (SSFP)), and imaging time during the cardiac cycle. Numerical and in vivo studies both in healthy and CHF subjects were performed to optimize and demonstrate the utility of CMR for coronary vein imaging. Magnetization transfer was superior to T(2) preparation for contrast enhancement. Both GRE and SSFP were viable imaging sequences, although GRE provided more robust results with better contrast. Imaging during the end-systolic quiescent period was preferable as it coincided with the maximum size of the coronary veins. (c) 2007 Wiley-Liss, Inc.

  8. Realise : reconstruction of reality from image sequences

    NARCIS (Netherlands)

    Leymarie, F.; de la Fortelle, A.; Koenderink, Jan J.; Kappers, A. M L; Stavridi, M.; van Ginneken, B.; Muller, S.; Krake, S.; Faugeras, O.; Robert, L.; Gauclin, C.; Laveau, S.; Zeller, C.; Anon,

    1996-01-01

    REALISE has for principal goals to extract from sequences of images, acquired with a moving camera, information necessary for determining the 3D (CAD-like) structure of a real-life scene together with information about the radiometric signatures of surfaces bounding the extracted 3D objects (e.g.

  9. Research on hyperspectral dynamic scene and image sequence simulation

    Science.gov (United States)

    Sun, Dandan; Gao, Jiaobo; Sun, Kefeng; Hu, Yu; Li, Yu; Xie, Junhu; Zhang, Lei

    2016-10-01

    This paper presents a simulation method of hyper-spectral dynamic scene and image sequence for hyper-spectral equipment evaluation and target detection algorithm. Because of high spectral resolution, strong band continuity, anti-interference and other advantages, in recent years, hyper-spectral imaging technology has been rapidly developed and is widely used in many areas such as optoelectronic target detection, military defense and remote sensing systems. Digital imaging simulation, as a crucial part of hardware in loop simulation, can be applied to testing and evaluation hyper-spectral imaging equipment with lower development cost and shorter development period. Meanwhile, visual simulation can produce a lot of original image data under various conditions for hyper-spectral image feature extraction and classification algorithm. Based on radiation physic model and material characteristic parameters this paper proposes a generation method of digital scene. By building multiple sensor models under different bands and different bandwidths, hyper-spectral scenes in visible, MWIR, LWIR band, with spectral resolution 0.01μm, 0.05μm and 0.1μm have been simulated in this paper. The final dynamic scenes have high real-time and realistic, with frequency up to 100 HZ. By means of saving all the scene gray data in the same viewpoint image sequence is obtained. The analysis results show whether in the infrared band or the visible band, the grayscale variations of simulated hyper-spectral images are consistent with the theoretical analysis results.

  10. Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy.

    Science.gov (United States)

    Chen, Shengpei; Li, Sheng; Xie, Weiwei; Li, Xuchao; Zhang, Chunlei; Jiang, Haojun; Zheng, Jing; Pan, Xiaoyu; Zheng, Hancheng; Liu, Jia Sophie; Deng, Yongqiang; Chen, Fang; Jiang, Hui

    2014-01-01

    Ultra-low coverage sequencing (ULCS) is one of the most promising strategies for sequencing based clinical application. These clinical applications, especially prenatal diagnosis, have a strict requirement of turn-around-time; therefore, the application of ULCS is restricted by current high throughput sequencing platforms. Recently, the emergence of rapid sequencing platforms, such as MiSeq and Ion Proton, brings ULCS strategy into a new era. The comparison of their performance could shed lights on their potential application in large-scale clinic trials. In this study, we performed ULCS (<0.1X coverage) on both MiSeq and Ion Proton platforms for 18 spontaneous abortion fetuses carrying aneuploidy and compared their performance on different levels. Overall basic data and GC bias showed no significant difference between these two platforms. We also found the sex and aneuploidy detection indicated 100% sensitivity and 100% specificity on both platforms. Our study generated essential data from these two rapid sequencing platforms, which provides useful reference for later research and potentially accelerates the clinical applications of ULCS.

  11. Rocuronium versus succinylcholine in air medical rapid-sequence intubation.

    Science.gov (United States)

    Hiestand, Brian; Cudnik, Michael T; Thomson, David; Werman, Howard A

    2011-01-01

    It is not known how rocuronium compares with succinylcholine in its effect on intubation success during air medical rapid-sequence intubation (RSI). To examine the impact of succinylcholine use on the odds of successful prehospital intubation. We performed a retrospective analysis of a critical care transport service administrative database containing patient encounters from 2004 to 2008. Rotor transports of patients ≥ 18 years old, requiring airway management (intubation or backup airway: laryngeal mask airway, Combitube, or cricothyrotomy), and receiving either rocuronium or succinylcholine were included in the analysis. Patients receiving both drugs were excluded. Multiple imputation was used to account for records that were missing data elements. A propensity score based on patient and encounter characteristics was calculated to control for the effect of clinical factors on the choice of drug by air medical personnel. Logistic regression was used to assess the impact of succinylcholine use on the odds of first-attempt intubation. Ordinal logistic regression was used to assess the impact of succinylcholine on the number of attempts required to intubate (1, 2, or ≥ 3 or backup airway). A total of 1,045 patients met the criteria for analysis; 761 (73%) were male, and the median age was 41 years (interquartile range 26-56). Eight hundred seventy-six (84%) were transported from the scene, and 484 (46%) received succinylcholine. Six hundred twelve (59%) were intubated on the first attempt, 322 (31%) required two attempts, 69 required three or more attempts (7%), and 42 required a backup airway (4%). After propensity score adjustment, succinylcholine was associated with a higher incidence of first-attempt intubation (odds ratio 1.4, 95% CI 1.1-1.8), as well as improved odds for requiring fewer attempts to intubate (odds ratio 1.5, 95% CI 1.2-1.9), as compared with rocuronium. Rapid-sequence intubation was more successful with fewer attempts in patients intubated

  12. An Imaging And Graphics Workstation For Image Sequence Analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-01-01

    This paper describes an application-specific engineering workstation designed and developed to analyze imagery sequences from a variety of sources. The system combines the software and hardware environment of the modern graphic-oriented workstations with the digital image acquisition, processing and display techniques. The objective is to achieve automation and high throughput for many data reduction tasks involving metric studies of image sequences. The applications of such an automated data reduction tool include analysis of the trajectory and attitude of aircraft, missile, stores and other flying objects in various flight regimes including launch and separation as well as regular flight maneuvers. The workstation can also be used in an on-line or off-line mode to study three-dimensional motion of aircraft models in simulated flight conditions such as wind tunnels. The system's key features are: 1) Acquisition and storage of image sequences by digitizing real-time video or frames from a film strip; 2) computer-controlled movie loop playback, slow motion and freeze frame display combined with digital image sharpening, noise reduction, contrast enhancement and interactive image magnification; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored image sequence; 4) automatic and manual field-of-view and spatial calibration; 5) image sequence data base generation and management, including the measurement data products; 6) off-line analysis software for trajectory plotting and statistical analysis; 7) model-based estimation and tracking of object attitude angles; and 8) interface to a variety of video players and film transport sub-systems.

  13. SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly.

    Science.gov (United States)

    Wala, Jeremiah; Beroukhim, Rameen

    2017-03-01

    We present SeqLib, a C ++ API and command line tool that provides a rapid and user-friendly interface to BAM/SAM/CRAM files, global sequence alignment operations and sequence assembly. Four C libraries perform core operations in SeqLib: HTSlib for BAM access, BWA-MEM and BLAT for sequence alignment and Fermi for error correction and sequence assembly. Benchmarking indicates that SeqLib has lower CPU and memory requirements than leading C ++ sequence analysis APIs. We demonstrate an example of how minimal SeqLib code can extract, error-correct and assemble reads from a CRAM file and then align with BWA-MEM. SeqLib also provides additional capabilities, including chromosome-aware interval queries and read plotting. Command line tools are available for performing integrated error correction, micro-assemblies and alignment. SeqLib is available on Linux and OSX for the C ++98 standard and later at github.com/walaj/SeqLib. SeqLib is released under the Apache2 license. Additional capabilities for BLAT alignment are available under the BLAT license. jwala@broadinstitue.org ; rameen@broadinstitute.org.

  14. Pediatric imaging. Rapid fire questions and answers

    Energy Technology Data Exchange (ETDEWEB)

    Quattromani, F.; Lampe, R. (eds.) [Texas Tech Univ. Health Sciences Center, School of Medicine, Lubbock, TX (United States); Handal, G.A. [Texas Tech Univ. Health Sciences Center, School of Medicine, El Paso, TX (United States)

    2008-07-01

    The book contains the following contributions: Airway, head, neck; allergy, immunology rheumatology; pediatric cardiac imaging; child abuse; chromosomal abnormalities; conscious sedation; contrast agents and radiation protection; pediatric gastrointestinal imaging; genetic disorders in infants and children; pediatric genitourinary imaging; pediatric hematology, oncology imaging; pediatric intenrventional radiology; metabolic and vitamin disorders; muscoskeletal disorders (osteoradiology); neonatology imaging; pediatric neuroimaging; imaging of the respiratory tract in infants and children; vascular anomalies.

  15. Space debris detection in optical image sequences.

    Science.gov (United States)

    Xi, Jiangbo; Wen, Desheng; Ersoy, Okan K; Yi, Hongwei; Yao, Dalei; Song, Zongxi; Xi, Shaobo

    2016-10-01

    We present a high-accuracy, low false-alarm rate, and low computational-cost methodology for removing stars and noise and detecting space debris with low signal-to-noise ratio (SNR) in optical image sequences. First, time-index filtering and bright star intensity enhancement are implemented to remove stars and noise effectively. Then, a multistage quasi-hypothesis-testing method is proposed to detect the pieces of space debris with continuous and discontinuous trajectories. For this purpose, a time-index image is defined and generated. Experimental results show that the proposed method can detect space debris effectively without any false alarms. When the SNR is higher than or equal to 1.5, the detection probability can reach 100%, and when the SNR is as low as 1.3, 1.2, and 1, it can still achieve 99%, 97%, and 85% detection probabilities, respectively. Additionally, two large sets of image sequences are tested to show that the proposed method performs stably and effectively.

  16. Development of rapid methods for relaxation time mapping and motion estimation using magnetic resonance imaging

    OpenAIRE

    Gilani, Syed Irtiza Ali

    2008-01-01

    Recent technological developments in the field of magnetic resonance imaging have resulted in advanced techniques that can reduce the total time to acquire images. For applications such as relaxation time mapping, which enables improved visualisation of in vivo structures, rapid imaging techniques are highly desirable. TAPIR is a Look- Locker-based sequence for high-resolution, multislice T1 relaxation time mapping. Despite the high accuracy and precision of TAPIR, an improveme...

  17. Disparity estimation from monocular image sequence

    Science.gov (United States)

    Zhang, Qieshi; Kamata, Sei-ichiro

    2015-02-01

    This paper proposes a novel method for estimating disparity accurately. To achieve the ideal result, an optimal adjusting framework is proposed to address the noise, occlusions, and outliners. Different from the typical multi-view stereo (MVS) methods, the proposed approach not only use the color constraint, but also use the geometric constraint associating multiple frame from the image sequence. The result shows the disparity with a good visual quality that most of the noise is eliminated, the errors in occlusion area are suppressed and the details of scene objects are preserved.

  18. A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

    Science.gov (United States)

    Hebert, Paul D N; Dewaard, Jeremy R; Zakharov, Evgeny V; Prosser, Sean W J; Sones, Jayme E; McKeown, Jaclyn T A; Mantle, Beth; La Salle, John

    2013-01-01

    DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.

  19. A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

    Directory of Open Access Journals (Sweden)

    Paul D N Hebert

    Full Text Available DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.

  20. Rapid MR spectroscopic imaging of lactate using compressed sensing

    Science.gov (United States)

    Vidya Shankar, Rohini; Agarwal, Shubhangi; Geethanath, Sairam; Kodibagkar, Vikram D.

    2015-03-01

    Imaging lactate metabolism in vivo may improve cancer targeting and therapeutics due to its key role in the development, maintenance, and metastasis of cancer. The long acquisition times associated with magnetic resonance spectroscopic imaging (MRSI), which is a useful technique for assessing metabolic concentrations, are a deterrent to its routine clinical use. The objective of this study was to combine spectral editing and prospective compressed sensing (CS) acquisitions to enable precise and high-speed imaging of the lactate resonance. A MRSI pulse sequence with two key modifications was developed: (1) spectral editing components for selective detection of lactate, and (2) a variable density sampling mask for pseudo-random under-sampling of the k-space `on the fly'. The developed sequence was tested on phantoms and in vivo in rodent models of cancer. Datasets corresponding to the 1X (fully-sampled), 2X, 3X, 4X, 5X, and 10X accelerations were acquired. The under-sampled datasets were reconstructed using a custom-built algorithm in MatlabTM, and the fidelity of the CS reconstructions was assessed in terms of the peak amplitudes, SNR, and total acquisition time. The accelerated reconstructions demonstrate a reduction in the scan time by up to 90% in vitro and up to 80% in vivo, with negligible loss of information when compared with the fully-sampled dataset. The proposed unique combination of spectral editing and CS facilitated rapid mapping of the spatial distribution of lactate at high temporal resolution. This technique could potentially be translated to the clinic for the routine assessment of lactate changes in solid tumors.

  1. Rapid SNP discovery and genetic mapping using sequenced RAD markers

    National Research Council Canada - National Science Library

    Baird, Nathan A; Etter, Paul D; Atwood, Tressa S; Currey, Mark C; Shiver, Anthony L; Lewis, Zachary A; Selker, Eric U; Cresko, William A; Johnson, Eric A

    2008-01-01

    .... Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run...

  2. Interpolation of missing data in image sequences.

    Science.gov (United States)

    Kokaram, A C; Morris, R D; Fitzgerald, W J; Rayner, P W

    1995-01-01

    This paper presents a number of model based interpolation schemes tailored to the problem of interpolating missing regions in image sequences. These missing regions may be of arbitrary size and of random, but known, location. This problem occurs regularly with archived film material. The film is abraded or obscured in patches, giving rise to bright and dark flashes, known as "dirt and sparkle" in the motion picture industry. Both 3-D autoregressive models and 3-D Markov random fields are considered in the formulation of the different reconstruction processes. The models act along motion directions estimated using a multiresolution block matching scheme. It is possible to address this sort of impulsive noise suppression problem with median filters, and comparisons with earlier work using multilevel median filters are performed. These comparisons demonstrate the higher reconstruction fidelity of the new interpolators.

  3. Rapid quantification of DNA libraries for next-generation sequencing.

    Science.gov (United States)

    Buehler, Bernd; Hogrefe, Holly H; Scott, Graham; Ravi, Harini; Pabón-Peña, Carlos; O'Brien, Scott; Formosa, Rachel; Happe, Scott

    2010-04-01

    The next-generation DNA sequencing workflows require an accurate quantification of the DNA molecules to be sequenced which assures optimal performance of the instrument. Here, we demonstrate the use of qPCR for quantification of DNA libraries used in next-generation sequencing. In addition, we find that qPCR quantification may allow improvements to current NGS workflows, including reducing the amount of library DNA required, increasing the accuracy in quantifying amplifiable DNA, and avoiding amplification bias by reducing or eliminating the need to amplify DNA before sequencing. Copyright 2010. Published by Elsevier Inc.

  4. Rapid identification of sequences for orphan enzymes to power accurate protein annotation.

    Directory of Open Access Journals (Sweden)

    Kevin R Ramkissoon

    Full Text Available The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the "back catalog" of enzymology--"orphan enzymes," those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC database alone. In this study, we demonstrate how this orphan enzyme "back catalog" is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology's "back catalog" another powerful tool to drive accurate genome annotation.

  5. Rapid Identification of Sequences for Orphan Enzymes to Power Accurate Protein Annotation

    Science.gov (United States)

    Ojha, Sunil; Watson, Douglas S.; Bomar, Martha G.; Galande, Amit K.; Shearer, Alexander G.

    2013-01-01

    The power of genome sequencing depends on the ability to understand what those genes and their proteins products actually do. The automated methods used to assign functions to putative proteins in newly sequenced organisms are limited by the size of our library of proteins with both known function and sequence. Unfortunately this library grows slowly, lagging well behind the rapid increase in novel protein sequences produced by modern genome sequencing methods. One potential source for rapidly expanding this functional library is the “back catalog” of enzymology – “orphan enzymes,” those enzymes that have been characterized and yet lack any associated sequence. There are hundreds of orphan enzymes in the Enzyme Commission (EC) database alone. In this study, we demonstrate how this orphan enzyme “back catalog” is a fertile source for rapidly advancing the state of protein annotation. Starting from three orphan enzyme samples, we applied mass-spectrometry based analysis and computational methods (including sequence similarity networks, sequence and structural alignments, and operon context analysis) to rapidly identify the specific sequence for each orphan while avoiding the most time- and labor-intensive aspects of typical sequence identifications. We then used these three new sequences to more accurately predict the catalytic function of 385 previously uncharacterized or misannotated proteins. We expect that this kind of rapid sequence identification could be efficiently applied on a larger scale to make enzymology’s “back catalog” another powerful tool to drive accurate genome annotation. PMID:24386392

  6. Microscopic imaging of slow flow and diffusion: a pulsed field gradient stimulated echo sequence combined with turbo spin echo imaging

    NARCIS (Netherlands)

    Scheenen, T.W.J.; Vergeldt, F.J.; Windt, C.W.; Jager, de P.A.; As, van H.

    2001-01-01

    In this paper we present a pulse sequence that combines a displacement-encoded stimulated echo with rapid sampling of k-space by means of turbo spin echo imaging. The stimulated echo enables the use of long observation times between the two pulsed field gradients that sample q-space completely.

  7. Rapid Multi-Locus Sequence Typing Using Microfluidic Biochips

    Science.gov (United States)

    2010-05-12

    Chlamydia (manuscript in preparation) and performed pilot studies on Staphylococcus aureus and Streptoccus pneumoniae (Data S4 and Text S2). Another potential...Found at: doi:10.1371/journal.pone.0010595.s009 (0.00 MB TXT) Text S2 mMLST sequencing of S. aureus and S. pneumoniae . Found at: doi:10.1371...provided S. aureus and S. pneumoniae strains. This publication made use of the Bacillus cereus Multi Locus Sequence Typing website (http://pubmlst.org

  8. RUCS: Rapid identification of PCR primers for unique core sequences

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik

    2017-01-01

    in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin...

  9. RUCS: rapid identification of PCR primers for unique core sequences.

    Science.gov (United States)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik; Kaya, Hülya; Lund, Ole

    2017-12-15

    Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. mcft@cbs.dtu.dk. Supplementary data are available at Bioinformatics online.

  10. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads.

    Science.gov (United States)

    Hunt, Martin; Mather, Alison E; Sánchez-Busó, Leonor; Page, Andrew J; Parkhill, Julian; Keane, Jacqueline A; Harris, Simon R

    2017-10-01

    Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customizable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods.

  11. Based on photogrammetry methodological sequence image 3D movement comparisons

    Science.gov (United States)

    Zhang, Chunsen; He, Shaojun

    2005-10-01

    The sequence image 3D movement analysis is method that estimates 3D movement parameter from 2D image sequence or 3D "image" (object side) sequence. In theory, monocular and binocular sequence image all can fulfill the three dimensions movement analyses, but there are distinctions in the complexity of computing and accuracy of computing result. In order to compare the accuracy of estimates 3D movement parameter from 2D image sequence or 3D "image" sequence, the article uses ideas of "relative orientation" and "space similitude transform" in photogrammetry for reference, presents an approach that connects the image data with real three dimensions space by making use of the result of calibration and other additional conditions to unify the computing result of monocular and binocular sequence image to object side coordinate system which origin point is one fixed point in object side, this make it possible to compare their results. The experiment results of real data, which use the method, are given.

  12. Cardiac tumors: optimal cardiac MR sequences and spectrum of imaging appearances.

    LENUS (Irish Health Repository)

    O'Donnell, David H

    2012-02-01

    OBJECTIVE: This article reviews the optimal cardiac MRI sequences for and the spectrum of imaging appearances of cardiac tumors. CONCLUSION: Recent technologic advances in cardiac MRI have resulted in the rapid acquisition of images of the heart with high spatial and temporal resolution and excellent myocardial tissue characterization. Cardiac MRI provides optimal assessment of the location, functional characteristics, and soft-tissue features of cardiac tumors, allowing accurate differentiation of benign and malignant lesions.

  13. Quality Assessment of Mapping Building Textures from Infrared Image Sequences

    Science.gov (United States)

    Hoegner, L.; Iwaszczuk, D.; Stilla, U.

    2012-07-01

    Generation and texturing of building models is a fast developing field of research. Several techniques have been developed to extract building geometry and textures from multiple images and image sequences. In this paper, these techniques are discussed and extended to automatically add new textures from infrared (IR) image sequences to existing building models. In contrast to existing work, geometry and textures are not generated together from the same dataset but the textures are extracted from the image sequence and matched to an existing geo-referenced 3D building model. The texture generation is divided in two main parts. The first part deals with the estimation and refinement of the exterior camera orientation. Feature points are extracted in the images and used as tie points in the sequence. A recorded exterior orientation of the camera s added to these homologous points and a bundle adjustment is performed starting on image pairs and combining the hole sequence. A given 3d model of the observed building is additionally added to introduce further constraint as ground control points in the bundle adjustment. The second part includes the extraction of textures from the images and the combination of textures from different images of the sequence. Using the reconstructed exterior camera orientation for every image of the sequence, the visible facades are projected into the image and texture is extracted. These textures normally contain only parts of the facade. The partial textures extracted from all images are combined to one facade texture. This texture is stored with a 3D reference to the corresponding facade. This allows searching for features in textures and localising those features in 3D space. It will be shown, that the proposed strategy allows texture extraction and mapping even for big building complexes with restricted viewing possibilities and for images with low optical resolution.

  14. Rapid imaging of free radicals in vivo using hybrid FISP field-cycled PEDRI

    Science.gov (United States)

    Youngdee, Wiwat; Lurie, David J.; Foster, Margaret A.

    2002-04-01

    A new pulse sequence for rapid imaging of free radicals is presented which combines snapshot imaging methods and conventional field-cycled proton electron double resonance imaging (FC-PEDRI). The new sequence allows the number of EPR irradiation periods to be optimized to obtain an acceptable SNR and spatial resolution of free radical distribution in the final image while reducing the RF power deposition and increasing the temporal resolution. Centric reordered phase encoding has been employed to counter the problem of rapid decay of the Overhauser-enhanced signal. A phase-correction scheme has also been used to correct problems arising from instability of the magnetic field following field-cycling. In vivo experiments were carried out using triaryl methyl free radical contrast agent, injected at a dose of 0.214 mmol kg-1 body weight in anaesthetized adult male Sprague-Dawley rats. Transaxial images through the abdomen were collected using 1, 2, 4 and 8 EPR irradiation periods. Using 4 EPR irradiation periods it was possible to generate free radical distributions of acceptable SNR and resolution. The EPR power deposition is reduced by a factor of 16 and the acquisition time is reduced by a factor of 4 compared to an acquisition using the conventional FC-PEDRI pulse sequence.

  15. Cross-utilizing hyperchaotic and DNA sequences for image encryption

    Science.gov (United States)

    Zhan, Kun; Wei, Dong; Shi, Jinhui; Yu, Jun

    2017-01-01

    The hyperchaotic sequence and the DNA sequence are utilized jointly for image encryption. A four-dimensional hyperchaotic system is used to generate a pseudorandom sequence. The main idea is to apply the hyperchaotic sequence to almost all steps of the encryption. All intensity values of an input image are converted to a serial binary digit stream, and the bitstream is scrambled globally by the hyperchaotic sequence. DNA algebraic operation and complementation are performed between the hyperchaotic sequence and the DNA sequence to obtain a robust encryption performance. The experiment results demonstrate that the encryption algorithm achieves the performance of the state-of-the-art methods in term of quality, security, and robustness against noise and cropping attack.

  16. Do the eyes scan dream images during rapid eye movement sleep? Evidence from the rapid eye movement sleep behaviour disorder model.

    Science.gov (United States)

    Leclair-Visonneau, Laurène; Oudiette, Delphine; Gaymard, Bertrand; Leu-Semenescu, Smaranda; Arnulf, Isabelle

    2010-06-01

    Rapid eye movements and complex visual dreams are salient features of human rapid eye movement sleep. However, it remains to be elucidated whether the eyes scan dream images, despite studies that have retrospectively compared the direction of rapid eye movements to the dream recall recorded after having awakened the sleeper. We used the model of rapid eye movement sleep behaviour disorder (when patients enact their dreams by persistence of muscle tone) to determine directly whether the eyes move in the same directions as the head and limbs. In 56 patients with rapid eye movement sleep behaviour disorder and 17 healthy matched controls, the eye movements were monitored by electrooculography in four (right, left, up and down) directions, calibrated with a target and synchronized with video and sleep monitoring. The rapid eye movement sleep behaviour disorder-associated behaviours occurred 2.1 times more frequently during rapid eye movement sleep with than without rapid eye movements, and more often during or after rapid eye movements than before. Rapid eye movement density, index and complexity were similar in patients with rapid eye movement sleep behaviour disorder and controls. When rapid eye movements accompanied goal-oriented motor behaviour during rapid eye movement sleep behaviour disorder (e.g. grabbing a fictive object, hand greetings, climbing a ladder), which happened in 19 sequences, 82% were directed towards the action of the patient (same plane and direction). When restricted to the determinant rapid eye movements, the concordance increased to 90%. Rapid eye movements were absent in 38-42% of behaviours. This directional coherence between limbs, head and eye movements during rapid eye movement sleep behaviour disorder suggests that, when present, rapid eye movements imitate the scanning of the dream scene. Since the rapid eye movements are similar in subjects with and without rapid eye movement sleep behaviour disorder, this concordance can be extended

  17. Rapid sequence induction and intubation with rocuronium-sugammadex compared with succinylcholine

    DEFF Research Database (Denmark)

    Sørensen, M K; Bretlau, C; Gätke, M R

    2012-01-01

    An unanticipated difficult airway may arise during rapid sequence induction and intubation (RSII). The aim of the trial was to assess how rapidly spontaneous ventilation could be re-established after RSII. We hypothesized that the time period from tracheal intubation to spontaneous ventilation...

  18. Differential conductance as a promising approach for rapid DNA sequencing with nanopore-embedded electrodes

    Science.gov (United States)

    He, Yuhui; Shao, Lubing; Scheicher, Ralph H.; Grigoriev, Anton; Ahuja, Rajeev; Long, Shibing; Ji, Zhuoyu; Yu, Zhaoan; Liu, Ming

    2010-07-01

    We propose an approach for nanopore-based DNA sequencing using characteristic transverse differential conductance. Molecular dynamics and electron transport simulations show that the transverse differential conductance during the translocation of DNA through the nanopore is distinguishable enough for the detection of the base sequence and can withstand electrical noise caused by DNA structure fluctuation. Our findings demonstrate several advantages of the transverse conductance approach, which may lead to important applications in rapid genome sequencing.

  19. Rapid eye movement sleep behavior disorder in Parkinson's disease: magnetic resonance imaging study.

    Science.gov (United States)

    Ford, Andrew H; Duncan, Gordon W; Firbank, Michael J; Yarnall, Alison J; Khoo, Tien K; Burn, David J; O'Brien, John T

    2013-06-01

    Rapid eye movement sleep behavior disorder has poor prognostic implications for Parkinson's disease. The authors recruited 124 patients with early Parkinson's disease to compare clinical and neuroimaging findings based on the presence of this sleep disorder. The presence of rapid eye movement sleep behavior disorder was assessed with the Mayo Sleep Questionnaire. Magnetic resonance imaging sequences were obtained for voxel-based morphometry and diffusion tensor imaging. Patients with sleep disorder had more advanced disease, but groups had similar clinical characteristics and cognitive performance. Those with sleep disorder had areas of reduced cortical grey matter volume and white matter changes compared with those who did not have sleep disorder. However, differences were slight and were not significant when the analyses were adjusted for multiple comparisons. Rapid eye movement sleep behavior disorder was associated with subtle changes in white matter integrity and grey matter volume in patients with early Parkinson's disease. Copyright © 2013 Movement Disorder Society.

  20. Fast Registration of Terrestrial LIDAR Point Cloud and Sequence Images

    Science.gov (United States)

    Shao, J.; Zhang, W.; Zhu, Y.; Shen, A.

    2017-09-01

    Image has rich color information, and it can help to promote recognition and classification of point cloud. The registration is an important step in the application of image and point cloud. In order to give the rich texture and color information for LiDAR point cloud, the paper researched a fast registration method of point cloud and sequence images based on the ground-based LiDAR system. First, calculating transformation matrix of one of sequence images based on 2D image and LiDAR point cloud; second, using the relationships of position and attitude information among multi-angle sequence images to calculate all transformation matrixes in the horizontal direction; last, completing the registration of point cloud and sequence images based on the collinear condition of image point, projective center and LiDAR point. The experimental results show that the method is simple and fast, and the stitching error between adjacent images is litter; meanwhile, the overall registration accuracy is high, and the method can be used in engineering application.

  1. Infrared thermal facial image sequence registration analysis and verification

    Science.gov (United States)

    Chen, Chieh-Li; Jian, Bo-Lin

    2015-03-01

    To study the emotional responses of subjects to the International Affective Picture System (IAPS), infrared thermal facial image sequence is preprocessed for registration before further analysis such that the variance caused by minor and irregular subject movements is reduced. Without affecting the comfort level and inducing minimal harm, this study proposes an infrared thermal facial image sequence registration process that will reduce the deviations caused by the unconscious head shaking of the subjects. A fixed image for registration is produced through the localization of the centroid of the eye region as well as image translation and rotation processes. Thermal image sequencing will then be automatically registered using the two-stage genetic algorithm proposed. The deviation before and after image registration will be demonstrated by image quality indices. The results show that the infrared thermal image sequence registration process proposed in this study is effective in localizing facial images accurately, which will be beneficial to the correlation analysis of psychological information related to the facial area.

  2. Pulseq: A rapid and hardware-independent pulse sequence prototyping framework.

    Science.gov (United States)

    Layton, Kelvin J; Kroboth, Stefan; Jia, Feng; Littin, Sebastian; Yu, Huijun; Leupold, Jochen; Nielsen, Jon-Fredrik; Stöcker, Tony; Zaitsev, Maxim

    2017-04-01

    Implementing new magnetic resonance experiments, or sequences, often involves extensive programming on vendor-specific platforms, which can be time consuming and costly. This situation is exacerbated when research sequences need to be implemented on several platforms simultaneously, for example, at different field strengths. This work presents an alternative programming environment that is hardware-independent, open-source, and promotes rapid sequence prototyping. A novel file format is described to efficiently store the hardware events and timing information required for an MR pulse sequence. Platform-dependent interpreter modules convert the file to appropriate instructions to run the sequence on MR hardware. Sequences can be designed in high-level languages, such as MATLAB, or with a graphical interface. Spin physics simulation tools are incorporated into the framework, allowing for comparison between real and virtual experiments. Minimal effort is required to implement relatively advanced sequences using the tools provided. Sequences are executed on three different MR platforms, demonstrating the flexibility of the approach. A high-level, flexible and hardware-independent approach to sequence programming is ideal for the rapid development of new sequences. The framework is currently not suitable for large patient studies or routine scanning although this would be possible with deeper integration into existing workflows. Magn Reson Med 77:1544-1552, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  3. An efficient image cryptosystem based on wolfram sequence and RNS

    African Journals Online (AJOL)

    In this paper we propose a novel encryption algorithm for digital images using the moduli set {2n+2, 2n+1, 2n}. The technique uses the Wolfram sequence for resizing, bitwise-XOR for pixel scrambling and modulus operation for pixel encoding. In the proposed scheme, a digital image is first segmented into many parts.

  4. Estimation of visual motion in image sequences

    DEFF Research Database (Denmark)

    Larsen, Rasmus

    1994-01-01

    are given. In particular we have investigated the use of smoothness of the second order derivatives, and the use of edge model and prior destributions for the field that favor discontinuities to characterize the motion field. A succesful implementation of a temporal interpolation in a sequence of weather...... of motion under an assumption of translatory motion has been considered. Furthermore we have described methods for quantifying the directional certainty with which we have measured the local displacement. A method based on local estimation of the spatio temporal orientation is generalized to give...

  5. Image-based temporal alignment of echocardiographic sequences

    Science.gov (United States)

    Danudibroto, Adriyana; Bersvendsen, Jørn; Mirea, Oana; Gerard, Olivier; D'hooge, Jan; Samset, Eigil

    2016-04-01

    Temporal alignment of echocardiographic sequences enables fair comparisons of multiple cardiac sequences by showing corresponding frames at given time points in the cardiac cycle. It is also essential for spatial registration of echo volumes where several acquisitions are combined for enhancement of image quality or forming larger field of view. In this study, three different image-based temporal alignment methods were investigated. First, a method based on dynamic time warping (DTW). Second, a spline-based method that optimized the similarity between temporal characteristic curves of the cardiac cycle using 1D cubic B-spline interpolation. Third, a method based on the spline-based method with piecewise modification. These methods were tested on in-vivo data sets of 19 echo sequences. For each sequence, the mitral valve opening (MVO) time was manually annotated. The results showed that the average MVO timing error for all methods are well under the time resolution of the sequences.

  6. Shuffled magnetization-prepared multicontrast rapid gradient-echo imaging.

    Science.gov (United States)

    Cao, Peng; Zhu, Xucheng; Tang, Shuyu; Leynes, Andrew; Jakary, Angela; Larson, Peder E Z

    2018-01-01

    To develop a novel acquisition and reconstruction method for magnetization-prepared 3-dimensional multicontrast rapid gradient-echo imaging, using Hankel matrix completion in combination with compressed sensing and parallel imaging. A random k-space shuffling strategy was implemented in simulation and in vivo human experiments at 7 T for 3-dimensional inversion recovery, T2 /diffusion preparation, and magnetization transfer imaging. We combined compressed sensing, based on total variation and spatial-temporal low-rank regularizations, and parallel imaging with pixel-wise Hankel matrix completion, allowing the reconstruction of tens of multicontrast 3-dimensional images from 3- or 6-min scans. The simulation result showed that the proposed method can reconstruct signal-recovery curves in each voxel and was robust for typical in vivo signal-to-noise ratio with 16-times acceleration. In vivo studies achieved 4 to 24 times accelerations for inversion recovery, T2 /diffusion preparation, and magnetization transfer imaging. Furthermore, the contrast was improved by resolving pixel-wise signal-recovery curves after magnetization preparation. The proposed method can improve acquisition efficiencies for magnetization-prepared MRI and tens of multicontrast 3-dimensional images could be recovered from a single scan. Furthermore, it was robust against noise, applicable for recovering multi-exponential signals, and did not require any previous knowledge of model parameters. Magn Reson Med 79:62-70, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  7. Carbon nanotube-based lateral flow biosensor for sensitive and rapid detection of DNA sequence.

    Science.gov (United States)

    Qiu, Wanwei; Xu, Hui; Takalkar, Sunitha; Gurung, Anant S; Liu, Bin; Zheng, Yafeng; Guo, Zebin; Baloda, Meenu; Baryeh, Kwaku; Liu, Guodong

    2015-02-15

    In this article, we describe a carbon nanotube (CNT)-based lateral flow biosensor (LFB) for rapid and sensitive detection of DNA sequence. Amine-modified DNA detection probe was covalently immobilized on the shortened multi-walled carbon nanotubes (MWCNTs) via diimide-activated amidation between the carboxyl groups on the CNT surface and amine groups on the detection DNA probes. Sandwich-type DNA hybridization reactions were performed on the LFB and the captured MWCNTs on test zone and control zone of LFB produced the characteristic black bands, enabling visual detection of DNA sequences. Combining the advantages of lateral flow chromatographic separation with unique physical properties of MWCNT (large surface area), the optimized LFB was capable of detecting of 0.1 nM target DNA without instrumentation. Quantitative detection could be realized by recording the intensity of the test line with the Image J software, and the detection limit of 40 pM was obtained. This detection limit is 12.5 times lower than that of gold nanoparticle (GNP)-based LFB (0.5 nM, Mao et al. Anal. Chem. 2009, 81, 1660-1668). Another important feature is that the preparation of MWCNT-DNA conjugates was robust and the use of MWCNT labels avoided the aggregation of conjugates and tedious preparation time, which were often met in the traditional GNP-based nucleic acid LFB. The applications of MWCNT-based LFB can be extended to visually detect protein biomarkers using MWCNT-antibody conjugates. The MWCNT-based LFB thus open a new door to prepare a new generation of LFB, and shows great promise for in-field and point-of-care diagnosis of genetic diseases and for the detection of infectious agents. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches

    OpenAIRE

    Rognes, Torbjørn

    2001-01-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of th...

  9. Image sequence analysis workstation for multipoint motion analysis

    Science.gov (United States)

    Mostafavi, Hassan

    1990-08-01

    This paper describes an application-specific engineering workstation designed and developed to analyze motion of objects from video sequences. The system combines the software and hardware environment of a modem graphic-oriented workstation with the digital image acquisition, processing and display techniques. In addition to automation and Increase In throughput of data reduction tasks, the objective of the system Is to provide less invasive methods of measurement by offering the ability to track objects that are more complex than reflective markers. Grey level Image processing and spatial/temporal adaptation of the processing parameters is used for location and tracking of more complex features of objects under uncontrolled lighting and background conditions. The applications of such an automated and noninvasive measurement tool include analysis of the trajectory and attitude of rigid bodies such as human limbs, robots, aircraft in flight, etc. The system's key features are: 1) Acquisition and storage of Image sequences by digitizing and storing real-time video; 2) computer-controlled movie loop playback, freeze frame display, and digital Image enhancement; 3) multiple leading edge tracking in addition to object centroids at up to 60 fields per second from both live input video or a stored Image sequence; 4) model-based estimation and tracking of the six degrees of freedom of a rigid body: 5) field-of-view and spatial calibration: 6) Image sequence and measurement data base management; and 7) offline analysis software for trajectory plotting and statistical analysis.

  10. Rapid whole genome sequencing for the detection and characterization of microorganisms directly from clinical samples

    DEFF Research Database (Denmark)

    Hasman, Henrik; Saputra, Dhany; Sicheritz-Pontén, Thomas

    2014-01-01

    Whole genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples this could further reduce diagnostic time and thereby improve control and treatment. A major bottle-neck is the availability of fast and reliable bioinformatics...... microbiology, WGS of isolated bacteria and by directly sequencing on pellets from the urine. A rapid method for analyzing the sequence data was developed. Bacteria were cultivated from 19 samples, but only in pure culture from 17. WGS improved the identification of the cultivated bacteria and almost complete...

  11. Extracting flat-field images from scene-based image sequences using phase correlation

    Energy Technology Data Exchange (ETDEWEB)

    Caron, James N., E-mail: Caron@RSImd.com [Research Support Instruments, 4325-B Forbes Boulevard, Lanham, Maryland 20706 (United States); Montes, Marcos J. [Naval Research Laboratory, Code 7231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States); Obermark, Jerome L. [Naval Research Laboratory, Code 8231, 4555 Overlook Avenue, SW, Washington, DC 20375 (United States)

    2016-06-15

    Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

  12. Extracting flat-field images from scene-based image sequences using phase correlation.

    Science.gov (United States)

    Caron, James N; Montes, Marcos J; Obermark, Jerome L

    2016-06-01

    Flat-field image processing is an essential step in producing high-quality and radiometrically calibrated images. Flat-fielding corrects for variations in the gain of focal plane array electronics and unequal illumination from the system optics. Typically, a flat-field image is captured by imaging a radiometrically uniform surface. The flat-field image is normalized and removed from the images. There are circumstances, such as with remote sensing, where a flat-field image cannot be acquired in this manner. For these cases, we developed a phase-correlation method that allows the extraction of an effective flat-field image from a sequence of scene-based displaced images. The method uses sub-pixel phase correlation image registration to align the sequence to estimate the static scene. The scene is removed from sequence producing a sequence of misaligned flat-field images. An average flat-field image is derived from the realigned flat-field sequence.

  13. Functional Brain Activation Differences in Stuttering Identified with a Rapid fMRI Sequence

    Science.gov (United States)

    Loucks, Torrey; Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

    2011-01-01

    The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech…

  14. Direct typing of Canine parvovirus (CPV) from infected dog faeces by rapid mini sequencing technique.

    Science.gov (United States)

    V, Pavana Jyothi; S, Akila; Selvan, Malini K; Naidu, Hariprasad; Raghunathan, Shwethaa; Kota, Sathish; Sundaram, R C Raja; Rana, Samir Kumar; Raj, G Dhinakar; Srinivasan, V A; Mohana Subramanian, B

    2016-12-01

    Canine parvovirus (CPV) is a non-enveloped single stranded DNA virus with an icosahedral capsid. Mini-sequencing based CPV typing was developed earlier to detect and differentiate all the CPV types and FPV in a single reaction. This technique was further evaluated in the present study by performing the mini-sequencing directly from fecal samples which avoided tedious virus isolation steps by cell culture system. Fecal swab samples were collected from 84 dogs with enteritis symptoms, suggestive of parvoviral infection from different locations across India. Seventy six of these samples were positive by PCR; the subsequent mini-sequencing reaction typed 74 of them as type 2a virus, and 2 samples as type 2b. Additionally, 25 of the positive samples were typed by cycle sequencing of PCR products. Direct CPV typing from fecal samples using mini-sequencing showed 100% correlation with CPV typing by cycle sequencing. Moreover, CPV typing was achieved by mini-sequencing even with faintly positive PCR amplicons which was not possible by cycle sequencing. Therefore, the mini-sequencing technique is recommended for regular epidemiological follow up of CPV types, since the technique is rapid, highly sensitive and high capacity method for CPV typing. Copyright © 2016. Published by Elsevier B.V.

  15. Rapid prototyping of biomimetic vascular phantoms for hyperspectral reflectance imaging.

    Science.gov (United States)

    Ghassemi, Pejhman; Wang, Jianting; Melchiorri, Anthony J; Ramella-Roman, Jessica C; Mathews, Scott A; Coburn, James C; Sorg, Brian S; Chen, Yu; Pfefer, T Joshua

    2015-01-01

    The emerging technique of rapid prototyping with three-dimensional (3-D) printers provides a simple yet revolutionary method for fabricating objects with arbitrary geometry. The use of 3-D printing for generating morphologically biomimetic tissue phantoms based on medical images represents a potentially major advance over existing phantom approaches. Toward the goal of image-defined phantoms, we converted a segmented fundus image of the human retina into a matrix format and edited it to achieve a geometry suitable for printing. Phantoms with vessel-simulating channels were then printed using a photoreactive resin providing biologically relevant turbidity, as determined by spectrophotometry. The morphology of printed vessels was validated by x-ray microcomputed tomography. Channels were filled with hemoglobin (Hb) solutions undergoing desaturation, and phantoms were imaged with a near-infrared hyperspectral reflectance imaging system. Additionally, a phantom was printed incorporating two disjoint vascular networks at different depths, each filled with Hb solutions at different saturation levels. Light propagation effects noted during these measurements—including the influence of vessel density and depth on Hb concentration and saturation estimates, and the effect of wavelength on vessel visualization depth—were evaluated. Overall, our findings indicated that 3-D-printed biomimetic phantoms hold significant potential as realistic and practical tools for elucidating light–tissue interactions and characterizing biophotonic system performance.

  16. Adaptive Robotic Welding Using A Rapid Image Pre-Processor

    Science.gov (United States)

    Dufour, M.; Begin, G.

    1984-02-01

    The rapid pre-processor initially developed by NRCC and Leigh Instruments Inc. as part of the visual aid system of the space shuttle arm 1 has been adapted to perform real time seam tracking of multipass butt weld and other adaptive welding functions. The weld preparation profile is first enhanced by a projected laser target formed by a line and dots. A standard TV camera is used to observe the target image at an angle. Displacement and distorsion of the target image on a monitor are simple functions of the preparation surface distance and shape respectively. Using the video signal, the pre-processor computes in real time the area and first moments of the white level figure contained within four independent rectangular windows in the field of view of the camera. The shape, size, and position of each window can be changed dynamically for each successive image at the standard 30 images/sec rate, in order to track some target image singularities. Visual sensing and welding are done simultaneously. As an example, it is shown that thin sheet metal welding can be automated using a single window for seam tracking, gap width measurement and torch height estimation. Using a second window, measurement of sheet misalignment and their orientation in space were also achieved. The system can be used at welding speed of up to 1 m/min. Simplicity, speed and effectiveness are the main advantages of this system.

  17. Visual Perceptual Echo Reflects Learning of Regularities in Rapid Luminance Sequences.

    Science.gov (United States)

    Chang, Acer Y-C; Schwartzman, David J; VanRullen, Rufin; Kanai, Ryota; Seth, Anil K

    2017-08-30

    A novel neural signature of active visual processing has recently been described in the form of the "perceptual echo", in which the cross-correlation between a sequence of randomly fluctuating luminance values and occipital electrophysiological signals exhibits a long-lasting periodic (∼100 ms cycle) reverberation of the input stimulus (VanRullen and Macdonald, 2012). As yet, however, the mechanisms underlying the perceptual echo and its function remain unknown. Reasoning that natural visual signals often contain temporally predictable, though nonperiodic features, we hypothesized that the perceptual echo may reflect a periodic process associated with regularity learning. To test this hypothesis, we presented subjects with successive repetitions of a rapid nonperiodic luminance sequence, and examined the effects on the perceptual echo, finding that echo amplitude linearly increased with the number of presentations of a given luminance sequence. These data suggest that the perceptual echo reflects a neural signature of regularity learning.Furthermore, when a set of repeated sequences was followed by a sequence with inverted luminance polarities, the echo amplitude decreased to the same level evoked by a novel stimulus sequence. Crucially, when the original stimulus sequence was re-presented, the echo amplitude returned to a level consistent with the number of presentations of this sequence, indicating that the visual system retained sequence-specific information, for many seconds, even in the presence of intervening visual input. Altogether, our results reveal a previously undiscovered regularity learning mechanism within the human visual system, reflected by the perceptual echo.SIGNIFICANCE STATEMENT How the brain encodes and learns fast-changing but nonperiodic visual input remains unknown, even though such visual input characterizes natural scenes. We investigated whether the phenomenon of "perceptual echo" might index such learning. The perceptual echo is a

  18. wzi Gene Sequencing, a Rapid Method for Determination of Capsular Type for Klebsiella Strains

    Science.gov (United States)

    Passet, Virginie; Haugaard, Anita Björk; Babosan, Anamaria; Kassis-Chikhani, Najiby; Struve, Carsten; Decré, Dominique

    2013-01-01

    Pathogens of the genus Klebsiella have been classified into distinct capsular (K) types for nearly a century. K typing of Klebsiella species still has important applications in epidemiology and clinical microbiology, but the serological method has strong practical limitations. Our objective was to evaluate the sequencing of wzi, a gene conserved in all capsular types of Klebsiella pneumoniae that codes for an outer membrane protein involved in capsule attachment to the cell surface, as a simple and rapid method for the prediction of K type. The sequencing of a 447-nucleotide region of wzi distinguished the K-type reference strains with only nine exceptions. A reference wzi sequence database was created by the inclusion of multiple strains representing K types associated with high virulence and multidrug resistance. A collection of 119 prospective clinical isolates of K. pneumoniae were then analyzed in parallel by wzi sequencing and classical K typing. Whereas K typing achieved typeability for 81% and discrimination for 94.4% of the isolates, these figures were 98.1% and 98.3%, respectively, for wzi sequencing. The prediction of K type once the wzi allele was known was 94%. wzi sequencing is a rapid and simple method for the determination of the K types of most K. pneumoniae clinical isolates. PMID:24088853

  19. Face reconstruction from image sequences for forensic face comparison

    NARCIS (Netherlands)

    van Dam, C.; Veldhuis, Raymond N.J.; Spreeuwers, Lieuwe Jan

    2016-01-01

    The authors explore the possibilities of a dense model-free three-dimensional (3D) face reconstruction method, based on image sequences from a single camera, to improve the current state of forensic face comparison. They propose a new model-free 3D reconstruction method for faces, based on the

  20. Safety Assessment of Advanced Imaging Sequences II: Simulations

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt

    2016-01-01

    An automatic approach for simulating the emitted pressure, intensity, and MI of advanced ultrasound imaging sequences is presented. It is based on a linear simulation of pressure fields using Field II, and it is hypothesized that linear simulation can attain the needed accuracy for predicting Mec...

  1. Finding trajectories of feature points in a monocular image sequence.

    Science.gov (United States)

    Sethi, I K; Jain, R

    1987-01-01

    Identifying the same physical point in more than one image, the correspondence problem, is vital in motion analysis. Most research for establishing correspondence uses only two frames of a sequence to solve this problem. By using a sequence of frames, it is possible to exploit the fact that due to inertia the motion of an object cannot change instantaneously. By using smoothness of motion, it is possible to solve the correspondence problem for arbitrary motion of several nonrigid objects in a scene. We formulate the correspondence problem as an optimization problem and propose an iterative algorithm to find trajectories of points in a monocular image sequence. A modified form of this algorithm is useful in case of occlusion also. We demonstrate the efficacy of this approach considering synthetic, laboratory, and real scenes.

  2. Functional brain activation differences in stuttering identified with a rapid fMRI sequence

    Science.gov (United States)

    Kraft, Shelly Jo; Choo, Ai Leen; Sharma, Harish; Ambrose, Nicoline G.

    2011-01-01

    The purpose of this study was to investigate whether brain activity related to the presence of stuttering can be identified with rapid functional MRI (fMRI) sequences that involved overt and covert speech processing tasks. The long-term goal is to develop sensitive fMRI approaches with developmentally appropriate tasks to identify deviant speech motor and auditory brain activity in children who stutter closer to the age at which recovery from stuttering is documented. Rapid sequences may be preferred for individuals or populations who do not tolerate long scanning sessions. In this report, we document the application of a picture naming and phoneme monitoring task in three minute fMRI sequences with adults who stutter (AWS). If relevant brain differences are found in AWS with these approaches that conform to previous reports, then these approaches can be extended to younger populations. Pairwise contrasts of brain BOLD activity between AWS and normally fluent adults indicated the AWS showed higher BOLD activity in the right inferior frontal gyrus (IFG), right temporal lobe and sensorimotor cortices during picture naming and and higher activity in the right IFG during phoneme monitoring. The right lateralized pattern of BOLD activity together with higher activity in sensorimotor cortices is consistent with previous reports, which indicates rapid fMRI sequences can be considered for investigating stuttering in younger participants. PMID:22133409

  3. Congruence analysis of point clouds from unstable stereo image sequences

    Directory of Open Access Journals (Sweden)

    C. Jepping

    2014-06-01

    Full Text Available This paper deals with the correction of exterior orientation parameters of stereo image sequences over deformed free-form surfaces without control points. Such imaging situation can occur, for example, during photogrammetric car crash test recordings where onboard high-speed stereo cameras are used to measure 3D surfaces. As a result of such measurements 3D point clouds of deformed surfaces are generated for a complete stereo sequence. The first objective of this research focusses on the development and investigation of methods for the detection of corresponding spatial and temporal tie points within the stereo image sequences (by stereo image matching and 3D point tracking that are robust enough for a reliable handling of occlusions and other disturbances that may occur. The second objective of this research is the analysis of object deformations in order to detect stable areas (congruence analysis. For this purpose a RANSAC-based method for congruence analysis has been developed. This process is based on the sequential transformation of randomly selected point groups from one epoch to another by using a 3D similarity transformation. The paper gives a detailed description of the congruence analysis. The approach has been tested successfully on synthetic and real image data.

  4. Optical flow estimation on image sequences with differently exposed frames

    Science.gov (United States)

    Bengtsson, Tomas; McKelvey, Tomas; Lindström, Konstantin

    2015-09-01

    Optical flow (OF) methods are used to estimate dense motion information between consecutive frames in image sequences. In addition to the specific OF estimation method itself, the quality of the input image sequence is of crucial importance to the quality of the resulting flow estimates. For instance, lack of texture in image frames caused by saturation of the camera sensor during exposure can significantly deteriorate the performance. An approach to avoid this negative effect is to use different camera settings when capturing the individual frames. We provide a framework for OF estimation on such sequences that contain differently exposed frames. Information from multiple frames are combined into a total cost functional such that the lack of an active data term for saturated image areas is avoided. Experimental results demonstrate that using alternate camera settings to capture the full dynamic range of an underlying scene can clearly improve the quality of flow estimates. When saturation of image data is significant, the proposed methods show superior performance in terms of lower endpoint errors of the flow vectors compared to a set of baseline methods. Furthermore, we provide some qualitative examples of how and when our method should be used.

  5. Innovative anisotropic phantoms for calibration of diffusion tensor imaging sequences.

    Science.gov (United States)

    Kłodowski, Krzysztof; Krzyżak, Artur Tadeusz

    2016-05-01

    The paper describes a novel type of anisotropic phantoms designed for b-matrix spatial distribution diffusion tensor imaging (BSD-DTI). Cubic plate anisotropic phantom, cylinder capillary phantom and water reference phantom are described as a complete set necessary for calibration, validation and normalization of BSD-DTI. An innovative design of the phantoms basing on enclosing the anisotropic cores in glass balls filled with liquid made for the first time possible BSD calibration with usage of echo planar imaging (EPI) sequence. Susceptibility artifacts prone to occur in EPI sequences were visibly reduced in the central region of the phantoms. The phantoms were designed for usage in a clinical scanner's head coil, but can be scaled for other coil or scanner types. The phantoms can be also used for a pre-calibration of imaging of other types of phantoms having more specific applications. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Sequences for real-time magnetic particle imaging

    Directory of Open Access Journals (Sweden)

    Weber Matthias

    2015-09-01

    Full Text Available Magnetic Particle Imaging (MPI is a new imaging modality with the potential to be a new medical tool for angiographic diagnostics. It is capable of visualizing the spatial distribution of super-paramagnetic nanoparticles in high temporal and spatial resolution. Furthermore, the new spatial encoding scheme of a field free line (FFL promises a ten-fold higher sensitivity. So far, all know imaging devices featuring this new technique feature slow data acquisition and thus, are far away from real-time imaging capability. An actual real-time approach requires a complex field generator and an application of currents with very precise amplitude and phase. Here, we present the first implementation and calibration of a dynamic FFL field sequence enabling the acquisition of 50 MPI images per second in a mouse sized scanner.

  7. Rapid and accurate identification of microorganisms contaminating cosmetic products based on DNA sequence homology.

    Science.gov (United States)

    Fujita, Y; Shibayama, H; Suzuki, Y; Karita, S; Takamatsu, S

    2005-12-01

    The aim of this study was to develop rapid and accurate procedures to identify microorganisms contaminating cosmetic products, based on the identity of the nucleotide sequences of the internal transcribed spacer (ITS) region of the ribosomal RNA coding DNA (rDNA). Five types of microorganisms were isolated from the inner portion of lotion bottle caps, skin care lotions, and cleansing gels. The rDNA ITS region of microorganisms was amplified through the use of colony-direct PCR or ordinal PCR using DNA extracts as templates. The nucleotide sequences of the amplified DNA were determined and subjected to homology search of a publicly available DNA database. Thereby, we obtained DNA sequences possessing high similarity with the query sequences from the databases of all the five organisms analyzed. The traditional identification procedure requires expert skills, and a time period of approximately 1 month to identify the microorganisms. On the contrary, 3-7 days were sufficient to complete all the procedures employed in the current method, including isolation and cultivation of organisms, DNA sequencing, and the database homology search. Moreover, it was possible to develop the skills necessary to perform the molecular techniques required for the identification procedures within 1 week. Consequently, the current method is useful for rapid and accurate identification of microorganisms, contaminating cosmetics.

  8. Scheduling algorithms for rapid imaging using agile Cubesat constellations

    Science.gov (United States)

    Nag, Sreeja; Li, Alan S.; Merrick, James H.

    2018-02-01

    Distributed Space Missions such as formation flight and constellations, are being recognized as important Earth Observation solutions to increase measurement samples over space and time. Cubesats are increasing in size (27U, ∼40 kg in development) with increasing capabilities to host imager payloads. Given the precise attitude control systems emerging in the commercial market, Cubesats now have the ability to slew and capture images within short notice. We propose a modular framework that combines orbital mechanics, attitude control and scheduling optimization to plan the time-varying, full-body orientation of agile Cubesats in a constellation such that they maximize the number of observed images and observation time, within the constraints of Cubesat hardware specifications. The attitude control strategy combines bang-bang and PD control, with constraints such as power consumption, response time, and stability factored into the optimality computations and a possible extension to PID control to account for disturbances. Schedule optimization is performed using dynamic programming with two levels of heuristics, verified and improved upon using mixed integer linear programming. The automated scheduler is expected to run on ground station resources and the resultant schedules uplinked to the satellites for execution, however it can be adapted for onboard scheduling, contingent on Cubesat hardware and software upgrades. The framework is generalizable over small steerable spacecraft, sensor specifications, imaging objectives and regions of interest, and is demonstrated using multiple 20 kg satellites in Low Earth Orbit for two case studies - rapid imaging of Landsat's land and coastal images and extended imaging of global, warm water coral reefs. The proposed algorithm captures up to 161% more Landsat images than nadir-pointing sensors with the same field of view, on a 2-satellite constellation over a 12-h simulation. Integer programming was able to verify that

  9. Radar image sequence analysis of inhomogeneous water surfaces

    Science.gov (United States)

    Seemann, Joerg; Senet, Christian M.; Dankert, Heiko; Hatten, Helge; Ziemer, Friedwart

    1999-10-01

    The radar backscatter from the ocean surface, called sea clutter, is modulated by the surface wave field. A method was developed to estimate the near-surface current, the water depth and calibrated surface wave spectra from nautical radar image sequences. The algorithm is based on the three- dimensional Fast Fourier Transformation (FFT) of the spatio- temporal sea clutter pattern in the wavenumber-frequency domain. The dispersion relation is used to define a filter to separate the spectral signal of the imaged waves from the background noise component caused by speckle noise. The signal-to-noise ratio (SNR) contains information about the significant wave height. The method has been proved to be reliable for the analysis of homogeneous water surfaces in offshore installations. Radar images are inhomogeneous because of the dependency of the image transfer function (ITF) on the azimuth angle between the wave propagation and the antenna viewing direction. The inhomogeneity of radar imaging is analyzed using image sequences of a homogeneous deep-water surface sampled by a ship-borne radar. Changing water depths in shallow-water regions induce horizontal gradients of the tidal current. Wave refraction occurs due to the spatial variability of the current and water depth. These areas cannot be investigated with the standard method. A new method, based on local wavenumber estimation with the multiple-signal classification (MUSIC) algorithm, is outlined. The MUSIC algorithm provides superior wavenumber resolution on local spatial scales. First results, retrieved from a radar image sequence taken from an installation at a coastal site, are presented.

  10. Investigating the Feasibility of Rapid MRI for Image-Guided Motion Management in Lung Cancer Radiotherapy

    Directory of Open Access Journals (Sweden)

    Amit Sawant

    2014-01-01

    Full Text Available Cycle-to-cycle variations in respiratory motion can cause significant geometric and dosimetric errors in the administration of lung cancer radiation therapy. A common limitation of the current strategies for motion management is that they assume a constant, reproducible respiratory cycle. In this work, we investigate the feasibility of using rapid MRI for providing long-term imaging of the thorax in order to better capture cycle-to-cycle variations. Two nonsmall-cell lung cancer patients were imaged (free-breathing, no extrinsic contrast, and 1.5 T scanner. A balanced steady-state-free-precession (b-SSFP sequence was used to acquire cine-2D and cine-3D (4D images. In the case of Patient 1 (right midlobe lesion, ~40 mm diameter, tumor motion was well correlated with diaphragmatic motion. In the case of Patient 2, (left upper-lobe lesion, ~60 mm diameter, tumor motion was poorly correlated with diaphragmatic motion. Furthermore, the motion of the tumor centroid was poorly correlated with the motion of individual points on the tumor boundary, indicating significant rotation and/or deformation. These studies indicate that image quality and acquisition speed of cine-2D MRI were adequate for motion monitoring. However, significant improvements are required to achieve comparable speeds for truly 4D MRI. Despite several challenges, rapid MRI offers a feasible and attractive tool for noninvasive, long-term motion monitoring.

  11. Student paramedic rapid sequence intubation in Johannesburg, South Africa: A case series

    Directory of Open Access Journals (Sweden)

    Christopher Stein

    2017-06-01

    Discussion: Students demonstrated a good intubation success and first pass-success rate. However, newly qualified paramedics require strict protocols, clinical governance, and support to gain experience and perform pre-hospital rapid sequence intubation at an acceptable level in operational practice. More research is needed to understand the low rate of post-intubation paralysis, along with non-uniform administration of post-intubation sedation and analgesia, and the 5% prevalence of cardiac arrest.

  12. Rapid evaluation and quality control of next generation sequencing data with FaQCs.

    Science.gov (United States)

    Lo, Chien-Chi; Chain, Patrick S G

    2014-11-19

    Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform's sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects. Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics. FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

  13. Normal Evoked Response to Rapid Sequences of Tactile Pulses in Autism Spectrum Disorders

    Directory of Open Access Journals (Sweden)

    Santosh Ganesan

    2016-09-01

    Full Text Available Autism spectrum disorder (ASD is a developmental disorder diagnosed behaviorally, with many documented neurophysiological abnormalities in cortical response properties. While abnormal sensory processing is not considered core to the disorder, most ASD individuals report sensory processing abnormalities. Yet, the neurophysiological correlates of these abnormalities have not been fully mapped. In the auditory domain, studies have shown that cortical responses in the early auditory cortex in ASD are abnormal in multiple ways. In particular, it has been shown that individuals with ASD who were also language impaired, have abnormal cortical auditory evoked responses to rapid, but not slow, sequences of tones. Here, we tested the somatosensory domain in ASD for abnormalities in rapid processing of tactile pulses, to determine whether abnormalities there parallel those observed in the auditory domain. Specifically, we tested the somatosensory cortex response to a sequence of two tactile pulses with different (short and long temporal separation. We analyzed the responses in cortical space, in primary somatosensory cortex. As expected, we found no group difference in the evoked response to pulses with long temporal separation. Contrary to findings in the auditory domain and to our hypothesis, we also found no group differences in the evoked responses to the sequence with a short temporal separation. These results suggest that rapid temporal processing deficits in ASD are not generalized across multiple sensory domains, and are unlikely to underlie the behavioral somatosensory abnormalities observed in ASD.

  14. Mapping soil heterogeneity using RapidEye satellite images

    Science.gov (United States)

    Piccard, Isabelle; Eerens, Herman; Dong, Qinghan; Gobin, Anne; Goffart, Jean-Pierre; Curnel, Yannick; Planchon, Viviane

    2016-04-01

    In the frame of BELCAM, a project funded by the Belgian Science Policy Office (BELSPO), researchers from UCL, ULg, CRA-W and VITO aim to set up a collaborative system to develop and deliver relevant information for agricultural monitoring in Belgium. The main objective is to develop remote sensing methods and processing chains able to ingest crowd sourcing data, provided by farmers or associated partners, and to deliver in return relevant and up-to-date information for crop monitoring at the field and district level based on Sentinel-1 and -2 satellite imagery. One of the developments within BELCAM concerns an automatic procedure to detect soil heterogeneity within a parcel using optical high resolution images. Such heterogeneity maps can be used to adjust farming practices according to the detected heterogeneity. This heterogeneity may for instance be caused by differences in mineral composition of the soil, organic matter content, soil moisture or soil texture. Local differences in plant growth may be indicative for differences in soil characteristics. As such remote sensing derived vegetation indices may be used to reveal soil heterogeneity. VITO started to delineate homogeneous zones within parcels by analyzing a series of RapidEye images acquired in 2015 (as a precursor for Sentinel-2). Both unsupervised classification (ISODATA, K-means) and segmentation techniques were tested. Heterogeneity maps were generated from images acquired at different moments during the season (13 May, 30 June, 17 July, 31 August, 11 September and 1 November 2015). Tests were performed using blue, green, red, red edge and NIR reflectances separately and using derived indices such as NDVI, fAPAR, CIrededge, NDRE2. The results for selected winter wheat, maize and potato fields were evaluated together with experts from the collaborating agricultural research centers. For a few fields UAV images and/or yield measurements were available for comparison.

  15. Rapid seismic reflection imaging in an urban environment

    Science.gov (United States)

    Liberty, L. M.

    2011-12-01

    Subsurface characterization in urban areas is important for city planners, municipalities, and engineers to estimate groundwater resources, track contaminants, assess earthquake or landslide hazards, and many other similar objectives. Improving geophysical imaging methods and results, while minimizing costs, provides greater opportunities for city/project planners and geophysicists alike to take advantage of the improved characterization afforded by the particular method. Seismic reflection results can provide hydrogeologic constraints for groundwater models, provide slip rate estimates for active faults, or simply map stratigraphy to provide target depth estimates. While many traditional urban seismic transects have included the use of vibroseis sources to improve reflection signals and attenuate cultural noise, low cost and high quality near-surface seismic reflection data can be obtained within an urban environment using impulsive sources at a variety of scales and at production rates that can significantly exceed those of swept sources. Sledgehammers and hydraulically powered accelerated weight drops allow rapid acquisition rates through dense urban corridors where the objective is to image targets in the upper one km depth range. In addition permit and land access issues; culturally noisy urban environments can provide additional challenges to producing high quality seismic reflection results. Acquisition methods designed to address both coherent and random noises include recording redundant, unstacked, unfiltered field records. Processing steps that improve data quality in this setting include diversity stacking to attenuate large-amplitude coherent (non-repeatable) vehicle noise and subtraction of power line signals via match filters to retain reflection signals near alternating current frequencies. These acquisition and processing approaches allow for rapid and low cost data acquisition at the expense of moderately increased computing time and disk space. I

  16. Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples.

    Science.gov (United States)

    Hasman, Henrik; Saputra, Dhany; Sicheritz-Ponten, Thomas; Lund, Ole; Svendsen, Christina Aaby; Frimodt-Møller, Niels; Aarestrup, Frank M

    2014-01-01

    Whole-genome sequencing (WGS) is becoming available as a routine tool for clinical microbiology. If applied directly on clinical samples, this could further reduce diagnostic times and thereby improve control and treatment. A major bottleneck is the availability of fast and reliable bioinformatic tools. This study was conducted to evaluate the applicability of WGS directly on clinical samples and to develop easy-to-use bioinformatic tools for the analysis of sequencing data. Thirty-five random urine samples from patients with suspected urinary tract infections were examined using conventional microbiology, WGS of isolated bacteria, and direct sequencing on pellets from the urine samples. A rapid method for analyzing the sequence data was developed. Bacteria were cultivated from 19 samples but in pure cultures from only 17 samples. WGS improved the identification of the cultivated bacteria, and almost complete agreement was observed between phenotypic and predicted antimicrobial susceptibilities. Complete agreement was observed between species identification, multilocus sequence typing, and phylogenetic relationships for Escherichia coli and Enterococcus faecalis isolates when the results of WGS of cultured isolates and urine samples were directly compared. Sequencing directly from the urine enabled bacterial identification in polymicrobial samples. Additional putative pathogenic strains were observed in some culture-negative samples. WGS directly on clinical samples can provide clinically relevant information and drastically reduce diagnostic times. This may prove very useful, but the need for data analysis is still a hurdle to clinical implementation. To overcome this problem, a publicly available bioinformatic tool was developed in this study.

  17. Rapid determination of anti-tuberculosis drug resistance from whole-genome sequences

    KAUST Repository

    Coll, Francesc

    2015-05-27

    Mycobacterium tuberculosis drug resistance (DR) challenges effective tuberculosis disease control. Current molecular tests examine limited numbers of mutations, and although whole genome sequencing approaches could fully characterise DR, data complexity has restricted their clinical application. A library (1,325 mutations) predictive of DR for 15 anti-tuberculosis drugs was compiled and validated for 11 of them using genomic-phenotypic data from 792 strains. A rapid online ‘TB-Profiler’ tool was developed to report DR and strain-type profiles directly from raw sequences. Using our DR mutation library, in silico diagnostic accuracy was superior to some commercial diagnostics and alternative databases. The library will facilitate sequence-based drug-susceptibility testing.

  18. In-Situ Imaging of Particles during Rapid Thermite Deflagrations

    Science.gov (United States)

    Grapes, Michael; Reeves, Robert; Densmore, John; Fezzaa, Kamel; van Buuren, Tony; Willey, Trevor; Sullivan, Kyle

    2017-06-01

    The dynamic behavior of rapidly deflagrating thermites is a highly complex process involving rapid decomposition, melting, and outgassing of intermediate and/or product gases. Few experimental techniques are capable of probing these phenomena in situ due to the small length and time scales associated with the reaction. Here we use a recently developed extended burn tube test, where we initiate a small pile of thermite on the closed end of a clear acrylic tube. The length of the tube is sufficient to fully contain the reaction as it proceeds and flows entrained particles down the tube. This experiment was brought to the Advanced Photon Source, and the particle formation was X-ray imaged at various positions down the tube. Several formulations, as well as formulation parameters were varied to investigate the size and morphology of the particles, as well as to look for dynamic behavior attributed to the reaction. In all cases, we see evidence of particle coalescence and condensed-phase interfacial reactions. The results improve our understanding of the procession of reactants to products in these systems. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-691140.

  19. Segmentation of medical image sequence by parallel active contour.

    Science.gov (United States)

    Fekir, Abdelkader; Benamrane, Nacéra

    2011-01-01

    This paper presents an original approach for detecting and tracking of objects in medical image sequence. We propose a multi-agent system (MAS) based on NetLogo platform for implementing parametric contour active model or snake. In NetLogo, mobile agents (turtles) move over a grid of stationary agents (patches). In our proposed MAS, each mobile agent represents a point of snake (snaxel) and it minimizes, in parallel with other turtles, the energy functional attached to its snaxel. Then, these turtles move over the image represented by a grid of patches. The set of these agents is supervised by Observer, the NetLogo global agent. In addition, Observer loads successively the frames of sequence and initializes the turtles in the first frame. The efficiency of our system is shown through some experimental results.

  20. Digital image capture and rapid prototyping of the maxillofacial defect.

    Science.gov (United States)

    Sabol, Jennifer V; Grant, Gerald T; Liacouras, Peter; Rouse, Stephen

    2011-06-01

    In order to restore an extraoral maxillofacial defect, a moulage impression is commonly made with traditional impression materials. This technique has some disadvantages, including distortion of the site due to the weight of the impression material, changes in tissue location with modifications of the patient position, and the length of time and discomfort for the patient due to the impression procedure and materials used. The use of the commercially available 3dMDface™ System creates 3D images of soft tissues to form an anatomically accurate 3D surface image. Rapid prototyping converts the virtual designs from the 3dMDface™ System into a physical model by converting the data to a ZPrint (ZPR) CAD format file and a stereolithography (STL) file. The data, in conjunction with a Zprinter(®) 450 or a Stereolithography Apparatus (SLA), can be used to fabricate a model for prosthesis fabrication, without the disadvantages of the standard moulage technique. This article reviews this technique and how it can be applied to maxillofacial prosthetics. © 2011 by The American College of Prosthodontists.

  1. Analysis of the cryptography security and steganography in images sequences

    OpenAIRE

    Fábio Borges de Oliveira

    2007-01-01

    Information security is being considered of great importance to the private and governamental institutions. For this reason, we opted to conduct a study of security in this dissertation. We started with an introduction to the information theory, and then we proposed a new kind of Perfect Secrecy cryptographic and finally made a study of steganography in an image sequence, in which we suggest a more aggressive steganography in coefficients of the discrete cosine transform. A segurança da in...

  2. Rapid non-contrast magnetic resonance imaging for post appendectomy intra-abdominal abscess in children

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Megan H. [Washington University School of Medicine in St. Louis, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Eutsler, Eric P.; Khanna, Geetika [Washington University School of Medicine in St. Louis, Pediatric Radiology, Mallinckrodt Institute of Radiology, St. Louis, MO (United States); Sheybani, Elizabeth F. [Mercy Hospital St. Louis, Department of Radiology, St. Louis, MO (United States)

    2017-07-15

    Acute appendicitis, especially if perforated at presentation, is often complicated by postoperative abscess formation. The detection of a postoperative abscess relies primarily on imaging. This has traditionally been done with contrast-enhanced computed tomography. Non-contrast magnetic resonance imaging (MRI) has the potential to accurately detect intra-abdominal abscesses, especially with the use of diffusion-weighted imaging (DWI). To evaluate our single-center experience with a rapid non-contrast MRI protocol evaluating post-appendectomy abscesses in children with persistent postsurgical symptoms. In this retrospective, institutional review board-approved study, all patients underwent a clinically indicated non-contrast 1.5- or 3-Tesla abdomen/pelvis MRI consisting of single-shot fast spin echo, inversion recovery and DWI sequences. All MRI studies were reviewed by two blinded pediatric radiologists to identify the presence of a drainable fluid collection. Each fluid collection was further characterized as accessible or not accessible for percutaneous or transrectal drainage. Imaging findings were compared to clinical outcome. Seven of the 15 patients had a clinically significant fluid collection, and 5 of these patients were treated with percutaneous drain placement or exploratory laparotomy. The other patients had a phlegmon or a clinically insignificant fluid collection and were discharged home within 48 h. Rapid non-contrast MRI utilizing fluid-sensitive and DWI sequences can be used to identify drainable fluid collections in post-appendectomy patients. This protocol can be used to triage patients between conservative management vs. abscess drainage without oral/intravenous contrast or exposure to ionizing radiation. (orig.)

  3. Perceptual distortion measure for edgelike artifacts in image sequences

    Science.gov (United States)

    Yeh, Edmund M.; Kokaram, Anil C.; Kingsbury, Nick G.

    1998-07-01

    This paper presents an objective perceptual distortion measure quantifying the visibility of edge-like blocking artifacts in coded image sequences resulting from popular transform coding techniques. The prime motivation for this work is the awareness that properties of the human visual system should be central to the design and evaluation of image coding algorithms. The perceptual metric is the output of a visual model incorporating both the spatial and temporal characteristics of the visual system. Parameters of the model are based on results from a number of visual experiments in which sensitivities to simulated blocking artifacts were measured under various spatio-temporal background conditions. The visual model takes a pair of original and distorted sequences as inputs. Distortions are calculated along the vertical and horizontal directions. Visibility dependencies on spatial, temporal and motion activities of the background are incorporated using linear filtering and motion estimation. Pixel-based distortions are combined over local spatial and temporal regions to generate an overall distortion measure for each orientation. The final model output is the sum of the vertical and horizontal distortion measures. The model was applied to coded image sequences and the resulting distortion measures were compared to outcomes of subjective ranking tests. Results indicate that the perceptual distortion measure agrees well with human evaluation.

  4. Quality evaluation of edge detection in a road image sequences

    Directory of Open Access Journals (Sweden)

    Rodrigo B. de A. Gallis

    2004-12-01

    Full Text Available Terrestrial mobile mapping systems map interest features along roads such as poles, traffic signs, curb lines, garbage cans etc. The lab work, concerned to the object reconstruction, consists of transforming the video into still images on which homologous points and features of the road sequence are selected and measured. By means of photogrammetric intersection the object coordinates of these features and points are computed for 3D reconstruction. Using Canny algorithm for the automatic edge detection in a road image sequence the article initially focuses on the empiric determination of the required parameters (standard deviation s and high Ta and low Tb threshold. Then it presents the quality in terms of displacement of the automatically detected edges similar to those visually (manually selected straight features extracted by a human operator that takes them as correct, therefore, as reference for the automatic extraction comparison and the quality evaluation. The results of the tests are discussed and show that the quality of the automatic detection – measured by a quantity of rights and wrongs – vary accordingly to the empirically determined standard deviation and high and low thresholds and also to the image sequence environment (street or road.

  5. SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

    Directory of Open Access Journals (Sweden)

    Patel Viren

    2010-09-01

    Full Text Available Abstract Background The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research. Results SeqAnt (Sequence Annotator is an open source web service and software package that rapidly annotates DNA sequence variants and identifies recessive or compound heterozygous loci in human, mouse, fly, and worm genome sequencing experiments. Variants are characterized with respect to their functional type, frequency, and evolutionary conservation. Annotated variants can be viewed on a web browser, downloaded in a tab-delimited text file, or directly uploaded in a BED format to the UCSC genome browser. To demonstrate the speed of SeqAnt, we annotated a series of publicly available datasets that ranged in size from 37 to 3,439,107 variant sites. The total time to completely annotate these data completely ranged from 0.17 seconds to 28 minutes 49.8 seconds. Conclusion SeqAnt is an open source web service and software package that overcomes a critical bottleneck facing research and clinical geneticists using second-generation sequencing platforms. SeqAnt will prove especially useful for those investigators who lack dedicated bioinformatics personnel or infrastructure in their laboratories.

  6. Non-rigid consistent registration of 2D image sequences

    Energy Technology Data Exchange (ETDEWEB)

    Arganda-Carreras, I; Sorzano, C O S; Marabini, R; Carazo, J M [Biocomputing Unit, National Centre for Biotechnology, CSIC, Darwin 3, Universidad Autonoma de Madrid, 28049 Madrid (Spain); Thevenaz, P [Biomedical Imaging Group, Ecole polytechnique federale de Lausanne (EPFL) (Switzerland); Munoz-Barrutia, A; Ortiz-de Solorzano, C [Cancer Imaging Laboratory, Centre for Applied Medical Research, University of Navarra, Pamplona (Spain); Kybic, J, E-mail: iarganda@cnb.csic.e [Center for Machine Perception, Czech Technical University, Prague (Czech Republic)

    2010-10-21

    We present a novel algorithm for the registration of 2D image sequences that combines the principles of multiresolution B-spline-based elastic registration and those of bidirectional consistent registration. In our method, consecutive triples of images are iteratively registered to gradually extend the information through the set of images of the entire sequence. The intermediate results are reused for the registration of the following triple. We choose to interpolate the images and model the deformation fields using B-spline multiresolution pyramids. Novel boundary conditions are introduced to better characterize the deformations at the boundaries. In the experimental section, we quantitatively show that our method recovers from barrel/pincushion and fish-eye deformations with subpixel error. Moreover, it is more robust against outliers-occasional strong noise and large rotations-than the state-of-the-art methods. Finally, we show that our method can be used to realign series of histological serial sections, which are often heavily distorted due to folding and tearing of the tissues.

  7. Non-rigid consistent registration of 2D image sequences

    Science.gov (United States)

    Arganda-Carreras, I.; Sorzano, C. O. S.; Thévenaz, P.; Muñoz-Barrutia, A.; Kybic, J.; Marabini, R.; Carazo, J. M.; Ortiz-de Solorzano, C.

    2010-10-01

    We present a novel algorithm for the registration of 2D image sequences that combines the principles of multiresolution B-spline-based elastic registration and those of bidirectional consistent registration. In our method, consecutive triples of images are iteratively registered to gradually extend the information through the set of images of the entire sequence. The intermediate results are reused for the registration of the following triple. We choose to interpolate the images and model the deformation fields using B-spline multiresolution pyramids. Novel boundary conditions are introduced to better characterize the deformations at the boundaries. In the experimental section, we quantitatively show that our method recovers from barrel/pincushion and fish-eye deformations with subpixel error. Moreover, it is more robust against outliers—occasional strong noise and large rotations—than the state-of-the-art methods. Finally, we show that our method can be used to realign series of histological serial sections, which are often heavily distorted due to folding and tearing of the tissues.

  8. ParAlign: a parallel sequence alignment algorithm for rapid and sensitive database searches.

    Science.gov (United States)

    Rognes, T

    2001-04-01

    There is a need for faster and more sensitive algorithms for sequence similarity searching in view of the rapidly increasing amounts of genomic sequence data available. Parallel processing capabilities in the form of the single instruction, multiple data (SIMD) technology are now available in common microprocessors and enable a single microprocessor to perform many operations in parallel. The ParAlign algorithm has been specifically designed to take advantage of this technology. The new algorithm initially exploits parallelism to perform a very rapid computation of the exact optimal ungapped alignment score for all diagonals in the alignment matrix. Then, a novel heuristic is employed to compute an approximate score of a gapped alignment by combining the scores of several diagonals. This approximate score is used to select the most interesting database sequences for a subsequent Smith-Waterman alignment, which is also parallelised. The resulting method represents a substantial improvement compared to existing heuristics. The sensitivity and specificity of ParAlign was found to be as good as Smith-Waterman implementations when the same method for computing the statistical significance of the matches was used. In terms of speed, only the significantly less sensitive NCBI BLAST 2 program was found to outperform the new approach. Online searches are available at http://dna.uio.no/search/

  9. Safety Assessment of Advanced Imaging Sequences II: Simulations.

    Science.gov (United States)

    Jensen, Jørgen Arendt

    2016-01-01

    An automatic approach for simulating the emitted pressure, intensity, and mechanical index (MI) of advanced ultrasound imaging sequences is presented. It is based on a linear simulation of pressure fields using Field II, and it is hypothesized that linear simulation can attain the needed accuracy for predicting MI and I(spta.3) as required by FDA. The method is performed on four different imaging schemes and compared to measurements conducted using the SARUS experimental scanner. The sequences include focused emissions with an F-number of 2 with 64 elements that generate highly nonlinear fields. The simulation time is between 0.67 and 2.8 ms per emission and imaging point, making it possible to simulate even complex emission sequences in less than 1 s for a single spatial position. The linear simulations yield a relative accuracy on MI between -12.1% and 52.3% and for I(spta.3) between -38.6% and 62.6%, when using the impulse response of the probe estimated from an independent measurement. The accuracy is increased to between -22% and 24.5% for MI and between -33.2% and 27.0% for I(spta.3), when using the pressure response measured at a single point to scale the simulation. The spatial distribution of MI and I(ta.3) closely matches that for the measurement, and simulations can, therefore, be used to select the region for measuring the intensities, resulting in a significant reduction in measurement time. It can validate emission sequences by showing symmetry of emitted pressure fields, focal position, and intensity distribution.

  10. Silhouette extraction from human gait images sequence using cosegmentation

    Science.gov (United States)

    Chen, Jinyan; Zhang, Yi

    2012-11-01

    Gait based human identification is very useful for automatic person recognize through visual surveillance and has attracted more and more researchers. A key step in gait based human identification is to extract human silhouette from images sequence. Current silhouette extraction methods are mainly based on simple color subtraction. These methods have a very poor performance when the color of some body parts is similar to the background. In this paper a cosegmentation based human silhouette extraction method is proposed. Cosegmentation is typically defined as the task of jointly segmenting "something similar" in a given set of images. We can divide the human gait images sequence into several step cycles and every step cycle consist of 10-15 frames. The frames in human gait images sequence have following similarity: every frame is similar to the next or previous frame; every frame is similar to the corresponding frame in the next or previous step cycle; every pixel can find similar pixel in other frames. The progress of cosegmentation based human silhouette extraction can be described as follows: Initially only points which have high contrast to background are used as foreground kernel points, the points in the background are used as background kernel points, then points similar to foreground points will be added to foreground points set and the points similar to background points will be added to background points set. The definition of the similarity consider the context of the point. Experimental result shows that our method has a better performance comparing to traditional human silhouette extraction methods. Keywords: Human gait

  11. Compression and Processing of Space Image Sequences of Northern Lights and Sprites

    DEFF Research Database (Denmark)

    Forchhammer, Søren Otto; Martins, Bo; Jensen, Ole Riis

    1999-01-01

    Compression of image sequences of auroral activity as northern lights and thunderstorms with sprites is investigated.......Compression of image sequences of auroral activity as northern lights and thunderstorms with sprites is investigated....

  12. Outward-looking circular motion analysis of large image sequences.

    Science.gov (United States)

    Jiang, Guang; Wei, Yichen; Quan, Long; Tsui, Hung-tat; Shum, Heung Yeung

    2005-02-01

    This paper presents a novel and simple method of analyzing the motion of a large image sequence captured by a calibrated outward-looking video camera moving on a circular trajectory for large-scale environment applications. Previous circular motion algorithms mainly focus on inward-looking turntable-like setups. They are not suitable for outward-looking motion where the conic trajectory of corresponding points degenerates to straight lines. The circular motion of a calibrated camera essentially has only one unknown rotation angle for each frame. The motion recovery for the entire sequence computes only one fundamental matrix of a pair of frames to extract the angular motion of the pair using Laguerre's formula and then propagates the computation of the unknown rotation angles to the other frames by tracking one point over at least three frames. Finally, a maximum-likelihood estimation is developed for the optimization of the whole sequence. Extensive experiments demonstrate the validity of the method and the feasibility of the application in image-based rendering.

  13. Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing.

    Directory of Open Access Journals (Sweden)

    Can-Xing Duan

    Full Text Available BACKGROUND: The adzuki bean weevil, Callosobruchus chinensis L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from C. chinensis via high-throughput sequencing. PRINCIPAL FINDINGS: In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with de novo assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 C. chinensis genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 C. chinensis populations. The results showed the twenty SSR loci were highly polymorphic among these populations. CONCLUSIONS: This study presents a first report of genome sequencing and de novo assembly for C. chinensis and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for C. chinensis research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among C. chinensis.

  14. Highly Rapid Amplification-Free and Quantitative DNA Imaging Assay

    Science.gov (United States)

    Klamp, Tobias; Camps, Marta; Nieto, Benjamin; Guasch, Francesc; Ranasinghe, Rohan T.; Wiedemann, Jens; Petrášek, Zdeněk; Schwille, Petra; Klenerman, David; Sauer, Markus

    2013-01-01

    There is an urgent need for rapid and highly sensitive detection of pathogen-derived DNA in a point-of-care (POC) device for diagnostics in hospitals and clinics. This device needs to work in a ‘sample-in-result-out’ mode with minimum number of steps so that it can be completely integrated into a cheap and simple instrument. We have developed a method that directly detects unamplified DNA, and demonstrate its sensitivity on realistically sized 5 kbp target DNA fragments of Micrococcus luteus in small sample volumes of 20 μL. The assay consists of capturing and accumulating of target DNA on magnetic beads with specific capture oligonucleotides, hybridization of complementary fluorescently labeled detection oligonucleotides, and fluorescence imaging on a miniaturized wide-field fluorescence microscope. Our simple method delivers results in less than 20 minutes with a limit of detection (LOD) of ~5 pM and a linear detection range spanning three orders of magnitude. PMID:23677392

  15. Optimal context quantization in lossless compression of image data sequences

    DEFF Research Database (Denmark)

    Forchhammer, Søren; Wu, X.; Andersen, Jakob Dahl

    2004-01-01

    In image compression context-based entropy coding is commonly used. A critical issue to the performance of context-based image coding is how to resolve the conflict of a desire for large templates to model high-order statistic dependency of the pixels and the problem of context dilution due...... to insufficient sample statistics of a given input image. We consider the problem of finding the optimal quantizer Q that quantizes the K-dimensional causal context C/sub t/=(X/sub t-t1/,X/sub t-t2/,...,X/sub t-tK/) of a source symbol X/sub t/ into one of a set of conditioning states. The optimality of context...... a random variable can be decomposed into a sequence of binary decisions, each of which is coded using optimal context quantization designed for the corresponding binary random variable. This optimized coding scheme is applied to digital maps and /spl alpha-/plane sequences. The proposed optimal context...

  16. Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.

    Science.gov (United States)

    Ioannidis, Panagiotis; Lu, Yong; Kumar, Nikhil; Creasy, Todd; Daugherty, Sean; Chibucos, Marcus C; Orvis, Joshua; Shetty, Amol; Ott, Sandra; Flowers, Melissa; Sengamalay, Naomi; Tallon, Luke J; Pick, Leslie; Dunning Hotopp, Julie C

    2014-08-29

    Halyomorpha halys (Stål) (Insecta:Hemiptera;Pentatomidae), commonly known as the Brown Marmorated Stink Bug (BMSB), is an invasive pest of the mid-Atlantic region of the United States, causing economically important damage to a wide range of crops. Native to Asia, BMSB was first observed in Allentown, PA, USA, in 1996, and this pest is now well-established throughout the US mid-Atlantic region and beyond. In addition to the serious threat BMSB poses to agriculture, BMSB has become a nuisance to homeowners, invading home gardens and congregating in large numbers in human-made structures, including homes, to overwinter. Despite its significance as an agricultural pest with limited control options, only 100 bp of BMSB sequence data was available in public databases when this project began. Transcriptome sequencing was undertaken to provide a molecular resource to the research community to inform the development of pest control strategies and to provide molecular data for population genetics studies of BMSB. Using normalized, strand-specific libraries, we sequenced pools of all BMSB life stages on the Illumina HiSeq. Trinity was used to assemble 200,000 putative transcripts in >100,000 components. A novel bioinformatic method that analyzed the strand-specificity of the data reduced this to 53,071 putative transcripts from 18,573 components. By integrating multiple other data types, we narrowed this further to 13,211 representative transcripts. Bacterial endosymbiont genes were identified in this dataset, some of which have a copy number consistent with being lateral gene transfers between endosymbiont genomes and Hemiptera, including ankyrin-repeat related proteins, lysozyme, and mannanase. Such genes and endosymbionts may provide novel targets for BMSB-specific biocontrol. This study demonstrates the utility of strand-specific sequencing in generating shotgun transcriptomes and that rapid sequencing shotgun transcriptomes is possible without the need for extensive

  17. Dynamical Segmentation of the Left Ventricle in Echocardiographic Image Sequences

    Science.gov (United States)

    2001-10-25

    1 DYNAMICAL SEGMENTATION OF THE LEFT VENTRICLE IN ECHOCARDIOGRAPHIC IMAGE SEQUENCES A. Bosnjak1,2, V. Burdin 1, V. Torrealba 2, G. Montilla 2, B...V, Bosnjak A, Acuña M, Hernández L, Roux C, Montilla G. “3D Dynamics Echocardiography. Workstation for the Acquisition, Reconstruction and...Torrealba V., Hernández L., Acuña M., Montilla G., Bosnjak A., Roux C. “Interpolación Espacial de Imágenes Médicas 3D basada en movimiento”. Avances

  18. Comparison of optical flow algorithms performance on flame image sequences

    Science.gov (United States)

    Tanaś, J.; Kotyra, A.

    2017-08-01

    Analyzing flame image sequences of co-combusting pulverized coal and biomass can be used to determine the state of this very complex process. Considering dynamic changes between successive frames of such video streams the optical flow algorithms could be applied for di-agnostic purposes. The paper discusses effectiveness and performance of two approaches (sparse and dense optical flow) applied for several video streams of co-combusting biomass and pulverized coal, recorded with different combustion settings with a high-speed camera at the laboratory stand.

  19. LUM Smoother with Smooth Control for Noisy Image Sequences

    Directory of Open Access Journals (Sweden)

    Lukàč Rastislav

    2001-01-01

    Full Text Available This paper focuses on adaptive structure of LUM (lower-upper-middle smoothers for noisy image sequences. For the balance between noise suppression and signal-detail preservation, the LUM smoothers are widely used in smoothing applications. The amount of smoothing done by LUM smoothers is controlled by tuning parameter. However, the smoothing level is fixed for whole image. Thus, the excessive or insufficient smoothing can be performed. This problem is solved by a new method based on the adaptive controlled level of smoothing. A new method has excellent performance of the noise reduction in the environments corrupted by the impulse noise. In addition, minimal signal-detail and motion blurring can be observed. The performance of proposed method is evaluated through objective criteria and compared with traditional temporal, spatial, and spatiotemporal LUM smoothers.

  20. Dopamine transporter imaging in rapid eye movement sleep behavior disorder

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yu Kyeong; Yoon, In Young; Kim, Jong Min; Jeong, Seok Hoon; Kim, Ji Sun; Lee, Byung Chul; Lee, Won Woo; Kim, Sang Eun [Seoul National Univ. College of Medicine, Seoul (Korea, Republic of)

    2007-07-01

    The pathogenesis of rapid eye movement (REM) sleep behavior disorder (RBD) is still unknown. However, involvement of dopaminergic system in RBD has been hypothesized because of frequent association with degenerative movement disorders such as Parkinson's disease. The purpose of this study was to examine the extent and pattern of loss of dopamine transporter in RBD using FP-CIT SPECT. Fourteen patient with idiopathic RBD (mean age:665 yrs, M:F=10:3) participated in this study. Polysonmography confirmed loss of REM atonia and determined RBD severities by amount of tonic/phasic muscle activity during REM sleep in all cases. To compare with RBD, 14 early idiopathic Parkinson's disease rated as Hoehn and Yahr stage 1 (IPD) and 12 healthy controls were also selected. All participants performed single-photon emission computed tomography (SPECT) imaging 3 hours after injection of [123I]FP-CIT. Regions of interest were drawn on bilateral caudate and putamen, whole striatum and occipital cortex. Specific binding for dopamine transporters (DAT) were calculated using region to occipital uptake ratio based on the transient equilibrium method. Overall mean of DAT density in the striatum was lower in RBD group than controls, and higher than IPD group, However, DAT density in most individual RBD was still within normal range, and total striatal DAT density was not correlated with severity of RBD. Meanwhile, the caudate to putamen uptake ratio (C/P ratio) in RBD group was insignificantly higher than those in healthy controls. Nevertheless, C/P ratio within RBD group was reversely correlated with the RBD severity. Our study suggested that nigrostriatal dopaminergic degeneration could be a part of the pathogenesis of RBD, but not essential for the development of RBD. Further longitudinal evaluation of presynaptic dopaminergic system in idiopathic RBD may guarantee the more understanding for RBD and associated neurodegenerative disease.

  1. An Extended Multilocus Sequence Typing (MLST Scheme for Rapid Direct Typing of Leptospira from Clinical Samples.

    Directory of Open Access Journals (Sweden)

    Sabrina Weiss

    2016-09-01

    Full Text Available Rapid typing of Leptospira is currently impaired by requiring time consuming culture of leptospires. The objective of this study was to develop an assay that provides multilocus sequence typing (MLST data direct from patient specimens while minimising costs for subsequent sequencing.An existing PCR based MLST scheme was modified by designing nested primers including anchors for facilitated subsequent sequencing. The assay was applied to various specimen types from patients diagnosed with leptospirosis between 2014 and 2015 in the United Kingdom (UK and the Lao Peoples Democratic Republic (Lao PDR. Of 44 clinical samples (23 serum, 6 whole blood, 3 buffy coat, 12 urine PCR positive for pathogenic Leptospira spp. at least one allele was amplified in 22 samples (50% and used for phylogenetic inference. Full allelic profiles were obtained from ten specimens, representing all sample types (23%. No nonspecific amplicons were observed in any of the samples. Of twelve PCR positive urine specimens three gave full allelic profiles (25% and two a partial profile. Phylogenetic analysis allowed for species assignment. The predominant species detected was L. interrogans (10/14 and 7/8 from UK and Lao PDR, respectively. All other species were detected in samples from only one country (Lao PDR: L. borgpetersenii [1/8]; UK: L. kirschneri [1/14], L. santarosai [1/14], L. weilii [2/14].Typing information of pathogenic Leptospira spp. was obtained directly from a variety of clinical samples using a modified MLST assay. This assay negates the need for time-consuming culture of Leptospira prior to typing and will be of use both in surveillance, as single alleles enable species determination, and outbreaks for the rapid identification of clusters.

  2. [Factors of the rapid startup for nitrosation in sequencing batch reactor].

    Science.gov (United States)

    Li, Dong; Tao, Xiao-Xiao; Li, Zhan; Wang, Jun-An; Zhang, Jie

    2011-08-01

    The approach and factors for realizing the rapid startup of nitrosation were researched at the low level of dissolved oxygen (DO) in sequencing batch reactor (SBR). The main parameters of the reactor were controlled as follows: DO were 0.15-0.40 mg/L, pH values kept from 7.52 to 8.30, temperature maintained at 22.3-27.1 degrees C, and time of aeration was 8 hours. The purpose of rapid startup for nitrosation was achieved after 57 cycles (36 d) with the alternative influent of high and low ammonium wastewater (the mean values were 245.28 mg/L and 58.08 mg/L respectively) in a SBR, and the nitrosation rate was even 100%. Factors of accumulation of nitrite were investigated and the effects of DO and pH were analyzed during the startup for nitrosation. The results showed that it could improve the efficiency of nitrosation when DO concentration was increased appropriately. The activity of nitrite oxidizing bacteria (NOB) was recovered gradually when DO was higher than 0.72 mg/L. The key factor of controlling nitrosation reaction was the concentration of free ammonia (FA), while the final factor was the concentration of DO. pH was a desired controlling parameter to show the end of nitrification in a SBR cycle, while DO concentration did not indicate the finishing of SBR nitrification accurately because it increased rapidly before ammonia nitrogen was oxidized absolutely.

  3. A phase field method for joint denoising, edge detection, and motion estimation in image sequence processing

    NARCIS (Netherlands)

    Preusser, T.; Droske, M.; Garbe, C. S.; Telea, A.; Rumpf, M.

    2007-01-01

    The estimation of optical flow fields from image sequences is incorporated in a Mumford-Shah approach for image denoising and edge detection. Possibly noisy image sequences are considered as input and a piecewise smooth image intensity, a piecewise smooth motion field, and a joint discontinuity set

  4. [Images of Alu-sequence in 7 DNA clones from the human genome].

    Science.gov (United States)

    Korotkov, E V

    1987-01-01

    Information theory methods were used for computer search of Alu-like sequences in human DNA and RNA. Eight new regions related to the Alu repeat sequence was revealed in 85 clones from the EMBL-5 data bank. Some of these regions are purine-pyrimidine images of Alu repeats sequence, the rest are more complex images of Alu repeat sequence. A new definition for the likeness of different sequences--information image of sequence--was introduced. This information theory application greatly increases the power of DNA sequences computer analysis.

  5. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence

    OpenAIRE

    Todd A. Castoe*; Poole, Alexander W.; Gu, Wanjun; A.P. Jason de Koning*; Daza, Juan M.; Eric N. Smith; Pollock, David D.

    2009-01-01

    Optimal integration of next-generation sequencing into mainstream research requires reevaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of ...

  6. A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer.

    Science.gov (United States)

    Mitsuhashi, Satomi; Kryukov, Kirill; Nakagawa, So; Takeuchi, Junko S; Shiraishi, Yoshiki; Asano, Koichiro; Imanishi, Tadashi

    2017-07-18

    We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial compositions rapidly. We tested our protocols using a mock bacterial community that contained equimolar 16S rDNA and a pleural effusion from a patient with empyema, for time effectiveness and accuracy. MinION sequencing targeting 16S rDNA detected all 20 of the bacterial species present in the mock bacterial community. Time course analysis indicated that the sequence data obtained during the first 5 minutes of sequencing (1,379 bacterial reads) were enough to detect all 20 bacteria in the mock sample and to determine species composition, consistent with results of those obtained from 4 hours of sequencing (24,202 reads). Additionally, using a clinical sample extracted from the empyema patient's pleural effusion, we could identify major bacterial pathogens in that effusion using our rapid sequencing and analysis protocol. All results are comparable to conventional 16S rDNA sequencing results using an IonPGM sequencer. Our results suggest that rapid sequencing and bacterial composition determination are possible within 2 hours after obtaining a DNA sample.

  7. Probabilistic multi-person localisation and tracking in image sequences

    Science.gov (United States)

    Klinger, T.; Rottensteiner, F.; Heipke, C.

    2017-05-01

    The localisation and tracking of persons in image sequences in commonly guided by recursive filters. Especially in a multi-object tracking environment, where mutual occlusions are inherent, the predictive model is prone to drift away from the actual target position when not taking context into account. Further, if the image-based observations are imprecise, the trajectory is prone to be updated towards a wrong position. In this work we address both these problems by using a new predictive model on the basis of Gaussian Process Regression, and by using generic object detection, as well as instance-specific classification, for refined localisation. The predictive model takes into account the motion of every tracked pedestrian in the scene and the prediction is executed with respect to the velocities of neighbouring persons. In contrast to existing methods our approach uses a Dynamic Bayesian Network in which the state vector of a recursive Bayes filter, as well as the location of the tracked object in the image, are modelled as unknowns. This allows the detection to be corrected before it is incorporated into the recursive filter. Our method is evaluated on a publicly available benchmark dataset and outperforms related methods in terms of geometric precision and tracking accuracy.

  8. A rapid screening with direct sequencing from blood samples for the diagnosis of Leigh syndrome

    Directory of Open Access Journals (Sweden)

    Hiroko Shimbo

    2014-01-01

    Full Text Available Large numbers of genes are responsible for Leigh syndrome (LS, making genetic confirmation of LS difficult. We screened our patients with LS using a limited set of 21 primers encompassing the frequently reported gene for the respiratory chain complexes I (ND1–ND6, and ND4L, IV(SURF1, and V(ATP6 and the pyruvate dehydrogenase E1α-subunit. Of 18 LS patients, we identified mutations in 11 patients, including 7 in mDNA (two with ATP6, 4 in nuclear (three with SURF1. Overall, we identified mutations in 61% of LS patients (11/18 individuals in this cohort. Sanger sequencing with our limited set of primers allowed us a rapid genetic confirmation of more than half of the LS patients and it appears to be efficient as a primary genetic screening in this cohort.

  9. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

    Directory of Open Access Journals (Sweden)

    Zhou Kaiya

    2011-10-01

    Full Text Available Abstract Background A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales, and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. Results An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae, and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Conclusions Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae, whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving

  10. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences.

    Science.gov (United States)

    Chen, Zhuo; Xu, Shixia; Zhou, Kaiya; Yang, Guang

    2011-10-27

    A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

  11. Images from the Mind: BCI image reconstruction based on Rapid Serial Visual Presentations of polygon primitives

    Directory of Open Access Journals (Sweden)

    Luís F Seoane

    2015-04-01

    Full Text Available We provide a proof of concept for an EEG-based reconstruction of a visual image which is on a user's mind. Our approach is based on the Rapid Serial Visual Presentation (RSVP of polygon primitives and Brain-Computer Interface (BCI technology. In an experimental setup, subjects were presented bursts of polygons: some of them contributed to building a target image (because they matched the shape and/or color of the target while some of them did not. The presentation of the contributing polygons triggered attention-related EEG patterns. These Event Related Potentials (ERPs could be determined using BCI classification and could be matched to the stimuli that elicited them. These stimuli (i.e. the ERP-correlated polygons were accumulated in the display until a satisfactory reconstruction of the target image was reached. As more polygons were accumulated, finer visual details were attained resulting in more challenging classification tasks. In our experiments, we observe an average classification accuracy of around 75%. An in-depth investigation suggests that many of the misclassifications were not misinterpretations of the BCI concerning the users' intent, but rather caused by ambiguous polygons that could contribute to reconstruct several different images. When we put our BCI-image reconstruction in perspective with other RSVP BCI paradigms, there is large room for improvement both in speed and accuracy. These results invite us to be optimistic. They open a plethora of possibilities to explore non-invasive BCIs for image reconstruction both in healthy and impaired subjects and, accordingly, suggest interesting recreational and clinical applications.

  12. Development of rapid methods for relaxation time mapping and motion estimation using magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Gilani, Syed Irtiza Ali

    2008-09-15

    Recent technological developments in the field of magnetic resonance imaging have resulted in advanced techniques that can reduce the total time to acquire images. For applications such as relaxation time mapping, which enables improved visualisation of in vivo structures, rapid imaging techniques are highly desirable. TAPIR is a Look- Locker-based sequence for high-resolution, multislice T{sub 1} relaxation time mapping. Despite the high accuracy and precision of TAPIR, an improvement in the k-space sampling trajectory is desired to acquire data in clinically acceptable times. In this thesis, a new trajectory, termed line-sharing, is introduced for TAPIR that can potentially reduce the acquisition time by 40 %. Additionally, the line-sharing method was compared with the GRAPPA parallel imaging method. These methods were employed to reconstruct time-point images from the data acquired on a 4T high-field MR research scanner. Multislice, multipoint in vivo results obtained using these methods are presented. Despite improvement in acquisition speed, through line-sharing, for example, motion remains a problem and artefact-free data cannot always be obtained. Therefore, in this thesis, a rapid technique is introduced to estimate in-plane motion. The presented technique is based on calculating the in-plane motion parameters, i.e., translation and rotation, by registering the low-resolution MR images. The rotation estimation method is based on the pseudo-polar FFT, where the Fourier domain is composed of frequencies that reside in an oversampled set of non-angularly, equispaced points. The essence of the method is that unlike other Fourier-based registration schemes, the employed approach does not require any interpolation to calculate the pseudo-polar FFT grid coordinates. Translation parameters are estimated by the phase correlation method. However, instead of two-dimensional analysis of the phase correlation matrix, a low complexity subspace identification of the phase

  13. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

    Science.gov (United States)

    Bradley, Phelim; Gordon, N. Claire; Walker, Timothy M.; Dunn, Laura; Heys, Simon; Huang, Bill; Earle, Sarah; Pankhurst, Louise J.; Anson, Luke; de Cesare, Mariateresa; Piazza, Paolo; Votintseva, Antonina A.; Golubchik, Tanya; Wilson, Daniel J.; Wyllie, David H.; Diel, Roland; Niemann, Stefan; Feuerriegel, Silke; Kohl, Thomas A.; Ismail, Nazir; Omar, Shaheed V.; Smith, E. Grace; Buck, David; McVean, Gil; Walker, A. Sarah; Peto, Tim E. A.; Crook, Derrick W.; Iqbal, Zamin

    2015-01-01

    The rise of antibiotic-resistant bacteria has led to an urgent need for rapid detection of drug resistance in clinical samples, and improvements in global surveillance. Here we show how de Bruijn graph representation of bacterial diversity can be used to identify species and resistance profiles of clinical isolates. We implement this method for Staphylococcus aureus and Mycobacterium tuberculosis in a software package (‘Mykrobe predictor') that takes raw sequence data as input, and generates a clinician-friendly report within 3 minutes on a laptop. For S. aureus, the error rates of our method are comparable to gold-standard phenotypic methods, with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics (using an independent validation set, n=470). For M. tuberculosis, our method predicts resistance with sensitivity/specificity of 82.6%/98.5% (independent validation set, n=1,609); sensitivity is lower here, probably because of limited understanding of the underlying genetic mechanisms. We give evidence that minor alleles improve detection of extremely drug-resistant strains, and demonstrate feasibility of the use of emerging single-molecule nanopore sequencing techniques for these purposes. PMID:26686880

  14. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications.

    Science.gov (United States)

    Chen, Xiaoyu; Schulz-Trieglaff, Ole; Shaw, Richard; Barnes, Bret; Schlesinger, Felix; Källberg, Morten; Cox, Anthony J; Kruglyak, Semyon; Saunders, Christopher T

    2016-04-15

    : We describe Manta, a method to discover structural variants and indels from next generation sequencing data. Manta is optimized for rapid germline and somatic analysis, calling structural variants, medium-sized indels and large insertions on standard compute hardware in less than a tenth of the time that comparable methods require to identify only subsets of these variant types: for example NA12878 at 50× genomic coverage is analyzed in less than 20 min. Manta can discover and score variants based on supporting paired and split-read evidence, with scoring models optimized for germline analysis of diploid individuals and somatic analysis of tumor-normal sample pairs. Call quality is similar to or better than comparable methods, as determined by pedigree consistency of germline calls and comparison of somatic calls to COSMIC database variants. Manta consistently assembles a higher fraction of its calls to base-pair resolution, allowing for improved downstream annotation and analysis of clinical significance. We provide Manta as a community resource to facilitate practical and routine structural variant analysis in clinical and research sequencing scenarios. Manta is released under the open-source GPLv3 license. Source code, documentation and Linux binaries are available from https://github.com/Illumina/manta. csaunders@illumina.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. Whole-exome sequencing enables rapid determination of xeroderma pigmentosum molecular etiology.

    Directory of Open Access Journals (Sweden)

    Oscar Ortega-Recalde

    Full Text Available Xeroderma pigmentosum (XP is a rare autosomal recessive disorder characterized by extreme sensitivity to actinic pigmentation changes in the skin and increased incidence of skin cancer. In some cases, patients are affected by neurological alterations. XP is caused by mutations in 8 distinct genes (XPA through XPG and XPV. The XP-V (variant subtype of the disease results from mutations in a gene (XPV, also named POLH which encodes for Polη, a member of the Y-DNA polymerase family. Although the presence and severity of skin and neurological dysfunctions differ between XP subtypes, there are overlapping clinical features among subtypes such that the sub-type cannot be deduced from the clinical features. In this study, in order to overcome this drawback, we undertook whole-exome sequencing in two XP sibs and their father. We identified a novel homozygous nonsense mutation (c.897T>G, p.Y299X in POLH which causes the disease. Our results demonstrate that next generation sequencing is a powerful approach to rapid determination of XP genetic etiology.

  16. Whole-Genome Sequencing of Native Sheep Provides Insights into Rapid Adaptations to Extreme Environments

    Science.gov (United States)

    Yang, Ji; Li, Wen-Rong; Lv, Feng-Hua; He, San-Gang; Tian, Shi-Lin; Peng, Wei-Feng; Sun, Ya-Wei; Zhao, Yong-Xin; Tu, Xiao-Long; Zhang, Min; Xie, Xing-Long; Wang, Yu-Tao; Li, Jin-Quan; Liu, Yong-Gang; Shen, Zhi-Qiang; Wang, Feng; Liu, Guang-Jian; Lu, Hong-Feng; Kantanen, Juha; Han, Jian-Lin; Li, Meng-Hua; Liu, Ming-Jun

    2016-01-01

    Global climate change has a significant effect on extreme environments and a profound influence on species survival. However, little is known of the genome-wide pattern of livestock adaptations to extreme environments over a short time frame following domestication. Sheep (Ovis aries) have become well adapted to a diverse range of agroecological zones, including certain extreme environments (e.g., plateaus and deserts), during their post-domestication (approximately 8–9 kya) migration and differentiation. Here, we generated whole-genome sequences from 77 native sheep, with an average effective sequencing depth of ∼5× for 75 samples and ∼42× for 2 samples. Comparative genomic analyses among sheep in contrasting environments, that is, plateau (>4,000 m above sea level) versus lowland (1500 m) versus low-altitude region (600 mm), and arid zone (400 mm), detected a novel set of candidate genes as well as pathways and GO categories that are putatively associated with hypoxia responses at high altitudes and water reabsorption in arid environments. In addition, candidate genes and GO terms functionally related to energy metabolism and body size variations were identified. This study offers novel insights into rapid genomic adaptations to extreme environments in sheep and other animals, and provides a valuable resource for future research on livestock breeding in response to climate change. PMID:27401233

  17. Rapid and Specific Detection of the Escherichia coli Sequence Type 648 Complex within Phylogroup F.

    Science.gov (United States)

    Johnson, James R; Johnston, Brian D; Gordon, David M

    2017-04-01

    The Escherichia coli sequence type 648 complex (STc648) is an emerging lineage within phylogroup F-formerly included within phylogroup D-that is associated with multidrug resistance. Here, we designed and validated a novel multiplex PCR-based assay for STc648 that took advantage of (i) four distinctive single-nucleotide polymorphisms in icd allele 96 and gyrB allele 87, two of the multilocus sequence typing alleles that define ST648; and (ii) the typical absence within STc648 of uidA, an E. coli-specific gene encoding β-glucuronidase. Within a diverse 212-strain validation set that included 109 STs other than STc648, from phylogroups A, B1, B2, C, D, E, and F, the assay exhibited 100% sensitivity (95% confidence interval [CI], 82% to 100%) and specificity (95% CI, 98% to 100%). It functioned similarly well in two distant laboratories that used boiled lysates or DNAzol-purified DNA as the template DNA. Thus, this novel multiplex PCR-based assay should enable any laboratory equipped for diagnostic PCR to rapidly, accurately, and economically screen E. coli isolates for membership in STc648. Copyright © 2017 American Society for Microbiology.

  18. DPS – A rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque

    DEFF Research Database (Denmark)

    Kot, Witold; Vogensen, Finn Kvist; Sørensen, Søren J.

    2014-01-01

    methods for characterization of phages is determination of the whole genome using high throughput sequencing approaches. Here a direct plaque sequencing (DPS) is described, which is a rapid method that allows easy full genome sequencing of DNA-containing phages using the Nextera XT™ kit. A combination...... of host-DNA removal followed by purification and concentration of the viral DNA, allowed the construction of Illumina-compatible sequencing libraries using the Nextera™ XT technology directly from single phage plaques without any whole genome amplification step. This method was tested on three...

  19. Symbolic representation and visual querying of left ventricular image sequences.

    Science.gov (United States)

    Baroni, M; Del Bimbo, A; Evangelist, A; Vicario, E

    1999-01-01

    In the evaluation of regional left ventricular function, relevant cardiac disorders manifest themselves not only in static features, such as shape descriptors and motion excursion in end-diastolic and end-systolic frames, but also in their temporal evolution. In common diagnostic practice, such dynamic patterns are analysed by direct inspection of frame sequences through the use of a moviola. This permits only a subjective and poorly defined evaluation of functional parameters, and definitely prevents a systematic and reproducible analysis of large sets of reports. Retrieval by contents techniques may overcome this limitation by permitting the automatic comparison of the reports in a database against queries expressing descriptive properties related to significant pathological conditions. A system is presented which is aimed at investigating the potential of this approach by supporting retrieval by contents from a database of cineangiographic or echocardiographic images. The system relies on a symbolic description of both geometrical and temporal properties of left ventricular contours. This is derived automatically by an image processing and interpretation module and associated with the report at its storage time. In the retrieval stage, queries are expressed by means of an iconic visual language which describes searched content properties over a computer screen. The system automatically interprets iconic statements and compares them against concrete descriptions in the database. This enables medical users to interact with the system to search for motion and shape abnormalities on a regional basis, in single or homogeneous groups of reports, so as to enable both prospective and retrospective diagnosis.

  20. Submillimeter Imaging of Dust Around Main Sequence Stars

    Science.gov (United States)

    Jewitt, David

    1998-01-01

    This grant was to image circumstellar dust disks surrounding main-sequence stars. The delivery of the SCUBA detector we had planned to use for this work was delayed repeatedly, leading us to undertake a majority of the observations with the UKT14 submillimeter detector at the JCMT (James Clerk Maxwell Telescope) and optical imagers and a coronagraph at the University of Hawaii 2.2-m telescope. Major findings under this grant include: (1) We discovered 5 asymmetries in the beta Pictoris regenerated dust disk. The discovery of these asymmetries was a surprise, since smearing due to Keplerian shear should eliminate most such features on timescales of a few thousand years. One exception is the "wing tilt" asymmetry, which we interpret as due to the scattering phase function of dust disk particles. From the wing tilt and a model of the phase function, we find a disk plane inclination to the line of sight of JCMT). It is possible, for instance, that the main 850 micro-m blob is merely a galaxy or other high-z source projected onto the beta Pic mid-plane.

  1. Abdominal MR imaging using a HASTE sequence : image comparison on the different echo times

    Energy Technology Data Exchange (ETDEWEB)

    Park, Kwang Bo; Lee, Moon Gyu; Lim, Tae Hwan; Jeong, Yoong Ki; Ha, Hyun Kwon; Kim, Pyo Nyun; Auh, Yong Ho [Ulsan Univ. College of Medicine, Asan Medical Center, Seoul (Korea, Republic of)

    1999-11-01

    To determine the optimal parameters of abdominal HASTE imaging by means of a comparison of intermediate and long TE (echo time). We evaluated 30 consecutive patients who had undergone liver MR during a three-month period. Twelve patients were diagnosed as normal, four as having liver cirrhosis, and 14 were found to be suffering form hepatic hemangioma. On the basis of measured signal intensity of the liver, spleen, pancreas and gallbladder, and of fat, muscle, hemangioma, and background, we calculated the ratios of signal to noise (S/N), signal difference to noise (SD/N), and signal intensity (SI). Image quality was compared using these three ratios, and using two HASTE sequences with TEs of 90 msec and 134 msec, images were qualitatively evaluated. S/N ratio of the liver was higher when TE was 90 msec(p<.05), though S/N, SD/N and SI rations of the spleen, gallbladder, and pancreas-and of hemangiom-were higher when TE was 134 msec (p<.05). However, in muscle, all these three ratios were higher at a TE of 90 msec. SD/N ratio and SI of fat were higher at a TE of 134 msec. Overall image quality was better at a TE of 134 msec than at one of 90msec. A HASTE sequence with a TE of 134msec showed greater tissue contrast and stronger T2-weighted images than one with a TE of 90msec.

  2. [Rapid total body fat measurement by magnetic resonance imaging: quantification and topography].

    Science.gov (United States)

    Vogt, F M; Ruehm, S; Hunold, P; de Greiff, A; Nuefer, M; Barkhausen, J; Ladd, S C

    2007-05-01

    To evaluate a rapid and comprehensive MR protocol based on a T1-weighted sequence in conjunction with a rolling table platform for the quantification of total body fat. 11 healthy volunteers and 50 patients were included in the study. MR data was acquired on a 1.5-T system (Siemens Magnetom Sonata). An axial T1-weighted flash 2D sequence (TR 101, TE 4.7, FA 70, FOV 50 cm, 205 x 256 matrix, slice thickness: 10 mm, 10 mm interslice gap) was used for data acquisition. Patients were placed in a supine position on a rolling table platform capable of acquiring multiple consecutive data sets by pulling the patient through the isocenter of the magnet. Data sets extending from the upper to lower extremities were collected. The images were analyzed with respect to the amount of intraabdominal, subcutaneous and total abdominal fat by semi-automated image segmentation software that employs a contour-following algorithm. The obtained MR images were able to be evaluated for all volunteers and patients. Excellent correlation was found between whole body MRI results in volunteers with DEXA (r (2) = 0.95) and bioimpedance (r (2) = 0.89) measurements, while the correlation coefficient was 0.66 between MRI and BMI, indicating only moderate reliability of the BMI method. Variations in patients with respect to the amount of total, subcutaneous, and intraabdominal adipose tissue was not related to standard anthropometric measurements and metabolic lipid profiles (r (2) = 0,001 to 0.48). The results showed that there was a significant variation in intraabdominal adipose tissue which could not be predicted from the total body fat (r (2) = 0.14) or subcutaneous adipose tissue (r (2) = 0.04). Although no significant differences in BMI could be found between females and males (p = 0.26), females showed significantly higher total and subcutaneous abdominal adipose tissue (p < 0.05). This MR protocol can be used for the rapid and non-invasive quantification of body fat. The missing

  3. Intraoperative Molecular Imaging for Rapid Assessment of Tumor Margins

    Science.gov (United States)

    2011-09-01

    approach in animal models using a the MRI- FMT imaging system (Task 5). A description of the primary accomplishments and ongoing efforts follows...guided fluorescence molecular tomography ( FMT ) of ( ) ( ) ( ) tBP k NTNTT etCBP kRktCRtC + − ∗    + ++= 12121 2 1 9 two fluorescent probes in...administration, mice were imaged for an hour at approximately two minutes per frame using an MR-coupled FMT system. The imaging system is a spectrometer

  4. BOLD imaging in the mouse brain using a turboCRAZED sequence at high magnetic fields.

    Science.gov (United States)

    Schneider, Johannes T; Faber, Cornelius

    2008-10-01

    Functional MRI (fMRI) based on the detection of intermolecular double-quantum coherences (iDQC) has previously been shown to provide pronounced activation signal. For fMRI in small animals at very high magnetic fields, the essential fast gradient echo-based readout methods become problematic. Here, rapid intermolecular double-quantum coherence (iDQC) imaging was implemented, combining the iDQC preparation sequence with a Turbo spin echo-like readout. Four-step phase cycling and a novel intensity-ordered k-space encoding scheme with separate acquisition of odd and even echoes were essential to optimize signal to noise ratio efficiency. Compared with a single echo readout of iDQC signal, acceleration of factor 16 was achieved in phantoms using the novel method at 17.6 Tesla. In vivo, echo trains consisting of 32 echoes were possible and images of the mouse brain were obtained in 30 s. The blood oxygen level dependent (BOLD) effect in the mouse brain upon change of breathing gas was observed as average signal change of (6.3 +/- 1.1)% in iDQC images. Signal changes in conventional multi spin echo images were (4.4 +/- 2.3)% and (8.3 +/- 3.8)% with gradient echo methods. Combination of T(2)*-weighting with the fast iDQC sequence may yield higher signal changes than with either method alone, and establish fast iDQC imaging a robust tool for high field fMRI in small animals. (c) 2008 Wiley-Liss, Inc.

  5. Real-time SPARSE-SENSE cardiac cine MR imaging: optimization of image reconstruction and sequence validation.

    Science.gov (United States)

    Goebel, Juliane; Nensa, Felix; Bomas, Bettina; Schemuth, Haemi P; Maderwald, Stefan; Gratz, Marcel; Quick, Harald H; Schlosser, Thomas; Nassenstein, Kai

    2016-12-01

    Improved real-time cardiac magnetic resonance (CMR) sequences have currently been introduced, but so far only limited practical experience exists. This study aimed at image reconstruction optimization and clinical validation of a new highly accelerated real-time cine SPARSE-SENSE sequence. Left ventricular (LV) short-axis stacks of a real-time free-breathing SPARSE-SENSE sequence with high spatiotemporal resolution and of a standard segmented cine SSFP sequence were acquired at 1.5 T in 11 volunteers and 15 patients. To determine the optimal iterations, all volunteers' SPARSE-SENSE images were reconstructed using 10-200 iterations, and contrast ratios, image entropies, and reconstruction times were assessed. Subsequently, the patients' SPARSE-SENSE images were reconstructed with the clinically optimal iterations. LV volumetric values were evaluated and compared between both sequences. Sufficient image quality and acceptable reconstruction times were achieved when using 80 iterations. Bland-Altman plots and Passing-Bablok regression showed good agreement for all volumetric parameters. 80 iterations are recommended for iterative SPARSE-SENSE image reconstruction in clinical routine. Real-time cine SPARSE-SENSE yielded comparable volumetric results as the current standard SSFP sequence. Due to its intrinsic low image acquisition times, real-time cine SPARSE-SENSE imaging with iterative image reconstruction seems to be an attractive alternative for LV function analysis. • A highly accelerated real-time CMR sequence using SPARSE-SENSE was evaluated. • SPARSE-SENSE allows free breathing in real-time cardiac cine imaging. • For clinically optimal SPARSE-SENSE image reconstruction, 80 iterations are recommended. • Real-time SPARSE-SENSE imaging yielded comparable volumetric results as the reference SSFP sequence. • The fast SPARSE-SENSE sequence is an attractive alternative to standard SSFP sequences.

  6. Rapid Acquisition Imaging Spectrograph (RAISE) Renewal Proposal Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The optical design of RAISE is based on a new class of UV/EUV imaging spectrometers that use  only two reflections to provide quasi-stigmatic performance...

  7. Direct sequencing for rapid detection of multidrug resistant Mycobacterium tuberculosis strains in Morocco

    Directory of Open Access Journals (Sweden)

    Zakham F

    2013-11-01

    Full Text Available Fathiah Zakham,1,4 Imane Chaoui,1 Amina Hadbae Echchaoui,2 Fouad Chetioui,3 My Driss Elmessaoudi,3 My Mustapha Ennaji,4 Mohammed Abid,2 Mohammed El Mzibri11Unité de Biologie et Recherché Médicale, Centre National de l'Energie, des Sciences et des Techniques Nucléaires (CNESTEN, Rabat, 2Laboratoire de Génétique Mycobacterienne, Institut Pasteur, Tangier, 3Laboratoire de Tuberculose Institut Pasteur, Casablanca, 4Laboratoire de Microbiologie, Hygiène et Virologie, Faculté des Sciences et Techniques, Mohammedia, MoroccoBackground: Tuberculosis (TB is a major public health problem with high mortality and morbidity rates, especially in low-income countries. Disturbingly, the emergence of multidrug resistant (MDR and extensively drug resistant (XDR TB cases has worsened the situation, raising concerns of a future epidemic of virtually untreatable TB. Indeed, the rapid diagnosis of MDR TB is a critical issue for TB management. This study is an attempt to establish a rapid diagnosis of MDR TB by sequencing the target fragments of the rpoB gene which linked to resistance against rifampicin and the katG gene and inhA promoter region, which are associated with resistance to isoniazid.Methods: For this purpose, 133 sputum samples of TB patients from Morocco were enrolled in this study. One hundred samples were collected from new cases, and the remaining 33 were from previously treated patients (drug relapse or failure, chronic cases and did not respond to anti-TB drugs after a sufficient duration of treatment. All samples were subjected to rpoB, katG and pinhA mutation analysis by polymerase chain reaction and DNA sequencing.Results: Molecular analysis showed that seven strains were isoniazid-monoresistant and 17 were rifampicin-monoresistant. MDR TB strains were identified in nine cases (6.8%. Among them, eight were traditionally diagnosed as critical cases, comprising four chronic and four drug-relapse cases. The last strain was isolated from a

  8. Intubating conditions following rapid sequence induction with three doses of succinylcholine

    Science.gov (United States)

    Prakash, Smita; Barde, Sushma; Thakur, Preeti; Gogia, Anoop Raj; Singh, Rajvir

    2012-01-01

    Background: The aim of this prospective, randomized, double-blind study was to compare tracheal intubating conditions and the duration of apnoea following administration of 0.4, 0.6 and 1.0 mg/kg of succinylcholine during simulated rapid sequence induction of anaesthesia. Methods: Anaesthesia was induced with fentanyl 2 μg/kg and propofol 2 mg/kg followed by application of cricoid pressure. Patients were randomly allocated to three groups according to the dose of succinylcholine administered (0.4, 0.6 or 1.0 mg/kg). Intubating conditions were assessed at 60 s after succinylcholine administration. Time to first diaphragmatic contraction (apnoea time) and time to resumption of regular spontaneous breathing were noted. Results: Excellent intubating conditions were obtained in 52.4%, 95.7% and 100% of the patients after 0.4, 0.6 and 1.0 mg/kg succinylcholine, respectively; P<0.001. Acceptable intubating conditions (excellent and good grade combined) were obtained in 66.7%, 100% and 100% of the patients after 0.4, 0.6 and 1.0 mg/ kg succinylcholine, respectively; P<0.001. Apnoea time and resumption of regular spontaneous breathing were dose-dependent. Apnoea time was 3.8±1.1 min, 4.3±0.9 min and 8.2±3.4 min in groups 0.4, 0.6 and 1.0 mg/kg, respectively; P<0.001. Time to regular spontaneous breathing was 5.3±1.2 min, 5.5±1.1 min and 8.9±3.5 min in groups 0.4, 0.6 and 1.0 mg/kg, respectively; P<0.001. Conclusion: A dose of 0.6 mg/kg succinylcholine can be used for rapid sequence induction of anaesthesia as it provides acceptable intubating conditions with a shorter apnoea time compared with a dose of 1 mg/kg. PMID:22701204

  9. Intubating conditions following rapid sequence induction with three doses of succinylcholine

    Directory of Open Access Journals (Sweden)

    Smita Prakash

    2012-01-01

    Full Text Available Background: The aim of this prospective, randomized, double-blind study was to compare tracheal intubating conditions and the duration of apnoea following administration of 0.4, 0.6 and 1.0 mg/kg of succinylcholine during simulated rapid sequence induction of anaesthesia. Methods: Anaesthesia was induced with fentanyl 2 μg/kg and propofol 2 mg/kg followed by application of cricoid pressure. Patients were randomly allocated to three groups according to the dose of succinylcholine administered (0.4, 0.6 or 1.0 mg/kg. Intubating conditions were assessed at 60 s after succinylcholine administration. Time to first diaphragmatic contraction (apnoea time and time to resumption of regular spontaneous breathing were noted. Results: Excellent intubating conditions were obtained in 52.4%, 95.7% and 100% of the patients after 0.4, 0.6 and 1.0 mg/kg succinylcholine, respectively; P<0.001. Acceptable intubating conditions (excellent and good grade combined were obtained in 66.7%, 100% and 100% of the patients after 0.4, 0.6 and 1.0 mg/ kg succinylcholine, respectively; P<0.001. Apnoea time and resumption of regular spontaneous breathing were dose-dependent. Apnoea time was 3.8±1.1 min, 4.3±0.9 min and 8.2±3.4 min in groups 0.4, 0.6 and 1.0 mg/kg, respectively; P<0.001. Time to regular spontaneous breathing was 5.3±1.2 min, 5.5±1.1 min and 8.9±3.5 min in groups 0.4, 0.6 and 1.0 mg/kg, respectively; P<0.001. Conclusion: A dose of 0.6 mg/kg succinylcholine can be used for rapid sequence induction of anaesthesia as it provides acceptable intubating conditions with a shorter apnoea time compared with a dose of 1 mg/kg.

  10. Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

    DEFF Research Database (Denmark)

    Larsen, P B; Hansen, E G; Jacobsen, L S

    2005-01-01

    conditions of standard doses of rocuronium 0.6 mg kg[-1] and succinylcholine 1.0 mg kg[-1] during a strict rapid-sequence induction regimen including propofol and alfentanil. Methods: Male and female patients (ASA I-III) older than 17 yr scheduled for emergency abdominal or gynaecological surgery...... not fulfil the inclusion criteria. Clinically acceptable intubation conditions were present in 93.5% and 96.1% of patients in the succinylcholine group (n=107) and the rocuronium group (n=102), respectively (P=0.59). Conclusions: During a rapid-sequence induction with alfentanil and propofol, both rocuronium...

  11. Next-Generation Sequencing-Aided Rapid Molecular Diagnosis of Occult Macular Dystrophy in a Chinese Family

    OpenAIRE

    Yu-He Qi; Feng-Juan Gao; Fang-Yuan Hu; Sheng-Hai Zhang; Jun-Yi Chen; Wan-Jing Huang; Guo-Hong Tian; Min Wang; De-Kang Gan; Ji-Hong Wu; Ge-Zhi Xu

    2017-01-01

    Purpose: To show early, rapid and accurate molecular diagnosis of occult macular dystrophy (OMD) in a four-generation Chinese family with inherited macular dystrophy.Methods: In the current study, we comprehensively screened 130 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the proband of a four-generation Chinese family that has suffered from maculopathy without a definitive diagnosis for over 10 years. Varian...

  12. Intraoperative Molecular Imaging for Rapid Assessment of Tumor Margins

    Science.gov (United States)

    2010-09-01

    determine the depth of embedded tumor fragments in the excise tissue or surgical cavity. Pilot animal data with the Licor IRDye800CW-2DG imaging agent in...and the tumor immediately removed with adjacent normal tissue. All tissue were soaked for 5 – 20 minutes in a solution of Licor IRDye800CW-2DG and... Licor IRDye800CW-2DG, showing a cross section of the tumor mass. These images show a significant amount of non-specific uptake of the probe in

  13. Rapid identification of rice blast resistance gene by specific length amplified fragment sequencing

    Directory of Open Access Journals (Sweden)

    Shen Chen

    2016-05-01

    Full Text Available Excavation of resistance genes is one of the most effective and environment-friendly measures to control the devastating rice disease caused by Magnaporthe oryzae. Many resistance genes have been mapped and characterized in the last century. Nevertheless, only a few of the total resistance genes could be really applied in the rice breeding program. Huazhan (HZ is a new native rice restorer line developed in China and widely used in hybrid rice in recent years. HZ and its crossed combinations usually show a broad spectrum of resistance against rice blast in different rice ecosystems in China. Dissection of the genetic background of HZ is very useful for its further application. In this study, a combined method based on bulked segregation analysis (BSA and specific length amplified fragment sequencing (SLAF-seq was used to identify blast resistance gene(s in HZ. A total of 56,187 SLAFs labels were captured and 9051 polymorphic SLAFs markers were analysed and procured in this study. One trait associated with candidate resistance genes region on chromosome 12 overlapping 10.2–17.6 Mb has been identified, in which 10 NBS-LRR (nucleotide-binding site-leucine-rich repeat coding genes were used as resistance gene candidates. Our result indicated that SLAF-seq with BSA is a rapid and effective method for initial identification of blast resistance genes. The identification of resistance gene in HZ will improve its molecular breeding and resistance variety application.

  14. Rapid Detection and Identification of Infectious Pathogens Based on High-throughput Sequencing

    Directory of Open Access Journals (Sweden)

    Pei-Xiang Ni

    2015-01-01

    Full Text Available Background: The dilemma of pathogens identification in patients with unidentified clinical symptoms such as fever of unknown origin exists, which not only poses a challenge to both the diagnostic and therapeutic process by itself, but also to expert physicians. Methods: In this report, we have attempted to increase the awareness of unidentified pathogens by developing a method to investigate hitherto unidentified infectious pathogens based on unbiased high-throughput sequencing. Results: Our observations show that this method supplements current diagnostic technology that predominantly relies on information derived five cases from the intensive care unit. This methodological approach detects viruses and corrects the incidence of false positive detection rates of pathogens in a much shorter period. Through our method is followed by polymerase chain reaction validation, we could identify infection with Epstein-Barr virus, and in another case, we could identify infection with Streptococcus viridians based on the culture, which was false positive. Conclusions: This technology is a promising approach to revolutionize rapid diagnosis of infectious pathogens and to guide therapy that might result in the improvement of personalized medicine.

  15. Quantitative Functional Imaging Using Dynamic Positron Computed Tomography and Rapid Parameter Estimation Techniques

    Science.gov (United States)

    Koeppe, Robert Allen

    Positron computed tomography (PCT) is a diagnostic imaging technique that provides both three dimensional imaging capability and quantitative measurements of local tissue radioactivity concentrations in vivo. This allows the development of non-invasive methods that employ the principles of tracer kinetics for determining physiological properties such as mass specific blood flow, tissue pH, and rates of substrate transport or utilization. A physiologically based, two-compartment tracer kinetic model was derived to mathematically describe the exchange of a radioindicator between blood and tissue. The model was adapted for use with dynamic sequences of data acquired with a positron tomograph. Rapid estimation techniques were implemented to produce functional images of the model parameters by analyzing each individual pixel sequence of the image data. A detailed analysis of the performance characteristics of three different parameter estimation schemes was performed. The analysis included examination of errors caused by statistical uncertainties in the measured data, errors in the timing of the data, and errors caused by violation of various assumptions of the tracer kinetic model. Two specific radioindicators were investigated. ('18)F -fluoromethane, an inert freely diffusible gas, was used for local quantitative determinations of both cerebral blood flow and tissue:blood partition coefficient. A method was developed that did not require direct sampling of arterial blood for the absolute scaling of flow values. The arterial input concentration time course was obtained by assuming that the alveolar or end-tidal expired breath radioactivity concentration is proportional to the arterial blood concentration. The scale of the input function was obtained from a series of venous blood concentration measurements. The method of absolute scaling using venous samples was validated in four studies, performed on normal volunteers, in which directly measured arterial concentrations

  16. Monitoring of rapid sand filters using an acoustic imaging technique

    NARCIS (Netherlands)

    Allouche, N.; Simons, D.G.; Rietveld, L.C.

    2012-01-01

    A novel instrument is developed to acoustically image sand filters used for water treatment and monitor their performance. The instrument consists of an omnidirectional transmitter that generates a chirp with a frequency range between 10 and 110 kHz, and an array of hydrophones. The instrument was

  17. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets.

    Directory of Open Access Journals (Sweden)

    Sean C Warren

    Full Text Available Fluorescence lifetime imaging (FLIM is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset. This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis

  18. Rapid global fitting of large fluorescence lifetime imaging microscopy datasets.

    Science.gov (United States)

    Warren, Sean C; Margineanu, Anca; Alibhai, Dominic; Kelly, Douglas J; Talbot, Clifford; Alexandrov, Yuriy; Munro, Ian; Katan, Matilda; Dunsby, Chris; French, Paul M W

    2013-01-01

    Fluorescence lifetime imaging (FLIM) is widely applied to obtain quantitative information from fluorescence signals, particularly using Förster Resonant Energy Transfer (FRET) measurements to map, for example, protein-protein interactions. Extracting FRET efficiencies or population fractions typically entails fitting data to complex fluorescence decay models but such experiments are frequently photon constrained, particularly for live cell or in vivo imaging, and this leads to unacceptable errors when analysing data on a pixel-wise basis. Lifetimes and population fractions may, however, be more robustly extracted using global analysis to simultaneously fit the fluorescence decay data of all pixels in an image or dataset to a multi-exponential model under the assumption that the lifetime components are invariant across the image (dataset). This approach is often considered to be prohibitively slow and/or computationally expensive but we present here a computationally efficient global analysis algorithm for the analysis of time-correlated single photon counting (TCSPC) or time-gated FLIM data based on variable projection. It makes efficient use of both computer processor and memory resources, requiring less than a minute to analyse time series and multiwell plate datasets with hundreds of FLIM images on standard personal computers. This lifetime analysis takes account of repetitive excitation, including fluorescence photons excited by earlier pulses contributing to the fit, and is able to accommodate time-varying backgrounds and instrument response functions. We demonstrate that this global approach allows us to readily fit time-resolved fluorescence data to complex models including a four-exponential model of a FRET system, for which the FRET efficiencies of the two species of a bi-exponential donor are linked, and polarisation-resolved lifetime data, where a fluorescence intensity and bi-exponential anisotropy decay model is applied to the analysis of live cell

  19. An Algorithm for Pedestrian Detection in Multispectral Image Sequences

    Science.gov (United States)

    Kniaz, V. V.; Fedorenko, V. V.

    2017-05-01

    The growing interest for self-driving cars provides a demand for scene understanding and obstacle detection algorithms. One of the most challenging problems in this field is the problem of pedestrian detection. Main difficulties arise from a diverse appearances of pedestrians. Poor visibility conditions such as fog and low light conditions also significantly decrease the quality of pedestrian detection. This paper presents a new optical flow based algorithm BipedDetet that provides robust pedestrian detection on a single-borad computer. The algorithm is based on the idea of simplified Kalman filtering suitable for realization on modern single-board computers. To detect a pedestrian a synthetic optical flow of the scene without pedestrians is generated using slanted-plane model. The estimate of a real optical flow is generated using a multispectral image sequence. The difference of the synthetic optical flow and the real optical flow provides the optical flow induced by pedestrians. The final detection of pedestrians is done by the segmentation of the difference of optical flows. To evaluate the BipedDetect algorithm a multispectral dataset was collected using a mobile robot.

  20. Direct Parametric Image Reconstruction in Reduced Parameter Space for Rapid Multi-Tracer PET Imaging.

    Science.gov (United States)

    Cheng, Xiaoyin; Li, Zhoulei; Liu, Zhen; Navab, Nassir; Huang, Sung-Cheng; Keller, Ulrich; Ziegler, Sibylle; Shi, Kuangyu

    2015-02-12

    The separation of multiple PET tracers within an overlapping scan based on intrinsic differences of tracer pharmacokinetics is challenging, due to limited signal-to-noise ratio (SNR) of PET measurements and high complexity of fitting models. In this study, we developed a direct parametric image reconstruction (DPIR) method for estimating kinetic parameters and recovering single tracer information from rapid multi-tracer PET measurements. This is achieved by integrating a multi-tracer model in a reduced parameter space (RPS) into dynamic image reconstruction. This new RPS model is reformulated from an existing multi-tracer model and contains fewer parameters for kinetic fitting. Ordered-subsets expectation-maximization (OSEM) was employed to approximate log-likelihood function with respect to kinetic parameters. To incorporate the multi-tracer model, an iterative weighted nonlinear least square (WNLS) method was employed. The proposed multi-tracer DPIR (MTDPIR) algorithm was evaluated on dual-tracer PET simulations ([18F]FDG and [11C]MET) as well as on preclinical PET measurements ([18F]FLT and [18F]FDG). The performance of the proposed algorithm was compared to the indirect parameter estimation method with the original dual-tracer model. The respective contributions of the RPS technique and the DPIR method to the performance of the new algorithm were analyzed in detail. For the preclinical evaluation, the tracer separation results were compared with single [18F]FDG scans of the same subjects measured 2 days before the dual-tracer scan. The results of the simulation and preclinical studies demonstrate that the proposed MT-DPIR method can improve the separation of multiple tracers for PET image quantification and kinetic parameter estimations.

  1. A framework for creating realistic synthetic fluorescence microscopy image sequences

    CSIR Research Space (South Africa)

    Mabaso, M

    2016-02-01

    Full Text Available Fluorescence microscopy imaging is an important tool in modern biological research, allowing insights into the processes of biological systems. Automated image analysis algorithms help in extracting information from these images. Validation...

  2. Rapid identification of thousands of copperhead snake (Agkistrodon contortrix) microsatellite loci from modest amounts of 454 shotgun genome sequence.

    Science.gov (United States)

    Castoe, Todd A; Poole, Alexander W; Gu, Wanjun; Jason de Koning, A P; Daza, Juan M; Smith, Eric N; Pollock, David D

    2010-03-01

    Optimal integration of next-generation sequencing into mainstream research requires re-evaluation of how problems can be reasonably overcome and what questions can be asked. One potential application is the rapid acquisition of genomic information to identify microsatellite loci for evolutionary, population genetic and chromosome linkage mapping research on non-model and not previously sequenced organisms. Here, we report on results using high-throughput sequencing to obtain a large number of microsatellite loci from the venomous snake Agkistrodon contortrix, the copperhead. We used the 454 Genome Sequencer FLX next-generation sequencing platform to sample randomly ∼27 Mbp (128 773 reads) of the copperhead genome, thus sampling about 2% of the genome of this species. We identified microsatellite loci in 11.3% of all reads obtained, with 14 612 microsatellite loci identified in total, 4564 of which had flanking sequences suitable for polymerase chain reaction primer design. The random sequencing-based approach to identify microsatellites was rapid, cost-effective and identified thousands of useful microsatellite loci in a previously unstudied species. © 2009 Blackwell Publishing Ltd.

  3. Featured Image: Making a Rapidly Rotating Black Hole

    Science.gov (United States)

    Kohler, Susanna

    2017-10-01

    These stills from a simulation show the evolution (from left to right and top to bottom) of a high-mass X-ray binary over 1.1 days, starting after the star on the right fails to explode as a supernova and then collapses into a black hole. Many high-mass X-ray binaries like the well-known Cygnus X-1, the first source widely accepted to be a black hole host rapidly spinning black holes. Despite our observations of these systems, however, were still not sure how these objects end up with such high rotation speeds. Using simulations like that shown above, a team of scientists led by Aldo Batta (UC Santa Cruz) has demonstrated how a failed supernova explosion can result in such a rapidly spinning black hole. The authors work shows that in a binary where one star attempts to explode as a supernova and fails it doesnt succeed in unbinding the star the large amount of fallback material can interact with the companion star and then accrete onto the black hole, spinning it up in the process. You can read more about the authors simulations and conclusions in the paper below.CitationAldo Batta et al 2017 ApJL 846 L15. doi:10.3847/2041-8213/aa8506

  4. Rapid HIFU autofocusing using the entire MR-ARFI image

    Energy Technology Data Exchange (ETDEWEB)

    Grissom, William A.; Kaye, Elena; Pauly, Kim Butts; Zur, Yuval; Yeo, Desmond; Medan, Yoav; Davis, Cynthia [Biomedical Engineering, Vanderbilt University, Nashville, Tennessee (United States); Electrical Engineering, Stanford University, Stanford, California (United States); Radiology, Stanford University, Stanford, California (United States); GE Healthcare, Haifa (Israel); GE Global Research, Niskayuna, New York (United States); Biomedical Engineering, Technion IIT, Haifa (Israel); GE Global Research, Niskayuna, New York (United States)

    2012-11-28

    Phase aberrations and attenuations caused by bone can defocus HIFU in the brain and organs behind the ribcage. To refocus the beam, MR-ARFI can be used to measure tissue displacements created by each element in the transducer, and optimize driving signal delays and amplitudes. We introduce a new MR-ARFI-based autofocusing method that requires many fewer image acquisitions than current methods. The method is validated in simulations of bone and brain HIFU transducers, and compared to a conventional method.

  5. Pressure applied by the healthcare staff on a cricoids cartilage simulator during Sellick's maneuver in rapid sequence intubation

    NARCIS (Netherlands)

    J.A. Calvache (Jose Andrés); L.C.B. Sandoval (Luz); W.A. Vargas (William Andres)

    2013-01-01

    textabstractBackground: Sellick's maneuver or cricoid pressure is a strategy used to prevent bronchoaspiration during the rapid intubation sequence. Several studies have described that the force required for an adequate maneuver is of 2.5-3.5 kg. The purpose of this paper was to determine the force

  6. Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

    DEFF Research Database (Denmark)

    Larsen, P B; Hansen, E G; Jacobsen, L S

    2005-01-01

    conditions of standard doses of rocuronium 0.6 mg kg[-1] and succinylcholine 1.0 mg kg[-1] during a strict rapid-sequence induction regimen including propofol and alfentanil. Methods: Male and female patients (ASA I-III) older than 17 yr scheduled for emergency abdominal or gynaecological surgery...

  7. Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

    DEFF Research Database (Denmark)

    Larsen, P B; Hansen, E G; Jacobsen, L S

    2005-01-01

    and with increased risk of pulmonary aspiration of gastric content were randomized to a rapid-sequence induction with succinylcholine 1.0 mg kg[-1] or rocuronium 0.6 mg kg[-1]. Patients with a predicted difficult airway were excluded. A senior anaesthesiologist 'blinded' for the randomization performed...

  8. Determination of exterior parameters for video image sequences from helicopter by block adjustment with combined vertical and oblique images

    Science.gov (United States)

    Zhang, Jianqing; Zhang, Yong; Zhang, Zuxun

    2003-09-01

    Determination of image exterior parameters is a key aspect for the realization of automatic texture mapping of buildings in the reconstruction of real 3D city models. This paper reports about an application of automatic aerial triangulation on a block with three video image sequences, one vertical image sequence to buildings' roofs and two oblique image sequences to buildings' walls. A new process procedure is developed in order to auto matching homologous points between images in oblique and vertical images. Two strategies are tested. One is treating three strips as independent blocks and executing strip block adjustment respectively, the other is creating a block with three strips, using the new image matching procedure to extract large number of tie points and executing block adjustment. The block adjustment results of these two strategies are also compared.

  9. Rapid interferometric imaging of printed drug laden multilayer structures

    DEFF Research Database (Denmark)

    Sandler, Niklas; Kassamakov, Ivan; Ehlers, Henrik

    2014-01-01

    /and active pharmaceutical ingredients (API) adhere to each other. This is crucial in order to have predetermined drug release profiles. We also demonstrate non-invasive measurement of a polymer structure in a microfluidic channel. It shown that traceable interferometric 3D microscopy is a viable technique......The developments in printing technologies allow fabrication of micron-size nano-layered delivery systems to personal specifications. In this study we fabricated layered polymer structures for drug-delivery into a microfluidic channel and aimed to interferometrically assure their topography...... and adherence to each other. We present a scanning white light interferometer (SWLI) method for quantitative assurance of the topography of the embedded structure. We determined rapidly in non-destructive manner the thickness and roughness of the structures and whether the printed layers containing polymers or...

  10. Computer Vision Tools for Finding Images and Video Sequences.

    Science.gov (United States)

    Forsyth, D. A.

    1999-01-01

    Computer vision offers a variety of techniques for searching for pictures in large collections of images. Appearance methods compare images based on the overall content of the image using certain criteria. Finding methods concentrate on matching subparts of images, defined in a variety of ways, in hope of finding particular objects. These ideas…

  11. Rapid identification of heterogeneous mixture components with hyperspectral coherent anti-Stokes Raman scattering imaging

    NARCIS (Netherlands)

    Garbacik, E.T.; Herek, Jennifer Lynn; Otto, Cornelis; Offerhaus, Herman L.

    2012-01-01

    For the rapid analysis of complicated heterogeneous mixtures, we have developed a method to acquire and intuitively display hyperspectral coherent anti-Stokes Raman scattering (CARS) images. The imaging is performed with a conventional optical setup based around an optical parametric oscillator.

  12. Rapid detection of a norovirus pseudo-outbreak by using real-time sequence based information

    NARCIS (Netherlands)

    Rahamat-Langendoen, J. C.; Lokate, M.; Scholvinck, E. H.; Friedrich, A. W.; Niesters, H. G. M.

    Background: Sequence based information is increasingly used to study the epidemiology of viruses, not only to provide insight in viral evolution, but also to understand transmission patterns during outbreaks. However, sequence analysis is not yet routinely performed by diagnostic laboratories,

  13. Supraglottic airway device use as a primary airway during rapid sequence intubation.

    Science.gov (United States)

    Frascone, Ralph J; Wewerka, Sandi S; Burnett, Aaron M; Griffith, Kent R; Salzman, Joshua G

    2013-01-01

    This study compared first-attempt placement success rates of the King LTS-D as a primary airway for patients requiring medication-assisted airway management (MAAM) against historical controls. Rotor-wing division of a single critical care transportation company 53 providers (RNs/EMT-P) consented to participation and were trained in the use of the King LTS-D. All patients in need of MAAM per agency treatment guidelines were screened for inclusion and exclusion criteria. After each placement attempt, providers completed data collection via telephone. The primary endpoint was comparison of first-attempt placement success rate between the King LTS-D and historical control endotracheal intubation (ETI) MAAM patients. Overall placement success, time to placement, pre- and post-placement SaO2, ETCO2 at 2 minutes after placement, and complications were also analyzed. 38 patients received rapid sequence intubation with the King LTS-D by 23 of 58 consented providers. First-attempt success rate was 76% (29/38), with an overall success rate of 84% (32/38). The primary endpoint analysis showed no difference in first-attempt success rate between historical control ETI MAAM data and King LTS-D (71% vs 76%; OR = 0.1.34 [95% CI Intubation time to insertion was 26 seconds (IQR = 12-46). Pre- and post-insertion SaO(1)2 values were 88.9 ± 12.6% and 92.1 ± 12.7%, respectively. Mean ETCO2 at 2 minutes after placement was 34.8 ± 4.0. Vomit in the patient's airway was the most frequently reported complication (46%). Success rates with the King LTS-D were not significantly different from historical control ETI data. Time to placement was comparable to previous reports. Copyright © 2013 Air Medical Journal Associates. Published by Elsevier Inc. All rights reserved.

  14. Effect of Intensive Physician Oversight on a Prehospital Rapid Sequence Induction Program

    Science.gov (United States)

    Cushman, Jeremy T.; Hettinger, A. Zachary; Farney, Aaron; Shah, Manish N.

    2010-01-01

    Objective To examine the effects of adding close concurrent and retrospective physician oversight, consistent with NAEMSP recommendations, to an existing regional prehospital rapid sequence induction (RSI) program. Methods This study involved a retrospective cohort of patients receiving RSI between January 1st, 2004 and July 31st, 2008. On January 1st, 2007 an updated program including additional concurrent and retrospective physician oversight, increased RSI specific continuing medical education, and cadaver lab training was implemented. Study patients were divided into pre- (1) and post- (2) intervention groups based on date of medical care. Data regarding baseline characteristics, airway management, medication usage, and performance factors were compared between groups. A retrospective review by two EMS physicians assessed if the RSI was “clearly indicated” based on a predetermined set of criteria Results There were 109 RSIs performed in Group 1, and 54 in Group 2. Absolute increases in the use of both BLS (5%, p=0.02) and ALS (41%, p=0.001) airway techniques were observed. Increases in post-intubation administration of midazolam (30%, p=0.001) and morphine (24%, p=0.001), and decrease for vecuronium (−28%, p=0.001) were observed. The intubation success rate (92 vs. 94%) and frequency of recognized esophageal ETT placement (5 vs. 6%) were not statistically different. The number of unrecognized esophageal ETT placements remained zero. Physician chart review demonstrated an absolute increase in “clearly indicated” RSIs (17%, p=0.013). Conclusions Close concurrent and retrospective physician oversight consistent with recommendations from the National Association of EMS Physicians is associated with improved cognitive skills in paramedics, including appropriate patient selection for RSI. Further research is warranted to validate this model and optimize where resources are best used to enhance patient safety and improve clinical management for this

  15. Role of rapid sequence whole-body MRI screening in SDH-associated hereditary paraganglioma families.

    Science.gov (United States)

    Jasperson, Kory W; Kohlmann, Wendy; Gammon, Amanda; Slack, Heidi; Buchmann, Luke; Hunt, Jason; Kirchhoff, Anne C; Baskin, Henry; Shaaban, Akram; Schiffman, Joshua D

    2014-06-01

    Patients with germline mutations in one of the SDH genes are at substantially increased risk of developing paragangliomas, pheochromocytomas (pheos), and other tumors (all combined referred to as SDH-related tumors). However, limited data exist on screening in SDH mutation carriers and no studies have evaluated whole-body MRI as a screening tool in asymptomatic patients. This was a single-center observational study. We evaluated the results of screening in 37 SDH carriers who underwent 45 whole-body MRIs and 47 biochemical tests. Screening included annual biochemical testing (catecholamines, metanephrines and chromogranin A) and biennial or annual rapid sequence whole-body MRI from the base of the skull to the pelvis beginning at age 10 years old. Six tumors (paragangliomas of the organ of Zuckerkandl, the aortocaval/vas deferens, of the carotid body times three, and a renal cell carcinoma) were diagnosed in five patients. In total, 13.5 % of all patients screened were diagnosed with SDH-related tumors. Whole-body MRI missed one tumor, while biochemical testing was normal in five patients with SDH-related tumors. The sensitivity of whole-body MRI was 87.5 % and the specificity was 94.7 %, while the sensitivity of biochemical testing was 37.5 % and the specificity was 94.9 %. Whole-body MRI had a higher sensitivity for SDH-related tumors than biochemical testing in patients undergoing screening due to their SDHB or SDHC mutation status. Whole-body MRI reduces radiation exposure compared to computed tomography scan and time compared to dedicated MRI of the head/neck, thorax, and abdomen/pelvis.

  16. Paramedic rapid sequence intubation in patients with non-traumatic coma.

    Science.gov (United States)

    Bernard, S A; Smith, K; Porter, R; Jones, C; Gailey, A; Cresswell, B; Cudini, D; Hill, S; Moore, B; St Clair, T

    2015-01-01

    Pre-hospital intubation by paramedics is widely used in comatose patients prior to transportation to hospital, but the optimal technique for intubation is uncertain. One approach is paramedic rapid sequence intubation (RSI), which may improve outcomes in adult patients with traumatic brain injury. However, many patients present to emergency medical services with coma of non-traumatic cause and the role of paramedic RSI in these patients remains uncertain. The electronic Victorian Ambulance Clinical Information System was searched for the term 'suxamethonium' between 2008 and 2011. We reviewed the patient care records and included patients with suspected non-traumatic coma who were treated and transported by road-based paramedics. Demographics, intubation conditions, vital signs (before and after drug administration) and complications were recorded. Younger patients (patients. There were 1152 paramedic RSI attempts of which 551 were for non-traumatic coma. The success rate for intubation was 97.5%. There was a significant drop in blood pressure in younger patients (patients, the systolic blood pressure also decreased significantly by 20 mm Hg (95% CI 17 to 24). Four patients suffered brief cardiac arrest during pre-hospital care, all of whom were successfully resuscitated and transported to hospital. Paramedic RSI in patients with non-traumatic coma has a high procedural success rate. Further studies are required to determine whether this procedure improves outcomes. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  17. Rapid MR imaging of cryoprotectant permeation in an engineered dermal replacement.

    Science.gov (United States)

    Bidault, N P; Hammer, B E; Hubel, A

    2000-02-01

    Magnetic resonance (MR) imaging is a powerful technique for monitoring the permeation of cryoprotective agents (CPAs) inside tissues. However, the techniques published until now suffer from inherently long imaging times, limiting the application of these techniques to slow diffusion processes and large CPA concentrations. In this study, we present a rapid MR imaging technique based on a CHESS-FLASH scheme combined with Keyhole image acquisition. This technique can image the fast permeation of Me(2)SO solutions into freeze-dried artificial dermal replacements for concentrations down to 10% v/v. Special attention is given to evaluating the technique for quantitative analysis. Copyright 2000 Academic Press.

  18. Quantitative sodium imaging with a flexible twisted projection pulse sequence

    National Research Council Canada - National Science Library

    Lu, Aiming; Atkinson, Ian C; Claiborne, Theodore C; Damen, Frederick C; Thulborn, Keith R

    2010-01-01

    The quantification of sodium MR images from an arbitrary intensity scale into a bioscale fosters image interpretation in terms of the spatially resolved biochemical process of sodium ion homeostasis...

  19. Rapid Sanger sequencing of the 16S rRNA gene for identification of some common pathogens.

    Directory of Open Access Journals (Sweden)

    Linxiang Chen

    Full Text Available Conventional Sanger sequencing remains time-consuming and laborious. In this study, we developed a rapid improved sequencing protocol of 16S rRNA for pathogens identification by using a new combination of SYBR Green I real-time PCR and Sanger sequencing with FTA® cards. To compare the sequencing quality of this method with conventional Sanger sequencing, 12 strains, including three kinds of strains (1 reference strain and 3 clinical strains, which were previously identified by biochemical tests, which have 4 Pseudomonas aeruginosa, 4 Staphyloccocus aureus and 4 Escherichia coli, were targeted. Additionally, to validate the sequencing results and bacteria identification, expanded specimens with 90 clinical strains, also comprised of the three kinds of strains which included 30 samples respectively, were performed as just described. The results showed that although statistical differences (P<0.05 were found in sequencing quality between the two methods, their identification results were all correct and consistent. The workload, the time consumption and the cost per batch were respectively light versus heavy, 8 h versus 11 h and $420 versus $400. In the 90 clinical strains, all of the Pseudomonas aeruginosa and Staphyloccocus aureus strains were correctly identified, but only 26.7% of the Escherichia coli strains were recognized as Escherichia coli, while 33.3% as Shigella sonnei and 40% as Shigella dysenteriae. The protocol described here is a rapid, reliable, stable and convenient method for 16S rRNA sequencing, and can be used for Pseudomonas aeruginosa and Staphyloccocus aureus identification, yet it is not completely suitable for discriminating Escherichia coli and Shigella strains.

  20. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

    OpenAIRE

    Torella, Joseph P.; Boehm, Christian R.; Lienert, Florian; Chen, Jan-Hung; Way, Jeffrey C.; Silver, Pamela A.

    2013-01-01

    In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly....

  1. Nonphysician Out-of-Hospital Rapid Sequence Intubation Success and Adverse Events: A Systematic Review and Meta-Analysis.

    Science.gov (United States)

    Fouche, Pieter F; Stein, Christopher; Simpson, Paul; Carlson, Jestin N; Doi, Suhail A

    2017-10-01

    Rapid sequence intubation performed by nonphysicians such as paramedics or nurses has become increasingly common in many countries; however, concerns have been stated in regard to the safe use and appropriateness of rapid sequence intubation when performed by these health care providers. The aim of our study is to compare rapid sequence intubation success and adverse events between nonphysician and physician in the out-of-hospital setting. A systematic literature search of key databases including MEDLINE, EMBASE, and the Cochrane Library was conducted. Eligibility, data extraction, and assessment of risk of bias were assessed independently by 2 reviewers. A bias-adjusted meta-analysis using a quality-effects model was conducted for the primary outcomes of overall intubation success and first-pass intubation success and for adverse events when possible. Eighty-three studies were included in the meta-analysis. There was a 2% difference in successful intubation proportion for physicians versus nonphysicians, 99% (95% confidence interval [CI] 98% to 99%) versus 97% (95% CI 95% to 99%). A 10% difference in first-pass rapid sequence intubation success was noted between physicians versus nonphysicians, 88% (95% CI 83% to 93%) versus 78% (95% CI 65% to 89%). For airway trauma, bradycardia, cardiac arrest, endobronchial intubation, hypertension, and hypotension, lower prevalences of adverse events were noted for physicians. However, nonphysicians had a lower prevalence of hypoxia and esophageal intubations. Similar proportions were noted for pulmonary aspiration and emesis. Nine adverse events estimates lacked precision, except for endobronchial intubation, and 4 adverse event analyses showed evidence of possible publication bias. Consequently, no reliable evidence exists for differences between physicians and nonphysicians for adverse events. This analysis shows that physicians have a higher rapid sequence intubation first-pass and overall success, as well as mostly lower

  2. Survival in Out-of-hospital Rapid Sequence Intubation of Non-Traumatic Brain Pathologies.

    Science.gov (United States)

    Fouche, Pieter Francsois; Jennings, Paul Andrew; Smith, Karen; Boyle, Malcolm; Blecher, Gabriel; Knott, Jonathan; Raji, Mani; Rosengarten, Pamela; Augello, Michael Roberto; Bernard, Stephen

    2017-01-01

    Rapid sequence intubation (RSI) is not only used in traumatic brain injuries in the out-of-hospital setting, but also for non-traumatic brain pathologies (NTBP) such as brain tumors, meningitis, encephalitis, hypoxic/anoxic brain injury, stroke, arteriovenous malformations, tumors, aneurysms, brain hemorrhage, as well as brain injury due to diabetes, seizures and toxicity, metabolic conditions, and alcohol and drug overdose. Previous research suggests that RSI is common in non-traumatic coma, but with an unknown prevalence of NTBP in those that receive RSI. If NTBP is common and if brain trauma RSI evidence is not valid for NTBP then a sizable proportion of NTBP receive this treatment without evidence of benefit. This study calculated the out-of-hospital NTBP prevalence in patients that had received RSI and explored factors that predicted survival. A retrospective cohort study based on data collected from an ambulance service and seven hospitals based in Melbourne, Australia. Non-traumatic brain pathologies were defined using ICD10-AM codes for the calculation of NTBP prevalence. Logistic regression modelled out-of-hospital predictors of survival to hospital discharge after adjustment for comorbidities. The seven participating hospitals treated 2,277 patients that received paramedic RSI for all illnesses and indications from January 1, 2008 to December 31, 2015, with survival data available for 1,940 (85%). Of the 1,940, 1,125 (58%) patients had at least one hospital-diagnosed NTBP. Sixty-nine percent all of NTBP survived to hospital discharge, compared to 65% for traumatic intracranial injury. Strokes were the most common and had poor survival to discharge (37%) compared to the second most common NTBP toxicity/toxic encephalopathy that had very high survival (98%). No out-of-hospital clinical intervention or prehospital time interval predicted survival. Factors that did predict survival include Glasgow Coma Scale (GCS), duration of mechanical ventilation, age, ICU

  3. DPS - a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque.

    Science.gov (United States)

    Kot, Witold; Vogensen, Finn K; Sørensen, Søren J; Hansen, Lars H

    2014-02-01

    Bacteriophages (phages) coexist with bacteria in all environments and influence microbial diversity, evolution and industrial production processes. As a result of this major impact of phages on microbes, tools that allow rapid characterization of phages are needed. Today, one of the most powerful methods for characterization of phages is determination of the whole genome using high throughput sequencing approaches. Here a direct plaque sequencing (DPS) is described, which is a rapid method that allows easy full genome sequencing of DNA-containing phages using the Nextera XT™ kit. A combination of host-DNA removal followed by purification and concentration of the viral DNA, allowed the construction of Illumina-compatible sequencing libraries using the Nextera™ XT technology directly from single phage plaques without any whole genome amplification step. This method was tested on three Caudovirales phages; ϕ29 Podoviridae, P113g Siphoviridae and T4 Myovirdae, which are representative of >96% of all known phages, and were sequenced using the Illumina MiSeq platform. Successful de novo assembly of the viral genomes was possible. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Scalable metagenomics alignment research tool (SMART): a scalable, rapid, and complete search heuristic for the classification of metagenomic sequences from complex sequence populations.

    Science.gov (United States)

    Lee, Aaron Y; Lee, Cecilia S; Van Gelder, Russell N

    2016-07-28

    Next generation sequencing technology has enabled characterization of metagenomics through massively parallel genomic DNA sequencing. The complexity and diversity of environmental samples such as the human gut microflora, combined with the sustained exponential growth in sequencing capacity, has led to the challenge of identifying microbial organisms by DNA sequence. We sought to validate a Scalable Metagenomics Alignment Research Tool (SMART), a novel searching heuristic for shotgun metagenomics sequencing results. After retrieving all genomic DNA sequences from the NCBI GenBank, over 1 × 10(11) base pairs of 3.3 × 10(6) sequences from 9.25 × 10(5) species were indexed using 4 base pair hashtable shards. A MapReduce searching strategy was used to distribute the search workload in a computing cluster environment. In addition, a one base pair permutation algorithm was used to account for single nucleotide polymorphisms and sequencing errors. Simulated datasets used to evaluate Kraken, a similar metagenomics classification tool, were used to measure and compare precision and accuracy. Finally using a same set of training sequences we compared Kraken, CLARK, and SMART within the same computing environment. Utilizing 12 computational nodes, we completed the classification of all datasets in under 10 min each using exact matching with an average throughput of over 1.95 × 10(6) reads classified per minute. With permutation matching, we achieved sensitivity greater than 83 % and precision greater than 94 % with simulated datasets at the species classification level. We demonstrated the application of this technique applied to conjunctival and gut microbiome metagenomics sequencing results. In our head to head comparison, SMART and CLARK had similar accuracy gains over Kraken at the species classification level, but SMART required approximately half the amount of RAM of CLARK. SMART is the first scalable, efficient, and rapid metagenomics classification algorithm

  5. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences

    OpenAIRE

    Lundblad, Eirik W.; Xiao, Gaoping; Ko, Jae-hyeong; Altman, Sidney

    2008-01-01

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few ho...

  6. Spatiotonal adaptivity in super-resolution of under-sampled image sequences

    NARCIS (Netherlands)

    Pham, T.Q.

    2006-01-01

    This thesis concerns the use of spatial and tonal adaptivity in improving the resolution of aliased image sequences under scene or camera motion. Each of the five content chapters focuses on a different subtopic of super-resolution: image registration (chapter 2), image fusion (chapter 3 and 4),

  7. Real-time UAV trajectory generation using feature points matching between video image sequences

    Science.gov (United States)

    Byun, Younggi; Song, Jeongheon; Han, Dongyeob

    2017-09-01

    Unmanned aerial vehicles (UAVs), equipped with navigation systems and video capability, are currently being deployed for intelligence, reconnaissance and surveillance mission. In this paper, we present a systematic approach for the generation of UAV trajectory using a video image matching system based on SURF (Speeded up Robust Feature) and Preemptive RANSAC (Random Sample Consensus). Video image matching to find matching points is one of the most important steps for the accurate generation of UAV trajectory (sequence of poses in 3D space). We used the SURF algorithm to find the matching points between video image sequences, and removed mismatching by using the Preemptive RANSAC which divides all matching points to outliers and inliers. The inliers are only used to determine the epipolar geometry for estimating the relative pose (rotation and translation) between image sequences. Experimental results from simulated video image sequences showed that our approach has a good potential to be applied to the automatic geo-localization of the UAVs system

  8. Rapid biocompatibility analysis of materials via in vivo fluorescence imaging of mouse models.

    Directory of Open Access Journals (Sweden)

    Kaitlin M Bratlie

    Full Text Available BACKGROUND: Many materials are unsuitable for medical use because of poor biocompatibility. Recently, advances in the high throughput synthesis of biomaterials has significantly increased the number of potential biomaterials, however current biocompatibility analysis methods are slow and require histological analysis. METHODOLOGY/PRINCIPAL FINDINGS: Here we develop rapid, non-invasive methods for in vivo quantification of the inflammatory response to implanted biomaterials. Materials were placed subcutaneously in an array format and monitored for host responses as per ISO 10993-6: 2001. Host cell activity in response to these materials was imaged kinetically, in vivo using fluorescent whole animal imaging. Data captured using whole animal imaging displayed similar temporal trends in cellular recruitment of phagocytes to the biomaterials compared to histological analysis. CONCLUSIONS/SIGNIFICANCE: Histological analysis similarity validates this technique as a novel, rapid approach for screening biocompatibility of implanted materials. Through this technique there exists the possibility to rapidly screen large libraries of polymers in vivo.

  9. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

    Directory of Open Access Journals (Sweden)

    Stephen J Salipante

    Full Text Available Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times and inexpensive for routine clinical use.

  10. Intubation conditions after rocuronium or succinylcholine for rapid sequence induction with alfentanil and propofol in the emergency patient

    DEFF Research Database (Denmark)

    Larsen, P B; Hansen, E G; Jacobsen, L S

    2005-01-01

    the intubation 60 s after injection of the neuromuscular blocker. Intubating conditions were evaluated according to an established guideline. Tracheal intubation not completed within 30 s was recorded as failed. Results: 222 patients were randomized. Three patients had their operation cancelled and 10 did......Background and objective: Previous studies mainly conducted on elective patients recommend doses of 0.9-1.2 mg kg[-1] rocuronium to obtain comparable intubation conditions with succinylcholine 1.0 mg kg[-1] after 60 s during a rapid-sequence induction. We decided to compare the overall intubating...... conditions of standard doses of rocuronium 0.6 mg kg[-1] and succinylcholine 1.0 mg kg[-1] during a strict rapid-sequence induction regimen including propofol and alfentanil. Methods: Male and female patients (ASA I-III) older than 17 yr scheduled for emergency abdominal or gynaecological surgery...

  11. Single-Trial Event-Related Potential Based Rapid Image Triage System

    Directory of Open Access Journals (Sweden)

    Ke Yu

    2011-06-01

    Full Text Available Searching for points of interest (POI in large-volume imagery is a challenging problem with few good solutions. In this work, a neural engineering approach called rapid image triage (RIT which could offer about a ten-fold speed up in POI searching is developed. It is essentially a cortically-coupled computer vision technique, whereby the user is presented bursts of images at a speed of 6–15 images per second and then neural signals called event-related potential (ERP is used as the ‘cue’ for user seeing images of high relevance likelihood. Compared to past efforts, the implemented system has several unique features: (1 it applies overlapping frames in image chip preparation, to ensure rapid image triage performance; (2 a novel common spatial-temporal pattern (CSTP algorithm that makes use of both spatial and temporal patterns of ERP topography is proposed for high-accuracy single-trial ERP detection; (3 a weighted version of probabilistic support-vector-machine (SVM is used to address the inherent unbalanced nature of single-trial ERP detection for RIT. High accuracy, fast learning, and real-time capability of the developed system shown on 20 subjects demonstrate the feasibility of a brainmachine integrated rapid image triage system for fast detection of POI from large-volume imagery.

  12. 3D noninvasive, high-resolution imaging using a photoacoustic tomography (PAT) system and rapid wavelength-cycling lasers

    Science.gov (United States)

    Sampathkumar, Ashwin; Gross, Daniel; Klosner, Marc; Chan, Gary; Wu, Chunbai; Heller, Donald F.

    2015-05-01

    Globally, cancer is a major health issue as advances in modern medicine continue to extend the human life span. Breast cancer ranks second as a cause of cancer death in women in the United States. Photoacoustic (PA) imaging (PAI) provides high molecular contrast at greater depths in tissue without the use of ionizing radiation. In this work, we describe the development of a PA tomography (PAT) system and a rapid wavelength-cycling Alexandrite laser designed for clinical PAI applications. The laser produces 450 mJ/pulse at 25 Hz to illuminate the entire breast, which eliminates the need to scan the laser source. Wavelength cycling provides a pulse sequence in which the output wavelength repeatedly alternates between 755 nm and 797 nm rapidly within milliseconds. We present imaging results of breast phantoms with inclusions of different sizes at varying depths, obtained with this laser source, a 5-MHz 128-element transducer and a 128-channel Verasonics system. Results include PA images and 3D reconstruction of the breast phantom at 755 and 797 nm, delineating the inclusions that mimic tumors in the breast.

  13. Rapid, low dose X-ray diffractive imaging of the malaria parasite Plasmodium falciparum

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Michael W.M., E-mail: michael.jones@latrobe.edu.au [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Dearnley, Megan K. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia); Riessen, Grant A. van [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Abbey, Brian [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Melbourne Centre for Nanofabrication, Victoria 3168 (Australia); Putkunz, Corey T. [ARC Centre of Excellence for Coherent X-Ray Science, School of Physics, The University of Melbourne, Victoria 3010 (Australia); Junker, Mark D. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Vine, David J. [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); McNulty, Ian [Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439 (United States); Centre for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439 (United States); Nugent, Keith A. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Peele, Andrew G. [ARC Centre of Excellence for Coherent X-Ray Science, Department of Physics, La Trobe University, Victoria 3086 (Australia); Australian Synchrotron, 800 Blackburn Road, Clayton 3168 (Australia); Tilley, Leann [ARC Centre of Excellence for Coherent X-Ray Science, Department of Biochemistry and Molecular Biology, Bio21 Institute, The University of Melbourne, Victoria 3010 (Australia)

    2014-08-01

    Phase-diverse X-ray coherent diffractive imaging (CDI) provides a route to high sensitivity and spatial resolution with moderate radiation dose. It also provides a robust solution to the well-known phase-problem, making on-line image reconstruction feasible. Here we apply phase-diverse CDI to a cellular sample, obtaining images of an erythrocyte infected by the sexual stage of the malaria parasite, Plasmodium falciparum, with a radiation dose significantly lower than the lowest dose previously reported for cellular imaging using CDI. The high sensitivity and resolution allow key biological features to be identified within intact cells, providing complementary information to optical and electron microscopy. This high throughput method could be used for fast tomographic imaging, or to generate multiple replicates in two-dimensions of hydrated biological systems without freezing or fixing. This work demonstrates that phase-diverse CDI is a valuable complementary imaging method for the biological sciences and ready for immediate application. - Highlights: • Phase-diverse coherent X-ray diffraction microscopy provides high-resolution and high-contrast images of intact biological samples. • Rapid nanoscale resolution imaging is demonstrated at orders of magnitude lower dose than previously possible. • Phase-diverse coherent X-ray diffraction microscopy is a robust technique for rapid, quantitative, and correlative X-ray phase imaging.

  14. Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Peter E Chen

    Full Text Available BACKGROUND: The anthrax letter attacks of 2001 highlighted the need for rapid identification of biothreat agents not only for epidemiological surveillance of the intentional outbreak but also for implementing appropriate countermeasures, such as antibiotic treatment, in a timely manner to prevent further casualties. It is clear from the 2001 cases that survival may be markedly improved by administration of antimicrobial therapy during the early symptomatic phase of the illness; i.e., within 3 days of appearance of symptoms. Microbiological detection methods are feasible only for organisms that can be cultured in vitro and cannot detect all genetic modifications with the exception of antibiotic resistance. Currently available immuno or nucleic acid-based rapid detection assays utilize known, organism-specific proteins or genomic DNA signatures respectively. Hence, these assays lack the ability to detect novel natural variations or intentional genetic modifications that circumvent the targets of the detection assays or in the case of a biological attack using an antibiotic resistant or virulence enhanced Bacillus anthracis, to advise on therapeutic treatments. METHODOLOGY/PRINCIPAL FINDINGS: We show here that the Roche 454-based pyrosequencing can generate whole genome draft sequences of deep and broad enough coverage of a bacterial genome in less than 24 hours. Furthermore, using the unfinished draft sequences, we demonstrate that unbiased identification of known as well as heretofore-unreported genetic modifications that include indels and single nucleotide polymorphisms conferring antibiotic and phage resistances is feasible within the next 12 hours. CONCLUSIONS/SIGNIFICANCE: Second generation sequencing technologies have paved the way for sequence-based rapid identification of both known and previously undocumented genetic modifications in cultured, conventional and newly emerging biothreat agents. Our findings have significant implications in

  15. Rapid focused sequencing: a multiplexed assay for simultaneous detection and strain typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis.

    Directory of Open Access Journals (Sweden)

    Rosemary S Turingan

    Full Text Available BACKGROUND: The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses. METHODOLOGY/PRINCIPAL FINDINGS: We have developed microfluidic multiplexed PCR and sequencing assays based on the simultaneous interrogation of three pathogens per assay and ten loci per pathogen. Microfluidic separation of amplified fluorescently labeled fragments generated characteristic electrophoretic signatures for identification of each agent. The three sets of primers allowed significant strain typing and discrimination from non-pathogenic closely-related species and environmental background strains based on amplicon sizes alone. Furthermore, sequencing of the 10 amplicons per pathogen, termed "Rapid Focused Sequencing," allowed an even greater degree of strain discrimination and, in some cases, can be used to determine virulence. Both amplification and sequencing assays were performed in microfluidic biochips developed for fast thermal cycling and requiring 7 µL per reaction. The 30-plex sequencing assay resulted in genotypic resolution of 84 representative strains belonging to each of the three biothreat species. CONCLUSIONS/SIGNIFICANCE: The microfluidic multiplexed assays allowed identification and strain differentiation of the biothreat agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis and clear discrimination from closely-related species and several environmental

  16. Rapid functional and sequence differentiation of a tandemly repeated species-specific multigene family in Drosophila

    DEFF Research Database (Denmark)

    Clifton, Bryan D.; Sanz, Pablo Librado; Yeh, Shu-Dan

    2017-01-01

    results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition. Using various types of massively parallel sequencing data, we studied...

  17. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data

    Science.gov (United States)

    Zomer, Aldert; Burghout, Peter; Bootsma, Hester J.; Hermans, Peter W. M.; van Hijum, Sacha A. F. T.

    2012-01-01

    High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality. PMID:22900082

  18. CT image sequence restoration based on sparse and low-rank decomposition.

    Directory of Open Access Journals (Sweden)

    Shuiping Gou

    Full Text Available Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA, Linearized Alternating Direction Method with Adaptive Penalty (LADMAP and Go Decomposition (GoDec. Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images.

  19. CT image sequence restoration based on sparse and low-rank decomposition.

    Science.gov (United States)

    Gou, Shuiping; Wang, Yueyue; Wang, Zhilong; Peng, Yong; Zhang, Xiaopeng; Jiao, Licheng; Wu, Jianshe

    2013-01-01

    Blurry organ boundaries and soft tissue structures present a major challenge in biomedical image restoration. In this paper, we propose a low-rank decomposition-based method for computed tomography (CT) image sequence restoration, where the CT image sequence is decomposed into a sparse component and a low-rank component. A new point spread function of Weiner filter is employed to efficiently remove blur in the sparse component; a wiener filtering with the Gaussian PSF is used to recover the average image of the low-rank component. And then we get the recovered CT image sequence by combining the recovery low-rank image with all recovery sparse image sequence. Our method achieves restoration results with higher contrast, sharper organ boundaries and richer soft tissue structure information, compared with existing CT image restoration methods. The robustness of our method was assessed with numerical experiments using three different low-rank models: Robust Principle Component Analysis (RPCA), Linearized Alternating Direction Method with Adaptive Penalty (LADMAP) and Go Decomposition (GoDec). Experimental results demonstrated that the RPCA model was the most suitable for the small noise CT images whereas the GoDec model was the best for the large noisy CT images.

  20. Simulation and Efficient Measurements of Intensities for Complex Imaging Sequences

    DEFF Research Database (Denmark)

    Jensen, Jørgen Arendt; Rasmussen, Morten Fischer; Stuart, Matthias Bo

    2014-01-01

    It is investigated how linear simulation can be used to predict both the magnitude of the intensities as well as the placement of the peak values. An ultrasound sequence is defined through the normal setup routines for the experimental SARUS scanner, and Field II is then used automatically on the...

  1. Comparison of breath-hold T1-weighted MR sequences for imaging of the liver.

    Science.gov (United States)

    Semelka, R C; Willms, A B; Brown, M A; Brown, E D; Finn, J P

    1994-01-01

    Three rapid T1-weighted gradient-echo techniques for imaging of the liver were compared: fast low-angle shot (FLASH) and section-selective (SSTF) and non-section-selective (NSTF) inversion-recovery TurboFLASH. Ten healthy volunteers were imaged at 1.5 T, with breath-hold images acquired in the transaxial and coronal planes and non-breath-hold images in the transaxial plane. Breath-hold images were evaluated quantitatively and qualitatively, and non-breath-hold images were evaluated qualitatively. FLASH images had significantly higher (P FLASH images than on NSTF and SSTF images. With breath hold, FLASH images were rated as having the highest quality in the axial plane, followed by NSTF and SSTF images. In the coronal plane, NSTF images were rated as having the highest quality. For images acquired during patient respiration, NSTF images had the highest quality and showed the least degradation. The results suggest that FLASH images have the highest SD/N and S/N for liver imaging and have the highest quality in the axial plane. In patients who cannot suspend respiration. NSTF images may be least affected by breathing artifact and provide reasonable image quality.

  2. Rapid identification of salmonella serotypes with stereo and hyperspectral microscope imaging Methods

    Science.gov (United States)

    The hyperspectral microscope imaging (HMI) method can reduce detection time within 8 hours including incubation process. The early and rapid detection with this method in conjunction with the high throughput capabilities makes HMI method a prime candidate for implementation for the food industry. Th...

  3. Click-Chemistry-Mediated Rapid Microbubble Capture for Acute Thrombus Ultrasound Molecular Imaging.

    Science.gov (United States)

    Wang, Tuantuan; Yuan, Chuxiao; Dai, Bingyang; Liu, Yang; Li, Mingxi; Feng, Zhenqiang; Jiang, Qing; Xu, Zhihong; Zhao, Ningwei; Gu, Ning; Yang, Fang

    2017-07-18

    Bioorthogonal coupling chemistry has been studied as a potentially advantageous approach for molecular imaging because it offers rapid, efficient, and strong binding, which might also benefit stability, production, and chemical conjugation. The inverse-electron-demand Diels-Alder reaction between a 1,2,4,5-tetrazine and trans-cyclooctene (TCO) is an example of a highly selective and rapid bioorthogonal coupling reaction that has been used successfully to prepare targeted molecular imaging probes. Here we report a fast, reliable, and highly sensitive approach, based on a two-step pretargeting bioorthogonal approach, to achieving activated-platelet-specific CD62p-targeted thrombus ultrasound molecular imaging. Tetrazine-modified microbubbles (tetra-MBs) could be uniquely and rapidly captured by subsequent click chemistry of thrombus tagged with a trans-cyclooctene-pretreated CD62p antibody. Moreover, such tetra-MBs showed great long-term stability under physiological conditions, thus offering the ability to monitor thrombus changes in real time. We demonstrated for the first time that a bioorthogonal targeting molecular ultrasound imaging strategy based on tetra-MBs could be a simple but powerful tool for rapid diagnosis of acute thrombosis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Elimination of motion and pulsation artifacts using BLADE sequences in shoulder MR imaging

    Energy Technology Data Exchange (ETDEWEB)

    Lavdas, E.; Zaloni, E. [Technological Education Institute of Athens, Greece, Department of Medical Radiological Technologists, Athens (Greece); Vlychou, M.; Vassiou, K.; Fezoulidis, I. [University of Thessaly, Department of Radiology, Faculty of Medicine, Larissa (Greece); Tsagkalis, A. [IASO Hospital, Department of Orthopedics, Larissa (Greece); Dailiana, Z. [University of Thessaly, Department of Orthopedics, Faculty of Medicine, Larissa (Greece)

    2015-11-15

    To evaluate the ability of proton-density with fat-suppression BLADE (proprietary name for periodically rotated overlapping parallel lines with enhanced reconstruction in MR systems from Siemens Healthcare, PDFS BLADE) and turbo inversion recovery magnitude-BLADE (TIRM BLADE) sequences to reduce motion and pulsation artifacts in shoulder magnetic resonance examinations. Forty-one consecutive patients who had been routinely scanned for shoulder examination participated in the study. The following pairs of sequences with and without BLADE were compared: (a) Oblique coronal proton-density sequence with fat saturation of 25 patients and (b) oblique sagittal T2 TIRM-weighed sequence of 20 patients. Qualitative analysis was performed by two experienced radiologists. Image motion and pulsation artifacts were also evaluated. In oblique coronal PDFS BLADE sequences, motion artifacts have been significantly eliminated, even in five cases of non-diagnostic value with conventional imaging. Similarly, in oblique sagittal T2 TIRM BLADE sequences, image quality has been improved, even in six cases of non-diagnostic value with conventional imaging. Furthermore, flow artifacts have been improved in more than 80% of all the cases. The use of BLADE sequences is recommended in shoulder imaging, especially in uncooperative patients because it effectively eliminates motion and pulsation artifacts. (orig.)

  5. Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool.

    Science.gov (United States)

    Helgason, Agnar; Lalueza-Fox, Carles; Ghosh, Shyamali; Sigurethardóttir, Sigrún; Sampietro, Maria Lourdes; Gigli, Elena; Baker, Adam; Bertranpetit, Jaume; Arnadóttir, Lilja; Thornorsteinsdottir, Unnur; Stefánsson, Kári

    2009-01-01

    A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA) control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

  6. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Tina T.; Pattyn, Pedro; Bakker, Erica G.; Cao, Jun; Cheng, Jan-Fang; Clark, Richard M.; Fahlgren, Noah; Fawcett, Jeffrey A.; Grimwood, Jane; Gundlach, Heidrun; Haberer, Georg; Hollister, Jesse D.; Ossowski, Stephan; Ottilar, Robert P.; Salamov, Asaf A.; Schneeberger, Korbinian; Spannagl, Manuel; Wang, Xi; Yang, Liang; Nasrallah, Mikhail E.; Bergelson, Joy; Carrington, James C.; Gaut, Brandon S.; Schmutz, Jeremy; Mayer, Klaus F. X.; Van de Peer, Yves; Grigoriev, Igor V.; Nordborg, Magnus; Weigel, Detlef; Guo, Ya-Long

    2011-04-29

    In our manuscript, we present a high-quality genome sequence of the Arabidopsis thaliana relative, Arabidopsis lyrata, produced by dideoxy sequencing. We have performed the usual types of genome analysis (gene annotation, dN/dS studies etc. etc.), but this is relegated to the Supporting Information. Instead, we focus on what was a major motivation for sequencing this genome, namely to understand how A. thaliana lost half its genome in a few million years and lived to tell the tale. The rather surprising conclusion is that there is not a single genomic feature that accounts for the reduced genome, but that every aspect centromeres, intergenic regions, transposable elements, gene family number is affected through hundreds of thousands of cuts. This strongly suggests that overall genome size in itself is what has been under selection, a suggestion that is strongly supported by our demonstration (using population genetics data from A. thaliana) that new deletions seem to be driven to fixation.

  7. Rapid and Easy Protocol for Quantification of Next-Generation Sequencing Libraries.

    Science.gov (United States)

    Hawkins, Steve F C; Guest, Paul C

    2018-01-01

    The emergence of next-generation sequencing (NGS) over the last 10 years has increased the efficiency of DNA sequencing in terms of speed, ease, and price. However, the exact quantification of a NGS library is crucial in order to obtain good data on sequencing platforms developed by the current market leader Illumina. Different approaches for DNA quantification are available currently and the most commonly used are based on analysis of the physical properties of the DNA through spectrophotometric or fluorometric methods. Although these methods are technically simple, they do not allow exact quantification as can be achieved using a real-time quantitative PCR (qPCR) approach. A qPCR protocol for DNA quantification with applications in NGS library preparation studies is presented here. This can be applied in various fields of study such as medical disorders resulting from nutritional programming disturbances.

  8. Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.

    Directory of Open Access Journals (Sweden)

    Todd A Castoe

    Full Text Available Identification of microsatellites, or simple sequence repeats (SSRs, can be a time-consuming and costly investment requiring enrichment, cloning, and sequencing of candidate loci. Recently, however, high throughput sequencing (with or without prior enrichment for specific SSR loci has been utilized to identify SSR loci. The direct "Seq-to-SSR" approach has an advantage over enrichment-based strategies in that it does not require a priori selection of particular motifs, or prior knowledge of genomic SSR content. It has been more expensive per SSR locus recovered, however, particularly for genomes with few SSR loci, such as bird genomes. The longer but relatively more expensive 454 reads have been preferred over less expensive Illumina reads. Here, we use Illumina paired-end sequence data to identify potentially amplifiable SSR loci (PALs from a snake (the Burmese python, Python molurus bivittatus, and directly compare these results to those from 454 data. We also compare the python results to results from Illumina sequencing of two bird genomes (Gunnison Sage-grouse, Centrocercus minimus, and Clark's Nutcracker, Nucifraga columbiana, which have considerably fewer SSRs than the python. We show that direct Illumina Seq-to-SSR can identify and characterize thousands of potentially amplifiable SSR loci for as little as $10 per sample--a fraction of the cost of 454 sequencing. Given that Illumina Seq-to-SSR is effective, inexpensive, and reliable even for species such as birds that have few SSR loci, it seems that there are now few situations for which prior hybridization is justifiable.

  9. Motion Estimation Using the Firefly Algorithm in Ultrasonic Image Sequence of Soft Tissue

    Directory of Open Access Journals (Sweden)

    Chih-Feng Chao

    2015-01-01

    Full Text Available Ultrasonic image sequence of the soft tissue is widely used in disease diagnosis; however, the speckle noises usually influenced the image quality. These images usually have a low signal-to-noise ratio presentation. The phenomenon gives rise to traditional motion estimation algorithms that are not suitable to measure the motion vectors. In this paper, a new motion estimation algorithm is developed for assessing the velocity field of soft tissue in a sequence of ultrasonic B-mode images. The proposed iterative firefly algorithm (IFA searches for few candidate points to obtain the optimal motion vector, and then compares it to the traditional iterative full search algorithm (IFSA via a series of experiments of in vivo ultrasonic image sequences. The experimental results show that the IFA can assess the vector with better efficiency and almost equal estimation quality compared to the traditional IFSA method.

  10. Rapid Multi-Tracer PET Tumor Imaging With 18F-FDG and Secondary Shorter-Lived Tracers

    OpenAIRE

    Black, Noel F.; McJames, Scott; Kadrmas, Dan J

    2009-01-01

    Rapid multi-tracer PET, where two to three PET tracers are rapidly scanned with staggered injections, can recover certain imaging measures for each tracer based on differences in tracer kinetics and decay. We previously showed that single-tracer imaging measures can be recovered to a certain extent from rapid dual-tracer 62Cu – PTSM (blood flow) + 62Cu — ATSM (hypoxia) tumor imaging. In this work, the feasibility of rapidly imaging 18F-FDG plus one or two of these shorter-lived secondary trac...

  11. SSR-patchwork: An optimized protocol to obtain a rapid and inexpensive SSR library using first-generation sequencing technology.

    Science.gov (United States)

    Di Maio, Antonietta; De Castro, Olga

    2013-01-01

    We have optimized a version of a microsatellite loci isolation protocol for first-generation sequencing (FGS) technologies. The protocol is optimized to reduce the cost and number of steps, and it combines some procedures from previous simple sequence repeat (SSR) protocols with several key improvements that significantly affect the final yield of the SSR library. This protocol may be accessible for laboratories with a moderate budget or for which next-generation sequencing (NGS) is not readily available. • We drew from classic protocols for library enrichment by digestion, ligation, amplification, hybridization, cloning, and sequencing. Three different systems were chosen: two with very different genome sizes (Galdieria sulphuraria, 10 Mbp; Pancratium maritimum, 30 000 Mbp), and a third with an undetermined genome size (Kochia saxicola). Moreover, we also report the optimization of the sequencing reagents. A good frequency of the obtained microsatellite loci was achieved. • The method presented here is very detailed; comparative tests with other SSR protocols are also reported. This optimized protocol is a promising tool for low-cost genetic studies and the rapid, simple construction of homemade SSR libraries for small and large genomes.

  12. Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances.

    Directory of Open Access Journals (Sweden)

    Alexander S Mikheyev

    Full Text Available BACKGROUND: The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha. PRINCIPAL FINDINGS: By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations. SIGNIFICANCE: De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.

  13. Rapid microsatellite isolation from a butterfly by de novo transcriptome sequencing: performance and a comparison with AFLP-derived distances.

    Science.gov (United States)

    Mikheyev, Alexander S; Vo, Tanya; Wee, Brian; Singer, Michael C; Parmesan, Camille

    2010-06-18

    The isolation of microsatellite markers remains laborious and expensive. For some taxa, such as Lepidoptera, development of microsatellite markers has been particularly difficult, as many markers appear to be located in repetitive DNA and have nearly identical flanking regions. We attempted to circumvent this problem by bioinformatic mining of microsatellite sequences from a de novo-sequenced transcriptome of a butterfly (Euphydryas editha). By searching the assembled sequence data for perfect microsatellite repeats we found 10 polymorphic loci. Although, like many expressed sequence tag-derived microsatellites, our markers show strong deviations from Hardy-Weinberg equilibrium in many populations, and, in some cases, a high incidence of null alleles, we show that they nonetheless provide measures of population differentiation consistent with those obtained by amplified fragment length polymorphism analysis. Estimates of pairwise population differentiation between 23 populations were concordant between microsatellite-derived data and AFLP analysis of the same samples (r = 0.71, p<0.00001, 425 individuals from 23 populations). De novo transcriptional sequencing appears to be a rapid and cost-effective tool for developing microsatellite markers for difficult genomes.

  14. Usefulness of the SPACE pulse sequence at 1.5T MR cholangiography: comparison of image quality and image acquisition time with conventional 3D-TSE sequence.

    Science.gov (United States)

    Nakaura, Takeshi; Kidoh, Masafumi; Maruyama, Natsuki; Kawahara, Tetsuya; Namimoto, Tomohiro; Sakai, Yoshinari; Harada, Kazunori; Yamashita, Yasuyuki

    2013-11-01

    To prospectively evaluate the image quality and image acquisition time at 3D magnetic resonance cholangiopancreatography (MRCP) using sampling perfection with application optimized contrasts (SPACE) and conventional turbo-spin-echo (TSE) sequences. We acquired navigator-triggered SPACE and conventional 3D-TSE MRCP images using the same parameters where possible for 30 patients and compared the image acquisition time, contrast, and contrast-to-noise ratio (CNR) of the common bile duct (CBD). Two radiologists performed qualitative analyses using a 4-point scale. Image acquisition time was 31% shorter with the SPACE than the conventional TSE sequence (248.9 ± 73.0 sec vs. 360.5 ± 99.9 sec, P TSE (39.4 ± 14.7 vs. 33.5 ± 14.2, P TSE sequence; there was a significant difference in motion artifacts and the depiction of the CBD and the left hepatic and main pancreatic duct (P TSE. Copyright © 2013 Wiley Periodicals, Inc.

  15. Imaging thiol redox status in murine tumors in vivo with rapid-scan electron paramagnetic resonance

    Science.gov (United States)

    Epel, Boris; Sundramoorthy, Subramanian V.; Krzykawska-Serda, Martyna; Maggio, Matthew C.; Tseytlin, Mark; Eaton, Gareth R.; Eaton, Sandra S.; Rosen, Gerald M.; Kao, Joseph P. Y.; Halpern, Howard J.

    2017-03-01

    Thiol redox status is an important physiologic parameter that affects the success or failure of cancer treatment. Rapid scan electron paramagnetic resonance (RS EPR) is a novel technique that has shown higher signal-to-noise ratio than conventional continuous-wave EPR in in vitro studies. Here we used RS EPR to acquire rapid three-dimensional images of the thiol redox status of tumors in living mice. This work presents, for the first time, in vivo RS EPR images of the kinetics of the reaction of 2H,15N-substituted disulfide-linked dinitroxide (PxSSPx) spin probe with intracellular glutathione. The cleavage rate is proportional to the intracellular glutathione concentration. Feasibility was demonstrated in a FSa fibrosarcoma tumor model in C3H mice. Similar to other in vivo and cell model studies, decreasing intracellular glutathione concentration by treating mice with L-buthionine sulfoximine (BSO) markedly altered the kinetic images.

  16. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly.

    Science.gov (United States)

    Torella, Joseph P; Boehm, Christian R; Lienert, Florian; Chen, Jan-Hung; Way, Jeffrey C; Silver, Pamela A

    2014-01-01

    In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.

  17. ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data.

    NARCIS (Netherlands)

    Zomer, A.L.; Burghout, P.J.; Bootsma, H.J.; Hermans, P.W.M.; Hijum, S.A.F.T. van

    2012-01-01

    High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon

  18. Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly

    Energy Technology Data Exchange (ETDEWEB)

    Torella, JP; Boehm, CR; Lienert, F; Chen, JH; Way, JC; Silver, PA

    2013-12-28

    In vitro recombination methods have enabled one-step construction of large DNA sequences from multiple parts. Although synthetic biological circuits can in principle be assembled in the same fashion, they typically contain repeated sequence elements such as standard promoters and terminators that interfere with homologous recombination. Here we use a computational approach to design synthetic, biologically inactive unique nucleotide sequences (UNSes) that facilitate accurate ordered assembly. Importantly, our designed UNSes make it possible to assemble parts with repeated terminator and insulator sequences, and thereby create insulated functional genetic circuits in bacteria and mammalian cells. Using UNS-guided assembly to construct repeating promoter-gene-terminator parts, we systematically varied gene expression to optimize production of a deoxychromoviridans biosynthetic pathway in Escherichia coli. We then used this system to construct complex eukaryotic AND-logic gates for genomic integration into embryonic stem cells. Construction was performed by using a standardized series of UNS-bearing BioBrick-compatible vectors, which enable modular assembly and facilitate reuse of individual parts. UNS-guided isothermal assembly is broadly applicable to the construction and optimization of genetic circuits and particularly those requiring tight insulation, such as complex biosynthetic pathways, sensors, counters and logic gates.

  19. Easy Leaf Area: Automated Digital Image Analysis for Rapid and Accurate Measurement of Leaf Area

    Directory of Open Access Journals (Sweden)

    Hsien Ming Easlon

    2014-07-01

    Full Text Available Premise of the study: Measurement of leaf areas from digital photographs has traditionally required significant user input unless backgrounds are carefully masked. Easy Leaf Area was developed to batch process hundreds of Arabidopsis rosette images in minutes, removing background artifacts and saving results to a spreadsheet-ready CSV file. Methods and Results: Easy Leaf Area uses the color ratios of each pixel to distinguish leaves and calibration areas from their background and compares leaf pixel counts to a red calibration area to eliminate the need for camera distance calculations or manual ruler scale measurement that other software methods typically require. Leaf areas estimated by this software from images taken with a camera phone were more accurate than ImageJ estimates from flatbed scanner images. Conclusions: Easy Leaf Area provides an easy-to-use method for rapid measurement of leaf area and nondestructive estimation of canopy area from digital images.

  20. EEG Sequence Imaging: A Markov Prior for the Variational Garrote

    DEFF Research Database (Denmark)

    Hansen, Sofie Therese; Hansen, Lars Kai

    2013-01-01

    We propose the following generalization of the Variational Garrote for sequential EEG imaging: A Markov prior to promote sparse, but temporally smooth source dynamics. We derive a set of modied Variational Garrote updates and analyze the role of the prior's hyperparameters. An experimental...

  1. Outdoor Illumination Estimation in Image Sequences for Augmented Reality

    DEFF Research Database (Denmark)

    Madsen, Claus B.; Lal, Brajesh Behari

    2011-01-01

    the detected shadows is used to estimate the radiance of the sun. The technique does not require special purpose objects in the scene, nor does it require High Dynamic Range imagery. Results are demonstrated by rendering augmented objects into real images with shading and shadows which are consistent...

  2. Large area super-resolution chemical imaging via rapid dithering of a nanoprobe

    Science.gov (United States)

    Languirand, Eric R.; Cullum, Brian M.

    2015-05-01

    Super-resolution chemical imaging via Raman spectroscopy provides a significant ability to simultaneously or pseudosimultaneously monitor numerous label-free analytes while elucidating their spatial distribution on the surface of the sample. However, spontaneous Raman is an inherently weak phenomenon making trace detection and thus superresolution imaging extremely difficult, if not impossible. To circumvent this and allow for trace detection of the few chemical species present in any sub-diffraction limited resolution element of an image, we have developed a surface enhanced Raman scattering (SERS) coherent fiber-optic imaging bundle probe consisting of 30,000 individual fiber elements. When the probes are tapered, etched and coated with metal, they provide circular Raman chemical images of a sample with a field of view of approximately 20μm (i.e. diameter) via the array of 30,000 individual 50 nm fiber elements. An acousto-optic tunable filter is used to rapidly scan or select discrete frequencies for multi- or hyperspectral analysis. Although the 50nm fiber element dimensions of this probe inherently provide spatial resolutions of approximately 100nm, further increases in the spatial resolution can be achieved by using a rapid dithering process. Using this process, additional images are obtained one-half fiber diameter translations in the x- and y- planes. A piezostage drives the movement, providing the accurate and reproducible shifts required for dithering. Optimal probability algorithms are then used to deconvolute the related images producing a final image with a three-fold increase in spatial resolution. This paper describes super-resolution chemical imaging using these probes and the dithering method as well as its potential applications in label-free imaging of lipid rafts and other applications within biology and forensics.

  3. Rapid detection of Clostridium difficile via magnetic bead aggregation in cost-effective polyester microdevices with cell phone image analysis.

    Science.gov (United States)

    DuVall, Jacquelyn A; Cabaniss, Scott T; Angotti, Morgan L; Moore, John H; Abhyankar, Mayuresh; Shukla, Nishant; Mills, Daniel L; Kessel, Bryan G; Garner, Gavin T; Swami, Nathan S; Landers, James P

    2016-10-07

    Pathogen detection has traditionally been accomplished by utilizing methods such as cell culture, immunoassays, and nucleic acid amplification tests; however, these methods are not easily implemented in resource-limited settings because special equipment for detection and thermal cycling is often required. In this study, we present a magnetic bead aggregation assay coupled to an inexpensive microfluidic fabrication technique that allows for cell phone detection and analysis of a notable pathogen in less than one hour. Detection is achieved through the use of a custom-built system that allows for fluid flow control via centrifugal force, as well as manipulation of magnetic beads with an adjustable rotating magnetic field. Cell phone image capture and analysis is housed in a 3D-printed case with LED backlighting and a lid-mounted Android phone. A custom-written application (app.) is employed to interrogate images for the extent of aggregation present following loop-mediated isothermal amplification (LAMP) coupled to product-inhibited bead aggregation (PiBA) for detection of target sequences. Clostridium difficile is a pathogen of increasing interest due to its causative role in intestinal infections following antibiotic treatment, and was therefore chosen as the pathogen of interest in the present study to demonstrate the rapid, cost-effective, and sequence-specific detection capabilities of the microfluidic platform described herein.

  4. Retrieval of Sentence Sequences for an Image Stream via Coherence Recurrent Convolutional Networks.

    Science.gov (United States)

    Park, Cesc; Kim, Youngjin; Kim, Gunhee

    2017-05-02

    We propose an approach for retrieving a sequence of natural sentences for an image stream. Since general users often take a series of pictures on their experiences, much online visual information exists in the form of image streams, for which it would better take into consideration of the whole image stream to produce natural language descriptions. While almost all previous studies have dealt with the relation between a single image and a single natural sentence, our work extends both input and output dimension to a sequence of images and a sequence of sentences. For retrieving a coherent flow of multiple sentences for a photo stream, we propose a multimodal neural architecture called coherence recurrent convolutional network (CRCN), which consists of convolutional neural networks, bidirectional long short-term memory (LSTM) networks, and an entity-based local coherence model. Our approach directly learns from vast user-generated resource of blog posts as text-image parallel training data. We collect more than 22K unique blog posts with 170K associated images for the travel topics of NYC, Disneyland, Australia, and Hawaii. We demonstrate that our approach outperforms other state-of-the-art image captioning methods for text sequence generation, using both quantitative measures and user studies via Amazon Mechanical Turk.

  5. DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays

    Directory of Open Access Journals (Sweden)

    Kenjiro Nagamine

    2015-01-01

    Full Text Available Using Streptococcus pyogenes as a model, we previously established a stepwise computational workflow to effectively identify species-specific DNA signatures that could be used as PCR primer sets to detect target bacteria with high specificity and sensitivity. In this study, we extended the workflow for the rapid development of PCR assays targeting Enterococcus faecalis, Enterococcus faecium, Clostridium perfringens, Clostridium difficile, Clostridium tetani , and Staphylococcus aureus , which are of safety concern for human tissue intended for transplantation. Twenty-one primer sets that had sensitivity of detecting 5–50 fg DNA from target bacteria with high specificity were selected. These selected primer sets can be used in a PCR array for detecting target bacteria with high sensitivity and specificity. The workflow could be widely applicable for the rapid development of PCR-based assays for a wide range of target bacteria, including those of biothreat agents.

  6. Lossless image data sequence compression using optimal context quantization

    DEFF Research Database (Denmark)

    Forchhammer, Søren; WU, Xiaolin; Andersen, Jakob Dahl

    2001-01-01

    Context based entropy coding often faces the conflict of a desire for large templates and the problem of context dilution. We consider the problem of finding the quantizer Q that quantizes the K-dimensional causal context Ci=(X(i-t1), X(i-t2), …, X(i-tK)) of a source symbol Xi into one of M...... and context quantization for coding the binary decisions is presented and applied to digital maps and α-plane sequences. The optimal context quantization is also used to evaluate existing heuristic context quantizations....

  7. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+".

    Directory of Open Access Journals (Sweden)

    Markus H Antwerpen

    Full Text Available The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  8. Rapid high resolution genotyping of Francisella tularensis by whole genome sequence comparison of annotated genes ("MLST+").

    Science.gov (United States)

    Antwerpen, Markus H; Prior, Karola; Mellmann, Alexander; Höppner, Sebastian; Splettstoesser, Wolf D; Harmsen, Dag

    2015-01-01

    The zoonotic disease tularemia is caused by the bacterium Francisella tularensis. This pathogen is considered as a category A select agent with potential to be misused in bioterrorism. Molecular typing based on DNA-sequence like canSNP-typing or MLVA has become the accepted standard for this organism. Due to the organism's highly clonal nature, the current typing methods have reached their limit of discrimination for classifying closely related subpopulations within the subspecies F. tularensis ssp. holarctica. We introduce a new gene-by-gene approach, MLST+, based on whole genome data of 15 sequenced F. tularensis ssp. holarctica strains and apply this approach to investigate an epidemic of lethal tularemia among non-human primates in two animal facilities in Germany. Due to the high resolution of MLST+ we are able to demonstrate that three independent clones of this highly infectious pathogen were responsible for these spatially and temporally restricted outbreaks.

  9. Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila.

    Science.gov (United States)

    Clifton, Bryan D; Librado, Pablo; Yeh, Shu-Dan; Solares, Edwin S; Real, Daphne A; Jayasekera, Suvini U; Zhang, Wanting; Shi, Mijuan; Park, Ronni V; Magie, Robert D; Ma, Hsiu-Ching; Xia, Xiao-Qin; Marco, Antonio; Rozas, Julio; Ranz, José M

    2017-01-01

    Gene clusters of recently duplicated genes are hotbeds for evolutionary change. However, our understanding of how mutational mechanisms and evolutionary forces shape the structural and functional evolution of these clusters is hindered by the high sequence identity among the copies, which typically results in their inaccurate representation in genome assemblies. The presumed testis-specific, chimeric gene Sdic originated, and tandemly expanded in Drosophila melanogaster, contributing to increased male-male competition. Using various types of massively parallel sequencing data, we studied the organization, sequence evolution, and functional attributes of the different Sdic copies. By leveraging long-read sequencing data, we uncovered both copy number and order differences from the currently accepted annotation for the Sdic region. Despite evidence for pervasive gene conversion affecting the Sdic copies, we also detected signatures of two episodes of diversifying selection, which have contributed to the evolution of a variety of C-termini and miRNA binding site compositions. Expression analyses involving RNA-seq datasets from 59 different biological conditions revealed distinctive expression breadths among the copies, with three copies being transcribed in females, opening the possibility to a sexually antagonistic effect. Phenotypic assays using Sdic knock-out strains indicated that should this antagonistic effect exist, it does not compromise female fertility. Our results strongly suggest that the genome consolidation of the Sdic gene cluster is more the result of a quick exploration of different paths of molecular tinkering by different copies than a mere dosage increase, which could be a recurrent evolutionary outcome in the presence of persistent sexual selection. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  10. After Nearly A Decade Of Rapid Growth, Use And Complexity Of Imaging Declined, 2008-14.

    Science.gov (United States)

    Levin, David C; Parker, Laurence; Palit, Charles D; Rao, Vijay M

    2017-04-01

    Imaging is an important cost driver in health care, and its use grew rapidly in the early 2000s. Several studies toward the end of the decade suggested that a leveling off was beginning to occur. In this study we examined more recent data to determine whether the slowdown had continued. Our data sources were the nationwide Medicare Part B databases for the period 2001-14. We calculated utilization rates per 1,000 enrollees for all advanced imaging modalities. We also calculated professional component relative value unit (RVU) rates per 1,000 beneficiaries for all imaging modalities, as RVU values provide a measure of complexity of imaging services and may in some ways be a better reflection of the amount of work involved in imaging. We found that utilization rates and RVU rates grew substantially until 2008 and 2009, respectively, and then began to drop. The downward trend in both rates persisted through 2014. Federal policies appear to have achieved the desired effect of ending the rapid growth of imaging that had been seen in earlier years. Project HOPE—The People-to-People Health Foundation, Inc.

  11. Sequences from first settlers reveal rapid evolution in Icelandic mtDNA pool.

    Directory of Open Access Journals (Sweden)

    Agnar Helgason

    2009-01-01

    Full Text Available A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations. Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time. Here, we show that a sample of mitochondrial DNA (mtDNA control region sequences from 68 early medieval Icelandic skeletal remains is more closely related to sequences from contemporary inhabitants of Scotland, Ireland, and Scandinavia than to those from the modern Icelandic population. Due to a faster rate of genetic drift in the Icelandic mtDNA pool during the last 1,100 years, the sequences carried by the first settlers were better preserved in their ancestral gene pools than among their descendants in Iceland. These results demonstrate the inferential power gained in ancient DNA studies through the application of population genetics analyses to relatively large samples.

  12. Voluntary hyperventilation before a rapid-sequence induction of anesthesia does not decrease postintubation PaCO2.

    Science.gov (United States)

    Choinière, A; Girard, F; Boudreault, D; Ruel, M; Girard, D C

    2001-11-01

    To prevent hypercapnia, voluntary hyperventilation is recommended for patients with increased intracranial pressure before the induction of general anesthesia. We sought to determine whether this maneuver results in a lower PaCO2 than breathing 3 min of oxygen 100% by face mask (preoxygenation) after intubation. Thirty patients requiring general anesthesia were randomly assigned to breathe either 3 min of oxygen 100% by face mask (Group P) or 1 min of oxygen 100% followed by 2 min of voluntary hyperventilation with oxygen 100% (Group H). All patients received a standard rapid-sequence induction of anesthesia followed by a 90-s period of apnea. Patients were then tracheally intubated and mechanically ventilated. Five arterial blood gas samples were taken: with room air, after preoxygenation or hyperventilation, after 60 and 90 s of apnea, and after tracheal intubation. Voluntary hyperventilation decreased PaCO2 before rapid-sequence induction (hyperventilation, 30.0 +/- 3.5 mm Hg versus preoxygenation, 37.9 +/- 5.2 mm Hg; P hyperventilation, 36.1 +/- 3.3 mm Hg versus preoxygenation, 35.6 +/- 3.4 mm Hg; P = 0.673), and no benefit was found after intubation (hyperventilation, 40.5 +/- 3.9 mm Hg versus preoxygenation, 41.4 +/- 2.7 mm Hg; P = 0.603). We conclude that voluntary hyperventilation before rapid-sequence induction does not provide protection against potential hypercapnia during intubation. Voluntary hyperventilation before anesthesia induction is recommended for patients with increased intracranial pressure to prevent hypercapnia. This randomized, prospective study demonstrated that this maneuver does not result in a lower postintubation PaCO2 than standard preoxygenation.

  13. Rapid selection of accessible and cleavable sites in RNA by Escherichia coli RNase P and random external guide sequences.

    Science.gov (United States)

    Lundblad, Eirik W; Xiao, Gaoping; Ko, Jae-Hyeong; Altman, Sidney

    2008-02-19

    A method of inhibiting the expression of particular genes by using external guide sequences (EGSs) has been improved in its rapidity and specificity. Random EGSs that have 14-nt random sequences are used in the selection procedure for an EGS that attacks the mRNA for a gene in a particular location. A mixture of the random EGSs, the particular target RNA, and RNase P is used in the diagnostic procedure, which, after completion, is analyzed in a gel with suitable control lanes. Within a few hours, the procedure is complete. The action of EGSs designed by an older method is compared with EGSs designed by the random EGS method on mRNAs from two bacterial pathogens.

  14. Preparation of 2D sequences of corneal images for 3D model building.

    Science.gov (United States)

    Elbita, Abdulhakim; Qahwaji, Rami; Ipson, Stanley; Sharif, Mhd Saeed; Ghanchi, Faruque

    2014-04-01

    A confocal microscope provides a sequence of images, at incremental depths, of the various corneal layers and structures. From these, medical practioners can extract clinical information on the state of health of the patient's cornea. In this work we are addressing problems associated with capturing and processing these images including blurring, non-uniform illumination and noise, as well as the displacement of images laterally and in the anterior-posterior direction caused by subject movement. The latter may cause some of the captured images to be out of sequence in terms of depth. In this paper we introduce automated algorithms for classification, reordering, registration and segmentation to solve these problems. The successful implementation of these algorithms could open the door for another interesting development, which is the 3D modelling of these sequences. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  15. Evaluation of rapid volume changes of substrate-adherent cells by conventional microscopy 3D imaging.

    Science.gov (United States)

    Boudreault, F; Grygorczyk, R

    2004-09-01

    Precise measurement of rapid volume changes of substrate-adherent cells is essential to understand many aspects of cell physiology, yet techniques to evaluate volume changes with sufficient precision and high temporal resolution are limited. Here, we describe a novel imaging method that surveys the rapid morphology modifications of living, substrate-adherent cells based on phase-contrast, digital video microscopy. Cells grown on a glass substrate are mounted in a custom-designed, side-viewing chamber and subjected to hypotonic swelling. Side-view images of the rapidly swelling cell, and at the end of the assay, an image of the same cell viewed from a perpendicular direction through the substrate, are acquired. Based on these images, off-line reconstruction of 3D cell morphology is performed, which precisely measures cell volume, height and surface at different points during cell volume changes. Volume evaluations are comparable to those obtained by confocal laser scanning microscopy (DeltaVolume microscopy without the need for cell staining or intense illumination to monitor cell volume make this system a promising new tool to investigate the fundamentals of cell volume physiology.

  16. Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues.

    Science.gov (United States)

    Wang, Yu; Woehrstein, Johannes B; Donoghue, Noah; Dai, Mingjie; Avendaño, Maier S; Schackmann, Ron C J; Zoeller, Jason J; Wang, Shan Shan H; Tillberg, Paul W; Park, Demian; Lapan, Sylvain W; Boyden, Edward S; Brugge, Joan S; Kaeser, Pascal S; Church, George M; Agasti, Sarit S; Jungmann, Ralf; Yin, Peng

    2017-10-11

    To decipher the molecular mechanisms of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit but are not widely adopted due to the common limitation of requiring multirounds of slow (typically over 2 h at room temperature to overnight at 4 °C in practice) immunostaining. We present here a practical and robust method, which we call DNA Exchange Imaging (DEI), for rapid in situ spectrally unlimited multiplexing. This technique overcomes speed restrictions by allowing for single-round immunostaining with DNA-barcoded antibodies, followed by rapid (less than 10 min) buffer exchange of fluorophore-bearing DNA imager strands. The programmability of DEI allows us to apply it to diverse microscopy platforms (with Exchange Confocal, Exchange-SIM, Exchange-STED, and Exchange-PAINT demonstrated here) at multiple desired resolution scales (from ∼300 nm down to sub-20 nm). We optimized and validated the use of DEI in complex biological samples, including primary neuron cultures and tissue sections. These results collectively suggest DNA exchange as a versatile, practical platform for rapid, highly multiplexed in situ imaging, potentially enabling new applications ranging from basic science, to drug discovery, and to clinical pathology.

  17. Rapid Development of Microsatellite Markers for Plantago ovata Forsk.: Using Next Generation Sequencing and Their Cross-Species Transferability

    Directory of Open Access Journals (Sweden)

    Ranbir Singh Fougat

    2014-06-01

    Full Text Available Isabgol (Plantago ovata Forsk. is an important medicinal plant having high pharmacological activity in its seed husk, which is substantially used in the food, beverages and packaging industries. Nevertheless, isabgol lags behind in research, particularly for genomic resources, like molecular markers, genetic maps, etc. Presently, molecular markers can be easily developed through next generation sequencing technologies, more efficiently, cost effectively and in less time than ever before. This study was framed keeping in view the need to develop molecular markers for this economically important crop by employing a microsatellite enrichment protocol using a next generation sequencing platform (ion torrent PGM™ to obtain simple sequence repeats (SSRs for Plantago ovata for the very first time. A total of 3447 contigs were assembled, which contained 249 SSRs. Thirty seven loci were randomly selected for primer development; of which, 30 loci were successfully amplified. The developed microsatellite markers showed the amplification of the expected size and cross-amplification in another six species of Plantago. The SSR markers were unable to show polymorphism within P. ovata, suggesting that low variability exists within genotypes of P. ovata. This study suggests that PGM™ sequencing is a rapid and cost-effective tool for developing SSR markers for non-model species, and the markers so-observed could be useful in the molecular breeding of P. ovata.

  18. Imaging inflammation in mouse colon using a rapid stage-scanning confocal fluorescence microscope.

    Science.gov (United States)

    Saldua, Meagan A; Olsovsky, Cory A; Callaway, Evelyn S; Chapkin, Robert S; Maitland, Kristen C

    2012-01-01

    Large area confocal microscopy may provide fast, high-resolution image acquisition for evaluation of tissue in pre-clinical studies with reduced tissue processing in comparison to histology. We present a rapid beam and stage-scanning confocal fluorescence microscope to image cellular and tissue features along the length of the entire excised mouse colon. The beam is scanned at 8,333 lines/sec by a polygon scanning mirror while the specimen is scanned in the orthogonal axis by a motorized translation stage with a maximum speed of 7 mm/sec. A single 1 × 60 mm(2) field of view image spanning the length of the mouse colon is acquired in 10 s. Z-projection images generated from axial image stacks allow high resolution imaging of the surface of non-flat specimens. In contrast to the uniform size, shape, and distribution of colon crypts in confocal images of normal colon, confocal images of chronic bowel inflammation exhibit heterogeneous tissue structure with localized severe crypt distortion.

  19. Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology

    Science.gov (United States)

    Reuter, Sandra; Ellington, Matthew J.; Cartwright, Edward J. P.; Köser, Claudio U.; Török, M. Estée; Gouliouris, Theodore; Harris, Simon R.; Brown, Nicholas M.; Holden, Matthew T. G.; Quail, Mike; Parkhill, Julian; Smith, Geoffrey P.; Bentley, Stephen D.; Peacock, Sharon J.

    2014-01-01

    IMPORTANCE The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens. OBJECTIVE To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens. DESIGN, SETTING, AND PARTICIPANTS A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information. MAIN OUTCOMES AND MEASURES Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data. RESULTS We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of

  20. Rapid visuomotor processing of phobic images in spider- and snake-fearful participants.

    Science.gov (United States)

    Haberkamp, Anke; Schmidt, Filipp; Schmidt, Thomas

    2013-10-01

    This study investigates enhanced visuomotor processing of phobic compared to fear-relevant and neutral stimuli. We used a response priming design to measure rapid, automatic motor activation by natural images (spiders, snakes, mushrooms, and flowers) in spider-fearful, snake-fearful, and control participants. We found strong priming effects in all tasks and conditions; however, results showed marked differences between groups. Most importantly, in the group of spider-fearful individuals, spider pictures had a strong and specific influence on even the fastest motor responses: Phobic primes entailed the largest priming effects, and phobic targets accelerated responses, both effects indicating speeded response activation by phobic images. In snake-fearful participants, this processing enhancement for phobic material was less pronounced and extended to both snake and spider images. We conclude that spider phobia leads to enhanced processing capacity for phobic images. We argue that this is enabled by long-term perceptual learning processes. © 2013.

  1. Rapid mapping of digital integrated circuit logic gates via multi-spectral backside imaging

    CERN Document Server

    Adato, Ronen; Zangeneh, Mahmoud; Zhou, Boyou; Joshi, Ajay; Goldberg, Bennett; Unlu, M Selim

    2016-01-01

    Modern semiconductor integrated circuits are increasingly fabricated at untrusted third party foundries. There now exist myriad security threats of malicious tampering at the hardware level and hence a clear and pressing need for new tools that enable rapid, robust and low-cost validation of circuit layouts. Optical backside imaging offers an attractive platform, but its limited resolution and throughput cannot cope with the nanoscale sizes of modern circuitry and the need to image over a large area. We propose and demonstrate a multi-spectral imaging approach to overcome these obstacles by identifying key circuit elements on the basis of their spectral response. This obviates the need to directly image the nanoscale components that define them, thereby relaxing resolution and spatial sampling requirements by 1 and 2 - 4 orders of magnitude respectively. Our results directly address critical security needs in the integrated circuit supply chain and highlight the potential of spectroscopic techniques to addres...

  2. On-site Rapid Diagnosis of Intracranial Hematoma using Portable Multi-slice Microwave Imaging System

    Science.gov (United States)

    Mobashsher, Ahmed Toaha; Abbosh, A. M.

    2016-11-01

    Rapid, on-the-spot diagnostic and monitoring systems are vital for the survival of patients with intracranial hematoma, as their conditions drastically deteriorate with time. To address the limited accessibility, high costs and static structure of currently used MRI and CT scanners, a portable non-invasive multi-slice microwave imaging system is presented for accurate 3D localization of hematoma inside human head. This diagnostic system provides fast data acquisition and imaging compared to the existing systems by means of a compact array of low-profile, unidirectional antennas with wideband operation. The 3D printed low-cost and portable system can be installed in an ambulance for rapid on-site diagnosis by paramedics. In this paper, the multi-slice head imaging system’s operating principle is numerically analysed and experimentally validated on realistic head phantoms. Quantitative analyses demonstrate that the multi-slice head imaging system is able to generate better quality reconstructed images providing 70% higher average signal to clutter ratio, 25% enhanced maximum signal to clutter ratio and with around 60% hematoma target localization compared to the previous head imaging systems. Nevertheless, numerical and experimental results demonstrate that previous reported 2D imaging systems are vulnerable to localization error, which is overcome in the presented multi-slice 3D imaging system. The non-ionizing system, which uses safe levels of very low microwave power, is also tested on human subjects. Results of realistic phantom and subjects demonstrate the feasibility of the system in future preclinical trials.

  3. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing.

    Science.gov (United States)

    Kowalsky, Caitlin A; Faber, Matthew S; Nath, Aritro; Dann, Hailey E; Kelly, Vince W; Liu, Li; Shanker, Purva; Wagner, Ellen K; Maynard, Jennifer A; Chan, Christina; Whitehead, Timothy A

    2015-10-30

    Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing.

    Science.gov (United States)

    Garcia, Virginie; Bres, Cécile; Just, Daniel; Fernandez, Lucie; Tai, Fabienne Wong Jun; Mauxion, Jean-Philippe; Le Paslier, Marie-Christine; Bérard, Aurélie; Brunel, Dominique; Aoki, Koh; Alseekh, Saleh; Fernie, Alisdair R; Fraser, Paul D; Rothan, Christophe

    2016-12-01

    The tomato is the model species of choice for fleshy fruit development and for the Solanaceae family. Ethyl methanesulfonate (EMS) mutants of tomato have already proven their utility for analysis of gene function in plants, leading to improved breeding stocks and superior tomato varieties. However, until recently, the identification of causal mutations that underlie particular phenotypes has been a very lengthy task that many laboratories could not afford because of spatial and technical limitations. Here, we describe a simple protocol for identifying causal mutations in tomato using a mapping-by-sequencing strategy. Plants displaying phenotypes of interest are first isolated by screening an EMS mutant collection generated in the miniature cultivar Micro-Tom. A recombinant F2 population is then produced by crossing the mutant with a wild-type (WT; non-mutagenized) genotype, and F2 segregants displaying the same phenotype are subsequently pooled. Finally, whole-genome sequencing and analysis of allele distributions in the pools allow for the identification of the causal mutation. The whole process, from the isolation of the tomato mutant to the identification of the causal mutation, takes 6-12 months. This strategy overcomes many previous limitations, is simple to use and can be applied in most laboratories with limited facilities for plant culture and genotyping.

  5. A rapid method for creating qualitative images indicative of thick oil emulsion on the ocean's surface from imaging spectrometer data

    Science.gov (United States)

    Kokaly, Raymond F.; Hoefen, Todd M.; Livo, K. Eric; Swayze, Gregg A.; Leifer, Ira; McCubbin, Ian B.; Eastwood, Michael L.; Green, Robert O.; Lundeen, Sarah R.; Sarture, Charles M.; Steele, Denis; Ryan, Thomas; Bradley, Eliza S.; Roberts, Dar A.; ,

    2010-01-01

    This report describes a method to create color-composite images indicative of thick oil:water emulsions on the surface of clear, deep ocean water by using normalized difference ratios derived from remotely sensed data collected by an imaging spectrometer. The spectral bands used in the normalized difference ratios are located in wavelength regions where the spectra of thick oil:water emulsions on the ocean's surface have a distinct shape compared to clear water and clouds. In contrast to quantitative analyses, which require rigorous conversion to reflectance, the method described is easily computed and can be applied rapidly to radiance data or data that have been atmospherically corrected or ground-calibrated to reflectance. Examples are shown of the method applied to Airborne Visible/Infrared Imaging Spectrometer data collected May 17 and May 19, 2010, over the oil spill from the Deepwater Horizon offshore oil drilling platform in the Gulf of Mexico.

  6. Novel Applications of Rapid Prototyping in Gamma-ray and X-ray Imaging

    Science.gov (United States)

    Miller, Brian W.; Moore, Jared W.; Gehm, Michael E.; Furenlid, Lars R.; Barrett, Harrison H.

    2010-01-01

    Advances in 3D rapid-prototyping printers, 3D modeling software, and casting techniques allow for the fabrication of cost-effective, custom components in gamma-ray and x-ray imaging systems. Applications extend to new fabrication methods for custom collimators, pinholes, calibration and resolution phantoms, mounting and shielding components, and imaging apertures. Details of the fabrication process for these components are presented, specifically the 3D printing process, cold casting with a tungsten epoxy, and lost-wax casting in platinum. PMID:22984341

  7. Comparison of 3 T and 7 T MRI clinical sequences for ankle imaging

    Energy Technology Data Exchange (ETDEWEB)

    Juras, Vladimir, E-mail: vladimir.juras@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Slovak Academy of Sciences, Institute of Measurement Science, Dubravska cesta 9, 84104 Bratislava (Slovakia); Welsch, Goetz, E-mail: welsch@bwh.harvard.edu [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Baer, Peter, E-mail: baerpeter@siemens.com [Siemens Healthcare, Richard-Strauss-Strasse 76, D81679 Munich (Germany); Kronnerwetter, Claudia, E-mail: claudia.kronnerwetter@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria); Fujita, Hiroyuki, E-mail: hiroyuki.fujita@qualedyn.com [Quality Electrodynamics, LCC, 777 Beta Dr, Cleveland, OH 44143-2336 (United States); Trattnig, Siegfried, E-mail: siegfried.trattnig@meduniwien.ac.at [Medical University of Vienna, Department of Radiology, Vienna General Hospital, Waeringer Guertel 18-20, A-1090 Vienna (Austria)

    2012-08-15

    The purpose of this study was to compare 3 T and 7 T signal-to-noise and contrast-to noise ratios of clinical sequences for imaging of the ankles with optimized sequences and dedicated coils. Ten healthy volunteers were examined consecutively on both systems with three clinical sequences: (1) 3D gradient-echo, T{sub 1}-weighted; (2) 2D fast spin-echo, PD-weighted; and (3) 2D spin-echo, T{sub 1}-weighted. SNR was calculated for six regions: cartilage; bone; muscle; synovial fluid; Achilles tendon; and Kager's fat-pad. CNR was obtained for cartilage/bone, cartilage/fluid, cartilage/muscle, and muscle/fat-pad, and compared by a one-way ANOVA test for repeated measures. Mean SNR significantly increased at 7 T compared to 3 T for 3D GRE, and 2D TSE was 60.9% and 86.7%, respectively. In contrast, an average SNR decrease of almost 25% was observed in the 2D SE sequence. A CNR increase was observed in 2D TSE images, and in most 3D GRE images. There was a substantial benefit from ultra high-field MR imaging of ankles with routine clinical sequences at 7 T compared to 3 T. Higher SNR and CNR at ultra-high field MR scanners may be useful in clinical practice for ankle imaging. However, carefully optimized protocols and dedicated extremity coils are necessary to obtain optimal results.

  8. A rapid method for counting nucleated erythrocytes on stained blood smears by digital image analysis

    Science.gov (United States)

    Gering, E.; Atkinson, C.T.

    2004-01-01

    Measures of parasitemia by intraerythrocytic hematozoan parasites are normally expressed as the number of infected erythrocytes per n erythrocytes and are notoriously tedious and time consuming to measure. We describe a protocol for generating rapid counts of nucleated erythrocytes from digital micrographs of thin blood smears that can be used to estimate intensity of hematozoan infections in nonmammalian vertebrate hosts. This method takes advantage of the bold contrast and relatively uniform size and morphology of erythrocyte nuclei on Giemsa-stained blood smears and uses ImageJ, a java-based image analysis program developed at the U.S. National Institutes of Health and available on the internet, to recognize and count these nuclei. This technique makes feasible rapid and accurate counts of total erythrocytes in large numbers of microscope fields, which can be used in the calculation of peripheral parasitemias in low-intensity infections.

  9. Shadow Areas Robust Matching Among Image Sequence in Planetary Landing

    Science.gov (United States)

    Ruoyan, Wei; Xiaogang, Ruan; Naigong, Yu; Xiaoqing, Zhu; Jia, Lin

    2017-01-01

    In this paper, an approach for robust matching shadow areas in autonomous visual navigation and planetary landing is proposed. The approach begins with detecting shadow areas, which are extracted by Maximally Stable Extremal Regions (MSER). Then, an affine normalization algorithm is applied to normalize the areas. Thirdly, a descriptor called Multiple Angles-SIFT (MA-SIFT) that coming from SIFT is proposed, the descriptor can extract more features of an area. Finally, for eliminating the influence of outliers, a method of improved RANSAC based on Skinner Operation Condition is proposed to extract inliers. At last, series of experiments are conducted to test the performance of the approach this paper proposed, the results show that the approach can maintain the matching accuracy at a high level even the differences among the images are obvious with no attitude measurements supplied.

  10. Relevance of 3D magnetic resonance imaging sequences in diagnosing basal subarachnoid neurocysticercosis.

    Science.gov (United States)

    Carrillo Mezo, Roger; Lara García, Javier; Arroyo, Mariana; Fleury, Agnès

    2015-12-01

    Imagenological diagnosis of subarachnoid neurocysticercosis is usually difficult when classical magnetic resonance imaging (MRI) sequences are used. The purpose of this study was to evaluate the advantages of 3D MRI sequences (Fast Imaging Employing Steady-state Acquisition (FIESTA) and Spoiled Gradient Recalled Echo (SPGR)) with respect to classical sequences (Fluid Attenuation Inversion Recovery (FLAIR) and T1) in visualizing Taenia solium cyst in these locations. Forty-seven T. solium cysts located in the basal cisterns of the subarachnoid space were diagnosed in eighteen Mexican patients. A pre-treatment MRI was performed on all patients, and all four sequences (FIESTA, FLAIR, T1 SPGR, and T2) were evaluated independently by two neuroradiologists. The sensitivity of each sequence to detect the parasite membrane and scolex was evaluated, along with its capacity to detect differences in signal intensity between cerebrospinal fluid (CSF) and cysts. FIESTA sequences allowed the visualization of cyst membrane in 87.2% of the parasites evaluated, FLAIR in 38.3%, SPGR in 23.4%, and T2 in 17.0%. The superiority of FIESTA sequences over the other three imaging methods was statistically significant (P0.05). Differences in signal intensity between CSF and parasite cysts were significant in FIESTA (P<0.0001), SPGR (P<0.0001), and FLAIR (P=0.005) sequences. For the first time, the usefulness of 3D MRI sequences to diagnose T. solium cysts located in the basal cisterns of the subarachnoid space was demonstrated. The routine use of these sequences could favor an earlier diagnosis and greatly improve the prognosis of patients affected by this severe form of the disease. Copyright © 2015 Elsevier B.V. All rights reserved.

  11. Comparison of Computer Vision and Photogrammetric Approaches for Epipolar Resampling of Image Sequence.

    Science.gov (United States)

    Kim, Jae-In; Kim, Taejung

    2016-03-22

    Epipolar resampling is the procedure of eliminating vertical disparity between stereo images. Due to its importance, many methods have been developed in the computer vision and photogrammetry field. However, we argue that epipolar resampling of image sequences, instead of a single pair, has not been studied thoroughly. In this paper, we compare epipolar resampling methods developed in both fields for handling image sequences. Firstly we briefly review the uncalibrated and calibrated epipolar resampling methods developed in computer vision and photogrammetric epipolar resampling methods. While it is well known that epipolar resampling methods developed in computer vision and in photogrammetry are mathematically identical, we also point out differences in parameter estimation between them. Secondly, we tested representative resampling methods in both fields and performed an analysis. We showed that for epipolar resampling of a single image pair all uncalibrated and photogrammetric methods tested could be used. More importantly, we also showed that, for image sequences, all methods tested, except the photogrammetric Bayesian method, showed significant variations in epipolar resampling performance. Our results indicate that the Bayesian method is favorable for epipolar resampling of image sequences.

  12. Comparison of Computer Vision and Photogrammetric Approaches for Epipolar Resampling of Image Sequence

    Directory of Open Access Journals (Sweden)

    Jae-In Kim

    2016-03-01

    Full Text Available Epipolar resampling is the procedure of eliminating vertical disparity between stereo images. Due to its importance, many methods have been developed in the computer vision and photogrammetry field. However, we argue that epipolar resampling of image sequences, instead of a single pair, has not been studied thoroughly. In this paper, we compare epipolar resampling methods developed in both fields for handling image sequences. Firstly we briefly review the uncalibrated and calibrated epipolar resampling methods developed in computer vision and photogrammetric epipolar resampling methods. While it is well known that epipolar resampling methods developed in computer vision and in photogrammetry are mathematically identical, we also point out differences in parameter estimation between them. Secondly, we tested representative resampling methods in both fields and performed an analysis. We showed that for epipolar resampling of a single image pair all uncalibrated and photogrammetric methods tested could be used. More importantly, we also showed that, for image sequences, all methods tested, except the photogrammetric Bayesian method, showed significant variations in epipolar resampling performance. Our results indicate that the Bayesian method is favorable for epipolar resampling of image sequences.

  13. Understanding 3D TSE Sequences: Advantages, Disadvantages, and Application in MSK Imaging.

    Science.gov (United States)

    Glaser, Christian; D'Anastasi, Melvin; Theisen, Daniel; Notohamiprodjo, Mike; Horger, Wilhelm; Paul, Dominik; Horng, Annie

    2015-09-01

    Three-dimensional (3D) turbo-spin echo (TSE) sequences have outgrown the stage of mere sequence optimization and by now are clinically applicable. Image blurring and acquisition times have been reduced, and contrast for T1-, T2-, and moderately T2-weighted (or intermediate-weighted) fat-suppressed variants has been optimized. Data on sound-to-noise ratio efficiency and contrast are available for moderately T2-weighted fat-saturated sequence protocols. The 3-T MRI scanners help to better exploit isotropic spatial resolution and multiplanar reformatting. Imaging times range from 5 to 10 minutes, and they are shorter than the cumulative acquisition times of three separate orthogonal two-dimensional (2D) sequences. Recent suggestions go beyond secondary reformations by using online 3D rendering for image evaluation. Comparative clinical studies indicate that the diagnostic performance of 3D TSE for imaging of internal derangements of joints is at least comparable with conventional 2D TSE with potential advantages of 3D TSE for small highly curved structures. But such studies, especially those with direct arthroscopic correlation, are still sparse. Whether 3D TSE will succeed in entering clinical routine imaging on a broader scale will depend on further published clinical evidence, on further reduction of imaging time, and on improvement of its integration into daily practice. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  14. A rapid and robust gradient measurement technique using dynamic single-point imaging.

    Science.gov (United States)

    Jang, Hyungseok; McMillan, Alan B

    2017-09-01

    We propose a new gradient measurement technique based on dynamic single-point imaging (SPI), which allows simple, rapid, and robust measurement of k-space trajectory. To enable gradient measurement, we utilize the variable field-of-view (FOV) property of dynamic SPI, which is dependent on gradient shape. First, one-dimensional (1D) dynamic SPI data are acquired from a targeted gradient axis, and then relative FOV scaling factors between 1D images or k-spaces at varying encoding times are found. These relative scaling factors are the relative k-space position that can be used for image reconstruction. The gradient measurement technique also can be used to estimate the gradient impulse response function for reproducible gradient estimation as a linear time invariant system. The proposed measurement technique was used to improve reconstructed image quality in 3D ultrashort echo, 2D spiral, and multi-echo bipolar gradient-echo imaging. In multi-echo bipolar gradient-echo imaging, measurement of the k-space trajectory allowed the use of a ramp-sampled trajectory for improved acquisition speed (approximately 30%) and more accurate quantitative fat and water separation in a phantom. The proposed dynamic SPI-based method allows fast k-space trajectory measurement with a simple implementation and no additional hardware for improved image quality. Magn Reson Med 78:950-962, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  15. Noise-bound method for detecting shadow-free scene changes in image sequences.

    Science.gov (United States)

    Irie, Kenji; McKinnon, Alan; Unsworth, Keith; Woodhead, Ian

    2010-02-01

    Many image processing applications are confounded by both sensor noise and cast shadows. All image sensors add noise to a captured image that can reduce algorithm sensitivity and performance, and global filters or fixed thresholds are often applied to limit their effects. Cast shadows can appear as scene changes and are difficult to adequately detect and remove from images and image sequences. We couple image-noise statistics with a dual-illumination shadow-detection algorithm to provide a novel color-based method for shadow-free scene-change detection whose performance is bound by metamerism and image noise, and has only one variable--the desired confidence interval for noise separation.

  16. Artificial Intelligence In Processing A Sequence Of Time-Varying Images

    Science.gov (United States)

    Siler, W.; Tucker, D.; Buckley, J.; Hess, R. G.; Powell, V. G.

    1985-04-01

    A computer system is described for unsupervised analysis of five sets of ultrasound images of the heart. Each set consists of 24 frames taken at 33 millisecond intervals. The images are acquired in real time with computer control of the ultrasound apparatus. After acquisition the images are segmented by a sequence of image-processing programs; features are extracted and stored in a version of the Carnegie- Mellon Blackboard. Region classification is accomplished by a fuzzy logic expert system FLOPS based on OPS5. Preliminary results are given.

  17. Rapid high-resolution three-dimensional mapping of T1 and age-dependent variations in the non-human primate brain using magnetization-prepared rapid gradient-echo (MPRAGE) sequence

    Science.gov (United States)

    Liu, Junjie V.; Bock, Nicholas A.; Silva, Afonso C.

    2011-01-01

    The use of quantitative T1 mapping in neuroscience and neurology has raised strong interest in the development of T1-mapping techniques that can measure T1 in the whole brain, with high accuracy and precision and within short imaging and computation times. Here, we present a new inversion-recovery (IR) based T1-mapping method using a standard 3D magnetization-prepared rapid gradient-echo (MPRAGE) sequence. By varying only the inversion time (TI), but keeping other parameters constant, MPRAGE image signals become linear to exp(−TI/T1), allowing for accurate T1 estimation without flip angle correction. We also show that acquiring data at just 3 TIs, with the three different TI values optimized, gives maximum T1 precision per unit time, allowing for new efficient approaches to measure and compute T1. We demonstrate the use of our method at 7 Tesla to obtain 3D T1 maps of the whole brain in common marmosets at 0.60 mm resolution and within 11 minutes. T1 maps from the same individuals were highly reproducible across different days. Across subjects, the peak of cerebral gray matter T1 distribution was 1735±52 ms, and the lower edge of cerebral white matter T1 distribution was 1270±43 ms. We found a significant decrease of T1 in both gray and white matter of the marmoset brain with age over a span of 14 years, in agreement with previous human studies. This application illustrates that MPRAGE-based 3D T1 mapping is rapid, accurate and precise, and can facilitate high-resolution anatomical studies in neuroscience and neurological diseases. PMID:21376814

  18. Parry-Romberg syndrome: findings in advanced magnetic resonance imaging sequences - case report

    Energy Technology Data Exchange (ETDEWEB)

    Paula, Rafael Alfenas de; Ribeiro, Bruno Niemeyer de Freitas, E-mail: alfenas85@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Hospital Universitario Clementino Fraga Filho; Bahia, Paulo Roberto Valle [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de radiologia; Ribeiro, Renato Niemeyer de Freitas [Hospital de Clinica de Jacarepagua, Rio de Janeiro, RJ (Brazil); Carvalho, Lais Balbi de [Universidade Presidente Antonio Carlos (Unipac), Juiz de Fora, MG (Brazil)

    2014-05-15

    Parry-Romberg syndrome is a rare disease characterized by progressive hemifacial atrophy associated with other systemic changes, including neurological symptoms. Currently, there are few studies exploring the utilization of advanced magnetic resonance sequences in the investigation of this disease. The authors report the case of a 45-year-old patient and describe the findings at structural magnetic resonance imaging and at advanced sequences, correlating them with pathophysiological data. (author)

  19. Hyperspectral Imaging as a Rapid Quality Control Method for Herbal Tea Blends

    Directory of Open Access Journals (Sweden)

    Majolie Djokam

    2017-03-01

    Full Text Available In South Africa, indigenous herbal teas are enjoyed due to their distinct taste and aroma. The acclaimed health benefits of herbal teas include the management of chronic diseases such as hypertension and diabetes. Quality control of herbal teas has become important due to the availability of different brands of varying quality and the production of tea blends. The potential of hyperspectral imaging as a rapid quality control method for herbal tea blends from rooibos (Aspalathus linearis, honeybush (Cyclopia intermedia, buchu (Agathosma Betulina and cancerbush (Sutherlandia frutescens was investigated. Hyperspectral images of raw materials and intact tea bags were acquired using a sisuChema shortwave infrared (SWIR hyperspectral pushbroom imaging system (920–2514 nm. Principal component analysis (PCA plots showed clear discrimination between raw materials. Partial least squares discriminant analysis (PLS-DA models correctly predicted the raw material constituents of each blend and accurately determined the relative proportions. The results were corroborated independently using ultra-high performance liquid chromatography coupled to mass spectrometry (UHPLC-MS. This study demonstrated the application of hyperspectral imaging coupled with chemometric modelling as a reliable, rapid and non-destructive quality control method for authenticating herbal tea blends and to determine relative proportions in a tea bag.

  20. MR imaging with fluid attenuated inversion recovery sequence of childhood adrenoleukodystrophy : comparison with T2 weighted spin echo imaging

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Asiry; Seo, Jeong-Jin; Jeong, Gwang Woo; Chung, Tae Woong; Jeong, Yong Yeon; Kang, Heoung Keun; Kook, Hoon; Woo, Young Jong; Hwang, Tai Joo [Chonnam Univ. Medical School, Seoul (Korea, Republic of)

    1999-03-01

    The purpose of this study was to evaluate the usefulness of FLAIR(Fluid Attenuated Inversion Recovery) MR imaging in childhood adrenoleukodystrophy by comparing with those of T2-weighted FSE imaging, and to correlate MRI findings with clinical manifestations. Axial FLAIR images(TR/TE/TI=10004/123/2200) and T2-weighted FSE images(TR/TE=4000/104) of brain in six male patients(age range : 6-17 years, mean age : 10.2 years) with biochemically confirmed adrenoleukodystrophy were compared visually by two radiologists for detection, conspicuity, and the extent of lesion. Quantitatively, we compared lesion/CSF contrast, lesion/CSF contrast to noise ratio(CNR), lesion/white matter(WM) contrast, and lesion/WM CNR between FLAIR and T2 weighted image. We correlated MR findings with clinical manifestations of neurologic symptoms and evaluated whether MRI could detect white matter lesions in neurologically asymptomatic patients. Visual detection of lesions was better with FLAIR images in 2 of the 6 cases and it was equal in the remainders. Visual conspicuity and detection of the extent of lesion were superior on FLAIR images than T2-weighted images in all 6 cases. In the quantitative assessment of lesions, FLAIR was superior to T2-weighted image for lesion/CSF contrast and lesion/CSF CNR, but was inferior to T2 weighted image for lesion/WM contrast and lesion/WM CNR. In one case, FLAIR images distinguished the portion of encephalomalacic change from lesions. MR findings of adrenoleukodystrophy were correlated with clinical manifestations in symptomatic 4 cases, and also detected white matter lesions in asymptomatic 2 cases. MR imaging with FLAIR sequence provided images that were equal or superior to T2-weighted images in the evaluation of childhood adrenoleukodystrophy. MRI findings were well correlated with clinical manifestations and could detect white matter lesions in neurologically asymptomatic adrenoleukodystrophy patients.

  1. Approach for moving small target detection in infrared image sequence based on reinforcement learning

    Science.gov (United States)

    Wang, Chuanyun; Qin, Shiyin

    2016-09-01

    Addressing the problems of moving small target detection in infrared image sequence caused by background clutter and target size variation with time, an approach for moving small target detection is proposed under a pipeline framework with an optimization strategy based on reinforcement learning. The pipeline framework is composed by pipeline establishment, target-background images separation, and target confirmation, in which the pipeline is established by designating several successive images with temporal sliding window, target-background images separation is dealt with low-rank and sparse matrix decomposition via robust principal component analysis, and target confirmation is achieved by employing a voting mechanism over more than one separated target images of the same input image. For unremitting optimization of target-background images separation, the weighting parameter of low-rank and sparse matrix decomposition is dynamically regulated by the way of reinforcement learning in consecutive detection, in which the complexity evaluation from sequential infrared images and results assessment of moving small target detection are integrated. The experiment results over four infrared small target image sequences with different cloudy sky backgrounds demonstrate the effectiveness and advantages of the proposed approach in both background clutter suppression and small target detection.

  2. Iteration and superposition encryption scheme for image sequences based on multi-dimensional keys

    Science.gov (United States)

    Han, Chao; Shen, Yuzhen; Ma, Wenlin

    2017-12-01

    An iteration and superposition encryption scheme for image sequences based on multi-dimensional keys is proposed for high security, big capacity and low noise information transmission. Multiple images to be encrypted are transformed into phase-only images with the iterative algorithm and then are encrypted by different random phase, respectively. The encrypted phase-only images are performed by inverse Fourier transform, respectively, thus new object functions are generated. The new functions are located in different blocks and padded zero for a sparse distribution, then they propagate to a specific region at different distances by angular spectrum diffraction, respectively and are superposed in order to form a single image. The single image is multiplied with a random phase in the frequency domain and then the phase part of the frequency spectrums is truncated and the amplitude information is reserved. The random phase, propagation distances, truncated phase information in frequency domain are employed as multiple dimensional keys. The iteration processing and sparse distribution greatly reduce the crosstalk among the multiple encryption images. The superposition of image sequences greatly improves the capacity of encrypted information. Several numerical experiments based on a designed optical system demonstrate that the proposed scheme can enhance encrypted information capacity and make image transmission at a highly desired security level.

  3. The method of parallel-hierarchical transformation for rapid recognition of dynamic images using GPGPU technology

    Science.gov (United States)

    Timchenko, Leonid; Yarovyi, Andrii; Kokriatskaya, Nataliya; Nakonechna, Svitlana; Abramenko, Ludmila; Ławicki, Tomasz; Popiel, Piotr; Yesmakhanova, Laura

    2016-09-01

    The paper presents a method of parallel-hierarchical transformations for rapid recognition of dynamic images using GPU technology. Direct parallel-hierarchical transformations based on cluster CPU-and GPU-oriented hardware platform. Mathematic models of training of the parallel hierarchical (PH) network for the transformation are developed, as well as a training method of the PH network for recognition of dynamic images. This research is most topical for problems on organizing high-performance computations of super large arrays of information designed to implement multi-stage sensing and processing as well as compaction and recognition of data in the informational structures and computer devices. This method has such advantages as high performance through the use of recent advances in parallelization, possibility to work with images of ultra dimension, ease of scaling in case of changing the number of nodes in the cluster, auto scan of local network to detect compute nodes.

  4. Cryptanalysis of an Image Encryption Algorithm Based on DNA Sequence Operation and Hyper-chaotic System

    Science.gov (United States)

    Xu, Ming

    2017-06-01

    Recently, chaotic image cipher using DNA sequence operation has been studied extensively. However, corresponding cryptanalysis is lacking, which impedes its further development. This paper cryptanalyzes a newly proposed chaotic image cipher based on DNA sequence operation. In this paper, we firstly analyze the security defects of the proposal. Then by applying chosen-plaintext attack, we show that all the secret parameters can be revealed. The effectiveness of the proposed chosen-plaintext attack is supported both by rigorous theoretical analysis and experimental results.

  5. Ultrasonic Shear Wave Elasticity Imaging (SWEI) Sequencing and Data Processing Using a Verasonics Research Scanner.

    Science.gov (United States)

    Deng, Yufeng; Rouze, Ned C; Palmeri, Mark L; Nightingale, Kathryn R

    2016-10-03

    Ultrasound elasticity imaging has been developed over the last decade to estimate tissue stiffness. Shear wave elasticity imaging (SWEI) quantifies tissue stiffness by measuring the speed of propagating shear waves following acoustic radiation force excitation. This work presents the sequencing and data processing protocols of SWEI using a Verasonics system. The selection of the sequence parameters in a Verasonics programming script is discussed in detail. The data processing pipeline to calculate group shear wave speed (SWS), including tissue motion estimation, data filtering, and SWS estimation is demonstrated. In addition, the procedures for calibration of beam position, scanner timing, and transducer face heating are provided to avoid SWS measurement bias and transducer damage.

  6. Ultrasonic Shear Wave Elasticity Imaging Sequencing and Data Processing Using a Verasonics Research Scanner.

    Science.gov (United States)

    Deng, Yufeng; Rouze, Ned C; Palmeri, Mark L; Nightingale, Kathryn R

    2017-01-01

    Ultrasound elasticity imaging has been developed over the last decade to estimate tissue stiffness. Shear wave elasticity imaging (SWEI) quantifies tissue stiffness by measuring the speed of propagating shear waves following acoustic radiation force excitation. This paper presents the sequencing and data processing protocols of SWEI using a Verasonics system. The selection of the sequence parameters in a Verasonics programming script is discussed in detail. The data processing pipeline to calculate group shear wave speed (SWS), including tissue motion estimation, data filtering, and SWS estimation, is demonstrated. In addition, the procedures for calibration of beam position, scanner timing, and transducer face heating are provided to avoid SWS measurement bias and transducer damage.

  7. ReagentTF: a rapid and versatile optical clearing method for biological imaging(Conference Presentation)

    Science.gov (United States)

    Yu, Tingting; Zhu, Jingtan; Li, Yusha; Qi, Yisong; Xu, Jianyi; Gong, Hui; Luo, Qingming; Zhu, Dan

    2017-02-01

    The emergence of various optical clearing methods provides a great potential for imaging deep inside tissues by combining with multiple-labelling and microscopic imaging techniques. They were generally developed for specific imaging demand thus presented some non-negligible limitations such as long incubation time, tissue deformation, fluorescence quenching, incompatibility with immunostaining or lipophilic tracers. In this study, we developed a rapid and versatile clearing method, termed ReagentTF, for deep imaging of various fluorescent samples. This method can not only efficiently clear embryos, neonatal whole-brains and adult thick brain sections by simple immersion in aqueous mixtures with minimal volume change, but also can preserve fluorescence of various fluorescent proteins and simultaneously be compatible with immunostaining and lipophilic neuronal dyes. We demonstrate the effectiveness of this method in reconstructing the cell distributions of mouse hippocampus, visualizing the neural projection from CA1 (Cornu Ammonis 1) to HDB (nucleus of the horizontal limb of the diagonal band), and observing the growth of forelimb plexus in whole-mount embryos. These results suggest that ReagentTF is useful for large-volume imaging and will be an option for the deep imaging of biological tissues.

  8. A rapid automatic analyzer and its methodology for effective bentonite content based on image recognition technology

    Directory of Open Access Journals (Sweden)

    Wei Long

    2016-09-01

    Full Text Available Fast and accurate determination of effective bentonite content in used clay bonded sand is very important for selecting the correct mixing ratio and mixing process to obtain high-performance molding sand. Currently, the effective bentonite content is determined by testing the ethylene blue absorbed in used clay bonded sand, which is usually a manual operation with some disadvantages including complicated process, long testing time and low accuracy. A rapid automatic analyzer of the effective bentonite content in used clay bonded sand was developed based on image recognition technology. The instrument consists of auto stirring, auto liquid removal, auto titration, step-rotation and image acquisition components, and processor. The principle of the image recognition method is first to decompose the color images into three-channel gray images based on the photosensitive degree difference of the light blue and dark blue in the three channels of red, green and blue, then to make the gray values subtraction calculation and gray level transformation of the gray images, and finally, to extract the outer circle light blue halo and the inner circle blue spot and calculate their area ratio. The titration process can be judged to reach the end-point while the area ratio is higher than the setting value.

  9. Rapid Texture Optimization of Three-Dimensional Urban Model Based on Oblique Images.

    Science.gov (United States)

    Zhang, Weilong; Li, Ming; Guo, Bingxuan; Li, Deren; Guo, Ge

    2017-04-20

    Seamless texture mapping is one of the key technologies for photorealistic 3D texture reconstruction. In this paper, a method of rapid texture optimization of 3D urban reconstruction based on oblique images is proposed aiming at the existence of texture fragments, seams, and inconsistency of color in urban 3D texture mapping based on low-altitude oblique images. First, we explore implementing radiation correction on the experimental images with a radiation procession algorithm. Then, an efficient occlusion detection algorithm based on OpenGL is proposed according to the mapping relation between the terrain triangular mesh surface and the images to implement the occlusion detection of the visible texture on the triangular facets as well as create a list of visible images. Finally, a texture clustering algorithm is put forward based on Markov Random Field utilizing the inherent attributes of the images and solve the energy function minimization by Graph-Cuts. The experimental results display that the method is capable of decreasing the existence of texture fragments, seams, and inconsistency of color in the 3D texture model reconstruction.

  10. Denoising time-resolved microscopy image sequences with singular value thresholding

    Energy Technology Data Exchange (ETDEWEB)

    Furnival, Tom, E-mail: tjof2@cam.ac.uk; Leary, Rowan K., E-mail: rkl26@cam.ac.uk; Midgley, Paul A., E-mail: pam33@cam.ac.uk

    2017-07-15

    Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second. - Highlights: • Correlations in space and time are harnessed to denoise microscopy image sequences. • A robust estimator provides automated selection of the denoising parameter. • Motion tracking and automated noise estimation provides a versatile algorithm. • Application to time-resolved STEM enables study of atomic and nanoparticle dynamics.

  11. Estimation of temporal evolution of the helium plasmasphere based on a sequence of IMAGE/EUV images

    Science.gov (United States)

    Nakano, S.; Fok, M.-C.; Brandt, P. C.; Higuchi, T.

    2014-05-01

    We have developed a technique for estimating the temporal evolution of the plasmaspheric helium ion density based on a sequence of extreme ultraviolet (EUV) data obtained from the IMAGE satellite. In the proposed technique, the estimation is obtained by incorporating EUV images from IMAGE into a two-dimensional fluid model of the plasmasphere using a data assimilation approach based on the ensemble transform Kalman filter. Since the motion and the spatial structure of the helium plasmasphere is strongly controlled by the electric field in the inner magnetosphere, the electric field around the plasmapause can also be estimated using the ensemble transform Kalman filter. We performed an experiment using synthetic images that were generated from the same numerical model under a certain condition. It was confirmed that the condition that generated the synthetic images was successfully reproduced. We also present some results obtained using real EUV imaging data. Finally, we discuss the possibility of estimating the density profile along a magnetic field line. Since each EUV image was taken from a different direction due to the motion of the IMAGE satellite, we could obtain the information on the density profile along a field line by combining multiple images.

  12. Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae, a mammalian family that experienced rapid speciation

    Directory of Open Access Journals (Sweden)

    Ryder Oliver A

    2007-10-01

    Full Text Available Abstract Background Despite the small number of ursid species, bear phylogeny has long been a focus of study due to their conservation value, as all bear genera have been classified as endangered at either the species or subspecies level. The Ursidae family represents a typical example of rapid evolutionary radiation. Previous analyses with a single mitochondrial (mt gene or a small number of mt genes either provide weak support or a large unresolved polytomy for ursids. We revisit the contentious relationships within Ursidae by analyzing complete mt genome sequences and evaluating the performance of both entire mt genomes and constituent mtDNA genes in recovering a phylogeny of extremely recent speciation events. Results This mitochondrial genome-based phylogeny provides strong evidence that the spectacled bear diverged first, while within the genus Ursus, the sloth bear is the sister taxon of all the other five ursines. The latter group is divided into the brown bear/polar bear and the two black bears/sun bear assemblages. These findings resolve the previous conflicts between trees using partial mt genes. The ability of different categories of mt protein coding genes to recover the correct phylogeny is concordant with previous analyses for taxa with deep divergence times. This study provides a robust Ursidae phylogenetic framework for future validation by additional independent evidence, and also has significant implications for assisting in the resolution of other similarly difficult phylogenetic investigations. Conclusion Identification of base composition bias and utilization of the combined data of whole mitochondrial genome sequences has allowed recovery of a strongly supported phylogeny that is upheld when using multiple alternative outgroups for the Ursidae, a mammalian family that underwent a rapid radiation since the mid- to late Pliocene. It remains to be seen if the reliability of mt genome analysis will hold up in studies of other

  13. Limited-sequence magnetic resonance imaging in the evaluation of the ultrasonographically indeterminate pelvic mass

    Energy Technology Data Exchange (ETDEWEB)

    Chang, S.D. [Univ. of British Columbia, Vancouver Hospital and Helath Services Centre, Dept. of Radiology, Vancouver, British Columbia (Canada)]. E-mail: schang@vanhosp.bc.ca; Cooperberg, P.L.; Wong, A.D. [Univ. of British Columbia, St. Paul' s Hospital, Dept. of Radiology, Vancouver, British Columbia (Canada); Llewellyn, P.A. [Lion' s Gate Hospital, Dept. of Radiology, North Vancouver, British Columbia (Canada); Bilbey, J.H. [Royal Inland Hospital, Dept. of Radiology, Kamloops, British Columbia (Canada)

    2004-04-01

    To evaluate the usefulness of limited-sequence magnetic resonance imaging (MRI) in the elucidation of ultrasonographically indeterminate pelvic masses. This study focused only on pelvic masses in which the origin of the mass (uterine v. extrauterine) could not be determined by ultrasonography (US). The origin of a pelvic mass has clinical implications. A mass arising from the uterus is most likely to be a leiomyoma, which is a benign lesion, whereas an extrauterine mass will have a higher likelihood of malignancy and usually requires surgery. Eighty-one female patients whose pelvic mass was of indeterminate origin on US also underwent limited-sequence MRI of the pelvis. Most of the MRI examinations were performed on the same day as the US. Limited-sequence MRI sequences included a quick gradient-echoT{sub 1}-weighted localizer and a fast spin-echoT{sub 2}-weighted sequence. Final diagnoses were established by surgical pathology or by clinical and imaging follow-up. Limited-sequence MRI was helpful in 79 of the 81 cases (98%). Fifty-two of the 81 masses (64%) were leiomyomas. One was a leiomyosarcoma. The extrauterine masses (26/81 [32%]) were identified as 14 ovarian malignancies, 4 endometriomas, 3 dermoids, an ovarian fibroma, an infarcted fibrothecoma, an infarcted hemorrhagic cyst, a sigmoid diverticular abscess and a gastrointestinal stromal tumour of the ileum. In the other 2 cases (2/81 [2%]), the origin of the pelvic mass remained indeterminate. Both of these indeterminate masses showed low signal onT{sub 2}-weighted images and were interpreted as probable leiomyomas. They were not surgically removed but were followed clinically and had a stable course. Limited-sequence MRI is a quick and efficient way to further evaluate ultrasonographically indeterminate pelvic masses. Limited-sequence MRI of the pelvis can suffice, in these cases, without requiring a full MRI examination. (author)

  14. Association of apneic oxygenation with decreased desaturation rates during rapid sequence intubation by a Chinese emergency medicine service

    Science.gov (United States)

    Mao, Yong; Qin, Zong-He

    2015-01-01

    Rapid and safe airway management has always been of paramount importance in successful management of critically ill and injured patients in the emergency department. The achievement rate of emergency medicine inhabitants in airway management improved enhanced essentially subsequent to finishing anaesthesiology turn. There was a slightly higher rate of quick sequence intubation in the postapneic oxygenation groups (preapneic oxygenation 6.4%; postapneic oxygenation 9.1%). The majority of patients intubated in both groups were men (preapneic oxygenation 72.3%; postapneic oxygenation 63.5%). A higher percentage of patients in the preapneic oxygenation group had a Cormack-Lehane grade III or worse view (23.2% versus 11.8%). Anaesthesiology turns should be considered as an essential component of emergency medicine training programs. A collateral curriculum of this nature should also focus on the acquisition of skills in airway management. PMID:26379959

  15. Multimodal imaging documentation of rapid evolution of retinal changes in handheld laser-induced maculopathy.

    Science.gov (United States)

    Dhrami-Gavazi, Elona; Lee, Winston; Balaratnasingam, Chandrakumar; Kayserman, Larisa; Yannuzzi, Lawrence A; Freund, K Bailey

    2015-01-01

    To use multimodal imaging to document the relatively rapid clinical evolution of handheld laser-induced maculopathy (HLIM). To demonstrate that inadvertent ocular injury can result from devices mislabeled with respect to their power specifications. The clinical course of a 17-year-old male who sustained self-inflicted, central macular damage from a 20-25 s direct stare at a red-spectrum, handheld laser pointer ordered from an internet retailer is provided. Retrospective review of multimodal imaging that includes fundus photography, fluorescein angiography, MultiColor reflectance, eye-tracked spectral domain optical coherence tomography (SD-OCT), fundus autofluorescence, and microperimetry is used to describe the evolving clinical manifestations of HLIM in the first 3 months. Curvilinear bands of dense hyperreflectivity extending from the outer retina and following the Henle fibers were seen on SD-OCT immediately after injury. This characteristic appearance had largely resolved by 2 weeks. There was significant non-uniformity in the morphological characteristics of HLIM lesions between autofluorescence and reflectance images. The pattern of lesion evolution was also significantly different between imaging modalities. Analysis of the laser device showed its wavelength to be correctly listed, but the power was found to be 102.5-105 mW, as opposed to the laser -induced maculopathy, this finding can undergo rapid resolution in the span of several days. In the absence of this finding, other multimodal imaging clues and a careful history may aid in recognizing this diagnosis. A greater awareness regarding inaccurate labeling on some of these devices could help reduce the frequency of this preventable entity.

  16. Brain activity-based image classification from rapid serial visual presentation.

    Science.gov (United States)

    Bigdely-Shamlo, Nima; Vankov, Andrey; Ramirez, Rey R; Makeig, Scott

    2008-10-01

    We report the design and performance of a brain-computer interface (BCI) system for real-time single-trial binary classification of viewed images based on participant-specific dynamic brain response signatures in high-density (128-channel) electroencephalographic (EEG) data acquired during a rapid serial visual presentation (RSVP) task. Image clips were selected from a broad area image and presented in rapid succession (12/s) in 4.1-s bursts. Participants indicated by subsequent button press whether or not each burst of images included a target airplane feature. Image clip creation and search path selection were designed to maximize user comfort and maintain user awareness of spatial context. Independent component analysis (ICA) was used to extract a set of independent source time-courses and their minimally-redundant low-dimensional informative features in the time and time-frequency amplitude domains from 128-channel EEG data recorded during clip burst presentations in a training session. The naive Bayes fusion of two Fisher discriminant classifiers, computed from the 100 most discriminative time and time-frequency features, respectively, was used to estimate the likelihood that each clip contained a target feature. This estimator was applied online in a subsequent test session. Across eight training/test session pairs from seven participants, median area under the receiver operator characteristic curve, by tenfold cross validation, was 0.97 for within-session and 0.87 for between-session estimates, and was nearly as high (0.83) for targets presented in bursts that participants mistakenly reported to include no target features.

  17. Rapid intracerebroventricular delivery of Cu-DOTA-etanercept after peripheral administration demonstrated by PET imaging

    Directory of Open Access Journals (Sweden)

    Chen Xiaoyuan

    2009-02-01

    Full Text Available Abstract Background The cytokines interleukin-1 and tumor necrosis factor (TNF, and the cytokine blocker interleukin-1 receptor antagonist, all have been demonstrated to enter the cerebrospinal fluid (CSF following peripheral administration. Recent reports of rapid clinical improvement in patients with Alzheimer's disease and related forms of dementia following perispinal administration of etanercept, a TNF antagonist, suggest that etanercept also has the ability to reach the brain CSF. To investigate, etanercept was labeled with a positron emitter to enable visualization of its intracranial distribution following peripheral administration by PET in an animal model. Findings Radiolabeling of etanercept with the PET emitter 64Cu was performed by DOTA (1,4,7,10-tetraazadodecane-N,N',N",N"'-tetraacetic acid conjugation of etanercept, followed by column purification and 64Cu labeling. MicroPET imaging revealed accumulation of 64Cu-DOTA-etanercept within the lateral and third cerebral ventricles within minutes of peripheral perispinal administration in a normal rat anesthesized with isoflurane anesthesia, with concentration within the choroid plexus and into the CSF. Conclusion Synthesis of 64Cu-DOTA-etanercept enabled visualization of its intracranial distribution by microPET imaging. MicroPET imaging documented rapid accumulation of 64Cu-DOTA-etanercept within the choroid plexus and the cerebrospinal fluid within the cerebral ventricles of a living rat after peripheral administration. Further study of the effects of etanercept and TNF at the level of the choroid plexus may yield valuable insights into the pathogenesis of Alzheimer's disease.

  18. The Java Image Science Toolkit (JIST) for Rapid Prototyping and Publishing of Neuroimaging Software

    Science.gov (United States)

    Lucas, Blake C.; Bogovic, John A.; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L.; Pham, Dzung

    2010-01-01

    Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). PMID:20077162

  19. Rapid and Quantitative Assessment of Cancer Treatment Response Using In Vivo Bioluminescence Imaging

    Directory of Open Access Journals (Sweden)

    Alnawaz Rehemtulla

    2000-01-01

    Full Text Available Current assessment of orthotopic tumor models in animals utilizes survival as the primary therapeutic end point. In vivo bioluminescence imaging (BLI is a sensitive imaging modality that is rapid and accessible, and may comprise an ideal tool for evaluating antineoplastic therapies [1 ]. Using human tumor cell lines constitutively expressing luciferase, the kinetics of tumor growth and response to therapy have been assessed in intraperitoneal [2], subcutaneous, and intravascular [3] cancer models. However, use of this approach for evaluating orthotopic tumor models has not been demonstrated. In this report, the ability of BLI to noninvasively quantitate the growth and therapeuticinduced cell kill of orthotopic rat brain tumors derived from 9L gliosarcoma cells genetically engineered to stably express firefly luciferase (9LLuc was investigated. Intracerebral tumor burden was monitored over time by quantitation of photon emission and tumor volume using a cryogenically cooled CCD camera and magnetic resonance imaging (MRI, respectively. There was excellent correlation (r=0.91 between detected photons and tumor volume. A quantitative comparison of tumor cell kill determined from serial MRI volume measurements and BLI photon counts following 1,3-bis(2-chloroethyl-1-nitrosourea (BCNU treatment revealed that both imaging modalities yielded statistically similar cell kill values (P=.951. These results provide direct validation of BLI imaging as a powerful and quantitative tool for the assessment of antineoplastic therapies in living animals.

  20. Computationally rapid method of estimating signal-to-noise ratio for phased array image reconstructions.

    Science.gov (United States)

    Wiens, Curtis N; Kisch, Shawn J; Willig-Onwuachi, Jacob D; McKenzie, Charles A

    2011-10-01

    Measuring signal-to-noise ratio (SNR) for parallel MRI reconstructions is difficult due to spatially dependent noise amplification. Existing approaches for measuring parallel MRI SNR are limited because they are not applicable to all reconstructions, require significant computation time, or rely on repeated image acquisitions. A new SNR estimation approach is proposed, a hybrid of the repeated image acquisitions method detailed in the National Electrical Manufacturers Association (NEMA) standard and the Monte Carlo based pseudo-multiple replica method, in which the difference between images reconstructed from the unaltered acquired data and that same data reconstructed after the addition of calibrated pseudo-noise is used to estimate the noise in the parallel MRI image reconstruction. This new noise estimation method can be used to rapidly compute the pixel-wise SNR of the image generated from any parallel MRI reconstruction of a single acquisition. SNR maps calculated with the new method are validated against existing SNR calculation techniques. Copyright © 2011 Wiley-Liss, Inc.

  1. Genome Sequencing and Mapping Reveal Loss of Heterozygosity as a Mechanism for Rapid Adaptation in the Vegetable Pathogen Phytophthora capsici

    Energy Technology Data Exchange (ETDEWEB)

    Lamour, Kurt H.; Mudge, Joann; Gobena, Daniel; Hurtado-Gonzales, Oscar P.; Schmutz, Jeremy; Kuo, Alan; Miller, Neil A.; Rice, Brandon J.; Raffaele, Sylvain; Cano, Liliana M.; Bharti, Arvind K.; Donahoo, Ryan S.; Finely, Sabra; Huitema, Edgar; Hulvey, Jon; Platt, Darren; Salamov, Asaf; Savidor, Alon; Sharma, Rahul; Stam, Remco; Sotrey, Dylan; Thines, Marco; Win, Joe; Haas, Brian J.; Dinwiddie, Darrell L.; Jenkins, Jerry; Knight, James R.; Affourtit, Jason P.; Han, Cliff S.; Chertkov, Olga; Lindquist, Erika A.; Detter, Chris; Grigoriev, Igor V.; Kamoun, Sophien; Kingsmore, Stephen F.

    2012-02-07

    The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30percent of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.

  2. Lncident: A Tool for Rapid Identification of Long Noncoding RNAs Utilizing Sequence Intrinsic Composition and Open Reading Frame Information

    Directory of Open Access Journals (Sweden)

    Siyu Han

    2016-01-01

    Full Text Available More and more studies have demonstrated that long noncoding RNAs (lncRNAs play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Here, we present a novel method for rapid identification of lncRNAs utilizing sequence intrinsic composition features and open reading frame information based on support vector machine model, named as Lncident (LncRNAs identification. The 10-fold cross-validation and ROC curve are used to evaluate the performance of Lncident. The main advantage of Lncident is high speed without the loss of accuracy. Compared with the exiting popular tools, Lncident outperforms Coding-Potential Calculator, Coding-Potential Assessment Tool, Coding-Noncoding Index, and PLEK. Lncident is also much faster than Coding-Potential Calculator and Coding-Noncoding Index. Lncident presents an outstanding performance on microorganism, which offers a great application prospect to the analysis of microorganism. In addition, Lncident can be trained by users’ own collected data. Furthermore, R package and web server are simultaneously developed in order to maximize the convenience for the users. The R package “Lncident” can be easily installed on multiple operating system platforms, as long as R is supported.

  3. Rapid formation and pollutant removal ability of aerobic granules in a sequencing batch airlift reactor at low temperature.

    Science.gov (United States)

    Jiang, Yu; Shang, Yu; Wang, Hongyu; Yang, Kai

    2016-12-01

    The start-up of an aerobic granular sludge (AGS) reactor at low temperature was more difficult than at ambient temperature.The rapid formation and characteristics of AGS in a sequencing batch airlift reactor at low temperature were investigated. The nutrient removal ability of the system was also evaluated. It was found that compact granules with clear boundary were formed within 10 days and steady state was achieved within 25 days. The settling properties of sludge were improved with the increasing secretion of extracellular polymeric substances and removal performances of pollutants were enhanced along with granulation. The average removal efficiencies of COD, NH4(+)-N, total nitrogen (TN), total phosphorus (TP) after aerobic granules maturing were over 90.9%, 94.7%, 75.4%, 80.2%, respectively. The rise of temperature had little impact on pollutant biodegradation while the variation of dissolved oxygen caused obvious changes in TN and TP removal rates. COD concentrations of effluents were below 30 mg l(-1) in most cycles of operation with a wide range of organic loading rates (0.6-3.0 kg COD m(-3) d(-1)). The rapid granulation and good performance of pollutant reduction by the system might provide an alternate for wastewater treatment in cold regions.

  4. Spatially Varying Image Based Lighting by Light Probe Sequences, Capture, Processing and Rendering

    OpenAIRE

    Unger, Jonas; Gustavson, Stefan; Ynnerman, Anders

    2007-01-01

    We present a novel technique for capturing spatially or temporally resolved light probe sequences, and using them for image based lighting. For this purpose we have designed and built a real-time light probe, a catadioptric imaging system that can capture the full dynamic range of the lighting incident at each point in space at video frame rates, while being moved through a scene. The real-time light probe uses a digital imaging system which we have programmed to capture high quality, photome...

  5. FREQ-Seq: a rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.

    Directory of Open Access Journals (Sweden)

    Lon M Chubiz

    Full Text Available Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq that leverages Illumina next-generation sequencing for localized, quantitative allele frequency detection. Analogous to RNA-Seq, FREQ-Seq relies upon counts from the >10(5 reads generated per locus per time-point to determine allele frequencies. Loci of interest are directly amplified from a mixed population via two rounds of PCR using inexpensive, user-designed oligonucleotides and a bar-coded bridging primer system that can be regenerated in-house. The resulting bar-coded PCR products contain the adapters needed for Illumina sequencing, eliminating further library preparation. We demonstrate the utility of FREQ-Seq by determining the order and dynamics of beneficial alleles that arose as a microbial population, founded with an engineered strain of Methylobacterium, evolved to grow on methanol. Quantifying allele frequencies with minimal bias down to 1% abundance allowed effective analysis of SNPs, small in-dels and insertions of transposable elements. Our data reveal large-scale clonal interference during the early stages of adaptation and illustrate the utility of FREQ-Seq as a cost-effective tool for tracking allele frequencies in populations.

  6. Image-model coupling: a simple information theoretic perspective for image sequences

    Directory of Open Access Journals (Sweden)

    N. D. Smith

    2009-03-01

    Full Text Available Images are widely used to visualise physical processes. Models may be developed which attempt to replicate those processes and their effects. The technique of coupling model output to images, which is here called "image-model coupling", may be used to help understand the underlying physical processes, and better understand the limitations of the models. An information theoretic framework is presented for image-model coupling in the context of communication along a discrete channel. The physical process may be regarded as a transmitter of images and the model as part of a receiver which decodes or recognises those images. Image-model coupling may therefore be interpreted as image recognition. Of interest are physical processes which exhibit "memory". The response of such a system is not only dependent on the current values of driver variables, but also on the recent history of drivers and/or system description. Examples of such systems in geophysics include the ionosphere and Earth's climate. The discrete channel model is used to help derive expressions for matching images and model output, and help analyse the coupling.

  7. Image-model coupling: a simple information theoretic perspective for image sequences

    Science.gov (United States)

    Smith, N. D.; Mitchell, C. N.; Budd, C. J.

    2009-03-01

    Images are widely used to visualise physical processes. Models may be developed which attempt to replicate those processes and their effects. The technique of coupling model output to images, which is here called "image-model coupling", may be used to help understand the underlying physical processes, and better understand the limitations of the models. An information theoretic framework is presented for image-model coupling in the context of communication along a discrete channel. The physical process may be regarded as a transmitter of images and the model as part of a receiver which decodes or recognises those images. Image-model coupling may therefore be interpreted as image recognition. Of interest are physical processes which exhibit "memory". The response of such a system is not only dependent on the current values of driver variables, but also on the recent history of drivers and/or system description. Examples of such systems in geophysics include the ionosphere and Earth's climate. The discrete channel model is used to help derive expressions for matching images and model output, and help analyse the coupling.

  8. Live cell imaging of repetitive DNA sequences via GFP-tagged polydactyl zinc finger proteins

    Science.gov (United States)

    Lindhout, Beatrice I.; Fransz, Paul; Tessadori, Federico; Meckel, Tobias; Hooykaas, Paul J.J.; van der Zaal, Bert J.

    2007-01-01

    Several techniques are available to study chromosomes or chromosomal domains in nuclei of chemically fixed or living cells. Current methods to detect DNA sequences in vivo are limited to trans interactions between a DNA sequence and a transcription factor from natural systems. Here, we expand live cell imaging tools using a novel approach based on zinc finger-DNA recognition codes. We constructed several polydactyl zinc finger (PZF) DNA-binding domains aimed to recognize specific DNA sequences in Arabidopsis and mouse and fused these with GFP. Plants and mouse cells expressing PZF:GFP proteins were subsequently analyzed by confocal microscopy. For Arabidopsis, we designed a PZF:GFP protein aimed to specifically recognize a 9-bp sequence within centromeric 180-bp repeat and monitored centromeres in living roots. Similarly, in mouse cells a PZF:GFP protein was targeted to a 9-bp sequence in the major satellite repeat. Both PZF:GFP proteins localized in chromocenters which represent heterochromatin domains containing centromere and other tandem repeats. The number of PZF:GFP molecules per centromere in Arabidopsis, quantified with near single-molecule precision, approximated the number of expected binding sites. Our data demonstrate that live cell imaging of specific DNA sequences can be achieved with artificial zinc finger proteins in different organisms. PMID:17704126

  9. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data.

    Science.gov (United States)

    Joensen, Katrine G; Tetzschner, Anna M M; Iguchi, Atsushi; Aarestrup, Frank M; Scheutz, Flemming

    2015-08-01

    Accurate and rapid typing of pathogens is essential for effective surveillance and outbreak detection. Conventional serotyping of Escherichia coli is a delicate, laborious, time-consuming, and expensive procedure. With whole-genome sequencing (WGS) becoming cheaper, it has vast potential in routine typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin genes fliC, flkA, fllA, flmA, and flnA were detected in 569 and 508 genome sequences, respectively. SerotypeFinder for WGS-based O and H typing predicted 560 of 569 O types and 504 of 508 H types, consistent with conventional serotyping. In combination with other available WGS typing tools, E. coli serotyping can be performed solely from WGS data, providing faster and cheaper typing than current routine procedures and making WGS typing a superior alternative to conventional typing strategies. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  10. Next-Generation Sequencing-Aided Rapid Molecular Diagnosis of Occult Macular Dystrophy in a Chinese Family

    Directory of Open Access Journals (Sweden)

    Yu-He Qi

    2017-08-01

    Full Text Available Purpose: To show early, rapid and accurate molecular diagnosis of occult macular dystrophy (OMD in a four-generation Chinese family with inherited macular dystrophy.Methods: In the current study, we comprehensively screened 130 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the proband of a four-generation Chinese family that has suffered from maculopathy without a definitive diagnosis for over 10 years. Variants were filtered and analyzed to identify possible disease-causing variants before validation by Sanger sequencing.Results: Two heterozygous mutations—RP1L1 c.133 C > T (p.Arg45Trp, which is a hot spot for OMD, and ABCA4 c.6119 G > A (p.Arg2040Gln, which was identified in Stargardt’s disease were found in three patients, but neither of the mutations was found in the unaffected individuals in the same family, who are phenotypically normal or in the normal control volunteers.Conclusion: These results cannot only confirm the diagnosis of OMD in the proband, but also provide presymptomatic diagnosis of the proband’s children before the onset of visual acuity impairment and guidance regarding the prognosis and management of these patients. Heterozygous mutations of RP1L1 c.133 C > T (p.Arg45Trp and ABCA4 c.6119 G > A (p.Arg2040Gln are likely responsible for OMD. Our results further extend our current understanding of the genetic basis of OMD, and emphasize the importance of molecular diagnosis and genetic counseling for OMD.

  11. Next-Generation Sequencing-Aided Rapid Molecular Diagnosis of Occult Macular Dystrophy in a Chinese Family.

    Science.gov (United States)

    Qi, Yu-He; Gao, Feng-Juan; Hu, Fang-Yuan; Zhang, Sheng-Hai; Chen, Jun-Yi; Huang, Wan-Jing; Tian, Guo-Hong; Wang, Min; Gan, De-Kang; Wu, Ji-Hong; Xu, Ge-Zhi

    2017-01-01

    Purpose: To show early, rapid and accurate molecular diagnosis of occult macular dystrophy (OMD) in a four-generation Chinese family with inherited macular dystrophy. Methods: In the current study, we comprehensively screened 130 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the proband of a four-generation Chinese family that has suffered from maculopathy without a definitive diagnosis for over 10 years. Variants were filtered and analyzed to identify possible disease-causing variants before validation by Sanger sequencing. Results: Two heterozygous mutations-RP1L1 c.133 C > T (p.Arg45Trp), which is a hot spot for OMD, and ABCA4 c.6119 G > A (p.Arg2040Gln), which was identified in Stargardt's disease were found in three patients, but neither of the mutations was found in the unaffected individuals in the same family, who are phenotypically normal or in the normal control volunteers. Conclusion: These results cannot only confirm the diagnosis of OMD in the proband, but also provide presymptomatic diagnosis of the proband's children before the onset of visual acuity impairment and guidance regarding the prognosis and management of these patients. Heterozygous mutations of RP1L1 c.133 C > T (p.Arg45Trp) and ABCA4 c.6119 G > A (p.Arg2040Gln) are likely responsible for OMD. Our results further extend our current understanding of the genetic basis of OMD, and emphasize the importance of molecular diagnosis and genetic counseling for OMD.

  12. Rapid susceptibility testing and microcolony analysis of Candida spp. cultured and imaged on porous aluminum oxide.

    Science.gov (United States)

    Ingham, Colin J; Boonstra, Sjoukje; Levels, Suzanne; de Lange, Marit; Meis, Jacques F; Schneeberger, Peter M

    2012-01-01

    Acquired resistance to antifungal agents now supports the introduction of susceptibility testing for species-drug combinations for which this was previously thought unnecessary. For pathogenic yeasts, conventional phenotypic testing needs at least 24 h. Culture on a porous aluminum oxide (PAO) support combined with microscopy offers a route to more rapid results. Microcolonies of Candida species grown on PAO were stained with the fluorogenic dyes Fun-1 and Calcofluor White and then imaged by fluorescence microscopy. Images were captured by a charge-coupled device camera and processed by publicly available software. By this method, the growth of yeasts could be detected and quantified within 2 h. Microcolony imaging was then used to assess the susceptibility of the yeasts to amphotericin B, anidulafungin and caspofungin (3.5 h culture), and voriconazole and itraconazole (7 h culture). Overall, the results showed good agreement with EUCAST (86.5% agreement; n = 170) and E-test (85.9% agreement; n = 170). The closest agreement to standard tests was found when testing susceptibility to amphotericin B and echinocandins (88.2 to 91.2%) and the least good for the triazoles (79.4 to 82.4%). Furthermore, large datasets on population variation could be rapidly obtained. An analysis of microcolonies revealed subtle effects of antimycotics on resistant strains and below the MIC of sensitive strains, particularly an increase in population heterogeneity and cell density-dependent effects of triazoles. Additionally, the method could be adapted to strain identification via germ tube extension. We suggest PAO culture is a rapid and versatile method that may be usefully adapted to clinical mycology and has research applications.

  13. Rapid susceptibility testing and microcolony analysis of Candida spp. cultured and imaged on porous aluminum oxide.

    Directory of Open Access Journals (Sweden)

    Colin J Ingham

    Full Text Available BACKGROUND: Acquired resistance to antifungal agents now supports the introduction of susceptibility testing for species-drug combinations for which this was previously thought unnecessary. For pathogenic yeasts, conventional phenotypic testing needs at least 24 h. Culture on a porous aluminum oxide (PAO support combined with microscopy offers a route to more rapid results. METHODS: Microcolonies of Candida species grown on PAO were stained with the fluorogenic dyes Fun-1 and Calcofluor White and then imaged by fluorescence microscopy. Images were captured by a charge-coupled device camera and processed by publicly available software. By this method, the growth of yeasts could be detected and quantified within 2 h. Microcolony imaging was then used to assess the susceptibility of the yeasts to amphotericin B, anidulafungin and caspofungin (3.5 h culture, and voriconazole and itraconazole (7 h culture. SIGNIFICANCE: Overall, the results showed good agreement with EUCAST (86.5% agreement; n = 170 and E-test (85.9% agreement; n = 170. The closest agreement to standard tests was found when testing susceptibility to amphotericin B and echinocandins (88.2 to 91.2% and the least good for the triazoles (79.4 to 82.4%. Furthermore, large datasets on population variation could be rapidly obtained. An analysis of microcolonies revealed subtle effects of antimycotics on resistant strains and below the MIC of sensitive strains, particularly an increase in population heterogeneity and cell density-dependent effects of triazoles. Additionally, the method could be adapted to strain identification via germ tube extension. We suggest PAO culture is a rapid and versatile method that may be usefully adapted to clinical mycology and has research applications.

  14. Single-heartbeat electromechanical wave imaging with optimal strain estimation using temporally unequispaced acquisition sequences.

    Science.gov (United States)

    Provost, Jean; Thiébaut, Stéphane; Luo, Jianwen; Konofagou, Elisa E

    2012-02-21

    Electromechanical Wave Imaging (EWI) is a non-invasive, ultrasound-based imaging method capable of mapping the electromechanical wave (EW) in vivo, i.e. the transient deformations occurring in response to the electrical activation of the heart. Optimal imaging frame rates, in terms of the elastographic signal-to-noise ratio, to capture the EW cannot be achieved due to the limitations of conventional imaging sequences, in which the frame rate is low and tied to the imaging parameters. To achieve higher frame rates, EWI is typically performed by combining sectors acquired during separate heartbeats, which are then combined into a single view. However, the frame rates achieved remain potentially sub-optimal and this approach precludes the study of non-periodic arrhythmias. This paper describes a temporally unequispaced acquisition sequence (TUAS) for which a wide range of frame rates are achievable independently of the imaging parameters, while maintaining a full view of the heart at high beam density. TUAS is first used to determine the optimal frame rate for EWI in a paced canine heart in vivo and then to image during ventricular fibrillation. These results indicate how EWI can be optimally performed within a single heartbeat, during free breathing and in real time, for both periodic and non-periodic cardiac events.

  15. SCALE-PWI: A pulse sequence for absolute quantitative cerebral perfusion imaging.

    Science.gov (United States)

    Srour, Jessy Mouannes; Shin, Wanyong; Shah, Saurabh; Sen, Anindya; Carroll, Timothy J

    2011-05-01

    The Bookend technique is a magnetic resonance imaging (MRI) dynamic susceptibility contrast method that provides reliable quantitative measurement of cerebral blood flow (CBF) and cerebral blood volume (CBV). The quantification is patient specific, is derived from a steady-state measurement of CBV, and is obtained from T(1) changes in the white matter and the blood pool after contrast agent injection. In the current implementation, the Bookend technique consists of three scanning steps requiring a cumulative scan time of 3 minutes 47 seconds, a well-trained technologist, and extra time for offline image reconstruction. We present an automation and acceleration of the multiscan Bookend protocol through a self-calibrating pulse sequence, namely Self-Calibrated Epi Perfusion-Weighted Imaging (SCALE-PWI). The SCALE-PWI is a single-shot echo-planar imaging pulse sequence with three modules and a total scan time of under 2 minutes. It provides the possibility of performing online, quantitative perfusion image reconstruction, which reduces the latency to obtain quantitative maps. A validation study in healthy volunteers (N=19) showed excellent agreement between SCALE-PWI and the conventional Bookend protocol (P>0.05 with Student's t-test, r=0.95/slope=0.98 for quantitative CBF, and r=0.91/slope=0.94 for quantitative CBV). A single MRI pulse sequence for absolute quantification of cerebral perfusion has been developed.

  16. Optimization of an on-board imaging system for extremely rapid radiation therapy

    Science.gov (United States)

    Cherry Kemmerling, Erica M.; Wu, Meng; Yang, He; Maxim, Peter G.; Loo, Billy W.; Fahrig, Rebecca

    2015-01-01

    Purpose: Next-generation extremely rapid radiation therapy systems could mitigate the need for motion management, improve patient comfort during the treatment, and increase patient throughput for cost effectiveness. Such systems require an on-board imaging system that is competitively priced, fast, and of sufficiently high quality to allow good registration between the image taken on the day of treatment and the image taken the day of treatment planning. In this study, three different detectors for a custom on-board CT system were investigated to select the best design for integration with an extremely rapid radiation therapy system. Methods: Three different CT detectors are proposed: low-resolution (all 4 × 4 mm pixels), medium-resolution (a combination of 4 × 4 mm pixels and 2 × 2 mm pixels), and high-resolution (all 1 × 1 mm pixels). An in-house program was used to generate projection images of a numerical anthropomorphic phantom and to reconstruct the projections into CT datasets, henceforth called “realistic” images. Scatter was calculated using a separate Monte Carlo simulation, and the model included an antiscatter grid and bowtie filter. Diagnostic-quality images of the phantom were generated to represent the patient scan at the time of treatment planning. Commercial deformable registration software was used to register the diagnostic-quality scan to images produced by the various on-board detector configurations. The deformation fields were compared against a “gold standard” deformation field generated by registering initial and deformed images of the numerical phantoms that were used to make the diagnostic and treatment-day images. Registrations of on-board imaging system data were judged by the amount their deformation fields differed from the corresponding gold standard deformation fields—the smaller the difference, the better the system. To evaluate the registrations, the pointwise distance between gold standard and realistic registration

  17. Seven neurons memorizing sequences of alphabetical images via spike-timing dependent plasticity.

    Science.gov (United States)

    Osogami, Takayuki; Otsuka, Makoto

    2015-09-16

    An artificial neural network, such as a Boltzmann machine, can be trained with the Hebb rule so that it stores static patterns and retrieves a particular pattern when an associated cue is presented to it. Such a network, however, cannot effectively deal with dynamic patterns in the manner of living creatures. Here, we design a dynamic Boltzmann machine (DyBM) and a learning rule that has some of the properties of spike-timing dependent plasticity (STDP), which has been postulated for biological neural networks. We train a DyBM consisting of only seven neurons in a way that it memorizes the sequence of the bitmap patterns in an alphabetical image "SCIENCE" and its reverse sequence and retrieves either sequence when a partial sequence is presented as a cue. The DyBM is to STDP as the Boltzmann machine is to the Hebb rule.

  18. Magnetic resonance imaging of the Achilles tendon using ultrashort TE (UTE) pulse sequences

    Energy Technology Data Exchange (ETDEWEB)

    Robson, M.D.; Benjamin, M.; Gishen, P.; Bydder, G.M. E-mail: gbydder@ucsd.edu

    2004-08-01

    AIM: To assess the potential value of imaging the Achilles tendon with ultrashort echo time (UTE) pulse sequences. MATERIALS AND METHODS: Four normal controls and four patients with chronic Achilles tendinopathy were examined in the sagittal and transverse planes. Three of the patients were examined before and after intravenous gadodiamide. RESULTS: The fascicular pattern was clearly demonstrated within the tendon and detail of the three distinct fibrocartilaginous components of an 'enthesis organ' was well seen. T2* measurements showed two short T2* components. Increase in long T2 components with reduction in short T2 components was seen in tendinopathy. Contrast enhancement was much more extensive than with conventional sequences in two cases of tendinopathy but in a third case, there was a region of reduced enhancement. CONCLUSION: UTE pulse sequences provide anatomical detail not apparent with conventional sequences, demonstrate differences in T2* and show patterns of both increased and decreased enhancement in tendinopathy.

  19. How Lovebirds Maneuver Rapidly Using Super-Fast Head Saccades and Image Feature Stabilization.

    Directory of Open Access Journals (Sweden)

    Daniel Kress

    Full Text Available Diurnal flying animals such as birds depend primarily on vision to coordinate their flight path during goal-directed flight tasks. To extract the spatial structure of the surrounding environment, birds are thought to use retinal image motion (optical flow that is primarily induced by motion of their head. It is unclear what gaze behaviors birds perform to support visuomotor control during rapid maneuvering flight in which they continuously switch between flight modes. To analyze this, we measured the gaze behavior of rapidly turning lovebirds in a goal-directed task: take-off and fly away from a perch, turn on a dime, and fly back and land on the same perch. High-speed flight recordings revealed that rapidly turning lovebirds perform a remarkable stereotypical gaze behavior with peak saccadic head turns up to 2700 degrees per second, as fast as insects, enabled by fast neck muscles. In between saccades, gaze orientation is held constant. By comparing saccade and wingbeat phase, we find that these super-fast saccades are coordinated with the downstroke when the lateral visual field is occluded by the wings. Lovebirds thus maximize visual perception by overlying behaviors that impair vision, which helps coordinate maneuvers. Before the turn, lovebirds keep a high contrast edge in their visual midline. Similarly, before landing, the lovebirds stabilize the center of the perch in their visual midline. The perch on which the birds land swings, like a branch in the wind, and we find that retinal size of the perch is the most parsimonious visual cue to initiate landing. Our observations show that rapidly maneuvering birds use precisely timed stereotypic gaze behaviors consisting of rapid head turns and frontal feature stabilization, which facilitates optical flow based flight control. Similar gaze behaviors have been reported for visually navigating humans. This finding can inspire more effective vision-based autopilots for drones.

  20. How Lovebirds Maneuver Rapidly Using Super-Fast Head Saccades and Image Feature Stabilization

    Science.gov (United States)

    Kress, Daniel; van Bokhorst, Evelien; Lentink, David

    2015-01-01

    Diurnal flying animals such as birds depend primarily on vision to coordinate their flight path during goal-directed flight tasks. To extract the spatial structure of the surrounding environment, birds are thought to use retinal image motion (optical flow) that is primarily induced by motion of their head. It is unclear what gaze behaviors birds perform to support visuomotor control during rapid maneuvering flight in which they continuously switch between flight modes. To analyze this, we measured the gaze behavior of rapidly turning lovebirds in a goal-directed task: take-off and fly away from a perch, turn on a dime, and fly back and land on the same perch. High-speed flight recordings revealed that rapidly turning lovebirds perform a remarkable stereotypical gaze behavior with peak saccadic head turns up to 2700 degrees per second, as fast as insects, enabled by fast neck muscles. In between saccades, gaze orientation is held constant. By comparing saccade and wingbeat phase, we find that these super-fast saccades are coordinated with the downstroke when the lateral visual field is occluded by the wings. Lovebirds thus maximize visual perception by overlying behaviors that impair vision, which helps coordinate maneuvers. Before the turn, lovebirds keep a high contrast edge in their visual midline. Similarly, before landing, the lovebirds stabilize the center of the perch in their visual midline. The perch on which the birds land swings, like a branch in the wind, and we find that retinal size of the perch is the most parsimonious visual cue to initiate landing. Our observations show that rapidly maneuvering birds use precisely timed stereotypic gaze behaviors consisting of rapid head turns and frontal feature stabilization, which facilitates optical flow based flight control. Similar gaze behaviors have been reported for visually navigating humans. This finding can inspire more effective vision-based autopilots for drones. PMID:26107413

  1. How Lovebirds Maneuver Rapidly Using Super-Fast Head Saccades and Image Feature Stabilization.

    Science.gov (United States)

    Kress, Daniel; van Bokhorst, Evelien; Lentink, David

    2015-01-01

    Diurnal flying animals such as birds depend primarily on vision to coordinate their flight path during goal-directed flight tasks. To extract the spatial structure of the surrounding environment, birds are thought to use retinal image motion (optical flow) that is primarily induced by motion of their head. It is unclear what gaze behaviors birds perform to support visuomotor control during rapid maneuvering flight in which they continuously switch between flight modes. To analyze this, we measured the gaze behavior of rapidly turning lovebirds in a goal-directed task: take-off and fly away from a perch, turn on a dime, and fly back and land on the same perch. High-speed flight recordings revealed that rapidly turning lovebirds perform a remarkable stereotypical gaze behavior with peak saccadic head turns up to 2700 degrees per second, as fast as insects, enabled by fast neck muscles. In between saccades, gaze orientation is held constant. By comparing saccade and wingbeat phase, we find that these super-fast saccades are coordinated with the downstroke when the lateral visual field is occluded by the wings. Lovebirds thus maximize visual perception by overlying behaviors that impair vision, which helps coordinate maneuvers. Before the turn, lovebirds keep a high contrast edge in their visual midline. Similarly, before landing, the lovebirds stabilize the center of the perch in their visual midline. The perch on which the birds land swings, like a branch in the wind, and we find that retinal size of the perch is the most parsimonious visual cue to initiate landing. Our observations show that rapidly maneuvering birds use precisely timed stereotypic gaze behaviors consisting of rapid head turns and frontal feature stabilization, which facilitates optical flow based flight control. Similar gaze behaviors have been reported for visually navigating humans. This finding can inspire more effective vision-based autopilots for drones.

  2. Rapid determination of biogenic amines in cooked beef using hyperspectral imaging with sparse representation algorithm

    Science.gov (United States)

    Yang, Dong; Lu, Anxiang; Ren, Dong; Wang, Jihua

    2017-11-01

    This study explored the feasibility of rapid detection of biogenic amines (BAs) in cooked beef during the storage process using hyperspectral imaging technique combined with sparse representation (SR) algorithm. The hyperspectral images of samples were collected in the two spectral ranges of 400-1000 nm and 1000-1800 nm, separately. The spectral data were reduced dimensionality by SR and principal component analysis (PCA) algorithms, and then integrated the least square support vector machine (LS-SVM) to build the SR-LS-SVM and PC-LS-SVM models for the prediction of BAs values in cooked beef. The results showed that the SR-LS-SVM model exhibited the best predictive ability with determination coefficients (RP2) of 0.943 and root mean square errors (RMSEP) of 1.206 in the range of 400-1000 nm of prediction set. The SR and PCA algorithms were further combined to establish the best SR-PC-LS-SVM model for BAs prediction, which had high RP2of 0.969 and low RMSEP of 1.039 in the region of 400-1000 nm. The visual map of the BAs was generated using the best SR-PC-LS-SVM model with imaging process algorithms, which could be used to observe the changes of BAs in cooked beef more intuitively. The study demonstrated that hyperspectral imaging technique combined with sparse representation were able to detect effectively the BAs values in cooked beef during storage and the built SR-PC-LS-SVM model had a potential for rapid and accurate determination of freshness indexes in other meat and meat products.

  3. JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

    Science.gov (United States)

    Lelièvre, Peter G.; Grey, Melissa

    2017-08-01

    Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

  4. Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.

    Directory of Open Access Journals (Sweden)

    Dario Cantu

    Full Text Available BACKGROUND: The wheat stripe rust fungus (Puccinia striiformis f. sp. tritici, PST is responsible for significant yield losses in wheat production worldwide. In spite of its economic importance, the PST genomic sequence is not currently available. Fortunately Next Generation Sequencing (NGS has radically improved sequencing speed and efficiency with a great reduction in costs compared to traditional sequencing technologies. We used Illumina sequencing to rapidly access the genomic sequence of the highly virulent PST race 130 (PST-130. METHODOLOGY/PRINCIPAL FINDINGS: We obtained nearly 80 million high quality paired-end reads (>50x coverage that were assembled into 29,178 contigs (64.8 Mb, which provide an estimated coverage of at least 88% of the PST genes and are available through GenBank. Extensive micro-synteny with the Puccinia graminis f. sp. tritici (PGTG genome and high sequence similarity with annotated PGTG genes support the quality of the PST-130 contigs. We characterized the transposable elements present in the PST-130 contigs and using an ab initio gene prediction program we identified and tentatively annotated 22,815 putative coding sequences. We provide examples on the use of comparative approaches to improve gene annotation for both PST and PGTG and to identify candidate effectors. Finally, the assembled contigs provided an inventory of PST repetitive elements, which were annotated and deposited in Repbase. CONCLUSIONS/SIGNIFICANCE: The assembly of the PST-130 genome and the predicted proteins provide useful resources to rapidly identify and clone PST genes and their regulatory regions. Although the automatic gene prediction has limitations, we show that a comparative genomics approach using multiple rust species can greatly improve the quality of gene annotation in these species. The PST-130 sequence will also be useful for comparative studies within PST as more races are sequenced. This study illustrates the power of NGS for

  5. Hierarchical Matching of Uncertain Building Models with Oblique View Airborne IR Image Sequences

    Science.gov (United States)

    Iwaszczuk, D.; Hoegner, L.; Schmitt, M.; Stilla, U.

    2012-07-01

    Thermal building textures can be used for detection of damaged and weak spots in the building structure. These textures can be extracted from airborne infrared (IR) image sequences by projecting the 3D building model into the images. However, the direct georeferencing is often not sufficiently accurate and the projected 3D model does not match the structures in the image. Thus we present a technique with the main goal to find the best fit between the existing 3D building model and the IR image sequence. For this purpose we developed a hierarchical approach consisting of two working stages. In the first stage we correct exterior orientation via line based matching. In the adjustment we consider both uncertainties: the ones of the model and the ones of the image. In the second stage we match each edge separately in its closest surrounding. Thanks to this approach a better fit between the 3D building model and the IR image was found. The originally unmodeled roof overlap was reconstructed.

  6. Current density imaging sequence for monitoring current distribution during delivery of electric pulses in irreversible electroporation.

    Science.gov (United States)

    Serša, Igor; Kranjc, Matej; Miklavčič, Damijan

    2015-01-01

    Electroporation is gaining its importance in everyday clinical practice of cancer treatment. For its success it is extremely important that coverage of the target tissue, i.e. treated tumor, with electric field is within the specified range. Therefore, an efficient tool for the electric field monitoring in the tumor during delivery of electroporation pulses is needed. The electric field can be reconstructed by the magnetic resonance electric impedance tomography method from current density distribution data. In this study, the use of current density imaging with MRI for monitoring current density distribution during delivery of irreversible electroporation pulses was demonstrated. Using a modified single-shot RARE sequence, where four 3000 V and 100 μs long pulses were included at the start, current distribution between a pair of electrodes inserted in a liver tissue sample was imaged. Two repetitions of the sequence with phases of refocusing radiofrequency pulses 90° apart were needed to acquire one current density image. For each sample in total 45 current density images were acquired to follow a standard protocol for irreversible electroporation where 90 electric pulses are delivered at 1 Hz. Acquired current density images showed that the current density in the middle of the sample increased from first to last electric pulses by 60%, i.e. from 8 kA/m2 to 13 kA/m2 and that direction of the current path did not change with repeated electric pulses significantly. The presented single-shot RARE-based current density imaging sequence was used successfully to image current distribution during delivery of short high-voltage electric pulses. The method has a potential to enable monitoring of tumor coverage by electric field during irreversible electroporation tissue ablation.

  7. Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

    Science.gov (United States)

    Segerman, Bo; De Medici, Dario; Ehling Schulz, Monika; Fach, Patrick; Fenicia, Lucia; Fricker, Martina; Wielinga, Peter; Van Rotterdam, Bart; Knutsson, Rickard

    2011-03-01

    The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams. Copyright © 2010 Elsevier B.V. All rights reserved.

  8. Rapid diagnosis and intraoperative margin assessment of human lung cancer with fluorescence lifetime imaging microscopy

    Directory of Open Access Journals (Sweden)

    Mengyan Wang

    2017-12-01

    Full Text Available A method of rapidly differentiating lung tumor from healthy tissue is extraordinarily needed for both the diagnosis and the intraoperative margin assessment. We assessed the ability of fluorescence lifetime imaging microscopy (FLIM for differentiating human lung cancer and normal tissues with the autofluorescence, and also elucidated the mechanism in tissue studies and cell studies. A 15-patient testing group was used to compare FLIM results with traditional histopathology diagnosis. Based on the endogenous fluorescence lifetimes of the testing group, a criterion line was proposed to distinguish normal and cancerous tissues. Then by blinded examined 41 sections from the validation group of other 16 patients, the sensitivity and specificity of FLIM were determined. The cellular metabolism was studied with specific perturbations of oxidative phosphorylation and glycolysis in cell studies. The fluorescence lifetime of cancerous lung tissues is consistently lower than normal tissues, and this is due to the both decrease of reduced nicotinamide adenine dinucleotide (NADH and flavin adenine dinucleotide (FAD lifetimes. A criterion line of lifetime at 1920 ps can be given for differentiating human lung cancer and normal tissues.The sensitivity and specificity of FLIM for lung cancer diagnosis were determined as 92.9% and 92.3%. These findings suggest that NADH and FAD can be used to rapidly diagnose lung cancer. FLIM is a rapid, accurate and highly sensitive technique in the judgment during lung cancer surgery and it can be potential in earlier cancer detection.

  9. Rapid diagnosis and intraoperative margin assessment of human lung cancer with fluorescence lifetime imaging microscopy.

    Science.gov (United States)

    Wang, Mengyan; Tang, Feng; Pan, Xiaobo; Yao, Longfang; Wang, Xinyi; Jing, Yueyue; Ma, Jiong; Wang, Guifang; Mi, Lan

    2017-12-01

    A method of rapidly differentiating lung tumor from healthy tissue is extraordinarily needed for both the diagnosis and the intraoperative margin assessment. We assessed the ability of fluorescence lifetime imaging microscopy (FLIM) for differentiating human lung cancer and normal tissues with the autofluorescence, and also elucidated the mechanism in tissue studies and cell studies. A 15-patient testing group was used to compare FLIM results with traditional histopathology diagnosis. Based on the endogenous fluorescence lifetimes of the testing group, a criterion line was proposed to distinguish normal and cancerous tissues. Then by blinded examined 41 sections from the validation group of other 16 patients, the sensitivity and specificity of FLIM were determined. The cellular metabolism was studied with specific perturbations of oxidative phosphorylation and glycolysis in cell studies. The fluorescence lifetime of cancerous lung tissues is consistently lower than normal tissues, and this is due to the both decrease of reduced nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FAD) lifetimes. A criterion line of lifetime at 1920 ps can be given for differentiating human lung cancer and normal tissues.The sensitivity and specificity of FLIM for lung cancer diagnosis were determined as 92.9% and 92.3%. These findings suggest that NADH and FAD can be used to rapidly diagnose lung cancer. FLIM is a rapid, accurate and highly sensitive technique in the judgment during lung cancer surgery and it can be potential in earlier cancer detection.

  10. Rapid acquisition of helium-3 and proton three-dimensional image sets of the human lung in a single breath-hold using compressed sensing.

    Science.gov (United States)

    Qing, Kun; Altes, Talissa A; Tustison, Nicholas J; Feng, Xue; Chen, Xiao; Mata, Jaime F; Miller, G Wilson; de Lange, Eduard E; Tobias, William A; Cates, Gordon D; Brookeman, James R; Mugler, John P

    2015-10-01

    To develop and validate a method for acquiring helium-3 ((3) He) and proton ((1) H) three-dimensional (3D) image sets of the human lung with isotropic spatial resolution within a 10-s breath-hold by using compressed sensing (CS) acceleration, and to assess the fidelity of undersampled images compared with fully sampled images. The undersampling scheme for CS acceleration was optimized and tested using (3) He ventilation data. Rapid 3D acquisition of both (3) He and (1) H data during one breath-hold was then implemented, based on a balanced steady-state free-precession pulse sequence, by random undersampling of k-space with reconstruction by means of minimizing the L1 norm and total variance. CS-reconstruction fidelity was evaluated quantitatively by comparing fully sampled and retrospectively undersampled image sets. Helium-3 and (1) H 3D image sets of the lung with isotropic 3.9-mm resolution were acquired during a single breath-hold in 12 s and 8 s using acceleration factors of 2 and 3, respectively. Comparison of fully sampled and retrospectively undersampled (3) He and (1) H images yielded mean absolute errors 0.9. By randomly undersampling k-space and using CS reconstruction, high-quality (3) He and (1) H 3D image sets with isotropic 3.9-mm resolution can be acquired within an 8-s breath-hold. © 2014 Wiley Periodicals, Inc.

  11. Effects of imaging gradients in sequences with varying longitudinal storage time-Case of diffusion exchange imaging

    DEFF Research Database (Denmark)

    Lasic, Samo; Lundell, Henrik; Topgaard, Daniel

    2017-01-01

    Purpose: To illustrate the potential bias caused by imaging gradients in correlation MRI sequences using longitudinal magnetization storage (LS) and examine the case of filter exchange imaging (FEXI) yielding maps of the apparent exchange rate (AXR). Methods: The effects of imaging gradients...... low-pass diffusion filtering during the LS interval, which is more pronounced at lower exchange rates. For a total exchange rate constant larger than 1 s-1, the AXR bias is expected to be negligible when slices thicker than 2.5mm are used. Conclusion: In correlation experiments like FEXI, relying...... in FEXI were observed on yeast cells. To analyze the AXR bias, signal evolution was calculated by applying matrix exponential operators. Results: A sharp threshold for the slice thickness was identified, below which the AXR is increasingly underestimated. The bias can be understood in terms of an extended...

  12. Ion torrent personal genome machine sequencing for genomic typing of Neisseria meningitidis for rapid determination of multiple layers of typing information.

    Science.gov (United States)

    Vogel, Ulrich; Szczepanowski, Rafael; Claus, Heike; Jünemann, Sebastian; Prior, Karola; Harmsen, Dag

    2012-06-01

    Neisseria meningitidis causes invasive meningococcal disease in infants, toddlers, and adolescents worldwide. DNA sequence-based typing, including multilocus sequence typing, analysis of genetic determinants of antibiotic resistance, and sequence typing of vaccine antigens, has become the standard for molecular epidemiology of the organism. However, PCR of multiple targets and consecutive Sanger sequencing provide logistic constraints to reference laboratories. Taking advantage of the recent development of benchtop next-generation sequencers (NGSs) and of BIGSdb, a database accommodating and analyzing genome sequence data, we therefore explored the feasibility and accuracy of Ion Torrent Personal Genome Machine (PGM) sequencing for genomic typing of meningococci. Three strains from a previous meningococcus serogroup B community outbreak were selected to compare conventional typing results with data generated by semiconductor chip-based sequencing. In addition, sequencing of the meningococcal type strain MC58 provided information about the general performance of the technology. The PGM technology generated sequence information for all target genes addressed. The results were 100% concordant with conventional typing results, with no further editing being necessary. In addition, the amount of typing information, i.e., nucleotides and target genes analyzed, could be substantially increased by the combined use of genome sequencing and BIGSdb compared to conventional methods. In the near future, affordable and fast benchtop NGS machines like the PGM might enable reference laboratories to switch to genomic typing on a routine basis. This will reduce workloads and rapidly provide information for laboratory surveillance, outbreak investigation, assessment of vaccine preventability, and antibiotic resistance gene monitoring.

  13. ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.

    Science.gov (United States)

    Lavender, Christopher A; Shapiro, Andrew J; Burkholder, Adam B; Bennett, Brian D; Adelman, Karen; Fargo, David C

    2017-06-02

    Established and emerging next generation sequencing (NGS)-based technologies allow for genome-wide interrogation of diverse biological processes. However, accessibility of NGS data remains a problem, and few user-friendly resources exist for integrative analysis of NGS data from different sources and experimental techniques. Here, we present Online Resource for Integrative Omics (ORIO; https://orio.niehs.nih.gov/), a web-based resource with an intuitive user interface for rapid analysis and integration of NGS data. To use ORIO, the user specifies NGS data of interest along with a list of genomic coordinates. Genomic coordinates may be biologically relevant features from a variety of sources, such as ChIP-seq peaks for a given protein or transcription start sites from known gene models. ORIO first iteratively finds read coverage values at each genomic feature for each NGS dataset. Data are then integrated using clustering-based approaches, giving hierarchical relationships across NGS datasets and separating individual genomic features into groups. In focusing its analysis on read coverage, ORIO makes limited assumptions about the analyzed data; this allows the tool to be applied across data from a variety of experiments and techniques. Results from analysis are presented in dynamic displays alongside user-controlled statistical tests, supporting rapid statistical validation of observed results. We emphasize the versatility of ORIO through diverse examples, ranging from NGS data quality control to characterization of enhancer regions and integration of gene expression information. Easily accessible on a public web server, we anticipate wide use of ORIO in genome-wide investigations by life scientists. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

  14. Determining the physical processes behind four large eruptions in rapid sequence in the San Juan caldera cluster (Colorado, USA)

    Science.gov (United States)

    Curry, Adam; Caricchi, Luca; Lipman, Peter

    2017-04-01

    Large, explosive volcanic eruptions can have both immediate and long-term negative effects on human societies. Statistical analyses of volcanic eruptions show that the frequency of the largest eruptions on Earth (> ˜450 km3) differs from that observed for smaller eruptions, suggesting different physical processes leading to eruption. This project will characterize the petrography, whole-rock geochemistry, mineral chemistry, and zircon geochronology of four caldera-forming ignimbrites from the San Juan caldera cluster, Colorado, to determine the physical processes leading to eruption. We collected outflow samples along stratigraphy of the three caldera-forming ignimbrites of the San Luis caldera complex: the Nelson Mountain Tuff (>500 km3), Cebolla Creek Tuff (˜250 km3), and Rat Creek Tuff (˜150 km3); and we collected samples of both outflow and intracaldera facies of the Snowshoe Mountain Tuff (>500 km3), which formed the Creede caldera. Single-crystal sanidine 40Ar/39Ar ages show that these eruptions occurred in rapid succession between 26.91 ± 0.02 Ma (Rat Creek) and 26.87 ± 0.02 Ma (Snowshoe Mountain), providing a unique opportunity to investigate the physical processes leading to a rapid sequence of large, explosive volcanic eruptions. Recent studies show that the average flux of magma is an important parameter in determining the frequency and magnitude of volcanic eruptions. High-precision isotope-dilution thermal ionization mass spectrometry (ID-TIMS) zircon geochronology will be performed to determine magma fluxes, and cross-correlation of chemical profiles in minerals will be performed to determine the periodicity of magma recharge that preceded these eruptions. Our project intends to combine these findings with similar data from other volcanic regions around the world to identify physical processes controlling the regional and global frequency-magnitude relationships of volcanic eruptions.

  15. A motion correction framework for time series sequences in microscopy images.

    Science.gov (United States)

    Kumar, Ankur N; Short, Kurt W; Piston, David W

    2013-04-01

    With the advent of in vivo laser scanning fluorescence microscopy techniques, time-series and three-dimensional volumes of living tissue and vessels at micron scales can be acquired to firmly analyze vessel architecture and blood flow. Analysis of a large number of image stacks to extract architecture and track blood flow manually is cumbersome and prone to observer bias. Thus, an automated framework to accomplish these analytical tasks is imperative. The first initiative toward such a framework is to compensate for motion artifacts manifest in these microscopy images. Motion artifacts in in vivo microscopy images are caused by respiratory motion, heart beats, and other motions from the specimen. Consequently, the amount of motion present in these images can be large and hinders further analysis of these images. In this article, an algorithmic framework for the correction of time-series images is presented. The automated algorithm is comprised of a rigid and a nonrigid registration step based on shape contexts. The framework performs considerably well on time-series image sequences of the islets of Langerhans and provides for the pivotal step of motion correction in the further automatic analysis of microscopy images.

  16. Optical scatter imaging: a microscopic modality for the rapid morphological assay of living cells

    Science.gov (United States)

    Boustany, Nada N.

    2007-02-01

    Tumors derived from epithelial cells comprise the majority of human tumors and their growth results from the accumulation of multiple mutations affecting cellular processes critical for tissue homeostasis, including cell proliferation and cell death. To understand these processes and address the complexity of cancer cell function, multiple cellular responses to different experimental conditions and specific genetic mutations must be analyzed. Fundamental to this endeavor is the development of rapid cellular assays in genetically defined cells, and in particular, the development of optical imaging methods that allow dynamic observation and real-time monitoring of cellular processes. In this context, we are developing an optical scatter imaging technology that is intended to bridge the gap between light and electron microscopy by rapidly providing morphometric information about the relative size and shape of non-spherical organelles, with sub-wavelength resolution. Our goal is to complement current microscopy techniques used to study cells in-vitro, especially in long-term time-lapse studies of living cells, where exogenous labels can be toxic, and electron microscopy will destroy the sample. The optical measurements are based on Fourier spatial filtering in a standard microscope, and could ultimately be incorporated into existing high-throughput diagnostic platforms for cancer cell research and histopathology of neoplastic tissue arrays. Using an engineered epithelial cell model of tumor formation, we are currently studying how organelle structure and function are altered by defined genetic mutations affecting the propensity for cell death and oncogenic potential, and by environmental conditions promoting tumor growth. This talk will describe our optical scatter imaging technology and present results from our studies on apoptosis, and the function of BCL-2 family proteins.

  17. Technical Note: Rapid prototyping of 3D grid arrays for image guided therapy quality assurance

    Energy Technology Data Exchange (ETDEWEB)

    Kittle, David; Holshouser, Barbara; Slater, James M.; Guenther, Bob D.; Pitsianis, Nikos P.; Pearlstein, Robert D. [Department of Radiation Medicine, Epilepsy Radiosurgery Research Program, Loma Linda University, Loma Linda, California 92354 (United States); Department of Radiology, Loma Linda University Medical Center, Loma Linda, California 92354 (United States); Department of Radiation Medicine, Loma Linda University, Loma Linda, California 92354 (United States); Department of Physics, Duke University, Durham, North Carolina 27708 (United States); Department of Electrical and Computer Engineering and Department of Computer Science, Duke University, Durham, North Carolina 27708 (United States); Department of Radiation Medicine, Epilepsy Radiosurgery Research Program, Loma Linda University, Loma Linda, California 92354 and Department of Surgery-Neurosurgery, Duke University and Medical Center, Durham, North Carolina 27710 (United States)

    2008-12-15

    Three dimensional grid phantoms offer a number of advantages for measuring imaging related spatial inaccuracies for image guided surgery and radiotherapy. The authors examined the use of rapid prototyping technology for directly fabricating 3D grid phantoms from CAD drawings. We tested three different fabrication process materials, photopolymer jet with acrylic resin (PJ/AR), selective laser sintering with polyamide (SLS/P), and fused deposition modeling with acrylonitrile butadiene styrene (FDM/ABS). The test objects consisted of rectangular arrays of control points formed by the intersections of posts and struts (2 mm rectangular cross section) and spaced 8 mm apart in the x, y, and z directions. The PJ/AR phantom expanded after immersion in water which resulted in permanent warping of the structure. The surface of the FDM/ABS grid exhibited a regular pattern of depressions and ridges from the extrusion process. SLS/P showed the best combination of build accuracy, surface finish, and stability. Based on these findings, a grid phantom for assessing machine-dependent and frame-induced MR spatial distortions was fabricated to be used for quality assurance in stereotactic neurosurgical and radiotherapy procedures. The spatial uniformity of the SLS/P grid control point array was determined by CT imaging (0.6x0.6x0.625 mm{sup 3} resolution) and found suitable for the application, with over 97.5% of the control points located within 0.3 mm of the position specified in CAD drawing and none of the points off by more than 0.4 mm. Rapid prototyping is a flexible and cost effective alternative for development of customized grid phantoms for medical physics quality assurance.

  18. Rapid total body fat measurement by magnetic resonance imaging: quantification and topography; Schnelle Ganzkoerperfettmessung mittels MRT: Quantifizierung und Topografie

    Energy Technology Data Exchange (ETDEWEB)

    Vogt, F.M.; Hunold, P.; Greiff, A. de; Nuefer, M.; Barkhausen, J.; Ladd, S.C. [Uniklinikum Essen (Germany). Inst. fuer Diagnostische und Interventionelle Radiologie; Ruehm, S. [David Geffen School of Medicine at UCLA (United States). Dept. of Radiology

    2007-05-15

    Purpose: To evaluate a rapid and comprehensive MR protocol based on a T1-weighted sequence in conjunction with a rolling table platform for the quantification of total body fat. Materials and Methods: 11 healthy volunteers and 50 patients were included in the study. MR data was acquired on a 1.5-T system (Siemens Magnetom Sonata). An axial T1-weighted flash 2D sequence (TR 101, TE 4.7, FA 70, FOV 50 cm, 205 x 256 matrix, slice thickness: 10 mm, 10 mm interslice gap) was used for data acquisition. Patients were placed in a supine position on a rolling table platform capable of acquiring multiple consecutive data sets by pulling the patient through the isocenter of the magnet. Data sets extending from the upper to lower extremities were collected. The images were analyzed with respect to the amount of intraabdominal, subcutaneous and total abdominal fat by semi-automated image segmentation software that employs a contour-following algorithm. Results: The obtained MR images were able to be evaluated for all volunteers and patients. Excellent correlation was found between whole body MRI results in volunteers with DEXA (r{sup 2} = 0.95) and bioimpedance (r{sup 2} = 0.89) measurements, while the correlation coefficient was 0.66 between MRI and BMI, indicating only moderate reliability of the BMI method. Variations in patients with respect to the amount of total, subcutaneous, and intraabdominal adipose tissue was not related to standard anthropometric measurements and metabolic lipid profiles (r{sup 2} = 0,001 to 0.48). The results showed that there was a significant variation in intraabdominal adipose tissue which could not be predicted from the total body fat (r{sup 2} = 0.14) or subcutaneous adipose tissue (r{sup 2} = 0.04). Although no significant differences in BMI could be found between females and males (p = 0.26), females showed significantly higher total and subcutaneous abdominal adipose tissue (p < 0.05). Conclusion. (orig.)

  19. Single-Heartbeat Electromechanical Wave Imaging with Optimal Strain Estimation Using Temporally-Unequispaced Acquisition Sequences

    Science.gov (United States)

    Provost, Jean; Thiébaut, Stéphane; Luo, Jianwen; Konofagou, Elisa E.

    2014-01-01

    Electromechanical Wave Imaging (EWI) is a non-invasive, ultrasound-based imaging method capable of mapping the electromechanical wave (EW) in vivo, i.e., the transient deformations occurring in response to the electrical activation of the heart. Achieving the optimal imaging frame rates, in terms of the elastographic signal-to-noise ratio, to capture the EW in a full-view of the heart poses a technical challenge due to the limitations of conventional imaging sequences, in which the frame rate is low and tied to the imaging parameters. To achieve higher frame rates, EWI is typically performed in multiple small regions of interest acquired over separate heartbeats, which are then combined into a single view. However, the reliance on multiple heartbeats has previously precluded the method from its application in non-periodic arrhythmias such as fibrillation. Moreover, the frame rates achieved remain sub-optimal, because they are determined by the imaging parameters rather than being optimized to image the EW. In this paper, we develop a temporally-unequispaced acquisition sequence (TUAS) for which a wide range of frame rates are achievable independently of the imaging parameters, while maintaining a full view of the heart at high beam density. TUAS is first used to determine the optimal frame rate for EWI in a paced canine heart in vivo. The feasibility of performing single-heartbeat EWI during ventricular fibrillation is then demonstrated. These results indicate that EWI can be performed optimally, within a single heartbeat, during free breathing, and implemented in real time for periodic and non-periodic cardiac events. PMID:22297208

  20. Synthesis of image sequences for Korean sign language using 3D shape model

    Science.gov (United States)

    Hong, Mun-Ho; Choi, Chang-Seok; Kim, Chang-Seok; Jeon, Joon-Hyeon

    1995-05-01

    This paper proposes a method for offering information and realizing communication to the deaf-mute. The deaf-mute communicates with another person by means of sign language, but most people are unfamiliar with it. This method enables to convert text data into the corresponding image sequences for Korean sign language (KSL). Using a general 3D shape model of the upper body leads to generating the 3D motions of KSL. It is necessary to construct the general 3D shape model considering the anatomical structure of the human body. To obtain a personal 3D shape model, this general model is to adjust to the personal base images. Image synthesis for KSL consists of deforming a personal 3D shape model and texture-mapping the personal images onto the deformed model. The 3D motions for KSL have the facial expressions and the 3D movements of the head, trunk, arms and hands and are parameterized for easily deforming the model. These motion parameters of the upper body are extracted from a skilled signer's motion for each KSL and are stored to the database. Editing the parameters according to the inputs of text data yields to generate the image sequences of 3D motions.

  1. QUALITY ANALYSIS OF VEHICLE-BASED SEQUENCE IMAGES RELATIVE ORIENTATION BASED ON COMPUTER VISION

    Directory of Open Access Journals (Sweden)

    L. Yan

    2012-08-01

    Full Text Available Analyzed the quality and its influence factors of relative orientation of vehicle-based sequence images by comparing with the result obtained from Position & Orientation System using Direct Geo-referencing. Studies have shown that, under normal circumstances, the image Relative Orientation based on Computer vision is more robust, and under special conditions, it is more practical for analyzing and increasing the quality of vision measurement. Besides these, the method can be borrowed by many surveying and mapping related fields, taking indoor robot mobile environment awareness and unmanned automobile for instance.

  2. Position and Attitude Estimation from a Image Sequence of a Circle

    OpenAIRE

    佐藤, 真知子; Machiko, SATO; Tokyo Institute of Polytechnics Faculty of Engineering

    1995-01-01

    A method to estimate the position and attitude of a helicopter with respect to the landing site from a image sequence of a heliport is presented. The method use the circle of the heliport marking as the visual cue. The projection of the circle on the successive image taken by on board camera will change, therefore a Kalman filter can be build for the recursive estimation. The method needs to know just there is a circle ; The size of the circle is not necessary. The result of the experiment on...

  3. Sparse-SEMAC: rapid and improved SEMAC metal implant imaging using SPARSE-SENSE acceleration.

    Science.gov (United States)

    Otazo, Ricardo; Nittka, Mathias; Bruno, Mary; Raithel, Esther; Geppert, Christian; Gyftopoulos, Soterios; Recht, Michael; Rybak, Leon

    2017-07-01

    To develop an accelerated SEMAC metal implant MRI technique (Sparse-SEMAC) with reduced scan time and improved metal distortion correction. Sparse-SEMAC jointly exploits the inherent sparsity along the additional phase-encoding dimension and multicoil encoding capabilities to significantly accelerate data acquisition. A prototype pulse sequence with pseudorandom ky -kz undersampling and an inline image reconstruction was developed for integration in clinical studies. Three patients with hip implants were imaged using the proposed Sparse-SEMAC with eight-fold acceleration and compared with the standard-SEMAC technique used in clinical studies (three-fold GRAPPA acceleration). Measurements were performed with SEMAC-encoding steps (SES) = 15 for Sparse-SEMAC and SES = 9 for Standard-SEMAC using high spatial resolution Proton Density (PD) and lower-resolution STIR acquisitions. Two expert musculoskeletal (MSK) radiologists performed a consensus reading to score image-quality parameters. Sparse-SEMAC enables up to eight-fold acceleration of data acquisition that results in two-fold scan time reductions, compared with Standard-SEMAC, with improved metal artifact correction for patients with hip implants without degrading spatial resolution. The high acceleration enabled by Sparse-SEMAC would enable clinically feasible examination times with improved correction of metal distortion. Magn Reson Med 78:79-87, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  4. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences.

    Directory of Open Access Journals (Sweden)

    Josephine A Reinhardt

    Full Text Available How non-coding DNA gives rise to new protein-coding genes (de novo genes is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs, while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important.

  5. Imaging Spectroscopy Techniques for Rapid Assessment of Geologic and Cryospheric Science Data from future Satellite Sensors

    Science.gov (United States)

    Calvin, W. M.; Hill, R.

    2016-12-01

    Several efforts are currently underway to develop and launch the next generation of imaging spectrometer systems on satellite platforms for a wide range of Earth Observation goals. Systems that include the reflected solar wavelength range up to 2.5 μm will be capable of detailed mapping of the composition of the Earth's surface. Sensors under development include EnMAP, HISUI, PRISMA, HERO, and HyspIRI. These systems are expected to be able to provide global data for insights and constraints on fundamental geological processes, natural and anthropogenic hazards, water, energy and mineral resource assessments. Coupled with the development of these sensors is the challenge of bringing a multi-channel user community (from Landsat, MODIS, and ASTER) into the rich science return available from imaging spectrometer systems. Most data end users will never be spectroscopy experts so that making the derived science products accessible to a wide user community is imperative. Simple band parameterizations have been developed for the CRISM instrument at Mars, including mafic and alteration minerals, frost and volatile ice indices. These products enhance and augment the use of that data set by broader group of scientists. Summary products for terrestrial geologic and water resource applications would help build a wider user base for future satellite systems, and rapidly key spectral experts to important regions for detailed spectral mapping. Summary products take advantage of imaging spectroscopy's narrow spectral channels with band depth calculations in addition to band ratios that are commonly used by multi-channel systems (e.g. NDVI, NDWI, NDSI). We are testing summary products for Earth geologic and snow scenes over California using AVIRIS data at 18m/pixel. This has resulted in several algorithms for rapid mineral discrimination and mapping and data collects over the melting Sierra snowpack in spring 2016 are expected to generate algorithms for snow grain size and surface

  6. Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging.

    Science.gov (United States)

    Nolte-Ernsting, C C; Tacke, J; Adam, G B; Haage, P; Jung, P; Jakse, G; Günther, R W

    2001-01-01

    The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p urography, the entire pelvicaliceal system was imaged by acquisition of a fast single-slice sequence and the conventional 2D GRE technique provided superior morphological accuracy than 2D GRE EPI projection images (p excretory MR urography especially in old or critically ill patients unable to suspend breathing for more than 20 s. Conventional GRE sequences are superior to EPI in high-resolution detail MR urograms and in projection imaging.

  7. Inversion in the steady state: contrast optimization and reduced imaging time with fast three-dimensional inversion-recovery-prepared GRE pulse sequences.

    Science.gov (United States)

    Foo, T K; Sawyer, A M; Faulkner, W H; Mills, D G

    1994-04-01

    To evaluate the differences in contrast between 1-second delay and zero delay (for magnetization recovery) before the preparation radio-frequency pulse in three-dimensional, inversion-recovery (IR) fast gradient-echo (GRE) acquisitions. Mathematical simulations and measurements of brain image contrast were performed with healthy volunteers and 10 patients. The zero-delay sequence generated T1-weighted contrast similar to that obtained with 1-second delay but was accompanied by a substantial reduction in imaging time. However, the zero delay prohibits full recovery of the longitudinal magnetization. Hence, the signal null characteristic of IR experiments is not easily observed, since it occurs (as a function of tissue T1) at very short inversion times (prepared rapid GRE sequences with a 1-second delay and preparation time (TP) of 600-700 msec can be achieved in less time by using a zero delay and a shorter TP (400-500 msec).

  8. Rain or Snow Detection in Image Sequences through use of a Histogram of Orientation of Streaks

    OpenAIRE

    Bossu, Jérémie; Hautiere, Nicolas; TAREL, Jean Philippe

    2011-01-01

    The detection of bad weather conditions is crucial for meteorological centers, specially with demand for air, sea and ground traffic management. In this article, a system based on computer vision is presented which detects the presence of rain or snow. To separate the foreground from the background in image sequences, a classical Gaussian Mixture Model is used. The foreground model serves to detect rain and snow, since these are dynamic weather phenomena. Selection rules based on photometry a...

  9. New Imaging Strategies Using a Motion-Resistant Liver Sequence in Uncooperative Patients

    Science.gov (United States)

    Kim, Bong Soo; Lee, Kyung Ryeol; Goh, Myeng Ju

    2014-01-01

    MR imaging has unique benefits for evaluating the liver because of its high-resolution capability and ability to permit detailed assessment of anatomic lesions. In uncooperative patients, motion artifacts can impair the image quality and lead to the loss of diagnostic information. In this setting, the recent advances in motion-resistant liver MR techniques, including faster imaging protocols (e.g., dual-echo magnetization-prepared rapid-acquisition gradient echo (MP-RAGE), view-sharing technique), the data under-sampling (e.g., gradient recalled echo (GRE) with controlled aliasing in parallel imaging results in higher acceleration (CAIPIRINHA), single-shot echo-train spin-echo (SS-ETSE)), and motion-artifact minimization method (e.g., radial GRE with/without k-space-weighted image contrast (KWIC)), can provide consistent, artifact-free images with adequate image quality and can lead to promising diagnostic performance. Understanding of the different motion-resistant options allows radiologists to adopt the most appropriate technique for their clinical practice and thereby significantly improve patient care. PMID:25243115

  10. Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Science.gov (United States)

    Rowe, Will; Baker, Kate S; Verner-Jeffreys, David; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan; Pearce, Gareth

    2015-01-01

    Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring. Here we present the Search Engine for Antimicrobial Resistance (SEAR), a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei. We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we show that SEAR

  11. Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data.

    Directory of Open Access Journals (Sweden)

    Will Rowe

    Full Text Available Antimicrobial resistance remains a growing and significant concern in human and veterinary medicine. Current laboratory methods for the detection and surveillance of antimicrobial resistant bacteria are limited in their effectiveness and scope. With the rapidly developing field of whole genome sequencing beginning to be utilised in clinical practice, the ability to interrogate sequencing data quickly and easily for the presence of antimicrobial resistance genes will become increasingly important and useful for informing clinical decisions. Additionally, use of such tools will provide insight into the dynamics of antimicrobial resistance genes in metagenomic samples such as those used in environmental monitoring.Here we present the Search Engine for Antimicrobial Resistance (SEAR, a pipeline and web interface for detection of horizontally acquired antimicrobial resistance genes in raw sequencing data. The pipeline provides gene information, abundance estimation and the reconstructed sequence of antimicrobial resistance genes; it also provides web links to additional information on each gene. The pipeline utilises clustering and read mapping to annotate full-length genes relative to a user-defined database. It also uses local alignment of annotated genes to a range of online databases to provide additional information. We demonstrate SEAR's application in the detection and abundance estimation of antimicrobial resistance genes in two novel environmental metagenomes, 32 human faecal microbiome datasets and 126 clinical isolates of Shigella sonnei.We have developed a pipeline that contributes to the improved capacity for antimicrobial resistance detection afforded by next generation sequencing technologies, allowing for rapid detection of antimicrobial resistance genes directly from sequencing data. SEAR uses raw sequencing data via an intuitive interface so can be run rapidly without requiring advanced bioinformatic skills or resources. Finally, we

  12. Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

    Directory of Open Access Journals (Sweden)

    Graner Andreas

    2008-10-01

    Full Text Available Abstract Background Barley has one of the largest and most complex genomes of all economically important food crops. The rise of new short read sequencing technologies such as Illumina/Solexa permits such large genomes to be effectively sampled at relatively low cost. Based on the corresponding sequence reads a Mathematically Defined Repeat (MDR index can be generated to map repetitive regions in genomic sequences. Results We have generated 574 Mbp of Illumina/Solexa sequences from barley total genomic DNA, representing about 10% of a genome equivalent. From these sequences we generated an MDR index which was then used to identify and mark repetitive regions in the barley genome. Comparison of the MDR plots with expert repeat annotation drawing on the information already available for known repetitive elements revealed a significant correspondence between the two methods. MDR-based annotation allowed for the identification of dozens of novel repeat sequences, though, which were not recognised by hand-annotation. The MDR data was also used to identify gene-containing regions by masking of repetitive sequences in eight de-novo sequenced bacterial artificial chromosome (BAC clones. For half of the identified candidate gene islands indeed gene sequences could be identified. MDR data were only of limited use, when mapped on genomic sequences from the closely related species Triticum monococcum as only a fraction of the repetitive sequences was recognised. Conclusion An MDR index for barley, which was obtained by whole-genome Illumina/Solexa sequencing, proved as efficient in repeat identification as manual expert annotation. Circumventing the labour-intensive step of producing a specific repeat library for expert annotation, an MDR index provides an elegant and efficient resource for the identification of repetitive and low-copy (i.e. potentially gene-containing sequences regions in uncharacterised genomic sequences. The restriction that a particular

  13. Visual processing in rapid-chase systems: Image processing, attention, and awareness

    Directory of Open Access Journals (Sweden)

    Thomas eSchmidt

    2011-07-01

    Full Text Available Visual stimuli can be classified so rapidly that their analysis may be based on a single sweep of feedforward processing through the visuomotor system. Behavioral criteria for feedforward processing can be evaluated in response priming tasks where speeded pointing or keypress responses are performed towards target stimuli which are preceded by prime stimuli. We apply this method to several classes of complex stimuli. 1 When participants classify natural images into animals or non-animals, the time course of their pointing responses indicates that prime and target signals remain strictly sequential throughout all processing stages, meeting stringent behavioral criteria for feedforward processing (rapid-chase criteria. 2 Such priming effects are boosted by selective visual attention for positions, shapes, and colors, in a way consistent with bottom-up enhancement of visuomotor processing, even when primes cannot be consciously identified. 3 Speeded processing of phobic images is observed in participants specifically fearful of spiders or snakes, suggesting enhancement of feedforward processing by long-term perceptual learning. 4 When the perceived brightness of primes in complex displays is altered by means of illumination or transparency illusions, priming effects in speeded keypress responses can systematically contradict subjective brightness judgments, such that one prime appears brighter than the other but activates motor responses as if it was darker. We propose that response priming captures the output of the first feedforward pass of visual signals through the visuomotor system, and that this output lacks some characteristic features of more elaborate, recurrent processing. This way, visuomotor measures may become dissociated from several aspects of conscious vision. We argue that "fast" visuomotor measures predominantly driven by feedforward processing should supplement "slow" psychophysical measures predominantly based on visual

  14. Rapidly destructive arthrosis of the shoulder joints: radiographic, magnetic resonance imaging, and histopathologic findings.

    Science.gov (United States)

    Kekatpure, Aashay L; Sun, Ji-Ho; Sim, Gyeong-Bo; Chun, Jae-Myeung; Jeon, In-Ho

    2015-06-01

    Rapidly destructive arthrosis of the humeral head is a rare condition with an elusive pathophysiologic mechanism. In this study, radiographic and histopathologic findings were analyzed to determine the clinical characteristics of this rare condition. We retrospectively analyzed 189 patients who underwent total shoulder arthroplasty from January 2001 to August 2012. Among them, 9 patients showed a particular pattern of rapid collapse of the humeral head on plain radiography and magnetic resonance imaging (MRI) within 12 months from symptom onset. Patients with trauma, rheumatoid arthritis, steroid intake, neurologic osteoarthropathy, osteonecrosis, renal osteoarthropathy, or gout were excluded. All patients were women, with a mean age of 72.0 years (range, 63-85 years). The right side was involved in 7 cases and the left in 2 cases. The mean duration of humeral head collapse was 5.6 months (range, 2-11 months) from the onset of shoulder pain. Plain radiographs of all patients showed a unique pattern of humeral head flattening, which appeared like a clean surgical cut with bone debris around the humeral head. MRI findings revealed significant joint effusion and bone marrow edema in the humeral head, without involvement of the glenoid. Pathologic findings showed both fragmentation and regeneration of bone matrix, representing fracture healing. The important features of rapidly destructive shoulder arthrosis are unique flattened humeral head collapse with MRI showing massive joint effusion and bone marrow edema in the remnant humeral head. This condition should be considered in the differential diagnosis of elderly women with insidious shoulder pain. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

  15. Rapid microwave-assisted synthesis of dextran-coated iron oxide nanoparticles for magnetic resonance imaging

    Science.gov (United States)

    Osborne, Elizabeth A.; Atkins, Tonya M.; Gilbert, Dustin A.; Kauzlarich, Susan M.; Liu, Kai; Louie, Angelique Y.

    2012-06-01

    Currently, magnetic iron oxide nanoparticles are the only nanosized magnetic resonance imaging (MRI) contrast agents approved for clinical use, yet commercial manufacturing of these agents has been limited or discontinued. Though there is still widespread demand for these particles both for clinical use and research, they are difficult to obtain commercially, and complicated syntheses make in-house preparation unfeasible for most biological research labs or clinics. To make commercial production viable and increase accessibility of these products, it is crucial to develop simple, rapid and reproducible preparations of biocompatible iron oxide nanoparticles. Here, we report a rapid, straightforward microwave-assisted synthesis of superparamagnetic dextran-coated iron oxide nanoparticles. The nanoparticles were produced in two hydrodynamic sizes with differing core morphologies by varying the synthetic method as either a two-step or single-step process. A striking benefit of these methods is the ability to obtain swift and consistent results without the necessity for air-, pH- or temperature-sensitive techniques; therefore, reaction times and complex manufacturing processes are greatly reduced as compared to conventional synthetic methods. This is a great benefit for cost-effective translation to commercial production. The nanoparticles are found to be superparamagnetic and exhibit properties consistent for use in MRI. In addition, the dextran coating imparts the water solubility and biocompatibility necessary for in vivo utilization.

  16. Fully automated attenuation measurement and motion correction in FLIP image sequences.

    Science.gov (United States)

    van de Giessen, Martijn; van der Laan, Annelies; Hendriks, Emile A; Vidorreta, Marta; Reiber, Johan H C; Jost, Carolina R; Tanke, Hans J; Lelieveldt, Boudewijn P F

    2012-02-01

    Fluorescence loss in photobleaching (FLIP) is a method to study compartment connectivity in living cells. A FLIP sequence is obtained by alternatively bleaching a spot in a cell and acquiring an image of the complete cell. Connectivity is estimated by comparing fluorescence signal attenuation in different cell parts. The measurements of the fluorescence attenuation are hampered by the low signal to noise ratio of the FLIP sequences, by sudden sample shifts and by sample drift. This paper describes a method that estimates the attenuation by modeling photobleaching as exponentially decaying signals. Sudden motion artifacts are minimized by registering the frames of a FLIP sequence to target frames based on the estimated model and by removing frames that contain deformations. Linear motion (sample drift) is reduced by minimizing the entropy of the estimated attenuation coefficients. Experiments on 16 in vivo FLIP sequences of muscle cells in Drosophila show that the proposed method results in fluorescence attenuations similar to the manually identified gold standard, but with standard deviations of approximately 50 times smaller. As a result of this higher precision, cell compartment edges and details such as cell nuclei become clearly discernible. The main value of this method is that it uses a model of the bleaching process to correct motion and that the model based fluorescence intensity and attenuation estimates can be interpreted easily. The proposed method is fully automatic, and runs in approximately one minute per sequence, making it suitable for unsupervised batch processing of large data series.

  17. A Bayesian framework for human body pose tracking from depth image sequences.

    Science.gov (United States)

    Zhu, Youding; Fujimura, Kikuo

    2010-01-01

    This paper addresses the problem of accurate and robust tracking of 3D human body pose from depth image sequences. Recovering the large number of degrees of freedom in human body movements from a depth image sequence is challenging due to the need to resolve the depth ambiguity caused by self-occlusions and the difficulty to recover from tracking failure. Human body poses could be estimated through model fitting using dense correspondences between depth data and an articulated human model (local optimization method). Although it usually achieves a high accuracy due to dense correspondences, it may fail to recover from tracking failure. Alternately, human pose may be reconstructed by detecting and tracking human body anatomical landmarks (key-points) based on low-level depth image analysis. While this method (key-point based method) is robust and recovers from tracking failure, its pose estimation accuracy depends solely on image-based localization accuracy of key-points. To address these limitations, we present a flexible Bayesian framework for integrating pose estimation results obtained by methods based on key-points and local optimization. Experimental results are shown and performance comparison is presented to demonstrate the effectiveness of the proposed approach.

  18. A Bayesian Framework for Human Body Pose Tracking from Depth Image Sequences

    Directory of Open Access Journals (Sweden)

    Youding Zhu

    2010-05-01

    Full Text Available This paper addresses the problem of accurate and robust tracking of 3D human body pose from depth image sequences. Recovering the large number of degrees of freedom in human body movements from a depth image sequence is challenging due to the need to resolve the depth ambiguity caused by self-occlusions and the difficulty to recover from tracking failure. Human body poses could be estimated through model fitting using dense correspondences between depth data and an articulated human model (local optimization method. Although it usually achieves a high accuracy due to dense correspondences, it may fail to recover from tracking failure. Alternately, human pose may be reconstructed by detecting and tracking human body anatomical landmarks (key-points based on low-level depth image analysis. While this method (key-point based method is robust and recovers from tracking failure, its pose estimation accuracy depends solely on image-based localization accuracy of key-points. To address these limitations, we present a flexible Bayesian framework for integrating pose estimation results obtained by methods based on key-points and local optimization. Experimental results are shown and performance comparison is presented to demonstrate the effectiveness of the proposed approach.

  19. A Bayesian Framework for Human Body Pose Tracking from Depth Image Sequences

    Science.gov (United States)

    Zhu, Youding; Fujimura, Kikuo

    2010-01-01

    This paper addresses the problem of accurate and robust tracking of 3D human body pose from depth image sequences. Recovering the large number of degrees of freedom in human body movements from a depth image sequence is challenging due to the need to resolve the depth ambiguity caused by self-occlusions and the difficulty to recover from tracking failure. Human body poses could be estimated through model fitting using dense correspondences between depth data and an articulated human model (local optimization method). Although it usually achieves a high accuracy due to dense correspondences, it may fail to recover from tracking failure. Alternately, human pose may be reconstructed by detecting and tracking human body anatomical landmarks (key-points) based on low-level depth image analysis. While this method (key-point based method) is robust and recovers from tracking failure, its pose estimation accuracy depends solely on image-based localization accuracy of key-points. To address these limitations, we present a flexible Bayesian framework for integrating pose estimation results obtained by methods based on key-points and local optimization. Experimental results are shown and performance comparison is presented to demonstrate the effectiveness of the proposed approach. PMID:22399933

  20. Rapid and noncontact photoacoustic tomography imaging system using an interferometer with high-speed phase modulation technique

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jun [School of Physics and Telecom Engineering, South China Normal University, Guangzhou 510006 (China); Tang, Zhilie; Wu, Yongbo [School of Physics and Telecom Engineering, South China Normal University, Guangzhou 510006 (China); GuangDong Province Key Laboratory of Quantum Engineering and Quantum Materials, South China Normal University, IMOT, Guangzhou 510006 (China); Wang, Yi [School of Control Engineering, Northeastern University at Qinhuangdao, Qinhuangdao 066004 (China)

    2015-04-15

    We designed, fabricated, and tested a rapid and noncontact photoacoustic tomography (PAT) imaging system using a low-coherence interferometer with high-speed phase modulation technique. Such a rapid and noncontact probing system can greatly decrease the time of imaging. The proposed PAT imaging system is experimentally verified by capturing images of a simulated tissue sample and the blood vessels within the ear flap of a mouse (pinna) in vivo. The axial and lateral resolutions of the system are evaluated at 45 and ∼15 μm, respectively. The imaging depth of the system is 1 mm in a special phantom. Our results show that the proposed system opens a promising way to realize noncontact, real-time PAT.

  1. Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution

    Directory of Open Access Journals (Sweden)

    Singh Rama S

    2008-08-01

    Full Text Available Abstract Background Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern of gene expression. Using the fully sequenced genomes of three Caenorhabditid nematode species as well as genome information from additional more distantly related organisms (fruit fly, mouse, and human we sought to identify orthologous TFs and characterized their patterns of evolution. Results We identified 988 TF genes in C. elegans, and inferred corresponding sets in C. briggsae and C. remanei, containing 995 and 1093 TF genes, respectively. Analysis of the three gene sets revealed 652 3-way reciprocal 'best hit' orthologs (nematode TF set, approximately half of which are zinc finger (ZF-C2H2 and ZF-C4/NHR types and HOX family members. Examination of the TF genes in C. elegans and C. briggsae identified the presence of significant tandem clustering on chromosome V, the majority of which belong to ZF-C4/NHR family. We also found evidence for lineage-specific duplications and rapid evolution of many of the TF genes in the two species. A search of the TFs conserved among nematodes in Drosophila melanogaster, Mus musculus and Homo sapiens revealed 150 reciprocal orthologs, many of which are associated with important biological processes and human diseases. Finally, a comparison of the sequence, gene interactions and function indicates that nematode TFs conserved across phyla exhibit significantly more interactions and are enriched in genes with annotated mutant phenotypes compared to those that lack orthologs in other species. Conclusion Our study represents the first comprehensive genome-wide analysis of TFs across three nematode species and other organisms. The findings indicate substantial conservation of transcription

  2. Dual-scanning optical coherence elastography for rapid imaging of two tissue volumes (Conference Presentation)

    Science.gov (United States)

    Fang, Qi; Frewer, Luke; Wijesinghe, Philip; Hamzah, Juliana; Ganss, Ruth; Allen, Wes M.; Sampson, David D.; Curatolo, Andrea; Kennedy, Brendan F.

    2017-02-01

    In many applications of optical coherence elastography (OCE), it is necessary to rapidly acquire images in vivo, or within intraoperative timeframes, over fields-of-view far greater than can be achieved in one OCT image acquisition. For example, tumour margin assessment in breast cancer requires acquisition over linear dimensions of 4-5 centimetres in under 20 minutes. However, the majority of existing techniques are not compatible with these requirements, which may present a hurdle to the effective translation of OCE. To increase throughput, we have designed and developed an OCE system that simultaneously captures two 3D elastograms from opposite sides of a sample. The optical system comprises two interferometers: a common-path interferometer on one side of the sample and a dual-arm interferometer on the other side. This optical system is combined with scanning mechanisms and compression loading techniques to realize dual-scanning OCE. The optical signals scattered from two volumes are simultaneously detected on a single spectrometer by depth-encoding the interference signal from each interferometer. To demonstrate dual-scanning OCE, we performed measurements on tissue-mimicking phantoms containing rigid inclusions and freshly isolated samples of murine hepatocellular carcinoma, highlighting the use of this technique to visualise 3D tumour stiffness. These findings indicate that our technique holds promise for in vivo and intraoperative applications.

  3. Rapid implementation of image processing onto FPGA using modular DSP C6201 VHDL model

    Science.gov (United States)

    Brost, V.; Yang, F.; Paindavoine, M.; Liu, X. J.

    2007-01-01

    Recent FPGA chips, with their large capacity memory and reconfigurability potential, have opened new frontiers for rapid prototyping of embedded systems. With the advent of high density FPGAs it is now feasible to implement a high-performance VLIW processor core in an FPGA. We describe research results of enabling the DSP TMS320 C6201 model for real-time image processing applications, by exploiting FPGA technology. The goals are, firstly, to keep the flexibility of DSP in order to shorten the development cycle, and secondly, to use powerful available resources on FPGA to a maximum in order to increase real-time performance. We present a modular DSP C6201 VHDL model which contains only the bare minimum number of instruction sets, or modules, necessary for each target application. This allows an optimal implementation on the FPGA. Some common algorithms of image processing were created and validated on an FPGA VirtexII-2000 multimedia board using the proposed application development cycle. Our results demonstrate that an algorithm can easily be, in an optimal manner, specified and then automatically converted to VHDL language and implemented on an FPGA device with system level software.

  4. Rapid in situ biosynthesis of gold nanoparticles in living platelets for multimodal biomedical imaging.

    Science.gov (United States)

    Jin, Juan; Liu, Taotao; Li, Mingxi; Yuan, Chuxiao; Liu, Yang; Tang, Jian; Feng, Zhenqiang; Zhou, Yue; Yang, Fang; Gu, Ning

    2018-01-10

    Inspired by the nature, the biomimetic nanomaterial design strategies have attracted great interest because the bioinspired nanoplatforms may enhance the functionality of current nanoparticles. Especially, the cell membrane-derived nanoparticles can more effectively navigate and interact with the complex biological microenvironment. In this study, we have explored a novel strategy to rapidly in situ biosynthesize gold nanoparticles (GNPs) in living platelets with the help of ultrasound energy. Firstly, under the ultrasound exposure, the biocompatible chloroauric acid salts (HAuCl 4 ) can be enhanced to permeate into the platelet cytoplasm. Then, by the assist of reducing agent (NaBH 4 and sodium citrate) and platelet enzyme, GNPs were fast in situ synthesized in intra-platelets. The biosynthesized GNPs had a size of about 5 nm and were uniformly distributed in the cytoplasm. Atomic absorption spectrometry (AAS) showed the synthesized amount of Au is (12.7 ± 2.4) × 10 -3  pg per one platelet. The GNPs in platelets can produce Raman enhancement effect and further be probed for both dark-field microscopy (DFM)-based imaging and computed tomography (CT) imaging. Moreover, the platelets were not activated and remained aggregation bioactivity when intra-platelet GNPs synthesis. Therefore, such mimicking GNPs-platelets with in situ GNPs components remain inherent platelet bioactivity will find potential theranostic implications with unique GNPs properties. Copyright © 2018 Elsevier B.V. All rights reserved.

  5. Nosocomial rapidly growing mycobacterial infections following laparoscopic surgery: CT imaging findings

    Energy Technology Data Exchange (ETDEWEB)

    Volpato, Richard [Cassiano Antonio de Moraes University Hospital, Department of Diagnostic Radiology, Vitoria, ES (Brazil); Campi de Castro, Claudio [University of Sao Paulo Medical School, Department of Radiology, Cerqueira Cesar, Sao Paulo (Brazil); Hadad, David Jamil [Cassiano Antonio de Moraes University Hospital, Nucleo de Doencas Infecciosas, Department of Internal Medicine, Vitoria, ES (Brazil); Silva Souza Ribeiro, Flavya da [Laboratorio de Patologia PAT, Department of Diagnostic Radiology, Unit 1473, Vitoria, ES (Brazil); Filho, Ezequiel Leal [UNIMED Diagnostico, Department of Diagnostic Radiology, Unit 1473, Vitoria, ES (Brazil); Marcal, Leonardo P. [The University of Texas M D Anderson Cancer Center, Department of Diagnostic Radiology, Unit 1473, Houston, TX (United States)

    2015-09-15

    To identify the distribution and frequency of computed tomography (CT) findings in patients with nosocomial rapidly growing mycobacterial (RGM) infection after laparoscopic surgery. A descriptive retrospective study in patients with RGM infection after laparoscopic surgery who underwent CT imaging prior to initiation of therapy. The images were analyzed by two radiologists in consensus, who evaluated the skin/subcutaneous tissues, the abdominal wall, and intraperitoneal region separately. The patterns of involvement were tabulated as: densification, collections, nodules (≥1.0 cm), small nodules (<1.0 cm), pseudocavitated nodules, and small pseudocavitated nodules. Twenty-six patients met the established criteria. The subcutaneous findings were: densification (88.5 %), small nodules (61.5 %), small pseudocavitated nodules (23.1 %), nodules (38.5 %), pseudocavitated nodules (15.4 %), and collections (26.9 %). The findings in the abdominal wall were: densification (61.5 %), pseudocavitated nodules (3.8 %), and collections (15.4 %). The intraperitoneal findings were: densification (46.1 %), small nodules (42.3 %), nodules (15.4 %), and collections (11.5 %). Subcutaneous CT findings in descending order of frequency were: densification, small nodules, nodules, small pseudocavitated nodules, pseudocavitated nodules, and collections. The musculo-fascial plane CT findings were: densification, collections, and pseudocavitated nodules. The intraperitoneal CT findings were: densification, small nodules, nodules, and collections. (orig.)

  6. C-MAC videolaryngoscope compared with direct laryngoscopy for rapid sequence intubation in an emergency department: A randomised clinical trial.

    Science.gov (United States)

    Sulser, Simon; Ubmann, Dirk; Schlaepfer, Martin; Brueesch, Martin; Goliasch, Georg; Seifert, Burkhardt; Spahn, Donat R; Ruetzler, Kurt

    2016-12-01

    Airway management in the emergency room can be challenging when patients suffer from life-threatening conditions. Mental stress, ignorance of the patient's medical history, potential cervical injury or immobilisation and the presence of vomit and/or blood may also contribute to a difficult airway. Videolaryngoscopes have been introduced into clinical practice to visualise the airway and ultimately increase the success rate of airway management. The aim of this study was to test the hypothesis that the C-MAC videolaryngoscope improves first-attempt intubation success rate compared with direct laryngoscopy in patients undergoing emergency rapid sequence intubation in the emergency room setting. A randomised clinical trial. Emergency Department of the University Hospital, Zurich, Switzerland. With approval of the local ethics committee, we prospectively enrolled 150 patients between 18 and 99 years of age requiring emergency rapid sequence intubation in the emergency room of the University Hospital Zurich. Patients were randomised (1 : 1) to undergo tracheal intubation using the C-MAC videolaryngoscope or by direct laryngoscopy. Owing to ethical considerations, patients who had sustained maxillo-facial trauma, immobilised cervical spine, known difficult airway or ongoing cardiopulmonary resuscitation were excluded from our study. All intubations were performed by one of three very experienced anaesthesia consultants. First-attempt success rate served as our primary outcome parameter. Secondary outcome parameters were time to intubation; total number of intubation attempts; Cormack and Lehane score; inadvertent oesophageal intubation; ease of intubation; complications including violations of the teeth, injury/bleeding of the larynx/pharynx and aspiration/regurgitation of gastric contents; necessity of using further alternative airway devices for successful intubation; maximum decrease of oxygen saturation and technical problems with the device. A total of 150

  7. Conceptualizing ¬the Abstractions of Earthquakes Through an Instructional Sequence Using SeisMac and the Rapid Earthquake Viewer

    Science.gov (United States)

    Taber, J.; Hubenthal, M.; Wysession, M.

    2007-12-01

    Newsworthy earthquakes provide an engaging hook for students in Earth science classes, particularly when discussing their effects on people and the landscape. However, engaging students in an analysis of earthquakes that extends beyond death and damage, is frequently hampered by the abstraction of recorded ground motion data in the form of raw seismograms and the inability of most students to personally relate to ground accelerations. To overcome these challenges, an educational sequence has been developed using two software tools: SeisMac by Daniel Griscom, and the Rapid Earthquake Viewer (REV) developed by the University of South Carolina in collaboration with IRIS and DLESE. This sequence presents a unique opportunity for Earth Science teachers to "create" foundational experiences for students as they construction a framework of understanding of abstract concepts. The first activity is designed to introduce the concept of a three-component seismogram and to directly address the very abstract nature of seismograms through a kinesthetic experience. Students first learn to take the pulse of their classroom through a guided exploration of SeisMac, which displays the output of the laptop's built-in Sudden Motion Sensor (a 3-component accelerometer). This exploration allows students to view a 3-component seismogram as they move or tap the laptop and encourages them to propose and carry out experiments to explain the meaning of the 3-component seismogram. Once completed students are then asked to apply this new knowledge to a real 3-component seismogram printed from REV. Next the activity guides students through the process of identifying P and S waves and using SeisMac to connect the physical motion of the laptop to the "wiggles" they see on the SeisMac display and then comparing those to the "wiggles" they see on their seismogram. At this point students are more fully prepared to engage in an S-P location exercise such as those included in many state standards

  8. Managing complex processing of medical image sequences by program supervision techniques

    Science.gov (United States)

    Crubezy, Monica; Aubry, Florent; Moisan, Sabine; Chameroy, Virginie; Thonnat, Monique; Di Paola, Robert

    1997-05-01

    Our objective is to offer clinicians wider access to evolving medical image processing (MIP) techniques, crucial to improve assessment and quantification of physiological processes, but difficult to handle for non-specialists in MIP. Based on artificial intelligence techniques, our approach consists in the development of a knowledge-based program supervision system, automating the management of MIP libraries. It comprises a library of programs, a knowledge base capturing the expertise about programs and data and a supervision engine. It selects, organizes and executes the appropriate MIP programs given a goal to achieve and a data set, with dynamic feedback based on the results obtained. It also advises users in the development of new procedures chaining MIP programs.. We have experimented the approach for an application of factor analysis of medical image sequences as a means of predicting the response of osteosarcoma to chemotherapy, with both MRI and NM dynamic image sequences. As a result our program supervision system frees clinical end-users from performing tasks outside their competence, permitting them to concentrate on clinical issues. Therefore our approach enables a better exploitation of possibilities offered by MIP and higher quality results, both in terms of robustness and reliability.

  9. Temporal statistics of natural image sequences generated by movements with insect flight characteristics.

    Directory of Open Access Journals (Sweden)

    Alexander Schwegmann

    Full Text Available Many flying insects, such as flies, wasps and bees, pursue a saccadic flight and gaze strategy. This behavioral strategy is thought to separate the translational and rotational components of self-motion and, thereby, to reduce the computational efforts to extract information about the environment from the retinal image flow. Because of the distinguishing dynamic features of this active flight and gaze strategy of insects, the present study analyzes systematically the spatiotemporal statistics of image sequences generated during saccades and intersaccadic intervals in cluttered natural environments. We show that, in general, rotational movements with saccade-like dynamics elicit fluctuations and overall changes in brightness, contrast and spatial frequency of up to two orders of magnitude larger than translational movements at velocities that are characteristic of insects. Distinct changes in image parameters during translations are only caused by nearby objects. Image analysis based on larger patches in the visual field reveals smaller fluctuations in brightness and spatial frequency composition compared to small patches. The temporal structure and extent of these changes in image parameters define the temporal constraints imposed on signal processing performed by the insect visual system under behavioral conditions in natural environments.

  10. Interannual Change Detection of Mediterranean Seagrasses Using RapidEye Image Time Series

    Directory of Open Access Journals (Sweden)

    Dimosthenis Traganos

    2018-02-01

    Full Text Available Recent research studies have highlighted the decrease in the coverage of Mediterranean seagrasses due to mainly anthropogenic activities. The lack of data on the distribution of these significant aquatic plants complicates the quantification of their decreasing tendency. While Mediterranean seagrasses are declining, satellite remote sensing technology is growing at an unprecedented pace, resulting in a wealth of spaceborne image time series. Here, we exploit recent advances in high spatial resolution sensors and machine learning to study Mediterranean seagrasses. We process a multispectral RapidEye time series between 2011 and 2016 to detect interannual seagrass dynamics in 888 submerged hectares of the Thermaikos Gulf, NW Aegean Sea, Greece (eastern Mediterranean Sea. We assess the extent change of two Mediterranean seagrass species, the dominant Posidonia oceanica and Cymodocea nodosa, following atmospheric and analytical water column correction, as well as machine learning classification, using Random Forests, of the RapidEye time series. Prior corrections are necessary to untangle the initially weak signal of the submerged seagrass habitats from satellite imagery. The central results of this study show that P. oceanica seagrass area has declined by 4.1%, with a trend of −11.2 ha/yr, while C. nodosa seagrass area has increased by 17.7% with a trend of +18 ha/yr throughout the 5-year study period. Trends of change in spatial distribution of seagrasses in the Thermaikos Gulf site are in line with reported trends in the Mediterranean. Our presented methodology could be a time- and cost-effective method toward the quantitative ecological assessment of seagrass dynamics elsewhere in the future. From small meadows to whole coastlines, knowledge of aquatic plant dynamics could resolve decline or growth trends and accurately highlight key units for future restoration, management, and conservation.

  11. Update on MRI Pulse Sequences for the Knee: Imaging of Cartilage, Meniscus, Tendon, and Hardware.

    Science.gov (United States)

    Ariyachaipanich, Aticha; Bae, Won C; Statum, Sheronda; Chung, Christine B

    2017-04-01

    Magnetic resonance imaging (MRI) is widely used in the clinical setting as well as for research applications. Since its inception, technical development has broadly progressed as a response to challenges in both the clinical and research settings. Higher magnetic field strength and advances in hardware and software have revolutionized the diagnostic potential of MRI and moved well beyond diagnosis to characterization of tissue metabolism, biochemistry, disease pathogenesis, and material property, to name a few. This article focuses on state-of-the-art clinical and cutting-edge novel pulse sequences applied to knee MRI. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  12. Novel permutation-diffusion image encryption algorithm with chaotic dynamic S-box and DNA sequence operation

    Science.gov (United States)

    Tian, Ye; Lu, Zhimao

    2017-08-01

    The development of the computer network makes image files transportation via network become more and more convenient. This paper is concerned with the image encryption algorithm design based on the chaotic S-box mechanism. This paper proposes an Image Encryption algorithm involving both chaotic dynamic S-boxes and DNA sequence operation(IESDNA). The contribution of this paper is three folded: Firstly, we design an external 256-bit key to get large key space; secondly, we design a chaotic system to scramble image pixels; thirdly, DNA sequence operations are adopted to diffuse the scrambled image pixels. Experimental results show that our proposed image encryption algorithm can meet multiple cryptographic criteria and obtain good image encryption effect.

  13. No Reference Prediction of Quality Metrics for H.264 Compressed Infrared Image Sequences for UAV Applications

    DEFF Research Database (Denmark)

    Hossain, Kabir; Mantel, Claire; Forchhammer, Søren

    2018-01-01

    The framework for this research work is the acquisition of Infrared (IR) images from Unmanned Aerial Vehicles (UAV). In this paper we consider the No-Reference (NR) prediction of Full Reference Quality Metrics for Infrared (IR) video sequences which are compressed and thus distorted by an H.264...... and temporal perceptual information. Those features are then mapped, using a machine learning (ML) algorithm, the Support Vector Regression (SVR), to the quality scores of Full Reference (FR) quality metrics. The novelty of this work is to design a NR framework for the prediction of quality metrics by applying...... with the true FR quality metrics scores of four images metrics: PSNR, NQM, SSIM and UQI and one video metric: VQM. Results show that our technique achieves a fairly reasonable performance. The improved performance obtained in SROCC and LCC is up to 0.99 and the RMSE is reduced to as little as 0.01 between...

  14. Bubbles: a unifying framework for low-level statistical properties of natural image sequences.

    Science.gov (United States)

    Hyvärinen, Aapo; Hurri, Jarmo; Väyrynen, Jaakko

    2003-07-01

    Recently, different models of the statistical structure of natural images have been proposed. These models predict properties of biological visual systems and can be used as priors in Bayesian inference. The fundamental model is independent component analysis, which can be estimated by maximization of the sparsenesses of linear filter outputs. This leads to the emergence of principal simple cell properties. Alternatively, simple cell properties are obtained by maximizing the temporal coherence in natural image sequences. Taking account of the basic dependencies of linear filter outputs permit modeling of complex cells and topographic organization as well. We propose a unifying framework for these statistical properties, based on the concept of spatiotemporal activity "bubbles."A bubble means here an activation of simple cells (linear filters) that is contiguous both in space (the cortical surface) and in time.

  15. Temporal and spatiotemporal coherence in simple-cell responses: a generative model of natural image sequences.

    Science.gov (United States)

    Hurri, Jarmo; Hyvärinen, Aapo

    2003-08-01

    We present a two-layer dynamic generative model of the statistical structure of natural image sequences. The second layer of the model is a linear mapping from simple-cell outputs to pixel values, as in most work on natural image statistics. The first layer models the dependencies of the activity levels (amplitudes or variances) of the simple cells, using a multivariate autoregressive model. The second layer shows the emergence of basis vectors that are localized, oriented and have different scales, just like in previous work. But in our new model, the first layer learns connections between the simple cells that are similar to complex cell pooling: connections are strong among cells with similar preferred location, frequency and orientation. In contrast to previous work in which one of the layers needed to be fixed in advance, the dynamic model enables us to estimate both of the layers simultaneously from natural data.

  16. Diuretic-enhanced gadolinium excretory MR urography: comparison of conventional gradient-echo sequences and echo-planar imaging

    Energy Technology Data Exchange (ETDEWEB)

    Nolte-Ernsting, C.C.A.; Tacke, J.; Adam, G.B.; Haage, P.; Guenther, R.W. [Univ. of Technology, Aachen (Germany). Dept. of Diagnostic Radiology; Jung, P.; Jakse, G. [Univ. of Technology, Aachen (Germany). Dept. of Urology

    2001-01-01

    The aim of this study was to investigate the utility of different gadolinium-enhanced T1-weighted gradient-echo techniques in excretory MR urography. In 74 urologic patients, excretory MR urography was performed using various T1-weighted gradient-echo (GRE) sequences after injection of gadolinium-DTPA and low-dose furosemide. The examinations included conventional GRE sequences and echo-planar imaging (GRE EPI), both obtained with 3D data sets and 2D projection images. Breath-hold acquisition was used primarily. In 20 of 74 examinations, we compared breath-hold imaging with respiratory gating. Breath-hold imaging was significantly superior to respiratory gating for the visualization of pelvicaliceal systems, but not for the ureters. Complete MR urograms were obtained within 14-20 s using 3D GRE EPI sequences and in 20-30 s with conventional 3D GRE sequences. Ghost artefacts caused by ureteral peristalsis often occurred with conventional 3D GRE imaging and were almost completely suppressed in EPI sequences (p < 0.0001). Susceptibility effects were more pronounced on GRE EPI MR urograms and calculi measured 0.8-21.7% greater in diameter compared with conventional GRE sequences. Increased spatial resolution degraded the image quality only in GRE-EPI urograms. (orig.)

  17. Design of deep convolutional networks for prediction of image rapid serial visual presentation events.

    Science.gov (United States)

    Zijing Mao; Wan Xiang Yao; Yufe Huang

    2017-07-01

    We report in this paper an investigation of convolutional neural network (CNN) models for target prediction in time-locked image rapid serial visual presentation (RSVP) experiment. We investigated CNN models with 11 different designs of convolution filters in capturing spatial and temporal correlations in EEG data. We showed that for both within-subject and cross-subject predictions, the CNN models outperform the state-of-the-art algorithms: Bayesian linear discriminant analysis (BLDA) and xDAWN spatial filtering and achieved >6% improvement. Among the 11 different CNN models, the global spatial filter and our proposed region of interest (ROI) achieved best performance. We also implemented the deconvolution network to show how we can visualize from activated hidden units for target/nontarget events learned by the ROI-CNN. Our study suggests that deep learning is a powerful tool for RSVP target prediction and the proposed model is applicable for general EEG-based classifications in brain computer interaction research. The code of this project is available at https://github.com/ZijingMao/ROICNN.

  18. Rapid wide-field Mueller matrix polarimetry imaging based on four photoelastic modulators with no moving parts.

    Science.gov (United States)

    Alali, Sanaz; Gribble, Adam; Vitkin, I Alex

    2016-03-01

    A new polarimetry method is demonstrated to image the entire Mueller matrix of a turbid sample using four photoelastic modulators (PEMs) and a charge coupled device (CCD) camera, with no moving parts. Accurate wide-field imaging is enabled with a field-programmable gate array (FPGA) optical gating technique and an evolutionary algorithm (EA) that optimizes imaging times. This technique accurately and rapidly measured the Mueller matrices of air, polarization elements, and turbid phantoms. The system should prove advantageous for Mueller matrix analysis of turbid samples (e.g., biological tissues) over large fields of view, in less than a second.

  19. Diffusion-weighted imaging of the sellar region: A comparison study of BLADE and single-shot echo planar imaging sequences

    Energy Technology Data Exchange (ETDEWEB)

    Yiping, Lu [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China); Hui, Liu [MR Collaboration NE Asia, Siemens Healthcare, Siemens Ltd., China, Shanghai 201318 (China); Kun, Zhou [MR PLM APPL, Siemens Shenzhen Magnetic Resonance Ltd., Shenzhen 518057 (China); Daoying, Geng, E-mail: GengdaoyingGDY@163.com [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China); Bo, Yin, E-mail: yinbo7@163.com [Department of Radiology, Huashan Hospital, Fudan University, 12 Wulumuqi Rd. Middle, Shanghai 200040 (China)

    2014-07-15

    Purpose: The purpose of this study is to compare BLADE diffusion-weighted imaging (DWI) with single-shot echo planar imaging (EPI) DWI on the aspects of feasibility of imaging the sellar region and image quality. Methods: A total of 3 healthy volunteers and 52 patients with suspected lesions in the sellar region were included in this prospective intra-individual study. All exams were performed at 3.0 T with a BLADE DWI sequence and a standard single-shot EP-DWI sequence. Phantom measurements were performed to measure the objective signal-to-noise ratio (SNR). Two radiologists rated the image quality according to the visualisation of the internal carotid arteries, optic chiasm, pituitary stalk, pituitary gland and lesion, and the overall image quality. One radiologist measured lesion sizes for detecting their relationship with the image score. Results: The SNR in BLADE DWI sequence showed no significant difference from the single-shot EPI sequence (P > 0.05). All of the assessed regions received higher scores in BLADE DWI images than single-shot EP-DWI.

  20. An accurate and rapid continuous wavelet dynamic time warping algorithm for unbalanced global mapping in nanopore sequencing

    KAUST Repository

    Han, Renmin

    2017-12-24

    Long-reads, point-of-care, and PCR-free are the promises brought by nanopore sequencing. Among various steps in nanopore data analysis, the global mapping between the raw electrical current signal sequence and the expected signal sequence from the pore model serves as the key building block to base calling, reads mapping, variant identification, and methylation detection. However, the ultra-long reads of nanopore sequencing and an order of magnitude difference in the sampling speeds of the two sequences make the classical dynamic time warping (DTW) and its variants infeasible to solve the problem. Here, we propose a novel multi-level DTW algorithm, cwDTW, based on continuous wavelet transforms with different scales of the two signal sequences. Our algorithm starts from low-resolution wavelet transforms of the two sequences, such that the transformed sequences are short and have similar sampling rates. Then the peaks and nadirs of the transformed sequences are extracted to form feature sequences with similar lengths, which can be easily mapped by the original DTW. Our algorithm then recursively projects the warping path from a lower-resolution level to a higher-resolution one by building a context-dependent boundary and enabling a constrained search for the warping path in the latter. Comprehensive experiments on two real nanopore datasets on human and on Pandoraea pnomenusa, as well as two benchmark datasets from previous studies, demonstrate the efficiency and effectiveness of the proposed algorithm. In particular, cwDTW can almost always generate warping paths that are very close to the original DTW, which are remarkably more accurate than the state-of-the-art methods including FastDTW and PrunedDTW. Meanwhile, on the real nanopore datasets, cwDTW is about 440 times faster than FastDTW and 3000 times faster than the original DTW. Our program is available at https://github.com/realbigws/cwDTW.

  1. Novel Spatiotemporal Filter for Dim Point Targets Detection in Infrared Image Sequences

    Directory of Open Access Journals (Sweden)

    Zhaohui Li

    2015-01-01

    Full Text Available Dim point target detection is of great importance in both civil and military fields. In this paper a novel spatiotemporal filter is proposed to incorporate both the spatial and temporal features of moving dim point targets. Since targets are expected to be detected as far as possible, in this situation, they have no texture features in spatial dimensions, appearing like isolated points. Based on the attributes, potential targets are extracted by searching the local maximum point in a sliding window. And the potential targets are then correlated based on target moving patterns. After combining local maximum points and target moving patterns, structure background in infrared scene is removed. Next, the temporal profiles of infrared sense are reviewed and examined. By a new max-median filter performing on temporal profiles, the intensity of target pulse signal is extracted. Finally, each temporal profile is divided into several pieces to estimate the variance of the temporal profiles, which leads to a new detection metric. The proposed approach is tested via several infrared image sequences. The results show that our proposed method can significantly reduce the complex background in aerial infrared image sequence and have a good detection performance.

  2. A Low-Complexity Algorithm for Static Background Estimation from Cluttered Image Sequences in Surveillance Contexts

    Directory of Open Access Journals (Sweden)

    Reddy Vikas

    2011-01-01

    Full Text Available Abstract For the purposes of foreground estimation, the true background model is unavailable in many practical circumstances and needs to be estimated from cluttered image sequences. We propose a sequential technique for static background estimation in such conditions, with low computational and memory requirements. Image sequences are analysed on a block-by-block basis. For each block location a representative set is maintained which contains distinct blocks obtained along its temporal line. The background estimation is carried out in a Markov Random Field framework, where the optimal labelling solution is computed using iterated conditional modes. The clique potentials are computed based on the combined frequency response of the candidate block and its neighbourhood. It is assumed that the most appropriate block results in the smoothest response, indirectly enforcing the spatial continuity of structures within a scene. Experiments on real-life surveillance videos demonstrate that the proposed method obtains considerably better background estimates (both qualitatively and quantitatively than median filtering and the recently proposed "intervals of stable intensity" method. Further experiments on the Wallflower dataset suggest that the combination of the proposed method with a foreground segmentation algorithm results in improved foreground segmentation.

  3. An unsupervised approach for measuring myocardial perfusion in MR image sequences

    Science.gov (United States)

    Discher, Antoine; Rougon, Nicolas; Preteux, Francoise

    2005-08-01

    Quantitatively assessing myocardial perfusion is a key issue for the diagnosis, therapeutic planning and patient follow-up of cardio-vascular diseases. To this end, perfusion MRI (p-MRI) has emerged as a valuable clinical investigation tool thanks to its ability of dynamically imaging the first pass of a contrast bolus in the framework of stress/rest exams. However, reliable techniques for automatically computing regional first pass curves from 2D short-axis cardiac p-MRI sequences remain to be elaborated. We address this problem and develop an unsupervised four-step approach comprising: (i) a coarse spatio-temporal segmentation step, allowing to automatically detect a region of interest for the heart over the whole sequence, and to select a reference frame with maximal myocardium contrast; (ii) a model-based variational segmentation step of the reference frame, yielding a bi-ventricular partition of the heart into left ventricle, right ventricle and myocardium components; (iii) a respiratory/cardiac motion artifacts compensation step using a novel region-driven intensity-based non rigid registration technique, allowing to elastically propagate the reference bi-ventricular segmentation over the whole sequence; (iv) a measurement step, delivering first-pass curves over each region of a segmental model of the myocardium. The performance of this approach is assessed over a database of 15 normal and pathological subjects, and compared with perfusion measurements delivered by a MRI manufacturer software package based on manual delineations by a medical expert.

  4. A survey of a population of anaesthesiologists from South India regarding practices for rapid sequence intubation in patients with head injury

    Directory of Open Access Journals (Sweden)

    Satyen Parida

    2016-01-01

    Full Text Available Background and Aims: Evidence and utility of the individual steps of the rapid sequence induction and tracheal intubation protocols have been debated, especially in the setting of traumatic brain injury. The purpose of this survey was to determine preferences in the current approach to rapid sequence intubation ( RSI in head injury patients among a population of anaesthesiologists from South India. Methods: A questionnaire was E-mailed to all the members of the Indian Society of Anaesthesiologists′ South Zone Chapter to ascertain their preferences, experience and comfort level with regard to their use of rapid sequence intubation techniques in adult patients with head injury. Participants were requested to indicate their practices for RSI technique for a head-injured patient upon arrival at the Emergency Medical Services department of their hospital. Results: The total response rate was 56.9% (530/932. Of the total respondents, 35% of the clinicians used cricoid pressure routinely, most respondents (68% stated that they pre-oxygenate the patients for about 3 min prior to RSI, thiopentone (61% and propofol (34% were commonly used prior to intubation. Rocuronium was the muscle relaxant of choice for RSI among the majority (44%, compared to succinylcholine (39%. Statistical analyses were performed after the initial entry onto a spreadsheet. Data were summarised descriptively using frequency distribution. Conclusion: In a rapid sequence intubation situation, the practice differed significantly among anaesthesiologists. Owing to disagreements and paucity of evidence-based data regarding the standards of RSI, it is apparent that RSI practice still has considerable variability in clinical practice.

  5. Rapid Assessment of Earthquakes with Radar and Optical Geodetic Imaging and Finite Fault Models (Invited)

    Science.gov (United States)

    Fielding, E. J.; Sladen, A.; Simons, M.; Rosen, P. A.; Yun, S.; Li, Z.; Avouac, J.; Leprince, S.

    2010-12-01

    Earthquake responders need to know where the earthquake has caused damage and what is the likely intensity of damage. The earliest information comes from global and regional seismic networks, which provide the magnitude and locations of the main earthquake hypocenter and moment tensor centroid and also the locations of aftershocks. Location accuracy depends on the availability of seismic data close to the earthquake source. Finite fault models of the earthquake slip can be derived from analysis of seismic waveforms alone, but the results can have large errors in the location of the fault ruptures and spatial distribution of slip, which are critical for estimating the distribution of shaking and damage. Geodetic measurements of ground displacements with GPS, LiDAR, or radar and optical imagery provide key spatial constraints on the location of the fault ruptures and distribution of slip. Here we describe the analysis of interferometric synthetic aperture radar (InSAR) and sub-pixel correlation (or pixel offset tracking) of radar and optical imagery to measure ground coseismic displacements for recent large earthquakes, and lessons learned for rapid assessment of future events. These geodetic imaging techniques have been applied to the 2010 Leogane, Haiti; 2010 Maule, Chile; 2010 Baja California, Mexico; 2008 Wenchuan, China; 2007 Tocopilla, Chile; 2007 Pisco, Peru; 2005 Kashmir; and 2003 Bam, Iran earthquakes, using data from ESA Envisat ASAR, JAXA ALOS PALSAR, NASA Terra ASTER and CNES SPOT5 satellite instruments and the NASA/JPL UAVSAR airborne system. For these events, the geodetic data provided unique information on the location of the fault or faults that ruptured and the distribution of slip that was not available from the seismic data and allowed the creation of accurate finite fault source models. In many of these cases, the fault ruptures were on previously unknown faults or faults not believed to be at high risk of earthquakes, so the area and degree of

  6. Using multimodal imaging techniques to monitor limb ischemia: a rapid noninvasive method for assessing extremity wounds

    Science.gov (United States)

    Luthra, Rajiv; Caruso, Joseph D.; Radowsky, Jason S.; Rodriguez, Maricela; Forsberg, Jonathan; Elster, Eric A.; Crane, Nicole J.

    2013-03-01

    Over 70% of military casualties resulting from the current conflicts sustain major extremity injuries. Of these the majority are caused by blasts from improvised explosive devices. The resulting injuries include traumatic amputations, open fractures, crush injuries, and acute vascular disruption. Critical tissue ischemia—the point at which ischemic tissues lose the capacity to recover—is therefore a major concern, as lack of blood flow to tissues rapidly leads to tissue deoxygenation and necrosis. If left undetected or unaddressed, a potentially salvageable limb may require more extensive debridement or, more commonly, amputation. Predicting wound outcome during the initial management of blast wounds remains a significant challenge, as wounds continue to "evolve" during the debridement process and our ability to assess wound viability remains subjectively based. Better means of identifying critical ischemia are needed. We developed a swine limb ischemia model in which two imaging modalities were combined to produce an objective and quantitative assessment of wound perfusion and tissue viability. By using 3 Charge-Coupled Device (3CCD) and Infrared (IR) cameras, both surface tissue oxygenation as well as overall limb perfusion could be depicted. We observed a change in mean 3CCD and IR values at peak ischemia and during reperfusion correlate well with clinically observed indicators for limb function and vitality. After correcting for baseline mean R-B values, the 3CCD values correlate with surface tissue oxygenation and the IR values with changes in perfusion. This study aims to not only increase fundamental understanding of the processes involved with limb ischemia and reperfusion, but also to develop tools to monitor overall limb perfusion and tissue oxygenation in a clinical setting. A rapid and objective diagnostic for extent of ischemic damage and overall limb viability could provide surgeons with a more accurate indication of tissue viability. This may

  7. Research on the Compression Algorithm of the Infrared Thermal Image Sequence Based on Differential Evolution and Double Exponential Decay Model

    Directory of Open Access Journals (Sweden)

    Jin-Yu Zhang

    2014-01-01

    Full Text Available This paper has proposed a new thermal wave image sequence compression algorithm by combining double exponential decay fitting model and differential evolution algorithm. This study benchmarked fitting compression results and precision of the proposed method was benchmarked to that of the traditional methods via experiment; it investigated the fitting compression performance under the long time series and improved model and validated the algorithm by practical thermal image sequence compression and reconstruction. The results show that the proposed algorithm is a fast and highly precise infrared image data processing method.

  8. Motion parameter estimation by tracking stationary three-dimensional straight lines in image sequences

    Science.gov (United States)

    Habib, Ayman

    The purpose of this work is to utilize extracted linear features from imagery collected by a Mobile Mapping System (MMS) for the purpose of motion parameter estimation. The MMS is assumed to be equipped with two or more cameras. The relative relationship between these cameras is rigid, i.e. it does not change from one epoch to the other and can be determined by a calibration procedure. An optimal (minimal) representation of 3-D straight lines that requires only four parameters is discussed. The perspective transformation of the extracted linear features back and forth between image and object space is derived. By tracking stationary linear features in successive image sequences, the motion parameters, rotation and displacement, between the system's position at the corresponding epochs can be estimated. The suggested algorithm works as follows. First, straight-line features are extracted from the imagery. Then, a model space coordinate system is defined for each system position at which an image set is collected. The origin of this system can be chosen as the perspective center of one of the cameras onboard. Then, the linear features in successive image sets are projected into the corresponding model space. It has to be noted that the projection procedure is performed separately for the image sets under consideration. The mathematical model that relates the parameters of the resulting conjugate lines to the motion parameters of the system is derived. The relationship is obtained by imposing four constraints on the four degrees of freedom of any conjugate lines. The suggested algorithm is used to estimate the motion parameters using conjugate linear features in successive stereo-pairs collected by the GPS van of the Ohio State University. This algorithm will be helpful in deriving the motion parameters of the vehicle during periods of failure of the positioning component onboard, e.g. GPS loss of lock for a long time interval.

  9. CONTRAILS: A tool for rapid identification of transgene integration sites in complex, repetitive genomes using low-coverage paired-end sequencing

    Science.gov (United States)

    Lambirth, Kevin C.; Whaley, Adam M.; Schlueter, Jessica A.; Bost, Kenneth L.; Piller, Kenneth J.

    2015-01-01

    Transgenic crops have become a staple in modern agriculture, and are typically characterized using a variety of molecular techniques involving proteomics and metabolomics. Characterization of the transgene insertion site is of great interest, as disruptions, deletions, and genomic location can affect product selection and fitness, and identification of these regions and their integrity is required for regulatory agencies. Here, we present CONTRAILS (Characterization of Transgene Insertion Locations with Sequencing), a straightforward, rapid and reproducible method for the identification of transgene insertion sites in highly complex and repetitive genomes using low coverage paired-end Illumina sequencing and traditional PCR. This pipeline requires little to no troubleshooting and is not restricted to any genome type, allowing use for many molecular applications. Using whole genome sequencing of in-house transgenic Glycine max, a legume with a highly repetitive and complex genome, we used CONTRAILS to successfully identify the location of a single T-DNA insertion to single base resolution. PMID:26697366

  10. Linear terrestrial laser scanning using array avalanche photodiodes as detectors for rapid three-dimensional imaging.

    Science.gov (United States)

    Cai, Yinqiao; Tong, Xiaohua; Tong, Peng; Bu, Hongyi; Shu, Rong

    2010-12-01

    As an active remote sensor technology, the terrestrial laser scanner is widely used for direct generation of a three-dimensional (3D) image of an object in the fields of geodesy, surveying, and photogrammetry. In this article, a new laser scanner using array avalanche photodiodes, as designed by the Shanghai Institute of Technical Physics of the Chinese Academy of Sciences, is introduced for rapid collection of 3D data. The system structure of the new laser scanner is first presented, and a mathematical model is further derived to transform the original data to the 3D coordinates of the object in a user-defined coordinate system. The performance of the new laser scanner is tested through a comprehensive experiment. The result shows that the new laser scanner can scan a scene with a field view of 30° × 30° in 0.2 s and that, with respect to the point clouds obtained on the wall and ground floor surfaces, the root mean square errors for fitting the two planes are 0.21 and 0.01 cm, respectively. The primary advantages of the developed laser scanner include: (i) with a line scanning mode, the new scanner achieves simultaneously the 3D coordinates of 24 points per single laser pulse, which enables it to scan faster than traditional scanners with a point scanning mode and (ii) the new scanner makes use of two galvanometric mirrors to deflect the laser beam in both the horizontal and the vertical directions. This capability makes the instrument smaller and lighter, which is more acceptable for users.

  11. Clinical Application of Picodroplet Digital PCR Technology for Rapid Detection of EGFR T790M in Next-Generation Sequencing Libraries and DNA from Limited Tumor Samples.

    Science.gov (United States)

    Borsu, Laetitia; Intrieri, Julie; Thampi, Linta; Yu, Helena; Riely, Gregory; Nafa, Khedoudja; Chandramohan, Raghu; Ladanyi, Marc; Arcila, Maria E

    2016-11-01

    Although next-generation sequencing (NGS) is a robust technology for comprehensive assessment of EGFR-mutant lung adenocarcinomas with acquired resistance to tyrosine kinase inhibitors, it may not provide sufficiently rapid and sensitive detection of the EGFR T790M mutation, the most clinically relevant resistance biomarker. Here, we describe a digital PCR (dPCR) assay for rapid T790M detection on aliquots of NGS libraries prepared for comprehensive profiling, fully maximizing broad genomic analysis on limited samples. Tumor DNAs from patients with EGFR-mutant lung adenocarcinomas and acquired resistance to epidermal growth factor receptor inhibitors were prepared for Memorial Sloan-Kettering-Integrated Mutation Profiling of Actionable Cancer Targets sequencing, a hybrid capture-based assay interrogating 410 cancer-related genes. Precapture library aliquots were used for rapid EGFR T790M testing by dPCR, and results were compared with NGS and locked nucleic acid-PCR Sanger sequencing (reference high sensitivity method). Seventy resistance samples showed 99% concordance with the reference high sensitivity method in accuracy studies. Input as low as 2.5 ng provided a sensitivity of 1% and improved further with increasing DNA input. dPCR on libraries required less DNA and showed better performance than direct genomic DNA. dPCR on NGS libraries is a robust and rapid approach to EGFR T790M testing, allowing most economical utilization of limited material for comprehensive assessment. The same assay can also be performed directly on any limited DNA source and cell-free DNA. Copyright © 2016 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

  12. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

    DEFF Research Database (Denmark)

    Kelstrup, Christian D; Jersie-Christensen, Rosa R; Batth, Tanveer Singh

    2014-01-01

    Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evalu......Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage...... in less than 24 hours of analysis time by offline high pH reversed-phase peptide fractionation from which we identify more than 140,000 unique peptide sequences. This is comparable to state-of-the-art multi-day, multi-enzyme efforts. Finally the acquisition methods are evaluated for single-shot...

  13. Rapid and Deep Proteomes by Faster Sequencing on a Benchtop Quadrupole Ultra-High-Field Orbitrap Mass Spectrometer

    DEFF Research Database (Denmark)

    Kelstrup, Christian D; Jersie-Christensen, Rosa R; Batth, Tanveer Singh

    2014-01-01

    Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage is evalu......Shotgun proteomics is a powerful technology for global analysis of proteins and their post-translational modifications. Here, we investigate faster sequencing speed of the latest Q Exactive HF mass spectrometer, which features an ultra-high-field Orbitrap mass analyzer. Proteome coverage...... per second or up to 600 new peptides sequenced per gradient minute. We identify 4400 proteins from one microgram of HeLa digest using a one hour gradient, which is an approximately 30% improvement compared to previous instrumentation. In addition, we show very deep proteome coverage can be achieved...

  14. Diagnostic implication of magnetic resonance imaging using STIR sequences in optic neuritis

    Energy Technology Data Exchange (ETDEWEB)

    Igarashi, Yasuo; Hashimoto, Masato; Ohyachi, Hiroaki; Nakamura, Yasushi; Ohguro, Hiroshi; Ohtsuka, Kenji; Nakagawa, Takashi (Sapporo Medical Coll. (Japan))

    1994-10-01

    We evaluated 23 patients with optic neuritis by magnetic resonance imaging (MRI) using STIR sequences. The series comprised 5 cases of multiple sclerosis and 18 of unknown etiology. Abnormal high-intensity area was observed in the optic nerve in at least one slice. The slices showing a high signal intensity averaged 3.4 in number. The abnormal finding was most frequent at 15 mm posterior to the eyeglobe in papillitis and retrobulbar optic neuritis. The incidence of abnormal finding was more frequent in papillitis than in retrobulbar neuritis. The high-intensity signal in the optic nerve was not correlated with the latency of major positivity of pattern-reversal VEPs and was rather associated with the clinical course and outcome of optic neuritis. (author).

  15. Rapid detection of parasite in muscle fibers of fishes using a portable microscope imaging technique (Conference Presentation)

    Science.gov (United States)

    Lee, Jayoung; Lee, Hoonsoo; Kim, Moon S.; Cho, Byoungkwan

    2017-05-01

    Fishes are a widely used food material in the world. Recently about 4% of the fishes are infected with Kudoa thyrsites in Asian ocean. Kudoa thyrsites is a parasite that is found within the muscle fibers of fishes. The infected fishes can be a reason of food poisoning, which should be sorted out before distribution and consumption. Although Kudoa thyrsites is visible to the naked eye, it could be easily overlooked due to the micro-scale size and similar color with fish tissue. In addition, the visual inspection is labor intensive works resulting in loss of money and time. In this study, a portable microscopic camera was utilized to obtain images of raw fish slices. The optimized image processing techniques with polarized transmittance images provided reliable performance. The result shows that the portable microscopic imaging method can be used to detect parasites rapidly and non-destructively, which could be an alternative to manual inspections.

  16. A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

    Directory of Open Access Journals (Sweden)

    Charbonnel Nathalie

    2010-05-01

    Full Text Available Abstract Background High-throughput sequencing technologies offer new perspectives for biomedical, agronomical and evolutionary research. Promising progresses now concern the application of these technologies to large-scale studies of genetic variation. Such studies require the genotyping of high numbers of samples. This is theoretically possible using 454 pyrosequencing, which generates billions of base pairs of sequence data. However several challenges arise: first in the attribution of each read produced to its original sample, and second, in bioinformatic analyses to distinguish true from artifactual sequence variation. This pilot study proposes a new application for the 454 GS FLX platform, allowing the individual genotyping of thousands of samples in one run. A probabilistic model has been developed to demonstrate the reliability of this method. Results DNA amplicons from 1,710 rodent samples were individually barcoded using a combination of tags located in forward and reverse primers. Amplicons consisted in 222 bp fragments corresponding to DRB exon 2, a highly polymorphic gene in mammals. A total of 221,789 reads were obtained, of which 153,349 were finally assigned to original samples. Rules based on a probabilistic model and a four-step procedure, were developed to validate sequences and provide a confidence level for each genotype. The method gave promising results, with the genotyping of DRB exon 2 sequences for 1,407 samples from 24 different rodent species and the sequencing of 392 variants in one half of a 454 run. Using replicates, we estimated that the reproducibility of genotyping reached 95%. Conclusions This new approach is a promising alternative to classical methods involving electrophoresis-based techniques for variant separation and cloning-sequencing for sequence determination. The 454 system is less costly and time consuming and may enhance the reliability of genotypes obtained when high numbers of samples are studied

  17. Spectral phasor analysis allows rapid and reliable unmixing of fluorescence microscopy spectral images

    NARCIS (Netherlands)

    Fereidouni, F.|info:eu-repo/dai/nl/372641431; Bader, A.N.|info:eu-repo/dai/nl/291137334; Gerritsen, H.C.|info:eu-repo/dai/nl/071548777

    2012-01-01

    A new global analysis algorithm to analyse (hyper-) spectral images is presented. It is based on the phasor representation that has been demonstrated to be very powerful for the analysis of lifetime imaging data. In spectral phasor analysis the fluorescence spectrum of each pixel in the image is

  18. Deformation analysis of the vocal folds from videostroboscopic image sequences of the larynx.

    Science.gov (United States)

    Saadah, A K; Galatsanos, N P; Bless, D; Ramos, C A

    1998-06-01

    Videostroboscopy is an examination which yields a permanent record of the moving vocal folds. Thus, it allows the diagnosis of abnormalities which contribute to voice disorders. In this paper, in order to find and quantify the deformation of the vocal folds in videostroboscopic recordings, an active contours- (snakes) based approach is used to delineate the vocal folds in each frame of the videostroboscopic image sequence. After this delineation, a new elastic registration algorithm is used to register the vocal fold contours between adjacent frames of the video sequence. This algorithm is based on the regularization principle and is very effective when large deformations are present. A least-squares approach is used to fit an affine model to the displacement vectors found by elastic registration. The parameters of this model, rotation, translation, and deformation along two principle axes, quantify the deformation and allow the succinct characterization of the videostroboscopic recordings based on the deformations that occurred. Experiments are shown with synthetic and real videostroboscopic data that demonstrate the value of the proposed approach.

  19. Fusion primer and nested integrated PCR (FPNI-PCR): a new high-efficiency strategy for rapid chromosome walking or flanking sequence cloning

    Science.gov (United States)

    2011-01-01

    Background The advent of genomics-based technologies has revolutionized many fields of biological enquiry. However, chromosome walking or flanking sequence cloning is still a necessary and important procedure to determining gene structure. Such methods are used to identify T-DNA insertion sites and so are especially relevant for organisms where large T-DNA insertion libraries have been created, such as rice and Arabidopsis. The currently available methods for flanking sequence cloning, including the popular TAIL-PCR technique, are relatively laborious and slow. Results Here, we report a simple and effective fusion primer and nested integrated PCR method (FPNI-PCR) for the identification and cloning of unknown genomic regions flanked known sequences. In brief, a set of universal primers was designed that consisted of various 15-16 base arbitrary degenerate oligonucleotides. These arbitrary degenerate primers were fused to the 3' end of an adaptor oligonucleotide which provided a known sequence without degenerate nucleotides, thereby forming the fusion primers (FPs). These fusion primers are employed in the first step of an integrated nested PCR strategy which defines the overall FPNI-PCR protocol. In order to demonstrate the efficacy of this novel strategy, we have successfully used it to isolate multiple genomic sequences namely, 21 orthologs of genes in various species of Rosaceace, 4 MYB genes of Rosa rugosa, 3 promoters of transcription factors of Petunia hybrida, and 4 flanking sequences of T-DNA insertion sites in transgenic tobacco lines and 6 specific genes from sequenced genome of rice and Arabidopsis. Conclusions The successful amplification of target products through FPNI-PCR verified that this novel strategy is an effective, low cost and simple procedure. Furthermore, FPNI-PCR represents a more sensitive, rapid and accurate technique than the established TAIL-PCR and hiTAIL-PCR procedures. PMID:22093809

  20. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

    Science.gov (United States)

    Li, Miaoxin; Li, Jiang; Li, Mulin Jun; Pan, Zhicheng; Hsu, Jacob Shujui; Liu, Dajiang J; Zhan, Xiaowei; Wang, Junwen; Song, Youqiang; Sham, Pak Chung

    2017-05-19

    Whole genome sequencing (WGS) is a promising strategy to unravel variants or genes responsible for human diseases and traits. However, there is a lack of robust platforms for a comprehensive downstream analysis. In the present study, we first proposed three novel algorithms, sequence gap-filled gene feature annotation, bit-block encoded genotypes and sectional fast access to text lines to address three fundamental problems. The three algorithms then formed the infrastructure of a robust parallel computing framework, KGGSeq, for integrating downstream analysis functions for whole genome sequencing data. KGGSeq has been equipped with a comprehensive set of analysis functions for quality control, filtration, annotation, pathogenic prediction and statistical tests. In the tests with whole genome sequencing data from 1000 Genomes Project, KGGSeq annotated several thousand more reliable non-synonymous variants than other widely used tools (e.g. ANNOVAR and SNPEff). It took only around half an hour on a small server with 10 CPUs to access genotypes of ∼60 million variants of 2504 subjects, while a popular alternative tool required around one day. KGGSeq's bit-block genotype format used 1.5% or less space to flexibly represent phased or unphased genotypes with multiple alleles and achieved a speed of over 1000 times faster to calculate genotypic correlation. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology.

    Directory of Open Access Journals (Sweden)

    Paolo Fontana

    Full Text Available BACKGROUND: Large-scale sequencing projects have now become routine lab practice and this has led to the development of a new generation of tools involving function prediction methods, bringing the latter back to the fore. The advent of Gene Ontology, with its structured vocabulary and paradigm, has provided computational biologists with an appropriate means for this task. METHODOLOGY: We present here a novel method called ARGOT (Annotation Retrieval of Gene Ontology Terms that is able to process quickly thousands of sequences for functional inference. The tool exploits for the first time an integrated approach which combines clustering of GO terms, based on their semantic similarities, with a weighting scheme which assesses retrieved hits sharing a certain number of biological features with the sequence to be annotated. These hits may be obtained by different methods and in this work we have based ARGOT processing on BLAST results. CONCLUSIONS: The extensive benchmark involved 10,000 protein sequences, the complete S. cerevisiae genome and a small subset of proteins for purposes of comparison with other available tools. The algorithm was proven to outperform existing methods and to be suitable for function prediction of single proteins due to its high degree of sensitivity, specificity and coverage.

  2. antiSMASH : rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

    NARCIS (Netherlands)

    Medema, Marnix H.; Blin, Kai; Cimermancic, Peter; de Jager, Victor; Zakrzewski, Piotr; Fischbach, Michael A.; Weber, Tilmann; Takano, Eriko; Breitling, Rainer

    Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide

  3. Time-sequenced and spectrally filtered Rayleigh imaging of shock wave and boundary layer structure for inlet characterization

    Science.gov (United States)

    Forkey, Joseph; Cogne, Sandrine; Smits, Alexander; Bogdonoff, Seymour; Lempert, Walter R.; Miles, Richard B.

    1993-01-01

    Multiple pulsed Rayleigh imaging and filtered Rayleigh scattering are used to generate images of a complex boundary layer structure, shock wave/boundary layer interactions, and crossing shock waves. Time-sequenced Rayleigh images taken with a visible, double-pulsed laser system show the evolution of boundary layer structure of the internal flow in a generic cross-shock inlet. The images taken in the inlet give insight into 3D effects caused by the inlet geometry and may be used for modeling the complex flows.

  4. Dynamic MR imaging of the temporomandibular joint arthrosis using spoiled GRASS sequence

    Energy Technology Data Exchange (ETDEWEB)

    Suenaga, Shigeaki; Hamamoto, Sadatoshi; Kawano, Kazunori (Kagoshima Univ. (Japan). Dental School) (and others)

    1994-07-01

    The purpose of this study was to quantitatively evaluate contrast enhancement effects of the posterior disk attachment in the temporomandibular joint arthrosis using dynamic MRI with bilateral surface coils. One hundred twenty-four temporomandibular joints in 96 symptomatic patients and 27 control subjects were examined with a spoiled GRASS pulse sequence (TR: 35 ms, TE: 8 ms, flip angle: 60deg). One sagittal scan was performed prior to injection, then 0.1 mmol/kg of Gd-DTPA was given as a rapid bolus injection, immediately after which scans were performed at 30 seconds intervals for a period of 5 minutes. Signal intensity (SI) was measured from the ROI of the posterior disk attachment region. The contrast enhancement effects may be calculated by SI ratio (SIR) = ( SI[sup post]-SI[sup pre])/SI[sup pre], where SI[sup post] and SI[sup pre] were the signal intensities after and before administration of contrast medium. The time intensity curve of SIR versus time after injection was obtained on each symptoms. Join pain group (85 joints) tended to show a rapid enhancement pattern, while control group (54 joints), joint sound or opening limitation group (39 joints), and asymptomatic group (68 joints) showed a relatively gradual enhancement pattern. The drop of SIR in four groups were hardly observed during examination. Mean peak SIR of control group, joint pain group, joint sound or opening limitation group, and asymptomatic group was 0.62[+-]0.24 (SD), 1.53[+-]0.69, 0.73[+-]0.38 and 0.78[+-]0.44 respectively. The mean SIR of pain group was significantly (P<0.001, t-test) higher than that of other groups. These results suggested that dynamic MRI of the temporomandibular joint may effectively depict the inflammatory changes of the posterior disk attachment. (author).

  5. Using a contrast-enhanced imaging sequence at 3-minute delay in 3-T magnetic resonance imaging for acute infarct evaluation.

    Science.gov (United States)

    Comte, Alexandre; Kastler, Bruno; Laborie, Laurent; Hadjidekov, Georges; Meneveau, Nicolas; Boulahdour, Hatem

    2008-09-01

    To investigate the performance of a delayed-enhancement (DE) sequence adapted for a 3-minute delay after bolus injection of a contrast media in cardiac magnetic resonance imaging (MRI) in acute reperfused myocardial infarction. Sixty-three patients with recent myocardial infarction underwent contrast-enhanced MRI. Sequences of first-pass (FP) perfusion imaging and DE imaging at 3 and 15 minutes were performed at the acute phase. Of these patients, 49 had a follow-up cardiac magnetic resonance examination. Infarct sizes were quantified by 2 experienced users with a 17-segment model at the acute phase (at FP and at 3- and 15-minute delay) and at the chronic phase (at 15 minutes because only fibrous areas hyperenhance late). Areas of hypoenhancement and hyperenhancement were also calculated. Results from the 3-minute imaging sequence at the acute phase were compared with the FP (taking into account dark signal areas), with the 15-minute DE imaging sequence results at the acute phase [taking into account dark signal and hyperenhanced (white plus dark signal) areas] and with the 15-minute DE imaging sequence from the chronic phase (taking into account hyperenhanced areas). Least squares regression and Bland-Altman plots were performed for the comparisons. For the evaluation of hyperenhancement, the comparison between imaging sequence results at 3 minutes versus 15-minute DE at the acute phase (respectively, at the chronic phase) shows a good correlation (r(2) = 0.941; respectively r(2) = 0.862, at the chronic phase) and the Bland-Altman plot indicates a good concordance (m =-0.43; SD = 2.69; respectively m = 2.76; SD = 3.92); For the evaluation of hypoenhancement, the comparison between imaging sequence results at 3 minutes versus FP (respectively, 15 minutes at the acute phase) also shows a good correlation (r(2) = 0.751; respectively r(2) = 0.71) and the Bland-Altman plot indicates a good concordance (m = -1.06; SD = 3.34; respectively m = 2.90; SD = 3.11). Finally

  6. Implementing an Accurate and Rapid Sparse Sampling Approach for Low-Dose Atomic Resolution STEM Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Kovarik, Libor; Stevens, Andrew J.; Liyu, Andrey V.; Browning, Nigel D.

    2016-10-17

    Aberration correction for scanning transmission electron microscopes (STEM) has dramatically increased spatial image resolution for beam-stable materials, but it is the sample stability rather than the microscope that often limits the practical resolution of STEM images. To extract physical information from images of beam sensitive materials it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in scan coils, we show that sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by factor of 5x relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dose issues.

  7. The rapid imaging renaissance: sparser samples, denser dimensions, and glimmerings of a grand unified tomography

    Science.gov (United States)

    Sodickson, Daniel K.; Feng, Li; Knoll, Florian; Cloos, Martijn; Ben-Eliezer, Noam; Axel, Leon; Chandarana, Hersh; Block, Tobias; Otazo, Ricardo

    2015-03-01

    The task of imaging is to gather spatiotemporal information which can be organized into a coherent map. Tomographic imaging in particular involves the use of multiple projections, or other interactions of a probe (light, sound, etc.) with a body, in order to determine cross-sectional information. Though the probes and the corresponding imaging modalities may vary, and though the methodology of particular imaging approaches is in constant ferment, the conceptual underpinnings of tomographic imaging have in many ways remained fixed for many decades. Recent advances in applied mathematics, however, have begun to roil this intellectual landscape. The advent of compressed sensing, anticipated in various algorithms dating back many years but unleashed in full theoretical force in the last decade, has changed the way imagers have begun to think about data acquisition and image reconstruction. The power of incoherent sampling and sparsity-enforcing reconstruction has been demonstrated in various contexts and, when combined with other modern fast imaging techniques, has enabled unprecedented increases in imaging efficiency. Perhaps more importantly, however, such approaches have spurred a shift in perspective, prompting us to focus less on nominal data sufficiency than on information content. Beginning with examples from MRI, then proceeding through selected other modalities such as CT and PET, as well as multimodality combinations, this paper explores the potential of newly evolving acquisition and reconstruction paradigms to change the way we do imaging in the lab and in the clinic.

  8. NDER: A novel web application using annotated whole slide images for rapid improvements in human pattern recognition

    Directory of Open Access Journals (Sweden)

    Nicholas P Reder

    2016-01-01

    Full Text Available Context: Whole-slide images (WSIs present a rich source of information for education, training, and quality assurance. However, they are often used in a fashion similar to glass slides rather than in novel ways that leverage the advantages of WSI. We have created a pipeline to transform annotated WSI into pattern recognition training, and quality assurance web application called novel diagnostic electronic resource (NDER. Aims: Create an efficient workflow for extracting annotated WSI for use by NDER, an attractive web application that provides high-throughput training. Materials and Methods: WSI were annotated by a resident and classified into five categories. Two methods of extracting images and creating image databases were compared. Extraction Method 1: Manual extraction of still images and validation of each image by four breast pathologists. Extraction Method 2: Validation of annotated regions on the WSI by a single experienced breast pathologist and automated extraction of still images tagged by diagnosis. The extracted still images were used by NDER. NDER briefly displays an image, requires users to classify the image after time has expired, then gives users immediate feedback. Results: The NDER workflow is efficient: annotation of a WSI requires 5 min and validation by an expert pathologist requires An additional one to 2 min. The pipeline is highly automated, with only annotation and validation requiring human input. NDER effectively displays hundreds of high-quality, high-resolution images and provides immediate feedback to users during a 30 min session. Conclusions: NDER efficiently uses annotated WSI to rapidly increase pattern recognition and evaluate for diagnostic proficiency.

  9. Scan time reduction in {sup 23}Na-Magnetic Resonance Imaging using the chemical shift imaging sequence. Evaluation of an iterative reconstruction method

    Energy Technology Data Exchange (ETDEWEB)

    Weingaertner, Sebastian; Konstandin, Simon; Schad, Lothar R. [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Wetterling, Friedrich [Heidelberg Univ., Mannheim (Germany). Computer Assisted Clinical Medicine; Dublin Univ. (Ireland) Trinity Inst. of Neuroscience; Fatar, Marc [Heidelberg Univ., Mannheim (Germany). Dept. of Neurology; Neumaier-Probst, Eva [Heidelberg Univ., Mannheim (Germany). Dept. of Neuroradiology

    2015-07-01

    To evaluate potential scan time reduction in {sup 23}Na-Magnetic Resonance Imaging with the chemical shift imaging sequence (CSI) using undersampled data of high-quality datasets, reconstructed with an iterative constrained reconstruction, compared to reduced resolution or reduced signal-to-noise ratio. CSI {sup 23}Na-images were retrospectively undersampled and reconstructed with a constrained reconstruction scheme. The results were compared to conventional methods of scan time reduction. The constrained reconstruction scheme used a phase constraint and a finite object support, which was extracted from a spatially registered {sup 1}H-image acquired with a double-tuned coil. The methods were evaluated using numerical simulations, phantom images and in-vivo images of a healthy volunteer and a patient who suffered from cerebral ischemic stroke. The constrained reconstruction scheme showed improved image quality compared to a decreased number of averages, images with decreased resolution or circular undersampling with weighted averaging for any undersampling factor. Brain images of a stroke patient, which were reconstructed from three-fold undersampled k-space data, resulted in only minor differences from the original image (normalized root means square error < 12%) and an almost identical delineation of the stroke region (mismatch < 6%). The acquisition of undersampled {sup 23}Na-CSI images enables up to three-fold scan time reduction with improved image quality compared to conventional methods of scan time saving.

  10. Rapid identification of a Mycobacterium tuberculosis full genetic drug resistance profile through whole genome sequencing directly from sputum

    Directory of Open Access Journals (Sweden)

    Camus Nimmo

    2017-09-01

    Discussion: Compared to rapid molecular tests (which can only examine a limited number of mutations and WGS of culture isolates (which requires a culture step, WGS directly from sputum can quickly generate a complete genetic drug resistance profile. In this case, WGS altered the clinical management of drug-resistant tuberculosis and demonstrated potential for guiding individualized drug treatment where second-line drug resistance is common.

  11. Rapid in vitro splicing of coding sequences from genomic DNA by isothermal recombination reaction-based PCR

    Directory of Open Access Journals (Sweden)

    Wenxuan Chen

    2016-09-01

    Full Text Available Cloning of coding sequence (CDS is an important step for gene function research. Here, we reported a simple and efficient strategy for assembling multiple-exon into an intron-free CDS from genomic DNA (gDNA by an isothermal recombination reaction-based PCR (IRR-PCR method. As an example, a 2067-bp full-length CDS of the anther-specific expression gene OsABCG15, which is composed of seven exons and six introns, was generated by IRR-PCR using genomic DNA of rice leaf as the template. Actually, this approach can be wildly applied to any DNA sequences assembly to achieve CDS cloning, gene fusion and multiple site-directed mutagenesis in functional genomics studies in vitro.

  12. Direct, rapid antimicrobial susceptibility test from positive blood cultures based on microscopic imaging analysis

    OpenAIRE

    Choi, Jungil; Jeong, Hyun Yong; Lee, Gi Yoon; Han, Sangkwon; Han, Shinhun; Jin, Bonghwan; Lim, Taegeun; Kim, Shin; Kim, Dong Young; Kim, Hee Chan; Kim, Eui-Chong; Song, Sang Hoon; Kim, Taek Soo; Kwon, Sunghoon

    2017-01-01

    For the timely treatment of patients with infections in bloodstream and cerebrospinal fluid, a rapid antimicrobial susceptibility test (AST) is urgently needed. Here, we describe a direct and rapid antimicrobial susceptibility testing (dRAST) system, which can determine the antimicrobial susceptibility of bacteria from a positive blood culture bottle (PBCB) in six hours. The positive blood culture sample is directly mixed with agarose and inoculated into a micropatterned plastic microchip wit...

  13. Shadow and feature recognition aids for rapid image geo-registration in UAV vision system architectures

    Science.gov (United States)

    Baer, Wolfgang; Kölsch, Mathias

    2009-05-01

    The problem of real-time image geo-referencing is encountered in all vision based cognitive systems. In this paper we present a model-image feedback approach to this problem and show how it can be applied to image exploitation from Unmanned Arial Vehicle (UAV) vision systems. By calculating reference images from a known terrain database, using a novel ray trace algorithm, we are able to eliminate foreshortening, elevation, and lighting distortions, introduce registration aids and reduce the geo-referencing problem to a linear transformation search over the two dimensional image space. A method for shadow calculation that maintains real-time performance is also presented. The paper then discusses the implementation of our model-image feedback approach in the Perspective View Nascent Technology (PVNT) software package and provides sample results from UAV mission control and target mensuration experiments conducted at China Lake and Camp Roberts, California.

  14. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    Science.gov (United States)

    2012-01-01

    Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS) technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin) as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA) sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible) in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM), and are now replacing the markers previously developed by a traditional DNA fingerprinting method for

  15. Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

    Directory of Open Access Journals (Sweden)

    Yang Huaan

    2012-07-01

    Full Text Available Abstract Background In the last 30 years, a number of DNA fingerprinting methods such as RFLP, RAPD, AFLP, SSR, DArT, have been extensively used in marker development for molecular plant breeding. However, it remains a daunting task to identify highly polymorphic and closely linked molecular markers for a target trait for molecular marker-assisted selection. The next-generation sequencing (NGS technology is far more powerful than any existing generic DNA fingerprinting methods in generating DNA markers. In this study, we employed a grain legume crop Lupinus angustifolius (lupin as a test case, and examined the utility of an NGS-based method of RAD (restriction-site associated DNA sequencing as DNA fingerprinting for rapid, cost-effective marker development tagging a disease resistance gene for molecular breeding. Results Twenty informative plants from a cross of RxS (disease resistant x susceptible in lupin were subjected to RAD single-end sequencing by multiplex identifiers. The entire RAD sequencing products were resolved in two lanes of the 16-lanes per run sequencing platform Solexa HiSeq2000. A total of 185 million raw reads, approximately 17 Gb of sequencing data, were collected. Sequence comparison among the 20 test plants discovered 8207 SNP markers. Filtration of DNA sequencing data with marker identification parameters resulted in the discovery of 38 molecular markers linked to the disease resistance gene Lanr1. Five randomly selected markers were converted into cost-effective, simple PCR-based markers. Linkage analysis using marker genotyping data and disease resistance phenotyping data on a F8 population consisting of 186 individual plants confirmed that all these five markers were linked to the R gene. Two of these newly developed sequence-specific PCR markers, AnSeq3 and AnSeq4, flanked the target R gene at a genetic distance of 0.9 centiMorgan (cM, and are now replacing the markers previously developed by a traditional DNA

  16. Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae.

    Directory of Open Access Journals (Sweden)

    Venu M Margam

    Full Text Available The legume pod borer, Maruca vitrata (Lepidoptera: Crambidae, is an insect pest species of crops grown by subsistence farmers in tropical regions of Africa. We present the de novo assembly of 3729 contigs from 454- and Sanger-derived sequencing reads for midgut, salivary, and whole adult tissues of this non-model species. Functional annotation predicted that 1320 M. vitrata protein coding genes are present, of which 631 have orthologs within the Bombyx mori gene model. A homology-based analysis assigned M. vitrata genes into a group of paralogs, but these were subsequently partitioned into putative orthologs following phylogenetic analyses. Following sequence quality filtering, a total of 1542 putative single nucleotide polymorphisms (SNPs were predicted within M. vitrata contig assemblies. Seventy one of 1078 designed molecular genetic markers were used to screen M. vitrata samples from five collection sites in West Africa. Population substructure may be present with significant implications in the insect resistance management recommendations pertaining to the release of biological control agents or transgenic cowpea that express Bacillus thuringiensis crystal toxins. Mutation data derived from transcriptome sequencing is an expeditious and economical source for genetic markers that allow evaluation of ecological differentiation.

  17. Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions.

    Science.gov (United States)

    Stadhouders, Ralph; Kolovos, Petros; Brouwer, Rutger; Zuin, Jessica; van den Heuvel, Anita; Kockx, Christel; Palstra, Robert-Jan; Wendt, Kerstin S; Grosveld, Frank; van Ijcken, Wilfred; Soler, Eric

    2013-03-01

    Chromosome conformation capture (3C) technology is a powerful and increasingly popular tool for analyzing the spatial organization of genomes. Several 3C variants have been developed (e.g., 4C, 5C, ChIA-PET, Hi-C), allowing large-scale mapping of long-range genomic interactions. Here we describe multiplexed 3C sequencing (3C-seq), a 4C variant coupled to next-generation sequencing, allowing genome-scale detection of long-range interactions with candidate regions. Compared with several other available techniques, 3C-seq offers a superior resolution (typically single restriction fragment resolution; approximately 1-8 kb on average) and can be applied in a semi-high-throughput fashion. It allows the assessment of long-range interactions of up to 192 genes or regions of interest in parallel by multiplexing library sequencing. This renders multiplexed 3C-seq an inexpensive, quick (total hands-on time of 2 weeks) and efficient method that is ideal for the in-depth analysis of complex genetic loci. The preparation of multiplexed 3C-seq libraries can be performed by any investigator with basic skills in molecular biology techniques. Data analysis requires basic expertise in bioinformatics and in Linux and Python environments. The protocol describes all materials, critical steps and bioinformatics tools required for successful application of 3C-seq technology.

  18. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

    Directory of Open Access Journals (Sweden)

    Villegas Andre

    2010-09-01

    Full Text Available Abstract Background The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq. Results Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST. The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset. Conclusion Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters. It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs

  19. Optimization of multi-pulse sequences for nonlinear contrast agent imaging using a cMUT array.

    Science.gov (United States)

    Novell, Anthony; Arena, Christopher B; Kasoji, Sandeep; Dayton, Paul A

    2015-04-21

    Capacitive micromachined ultrasonic transducer (cMUT) technology provides advantages such as wide frequency bandwidth, which can be exploited for contrast agent imaging. Nevertheless, the efficiency of traditional multi-pulse imaging schemes, such as pulse inversion (PI), remains limited because of the intrinsic nonlinear character of cMUTs. Recently, a new contrast imaging sequence, called bias voltage modulation sequence (BVM), has been specifically developed for cMUTs to suppress their unwanted nonlinear behavior. In this study, we propose to optimize contrast agent detection by combining the BVM sequence with PI and/or chirp reversal (CR). An aqueous dispersion of lipid encapsulated microbubbles was exposed to several combinations of multi-pulse imaging sequences. Approaches were evaluated in vitro using 9 inter-connected elements of a cMUT linear array (excitation frequency of 4 MHz; peak negative pressure of 100 kPa). For sequences using chirp excitations, a specific compression filter was designed to compress and extract several nonlinear components from the received microbubble responses. A satisfactory cancellation of the nonlinear signal from the source is achieved when BVM is combined with PI and CR. In comparison with PI and CR imaging modes alone, using sequences incorporating BVM increases the contrast-to-tissue ratio by 10.0 dB and 4.6 dB, respectively. Furthermore, the combination of BVM with CR and PI results in a significant increase of the contrast-to-noise ratio (+29 dB). This enhancement is attributed to the use of chirps as excitation signals and the improved preservation of several nonlinear components contained within the contrast agent response.

  20. Rapid Retrieval of Lung Nodule CT Images Based on Hashing and Pruning Methods

    Directory of Open Access Journals (Sweden)

    Ling Pan

    2016-01-01

    Full Text Available The similarity-based retrieval of lung nodule computed tomography (CT images is an important task in the computer-aided diagnosis of lung lesions. It can provide similar clinical cases for physicians and help them make reliable clinical diagnostic decisions. However, when handling large-scale lung images with a general-purpose computer, traditional image retrieval methods may not be efficient. In this paper, a new retrieval framework based on a hashing method for lung nodule CT images is proposed. This method can translate high-dimensional image features into a compact hash code, so the retrieval time and required memory space can be reduced greatly. Moreover, a pruning algorithm is presented to further improve the retrieval speed, and a pruning-based decision rule is presented to improve the retrieval precision. Finally, the proposed retrieval method is validated on 2,450 lung nodule CT images selected from the public Lung Image Database Consortium (LIDC database. The experimental results show that the proposed pruning algorithm effectively reduces the retrieval time of lung nodule CT images and improves the retrieval precision. In addition, the retrieval framework is evaluated by differentiating benign and malignant nodules, and the classification accuracy can reach 86.62%, outperforming other commonly used classification methods.

  1. Rapid Retrieval of Lung Nodule CT Images Based on Hashing and Pruning Methods.

    Science.gov (United States)

    Pan, Ling; Qiang, Yan; Yuan, Jie; Wu, Lidong

    2016-01-01

    The similarity-based retrieval of lung nodule computed tomography (CT) images is an important task in the computer-aided diagnosis of lung lesions. It can provide similar clinical cases for physicians and help them make reliable clinical diagnostic decisions. However, when handling large-scale lung images with a general-purpose computer, traditional image retrieval methods may not be efficient. In this paper, a new retrieval framework based on a hashing method for lung nodule CT images is proposed. This method can translate high-dimensional image features into a compact hash code, so the retrieval time and required memory space can be reduced greatly. Moreover, a pruning algorithm is presented to further improve the retrieval speed, and a pruning-based decision rule is presented to improve the retrieval precision. Finally, the proposed retrieval method is validated on 2,450 lung nodule CT images selected from the public Lung Image Database Consortium (LIDC) database. The experimental results show that the proposed pruning algorithm effectively reduces the retrieval time of lung nodule CT images and improves the retrieval precision. In addition, the retrieval framework is evaluated by differentiating benign and malignant nodules, and the classification accuracy can reach 86.62%, outperforming other commonly used classification methods.

  2. Rapid Assessment of Tablet Film Coating Quality by Multispectral UV Imaging

    DEFF Research Database (Denmark)

    Klukkert, Marten; Wu, Jian X.; Rantanen, Jukka

    2016-01-01

    and coated with a polyvinyl alcohol-polyethylene glycol graft copolymer using a pan coater. It was demonstrated that the coating intactness can be assessed accurately and fast by UV imaging. The different types of coating defects could be differentiated and localized based on multivariate image analysis...

  3. A rapid and effective method for screening, sequencing and reporter verification of engineered frameshift mutations in zebrafish

    Directory of Open Access Journals (Sweden)

    Sergey V. Prykhozhij

    2017-06-01

    Full Text Available Clustered regularly interspaced palindromic repeats (CRISPR/Cas-based adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing. This problem is compounded by the relatively few antibodies available for zebrafish proteins, limiting validation at the protein level. To address these issues, we developed a detailed protocol to screen F1 mutation carriers, and clone and sequence identified mutations. In order to verify that mutations actually cause frameshifts, we created a fluorescent reporter system that can detect frameshift efficiency based on the cloning of wild-type and mutant cDNA fragments and their expression levels. As proof of principle, we applied this strategy to three CRISPR/Cas9-induced mutations in pycr1a, chd7 and hace1 genes. An insertion of seven nucleotides in pycr1a resulted in the first reported observation of exon skipping by CRISPR/Cas9-induced mutations in zebrafish. However, of these three mutant genes, the fluorescent reporter revealed effective frameshifting exclusively in the case of a two-nucleotide deletion in chd7, suggesting activity of alternative translation sites in the other two mutants even though pycr1a exon-skipping deletion is likely to be deleterious. This article provides a protocol for characterizing frameshift mutations in zebrafish, and highlights the importance of checking mutations at the mRNA level and verifying their effects on translation by fluorescent reporters when antibody detection of protein loss is not possible.

  4. A rapid and effective method for screening, sequencing and reporter verification of engineered frameshift mutations in zebrafish.

    Science.gov (United States)

    Prykhozhij, Sergey V; Steele, Shelby L; Razaghi, Babak; Berman, Jason N

    2017-06-01

    Clustered regularly interspaced palindromic repeats (CRISPR)/Cas-based adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio) to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing. This problem is compounded by the relatively few antibodies available for zebrafish proteins, limiting validation at the protein level. To address these issues, we developed a detailed protocol to screen F1 mutation carriers, and clone and sequence identified mutations. In order to verify that mutations actually cause frameshifts, we created a fluorescent reporter system that can detect frameshift efficiency based on the cloning of wild-type and mutant cDNA fragments and their expression levels. As proof of principle, we applied this strategy to three CRISPR/Cas9-induced mutations in pycr1a, chd7 and hace1 genes. An insertion of seven nucleotides in pycr1a resulted in the first reported observation of exon skipping by CRISPR/Cas9-induced mutations in zebrafish. However, of these three mutant genes, the fluorescent reporter revealed effective frameshifting exclusively in the case of a two-nucleotide deletion in chd7, suggesting activity of alternative translation sites in the other two mutants even though pycr1a exon-skipping deletion is likely to be deleterious. This article provides a protocol for characterizing frameshift mutations in zebrafish, and highlights the importance of checking mutations at the mRNA level and verifying their effects on translation by fluorescent reporters when antibody detection of protein loss is not possible. © 2017. Published by

  5. Automated method for tracing leading and trailing processes of migrating neurons in confocal image sequences

    Science.gov (United States)

    Kerekes, Ryan A.; Gleason, Shaun S.; Trivedi, Niraj; Solecki, David J.

    2010-03-01

    Segmentation, tracking, and tracing of neurons in video imagery are important steps in many neuronal migration studies and can be inaccurate and time-consuming when performed manually. In this paper, we present an automated method for tracing the leading and trailing processes of migrating neurons in time-lapse image stacks acquired with a confocal fluorescence microscope. In our approach, we first locate and track the soma of the cell of interest by smoothing each frame and tracking the local maxima through the sequence. We then trace the leading process in each frame by starting at the center of the soma and stepping repeatedly in the most likely direction of the leading process. This direction is found at each step by examining second derivatives of fluorescent intensity along curves of constant radius around the current point. Tracing terminates after a fixed number of steps or when fluorescent intensity drops below a fixed threshold. We evolve the resulting trace to form an improved trace that more closely follows the approximate centerline of the leading process. We apply a similar algorithm to the trailing process of the cell by starting the trace in the opposite direction. We demonstrate our algorithm on two time-lapse confocal video sequences of migrating cerebellar granule neurons (CGNs). We show that the automated traces closely approximate ground truth traces to within 1 or 2 pixels on average. Additionally, we compute line intensity profiles of fluorescence along the automated traces and quantitatively demonstrate their similarity to manually generated profiles in terms of fluorescence peak locations.

  6. Implementing an accurate and rapid sparse sampling approach for low-dose atomic resolution STEM imaging

    Science.gov (United States)

    Kovarik, L.; Stevens, A.; Liyu, A.; Browning, N. D.

    2016-10-01

    While aberration correction for scanning transmission electron microscopes (STEMs) dramatically increased the spatial resolution obtainable in the images of materials that are stable under the electron beam, the practical resolution of many STEM images is now limited by the sample stability rather than the microscope. To extract physical information from the images of beam sensitive materials, it is becoming clear that there is a critical dose/dose-rate below which the images can be interpreted as representative of the pristine material, while above it the observation is dominated by beam effects. Here, we describe an experimental approach for sparse sampling in the STEM and in-painting image reconstruction in order to reduce the electron dose/dose-rate to the sample during imaging. By characterizing the induction limited rise-time and hysteresis in the scan coils, we show that a sparse line-hopping approach to scan randomization can be implemented that optimizes both the speed of the scan and the amount of the sample that needs to be illuminated by the beam. The dose and acquisition time for the sparse sampling is shown to be effectively decreased by at least a factor of 5× relative to conventional acquisition, permitting imaging of beam sensitive materials to be obtained without changing the microscope operating parameters. The use of sparse line-hopping scan to acquire STEM images is demonstrated with atomic resolution aberration corrected the Z-contrast images of CaCO3, a material that is traditionally difficult to image by TEM/STEM because of dosage issues.

  7. Compared with the Conventional MR Imaging, Do the Constructive Interference Steady State Sequence and Diffusion Weighted Imaging Aid in the Diagnosis of Lumbar Disc Hernias?

    Science.gov (United States)

    Aydin, Hasan; Kizilgoz, Volkan; Hekimoglu, Baki

    2011-12-01

    Our aim was to evaluate the efficacy of Diffusion Weighted Imaging (DWI) and Constructive Interference Steady State (CISS) sequences in the depiction of lumbar disc hernias, including sequestrated and extruded discs. 100 patients; 35 males and 65 females, with 3 sequestration-16 extruded and 81 protruded all together 100 herniated discs were involved in this study. If a patient had more than one herniated disc, then the more precise herniation was included. All the MRI procedures were handled in Siemens Symphony Power 1.5 T. magnet. DWI- Apparent diffusion coefficient (ADC mapping) and CISS sequences were obtained in axial planes. Statistical analysis of CISS and DWI results were analysed by fischer's test, chi square statistics. CISS sequence had a 89% sensitivity, 100% specificity for all lumbar disc hernias, had 100% sensitivity and specificity in the evaluation of sequestrated and extruded discs. DWI had a 77% sensitivity and %100 specificity, had 100% sensitivity and 50% specificity in the evaluation of extrusion, 100% sensitivity and specificity in the evaluation of sequestration. CISS sequence and quantitative DWI may be alternative imaging modalities to the routine MR imaging sequences in the depiction of lumbar disc hernias, including sequestration and extruded discs.

  8. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.

    KAUST Repository

    Domina, Maria

    2014-12-04

    There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.

  9. Batch-processing of imaging or liquid-chromatography mass spectrometry datasets and De Novo sequencing of polyketide siderophores

    Czech Academy of Sciences Publication Activity Database

    Novák, Jiří; Sokolová, Lucie; Lemr, Karel; Pluháček, Tomáš; Palyzová, Andrea; Havlíček, Vladimír

    2017-01-01

    Roč. 1865, č. 7 (2017), s. 768-775 ISSN 1570-9639 R&D Projects: GA ČR(CZ) GA16-20229S; GA MŠk(CZ) LO1509 Institutional support: RVO:61388971 Keywords : Mass spectrometry imaging * De novo sequencing * Siderophores Subject RIV: EE - Microbiology, Virology Impact factor: 2.773, year: 2016

  10. Variability in prostate and seminal vesicle delineations defined on magnetic resonance images, a multi-observer, -center and -sequence study

    DEFF Research Database (Denmark)

    Nyholm, Tufve; Jonsson, Joakim; Söderström, Karin

    2013-01-01

    and approximately equal for the prostate and seminal vesicles. Large differences in variability were observed for individual patients, and also for individual imaging sequences used at the different centers. There was however no indication of decreased variability with higher field strength. CONCLUSION: The overall...

  11. Television, disordered eating, and young women in Fiji: negotiating body image and identity during rapid social change.

    Science.gov (United States)

    Becker, Anne E

    2004-12-01

    Although the relationship between media exposure and risk behavior among youth is established at a population level, the specific psychological and social mechanisms mediating the adverse effects of media on youth remain poorly understood. This study reports on an investigation of the impact of the introduction of television to a rural community in Western Fiji on adolescent ethnic Fijian girls in a setting of rapid social and economic change. Narrative data were collected from 30 purposively selected ethnic Fijian secondary school girls via semi-structured, open-ended interviews. Interviews were conducted in 1998, 3 years after television was first broadcast to this region of Fiji. Narrative data were analyzed for content relating to response to television and mechanisms that mediate self and body image in Fijian adolescents. Data in this sample suggest that media imagery is used in both creative and destructive ways by adolescent Fijian girls to navigate opportunities and conflicts posed by the rapidly changing social environment. Study respondents indicated their explicit modeling of the perceived positive attributes of characters presented in television dramas, but also the beginnings of weight and body shape preoccupation, purging behavior to control weight, and body disparagement. Response to television appeared to be shaped by a desire for competitive social positioning during a period of rapid social transition. Understanding vulnerability to images and values imported with media will be critical to preventing disordered eating and, potentially, other youth risk behaviors in this population, as well as other populations at risk.

  12. Development of a symmetric echo planar imaging framework for clinical translation of rapid dynamic hyperpolarized 13 C imaging.

    Science.gov (United States)

    Gordon, Jeremy W; Vigneron, Daniel B; Larson, Peder E Z

    2017-02-01

    To develop symmetric echo planar imaging (EPI) and a reference scan framework for hyperpolarized 13 C metabolic imaging. Symmetric, ramp-sampled EPI with partial Fourier reconstruction was implemented on a 3T scanner. The framework for acquiring a reference scan on the 1 H channel and applied to 13 C data was described and validated in both phantoms and in vivo metabolism of [1-13 C]pyruvate. Ramp-sampled, symmetric EPI provided a substantial increase in the signal-to-noise ratio of the phantom experiments. The reference scan acquired on the 1 H channel yielded 13 C phantom images that varied in mean signal intensity Ramp-sampled, symmetric EPI with spectral-spatial excitation of a single metabolite provides a fast, robust, and clinically efficacious approach to acquire hyperpolarized 13 C dynamic molecular imaging data. The gains of this efficient sampling, combined with partial Fourier methods, enables large matrix sizes required for human studies. Magn Reson Med 77:826-832, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  13. Rapid-Sequence Intubation in the Left-Lateral Tilt Position in a Pregnant Woman with Premature Placental Abruption Utilizing a Videolaryngoscope

    Directory of Open Access Journals (Sweden)

    Kenta Nakao

    2015-04-01

    Full Text Available Case - A 24-year-old pregnant woman was admitted to our hospital with decreased fetal heart rate. Obstetric examination revealed premature placental abruption; emergent caesarean section was planned under general anesthesia. On entering the operating room, the patient showed severe vital sign deterioration (blood pressure, 75/45 mm Hg; heart rate, 142 beats per minute. As left uterine displacement may worsen the premature placental abruption, the patient was placed in the left-lateral tilt position by rotating the operating table to release compression on the inferior vena cava by theuterus. To avoid circulatory collapse, rapid-sequence intubation was performed in this position. Tracheal intubation was performed with the Pentax-AWS Airwayscope (AWS videolaryngoscope, AWS; HOYA, Japan to obtain a good laryngeal view and minimize stress from laryngoscopy. After sufficient oxygenation, 120 mg of thiopental was administered. A second anesthesiologist performed cricoid pressure and 50 mg of rocuronium was administered after confirming loss of consciousness. This was followed by insertion of the AWS with a thin intlock into the mouth. Tracheal intubation was performed uneventfully. Discussion - Rapid-sequence intubation in the left-lateral tilted position with the AWS videolaryngoscope may be beneficial for pregnant women with vital sign deterioration.

  14. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae)

    Science.gov (United States)

    Kingston, Sarah E; Adams, Lara D; Rosel, Patricia E

    2009-01-01

    Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference. PMID:19811651

  15. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae).

    Science.gov (United States)

    Kingston, Sarah E; Adams, Lara D; Rosel, Patricia E

    2009-10-07

    Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA) control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP) analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

  16. Testing mitochondrial sequences and anonymous nuclear markers for phylogeny reconstruction in a rapidly radiating group: molecular systematics of the Delphininae (Cetacea: Odontoceti: Delphinidae

    Directory of Open Access Journals (Sweden)

    Kingston Sarah E

    2009-10-01

    Full Text Available Abstract Background Many molecular phylogenetic analyses rely on DNA sequence data obtained from single or multiple loci, particularly mitochondrial DNA loci. However, phylogenies for taxa that have undergone recent, rapid radiation events often remain unresolved. Alternative methodologies for discerning evolutionary relationships under these conditions are desirable. The dolphin subfamily Delphininae is a group that has likely resulted from a recent and rapid radiation. Despite several efforts, the evolutionary relationships among the species in the subfamily remain unclear. Results Here, we compare a phylogeny estimated using mitochondrial DNA (mtDNA control region sequences to a multi-locus phylogeny inferred from 418 polymorphic genomic markers obtained from amplified fragment length polymorphism (AFLP analysis. The two sets of phylogenies are largely incongruent, primarily because the mtDNA tree provides very poor resolving power; very few species' nodes in the tree are supported by bootstrap resampling. The AFLP phylogeny is considerably better resolved and more congruent with relationships inferred from morphological data. Both phylogenies support paraphyly for the genera Stenella and Tursiops. The AFLP data indicate a close relationship between the two spotted dolphin species and recent ancestry between Stenella clymene and S. longirostris. The placement of the Lagenodelphis hosei lineage is ambiguous: phenetic analysis of the AFLP data is consistent with morphological expectations but the phylogenetic analysis is not. Conclusion For closely related, recently diverged taxa, a multi-locus genome-wide survey is likely the most comprehensive approach currently available for phylogenetic inference.

  17. hnCOcaNH and hncoCANH pulse sequences for rapid and unambiguous backbone assignment in (13C, 15N) labeled proteins.

    Science.gov (United States)

    Kumar, Dinesh; Reddy, Jithender G; Hosur, Ramakrishna V

    2010-09-01

    Time-saving in data acquisition is a major thrust of NMR pulse sequence development in the context of structural proteomics research. The conventional HNCA and HN(CA)CO pulse sequences, routinely used for sequential backbone assignment, have the limitation that they cannot distinguish inter- and intra-residue correlations. In order to remove this ambiguity, one has to record HNCO and HN(CO)CA or sequential HNCA experiments which provide unambiguous information of sequential correlations. However, this almost doubles the experimental time. Besides, they require repeated scanning through the (15)N planes to search for the matching peaks along the carbon dimension. In this background, we present here two pulse sequences, termed as hncoCANH and hnCOcaNH that lead to spectra equivalent to HNCA and HN(CA)CO spectra, respectively, but with direct distinction of inter- and intra-residue peaks; these occur with opposite signs in the new experiments. The two pulse sequences have been derived by simple modification of the previously described HN(C)N pulse sequence [Panchal et al., J. Biomol. NMR 20 (2001) 135-147] to frequency-label (13)C(alpha) or (13)C' instead of (15)N during the t(1) period. Like HN(C)N, these spectra also exhibit special patterns of self and sequential peaks around glycines and prolines, which enable direct identification of certain triplets of residues and thus provide internal checks during the sequential assignment walk. The spectra enable rapid and unambiguous assignment of H(N), (15)N and (13)C(alpha) (or (13)C') in a single experiment, and thus would be of great value in high-throughput structural proteomics. (c) 2010. Published by Elsevier Inc.

  18. Process for rapid detection of fratricidal defects on optics using Linescan Phase Differential Imaging

    Energy Technology Data Exchange (ETDEWEB)

    Ravizza, F L; Nostrand, M C; Kegelmeyer, L M; Hawley, R A; Johnson, M A

    2009-11-05

    Phase-defects on optics used in high-power lasers can cause light intensification leading to laser-induced damage of downstream optics. We introduce Linescan Phase Differential Imaging (LPDI), a large-area dark-field imaging technique able to identify phase-defects in the bulk or surface of large-aperture optics with a 67 second scan-time. Potential phase-defects in the LPDI images are indentified by an image analysis code and measured with a Phase Shifting Diffraction Interferometer (PSDI). The PSDI data is used to calculate the defects potential for downstream damage using an empirical laser-damage model that incorporates a laser propagation code. A ray tracing model of LPDI was developed to enhance our understanding of its phase-defect detection mechanism and reveal limitations.

  19. Lobster-eye x-ray optics: a rapid evaluation of the image distribution.

    Science.gov (United States)

    Peele, A G; Nugent, K A

    1998-02-01

    A method for calculating the image distribution for one-dimensional lobster-eye optics is presented. This method gives the image distribution exactly for certain cases and offers improved speed over the method of ray tracing. Examples of the use of the algorithm are given. We show that the algorithm gives the same results as detailed ray-tracing codes. Extension of the method to the two-dimensional case is discussed.

  20. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data

    DEFF Research Database (Denmark)

    Joensen, Katrine Grimstrup; Tetzschner, Anna M. M.; Iguchi, Atsushi

    2015-01-01

    typing and surveillance. The aim of this study was to establish a valid and publicly available tool for WGS-based in silico serotyping of E. coli applicable for routine typing and surveillance. A FASTA database of specific O-antigen processing system genes for O typing and flagellin genes for H typing...... was created as a component of the publicly available Web tools hosted by the Center for Genomic Epidemiology (CGE) (www.genomicepidemiology.org). All E. coli isolates available with WGS data and conventional serotype information were subjected to WGS-based serotyping employing this specific SerotypeFinder CGE...... tool. SerotypeFinder was evaluated on 682 E. coli genomes, 108 of which were sequenced for this study, where both the whole genome and the serotype were available. In total, 601 and 509 isolates were included for O and H typing, respectively. The O-antigen genes wzx, wzy, wzm, and wzt and the flagellin...

  1. [Rapid 2D-3D medical image registration based on CUDA].

    Science.gov (United States)

    Li, Lingzhi; Zou, Beiji

    2014-08-01

    The medical image registration between preoperative three-dimensional (3D) scan data and intraoperative two-dimensional (2D) image is a key technology in the surgical navigation. Most previous methods need to generate 2D digitally reconstructed radiographs (DRR) images from the 3D scan volume data, then use conventional image similarity function for comparison. This procedure includes a large amount of calculation and is difficult to archive real-time processing. In this paper, with using geometric feature and image density mixed characteristics, we proposed a new similarity measure function for fast 2D-3D registration of preoperative CT and intraoperative X-ray images. This algorithm is easy to implement, and the calculation process is very short, while the resulting registration accuracy can meet the clinical use. In addition, the entire calculation process is very suitable for highly parallel numerical calculation by using the algorithm based on CUDA hardware acceleration to satisfy the requirement of real-time application in surgery.

  2. Automated Formosat Image Processing System for Rapid Response to International Disasters

    Science.gov (United States)

    Cheng, M. C.; Chou, S. C.; Chen, Y. C.; Chen, B.; Liu, C.; Yu, S. J.

    2016-06-01

    FORMOSAT-2, Taiwan's first remote sensing satellite, was successfully launched in May of 2004 into the Sun-synchronous orbit at 891 kilometers of altitude. With the daily revisit feature, the 2-m panchromatic, 8-m multi-spectral resolution images captured have been used for researches and operations in various societal benefit areas. This paper details the orchestration of various tasks conducted in different institutions in Taiwan in the efforts responding to international disasters. The institutes involved including its space agency-National Space Organization (NSPO), Center for Satellite Remote Sensing Research of National Central University, GIS Center of Feng-Chia University, and the National Center for High-performance Computing. Since each institution has its own mandate, the coordinated tasks ranged from receiving emergency observation requests, scheduling and tasking of satellite operation, downlink to ground stations, images processing including data injection, ortho-rectification, to delivery of image products. With the lessons learned from working with international partners, the FORMOSAT Image Processing System has been extensively automated and streamlined with a goal to shorten the time between request and delivery in an efficient manner. The integrated team has developed an Application Interface to its system platform that provides functions of search in archive catalogue, request of data services, mission planning, inquiry of services status, and image download. This automated system enables timely image acquisition and substantially increases the value of data product. Example outcome of these efforts in recent response to support Sentinel Asia in Nepal Earthquake is demonstrated herein.

  3. Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Nash John HE

    2008-08-01

    Full Text Available Abstract Background Multi-Locus Sequence Typing (MLST has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci. Results Our results indicate that, in general, there is significant concordance between strain relationships established by MLST and those based on shared gene content as established by CGH. While MLST has significant predictive power with respect to overall genome similarity of isolates, we also found evidence for significant differences in genomic content among strains that would otherwise appear to be highly related based on their MLST profiles. Conclusion The extensive genomic mosaicism between closely related strains has important implications in the context of establishing strain to strain relationships because it suggests that the exact gene content of strains, and by extension their phenotype, is less likely to be "predicted" based on a small number of typing loci. This in turn suggests that a greater emphasis should be placed on analyzing genes of clinical interest as we forge ahead with the next generation of molecular typing methods.

  4. INTEGRATED GEOREFERENCING OF STEREO IMAGE SEQUENCES CAPTURED WITH A STEREOVISION MOBILE MAPPING SYSTEM – APPROACHES AND PRACTICAL RESULTS

    Directory of Open Access Journals (Sweden)

    H. Eugster

    2012-07-01

    Full Text Available Stereovision based mobile mapping systems enable the efficient capturing of directly georeferenced stereo pairs. With today's camera and onboard storage technologies imagery can be captured at high data rates resulting in dense stereo sequences. These georeferenced stereo sequences provide a highly detailed and accurate digital representation of the roadside environment which builds the foundation for a wide range of 3d mapping applications and image-based geo web-services. Georeferenced stereo images are ideally suited for the 3d mapping of street furniture and visible infrastructure objects, pavement inspection, asset management tasks or image based change detection. As in most mobile mapping systems, the georeferencing of the mapping sensors and observations – in our case of the imaging sensors – normally relies on direct georeferencing based on INS/GNSS navigation sensors. However, in urban canyons the achievable direct georeferencing accuracy of the dynamically captured stereo image sequences is often insufficient or at least degraded. Furthermore, many of the mentioned application scenarios require homogeneous georeferencing accuracy within a local reference frame over the entire mapping perimeter. To achieve these demands georeferencing approaches are presented and cost efficient workflows are discussed which allows validating and updating the INS/GNSS based trajectory with independently estimated positions in cases of prolonged GNSS signal outages in order to increase the georeferencing accuracy up to the project requirements.

  5. Integrated Georeferencing of Stereo Image Sequences Captured with a Stereovision Mobile Mapping System - Approaches and Practical Results

    Science.gov (United States)

    Eugster, H.; Huber, F.; Nebiker, S.; Gisi, A.

    2012-07-01

    Stereovision based mobile mapping systems enable the efficient capturing of directly georeferenced stereo pairs. With today's camera and onboard storage technologies imagery can be captured at high data rates resulting in dense stereo sequences. These georeferenced stereo sequences provide a highly detailed and accurate digital representation of the roadside environment which builds the foundation for a wide range of 3d mapping applications and image-based geo web-services. Georeferenced stereo images are ideally suited for the 3d mapping of street furniture and visible infrastructure objects, pavement inspection, asset management tasks or image based change detection. As in most mobile mapping systems, the georeferencing of the mapping sensors and observations - in our case of the imaging sensors - normally relies on direct georeferencing based on INS/GNSS navigation sensors. However, in urban canyons the achievable direct georeferencing accuracy of the dynamically captured stereo image sequences is often insufficient or at least degraded. Furthermore, many of the mentioned application scenarios require homogeneous georeferencing accuracy within a local reference frame over the entire mapping perimeter. To achieve these demands georeferencing approaches are presented and cost efficient workflows are discussed which allows validating and updating the INS/GNSS based trajectory with independently estimated positions in cases of prolonged GNSS signal outages in order to increase the georeferencing accuracy up to the project requirements.

  6. Rapid Automatic Lighting Control of a Mixed Light Source for Image Acquisition using Derivative Optimum Search Methods

    Directory of Open Access Journals (Sweden)

    Kim HyungTae

    2015-01-01

    Full Text Available Automatic lighting (auto-lighting is a function that maximizes the image quality of a vision inspection system by adjusting the light intensity and color.In most inspection systems, a single color light source is used, and an equal step search is employed to determine the maximum image quality. However, when a mixed light source is used, the number of iterations becomes large, and therefore, a rapid search method must be applied to reduce their number. Derivative optimum search methods follow the tangential direction of a function and are usually faster than other methods. In this study, multi-dimensional forms of derivative optimum search methods are applied to obtain the maximum image quality considering a mixed-light source. The auto-lighting algorithms were derived from the steepest descent and conjugate gradient methods, which have N-size inputs of driving voltage and one output of image quality. Experiments in which the proposed algorithm was applied to semiconductor patterns showed that a reduced number of iterations is required to determine the locally maximized image quality.

  7. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection

    Science.gov (United States)

    Sanders-Buell, Eric; Chenine, Agnes-Laurence; Goonetilleke, Nilu; Thomas, Rasmi; Harbolick, Elizabeth A.; Bose, Meera; Pham, Phuc; Oropeza, Celina; Poltavee, Kultida; O’Sullivan, Anne Marie; Costanzo, Margaret C.; Warren, Joanna A.; Slike, Bonnie; Li, Hui; Peachman, Kristina K.; Gao, Feng; Cicala, Claudia; Arthos, James; O’Connell, Robert J.; Sinei, Samuel; Maganga, Lucas; Rao, Mangala; Marovich, Mary A.; Krebs, Shelly J.; Rolland, Morgane; Shaw, George M.

    2017-01-01

    In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection. PMID:28759651

  8. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection.

    Directory of Open Access Journals (Sweden)

    Gustavo H Kijak

    2017-07-01

    Full Text Available In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI. Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F viruses revealed novel viral profiles that included: a the low-level persistence of minor T/F variants, b the rapid replacement of the major T/F by a minor T/F, and c an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.

  9. AOTF-based near-infrared imaging spectrometer for rapid identification of camouflaged target

    Science.gov (United States)

    Gao, Zhifan; Zeng, Libo; Wu, Qiongshui

    2014-11-01

    Acousto-optic tunable filter (AOTF) is a novel device for spectrometer. The electronic tunability qualifies it with the most compelling advantages of higher wavelength scan rate over the conventional spectrometers that are mechanically tuned, and the feature of large angular aperture makes the AOTF particularly suitable in imaging applications. In this research, an AOTF-based near-infrared imaging spectrometer was developed. The spectrometer consists of a TeO2 AOTF module, a near-infrared imaging lens assembly, an AOTF controller, an InGaAs array detector, an image acquisition card, and a PC. A precisely designed optical wedge is placed at the emergent surface of the AOTF to deal with the inherent dispersion of the TeO2 that may degrade the spatial resolution. The direct digital synthesizer (DDS) techniques and the phase locked loop (PLL) techniques are combined for radio frequency (RF) signal synthesis. The PLL is driven by the DDS to take advantage of both their merits of high frequency resolution, high frequency scan rate and strong spurious signals resistance capability. All the functions relating to wavelength scan, image acquisition, processing, storge and display are controlled by the PC. Calibration results indicate that the spectral range is 898~1670 nm, the spectral resolution is 6.8 nm(@1064 nm), the wavelength separation between frames in the spectral image assembly is 1.0 nm, and the processing time of a single image is less than 1 ms if a TV camera with 640×512 detector is incorporated. A prototype device was assembled to test the capability of differentiating samples with similar appearances, and satisfactory results were achieved. By this device, the chemical compositions and the distribution information can be obtained simultaneously. This system has the most advantages of no moving parts, fast wavelength scan and strong vibration resistance. The proposed imaging spectrometer has a significant application prospect in the area of identification of

  10. Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success.

    Science.gov (United States)

    Peters, Ralph S; Niehuis, Oliver; Gunkel, Simon; Bläser, Marcel; Mayer, Christoph; Podsiadlowski, Lars; Kozlov, Alexey; Donath, Alexander; van Noort, Simon; Liu, Shanlin; Zhou, Xin; Misof, Bernhard; Heraty, John; Krogmann, Lars

    2017-12-13

    Chalcidoidea are a megadiverse group of mostly parasitoid wasps of major ecological and economical importance that are omnipresent in almost all extant terrestrial habitats. The timing and pattern of chalcidoid diversification is so far poorly understood and has left many important questions on the evolutionary history of Chalcidoidea unanswered. In this study, we infer the early divergence events within Chalcidoidea and address the question of whether or not ancestral chalcidoids were small egg parasitoids. We also trace the evolution of some key traits: jumping ability, development of enlarged hind femora, and associations with figs. Our phylogenetic inference is based on the analysis of 3,239 single-copy genes across 48 chalcidoid wasps and outgroups representatives. We applied an innovative a posteriori evaluation approach to molecular clock-dating based on nine carefully validated fossils, resulting in the first molecular clock-based estimation of deep Chalcidoidea divergence times. Our results suggest a late Jurassic origin of Chalcidoidea, with a first divergence of morphologically and biologically distinct groups in the early to mid Cretaceous, between 129 and 81 million years ago (mya). Diversification of most extant lineages happened rapidly after the Cretaceous in the early Paleogene, between 75 and 53 mya. The inferred Chalcidoidea tree suggests a transition from ancestral minute egg parasitoids to larger-bodied parasitoids of other host stages during the early history of chalcidoid evolution. The ability to jump evolved independently at least three times, namely in Eupelmidae, Encyrtidae, and Tanaostigmatidae. Furthermore, the large-bodied strongly sclerotized species with enlarged hind femora in Chalcididae and Leucospidae are not closely related. Finally, the close association of some chalcidoid wasps with figs, either as pollinators, or as inquilines/gallers or as parasitoids, likely evolved at least twice independently: in the Eocene, giving rise

  11. Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum.

    Science.gov (United States)

    Zhuang, Xiaofeng; McPhee, Kevin E; Coram, Tristan E; Peever, Tobin L; Chilvers, Martin I

    2012-11-26

    White mold, caused by Sclerotinia sclerotiorum, is one of the most important diseases of pea (Pisum sativum L.), however, little is known about the genetics and biochemistry of this interaction. Identification of genes underlying resistance in the host or pathogenicity and virulence factors in the pathogen will increase our knowledge of the pea-S. sclerotiorum interaction and facilitate the introgression of new resistance genes into commercial pea varieties. Although the S. sclerotiorum genome sequence is available, no pea genome is available, due in part to its large genome size (~3500 Mb) and extensive repeated motifs. Here we present an EST data set specific to the interaction between S. sclerotiorum and pea, and a method to distinguish pathogen and host sequences without a species-specific reference genome. 10,158 contigs were obtained by de novo assembly of 128,720 high-quality reads generated by 454 pyrosequencing of the pea-S. sclerotiorum interactome. A method based on the tBLASTx program was modified to distinguish pea and S. sclerotiorum ESTs. To test this strategy, a mixture of known ESTs (18,490 pea and 17,198 S. sclerotiorum ESTs) from public databases were pooled and parsed; the tBLASTx method successfully separated 90.1% of the artificial EST mix with 99.9% accuracy. The tBLASTx method successfully parsed 89.4% of the 454-derived EST contigs, as validated by PCR, into pea (6,299 contigs) and S. sclerotiorum (2,780 contigs) categories. Two thousand eight hundred and forty pea ESTs and 996 S. sclerotiorum ESTs were predicted to be expressed specifically during the pea-S. sclerotiorum interaction as determined by homology search against 81,449 pea ESTs (from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings) and 57,751 S. sclerotiorum ESTs (from mycelia at neutral pH, developing apothecia and developing sclerotia). Among those ESTs specifically expressed, 277 (9.8%) pea ESTs were predicted to be

  12. Rapid transcriptome characterization and parsing of sequences in a non-model host-pathogen interaction; pea-Sclerotinia sclerotiorum

    Directory of Open Access Journals (Sweden)

    Zhuang Xiaofeng

    2012-11-01

    Full Text Available Abstract Background White mold, caused by Sclerotinia sclerotiorum, is one of the most important diseases of pea (Pisum sativum L., however, little is known about the genetics and biochemistry of this interaction. Identification of genes underlying resistance in the host or pathogenicity and virulence factors in the pathogen will increase our knowledge of the pea-S. sclerotiorum interaction and facilitate the introgression of new resistance genes into commercial pea varieties. Although the S. sclerotiorum genome sequence is available, no pea genome is available, due in part to its large genome size (~3500 Mb and extensive repeated motifs. Here we present an EST data set specific to the interaction between S. sclerotiorum and pea, and a method to distinguish pathogen and host sequences without a species-specific reference genome. Results 10,158 contigs were obtained by de novo assembly of 128,720 high-quality reads generated by 454 pyrosequencing of the pea-S. sclerotiorum interactome. A method based on the tBLASTx program was modified to distinguish pea and S. sclerotiorum ESTs. To test this strategy, a mixture of known ESTs (18,490 pea and 17,198 S. sclerotiorum ESTs from public databases were pooled and parsed; the tBLASTx method successfully separated 90.1% of the artificial EST mix with 99.9% accuracy. The tBLASTx method successfully parsed 89.4% of the 454-derived EST contigs, as validated by PCR, into pea (6,299 contigs and S. sclerotiorum (2,780 contigs categories. Two thousand eight hundred and forty pea ESTs and 996 S. sclerotiorum ESTs were predicted to be expressed specifically during the pea-S. sclerotiorum interaction as determined by homology search against 81,449 pea ESTs (from flowers, leaves, cotyledons, epi- and hypocotyl, and etiolated and light treated etiolated seedlings and 57,751 S. sclerotiorum ESTs (from mycelia at neutral pH, developing apothecia and developing sclerotia. Among those ESTs specifically expressed

  13. Tissue viability (TiVi) imaging: utility in assessment of rapid changes in the cutaneous microvasculature

    Science.gov (United States)

    McNamara, Paul M.; O'Doherty, Jim; O'Connell, Marie-Louise; Fitzgerald, Barry W.; Anderson, Chris D.; Nilsson, Gert E.; Leahy, Martin J.

    2010-02-01

    This report outlines results from an independent study assessing the clinical potential of an emerging, contemporary imaging technology. Tissue Viability (TiVi) imaging is an easily implemented, non-invasive, and portable technique which maps the blood circulation in the surface dermal layer. However, its routine clinical implementation awaits the development of the necessary standardised protocols. Thus the pilot study examines the efficacy of a novel TiVi imaging device within a localised skin blood flow occlusion protocol. The test was administered to the upper volar forearm of 19 healthy subjects (10:9 Female:Male) for 5 different time periods ranging from 5 to 25 seconds. Dermal areas corresponding to 100 × 100 pixels (2.89 cm2) were monitored for 60 seconds prior to, during and after each occlusal test. Our results support the relevance of a TiVi occlusion protocol for physiological assessment of the skin microcirculation.

  14. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.

    Directory of Open Access Journals (Sweden)

    Hangfei Qi

    2014-04-01

    Full Text Available Widely used chemical genetic screens have greatly facilitated the identification of many antiviral agents. However, the regions of interaction and inhibitory mechanisms of many therapeutic candidates have yet to be elucidated. Previous chemical screens identified Daclatasvir (BMS-790052 as a potent nonstructural protein 5A (NS5A inhibitor for Hepatitis C virus (HCV infection with an unclear inhibitory mechanism. Here we have developed a quantitative high-resolution genetic (qHRG approach to systematically map the drug-protein interactions between Daclatasvir and NS5A and profile genetic barriers to Daclatasvir resistance. We implemented saturation mutagenesis in combination with next-generation sequencing technology to systematically quantify the effect of every possible amino acid substitution in the drug-targeted region (domain IA of NS5A on replication fitness and sensitivity to Daclatasvir. This enabled determination of the residues governing drug-protein interactions. The relative fitness and drug sensitivity profiles also provide a comprehensive reference of the genetic barriers for all possible single amino acid changes during viral evolution, which we utilized to predict clinical outcomes using mathematical models. We envision that this high-resolution profiling methodology will be useful for next-generation drug development to select drugs with higher fitness costs to resistance, and also for informing the rational use of drugs based on viral variant spectra from patients.

  15. Rapid Targeted Next-Generation Sequencing Platform for Molecular Screening and Clinical Genotyping in Subjects with Hemoglobinopathies

    Directory of Open Access Journals (Sweden)

    Xuan Shang

    2017-09-01

    Full Text Available Hemoglobinopathies are among the most common autosomal-recessive disorders worldwide. A comprehensive next-generation sequencing (NGS test would greatly facilitate screening and diagnosis of these disorders. An NGS panel targeting the coding regions of hemoglobin genes and four modifier genes was designed. We validated the assay by using 2522 subjects affected with hemoglobinopathies and applied it to carrier testing in a cohort of 10,111 couples who were also screened through traditional methods. In the clinical genotyping analysis of 1182 β-thalassemia subjects, we identified a group of additional variants that can be used for accurate diagnosis. In the molecular screening analysis of the 10,111 couples, we detected 4180 individuals in total who carried 4840 mutant alleles, and identified 186 couples at risk of having affected offspring. 12.1% of the pathogenic or likely pathogenic variants identified by our NGS assay, which were undetectable by traditional methods. Compared with the traditional methods, our assay identified an additional at-risk 35 couples. We describe a comprehensive NGS-based test that offers advantages over the traditional screening/molecular testing methods. To our knowledge, this is among the first large-scale population study to systematically evaluate the application of an NGS technique in carrier screening and molecular diagnosis of hemoglobinopathies.

  16. AUTOMATED FORMOSAT IMAGE PROCESSING SYSTEM FOR RAPID RESPONSE TO INTERNATIONAL DISASTERS

    Directory of Open Access Journals (Sweden)

    M. C. Cheng

    2016-06-01

    Full Text Available FORMOSAT-2, Taiwan’s first remote sensing satellite, was successfully launched in May of 2004 into the Sun-synchronous orbit at 891 kilometers of altitude. With the daily revisit feature, the 2-m panchromatic, 8-m multi-spectral resolution images captured have been used for researches and operations in various societal benefit areas. This paper details the orchestration of various tasks conducted in different institutions in Taiwan in the efforts responding to international disasters. The institutes involved including its space agency-National Space Organization (NSPO, Center for Satellite Remote Sensing Research of National Central University, GIS Center of Feng-Chia University, and the National Center for High-performance Computing. Since each institution has its own mandate, the coordinated tasks ranged from receiving emergency observation requests, scheduling and tasking of satellite operation, downlink to ground stations, images processing including data injection, ortho-rectification, to delivery of image products. With the lessons learned from working with international partners, the FORMOSAT Image Processing System has been extensively automated and streamlined with a goal to shorten the time between request and delivery in an efficient manner. The integrated team has developed an Application Interface to its system platform that provides functions of search in archive catalogue, request of data services, mission planning, inquiry of services status, and image download. This automated system enables timely image acquisition and substantially increases the value of data product. Example outcome of these efforts in recent response to support Sentinel Asia in Nepal Earthquake is demonstrated herein.

  17. Rapid Cancer Fluorescence Imaging Using A γ-Glutamyltranspeptidase-Specific Probe For Primary Lung Cancer

    Directory of Open Access Journals (Sweden)

    Haruaki Hino

    2016-06-01

    Full Text Available BACKGROUND: We set out to examine the activity of γ-glutamyltranspeptidase (GGT in lung cancer and the validity of γ-glutamyl hydroxymethyl rhodamine green (gGlu-HMRG for intraoperative imaging of primary lung cancer. METHODS: GGT activities and mRNA expression levels of GGT1 (one of the GGT subtypes in five human lung cancer cell lines were examined by fluorescence imaging and quantitative reverse transcription polymerase chain reaction. In vivo imaging of an orthotopic A549 xenograft model in nude mice was performed to confirm its applicability to intraoperative imaging. Furthermore, ex vivo imaging of 73 specimens from lung cancer patients were performed and analyzed to calculate the sensitivity/specificity of gGlu-HMRG for lung cancer diagnosis. RESULTS: GGT activities and mRNA expression levels of GGT1 are diverse depending on cell type; A549, H441, and H460 showed relatively high GGT activities and expression levels, whereas H82 and H226 showed lower values. In the in vivo mouse model study, tiny pleural dissemination and hilar/mediastinal lymph node metastasis (less than 1 mm in diameter were clearly detected 15 minutes after topical application of gGlu-HMRG. In the ex vivo study of specimens from patients, the sensitivity and specificity of gGlu-HMRG were calculated to be 43.8% (32/73 and 84.9% (62/73, respectively. When limited to female patients, never smokers, and adenocarcinomas, these values were 78.9% (15/19 and 73.7% (14/19, respectively. CONCLUSIONS: Although GGT activity of lung cancer cells vary, gGlu-HMRG can serve as an intraoperative imaging tool to detect small foci of lung cancer when such cells have sufficient GGT activity.

  18. Imaging sequences for intraoperative MR-guided laparoscopic liver resection in 1.0-T high field open MRI

    Energy Technology Data Exchange (ETDEWEB)

    Chopra, S.S.; Schmidt, S.C.; Schumacher, G. [University Medicine Berlin, Department of General, Visceral and Transplantation Surgery, Charite Campus Virchow Clinic, Berlin (Germany); Rump, J.; Streitparth, F.; Teichgraeber, U. [University Medicine Berlin, Department of Radiology, Charite Campus Mitte, Berlin (Germany); Seebauer, C. [University Medicine Berlin, Department of Trauma Surgery, Charite Campus Virchow Clinic, Berlin (Germany); Voort, I.V. der [University Medicine Berlin, Department of Gastroenterology, Charite Campus Virchow Clinic, Berlin (Germany)

    2009-09-15

    The aim of this study was to identify suitable interactive (dynamic) magnetic resonance (MR) sequences for real-time MR-guided liver dissection in a 1.0-T high field open MRI system. Four dynamic sequences encompassing balanced steady state free precession (bSSFP), T1W gradient echo (GRE), T2W GRE and T2W fast spin echo (FSE) were analysed regarding the image quality, artefact susceptibility and the performance of SNR and CNR. The T2W FSE sequence (1.5 s/image) was considered superior because of an intraoperative SNR of 6.9 ({+-}0.7) and CNR (vessel to parenchyma) of 5.6 ({+-}1.7) in the interventional setting. As a proof of concept, MR-guided laparoscopic liver resection was performed in two healthy domestic pigs by using the T2W FSE sequence. The additional MR images offered simultaneous multiplanar real-time visualisation of the liver vessels during the intervention and thereby increased the anatomical orientation of the surgeon. (orig.)

  19. Protocol optimization of sacroiliac joint MR Imaging at 3 Tesla: Impact of coil design and motion resistant sequences on image quality.

    Science.gov (United States)

    Gondim Teixeira, P A; Bravetti, M; Hossu, G; Lecocq, S; Petit, D; Loeuille, D; Blum, A

    2017-07-21

    To evaluate the impact of coil design and motion-resistant sequences on the quality of sacroiliac magnetic resonance imaging (MRI) examination in patients with spondyloarthropathy. One hundred and twenty-one patients with suspected sacroiliitis and referred for MRI of the sacroiliac joints were retrospectively evaluated with MRI at 3-Tesla. There were 78 women and 43 men with a mean age of 36.7±11.5 (SD) years (range: 15.8-78.4 years). Conventional and motion-resistant fat-saturated fast-spin echo T2-weighted sequences were performed with two different coils. Image quality was subjectively evaluated by two independent readers (R1 and R2) using a four-point scale. Confidence in the identification of bone marrow edema pattern (BMEP) was also evaluated subjectively using a three-point scale. Phased array body coil yielded improved image quality compared to surface coil (14.1 to 30.4% for R1 and 14.6 to 25.7% for R2; Pbody coil with motion-resistant T2-weighted sequence (kappa 0.990). The smallest number of indeterminate BMEP zones was seen on MRI set acquired with the phased-array body coil and motion-resistant T2-weighted sequence. Phased array body coil and motion-resistant T2-weighted sequences perform better than surface coil and conventional T2-weighted sequences for the evaluation of sacroiliac joints, increasing confidence in the identification of BMEP. Copyright © 2017 Editions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

  20. [Rapid Identification of Epicarpium Citri Grandis via Infrared Spectroscopy and Fluorescence Spectrum Imaging Technology Combined with Neural Network].

    Science.gov (United States)

    Pan, Sha-sha; Huang, Fu-rong; Xiao, Chi; Xian, Rui-yi; Ma, Zhi-guo

    2015-10-01

    To explore rapid reliable methods for detection of Epicarpium citri grandis (ECG), the experiment using Fourier Transform Attenuated Total Reflection Infrared Spectroscopy (FTIR/ATR) and Fluorescence Spectrum Imaging Technology combined with Multilayer Perceptron (MLP) Neural Network pattern recognition, for the identification of ECG, and the two methods are compared. Infrared spectra and fluorescence spectral images of 118 samples, 81 ECG and 37 other kinds of ECG, are collected. According to the differences in tspectrum, the spectra data in the 550-1 800 cm(-1) wavenumber range and 400-720 nm wavelength are regarded as the study objects of discriminant analysis. Then principal component analysis (PCA) is applied to reduce the dimension of spectroscopic data of ECG and MLP Neural Network is used in combination to classify them. During the experiment were compared the effects of different methods of data preprocessing on the model: multiplicative scatter correction (MSC), standard normal variable correction (SNV), first-order derivative(FD), second-order derivative(SD) and Savitzky-Golay (SG). The results showed that: after the infrared spectra data via the Savitzky-Golay (SG) pretreatment through the MLP Neural Network with the hidden layer function as sigmoid, we can get the best discrimination of ECG, the correct percent of training set and testing set are both 100%. Using fluorescence spectral imaging technology, corrected by the multiple scattering (MSC) results in the pretreatment is the most ideal. After data preprocessing, the three layers of the MLP Neural Network of the hidden layer function as sigmoid function can get 100% correct percent of training set and 96.7% correct percent of testing set. It was shown that the FTIR/ATR and fluorescent spectral imaging technology combined with MLP Neural Network can be used for the identification study of ECG and has the advantages of rapid, reliable effect.

  1. A rapid ex vivo tissue model for optimising drug detection and ionisation in MALDI imaging studies.

    Science.gov (United States)

    Huber, K; Aichler, M; Sun, N; Buck, A; Li, Z; Fernandez, I E; Hauck, S M; Zitzelsberger, H; Eickelberg, O; Janssen, K P; Keller, U; Walch, A

    2014-10-01

    The aim of this study was to establish an ex vivo model for a faster optimisation of sample preparation procedures, for example matrix choice, in matrix-assisted laser desorption/ionisation (MALDI) drug imaging studies. The ionisation properties of four drugs, afatinib, erlotinib, irinotecan and pirfenidone, were determined in an ex vivo tissue experiment by spotting decreasing dilution series onto liver sections. Hereby, the drug signals were distinctly detectable using different matrix compounds, which allowed the selection of the optimal matrix for each drug. The analysis of afatinib and erlotinib yielded high drug signals with α-cyano-4-hydroxycinnamic acid matrix, whereas 2,3-dihydroxybenzoic acid was identified as optimal matrix for irinotecan and pirfenidone detection. Our method was validated by a MALDI drug imaging approach of in vivo treated mouse tissue resulting in corresponding findings, indicating the spotting method as an appropriate approach to determine the matrix of choice. The present study shows the accordance between the detection of ex vivo spotted drugs and in vivo administered drugs by MALDI-TOF and MALDI-FT-ICR imaging, which has not been demonstrated so far. Our data suggest the ex vivo tissue spotting method as an easy and reliable model to optimise MALDI imaging measurements and to predict drug detection in tissue sections derived from treated mice prior to the recruitment of laboratory animals, which helps to save animals, time and costs.

  2. How lovebirds maneuver rapidly using super-fast head saccades and image feature stabilization

    NARCIS (Netherlands)

    Kress, Daniel; Bokhorst, Van Evelien; Lentink, David

    2015-01-01

    Diurnal flying animals such as birds depend primarily on vision to coordinate their flight path during goal-directed flight tasks. To extract the spatial structure of the surrounding environment, birds are thought to use retinal image motion (optical flow) that is primarily induced by motion of

  3. Evaluation of pneumonia in children: comparison of MRI with fast imaging sequences at 1.5T with chest radiographs

    Energy Technology Data Exchange (ETDEWEB)

    Yikilmaz, Ali; Koc, Ali; Coskun, Abdulhakim (Dept. of Radiology, Erciyes Medical School, Kayseri (Turkey)); Ozturk, Mustafa K (Dept. of Pediatric Infectious Diseases, Erciyes Medical School, Kayseri (Turkey)); Mulkern, Robert V; Lee, Edward Y (Dept. of Radiology and Dept. of Medicine, Pulmonary Div., Children' s Hospital Boston and Harvard Medical School, Boston (United States)), email: Edward.lee@childrens.harvard.edu

    2011-10-15

    Background Although there has been a study aimed at magnetic resonance imaging (MRI) evaluation of pneumonia in children at a low magnetic field (0.2T), there is no study which assessed the efficacy of MRI, particularly with fast imaging sequences at 1.5T, for evaluating pneumonia in children. Purpose To investigate the efficacy of chest MRI with fast imaging sequences at 1.5T for evaluating pneumonia in children by comparing MRI findings with those of chest radiographs. Material and Methods This was an Institutional Review Board-approved, HIPPA-compliant prospective study of 40 consecutive pediatric patients (24 boys, 16 girls; mean age 7.3 years +- 6.6 years) with pneumonia, who underwent PA and lateral chest radiographs followed by MRI within 24 h. All MRI studies were obtained in axial and coronal planes with two different fast imaging sequences: T1-weighted FFE (Fast Field Echo) (TR/TE: 83/4.6) and T2-weighted B-FFE M2D (Balanced Fast Field Echo Multiple 2D Dimensional) (TR/TE: 3.2/1.6). Two experienced pediatric radiologists reviewed each chest radiograph and MRI for the presence of consolidation, necrosis/abscess, bronchiectasis, and pleural effusion. Chest radiograph and MRI findings were compared with Kappa statistics. Results All consolidation, lung necrosis/abscess, bronchiectasis, and pleural effusion detected with chest radiographs were also detected with MRI. There was statistically substantial agreement between chest radiographs and MRI in detecting consolidation (k = 0.78) and bronchiectasis (k = 0.72) in children with pneumonia. The agreement between chest radiographs and MRI was moderate for detecting necrosis/abscess (k = 0.49) and fair for detecting pleural effusion (k = 0.30). Conclusion MRI with fast imaging sequences is comparable to chest radiographs for evaluating underlying pulmonary consolidation, bronchiectasis, necrosis/abscess, and pleural effusion often associated with pneumonia in children

  4. Active machine learning for rapid landslide inventory mapping with VHR satellite images (Invited)

    Science.gov (United States)

    Stumpf, A.; Lachiche, N.; Malet, J.; Kerle, N.; Puissant, A.

    2013-12-01

    VHR satellite images have become a primary source for landslide inventory mapping after major triggering events such as earthquakes and heavy rainfalls. Visual image interpretation is still the prevailing standard method for operational purposes but is time-consuming and not well suited to fully exploit the increasingly better supply of remote sensing data. Recent studies have addressed the development of more automated image analysis workflows for landslide inventory mapping. In particular object-oriented approaches that account for spatial and textural image information have been demonstrated to be more adequate than pixel-based classification but manually elaborated rule-based classifiers are difficult to adapt under changing scene characteristics. Machine learning algorithm allow learning classification rules for complex image patterns from labelled examples and can be adapted straightforwardly with available training data. In order to reduce the amount of costly training data active learning (AL) has evolved as a key concept to guide the sampling for many applications. The underlying idea of AL is to initialize a machine learning model with a small training set, and to subsequently exploit the model state and data structure to iteratively select the most valuable samples that should be labelled by the user. With relatively few queries and labelled samples, an AL strategy yields higher accuracies than an equivalent classifier trained with many randomly selected samples. This study addressed the development of an AL method for landslide mapping from VHR remote sensing images with special consideration of the spatial distribution of the samples. Our approach [1] is based on the Random Forest algorithm and considers the classifier uncertainty as well as the variance of potential sampling regions to guide the user towards the most valuable sampling areas. The algorithm explicitly searches for compact regions and thereby avoids a spatially disperse sampling pattern

  5. Validation of the Dominant Sequence Paradigm and Role of Dynamic Contrast-enhanced Imaging in PI-RADS Version 2.

    Science.gov (United States)

    Greer, Matthew D; Shih, Joanna H; Lay, Nathan; Barrett, Tristan; Kayat Bittencourt, Leonardo; Borofsky, Samuel; Kabakus, Ismail M; Law, Yan Mee; Marko, Jamie; Shebel, Haytham; Mertan, Francesca V; Merino, Maria J; Wood, Bradford J; Pinto, Peter A; Summers, Ronald M; Choyke, Peter L; Turkbey, Baris

    2017-12-01

    Purpose To validate the dominant pulse sequence paradigm and limited role of dynamic contrast material-enhanced magnetic resonance (MR) imaging in the Prostate Imaging Reporting and Data System (PI-RADS) version 2 for prostate multiparametric MR imaging by using data from a multireader study. Materials and Methods This HIPAA-compliant retrospective interpretation of prospectively acquired data was approved by the local ethics committee. Patients were treatment-naïve with endorectal coil 3-T multiparametric MR imaging. A total of 163 patients were evaluated, 110 with prostatectomy after multiparametric MR imaging and 53 with negative multiparametric MR imaging and systematic biopsy findings. Nine radiologists participated in this study and interpreted images in 58 patients, on average (range, 56-60 patients). Lesions were detected with PI-RADS version 2 and were compared with whole-mount prostatectomy findings. Probability of cancer detection for overall, T2-weighted, and diffusion-weighted (DW) imaging PI-RADS scores was calculated in the peripheral zone (PZ) and transition zone (TZ) by using generalized estimating equations. To determine dominant pulse sequence and benefit of dynamic contrast-enhanced (DCE) imaging, odds ratios (ORs) were calculated as the ratio of odds of cancer of two consecutive scores by logistic regression. Results A total of 654 lesions (420 in the PZ) were detected. The probability of cancer detection for PI-RADS category 2, 3, 4, and 5 lesions was 15.7%, 33.1%, 70.5%, and 90.7%, respectively. DW imaging outperformed T2-weighted imaging in the PZ (OR, 3.49 vs 2.45; P = .008). T2-weighted imaging performed better but did not clearly outperform DW imaging in the TZ (OR, 4.79 vs 3.77; P = .494). Lesions classified as PI-RADS category 3 at DW MR imaging and as positive at DCE imaging in the PZ showed a higher probability of cancer detection than did DCE-negative PI-RADS category 3 lesions (67.8% vs 40.0%, P = .02). The addition of DCE imaging

  6. PET/MR - a rapidly growing technique of imaging in oncology and neurology.

    Science.gov (United States)

    Sałyga, Alicja; Guzikowska-Ruszkowska, Izabela; Czepczyński, Rafał; Ruchała, Marek

    2016-01-01

    The combination of positron emission tomography (PET) and magnetic resonance (MR) has become a subject of interest for researchers in the recent several years. Positron emission tomography in combination with magnetic resonance (PET/MR) is the most recent imaging technique classified in the so called hybrid systems category. This review briefly discusses the development history of PET/MR scanners, the principle of their operation, of tandem systems, as well as fully integrated devices. Further, it summarizes recent reports on the application of PET/MR scans and their possible future role in oncological and non-oncological diagnostics. Recent reports regarding the application of PET/MR scanners show huge potential of simultaneously received images, which exceed the advantages of either of those scans used separately. However, the results so far remain uncertain and require further investigations, especially in terms of clinical studies, not only for scientific purposes.

  7. Multi-Frequency Encoding for Rapid Color Flow and Quadroplex Imaging

    DEFF Research Database (Denmark)

    Oddershede, Niels; Gran, Fredrik; Jensen, Jørgen Arendt

    2007-01-01

    Ultrasonic color flow maps are made by estimating the velocities line by line over the region of interest. For each velocity estimate, multiple repetitions are needed. This sets a limit on the frame rate, which becomes increasingly severe when imaging deeper lying structures or when simultaneously...... acquiring spectrogram data for triplex imaging. This paper proposes a method for decreasing the data acquisition time by simultaneously sampling multiple lines at different spatial positions for the color flow map using narrow band signals with disjoint spectral support. The signals are separated...... in the receiver by filters matched to the emitted waveforms and the autocorrelation estimator is applied. Alternatively, one spectral band can be used for creating a color flow map, while data for a number of spectrograms are acquired simultaneously. Using three disjoint spectral bands, this will result...

  8. Rapid reconstruction of 3D neuronal morphology from light microscopy images with augmented rayburst sampling.

    Directory of Open Access Journals (Sweden)

    Xing Ming

    Full Text Available Digital reconstruction of three-dimensional (3D neuronal morphology from light microscopy images provides a powerful technique for analysis of neural circuits. It is time-consuming to manually perform this process. Thus, efficient computer-assisted approaches are preferable. In this paper, we present an innovative method for the tracing and reconstruction of 3D neuronal morphology from light microscopy images. The method uses a prediction and refinement strategy that is based on exploration of local neuron structural features. We extended the rayburst sampling algorithm to a marching fashion, which starts from a single or a few seed points and marches recursively forward along neurite branches to trace and reconstruct the whole tree-like structure. A local radius-related but size-independent hemispherical sampling was used to predict the neurite centerline and detect branches. Iterative rayburst sampling was performed in the orthogonal plane, to refine the centerline location and to estimate the local radius. We implemented the method in a cooperative 3D interactive visualization-assisted system named flNeuronTool. The source code in C++ and the binaries are freely available at http://sourceforge.net/projects/flneurontool/. We validated and evaluated the proposed method using synthetic data and real datasets from the Digital Reconstruction of Axonal and Dendritic Morphology (DIADEM challenge. Then, flNeuronTool was applied to mouse brain images acquired with the Micro-Optical Sectioning Tomography (MOST system, to reconstruct single neurons and local neural circuits. The results showed that the system achieves a reasonable balance between fast speed and acceptable accuracy, which is promising for interactive applications in neuronal image analysis.

  9. Recent advances in rapid and non-destructive assessment of meat quality using hyperspectral imaging

    Science.gov (United States)

    Tao, Feifei; Ngadi, Michael

    2016-05-01

    Meat is an important food item in human diet. Its production and consumption has greatly increased in the last decades with the development of economies and improvement of peoples' living standards. However, most of the traditional methods for evaluation of meat quality are time-consuming, laborious, inconsistent and destructive to samples, which make them not appropriate for a fast-paced production and processing environment. Development of innovative and non-destructive optical sensing techniques to facilitate simple, fast, and accurate evaluation of quality are attracting increasing attention in the food industry. Hyperspectral imaging is one of the promising techniques. It integrates the combined merits of imaging and spectroscopic techniques. This paper provides a comprehensive review on recent advances in evaluation of the important quality attributes of meat including color, marbling, tenderness, pH, water holding capacity, and also chemical composition attributes such as moisture content, protein content and fat content in pork, beef and lamb. In addition, the future potential applications and trends of hyperspectral imaging are also discussed in this paper.

  10. Rapid image recognition of body parts scanned in computed tomography datasets.

    Science.gov (United States)

    Dicken, Volker; Lindow, B; Bornemann, L; Drexl, J; Nikoubashman, A; Peitgen, H-O

    2010-09-01

    Automatic CT dataset classification is important to efficiently create reliable database annotations, especially when large collections of scans must be analyzed. An automated segmentation and labeling algorithm was developed based on a fast patient segmentation and extraction of statistical density class features from the CT data. The method also delivers classifications of image noise level and patient size. The approach is based on image information only and uses an approximate patient contour detection and statistical features of the density distribution. These are obtained from a slice-wise analysis of the areas filled by various materials related to certain density classes and the spatial spread of each class. The resulting families of curves are subsequently classified using rules derived from knowledge about features of the human anatomy. The method was successfully applied to more than 5,000 CT datasets. Evaluation was performed via expert visual inspection of screenshots showing classification results and detected characteristic positions along the main body axis. Accuracy per body region was very satisfactory in the trunk (lung/liver >99.5% detection rate, presence of abdomen >97% or pelvis >95.8%) improvements are required for zoomed scans. The method performed very reliably. A test on 1,860 CT datasets collected from an oncological trial showed that the method is feasible, efficient, and is promising as an automated tool for image post-processing.

  11. Time-gated FRET nanoassemblies for rapid and sensitive intra- and extracellular fluorescence imaging.

    Science.gov (United States)

    Afsari, Hamid Samareh; Cardoso Dos Santos, Marcelina; Lindén, Stina; Chen, Ting; Qiu, Xue; van Bergen En Henegouwen, Paul M P; Jennings, Travis L; Susumu, Kimihiro; Medintz, Igor L; Hildebrandt, Niko; Miller, Lawrence W

    2016-06-01

    Time-gated Förster resonance energy transfer (FRET) using the unique material combination of long-lifetime terbium complexes (Tb) and semiconductor quantum dots (QDs) provides many advantages for highly sensitive and multiplexed biosensing. Although time-gated detection can efficiently suppress sample autofluorescence and background fluorescence from directly excited FRET acceptors, Tb-to-QD FRET has rarely been exploited for biomolecular imaging. We demonstrate Tb-to-QD time-gated FRET nanoassemblies that can be applied for intra- and extracellular imaging. Immunostaining of different epitopes of the epidermal growth factor receptor (EGFR) with Tb- and QD-conjugated antibodies and nanobodies allowed for efficient Tb-to-QD FRET on A431 cell membranes. The broad usability of Tb-to-QD FRET was further demonstrated by intracellular Tb-to-QD FRET and Tb-to-QD-to-dye FRET using microinjection as well as cell-penetrating peptide-mediated endocytosis with HeLa cells. Effective brightness enhancement by FRET from several Tb to the same QD, the use of low nanomolar concentrations, and the quick and sensitive detection void of FRET acceptor background fluorescence are important advantages for advanced intra- and extracellular imaging of biomolecular interactions.

  12. MR Diffusion Tensor Imaging Detects Rapid Microstructural Changes in Amygdala and Hippocampus Following Fear Conditioning in Mice

    Science.gov (United States)

    Ding, Abby Y.; Li, Qi; Zhou, Iris Y.; Ma, Samantha J.; Tong, Gehua; McAlonan, Grainne M.; Wu, Ed X.

    2013-01-01

    Background Following fear conditioning (FC), ex vivo evidence suggests that early dynamics of cellular and molecular plasticity in amygdala and hippocampal circuits mediate responses to fear. Such altered dynamics in fear circuits are thought to be etiologically related to anxiety disorders including posttraumatic stress disorder (PTSD). Consistent with this, neuroimaging studies of individuals with established PTSD in the months after trauma have revealed changes in brain regions responsible for processing fear. However, whether early changes in fear circuits can be captured in vivo is not known. Methods We hypothesized that in vivo magnetic resonance diffusion tensor imaging (DTI) would be sensitive to rapid microstructural changes elicited by FC in an experimental mouse PTSD model. We employed a repeated measures paired design to compare in vivo DTI measurements before, one hour after, and one day after FC-exposed mice (n = 18). Results Using voxel-wise repeated measures analysis, fractional anisotropy (FA) significantly increased then decreased in amygdala, decreased then increased in hippocampus, and was increasing in cingulum and adjacent gray matter one hour and one day post-FC respectively. These findings demonstrate that DTI is sensitive to early changes in brain microstructure following FC, and that FC elicits distinct, rapid in vivo responses in amygdala and hippocampus. Conclusions Our results indicate that DTI can detect rapid microstructural changes in brain regions known to mediate fear conditioning in vivo. DTI indices could be explored as a translational tool to capture potential early biological changes in individuals at risk for developing PTSD. PMID:23382811

  13. Rapid Stereomicroscopic Imaging of HER2 Overexpression in Ex Vivo Breast Tissue Using Topically Applied Silica-Based Gold Nanoshells

    Directory of Open Access Journals (Sweden)

    Lissett R. Bickford

    2012-01-01

    Full Text Available Tumor margin detection for patients undergoing breast conservation surgery primarily occurs postoperatively. Previously, we demonstrated that gold nanoshells rapidly enhance contrast of HER2 overexpression in ex vivo tissue sections. Our ultimate objective, however, is to discern HER2 overexpressing tissue from normal tissue in whole, nonsectioned, specimens to facilitate rapid diagnoses. Here, we use targeted nanoshells to quickly and effectively visualize HER2 receptor expression in intact ex vivo human breast tissue specimens. Punch biopsies of human breast tissue were analyzed after a brief 5-minute incubation with and without HER2-targeted silica-gold nanoshells using two-photon microscopy and stereomicroscopy. Labeling was subsequently verified using reflectance confocal microscopy, darkfield hyperspectral imaging, and immunohistochemistry to confirm levels of HER2 expression. Our results suggest that anti-HER2 nanoshells used in tandem with a near-infrared reflectance confocal microscope and a standard stereomicroscope may potentially be used to discern HER2-overexpressing cancerous tissue from normal tissue in near real time and offer a rapid supplement to current diagnostic techniques.

  14. Rapidly updated hyperspectral sounding and imaging data for severe storm prediction

    Science.gov (United States)

    Bingham, Gail; Jensen, Scott; Elwell, John; Cardon, Joel; Crain, David; Huang, Hung-Lung (Allen); Smith, William L.; Revercomb, Hank E.; Huppi, Ronald J.

    2013-09-01

    Several studies have shown that a geostationary hyperspectral imager/sounder can provide the most significant value increase in short term, regional numerical prediction weather models over a range of other options. In 1998, the Geostationary Imaging Fourier Transform Spectrometer (GIFTS) proposal was selected by NASA as the New Millennium Earth Observation 3 program over several other geostationary instrument development proposals. After the EO3 GIFTS flight demonstration program was changed to an Engineering Development Unit (EDU) due to funding limitations by one of the partners, the EDU was subjected to flight-like thermal vacuum calibration and testing and successfully validated the breakthrough technologies needed to make a successful observatory. After several government stops and starts, only EUMETSAT's Meteosat Third Generation (MTG-S) sounder is in operational development. Recently, a commercial partnership has been formed to fill the significant data gap. AsiaSat has partnered with GeoMetWatch (GMW)1 to fund the development and launch of the Sounding and Tracking Observatory for Regional Meteorology (STORMTM) sensor, a derivative of the Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS) EDU that was designed, built, and tested by Utah State University (USU). STORMTM combines advanced technologies to observe surface thermal properties, atmospheric weather, and chemistry variables in four dimensions to provide high vertical resolution temperature and moisture sounding information, with the fourth dimension (time) provided by the geosynchronous satellite platform ability to measure a location as often as desired. STORMTM will enhance the polar orbiting imaging and sounding measurements by providing: (1) a direct measure of moisture flux and altitude-resolved water vapor and cloud tracer winds throughout the troposphere, (2) an observation of the time varying atmospheric thermodynamics associated with storm system development, and (3) the

  15. Magnetic Resonance Image Sequence Influences the Relationship between Bone Marrow Lesions Volume and Pain: Data from the Osteoarthritis Initiative

    Directory of Open Access Journals (Sweden)

    Ming Zhang

    2015-01-01

    Full Text Available Subchondral bone marrow lesions (BMLs are related to structural and symptomatic osteoarthritis progression. However, it is unclear how sequence selection influences a quantitative BML measurement and its construct validity. We compared quantitative assessment of BMLs on intermediate-weighted fat suppressed (IW FS turbo spin echo and 3-dimensional dual echo steady state (3D DESS sequences. We used a customized software to measure 30 knees’ (24- and 48-month MR images BMLs on both sequences. The results showed that the IW FS sequences have much larger BML volumes (median: IW FS = 1840 mm3; DESS = 191 mm3 and BML volume change (between 24 and 48 months than DESS sequence and demonstrate more BML volume change. The 24-month BML volume on IW FS is correlated with BML volume on DESS (rs = 0.83. BML volume change on IW FS is not significantly correlated with change on DESS. The 24-month WOMAC pain is correlated with the 24-month BMLs on IW FS (rs = 0.39 but not DESS. The change in WOMAC pain is correlated with BML volume change on IW FS (rs = 0.37 but not DESS. Overall, BML quantification on IW FS offers better validity and statistical power than BML quantification on a 3D DESS sequence.

  16. Priming from distractors in rapid serial visual presentation is modulated by image properties and attention.

    Science.gov (United States)

    Harris, Irina M; Benito, Claire T; Dux, Paul E

    2010-12-01

    We investigated distractor processing in a dual-target rapid serial visual presentation (RSVP) task containing familiar objects, by measuring repetition priming from a priming distractor (PD) to Target 2 (T2). Priming from a visually identical PD was contrasted with priming from a PD in a different orientation from T2. We also tested the effect of attention on distractor processing, by placing the PD either within or outside the attentional blink (AB). PDs outside the AB induced positive priming when they were in a different orientation to T2 and no priming, or negative priming, when they were perceptually identical to T2. PDs within the AB induced positive priming regardless of orientation. These findings demonstrate (1) that distractors are processed at multiple levels of representation; (2) that the view-specific representations of distractors are actively suppressed during RSVP; and (3) that this suppression fails in the absence of attention.

  17. Registration techniques for speckle suppression in 2D LADAR image sequences

    Science.gov (United States)

    Sabo, Darren R.; Cain, Stephen C.

    2005-03-01

    Air Force Research Labs, Sensors Directorate has constructed and tested a coherent imaging system. The Laservision coherent imaging system resolution goals are compatible with long-range target identification based on the image characteristics of the target. The system received reflected coherent light from the laser using an optical telescope, which fed a CCD detector to collect the scene intensity. Registration of individual images remains a significant problem in the generation of accurate images collected using coherent imaging systems. An investigation of the performance of an image registration algorithm was conducted using data collected from a coherent optical imaging. The algorithm under study was implemented on a general-purpose computer running the MATLAB simulation environment. This paper documents the performance of the proposed technique compared to that of the cross-correlation algorithm.

  18. Imaging of acute pulmonary embolism using a dual energy CT system with rapid kVp switching: Initial results

    Energy Technology Data Exchange (ETDEWEB)

    Geyer, Lucas L., E-mail: Lucas.Geyer@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany); Scherr, Michael, E-mail: michael.scherr@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany); Körner, Markus, E-mail: markus.koerner@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany); Wirth, Stefan, E-mail: stefan.wirth@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany); Deak, Paul, E-mail: paul.deak@ge.com [GE Healthcare, Oskar-Schlemmer-Straße 11, 80807 Munich (Germany); Reiser, Maximilian F., E-mail: maximilian.reiser@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany); Linsenmaier, Ulrich, E-mail: ulrich.linsenmaier@med.uni-muenchen.de [Department of Clinical Radiology, Medical Center of the University of Munich, Nussbaumstraße 20, 80336 Munich (Germany)

    2012-12-15

    Purpose: Computed tomography pulmonary angiography (CTPA) is considered as clinical gold standard for diagnosing pulmonary embolism (PE). Whereas conventional CTPA only offers anatomic information, dual energy CT (DECT) provides functional information on blood volume as surrogate of perfusion by assessing the pulmonary iodine distribution. The purpose of this study was to evaluate the feasibility of lung perfusion imaging using a single-tube DECT scanner with rapid kVp switching. Materials and methods: Fourteen patients with suspicion of acute PE underwent DECT. Two experienced radiologists assessed the CTPA images and lung perfusion maps regarding the presence of PE. The image quality was rated using a semi-quantitative 5-point scale: 1 (=excellent) to 5 (=non-diagnostic). Iodine concentrations were quantified by a ROI analysis. Results: Seventy perfusion defects were identified in 266 lung segments: 13 (19%) were rated as consistent with PE. Five patients had signs of PE at CTPA. All patients with occlusive clots were correctly identified by DECT perfusion maps. On a per patient basis the sensitivity and specificity were 80.0% and 88.9%, respectively, while on a per segment basis it was 40.0% and 97.6%, respectively. None of the patients with a homogeneous perfusion map had an abnormal CTPA. The overall image quality of the perfusion maps was rated with a mean score of 2.6 ± 0.6. There was a significant ventrodorsal gradient of the median iodine concentrations (1.1 mg/cm{sup 3} vs. 1.7 mg/cm{sup 3}). Conclusion: Lung perfusion imaging on a DE CT-system with fast kVp-switching is feasible. DECT might be a helpful adjunct to assess the clinical severity of PE.

  19. Wavelength optimization for rapid chromophore mapping using spatial frequency domain imaging

    Science.gov (United States)

    Mazhar, Amaan; Dell, Steven; Cuccia, David J.; Gioux, Sylvain; Durkin, Anthony J.; Frangioni, John V.; Tromberg, Bruce J.

    2010-11-01

    Spatial frequency-domain imaging (SFDI) utilizes multiple-frequency structured illumination and model-based computation to generate two-dimensional maps of tissue absorption and scattering properties. SFDI absorption data are measured at multiple wavelengths and used to fit for the tissue concentration of intrinsic chromophores in each pixel. This is done with a priori knowledge of the basis spectra of common tissue chromophores, such as oxyhemoglobin (ctO2Hb), deoxyhemoglobin (ctHHb), water (ctH2O), and bulk lipid. The quality of in vivo SFDI fits for the hemoglobin parameters ctO2Hb and ctHHb is dependent on wavelength selection, fitting parameters, and acquisition rate. The latter is critical because SFDI acquisition time is up to six times longer than planar two-wavelength multispectral imaging due to projection of multiple-frequency spatial patterns. Thus, motion artifact during in vivo measurements compromises the quality of the reconstruction. Optimal wavelength selection is examined through matrix decomposition of basis spectra, simulation of data, and dynamic in vivo measurements of a human forearm during cuff occlusion. Fitting parameters that minimize cross-talk from additional tissue chromophores, such as water and lipid, are determined. On the basis of this work, a wavelength pair of 670 nm/850 nm is determined to be the optimal two-wavelength combination for in vivo hemodynamic tissue measurements provided that assumptions for water and lipid fractions are made in the fitting process. In our SFDI case study, wavelength optimization reduces acquisition time over 30-fold to 1.5s compared to 50s for a full 34-wavelength acquisition. The wavelength optimization enables dynamic imaging of arterial occlusions with improved spatial resolution due to reduction of motion artifacts.

  20. Internal transcribed spacer sequence-based rapid molecular identification of Prototheca zopfii and Prototheca blaschkeae directly from milk of infected cows.

    Science.gov (United States)

    Marques, S; Huss, V A R; Pfisterer, K; Grosse, C; Thompson, G

    2015-05-01

    The increasing incidence of rare mastitis-causing pathogens has urged the implementation of fast and efficient diagnostic and control measures. Prototheca algae are known to be associated with diseases in humans and animals. In the latter, the most prevalent form of protothecosis is bovine mastitis with Prototheca zopfii and Prototheca blaschkeae representing the most common pathogenic species. These nonphotosynthetic and colorless green algae are ubiquitous in different environments and are widely resistant against harmful conditions and antimicrobials. Hence, the association of Prototheca with bovine mastitis represents a herd problem, requiring fast and easy identification of the infectious agent. The purpose of this study was to develop a reliable and rapid method, based on the internal transcribed spacer (ITS) sequences of ribosomal DNA, for molecular identification and discrimination between P. zopfii and P. blaschkeae in bovine mastitic milk. The complete ITS sequences of 32 Prototheca isolates showed substantial interspecies but moderate intraspecies variability facilitating the design of species-specific PCR amplification primers. The species-specific PCR was successfully applied to the identification of P. zopfii and P. blaschkeae directly from milk samples. The intraspecific ITS phylogeny was compared for each species with the geographical distribution of the respective Prototheca isolates, but no significant correlation was found. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  1. Sequence-specific cleavage of 16S rRNA for rapid and quantitative detection of particular groups of anaerobes in bioreactors.

    Science.gov (United States)

    Sekiguchi, Y; Uyeno, Y; Sunaga, A; Yoshida, H; Kamagata, Y

    2005-01-01

    We developed a rapid and simple method for rRNA-based quantitative detection of a specific group of microorganisms in complex ecosystems. The method relies on the sequence-specific scission of 16S rRNA with ribonuclease H (RNase H) and oligonucleotides that specifically hybridize with targeted rRNA molecules. RNAs from a complex community were first mixed with an oligonucleotide and were subsequently digested with RNase H to achieve sequence-dependent rRNA cleavage at the hybridization site. For the quantitative detection of targeted rRNAs, the resulting RNA fragment patterns were analyzed by gel-electrophoresis, which separated and quantified cleaved and intact rRNA fragments. This method enabled the quantitative detection of microbes in a complex microbial community by a relatively simple and fast experimental procedure. We then applied the cleavage method to actual anaerobic microbial communities such as digested sewage sludge and UASB sludges. The results demonstrated that the present method was fully applicable to anaerobic digestor ecosystems containing complex anaerobic microorganisms.

  2. Optical Aptamer Probes of Fluorescent Imaging to Rapid Monitoring of Circulating Tumor Cell

    Directory of Open Access Journals (Sweden)

    Ji Yeon Hwang

    2016-11-01

    Full Text Available Fluorescence detecting of exogenous EpCAM (epithelial cell adhesion molecule or muc1 (mucin1 expression correlated to cancer metastasis using nanoparticles provides pivotal information on CTC (circulating tumor cell occurrence in a noninvasive tool. In this study, we study a new skill to detect extracellular EpCAM/muc1 using quantum dot-based aptamer beacon (QD-EpCAM/muc1 ALB (aptamer linker beacon. The QD-EpCAM/muc1 ALB was designed using QDs (quantum dots and probe. The EpCAM/muc1-targeting aptamer contains a Ep-CAM/muc1 binding sequence and BHQ1 (black hole quencher 1 or BHQ2 (black hole quencher2. In the absence of target EpCAM/muc1, the QD-EpCAM/muc1 ALB forms a partial duplex loop-like aptamer beacon and remained in quenched state because the BHQ1/2 quenches the fluorescence signal-on of the QD-EpCAM/muc1 ALB. The binding of EpCAM/muc1 of CTC to the EpCAM/muc1 binding aptamer sequence of the EpCAM/muc1-targeting oligonucleotide triggered the dissociation of the BHQ1/2 quencher and subsequent signal-on of a green/red fluorescence signal. Furthermore, acute inflammation was stimulated by trigger such as caerulein in vivo, which resulted in increased fluorescent signal of the cy5.5-EpCAM/muc1 ALB during cancer metastasis due to exogenous expression of EpCAM/muc1 in Panc02-implanted mouse model.

  3. Multichannel microfluidic chip for rapid and reliable trapping and imaging plant-parasitic nematodes

    Science.gov (United States)

    Amrit, Ratthasart; Sripumkhai, Witsaroot; Porntheeraphat, Supanit; Jeamsaksiri, Wutthinan; Tangchitsomkid, Nuchanart; Sutapun, Boonsong

    2013-05-01

    Faster and reliable testing technique to count and identify nematode species resided in plant roots is therefore essential for export control and certification. This work proposes utilizing a multichannel microfluidic chip with an integrated flow-through microfilter to retain the nematodes in a trapping chamber. When trapped, it is rather simple and convenient to capture images of the nematodes and later identify their species by a trained technician. Multiple samples can be tested in parallel using the proposed microfluidic chip therefore increasing number of samples tested per day.

  4. Evaluation of the Ion Torrent PGM sequencing workflow for the routine rapid detection of BRCA1 and BRCA2 germline mutations.

    Science.gov (United States)

    Zanella, Isabella; Merola, Francesca; Biasiotto, Giorgio; Arche