WorldWideScience

Sample records for computational time-lapse study

  1. Time-lapse photogrammetry in geomorphic studies

    Science.gov (United States)

    Eltner, Anette; Kaiser, Andreas

    2017-04-01

    Image based approaches to reconstruct the earth surface (Structure from Motion - SfM) are establishing as a standard technology for high resolution topographic data. This is amongst other advantages due to the comparatively ease of use and flexibility of data generation. Furthermore, the increased spatial resolution led to its implementation at a vast range of applications from sub-mm to tens-of-km scale. Almost fully automatic calculation of referenced digital elevation models allows for a significant increase of temporal resolution, as well, potentially up to sub-second scales. Thereby, the setup of a time-lapse multi-camera system is necessary and different aspects need to be considered: The camera array has to be temporary stable or potential movements need to be compensated by temporary stable reference targets/areas. The stability of the internal camera geometry has to be considered due to a usually significantly lower amount of images of the scene, and thus redundancy for parameter estimation, compared to more common SfM applications. Depending on the speed of surface change, synchronisation has to be very accurate. Due to the usual application in the field, changing environmental conditions important for lighting and visual range are also crucial factors to keep in mind. Besides these important considerations much potential is comprised by time-lapse photogrammetry. The integration of multi-sensor systems, e.g. using thermal cameras, enables the potential detection of other processes not visible with RGB-images solely. Furthermore, the implementation of low-cost sensors allows for a significant increase of areal coverage and their setup at locations, where a loss of the system cannot be ruled out. The usage of micro-computers offers smart camera triggering, e.g. acquiring images with increased frequency controlled by a rainfall-triggered sensor. In addition these micro-computers can enable on-site data processing, e.g. recognition of increased surface

  2. Remotely Measuring Trash Fluxes in the Flood Canals of Megacities with Time Lapse Cameras and Computer Vision Algorithms - a Case Study from Jakarta, Indonesia.

    Science.gov (United States)

    Sedlar, F.; Turpin, E.; Kerkez, B.

    2014-12-01

    As megacities around the world continue to develop at breakneck speeds, future development, investment, and social wellbeing are threatened by a number of environmental and social factors. Chief among these is frequent, persistent, and unpredictable urban flooding. Jakarta, Indonesia with a population of 28 million, is a prime example of a city plagued by such flooding. Yet although Jakarta has ample hydraulic infrastructure already in place with more being constructed, the increasingly severity of the flooding it experiences is not from a lack of hydraulic infrastructure but rather a failure of existing infrastructure. As was demonstrated during the most recent floods in Jakarta, the infrastructure failure is often the result of excessive amounts of trash in the flood canals. This trash clogs pumps and reduces the overall system capacity. Despite this critical weakness of flood control in Jakarta, no data exists on the overall amount of trash in the flood canals, much less on how it varies temporally and spatially. The recent availability of low cost photography provides a means to obtain such data. Time lapse photography postprocessed with computer vision algorithms yields a low cost, remote, and automatic solution to measuring the trash fluxes. When combined with the measurement of key hydrological parameters, a thorough understanding of the relationship between trash fluxes and the hydrology of massive urban areas becomes possible. This work examines algorithm development, quantifying trash parameters, and hydrological measurements followed by data assimilation into existing hydraulic and hydrological models of Jakarta. The insights afforded from such an approach allows for more efficient operating of hydraulic infrastructure, knowledge of when and where critical levels of trash originate from, and the opportunity for community outreach - which is ultimately needed to reduce the trash in the flood canals of Jakarta and megacities around the world.

  3. Composite time-lapse computed tomography and micro finite element simulations: A new imaging approach for characterizing cement flows and mechanical benefits of vertebroplasty.

    Science.gov (United States)

    Stadelmann, Vincent A; Zderic, Ivan; Baur, Annick; Unholz, Cynthia; Eberli, Ursula; Gueorguiev, Boyko

    2016-02-01

    Vertebroplasty has been shown to reinforce weak vertebral bodies and reduce fracture risks, yet cement leakage is a major problem that can cause severe complications. Since cement flow is nearly impossible to control during surgery, small volumes of cement are injected, but then mechanical benefits might be limited. A better understanding of cement flows within bone structure is required to further optimize vertebroplasty and bone augmentation in general. We developed a novel imaging method, composite time-lapse CT, to characterize cement flow during injection. In brief, composite-resolution time-lapse CT exploits the qualities of microCT and clinical CT. The method consists in overlaying low-resolution time-lapse CT scans acquired during injection onto pre-operative high-resolution microCT scans, generating composite-resolution time-lapse CT series of cement flow within bone. In this in vitro study, composite-resolution time-lapse CT was applied to eight intact and five artificially fractured cadaveric vertebrae during vertebroplasty. The time-lapse scans were acquired at one-milliliter cement injection steps until a total of 10 ml cement was injected. The composite-resolution series were then converted into micro finite element models to compute strains distribution under virtual axial loading. Relocation of strain energy density within bone structure was observed throughout the progression of the procedure. Interestingly, the normalized effect of cement injection on the overall stiffness of the vertebrae was similar between intact and fractured specimens, although at different orders of magnitude. In conclusion, composite time-lapse CT can picture cement flows during bone augmentation. The composite images can also be easily converted into finite element models to compute virtual strain distributions under loading at every step of an injection, providing deeper understanding on the biomechanics of vertebroplasty. Copyright © 2015 IPEM. Published by Elsevier Ltd

  4. Effect of time lapse on the diagnostic accuracy of cone beam computed tomography for detection of vertical root fractures

    Energy Technology Data Exchange (ETDEWEB)

    Eskandarloo, Amir; Shokri, Abbas, E-mail: Dr.a.shokri@gmail.com [Dental Research Center, Department of Oral and Maxillofacial Radiology, Hamadan University of Medical Sciences, Hamadan (Iran, Islamic Republic of); Asl, Amin Mahdavi [Department of Oral and Maxillofacial Radiology, Golestan University of Medical Sciences, Gorgan (Iran, Islamic Republic of); Jalalzadeh, Mohsen [Department of Endodontics, Hamadan University of Medical Sciences, Hamadan (Iran, Islamic Republic of); Tayari, Maryam [Department of Pedodontics, Golestan University of Medical Sciences, Gorgan (Iran, Islamic Republic of); Hosseinipanah, Mohammad [Department of Anatomy, School of Medicine, Hamadan University of Medical Sciences, Hamadan (Iran, Islamic Republic of); Fardmal, Javad [Research Center for Health Sciences and Department of Epidemiology and Biostatistics, School of Public Health, Hamadan University of Medical Sciences, Hamadan (Iran, Islamic Republic of)

    2016-01-15

    Accurate and early diagnosis of vertical root fractures (VRFs) is imperative to prevent extensive bone loss and unnecessary endodontic and prosthodontic treatments. The aim of this study was to assess the effect of time lapse on the diagnostic accuracy of cone beam computed tomography (CBCT) for VRFs in endodontically treated dog’s teeth. Forty eight incisors and premolars of three adult male dogs underwent root canal therapy. The teeth were assigned to two groups: VRFs were artificially induced in the first group (n=24) while the teeth in the second group remained intact (n=24). The CBCT scans were obtained by NewTom 3G unit immediately after inducing VRFs and after one, two, three, four, eight, 12 and 16 weeks. Three oral and maxillofacial radiologists blinded to the date of radiographs assessed the presence/absence of VRFs on CBCT scans. The sensitivity, specificity and accuracy values were calculated and data were analyzed using SPSS v.16 software and ANOVA. The total accuracy of detection of VRFs immediately after surgery, one, two, three, four, eight, 12 and 16 weeks was 67.3%, 68.7%, 66.6%, 64.6%, 64.5%, 69.4%, 68.7%, 68% respectively. The effect of time lapse on detection of VRFs was not significant (p>0.05). Overall sensitivity, specificity and accuracy of CBCT for detection of VRFs were 74.3%, 62.2%, 67.2% respectively. Cone beam computed tomography is a valuable tool for detection of VRFs. Time lapse (four months) had no effect on detection of VRFs on CBCT scans. (author)

  5. A study on quality-adjusted impact of time lapse on iris recognition

    Science.gov (United States)

    Sazonova, Nadezhda; Hua, Fang; Liu, Xuan; Remus, Jeremiah; Ross, Arun; Hornak, Lawrence; Schuckers, Stephanie

    2012-06-01

    Although human iris pattern is widely accepted as a stable biometric feature, recent research has found some evidences on the aging effect of iris system. In order to investigate changes in iris recognition performance due to the elapsed time between probe and gallery iris images, we examine the effect of elapsed time on iris recognition utilizing 7,628 iris images from 46 subjects with an average of ten visits acquired over two years from a legacy database at Clarkson University. Taken into consideration the impact of quality factors such as local contrast, illumination, blur and noise on iris recognition performance, regression models are built with and without quality metrics to evaluate the degradation of iris recognition performance based on time lapse factors. Our experimental results demonstrate the decrease of iris recognition performance along with increased elapsed time based on two iris recognition system (the modified Masek algorithm and a commercial software VeriEye SDK). These results also reveal the significance of quality factors in iris recognition regression indicating the variability in match scores. According to the regression analysis, our study in this paper helps provide the quantified decrease on match scores with increased elapsed time, which indicates the possibility to implement the prediction scheme for iris recognition performance based on learning of impact on time lapse factors.

  6. Micromechanical Time-Lapse X-ray CT Study of Fatigue Damage in Uni-Directional Fibre Composites

    DEFF Research Database (Denmark)

    Jespersen, Kristine Munk; Lowe, Tristan; Withers, Philip J.

    2015-01-01

    . In the current study 3D X-ray Computed Tomography (XCT) is used to characterise the fatigue damage in the material at three different stages of the fatigue life of a tension-tension fatigue test. 3D XCT is performed on rectangular samples (4x4x110mm) cut out from pre-fatigued full-size fatigue test specimens......This study considers fatigue damage evolution in a uni-directional (UD) glass fibre composite used for wind turbine blades which is manufactured from a non-crimp fabric. It is the initial part of a time-lapse study where the damage progression is followed in a sample during a fatigue test....... The geometry of the cut-out is similar to that which will be used in the time-lapse study. As the micro-mechanical damage mechanisms are small features, it is necessary to obtain a high scan resolution which sets a limit to how large the field of view can be. Therefore, it is necessary to perform several scans...

  7. Optimal Live Cell Tracking for Cell Cycle Study Using Time-Lapse Fluorescent Microscopy Images

    Science.gov (United States)

    Li, Fuhai; Zhou, Xiaobo; Wong, Stephen T. C.

    Cell cycle study using time-lapse fluorescent microscopy images is important for understanding the mechanisms of cell division and screening of anti-cancer drugs. Cell tracking is necessary for quantifying cell behaviors. However, the complex behaviors and similarity of individual cells in a dense population make the cell population tracking challenging. To deal with these challenges, we propose a novel tracking algorithm, in which the local neighboring information is introduced to distinguish the nearby cells with similar morphology, and the Interacting Multiple Model (IMM) filter is employed to compensate for cell migrations. Based on a similarity metric, integrating the local neighboring information, migration prediction, shape and intensity, the integer programming is used to achieve the most stable association between cells in two consecutive frames. We evaluated the proposed method on the high content screening assays of HeLa cancer cell populations, and achieved 92% average tracking accuracy.

  8. Assessing Uncertainty and Repeatability in Time-Lapse VSP Monitoring of CO2 Injection in a Brine Aquifer, Frio Formation, Texas (A Case Study)

    Energy Technology Data Exchange (ETDEWEB)

    Nazari, Siamak [Univ. of California, Berkeley, CA (United States). Dept. of Civil and Environmental Engineering; Daley, Thomas M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division

    2013-02-07

    This study was done to assess the repeatability and uncertainty of time-lapse VSP response to CO2 injection in the Frio formation near Houston Texas. A work flow was built to assess the effect of time-lapse injected CO2 into two Frio brine reservoir intervals, the ‘C’ sand (Frio1) and the ‘Blue sand’ (Frio2). The time-lapse seismic amplitude variations with sensor depth for both reservoirs Frio1 and Frio2 were computed by subtracting the seismic response of the base survey from each of the two monitor seismic surveys. Source site 1 has been considered as one of the best sites for evaluating the time-lapse response after injection. For site 1, the computed timelapse NRMS levels after processing had been compared to the estimated time-lapse NRMS level before processing for different control reflectors, and for brine aquifers Frio1, and Frio2 to quantify detectability of amplitude difference. As the main interest is to analyze the time-lapse amplitude variations, different scenarios have been considered. Three different survey scenarios were considered: the base survey which was performed before injection, monitor1 performed after the first injection operation, and monitor2 which was after the second injection. The first scenario was base-monitor1, the second was basemonitor2, and the third was monitor1-monitor2. We considered three ‘control’ reflections above the Frio to assist removal of overburden changes, and concluded that third control reflector (CR3) is the most favorable for the first scenario in terms of NRMS response, and first control reflector (CR1) is the most favorable for the second and third scenarios in terms of NRMS response. The NRMS parameter is shown to be a useful measure to assess the effect of processing on time-lapse data. The overall NRMS for the Frio VSP data set was found to be in the range of 30% to 80% following basic processing. This could be considered as an estimated baseline in assessing the utility

  9. In-situ, time-lapse study of extracellular polymeric substance discharge in Streptococcus mutans biofilm.

    Science.gov (United States)

    Liu, Bernard Haochih; Yu, Li-Chieh

    2017-02-01

    Streptococcus mutans is one of the main pathogens that cause tooth decay. By metabolizing carbohydrates, S. mutans emits extracellular polymeric substance (EPS) that adheres to the tooth surface and forms layers of biofilm. Periodontal disease occurs due to the low pH environment created by S. mutans biofilm, and such an acidic environment gradually erodes tooth enamel. Since the existence of EPS is essential in the formation of biofilm, the in-situ investigation of its generation and distribution in real time is the key to the control and suppression of S. mutans biofilm. Prior studies of the biofilm formation process by fluorescence microscope, scanning electron microscope, or spectroscope have roughly divided the mechanism into three stages: (1) initial attachment; (2) microcolonies; and (3) maturation. However, these analytical methods are incapable to observe real-time changes in different locations of the extracellular matrix, and to analyze mechanical properties for single bacteria in micro and nanoscale. Since atomic force microscopy (AFM) operates by precise control of tip-sample interaction forces in liquid and in air, living microorganisms can be analyzed under near-physiological conditions. Thus, analytical techniques based on AFM constitute powerful tools for the study of biological samples, both qualitatively and quantitatively. In this study, we used AFM to quantitatively track the changes of multiple nanomechanical properties of S. mutans, including dissipation energy, adhesion force, deformation, and elastic modulus at different metabolic stages. The data revealed that the bacterial extracellular matrix has a gradient distribution in stickiness, in which different stickiness indicates the variation of EPS compositions, freshness, and metabolic stages. In-situ, time-lapse AFM images showed the local generation and distribution of EPS at different times, in which the highest adhesion distributed along sides of the S. mutans cells. Through time-lapse

  10. A clustering approach applied to time-lapse ERT interpretation - Case study of Lascaux cave

    Science.gov (United States)

    Xu, Shan; Sirieix, Colette; Riss, Joëlle; Malaurent, Philippe

    2017-09-01

    The Lascaux cave, located in southwest France, is one of the most important prehistoric cave in the world that shows Paleolithic paintings. This study aims to characterize the structure of the weathered epikarst setting located above the cave using Time-Lapse Electrical Resistivity Tomography (ERT) combined with local hydrogeological and climatic environmental data. Twenty ERT profiles were carried out for two years and helped us to record the seasonal and spatial variations of the electrical resistivity of the hydraulic upstream area of the Lascaux cave. The 20 interpreted resistivity models were merged into a single synthetic model using a multidimensional statistical method (Hierarchical Agglomerative Clustering). The individual blocks from the synthetic model associated with a similar resistivity variability were gathered into 7 clusters. We combined the resistivity temporal variations with climatic and hydrogeological data to propose a geo-electrical model that relates to a conceptual geological model. We provide a geological interpretation for each cluster regarding epikarst features. The superficial clusters (no 1 & 2) are linked to effective rainfall and trees, probably a fractured limestone. Another two clusters (no 6 & 7) are linked to detrital formations (sand and clay respectively). The cluster 3 may correspond to a marly limestone that forms a non-permeable horizon. Finally, the electrical behavior of the last two clusters (no 4 & 5) is correlated with the variation of flow rate; they may be a privileged feed zone of the flow in the cave.

  11. The Relationship between Cell Number, Division Behavior and Developmental Potential of Cleavage Stage Human Embryos: A Time-Lapse Study.

    Science.gov (United States)

    Kong, Xiangyi; Yang, Shuting; Gong, Fei; Lu, Changfu; Zhang, Shuoping; Lu, Guangxiu; Lin, Ge

    2016-01-01

    Day 3 cleavage embryo transfer is routine in many assisted reproductive technology centers today. Embryos are usually selected according to cell number, cell symmetry and fragmentation for transfer. Many studies have showed the relationship between cell number and embryo developmental potential. However, there is limited understanding of embryo division behavior and their association with embryo cell number and developmental potential. A retrospective and observational study was conducted to investigate how different division behaviors affect cell number and developmental potential of day 3 embryos by time-lapse imaging. Based on cell number at day 3, the embryos (from 104 IVF/intracytoplasmic sperm injection (ICSI) treatment cycles, n = 799) were classified as follows: less than 5 cells (10C; n = 42). Division behavior, morphokinetic parameters and blastocyst formation rate were analyzed in 5 groups of day 3 embryos with different cell numbers. In 10C embryos increased compared to 7-8C embryos (45.8%, 33.3% vs. 11.1%, respectively). In ≥5C embryos, FR and DC significantly reduced developmental potential, whereas potential irrespective of division behaviors. In NB embryos, the blastocyst formation rate increased with cell number from 7.4% (10C). In NB embryos, the cell cycle elongation or shortening was the main cause for abnormally low or high cell number, respectively. After excluding embryos with abnormal division behaviors, the developmental potential, implantation rate and live birth rate of day 3 embryos increased with cell number.

  12. The Relationship between Cell Number, Division Behavior and Developmental Potential of Cleavage Stage Human Embryos: A Time-Lapse Study.

    Directory of Open Access Journals (Sweden)

    Xiangyi Kong

    Full Text Available Day 3 cleavage embryo transfer is routine in many assisted reproductive technology centers today. Embryos are usually selected according to cell number, cell symmetry and fragmentation for transfer. Many studies have showed the relationship between cell number and embryo developmental potential. However, there is limited understanding of embryo division behavior and their association with embryo cell number and developmental potential. A retrospective and observational study was conducted to investigate how different division behaviors affect cell number and developmental potential of day 3 embryos by time-lapse imaging. Based on cell number at day 3, the embryos (from 104 IVF/intracytoplasmic sperm injection (ICSI treatment cycles, n = 799 were classified as follows: less than 5 cells (10C; n = 42. Division behavior, morphokinetic parameters and blastocyst formation rate were analyzed in 5 groups of day 3 embryos with different cell numbers. In 10C embryos increased compared to 7-8C embryos (45.8%, 33.3% vs. 11.1%, respectively. In ≥5C embryos, FR and DC significantly reduced developmental potential, whereas 10C. In NB embryos, the cell cycle elongation or shortening was the main cause for abnormally low or high cell number, respectively. After excluding embryos with abnormal division behaviors, the developmental potential, implantation rate and live birth rate of day 3 embryos increased with cell number.

  13. Application of time-lapse ERT to Characterize Soil-Water-Disease Interactions of Citrus Orchard - Case Study

    Science.gov (United States)

    Peddinti, S. R.; Kbvn, D. P.; Ranjan, S.; Suradhaniwar, S.; J, P. A.; R M, G.

    2015-12-01

    Vidarbha region in Maharashtra, India (home for mandarin Orange) experience severe climatic uncertainties resulting in crop failure. Phytopthora are the soil-borne fungal species that accumulate in the presence of moisture, and attack the root / trunk system of Orange trees at any stage. A scientific understanding of soil-moisture-disease relations within the active root zone under different climatic, irrigation, and crop cycle conditions can help in practicing management activities for improved crop yield. In this study, we developed a protocol for performing 3-D time-lapse electrical resistivity tomography (ERT) at micro scale resolution to monitor the changes in resistivity distribution within the root zone of Orange trees. A total of 40 electrodes, forming a grid of 3.5 m x 2 m around each Orange tree were used in ERT survey with gradient and Wenner configurations. A laboratory test on un-disturbed soil samples of the region was performed to plot the variation of electrical conductivity with saturation. Curve fitting techniques were applied to get the modified Archie's model parameters. The calibrated model was further applied to generate the 3-D soil moisture profiles of the study area. The point estimates of soil moisture were validated using TDR probe measurements at 3 different depths (10, 20, and 40 cm) near to the root zone. In order to understand the effect of soil-water relations on plant-disease relations, we performed ERT analysis at two locations, one at healthy and other at Phytopthora affected Orange tree during the crop cycle, under dry and irrigated conditions. The degree to which an Orange tree is affected by Phytopthora under each condition is evaluated using 'grading scale' approach following visual inspection of the canopy features. Spatial-temporal distribution of moisture profiles is co-related with grading scales to comment on the effect of climatic and irrigation scenarios on the degree and intensity of crop disease caused by Phytopthora.

  14. A-3 Construction Time Lapse

    Science.gov (United States)

    2009-01-01

    A time lapse from start to finish of steel erection for the 235-foot tall A-3 Test Stand. Ground work for the stand was broken in August 2008 and the final structural steel beam was placed April 9, 2009.

  15. Multimodal and time-lapse skin registration.

    Science.gov (United States)

    Madan, S; Dana, K J; Cula, G O

    2015-08-01

    Computational skin analysis is revolutionizing modern dermatology. Patterns extracted from image sequences enable algorithmic evaluation. Stacking multiple images to analyze pattern variation implicitly assumes that the images are aligned per-pixel. However, breathing and involuntary motion of the patient causes significant misalignment. Alignment algorithms designed for multimodal and time-lapse skin images can solve this problem. Sequences from multi-modal imaging capture unique appearance features in each modality. Time-lapse image sequences capture skin appearance change over time. Multimodal skin images have been acquired under five different modalities: three in reflectance (visible, parallel-polarized, and cross-polarized) and two in fluorescence mode (UVA and blue light excitation). For time-lapse imagery, 39 images of acne lesions over a 3-month period have been collected. The method detects micro-level features like pores, wrinkles, and other skin texture markings in the acquired images. Images are automatically registered to subpixel accuracy. The proposed registration approach precisely aligns multimodal and time-lapse images. Subsurface recovery from multimodal images has misregistration artefacts that can be eliminated using this approach. Registered time-lapse imaging captures the evolution of appearance of skin regions with time. Misalignment in skin imaging has significant impact on any quantitative or qualitative image evaluation. Micro-level features can be used to obtain highly accurate registration. Multimodal images can be organized with maximal overlap for successful registration. The resulting point-to-point alignment improves the quality of skin image analysis. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Guide to making time-lapse graphics using the facilities of the National Magnetic Fusion Energy Computing Center

    Energy Technology Data Exchange (ETDEWEB)

    Munro, J.K. Jr.

    1980-05-01

    The advent of large, fast computers has opened the way to modeling more complex physical processes and to handling very large quantities of experimental data. The amount of information that can be processed in a short period of time is so great that use of graphical displays assumes greater importance as a means of displaying this information. Information from dynamical processes can be displayed conveniently by use of animated graphics. This guide presents the basic techniques for generating black and white animated graphics, with consideration of aesthetic, mechanical, and computational problems. The guide is intended for use by someone who wants to make movies on the National Magnetic Fusion Energy Computing Center (NMFECC) CDC-7600. Problems encountered by a geographically remote user are given particular attention. Detailed information is given that will allow a remote user to do some file checking and diagnosis before giving graphics files to the system for processing into film in order to spot problems without having to wait for film to be delivered. Source listings of some useful software are given in appendices along with descriptions of how to use it. 3 figures, 5 tables.

  17. Differentiation of human neural progenitor cell-derived spiral ganglion-like neurons: a time-lapse video study.

    Science.gov (United States)

    Edin, Fredrik; Liu, Wei; Boström, Marja; Magnusson, Peetra U; Rask-Andersen, Helge

    2014-05-01

    Human neural progenitor cells can differentiate into spiral ganglion-like cells when exposed to inner ear-associated growth factors. The phenotype bears resemblance to human sphere-derived neurons. To establish an in vitro model for the human auditory nerve to replace and complement in vivo animal experiments and ultimately human in vivo transplantation. Human neural progenitors were differentiated under conditions developed for in vitro survival of human primary spiral ganglion culture with media containing growth factors associated with inner ear development. Differentiation was documented using time-lapse video microscopy. Time-dependent marker expression was evaluated using immunocytochemistry with fluorescence and laser confocal microscopy. Within 14 days of differentiation, neural progenitors adopted neural phenotype and expressed spiral ganglion-associated markers.

  18. Study of time-lapse processing for dynamic hydrologic conditions. [electronic satellite image analysis console for Earth Resources Technology Satellites imagery

    Science.gov (United States)

    Serebreny, S. M.; Evans, W. E.; Wiegman, E. J.

    1974-01-01

    The usefulness of dynamic display techniques in exploiting the repetitive nature of ERTS imagery was investigated. A specially designed Electronic Satellite Image Analysis Console (ESIAC) was developed and employed to process data for seven ERTS principal investigators studying dynamic hydrological conditions for diverse applications. These applications include measurement of snowfield extent and sediment plumes from estuary discharge, Playa Lake inventory, and monitoring of phreatophyte and other vegetation changes. The ESIAC provides facilities for storing registered image sequences in a magnetic video disc memory for subsequent recall, enhancement, and animated display in monochrome or color. The most unique feature of the system is the capability to time lapse the imagery and analytic displays of the imagery. Data products included quantitative measurements of distances and areas, binary thematic maps based on monospectral or multispectral decisions, radiance profiles, and movie loops. Applications of animation for uses other than creating time-lapse sequences are identified. Input to the ESIAC can be either digital or via photographic transparencies.

  19. The type of GnRH analogue used during controlled ovarian stimulation influences early embryo developmental kinetics: a time-lapse study.

    Science.gov (United States)

    Muñoz, Manuel; Cruz, María; Humaidan, Peter; Garrido, Nicolás; Pérez-Cano, Inmaculada; Meseguer, Marcos

    2013-06-01

    To explore if the GnRH analogue used for controlled ovarian stimulation (COS) and the ovulation triggering factor (GnRH agonist + hCG triggering versus GnRH antagonist + GnRH agonist triggering) affect embryo development and kinetics. In a retrospective cohort study in the Instituto Valenciano de Infertilidad (IVI) Alicante and the Instituto Universitario-IVI Valencia, Spain, 2817 embryos deriving from 400 couples undergoing oocyte donation were analysed. After controlled ovarian stimulation and IVF/intracytoplamic sperm injection, the timing of embryonic cleavages was assessed by a video time-lapse system. The results were analysed using Student's t test for comparison of timings (hours) and Chi-squared test for comparison of proportions. A p-value < 0.05 was considered to be statistically significant. Embryos from cycles co-treated with GnRH antagonist + GnRH agonist (n = 2101) cleaved faster than embryos deriving from patients co-treated with GnRH agonist + hCG (n = 716): these differences were significant at the first stages of development but they disappeared as long as the embryo developed. Assessing embryo quality in terms of morphokinetic characteristics, we did not find significant differences between the two groups. By adopting a time-lapse video system, we can suggest that the type of protocol used for controlled ovarian stimulation influences embryo kinetics of development but these variations are not reflected in embryo quality. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  20. Eight-Year Retrospective Study of the Critical Time Lapse between Root Canal Completion and Crown Placement: Its Influence on the Survival of Endodontically Treated Teeth.

    Science.gov (United States)

    Pratt, Isaac; Aminoshariae, Anita; Montagnese, Thomas A; Williams, Kristin A; Khalighinejad, Navid; Mickel, Andre

    2016-11-01

    The purpose of this study was to investigate the effects of factors associated with various coronal restorative modalities after root canal treatment (RCT) on the survival of endodontically treated teeth (ETT) and to assess the effect of time lapse between RCT and crown placement after RCT to form a tooth loss hazard model. Computerized analysis was performed for all patients who received posterior RCT from 2008 to 2016 in the graduate endodontic department. Data collected included dates of RCT, type of post-endodontic restoration, and time of extraction if extracted. Teeth that received crown after RCT were also divided into 2 groups: receiving crown before 4 months and after 4 months after RCT. Data were analyzed by using Kaplan-Meier log-rank test and Cox regression model (α = 0.05) by using SPPS Statistic 21. Type of restoration after RCT significantly affected the survival of ETT (P = .001). ETT that received composite/amalgam buildup restorations were 2.29 times more likely to be extracted compared with ETT that received crown (hazard ratio, 2.29; confidence interval, 1.29-4.06; P = .005). Time of crown placement after RCT was also significantly correlated with survival rate of ETT (P = .001). Teeth that received crown 4 months after RCT were almost 3 times more likely to get extracted compared with teeth that received crown within 4 months of RCT (hazard ratio, 3.38; confidence interval, 1.56-6.33; P = .002). Patients may benefit by maintaining their natural dentition by timely placement of crown after RCT, which otherwise may have been extracted and replaced by implant because of any delay in crown placement. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  1. Time-lapse monitoring of localized changes within heterogeneous media with scattered waves

    Science.gov (United States)

    Chinaemerem, Kanu

    Time-lapse monitoring of geological and mechanical media has been the focus of various studies over the past four decades because of the information that the inferred changes within the medium provides insight into the dynamic characteristics of the medium. Time-lapse changes within a medium can be used to characterize the temporal evolution of the medium, evaluate the forces driving the changes within the medium and make predictions on the future state of the monitored medium. The detectability of the changes within a material depends on the characteristics of the change to be imaged, the sensitivity of the monitoring data to the change, and the time-lapse monitoring parameters such as the monitoring source-receiver array and the spectral content of the monitoring waves. Various time-lapse monitoring tools have been used to monitor changes within media ranging from the earth's surface to tumors within the human body. These monitoring tools include the use of 4D active surveys were an imprint of the change within the medium is extracted from the time-lapse surveys and the use of interferometric techniques that use singly or multiply scattered waves. My major goal in this study is to image and localize changes present within a scattering medium using time-lapse multiply scattered waves generated within the monitored medium. The changes to be imaged are generally localized in space. This work is an extension of coda wave interferometry. Coda wave interferometry focuses on the identification and extraction of average velocity change occurring within a scattering medium. Due to the non-linear characteristics of multiply scattered waves and limited information of the origin of the multiply scattered waves, coda wave interferometry resolves the average velocity change within the scattering medium with no or limited indication of the location of the change. In this study, I demonstrate that time-lapse changes can be imaged and localized within scattering media using

  2. TimeLapseAnalyzer: Multi-target analysis for live-cell imaging and time-lapse microscopy

    DEFF Research Database (Denmark)

    Huth, Johannes; Buchholz, Malte; Kraus, Johann M.

    2011-01-01

    The direct observation of cells over time using time-lapse microscopy can provide deep insights into many important biological processes. Reliable analyses of motility, proliferation, invasive potential or mortality of cells are essential to many studies involving live cell imaging and can aid...

  3. MONITORING EROSION OF STONE SURFACES USING TIME-LAPSE AND PTM PHOTOGRAPHY: FIELD STUDY OF A 14TH CENTURY MONASTERY IN YORKSHIRE

    Science.gov (United States)

    Doehne, E.; Pinchin, S.

    2009-12-01

    Evaluating stone weathering rates and their relationship to environmental fluctuations is an important challenge in understanding the critical zone and also in efforts to prevent the loss of important cultural heritage in stone, such as monuments, sculpture and archaeological sites. Repeat photography has been widely used to evaluate geological processes such as the retreat of glaciers and the weathering of stone surfaces. However, a fundamental difficulty is that the images are often shot under differing lighting conditions, making the interpretation of stone surface loss particularly challenging. Two developments in photographic documentation show promise for improving the situation. One is the use of digital time-lapse methods to provide more frequent images to correlate stone surface loss with ongoing environmental changes. The other is a relatively new method known as polynomial transform mapping (PTM), which integrates multiple photographs taken at different angles to document more comprehensively the texture of stone surfaces. Using Java-based software, the viewer can control the precise angle of the light source in an interpolated, high-quality image. PTM can produce raking light images from any angle, as well as images with ‘normal’ illumination. We present here results based on several years of macro-photography, time-lapse imaging, and PTM imaging of rapidly eroding stone surfaces at the site of Howden Minster in Yorkshire, UK, which suffers from salt weathering. The images show that surface loss is episodic rather than continuous and in some cases is related to unusual environmental conditions, such as high winds and condensation events. Damage was also found to be synchronous, with surface change (flaking, granular disintegration, and loss of flakes) occurring at the same time in different stone blocks. Crystallization pressure from phase transitions in magnesium sulfate salts appears to be the main cause of the loss of stone surfaces.

  4. Capturing change: the duality of time-lapse imagery to acquire data and depict ecological dynamics

    Science.gov (United States)

    Brinley Buckley, Emma M.; Allen, Craig R.; Forsberg, Michael; Farrell, Michael; Caven, Andrew J.

    2017-01-01

    We investigate the scientific and communicative value of time-lapse imagery by exploring applications for data collection and visualization. Time-lapse imagery has a myriad of possible applications to study and depict ecosystems and can operate at unique temporal and spatial scales to bridge the gap between large-scale satellite imagery projects and observational field research. Time-lapse data sequences, linking time-lapse imagery with data visualization, have the ability to make data come alive for a wider audience by connecting abstract numbers to images that root data in time and place. Utilizing imagery from the Platte Basin Timelapse Project, water inundation and vegetation phenology metrics are quantified via image analysis and then paired with passive monitoring data, including streamflow and water chemistry. Dynamic and interactive time-lapse data sequences elucidate the visible and invisible ecological dynamics of a significantly altered yet internationally important river system in central Nebraska.

  5. Calibrating vadose zone models with time-lapse gravity data

    DEFF Research Database (Denmark)

    Christiansen, Lars; Binning, Philip John; Rosbjerg, Dan

    2011-01-01

    The vadose zone plays an important role in the hydrologic cycle. Various geophysical methods can determine soil water content variations in time and space in volumes ranging from a few cubic centimeters to several cubic meters. In contrast to the established methods, time-lapse gravity measurements...... of changes in soil water content do not rely on a petrophysical relationship between the measured quantity and the water content but give a direct measure of the mass change in the soil. Only recently has the vadose zone been systematically incorporated when ground-based gravity data are used to infer...... hydrologic information. In this study, changes in the soil water content gave rise to a measurable signal in a forced infiltration experiment on a 107-m2 grassland area. Time-lapse gravity data were able to constrain the van Genuchten soil hydraulic parameters in both a synthetic example and a field...

  6. Different effectiveness of closed embryo culture system with time-lapse imaging (EmbryoScope(TM)) in comparison to standard manual embryology in good and poor prognosis patients: a prospectively randomized pilot study.

    Science.gov (United States)

    Wu, Yan-Guang; Lazzaroni-Tealdi, Emanuela; Wang, Qi; Zhang, Lin; Barad, David H; Kushnir, Vitaly A; Darmon, Sarah K; Albertini, David F; Gleicher, Norbert

    2016-08-24

    Previously manual human embryology in many in vitro fertilization (IVF) centers is rapidly being replaced by closed embryo incubation systems with time-lapse imaging. Whether such systems perform comparably to manual embryology in different IVF patient populations has, however, never before been investigated. We, therefore, prospectively compared embryo quality following closed system culture with time-lapse photography (EmbryoScope™) and standard embryology. We performed a two-part prospectively randomized study in IVF (clinical trial # NCT92256309). Part A involved 31 infertile poor prognosis patients prospectively randomized to EmbryoScope™ and standard embryology. Part B involved embryos from 17 egg donor-recipient cycles resulting in large egg/embryo numbers, thus permitting prospectively alternative embryo assignments to EmbryoScope™ and standard embryology. We then compared pregnancy rates and embryo quality on day-3 after fertilization and embryologist time utilized per processed embryo. Part A revealed in poor prognosis patients no differences in day-3 embryo scores, implantation and clinical pregnancy rates between EmbryoScope™ and standard embryology. The EmbryoScope™, however, more than doubled embryology staff time (P embryology. Appropriately designed and powered prospectively randomized studies appear urgently needed in well-defined patient populations before the uncontrolled utilization of these instruments further expands. NCT02246309 Registered September 18, 2014.

  7. Ex-situ time-lapse x-ray CT study of 3D micro-structural fatigue damage evolution in uni-directional composites

    DEFF Research Database (Denmark)

    Jespersen, Kristine Munk; Wang, Ying; Zangenberg Hansen, Jens

    2016-01-01

    In this study, the progress of damage under tension-tension fatigue of a uni-directional (UD) glass fibre composite made from a non-crimp fabric is studied using transilluminated white light imaging (TWLI) and X-ray computed tomography (CT). TWLI images are automatically captured throughout...

  8. Calibrating Vadose Zone Models with Time-Lapse Gravity Data

    DEFF Research Database (Denmark)

    Christiansen, Lars; Hansen, A. B.; Looms, M. C.

    2009-01-01

    A change in soil water content is a change in mass stored in the subsurface. Given that the mass change is big enough, the change can be measured with a gravity meter. Attempts have been made with varying success over the last decades to use ground-based time-lapse gravity measurements to infer...... experiment on 10m by 10m grass land. Simulation studies show a potential for vadose zone model calibration using gravity data in conjunction with other geophysical data, e.g. cross-borehole georadar. We present early field data and calibration results from a forced infiltration experiment conducted over 30...

  9. Time-lapse 3D imaging of calcite precipitation in a microporous column

    Science.gov (United States)

    Godinho, Jose R. A.; Withers, Philip J.

    2018-02-01

    Time-lapse X-ray computed tomography is used to image the evolution of calcite precipitation during flow through microporous quartz over the course of 400 h. The growth rate decreases by more than seven times, which is linked to the clogging of flow paths that restricts flow to some regions of the column. Fewer precipitates are observed as a function of column depth, which is found to be related to a differential nucleation density along the sample. A higher nucleation density closer to the inlet implies more crystal volume increase per unit of time without affecting the rate if normalized to the surface area of crystals. Our overall growth rates measured in porous media are orders of magnitude slower than growth rates derived from traditional precipitation experiments on free surfaces. Based on our time-lapse results we hypothesize a scenario where the evolving distribution of precipitates within a pore structure during precipitation progressively modifies the local transport through the pores. Within less permeable regions the saturation index may be lower than along the main flow paths. Therefore, the reactive crystal surfaces within those regions grow at a slower rate than that expected from the bulk fluid composition. Since the amount of reactive surface area within these less permeable regions increases over time, the overall growth rate decreases without a necessary significant change of the bulk fluid composition along more permeable flow paths. In conclusion, the overall growth rates in an evolving porous media expected from bulk fluid compositions alone can be overestimated due to the development of stagnant sub-regions where the reactive surface area is bath by a solution with lower saturation index. In this context we highlight the value of time-lapse 3D studies for understanding the dynamics of mineral precipitation in porous media.

  10. A randomized clinical trial comparing embryo culture in a conventional incubator with a time-lapse incubator

    DEFF Research Database (Denmark)

    Kirkegaard, Kirstine; Hindkjaer, Johnny Juhl; Grøndahl, Marie Louise

    2012-01-01

    Time-lapse monitoring allows for a flexible embryo evaluation and potentially provides new dynamic markers of embryo competence. Before introducing time-lapse monitoring in a clinical setting, the safety of the instrument must be properly documented. Accordingly, the aim of this study was to eval...

  11. Seismic time-lapse monitoring of potential gas hydrate dissociation around boreholes : could it be feasible? A conceptual 2D study linking geomechanical and seismic FD models

    Energy Technology Data Exchange (ETDEWEB)

    Pecher, I.; Yang, J.; Anderson, R.; Tohidi, B.; MacBeth, C. [Heriot-Watt Univ., Edinburgh (United Kingdom). Inst. of Petroleum Engineering; Freij-Ayoub, R.; Clennell, B. [CSIRO Petroleum, Bentley, WA (Australia)

    2008-07-01

    Dissociation of gas hydrate to water and potentially overpressured gas around boreholes may pose a hazard for deep-water hydrocarbon production. Strategies to mitigate this risk include monitoring for early detection of dissociation. Seismic methods are especially promising, primarily because of a high sensitivity of P-wave velocity to gas in the pore space of unconsolidated sediments. This paper presented a study that applied commonly used rock physics modeling to predict the seismic response to gas hydrate dissociation with a focus on P-impedance and performed sensitivity tests. The geomechanical model was translated into seismic models. In order to determine which parameters needed to be particularly well calibrated in experimental and modeling studies, the sensitivity of seismic properties to a variation of input parameters was estimated. The seismic response was predicted from dissociating gas hydrates using two-dimensional finite-difference wave-propagation modeling to demonstrate that despite the small predicted lateral extent of hydrate dissociation, its pronounced effect on seismic properties should allow detection with a seismic source on a drilling platform and receivers on the seafloor. The paper described the methods, models, and results of the study. It was concluded that the key factors for predicting the seismic response of sediments to hydrate dissociation were the mode of gas hydrate distribution, gas distribution in the sediments, gas saturation, and pore pressure. 33 refs., 3 tabs., 8 figs.

  12. Stretching silk-elastin-like peptide polymers induces nucleation of amyloid nanofibers: Mechanistic study using time-lapse lateral force microscopy

    Science.gov (United States)

    Varongchayakul, Nitinun; Quabili, Trina; Johnson, Sara; Seog, Joonil

    2013-03-01

    We studied the nucleation mechanism of silk-elastin-like peptide (SELP) nanofibers using lateral force microscopy. When a single line was repeatedly scanned on SELP coated mica surface, a sudden height increase was observed, indicating that the nucleus of amyloid fiber was formed during lateral scanning. The detailed analysis of frictional force profiles revealed that increase of frictional force was followed by a nucleus formation. The profile of increased frictional force was well fitted with exponential function, suggesting that AFM tip stretches multiple SELP molecules to the scanning direction. The probability of nucleus formation was highly dependent on the maximum level of increased frictional force, implying that the highly stretched SELPs are more likely to form nucleus for nanofiber growth. The authors gratefully acknowledge the support of NSF Ca-reer Award #1056552.

  13. Low-Cost Motility Tracking System (LOCOMOTIS) for Time-Lapse Microscopy Applications and Cell Visualisation

    Science.gov (United States)

    Lynch, Adam E.; Triajianto, Junian; Routledge, Edwin

    2014-01-01

    Direct visualisation of cells for the purpose of studying their motility has typically required expensive microscopy equipment. However, recent advances in digital sensors mean that it is now possible to image cells for a fraction of the price of a standard microscope. Along with low-cost imaging there has also been a large increase in the availability of high quality, open-source analysis programs. In this study we describe the development and performance of an expandable cell motility system employing inexpensive, commercially available digital USB microscopes to image various cell types using time-lapse and perform tracking assays in proof-of-concept experiments. With this system we were able to measure and record three separate assays simultaneously on one personal computer using identical microscopes, and obtained tracking results comparable in quality to those from other studies that used standard, more expensive, equipment. The microscopes used in our system were capable of a maximum magnification of 413.6×. Although resolution was lower than that of a standard inverted microscope we found this difference to be indistinguishable at the magnification chosen for cell tracking experiments (206.8×). In preliminary cell culture experiments using our system, velocities (mean µm/min ± SE) of 0.81±0.01 (Biomphalaria glabrata hemocytes on uncoated plates), 1.17±0.004 (MDA-MB-231 breast cancer cells), 1.24±0.006 (SC5 mouse Sertoli cells) and 2.21±0.01 (B. glabrata hemocytes on Poly-L-Lysine coated plates), were measured and are consistent with previous reports. We believe that this system, coupled with open-source analysis software, demonstrates that higher throughput time-lapse imaging of cells for the purpose of studying motility can be an affordable option for all researchers. PMID:25121722

  14. Inter and intra-observer variability of time-lapse annotations

    DEFF Research Database (Denmark)

    Sundvall Germeys, Linda Karin M; Ingerslev, Hans Jakob; Knudsen, Ulla Breth

    Study question: How consistent is the time-lapse annotation of dynamic and static morphologic parameters of embryo development, within and between observers? Summary answer: The assessment of dynamic parameters is characterized by almost perfect agreement within and between observers. What is kno...

  15. Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy

    DEFF Research Database (Denmark)

    Fredborg, M; Rosenvinge, F S; Spillum, E

    2015-01-01

    Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the oCelloScope s...

  16. Time-lapse Geophysical Data from a Stressed Environment

    Science.gov (United States)

    Milkereit, B.; Tibbo, M.; Kassam, A.; Carey, A.; Schmitt, D. R.; Mohammed, T. E.; Malehmir, R.; Guo, K.

    2015-12-01

    A complication in geophysical monitoring of deep mines is the high-stress dependency of the physical properties of hard rocks. This project is part of a comprehensive, exploration geophysical study in a deep, highly stressed mine located in Sudbury, Ontario, Canada. Data from in situ monitoring of the mining induced seismicity, conductivity, and stress dependent physical properties have been obtained from two boreholes located in this mine. These borehole are approximately 400 m long with NQ diameters and depths of about 1300 - 1600 m and 1700 - 2000 m. Two borehole logging surveys were performed on both boreholes, October 2013 and July 2015, in order to perform a time-lapse analysis of the geophysical changes in the mine. These multi-parameter surveys include caliper, full waveform sonic, televiewer, chargeability (IP), and resistivity. Multi-electrode array DC/IP borehole and borehole-to-borehole surveys were also conducted in 2014, showing an increase in resistivity only in the 1300 m borehole near the active mining area, possibly due to stress induced closing of fractures. There is only exploration activity near the 1700 m borehole over this time period, and it therefore shows no changes in resistivity. Laboratory experiments have been performed on borehole core samples from each borehole. These experiments have measured the geophysical properties including elastic modulus, bulk modulus, P- and S-wave velocities, and density.

  17. Terahertz time-lapse imaging of hydration in physiological tissues

    Science.gov (United States)

    Bennett, David B.; Taylor, Zachary D.; Bajwa, Neha; Tewari, Priyamvada; Maccabi, Ashkan; Sung, Shijun; Singh, Rahul S.; Culjat, Martin O.; Grundfest, Warren S.; Brown, Elliott R.

    2011-02-01

    This study describes terahertz (THz) imaging of hydration changes in physiological tissues with high water concentration sensitivity. A fast-scanning, pulsed THz imaging system (centered at 525 GHz; 125 GHz bandwidth) was utilized to acquire a 35 mm x 35 mm field-of-view with 0.5 mm x 0.5 mm pixels in less than two minutes. THz time-lapsed images were taken on three sample systems: (1) a simple binary system of water evaporating from a polypropylene towel, (2) the accumulation of fluid at the site of a sulfuric acid burn on ex vivo porcine skin, and (3) the evaporative dehydration of an ex vivo porcine cornea. The diffusion-regulating behavior of corneal tissue is elucidated, and the correlation of THz reflectivity with tissue hydration is measured using THz spectroscopy on four ex vivo corneas. We conclude that THz imaging can discern small differences in the distribution of water in physiological tissues and is a good candidate for burn and corneal imaging.

  18. Using Digital Time-Lapse Videos to Teach Geomorphic Processes to Undergraduates

    Science.gov (United States)

    Clark, D. H.; Linneman, S. R.; Fuller, J.

    2004-12-01

    We demonstrate the use of relatively low-cost, computer-based digital imagery to create time-lapse videos of two distinct geomorphic processes in order to help students grasp the significance of the rates, styles, and temporal dependence of geologic phenomena. Student interviews indicate that such videos help them to understand the relationship between processes and landform development. Time-lapse videos have been used extensively in some sciences (e.g., biology - http://sbcf.iu.edu/goodpract/hangarter.html, meteorology - http://www.apple.com/education/hed/aua0101s/meteor/, chemistry - http://www.chem.yorku.ca/profs/hempsted/chemed/home.html) to demonstrate gradual processes that are difficult for many students to visualize. Most geologic processes are slower still, and are consequently even more difficult for students to grasp, yet time-lapse videos are rarely used in earth science classrooms. The advent of inexpensive web-cams and computers provides a new means to explore the temporal dimension of earth surface processes. To test the use of time-lapse videos in geoscience education, we are developing time-lapse movies that record the evolution of two landforms: a stream-table delta and a large, natural, active landslide. The former involves well-known processes in a controlled, repeatable laboratory experiment, whereas the latter tracks the developing dynamics of an otherwise poorly understood slope failure. The stream-table delta is small and grows in ca. 2 days; we capture a frame on an overhead web-cam every 3 minutes. Before seeing the video, students are asked to hypothesize how the delta will grow through time. The final time-lapse video, ca. 20-80 MB, elegantly shows channel migration, progradation rates, and formation of major geomorphic elements (topset, foreset, bottomset beds). The web-cam can also be "zoomed-in" to show smaller-scale processes, such as bedload transfer, and foreset slumping. Post-lab tests and interviews with students indicate that

  19. An instrumented sample holder for time-lapse microtomography measurements of snow under advective airflow

    Directory of Open Access Journals (Sweden)

    P. P. Ebner

    2014-09-01

    Full Text Available An instrumented sample holder was developed for time-lapse microtomography of snow samples to enable in situ nondestructive spatial and temporal measurements under controlled advective airflows, temperature gradients, and air humidities. The design was aided by computational fluid dynamics simulations to evaluate the airflow uniformity across the snow sample. Morphological and mass transport properties were evaluated during a 4-day test run. This instrument allows the experimental characterization of metamorphism of snow undergoing structural changes with time.

  20. Time-lapse controlled-source electromagnetics using interferometry

    NARCIS (Netherlands)

    Hunziker, J.W.; Slob, E.C.; Wapenaar, C.P.A.

    In time-lapse controlled-source electromagnetics, it is crucial that the source and the receivers are positioned at exactly the same location at all times of measurement. We use interferometry by multidimensional deconvolution (MDD) to overcome problems in repeatability of the source location.

  1. Probabilistic 3-D time-lapse inversion of magnetotelluric data: Application to an enhanced geothermal system

    Science.gov (United States)

    Rosas-Carbajal, Marina; Linde, Nicolas; Peacock, Jared R.; Zyserman, F. I.; Kalscheuer, Thomas; Thiel, Stephan

    2015-01-01

    Surface-based monitoring of mass transfer caused by injections and extractions in deep boreholes is crucial to maximize oil, gas and geothermal production. Inductive electromagnetic methods, such as magnetotellurics, are appealing for these applications due to their large penetration depths and sensitivity to changes in fluid conductivity and fracture connectivity. In this work, we propose a 3-D Markov chain Monte Carlo inversion of time-lapse magnetotelluric data to image mass transfer following a saline fluid injection. The inversion estimates the posterior probability density function of the resulting plume, and thereby quantifies model uncertainty. To decrease computation times, we base the parametrization on a reduced Legendre moment decomposition of the plume. A synthetic test shows that our methodology is effective when the electrical resistivity structure prior to the injection is well known. The centre of mass and spread of the plume are well retrieved.We then apply our inversion strategy to an injection experiment in an enhanced geothermal system at Paralana, South Australia, and compare it to a 3-D deterministic time-lapse inversion. The latter retrieves resistivity changes that are more shallow than the actual injection interval, whereas the probabilistic inversion retrieves plumes that are located at the correct depths and oriented in a preferential north-south direction. To explain the time-lapse data, the inversion requires unrealistically large resistivity changes with respect to the base model. We suggest that this is partly explained by unaccounted subsurface heterogeneities in the base model from which time-lapse changes are inferred.

  2. Time-lapse stereo-photogrammetric monitoring of volcanic slopes

    OpenAIRE

    Dewez, Thomas; Moser, Simon

    2013-01-01

    Piton de la Fournaise volcano (La Reunion Island) due to its crater collapse of April 2007 which created 200m to 300-m-high sub-vertical cliffs in a matter of minutes offers a rare opportunity to observe the morphological fingerprint of numerous rock avalanches. In the framework of ANR-Undervolc, a research project funded by the French Research Council to investigate geophysical determinants of volcano construction and destruction, a pair of time lapse photogrammetric packages was deployed al...

  3. Calixarenes and cations: a time-lapse photography of the big-bang.

    Science.gov (United States)

    Casnati, Alessandro

    2013-08-07

    The outstanding cation complexation properties emerging from the pioneering studies on calixarene ligands during a five-year period in the early 1980s triggered a big-bang burst of publications on such macrocycles that is still lasting at a distance of more than 30 years. A time-lapse photography of this timeframe is proposed which allows the readers to pinpoint the contributions of the different research groups.

  4. Imaging Hydrological Processes in Headwater Riparian Seeps with Time-Lapse Electrical Resistivity.

    Science.gov (United States)

    Williams, Mark R; Buda, Anthony R; Singha, Kamini; Folmar, Gordon J; Elliott, Herschel A; Schmidt, John P

    2017-01-01

    Delineating hydrologic and pedogenic factors influencing groundwater flow in riparian zones is central in understanding pathways of water and nutrient transport. In this study, we combined two-dimensional time-lapse electrical resistivity imaging (ERI) (depth of investigation approximately 2 m) with hydrometric monitoring to examine hydrological processes in the riparian area of FD-36, a small (0.4 km(2) ) agricultural headwater basin in the Valley and Ridge region of east-central Pennsylvania. We selected two contrasting study sites, including a seep with groundwater discharge and an adjacent area lacking such seepage. Both sites were underlain by a fragipan at 0.6 m. We then monitored changes in electrical resistivity, shallow groundwater, and nitrate-N concentrations as a series of storms transitioned the landscape from dry to wet conditions. Time-lapse ERI revealed different resistivity patterns between seep and non-seep areas during the study period. Notably, the seep displayed strong resistivity reductions (∼60%) along a vertically aligned region of the soil profile, which coincided with strong upward hydraulic gradients recorded in a grid of nested piezometers (0.2- and 0.6-m depth). These patterns suggested a hydraulic connection between the seep and the nitrate-rich shallow groundwater system below the fragipan, which enabled groundwater and associated nitrate-N to discharge through the fragipan to the surface. In contrast, time-lapse ERI indicated no such connections in the non-seep area, with infiltrated rainwater presumably perched above the fragipan. Results highlight the value of pairing time-lapse ERI with hydrometric and water quality monitoring to illuminate possible groundwater and nutrient flow pathways to seeps in headwater riparian areas. © 2016, National Ground Water Association.

  5. Time-lapse electrical surveys to locate infiltration zones in weathered hard rock tropical areas

    Science.gov (United States)

    Wubda, M.; Descloitres, M.; Yalo, N.; Ribolzi, O.; Vouillamoz, J. M.; Boukari, M.; Hector, B.; Séguis, L.

    2017-07-01

    In West Africa, infiltration and groundwater recharge processes in hard rock areas are depending on climatic, surface and subsurface conditions, and are poorly documented. Part of the reason is that identification, location and monitoring of these processes is still a challenge. Here, we explore the potential for time-lapse electrical surveys to bring additional information on these processes for two different climate situations: a semi-arid Sahelian site (north of Burkina and a humid Sudanian site (north of Benin), respectively focusing on indirect (localized) and direct (diffuse) recharge processes. The methodology is based on surveys in dry season and rainy season on typical pond or gully using Electrical Resistivity Tomography (ERT) and frequency electromagnetic (FEM) apparent conductivity mapping. The results show that in the Sahelian zone an indirect recharge occurs as expected, but infiltration doesn't takes place at the center of the pond to the aquifer, but occurs laterally in the banks. In Sudanian zone, the ERT survey shows a direct recharge process as expected, but also a complicated behavior of groundwater dilution, as well as the role of hardpans for fast infiltration. These processes are ascertained by groundwater monitoring in adjacent observing wells. At last, FEM time lapse mapping is found to be difficult to quantitatively interpreted due to the non-uniqueness of the model, clearly evidenced comparing FEM result to auger holes monitoring. Finally, we found that time-lapse ERT can be an efficient way to track infiltration processes across ponds and gullies in both climatic conditions, the Sahelian setting providing results easier to interpret, due to significant resistivity contrasts between dry and rain seasons. Both methods can be used for efficient implementation of punctual sensors for complementary studies. However, FEM time-lapse mapping remains difficult to practice without external information that renders this method less attractive for

  6. Live time-lapse dataset of in vitro wound healing experiments.

    Science.gov (United States)

    Zaritsky, Assaf; Natan, Sari; Kaplan, Doron; Ben-Jacob, Eshel; Tsarfaty, Ilan

    2015-01-01

    The wound healing assay is the common method to study collective cell migration in vitro. Computational analyses of live imaging exploit the rich temporal information and significantly improve understanding of complex phenomena that emerge during this mode of collective motility. Publicly available experimental data can allow application of new analyses to promote new discoveries, and assess algorithms' capabilities to distinguish between different experimental conditions. A freely-available dataset of 31 time-lapse in vitro wound healing experiments of two cell lines is presented. It consists of six different experimental conditions with 4-6 replicates each, gathered to study the effects of a growth factor on collective cell migration. The raw data is available at 'The Cell: an Image Library' repository. This Data Note provides detailed description of the data, intermediately processed data, scripts and experimental validations that have not been reported before and are currently available at GigaDB. This is the first publicly available repository of live collective cell migration data that includes independent replicates for each set of conditions. This dataset has the potential for extensive reuse. Some aspects in the data remain unexplored and can be exploited extensively to reveal new insight. The dataset could also be used to assess the performance of available and new quantification methods by demonstrating phenotypic discriminatory capabilities between the different experimental conditions. It may allow faster and more elaborated, reproducible and effective analyses, which will likely lead to new biological and biophysical discoveries.

  7. Effect of oxygen concentration on human embryo development evaluated by time-lapse monitoring

    DEFF Research Database (Denmark)

    Ingerslev, Hans Jakob; Hindkjær, Johnny Juhl; Kirkegaard, Kirstine

    2012-01-01

    was to evaluate the influence of oxygen tension on human pre-implantation development using time-lapse monitoring. Materials and methods: Human embryos were cultured to the blastocyst stage in a time-lapse incubator (EmbryoScope™) in 20% O2 (group 1), 20% O2 for 24 hours followed by culture in 5% O2 (group 2......) or in 5% O2 (group 3). Eligible were patients with age 8 oocytes retrieved. Group 1 consisted of 120 IVF/ICSI embryos from 26 patients recruited to a study conducted to evaluate the safety of the time-lapse incubator by randomising 1:1 embryos from a patient to culture......-points for each cell division and blastocyst stages were registered until 120 hours after oocyte retrieval. Only 2PN embryos completing the first cleavage were evaluated. The groups were compared using one-way ANOVA or Kruskall-Wallis test. Estimates are reported as medians with 95% confidence intervals. Time...

  8. Interferometric full-waveform inversion of time-lapse data

    KAUST Repository

    Sinha, Mrinal

    2017-08-17

    One of the key challenges associated with time-lapse surveys is ensuring the repeatability between the baseline and monitor surveys. Non-repeatability between the surveys is caused by varying environmental conditions over the course of different surveys. To overcome this challenge, we propose the use of interferometric full waveform inversion (IFWI) for inverting the velocity model from data recorded by baseline and monitor surveys. A known reflector is used as the reference reflector for IFWI, and the data are naturally redatumed to this reference reflector using natural reflections as the redatuming operator. This natural redatuming mitigates the artifacts introduced by the repeatability errors that originate above the reference reflector.

  9. Estimating the hydrogeological parameters of an unconfined aquifer with the time-lapse resistivity-imaging method during pumping tests: Case studies at the Pengtsuo and Dajou sites, Taiwan

    Science.gov (United States)

    Chang, Ping-Yu; Chang, Lian-Cheng; Hsu, Shao-Yiu; Tsai, Jui-Pin; Chen, Wen-Fu

    2017-09-01

    We conducted time-lapse resistivity imaging during pumping tests at the Pengtsuo and Dajou test sites in Taiwan in order to examine the feasibility of estimating hydrogeological parameters with resistivity variations. Core logs reveal that the subsurface consists mainly of at least 100-m-thick gravel and sand at the two test sites. The resistivity differences between the pumping stages and pre-pumping background are well correlated to water level changes that are due to the dewatering of pumping activity. Therefore, it is possible to use the geometry of resistivity anomalies to estimate the hydraulic conductivity of the unconfined aquifer using the distance-drawdown equation for pumping tests in unsaturated aquifers. For each site, we used the contours of resistivity variations and recorded water levels in the pumping well to depict the bottom of the drawdown cone. The estimated hydraulic conductivity and specific yield, respectively, are 1.33 × 10- 4 m/s and 0.12 at the Pengtsuo site, and are 2.50 × 10- 4 m/s and 0.22 at the Dajou site. These values are consistent with the parameters that engineers from Taiwan Sugar Company calculated previously regarding groundwater-level variations in multiple wells (9.65 × 10- 5 m/s and 0.13 at Pengtsuo, and 1.00 × 10- 3 m/s and 0.19 at Dajou). This consistency suggests that resistivity imaging can perhaps serve as an alternative way to yield information about hydrogeological parameters.

  10. Inter-laboratory agreement on embryo classification and clinical decision: Conventional morphological assessment vs. time lapse.

    Directory of Open Access Journals (Sweden)

    Luis Martínez-Granados

    Full Text Available The aim of this study is to determine inter-laboratory variability on embryo assessment using time-lapse platform and conventional morphological assessment. This study compares the data obtained from a pilot study of external quality control (EQC of time lapse, performed in 2014, with the classical EQC of the Spanish Society for the Study of Reproductive Biology (ASEBIR performed in 2013 and 2014. In total, 24 laboratories (8 using EmbryoScope™, 15 using Primo Vision™ and one with both platforms took part in the pilot study. The clinics that used EmbryoScope™ analysed 31 embryos and those using Primo Vision™ analysed 35. The classical EQC was implemented by 39 clinics, based on an analysis of 25 embryos per year. Both groups were required to evaluate various qualitative morphological variables (cell fragmentation, the presence of vacuoles, blastomere asymmetry and multinucleation, to classify the embryos in accordance with ASEBIR criteria and to stipulate the clinical decision taken. In the EQC time-lapse pilot study, the groups were asked to determine, as well as the above characteristics, the embryo development times, the number, opposition and size of pronuclei, the direct division of 1 into 3 cells and/or of 3 into 5 cells and false divisions. The degree of agreement was determined by calculating the intra-class correlation coefficients and the coefficient of variation for the quantitative variables and the Gwet index for the qualitative variables. For both EmbryoScope™ and Primo Vision™, two periods of greater inter-laboratory variability were observed in the times of embryo development events. One peak of variability was recorded among the laboratories addressing the first embryo events (extrusion of the second polar body and the appearance of pronuclei; the second peak took place between the times corresponding to the 8-cell and morula stages. In most of the qualitative variables analysed regarding embryo development, there

  11. Entropy-Bayesian Inversion of Time-Lapse Tomographic GPR data for Monitoring Dielectric Permittivity and Soil Moisture Variations

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Z; Terry, N; Hubbard, S S; Csatho, B

    2013-02-12

    In this study, we evaluate the possibility of monitoring soil moisture variation using tomographic ground penetrating radar travel time data through Bayesian inversion, which is integrated with entropy memory function and pilot point concepts, as well as efficient sampling approaches. It is critical to accurately estimate soil moisture content and variations in vadose zone studies. Many studies have illustrated the promise and value of GPR tomographic data for estimating soil moisture and associated changes, however, challenges still exist in the inversion of GPR tomographic data in a manner that quantifies input and predictive uncertainty, incorporates multiple data types, handles non-uniqueness and nonlinearity, and honors time-lapse tomograms collected in a series. To address these challenges, we develop a minimum relative entropy (MRE)-Bayesian based inverse modeling framework that non-subjectively defines prior probabilities, incorporates information from multiple sources, and quantifies uncertainty. The framework enables us to estimate dielectric permittivity at pilot point locations distributed within the tomogram, as well as the spatial correlation range. In the inversion framework, MRE is first used to derive prior probability distribution functions (pdfs) of dielectric permittivity based on prior information obtained from a straight-ray GPR inversion. The probability distributions are then sampled using a Quasi-Monte Carlo (QMC) approach, and the sample sets provide inputs to a sequential Gaussian simulation (SGSim) algorithm that constructs a highly resolved permittivity/velocity field for evaluation with a curved-ray GPR forward model. The likelihood functions are computed as a function of misfits, and posterior pdfs are constructed using a Gaussian kernel. Inversion of subsequent time-lapse datasets combines the Bayesian estimates from the previous inversion (as a memory function) with new data. The memory function and pilot point design takes

  12. Entropy-Bayesian Inversion of Time-Lapse Tomographic GPR data for Monitoring Dielectric Permittivity and Soil Moisture Variations

    Energy Technology Data Exchange (ETDEWEB)

    Hou, Zhangshuan; Terry, Neil C.; Hubbard, Susan S.

    2013-02-22

    In this study, we evaluate the possibility of monitoring soil moisture variation using tomographic ground penetrating radar travel time data through Bayesian inversion, which is integrated with entropy memory function and pilot point concepts, as well as efficient sampling approaches. It is critical to accurately estimate soil moisture content and variations in vadose zone studies. Many studies have illustrated the promise and value of GPR tomographic data for estimating soil moisture and associated changes, however, challenges still exist in the inversion of GPR tomographic data in a manner that quantifies input and predictive uncertainty, incorporates multiple data types, handles non-uniqueness and nonlinearity, and honors time-lapse tomograms collected in a series. To address these challenges, we develop a minimum relative entropy (MRE)-Bayesian based inverse modeling framework that non-subjectively defines prior probabilities, incorporates information from multiple sources, and quantifies uncertainty. The framework enables us to estimate dielectric permittivity at pilot point locations distributed within the tomogram, as well as the spatial correlation range. In the inversion framework, MRE is first used to derive prior probability density functions (pdfs) of dielectric permittivity based on prior information obtained from a straight-ray GPR inversion. The probability distributions are then sampled using a Quasi-Monte Carlo (QMC) approach, and the sample sets provide inputs to a sequential Gaussian simulation (SGSIM) algorithm that constructs a highly resolved permittivity/velocity field for evaluation with a curved-ray GPR forward model. The likelihood functions are computed as a function of misfits, and posterior pdfs are constructed using a Gaussian kernel. Inversion of subsequent time-lapse datasets combines the Bayesian estimates from the previous inversion (as a memory function) with new data. The memory function and pilot point design takes advantage of

  13. Fast and robust optical flow for time-lapse microscopy using super-voxels.

    Science.gov (United States)

    Amat, Fernando; Myers, Eugene W; Keller, Philipp J

    2013-02-01

    Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 × faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions. Source code freely available in the Software section at http://janelia.org/lab/keller-lab.

  14. A Prototype System for Time-Lapse Electrical Resistivity Tomographies

    Directory of Open Access Journals (Sweden)

    Raffaele Luongo

    2012-01-01

    Full Text Available A prototype system for time-lapse acquisition of 2D electrical resistivity tomography (ERT and time domain reflectometry (TDR measurements was installed in a test site affected by a landslide in Basilicata region (southern Italy. The aim of the system is to monitor in real-time the rainwater infiltration into the soil and obtain information about the variation of the water content in the first layers of the subsoil and the possible influence of this variation on landslide activity. A rain gauge placed in the test site gives information on the rainfall intensity and frequency and suggests the acquisition time interval. The installed system and the preliminary results are presented in this paper.

  15. OPTICAL FLOW APPLIED TO TIME-LAPSE IMAGE SERIES TO ESTIMATE GLACIER MOTION IN THE SOUTHERN PATAGONIA ICE FIELD

    Directory of Open Access Journals (Sweden)

    E. Lannutti

    2016-06-01

    Full Text Available In this work, we assessed the feasibility of using optical flow to obtain the motion estimation of a glacier. In general, former investigations used to detect glacier changes involve solutions that require repeated observations which are many times based on extensive field work. Taking into account glaciers are usually located in geographically complex and hard to access areas, deploying time-lapse imaging sensors, optical flow may provide an efficient solution at good spatial and temporal resolution to describe mass motion. Several studies in computer vision and image processing community have used this method to detect large displacements. Therefore, we carried out a test of the proposed Large Displacement Optical Flow method at the Viedma Glacier, located at South Patagonia Icefield, Argentina. We collected monoscopic terrestrial time-lapse imagery, acquired by a calibrated camera at every 24 hour from April 2014 until April 2015. A filter based on temporal correlation and RGB color discretization between the images was applied to minimize errors related to changes in lighting, shadows, clouds and snow. This selection allowed discarding images that do not follow a sequence of similarity. Our results show a flow field in the direction of the glacier movement with acceleration in the terminus. We analyzed the errors between image pairs, and the matching generally appears to be adequate, although some areas show random gross errors related to the presence of changes in lighting. The proposed technique allowed the determination of glacier motion during one year, providing accurate and reliable motion data for subsequent analysis.

  16. Rock Slope Monitoring from 4D Time-Lapse Structure from Motion Analysis

    Science.gov (United States)

    Kromer, Ryan; Abellan, Antonio; Chyz, Alex; Hutchinson, Jean

    2017-04-01

    Structure from Motion (SfM) photogrammetry has become an important tool for studying earth surface processes because of its flexibility, ease of use, low cost and its capability of producing high quality 3-D surface models. A major benefit of SfM is that model accuracy is fit for purpose and surveys can be designed to meet a large range of spatial and temporal scales. In the Earth sciences, research in time-lapse SfM photogrammetry or videogrammetry is an area that is difficult to undertake due to complexities in acquiring, processing and managing large 4D datasets and represents an area with significant advancement potential (Eltner et al. 2016). In this study, we investigate the potential of 4D time-lapse SfM to monitor unstable rock slopes. We tested an array of statically mounted cameras collecting time-lapse photos of a limestone rock slope located along a highway in Canada. Our setup consisted of 8 DSLR cameras with 50 mm prime lenses spaced 2-3 m apart at a distance of 10 m from the slope. The portion of the rock slope monitored was 20 m wide and 6 m high. We collected data in four phases, each having 50 photographs taken simultaneously by each camera. The first phase of photographs was taken of the stable slope. In each successive phase, we gradually moved small, discrete blocks within the rock slope by 5-15 mm, simulating pre-failure deformation of rockfall. During the last phase we also removed discrete rock blocks, simulating rockfall. We used Agisoft Photoscan's 4D processing functionality and timeline tools to create 3D point clouds from the time-lapse photographs. These tools have the benefit of attaining better accuracy photo alignments as a greater number of photos are used. For change detection, we used the 4D filtering and calibration technique proposed by Kromer et al. (2015), which takes advantage of high degrees of spatial and temporal point redundancy to decrease measurement uncertainty. Preliminary results show that it is possible to attain

  17. [Assessing the effect of compulsory ambulatory treatment orders on the time lapse out of hospitalization for patients suffering from schizophrenia].

    Science.gov (United States)

    Spinzy, Yaniv; Israel, Krieger

    2012-03-01

    Schizophrenia is the most severe mental disorder, characterized in many cases by poor insight and low adherence to drug treatment. In Israel, as in many countries, Laws have been Legislated to allow the issuance of compuLsory ambulatory treatment orders (CATO) to patients whose medical condition poses a risk to themselves or the environment. In the Limited existing literature, no conclusive evidence has been found on the efficacy of CATO on patients' outcome. We examined the medical files of all the patients in "Shalvata" Mental Health Center, who were treated under the compulsory ambulatory treatment order during the years 2003-2010. We examined the effect of the CATO on the time Lapse out of hospitalization during a 3 year period before and after issuing the order. The study group was composed of 77 patients and each patient served as his own control. We conducted paired samples t-test and found that the average time lapse out of hospitalization after issuing CATO was higher (M = 426 days, SD = 3921 compared to the average time lapse out of hospitalization before issuing CATO (M = 345 days, SD = 366, N = 77), but the difference was not statistically significant (t = -1.34, p = 0.2). Our research shows that there was no significant beneficial effect of the CATO in the group of patients that we examined. We found that the average time lapse out of hospitalization did not increase significantly. Our study raises questions regarding the importance of the compulsory ambulatory treatment and its implementation measures.

  18. Estimation and discrimination of stochastic biochemical circuits from time-lapse microscopy data.

    Directory of Open Access Journals (Sweden)

    David Thorsley

    Full Text Available The ability of systems and synthetic biologists to observe the dynamics of cellular behavior is hampered by the limitations of the sensors, such as fluorescent proteins, available for use in time-lapse microscopy. In this paper, we propose a generalized solution to the problem of estimating the state of a stochastic chemical reaction network from limited sensor information generated by microscopy. We mathematically derive an observer structure for cells growing under time-lapse microscopy and incorporates the effects of cell division in order to estimate the dynamically-changing state of each cell in the colony. Furthermore, the observer can be used to discrimate between models by treating model indices as states whose values do not change with time. We derive necessary and sufficient conditions that specify when stochastic chemical reaction network models, interpreted as continuous-time Markov chains, can be distinguished from each other under both continual and periodic observation. We validate the performance of the observer on the Thattai-van Oudenaarden model of transcription and translation. The observer structure is most effective when the system model is well-parameterized, suggesting potential applications in synthetic biology where standardized biological parts are available. However, further research is necessary to develop computationally tractable approximations to the exact generalized solution presented here.

  19. Calibrating vadose zone models with time-lapse gravity data: a forced infiltration experiment

    DEFF Research Database (Denmark)

    Christiansen, Lars; Hansen, Allan Bo; Zibar, Majken Caroline Looms

    A change in soil water content is a change in mass stored in the subsurface, and when large enough, can be measured with a gravity meter. Over the last few decades there has been increased use of ground-based time-lapse gravity measurements to infer hydrogeological parameters. These studies have...... in the unsaturated zone. These results are confirmed by field measurements of gravity and georadar data at a forced infiltration experiment conducted over 14 days on a grassland area of 10 m by 10 m. An unsaturated zone infiltration model can be calibrated using the gravity data with good agreement to the field data...

  20. Live-streaming: Time-lapse video evidence of novel streamer formation mechanism and varying viscosity.

    Science.gov (United States)

    Parvinzadeh Gashti, Mazeyar; Bellavance, Julien; Kroukamp, Otini; Wolfaardt, Gideon; Taghavi, Seyed Mohammad; Greener, Jesse

    2015-07-01

    Time-lapse videos of growing biofilms were analyzed using a background subtraction method, which removed camouflaging effects from the heterogeneous field of view to reveal evidence of streamer formation from optically dense biofilm segments. In addition, quantitative measurements of biofilm velocity and optical density, combined with mathematical modeling, demonstrated that streamer formation occurred from mature, high-viscosity biofilms. We propose a streamer formation mechanism by sudden partial detachment, as opposed to continuous elongation as observed in other microfluidic studies. Additionally, streamer formation occurred in straight microchannels, as opposed to serpentine or pseudo-porous channels, as previously reported.

  1. A state-space Bayesian framework for estimating biogeochemical transformations using time-lapse geophysical data

    Energy Technology Data Exchange (ETDEWEB)

    Chen, J.; Hubbard, S.; Williams, K.; Pride, S.; Li, L.; Steefel, C.; Slater, L.

    2009-04-15

    We develop a state-space Bayesian framework to combine time-lapse geophysical data with other types of information for quantitative estimation of biogeochemical parameters during bioremediation. We consider characteristics of end-products of biogeochemical transformations as state vectors, which evolve under constraints of local environments through evolution equations, and consider time-lapse geophysical data as available observations, which could be linked to the state vectors through petrophysical models. We estimate the state vectors and their associated unknown parameters over time using Markov chain Monte Carlo sampling methods. To demonstrate the use of the state-space approach, we apply it to complex resistivity data collected during laboratory column biostimulation experiments that were poised to precipitate iron and zinc sulfides during sulfate reduction. We develop a petrophysical model based on sphere-shaped cells to link the sulfide precipitate properties to the time-lapse geophysical attributes and estimate volume fraction of the sulfide precipitates, fraction of the dispersed, sulfide-encrusted cells, mean radius of the aggregated clusters, and permeability over the course of the experiments. Results of the case study suggest that the developed state-space approach permits the use of geophysical datasets for providing quantitative estimates of end-product characteristics and hydrological feedbacks associated with biogeochemical transformations. Although tested here on laboratory column experiment datasets, the developed framework provides the foundation needed for quantitative field-scale estimation of biogeochemical parameters over space and time using direct, but often sparse wellbore data with indirect, but more spatially extensive geophysical datasets.

  2. Feeling the Heat: Supraglacial Lake Changes as Observed via Time-Lapse Photography, Ngozumpa Glacier, Nepal

    Science.gov (United States)

    Horodyskyj, U. N.; Breashears, D.; Bilham, R. G.

    2011-12-01

    Supraglacial lakes are suspected of playing a catalytic role in the current rapid melting rate of temperate glaciers. Our field work on the Ngozumpa glacier, in the Nepalese Himalaya, was targeted to quantify the physics of this process. A field season was conducted in June 2011 to investigate the formation and evolution of these lakes via time-lapse photography. One supraglacial lake in particular was chosen for more intensive study. A pressure transducer recorded lake level changes throughout the field season; probes measured surface water temperature, water temperature at depth, and air temperature; and solar irradiation (incoming and outgoing) was measured with a pair of silicon pyranometers. Depth surveys were conducted, water samples were collected, and melt rates on north and south facing ice walls also were measured with a laser rangefinder during hours of peak insolation. During the course of the field season, 28 cm of overall water rise was measured in the lake. Two major icefall events a week apart contributed to 8 and 6 cm, respectively, rise alone. Surface water and air temperatures increased during this time, along with the amount of solar irradiation reaching the surface of the lake. South-facing ice walls were found to melt faster, but no walls were found to be immune to melt and collapse. Hourly time-lapse photography captured a major icefall in this lake, while another camera captured a larger lake farther upglacier draining more than 3 meters overnight. A third camera, aimed near the terminus, captured a lake changing in color (from milky blue to brown) and doubling in size during the field season. These initial results show substantial change in a short amount of time. Continued time-lapse photography should provide us with an even better record of surface evolution on this climatically sensitive glacier in the Himalaya.

  3. Monitoring hydraulic processes with automated time-lapse electrical resistivity tomography (ALERT)

    Science.gov (United States)

    Kuras, Olivier; Pritchard, Jonathan D.; Meldrum, Philip I.; Chambers, Jonathan E.; Wilkinson, Paul B.; Ogilvy, Richard D.; Wealthall, Gary P.

    2009-10-01

    Hydraulic processes in porous media can be monitored in a minimally invasive fashion by time-lapse electrical resistivity tomography (ERT). The permanent installation of specifically designed ERT instrumentation, telemetry and information technology (IT) infrastructure enables automation of data collection, transfer, processing, management and interpretation. Such an approach gives rise to a dramatic increase in temporal resolution, thus providing new insight into rapidly occurring subsurface processes. In this paper, we discuss a practical implementation of automated time-lapse ERT. We present the results of a recent study in which we used controlled hydraulic experiments in two test cells at reduced field scale to explore the limiting conditions for process monitoring with cross-borehole ERT measurements. The first experiment used three adjacent boreholes to monitor rapidly rising and falling water levels. For the second experiment, we injected a saline tracer into a homogeneous flow field in freshwater-saturated sand; the dynamics of the plume were then monitored with 2D measurements across a 9-borehole fence and 3D measurements across a 3 × 3 grid of boreholes. We investigated different strategies for practical data acquisition and show that simple re-ordering of ERT measurement schemes can help harmonise data collection with the nature of the monitored process. The methodology of automated time-lapse ERT was found to perform well in different monitoring scenarios (2D/3D plus time) at time scales associated with realistic subsurface processes. The limiting factor is the finite amount of time needed for the acquisition of sufficiently comprehensive datasets. We found that, given the complexity of our monitoring scenarios, typical frame rates of at least 1.5-3 images per hour were possible without compromising image quality.

  4. Exploring the Resolution of Time-Lapse Microgravity at an Aquifer Storage and Recovery Site

    Science.gov (United States)

    Bradley, C. C.; Ali, M.; Levannier, A.

    2008-12-01

    Time-Lapse Microgravity can reveal relatively small underground fluid displacements via the redistribution of density-contrast at fluid boundaries. The method has, for example, been successfully demonstrated in underground natural gas storage and carbon sequestration studies, and has clear potential for hydrological research and applications such as mining and hydrocarbon reservoir management. For surveys based on modern spring-type gravimeters, the technique's basic measurement resolution is limited by instrument drift, offset errors, and viscoelastic strain hysteresis of the sensor. Despite the sophistication of modern instruments, actual field performance of gravimeters still depends on operator technique and survey conditions. To explore the ultimate resolution of field microgravity (and time-lapse measurements, in particular), we have made repeated gravity surveys of a shallow aquifer storage and recovery test site in the UAE, where injection produces a 'water mound' - localized vertical water-level shifts - monitored by a set of instrumented wells. Based on field measurements and additional laboratory testing of our Scintrex CG-5 gravimeter, we find that the main limit on measurement resolution is from orientation strain hysteresis - a variable amplitude error that decays in approximately 30 minutes, typically in response to orientation during transport between measurement stations. Still, carefully conducted surveys (during the summer, in the desert conditions of the UAE) demonstrate time-lapse microgravity resolution of about 3 microGals, corresponding to a water-level shift of about 0.3 m for this aquifer. In this paper, we will discuss what a 'careful survey' requires and present our detailed testing and survey results.

  5. Time-lapse electrical geophysical monitoring of amendment-based biostimulation

    Science.gov (United States)

    Johnson, Timothy C.; Versteeg, Roelof J.; Day-Lewis, Frederick D.; Major, William; Lane, John W.

    2015-01-01

    Biostimulation is increasingly used to accelerate microbial remediation of recalcitrant groundwater contaminants. Effective application of biostimulation requires successful emplacement of amendment in the contaminant target zone. Verification of remediation performance requires postemplacement assessment and contaminant monitoring. Sampling-based approaches are expensive and provide low-density spatial and temporal information. Time-lapse electrical resistivity tomography (ERT) is an effective geophysical method for determining temporal changes in subsurface electrical conductivity. Because remedial amendments and biostimulation-related biogeochemical processes often change subsurface electrical conductivity, ERT can complement and enhance sampling-based approaches for assessing emplacement and monitoring biostimulation-based remediation.Field studies demonstrating the ability of time-lapse ERT to monitor amendment emplacement and behavior were performed during a biostimulation remediation effort conducted at the Department of Defense Reutilization and Marketing Office (DRMO) Yard, in Brandywine, Maryland, United States. Geochemical fluid sampling was used to calibrate a petrophysical relation in order to predict groundwater indicators of amendment distribution. The petrophysical relations were field validated by comparing predictions to sequestered fluid sample results, thus demonstrating the potential of electrical geophysics for quantitative assessment of amendment-related geochemical properties. Crosshole radar zero-offset profile and borehole geophysical logging were also performed to augment the data set and validate interpretation.In addition to delineating amendment transport in the first 10 months after emplacement, the time-lapse ERT results show later changes in bulk electrical properties interpreted as mineral precipitation. Results support the use of more cost-effective surface-based ERT in conjunction with limited field sampling to improve spatial

  6. Proposed guidelines on the nomenclature and annotation of dynamic human embryo monitoring by a time-lapse user group.

    Science.gov (United States)

    Ciray, H Nadir; Campbell, Alison; Agerholm, Inge Errebo; Aguilar, Jesús; Chamayou, Sandrine; Esbert, Marga; Sayed, Shabana

    2014-12-01

    planes, this technology does not currently allow continuous monitoring such that the entire process of preimplantation embryo development may be visualized. This is the first time that a group of experienced time-lapse users has systematically evaluated current evidence and theoretical aspects of morphokinetic monitoring to propose guidelines for a standard methodology and terminology of its use and study, and its clinical application in IVF. The adoption of a more uniform approach to the terminology and definitions of morphokinetic variables within this developing field of clinical embryology would allow practitioners to benefit from improved interpretation of data and the sharing of best practice and experience, which could impact positively and more swiftly on patient treatment outcome. There was no specific funding for the preparation of these proposed guidelines. Meetings were held opportunistically during scientific conferences and using online communication tools. H.N.C. is a scientific consultant for ESCO, supplier of Miri TL. I.E.A. is a minor shareholder in Unisense Fertilitech, supplier of the EmbryoScope. Full disclosures of all participants are presented herein. The remaining authors have no conflict of interest. © The Author 2014. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  7. Network analysis of time-lapse microscopy recordings.

    Science.gov (United States)

    Smedler, Erik; Malmersjö, Seth; Uhlén, Per

    2014-01-01

    Multicellular organisms rely on intercellular communication to regulate important cellular processes critical to life. To further our understanding of those processes there is a need to scrutinize dynamical signaling events and their functions in both cells and organisms. Here, we report a method and provide MATLAB code that analyzes time-lapse microscopy recordings to identify and characterize network structures within large cell populations, such as interconnected neurons. The approach is demonstrated using intracellular calcium (Ca(2+)) recordings in neural progenitors and cardiac myocytes, but could be applied to a wide variety of biosensors employed in diverse cell types and organisms. In this method, network structures are analyzed by applying cross-correlation signal processing and graph theory to single-cell recordings. The goal of the analysis is to determine if the single cell activity constitutes a network of interconnected cells and to decipher the properties of this network. The method can be applied in many fields of biology in which biosensors are used to monitor signaling events in living cells. Analyzing intercellular communication in cell ensembles can reveal essential network structures that provide important biological insights.

  8. Network Analysis of Time-Lapse Microscopy Recordings

    Directory of Open Access Journals (Sweden)

    Erik eSmedler

    2014-09-01

    Full Text Available Multicellular organisms rely on intercellular communication to regulate important cellular processes critical to life. To further our understanding of those processes there is a need to scrutinize dynamical signaling events and their functions in both cells and organisms. Here, we report a method and provide MATLAB code that analyzes time-lapse microscopy recordings to identify and characterize network structures within large cell populations, such as interconnected neurons. The approach is demonstrated using intracellular calcium (Ca2+ recordings in neural progenitors and cardiac myocytes, but could be applied to a wide variety of biosensors employed in diverse cell types and organisms. In this method, network structures are analyzed by applying cross-correlation signal processing and graph theory to single-cell recordings. The goal of the analysis is to determine if the single cell activity constitutes a network of interconnected cells and to decipher the properties of this network. The method can be applied in many fields of biology in which biosensors are used to monitor signaling events in living cells. Analyzing intercellular communication in cell ensembles can reveal essential network structures that provide important biological insights.

  9. The critical time-lapse between various restoration placements and subsequent endodontic intervention.

    Science.gov (United States)

    Kwang, Sarah; Aminoshariae, Anita; Harding, Jarrod; Montagnese, Thomas A; Mickel, Andre

    2014-12-01

    The purpose of this study was 2-fold: (1) to investigate the critical time-lapse of endodontic intervention subsequent to various restorations and tooth surfaces and (2) to assess and compare the risk factors associated with the restorations, tooth surfaces, and endodontic treatment. A comprehensive computerized analysis of all dental school patients at the Case Western Reserve University School of Dental Medicine who received restorations from 2008-2013 was obtained. Inclusion and exclusion criteria were applied. The sample size was limited to teeth with endodontic treatment completed by the endodontic postgraduate dental clinic. Data collected included restoration type, restored tooth surfaces, tooth type, and the dates of restoration and subsequent endodontic treatment. A 2-sample paired t test (95% confidence interval, P endodontic intervention was 270 days, with a mean difference of 247-294 days (P endodontic intervention. Teeth with 2 or more restorative surfaces required endodontic intervention (P endodontic treatment after restoration placement, the critical time-lapse was 9 months. Composite restorations and teeth with 2 or more restorative surfaces were significantly associated with endodontic treatment. From the results of the current study, we recommended that all dental practitioners should perform a thorough endodontic evaluation and diagnosis before, during, and after all restorative procedures. Copyright © 2014 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  10. 4D reconstruction of soil surface changes with time-lapse cameras

    Science.gov (United States)

    Eltner, Anette; Kaiser, Andreas; Schindewolf, Marcus

    2017-04-01

    Time-lapse photogrammetry enables fascinating visual insights into earth surface processes by compressing time. Recent advances in spatially high resolution topographic data are made possible due to Structure-from-Motion (SfM) photogrammetry. In a next step increasing the temporal resolution can allow for continuous 4D monitoring of soil surface processes. Two case studies are presented where 4D reconstruction is performed utilising a time-lapse system with a multi-angle camera setup of three SLR cameras, which enables repeated calculation of digital elevation models (DEMs) of difference. A thunderstorm event was captured at a field with 15 seconds interval and a rainfall simulation has been observed at plot scale with a temporal resolution of 10 seconds. A workflow is introduced for fully automatic data generation. Thereby, special care needs to be taken regarding camera calibration and subsequent image correction. Furthermore, camera movements are compensated for via template matching of stable ground control points. In addition, temporal filtering is applied to the resulting surface change models to account for random noise and to increase the reliability of the measurement of signals of change with low intensity. Results reveal significant surface changes during the events. Ripple and pool sequences become obvious in both case studies. Additionally, roughness changes and hydrostatic effects are apparent along the temporal domain at the plot scale.

  11. Time lapse seismic observations and effects of reservoir compressibility at Teal South oil field

    Science.gov (United States)

    Islam, Nayyer

    One of the original ocean-bottom time-lapse seismic studies was performed at the Teal South oil field in the Gulf of Mexico during the late 1990's. This work reexamines some aspects of previous work using modern analysis techniques to provide improved quantitative interpretations. Using three-dimensional volume visualization of legacy data and the two phases of post-production time-lapse data, I provide additional insight into the fluid migration pathways and the pressure communication between different reservoirs, separated by faults. This work supports a conclusion from previous studies that production from one reservoir caused regional pressure decline that in turn resulted in liberation of gas from multiple surrounding unproduced reservoirs. I also provide an explanation for unusual time-lapse changes in amplitude-versus-offset (AVO) data related to the compaction of the producing reservoir which, in turn, changed an isotropic medium to an anisotropic medium. In the first part of this work, I examine regional changes in seismic response due to the production of oil and gas from one reservoir. The previous studies primarily used two post-production ocean-bottom surveys (Phase I and Phase II), and not the legacy streamer data, due to the unavailability of legacy prestack data and very different acquisition parameters. In order to incorporate the legacy data in the present study, all three post-stack data sets were cross-equalized and examined using instantaneous amplitude and energy volumes. This approach appears quite effective and helps to suppress changes unrelated to production while emphasizing those large-amplitude changes that are related to production in this noisy (by current standards) suite of data. I examine the multiple data sets first by using the instantaneous amplitude and energy attributes, and then also examine specific apparent time-lapse changes through direct comparisons of seismic traces. In so doing, I identify time-delays that, when

  12. Possible mechanism of polyspermy block in human oocytes observed by time-lapse cinematography.

    Science.gov (United States)

    Mio, Yasuyuki; Iwata, Kyoko; Yumoto, Keitaro; Kai, Yoshiteru; Sargant, Haruka C; Mizoguchi, Chizuru; Ueda, Minako; Tsuchie, Yuka; Imajo, Akifumi; Iba, Yumiko; Nishikori, Kyoko

    2012-09-01

    To analyze the fertilization process related to polyspermy block in human oocytes using an in vitro culturing system for time-lapse cinematography. We had 122 oocytes donated for this study from couples that provided informed consent. We recorded human oocytes at 2,000 to 2,800 frames every 10 s during the fertilization process and thereafter every 2 min using a new in vitro culture system originally developed by the authors for time-lapse cinematography. We displayed 30 frames per second for analysis of the polyspermy block during fertilization. Three oocytes showed the leading and following sperm within the zona pellucida in the same microscopic field. The dynamic images obtained during the fertilization process using this new system revealed that once a leading sperm penetrated the zona pellucida and attached to the oocyte membrane, a following sperm was arrested from further penetration into the zona pellucida within 10 s. The present results strongly suggest the existence of a novel mechanism of polyspermy block that takes place at the zona pellucida immediately after fertilization. These findings are clearly different from previous mechanisms describing polyspermy block as the oocyte membrane block to sperm penetration and the zona reaction. The finding presented herein thus represents a novel discovery about the highly complicated polyspermy block mechanism occurring in human oocytes.

  13. Time-Lapse Electrical Resistivity Investigations for Imaging the Grouting Injection in Shallow Subsurface Cavities

    Directory of Open Access Journals (Sweden)

    Muhammad Farooq

    2014-01-01

    Full Text Available The highway of Yongweol-ri, Muan-gun, south-western part of the South Korean Peninsula, is underlain by the abandoned of subsurface cavities, which were discovered in 2005. These cavities lie at shallow depths with the range of 5∼15 meters below the ground surface. Numerous subsidence events have repeatedly occurred in the past few years, damaging infrastructure and highway. As a result of continuing subsidence issues, the Korean Institute of Geosciences and Mineral Resources (KIGAM was requested by local administration to resolve the issue. The KIGAM used geophysical methods to delineate subsurface cavities and improve more refined understanding of the cavities network in the study area. Cement based grouting has been widely employed in the construction industry to reinforce subsurface ground. In this research work, time-lapse electrical resistivity surveys were accomplished to monitor the grouting injection in the subsurface cavities beneath the highway, which have provided a quasi-real-time monitoring for modifying the subsurface cavities related to ground reinforcement, which would be difficult with direct methods. The results obtained from time-lapse electrical resistivity technique have satisfactory imaged the grouting injection experiment in the subsurface cavities beneath the highway. Furthermore, the borehole camera confirmed the presence of grouting material in the subsurface cavities, and hence this procedure increases the mechanical resistance of subsurface cavities below the highway.

  14. Analyzing dynamic cellular morphology in time-lapsed images enabled by cellular deformation pattern recognition.

    Science.gov (United States)

    Li, Heng; Liu, Zhiwen; Pang, Fengqian; Fan, Zhiyi; Shi, Yonggang

    2015-01-01

    Computational analysis of cellular morphology aims to provide quantitative information of the global organizational and physiological state of cells, and has long been a major topic of biomedical research. Instead of analyzing morphology of static cells, we concentrate on live-cell deformation in a period of time. According to our observation of dynamic cell behavior, we have assumed that the pattern of cellular deformation is relevant to the cellular state. Moreover, based on our assumption an innovative approach for characterizing the deformation pattern is described and applied into cell classification. After normalizing and aligning cell image sequences, we extract the continuity of deformation at each angle through time-lapse. Then the deformation pattern is given by the histogram of the continuity of deformation. Experimental results demonstrate that the cellular deformation pattern provided by our approach can be applied to discriminate cellular activation. In addition, the deformation pattern recognition makes remarkable progress in the classification of cells.

  15. Exploring Time-Lapse Photography as a Means for Qualitative Data Collection

    Science.gov (United States)

    Persohn, Lindsay

    2015-01-01

    Collecting information via time-lapse photography is nothing new. Scientists and artists have been using this kind of data since the late 1800s. However, my research and experiments with time-lapse have shown that great potential may lie in its application to educational and social scientific research methods. This article is part history, part…

  16. Estimation of turbulence from time-lapse imagery

    Science.gov (United States)

    McCrae, Jack E.; Bose-Pillai, Santasri R.; Fiorino, Steven T.

    2017-07-01

    Atmospheric turbulence parameters are estimated for an imaging path based on time-lapse imaging results. Atmospheric turbulence causes frame-to-frame shifts of the entire image as well as parts of the image. The statistics of these shifts encode information about the turbulence strength (as characterized by Cn2, the refractive index structure function constant) along the optical path. The shift variance observed is simply proportional to the variance of the tilt of the optical field averaged over the area being tracked and averaged over the camera aperture. By presuming this turbulence follows the Kolmogorov spectrum, weighting functions, which relate the turbulence strength along the path to the shifts measured, are derived. These weighting functions peak at the camera and fall to zero at the object. The larger the area observed, the more quickly the weighting function decays. One parameter we would like to estimate is r0 (the Fried parameter or atmospheric coherence diameter.) The weighting functions derived for pixel sized or larger parts of the image all fall faster than the weighting function appropriate for estimating the spherical wave r0. If we were to presume that Cn2 is constant along the path, then an estimate for r0 could be obtained for each area tracked, but since the weighting function for r0 differs substantially from that for every realizable tracked area, it can be expected that this approach would yield a poor estimate. Instead, the weighting functions for a number of different patch sizes can be combined through the Moore-Penrose pseudoinverse to create a weighting function that yields the least-squares optimal linear combination of measurements for the estimation of r0. This approach is carried out for one example and is shown to give noisy results. A modified version of this approach that creates larger patches by averaging several smaller patches together solves this noise issue. This approach can also work to estimate other atmospheric

  17. Seismic imaging of reservoir flow properties: Time-lapse amplitude changes

    Energy Technology Data Exchange (ETDEWEB)

    Vasco, D.W.; Datta-Gupta, Akhil; Behrens, Ron; Condon, Pat; Rickett, Jame s

    2003-03-13

    Asymptotic methods provide an efficient means by which to infer reservoir flow properties, such as permeability, from time-lapse seismic data. A trajectory-based methodology, much like ray-based methods for medical and seismic imaging, is the basis for an iterative inversion of time-lapse amplitude changes. In this approach a single reservoir simulation is required for each iteration of the algorithm. A comparison between purely numerical and the trajectory-based sensitivities demonstrates their accuracy. An application to a set of synthetic amplitude changes indicates that they can recover large-scale reservoir permeability variations from time-lapse data. In an application of actual time-lapse amplitude changes from the Bay Marchand field in the Gulf of Mexico we are able to reduce the misfit by 81% in twelve iterations. The time-lapse observations indicate lower permeabilities are required in the central portion of the reservoir.

  18. Time-lapse VSP data processing for monitoring CO2 injection

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Lianjie [Los Alamos National Laboratory; Rutledge, James [Los Alamos National Laboratory; Cheng, Arthur [CAMBRIDGE GEOSCIENCES

    2009-01-01

    As a part of the effort of the Southwest Regional Partnership on Carbon Sequestration supported by U.S. Department of Energy and managed by the National Energy Technology Laboratory, two sets of time-lapse VSPs were acquired and processed in oil fields undergoing CO{sub 2} injection. One set of VSPs was acquired at the Aneth oil field in Utah, the other set at the Scurry Area Canyon Reef Operators Committee (SACROC) field in West Texas. One baseline and two repeat VSP surveys were conducted from 2007 to 2009 at the Aneth oil field in Utah for monitoring CO{sub 2} injection. The aim of the time-lapse VSP surveys is to study the combined enhanced oil recovery (EOR) and CO{sub 2} sequestration in collaboration with Resolute Natural Resources, Inc. VSP data were acquired using a cemented geophone string with 60 levels at depth from 805 m to 1704 m, and CO{sub 2} is injected into a horizontal well nearby within the reservoir at depth approximately from 1730 m to 1780 m. For each VSP survey, the data were acquired for one zero-offset source location and seven offset source locations (Figure 1). The baseline VSP survey was conducted before the CO{sub 2} injection. More than ten thousand tons of CO{sub 2} was injected between each of the two repeat VSP surveys. There are three horizontal injection wells, all originating from the same vertical well. One is drilled towards Southeast, directly towards the monitoring well (Figure 2), and the other two towards Northwest, directly away from the monitoring well. The injection is into the top portion of the Desert Creek formation, just beneath the Gothic shale, which acts as the reservoir seal. The initial baseline acquisition was done in October 2007; subsequent time-lapse acquisitions were conducted in July 2008, and January 2009. The acquisition geometry is shown in Figure 1. Shot point 1 is the zero-offset source location, Shot points 2 to 8 are the seven offset VSPs, arranged in a quarter circle on the Northwest side of the

  19. A Modular and Affordable Time-Lapse Imaging and Incubation System Based on 3D-Printed Parts, a Smartphone, and Off-The-Shelf Electronics.

    Science.gov (United States)

    Hernández Vera, Rodrigo; Schwan, Emil; Fatsis-Kavalopoulos, Nikos; Kreuger, Johan

    2016-01-01

    Time-lapse imaging is a powerful tool for studying cellular dynamics and cell behavior over long periods of time to acquire detailed functional information. However, commercially available time-lapse imaging systems are expensive and this has limited a broader implementation of this technique in low-resource environments. Further, the availability of time-lapse imaging systems often present workflow bottlenecks in well-funded institutions. To address these limitations we have designed a modular and affordable time-lapse imaging and incubation system (ATLIS). The ATLIS enables the transformation of simple inverted microscopes into live cell imaging systems using custom-designed 3D-printed parts, a smartphone, and off-the-shelf electronic components. We demonstrate that the ATLIS provides stable environmental conditions to support normal cell behavior during live imaging experiments in both traditional and evaporation-sensitive microfluidic cell culture systems. Thus, the system presented here has the potential to increase the accessibility of time-lapse microscopy of living cells for the wider research community.

  20. Quantifying Effusion Rates at Active Volcanoes through Integrated Time-Lapse Laser Scanning and Photography

    Directory of Open Access Journals (Sweden)

    Neil Slatcher

    2015-11-01

    Full Text Available During volcanic eruptions, measurements of the rate at which magma is erupted underpin hazard assessments. For eruptions dominated by the effusion of lava, estimates are often made using satellite data; here, in a case study at Mount Etna (Sicily, we make the first measurements based on terrestrial laser scanning (TLS, and we also include explosive products. During the study period (17–21 July 2012, regular Strombolian explosions were occurring within the Bocca Nuova crater, producing a ~50 m-high scoria cone and a small lava flow field. TLS surveys over multi-day intervals determined a mean cone growth rate (effusive and explosive products of ~0.24 m3·s−1. Differences between 0.3-m resolution DEMs acquired at 10-minute intervals captured the evolution of a breakout lava flow lobe advancing at 0.01–0.03 m3·s−1. Partial occlusion within the crater prevented similar measurement of the main flow, but integrating TLS data with time-lapse imagery enabled lava viscosity (7.4 × 105 Pa·s to be derived from surface velocities and, hence, a flux of 0.11 m3·s−1 to be calculated. Total dense rock equivalent magma discharge estimates are ~0.1–0.2 m3·s−1 over the measurement period and suggest that simultaneous estimates from satellite data are somewhat overestimated. Our results support the use of integrated TLS and time-lapse photography for ground-truthing space-based measurements and highlight the value of interactive image analysis when automated approaches, such as particle image velocimetry (PIV, fail.

  1. Limiting aspects of using geophysical time-lapse measurements for contaminant site monitoring

    Science.gov (United States)

    French, H. K.; Bloem, E.

    2010-12-01

    Winter maintenance at airports and roads in the areas with winter frost requires the use of large quantities of de-icing chemicals. These chemicals infiltrate the unsaturated zone during winter and spring due to the mixing with snow next to the roads or runways and may hence pollute the groundwater. Geophysical methods provide insight into soil heterogeneity and characteristics and may, when used in time-lapse mode, serve as a monitoring technique for contaminant transport over larger areas than traditional sampling techniques such as suction cups, soil sampling techniques and groundwater wells. The presence of a mixture of materials and contaminants in the subsurface, as well as the natural temporal variable conditions such as temperature and water saturation are among the challenges of geophysical monitoring of flow and transport processes in the unsaturated zone. Some examples of the use of geophysical measurements for contaminant site monitoring from the literature will be given as well as insight to more specific challenges both practical and scientifically for a case study in Norway. The case study shows results of electrical resistivity measurements along two profiles next to one of the runways at Oslo airport, Gardermoen. One profile is located parallel to the runway and within the zone affected by contaminated snow, while the other set of surface electrodes are installed at an angle from the runway and covers areas both affected and unaffected by de-icing chemicals. In addition to time-lapse electrical resistivity measurements, the soil temperature, volumetric water content and the electrical conductivity of the soil water is measured at 4 depths at the crossing point of the two cables. Theoretical improvements and managerial aspects still required for the applicability of this monitoring technique at contaminated sites will be discussed.

  2. Time-lapse imaging of red blood cell invasion by the rodent malaria parasite Plasmodium yoelii.

    Directory of Open Access Journals (Sweden)

    Kazuhide Yahata

    Full Text Available In order to propagate within the mammalian host, malaria parasites must invade red blood cells (RBCs. This process offers a window of opportunity in which to target the parasite with drugs or vaccines. However, most of the studies relating to RBC invasion have analyzed the molecular interactions of parasite proteins with host cells under static conditions, and the dynamics of these interactions remain largely unstudied. Time-lapse imaging of RBC invasion is a powerful technique to investigate cell invasion and has been reported for Plasmodium knowlesi and Plasmodium falciparum. However, experimental modification of genetic loci is laborious and time consuming for these species. We have established a system of time-lapse imaging for the rodent malaria parasite Plasmodium yoelii, for which modification of genetic loci is quicker and simpler. We compared the kinetics of RBC invasion by P. yoelii with that of P. falciparum and found that the overall kinetics during invasion were similar, with some exceptions. The most striking of these differences is that, following egress from the RBC, the shape of P. yoelii merozoites gradually changes from flat elongated ovals to spherical bodies, a process taking about 60 sec. During this period merozoites were able to attach to and deform the RBC membrane, but were not able to reorient and invade. We propose that this morphological change of P. yoelii merozoites may be related to the secretion or activation of invasion-related proteins. Thus the P. yoelii merozoite appears to be an excellent model to analyze the molecular dynamics of RBC invasion, particularly during the morphological transition phase, which could serve as an expanded window that cannot be observed in P. falciparum.

  3. On the Resolvability of Steam Assisted Gravity Drainage Reservoirs Using Time-Lapse Gravity Gradiometry

    Science.gov (United States)

    Elliott, E. Judith; Braun, Alexander

    2017-11-01

    Unconventional heavy oil resource plays are important contributors to oil and gas production, as well as controversial for posing environmental hazards. Monitoring those reservoirs before, during, and after operations would assist both the optimization of economic benefits and the mitigation of potential environmental hazards. This study investigates how gravity gradiometry using superconducting gravimeters could resolve depletion areas in steam assisted gravity drainage (SAGD) reservoirs. This is achieved through modelling of a SAGD reservoir at 1.25 and 5 years of operation. Specifically, the density change structure identified from geological, petrological, and seismic observations is forward modelled for gravity and gradients. Three main parameters have an impact on the resolvability of bitumen depletion volumes and are varied through a suitable parameter space: well pair separation, depth to the well pairs, and survey grid sampling. The results include a resolvability matrix, which identifies reservoirs that could benefit from time-lapse gravity gradiometry monitoring. After 1.25 years of operation, during the rising phase, the resolvable maximum reservoir depth ranges between the surface and 230 m, considering a well pair separation between 80 and 200 m. After 5 years of production, during the spreading phase, the resolvability of depletion volumes around single well pairs is greatly compromised as the depletion volume is closer to the surface, which translates to a larger portion of the gravity signal. The modelled resolvability matrices were derived from visual inspection and spectral analysis of the gravity gradient signatures and can be used to assess the applicability of time-lapse gradiometry to monitor reservoir density changes.

  4. Time-Lapse Monitoring of Soil Water Content Using Electromagnetic Conductivity Imaging

    Science.gov (United States)

    Triantafilis, J.; Huang, J.

    2016-12-01

    The volumetric soil water content (θ) is fundamental to agriculture because its spatio-temporal variation in soil affects plant growth. The universally accepted thermogravimetric method for estimating θ is labour intensive and time-consuming to use for field-scale monitoring. Electromagnetic (EM) induction has proven useful in mapping spatio-temporal variation of θ. However, depth-specific variation, which is important for irrigation management has been little explored. In this study we develop a relationship between θ and estimates of true electrical conductivity (σ) and use this to develop time-lapse images of θ beneath a center-pivot irrigated alfalfa (Medicago sativa L.) field in San Jacinto, California, USA. We measure the bulk apparent electrical conductivity (ECa - mS/m) using a DUALEM-421 over a period of 12 days after an irrigation event (i.e., days 1, 2, 3, 4, 6, 8 and 12). We use EM4Soil to generate electromagnetic conductivity images (EMCI). Testing the scenario where no soil information is available, we used a 3-parameter exponential model to relate θ to σ and then to map θ along the transect on different days. The results allow us to monitor the spatio-temporal variations of θ over the 12-day period. In this regard we were able to map the soil close to field capacity (0.27 cm3/cm3) and approaching permanent wilting point (0.03 cm3/cm3). The time-lapse θ monitoring approach, has implications for soil and water-use and management and allows farmers to identify inefficiencies in water application rates and use. It can also be used as a research tool to potentially assist precision irrigation practices and to test the efficacy of different methods of irrigation in terms of water delivery and efficiency in water use in near real-time.

  5. History matching of time-lapse crosswell data using ensemble kalman filtering

    KAUST Repository

    de Matos Ravanelli, Fabio Miguel

    2015-09-03

    Data from crosswell seismic surveys is processed to provide crosswell time-lapse data to map fluid changes in a reservoir where time-lapse or 4D seismic data is unavailable or unreliable, such as in onshore reservoirs. The resultant processing results provide quantitative information for history matching purposes using a probabilistic approach to take in account uncertainties in the geological model and reduce uncertainties in reservoir production forecasts.

  6. Examining the information content of time-lapse crosshole GPR data collected under different infiltration conditions to estimate unsaturated soil hydraulic properties

    DEFF Research Database (Denmark)

    Scholer, M.; Irving, J.; Zibar, Majken Caroline Looms

    2013-01-01

    Time-lapse geophysical data acquired during transient hydrological experiments are being increasingly employed to estimate subsurface hydraulic properties at the field scale. In particular, crosshole ground-penetrating radar (GPR) data, collected while water infiltrates into the subsurface either...... by natural or artificial means, have been demonstrated in a number of studies to contain valuable information concerning the hydraulic properties of the unsaturated zone. Previous work in this domain has considered a variety of infiltration conditions and different amounts of time-lapse GPR data...... of time-lapse zero-offset-profile (ZOP) GPR traveltime data, collected under three different infiltration conditions, for the estimation of van Genuchten–Mualem (VGM) parameters in a layered subsurface medium. Specifically, we systematically analyze synthetic and field GPR data acquired under natural...

  7. Harmonic oscillator in heat bath: Exact simulation of time-lapse-recorded data and exact analytical benchmark statistics

    DEFF Research Database (Denmark)

    Nørrelykke, Simon F; Flyvbjerg, Henrik

    2011-01-01

    -lapse recordings. Three applications are discussed: (i) The effects of finite sampling rate and time, described exactly here, are similar for other stochastic dynamical systems-e.g., motile microorganisms and their time-lapse-recorded trajectories. (ii) The same statistics is satisfied by any experimental system......The stochastic dynamics of the damped harmonic oscillator in a heat bath is simulated with an algorithm that is exact for time steps of arbitrary size. Exact analytical results are given for correlation functions and power spectra in the form they acquire when computed from experimental time...... of finite sampling rate and sampling time for these models as well....

  8. Combined time-lapse magnetic resonance imaging and modeling to investigate colloid deposition and transport in porous media.

    Science.gov (United States)

    Lehoux, Alizée P; Faure, Pamela; Lafolie, François; Rodts, Stéphane; Courtier-Murias, Denis; Coussot, Philippe; Michel, Eric

    2017-10-15

    Colloidal particles can act as vectors of adsorbed pollutants in the subsurface, or be themselves pollutants. They can reach the aquifer and impair groundwater quality. The mechanisms of colloid transport and deposition are often studied in columns filled with saturated porous media. Time-lapse profiles of colloid concentration inside the columns have occasionally been derived from magnetic resonance imaging (MRI) data recorded in transport experiments. These profiles are valuable, in addition to particle breakthrough curves (BTCs), for testing and improving colloid transport models. We show that concentrations could not be simply computed from MRI data when both deposited and suspended colloids contributed to the signal. We propose a generic method whereby these data can still be used to quantitatively appraise colloid transport models. It uses the modeled suspended and deposited particle concentrations to compute modeled MRI data that are compared to the experimental data. We tested this method by performing transport experiments with sorbing colloids in sand, and assessed for the first time the capacity of the model calibrated from BTCs to reproduce the MRI data. Interestingly, the dispersion coefficient and deposition rate calibrated from the BTC were respectively overestimated and underestimated compared with those calibrated from the MRI data, suggesting that these quantities, when determined from BTCs, need to be interpreted with care. In a broader perspective, we consider that combining MRI and modeling offers great potential for the quantitative analysis of complex MRI data recorded during transport experiments in complex environmentally relevant porous media, and can help improve our understanding of the fate of colloids and solutes, first in these media, and later in soils. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Time-lapse electrical resistivity tomography: a powerful tool for landslide monitoring?

    Science.gov (United States)

    Perrone, A.

    2011-12-01

    The extreme rainfall events and the quick snowmelt occurrences play an important role in the triggering of the landslides. The occurrence of one of these factors can determine the variation of water content in the first layers of the subsoil and as a consequence a quick soil saturation inducing both an increase in pore-water pressures and the overloaded of the slopes progressively collapsing. The electrical resistivity, self-potential, electromagnetic induction and GPR methods can be considered as the most appropriate for assessing the presence of water in the underground. Such methods allow us to study the behavior of water content over much wider and deeper areas than those offered by traditional methods (thermo-gravimetric, tensiometric, TDR, etc) based on spot measures and concerning small volumes. In particular, the Electrical Resistivity Tomography (ERT), which has already proved to be a powerful tool both for the geometrical reconstruction of a landslide body (location of sliding surface, estimation of the thickness of the slide material) and the individuation of high water content areas, can be considered as an alternative tool to be employed for a qualitative and quantitative water content monitoring in the first layers of the subsoil. Indeed, time-lapse 2D ERT can be tested in order to gather information on the temporal and spatial patterns of water infiltration processes and water content variation. This work reports the preliminary results from a new prototype system planned to obtain time-lapse 2D ERTs, TDR and precipitation measurements in two landslide areas located in the Southern Apennine chain (Italy). The system was planned with the aim to estimate the variation of the resistivity parameter on a long period considering the water content variation, the rain water infiltration and the seasonal changes. The prototype system, linked to a pc used for storing data and managing the time interval acquisition, consists of: a resistivimeter connected to a

  10. Monitoring channel head erosion processes in response to an artificially induced abrupt base level change using time-lapse photography 2301

    Science.gov (United States)

    Headcut and channel extension in response to an abrupt base level change in 2004 of approximately 1m was studied in a 1.29 ha semiarid headwater drainage on the Walnut Gulch Experimental Watershed (WGEW) in southeastern Arizona, USA. Field observations and time-lapse photography were coupled with hy...

  11. Time-lapse and UAV Thermal Imaging of Glacial and Periglacial Environments in the Peruvian Andes (Cordillera Blanca, Peru)

    Science.gov (United States)

    McKenzie, J. M.; Wigmore, O.; Aubry-Wake, C.; Mark, B. G.; Hellstrom, R. A.; Lautz, L.

    2015-12-01

    In the tropics, the acquisition of high-resolution geospatial data of high-mountain glacial and periglacial systems presents unique challenges due to remote site access and very high elevations. For glaciers and hydrologic systems, a key variable of interest is surface temperature as it constrains glacier melt rates, traces hydrologic processes, and is needed for the calibration of energy budget models. We present results from two studies that acquired high resolution temperature data from the Cuchillacocha Glacier, Peru (9.24°S, 77.21°W). The glacier resides on the western drainage of the Cordillera Blanca with an elevation range of 4700 to 6096 m. In the first study we use high resolution time-lapse infrared imagery (5-10 minute interval over 3 days; 0.6 m2 pixel size) to observe diel changes in the surface energy budget of the glacier and to demonstrate how radiation from bare rock adjacent to the glacier may affect melt rates. In the second study we use a newly developed, inexpensive unmanned aerial vehicle (UAV) for high resolution multispectral mapping of the glacier (2 cm resolution orthomosaic and 5 cm resolution DEM). We present results showing how the time-lapse and the high-resolution UAV imagery can be combined to further strengthen our understanding of the Cuchillacocha Glacier's energy budget and possible insights about turbulent heat fluxes. While the new instruments provide unprecedented data acquisition capabilities, there is an outstanding need for proper data correction. Spatial/thermal control points and post-processing algorithms are needed to produce quantifiable datasets. For example, our post-processed time-lapse imagery has an r2 > 0.9 after emissivity, transmissivity and offset corrections.

  12. Obstetric and perinatal outcomes of pregnancies conceived with embryos cultured in a time-lapse monitoring system.

    Science.gov (United States)

    Insua, Maria Fernanda; Cobo, Ana Cristina; Larreategui, Zaloa; Ferrando, Marcos; Serra, Vicente; Meseguer, Marcos

    2017-09-01

    To compare obstetric and perinatal outcomes of singleton pregnancies resulting from embryos incubated in a time-lapse system (TLS) with those of embryos grown in standard IVF incubators (SI). Retrospective description of a cohort of patients who conceived during a randomized, controlled trial. Private university-affiliated IVF center. Of 856 randomized patients, 378 gave birth to a live-born infant: 216 of the deliveries originated from embryos incubated in TLS, and 162 deliveries were from embryos cultured in SI. Embryo incubation and selection in TLS. Delivery and neonatal outcomes. No significant differences were observed in the baseline characteristics of the study population. The delivery rate was 49.3% (TLS) vs. 40.0% (SI), and multiple deliveries were higher in the TLS group: 31.0% (67 of 216) vs. 24.7% (40 of 162) in the SI group. When singleton pregnancies were analyzed no differences were found between the two groups in the rate of obstetric problems with respect to weeks at delivery: 38.8 (95% confidence interval [CI] 38.4-39.1) (TLS) vs. 39.5 (95% CI 38.0-39.9) (SI); preterm births (outcomes such as birth weight: 3,163 g (95% CI 3,035-3,292 g) (TLS) vs. 3,074 (95% CI 2,913-3,236) (SI); low birth weight (obstetric and perinatal outcomes when a time-lapse incubator was used rather than a more widely used conventional incubator. As far as we know this is the first report from a randomized study of the neonatal outcomes of time-lapse monitoring. Our results suggest that this technology is an effective and safe alternative for embryo incubation, though trials of larger numbers of patients are required to further confirm our conclusions. NCT01549262. Copyright © 2017 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

  13. Forward modeling to investigate inversion artifacts resulting from time-lapse electrical resistivity tomography during rainfall simulations

    Science.gov (United States)

    Carey, Austin M.; Paige, Ginger B.; Carr, Bradley J.; Dogan, Mine

    2017-10-01

    Time-lapse electrical resistivity tomography (ERT) is commonly used as a minimally invasive tool to study infiltration processes. In 2014, we conducted field studies coupling variable intensity rainfall simulation with high-resolution ERT to study the real-time partitioning of rainfall into surface and subsurface response. The significant contrast in resistivity in the subsurface from large changes in subsurface moisture resulted in artifacts during the inversion process of the time-lapse ERT data collected using a dipole-dipole electrode array. These artifacts, which are not representative of real subsurface moisture dynamics, have been shown to arise during time-lapse inversion of ERT data and may be subject to misinterpretation. Forward modeling of the infiltration process post field experiments using a two-layer system (saprolite overlain by a soil layer) was used to generate synthetic datasets. The synthetic data were used to investigate the influence of both changes in volumetric moisture content and electrode configuration on the development of the artifacts identified in the field datasets. For the dipole-dipole array, we found that a decrease in the resistivity of the bottom layer by 67% resulted in a 50% reduction in artifact development. Artifacts for the seven additional array configurations tested, ranged from a 19% increase in artifact development (using an extended dipole-dipole array) to as much as a 96% decrease in artifact development (using a wenner-alpha array), compared to that of the dipole-dipole array. Moreover, these arrays varied in their ability to accurately delineate the infiltration front. Model results showed that the modified pole-dipole array was able to accurately image the infiltration zone and presented fewer artifacts for our experiments. In this study, we identify an optimal array type for imaging rainfall-infiltration dynamics that reduces artifacts. The influence of moisture contrast between the infiltrating water and the

  14. TIME-LAPSE MICROSCOPY ROLE IN IMPROVING THE OUTCOME OF IVF/ICSI CYCLES BY MONITORING AND SELECTION OF EARLY EMBRYO

    Directory of Open Access Journals (Sweden)

    Gabriela SIMIONESCU

    2016-12-01

    Full Text Available In vitro fertilization (IVF and intracytoplasmatic sperm injection (ICSI are well-established assisted reproductive biotechnologies used to overcome infertility in couples. Time-lapse monitoring is an imagistic technology which was elaborated to fulfill the need for observing the dynamics of the mammalian embryonic development in a continuous, non-invasive manner, without removing the embryos from the optimal culturing conditions. This technology offers unique information regarding the cleavage process, as well as morphological and structural modifications thus enabling the embryologists to select the embryos with elevated implantation potential. Aim of the study: to identify, evaluate and summarize the available data regarding the role of time-lapse microscopy in improving the outcome of IVF and ICSI by monitoring and selection of early embryos Material and methods: we systematically reviewed the available evidence regarding the assessment of embryo quality through both conventional monitoring and time-lapse microscopy for couples undergoing in vitro fertilization (IVF or intracytoplasmic sperm injection (ICSI. The meta analysis included randomized trials and published data encountered on ISI Web of Knowledge Science, MedLine and Pubmed using the following keywords: time-lapse microscopy, IVF, ICSI, embryo, outcome, pregnancy. As criteria of differentiation, only studies that reported information regarding the implantation rate, aspects regarding clinical pregnancy or live birth were considered for analysis. Results: the info from the studies was extracted and included in the meta-analysis. A part of the retrospective studies conducted after 2010 have highlighted a correlation between time-lapse parameters and embryo viability as defined by the developmental competence and subsequently by the confirmation of clinical pregnancy. Other authors undertook a critical appraisal on potential benefit time-lapse monitoring may bring to ART. Conclusion

  15. PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

    Science.gov (United States)

    Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

    2017-02-01

    Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev.

  16. PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

    2017-02-01

    Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of changes subsurface electrical conductivity, in both the saturated and unsaturated zones, arising from water table changes and from river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev .

  17. Soundscape and Noise Exposure Monitoring in a Marine Protected Area Using Shipping Data and Time-Lapse Footage.

    Science.gov (United States)

    Merchant, Nathan D; Pirotta, Enrico; Barton, Tim R; Thompson, Paul M

    2016-01-01

    We review recent work that developed new techniques for underwater noise assessment that integrate acoustic monitoring with automatic identification system (AIS) shipping data and time-lapse video, meteorological, and tidal data. Two sites were studied within the Moray Firth Special Area of Conservation (SAC) for bottlenose dolphins, where increased shipping traffic is expected from construction of offshore wind farms outside the SAC. Noise exposure varied markedly between the sites, and natural and anthropogenic contributions were characterized using multiple data sources. At one site, AIS-operating vessels accounted for total cumulative sound exposure (0.1-10 kHz), suggesting that noise modeling using the AIS would be feasible.

  18. Advances in interpretation of subsurface processes with time-lapse electrical imaging

    Science.gov (United States)

    Singha, Kaminit; Day-Lewis, Frederick D.; Johnson, Tim B.; Slater, Lee D.

    2015-01-01

    Electrical geophysical methods, including electrical resistivity, time-domain induced polarization, and complex resistivity, have become commonly used to image the near subsurface. Here, we outline their utility for time-lapse imaging of hydrological, geochemical, and biogeochemical processes, focusing on new instrumentation, processing, and analysis techniques specific to monitoring. We review data collection procedures, parameters measured, and petrophysical relationships and then outline the state of the science with respect to inversion methodologies, including coupled inversion. We conclude by highlighting recent research focused on innovative applications of time-lapse imaging in hydrology, biology, ecology, and geochemistry, among other areas of interest.

  19. A multimethod Global Sensitivity Analysis to aid the calibration of geomechanical models via time-lapse seismic data

    Science.gov (United States)

    Price, D. C.; Angus, D. A.; Garcia, A.; Fisher, Q. J.; Parsons, S.; Kato, J.

    2018-03-01

    Time-lapse seismic attributes are used extensively in the history matching of production simulator models. However, although proven to contain information regarding production induced stress change, it is typically only loosely (i.e. qualitatively) used to calibrate geomechanical models. In this study we conduct a multimethod Global Sensitivity Analysis (GSA) to assess the feasibility and aid the quantitative calibration of geomechanical models via near-offset time-lapse seismic data. Specifically, the calibration of mechanical properties of the overburden. Via the GSA, we analyse the near-offset overburden seismic traveltimes from over 4000 perturbations of a Finite Element (FE) geomechanical model of a typical High Pressure High Temperature (HPHT) reservoir in the North Sea. We find that, out of an initially large set of material properties, the near-offset overburden traveltimes are primarily affected by Young's modulus and the effective stress (i.e. Biot) coefficient. The unexpected significance of the Biot coefficient highlights the importance of modelling fluid flow and pore pressure outside of the reservoir. The FE model is complex and highly nonlinear. Multiple combinations of model parameters can yield equally possible model realizations. Consequently, numerical calibration via a large number of random model perturbations is unfeasible. However, the significant differences in traveltime results suggest that more sophisticated calibration methods could potentially be feasible for finding numerous suitable solutions. The results of the time-varying GSA demonstrate how acquiring multiple vintages of time-lapse seismic data can be advantageous. However, they also suggest that significant overburden near-offset seismic time-shifts, useful for model calibration, may take up to 3 yrs after the start of production to manifest. Due to the nonlinearity of the model behaviour, similar uncertainty in the reservoir mechanical properties appears to influence overburden

  20. Summer-time Mass Balance of Wolverine Glacier, Alaska, Derived from Ground-based Time-lapse Microgravity Measurements

    Science.gov (United States)

    Young, E. V.; Muto, A.; Babcock, E.

    2016-12-01

    Monitoring the mass balance of alpine glaciers is important because alpine glaciers presently account for about half of the cryospheric contribution to the global sea-level rise. Mass balance measurements of alpine glaciers have predominantly relied upon glaciological and hydrological methods. However, these methods can be logistically costly and have potential extrapolation errors. Remote sensing approaches, such as gravimetric methods using data from GRACE satellite missions, have provided monthly mass-balance estimates of aggregates of alpine glaciers but their spatial resolution is far too large for studying a single glacier. On the other hand, ground-based time-lapse microgravity geophysical measurements can potentially circumvent some of the disadvantages of the glaciological and hydrological methods. It may detect the change in a single glacier's mass and its spatial distribution. We conducted ground-based time-lapse microgravity surveys on Wolverine Glacier, Alaska, in May and August of 2016, using a Scintrex CG-5 Autograv gravimeter. We collected data at seventy-nine individual stations on the glacier, roughly five stations per square kilometer. We included repeat-station and base-station measurements made at least twice a day for instrumental drift control. The uncertainty of our gravity measurements is better than 0.03 mGal, which is about 0.7 meters water equivalent of surface mass balance. Our summer-time mass balance of Wolverine Glacier determined from the time-lapse gravity measurements is independent of that derived from the stake-network or stream-gauge measurements, and could provide spatial insight into the mass balance process on Wolverine Glacier and similar glaciers.

  1. Analysis of Zebrafish Kidney Development with Time-lapse Imaging Using a Dissecting Microscope Equipped for Optical Sectioning.

    Science.gov (United States)

    Perner, Birgit; Schnerwitzki, Danny; Graf, Michael; Englert, Christoph

    2016-04-07

    In order to understand organogenesis, the spatial and temporal alterations that occur during development of tissues need to be recorded. The method described here allows time-lapse analysis of normal and impaired kidney development in zebrafish embryos by using a fluorescence dissecting microscope equipped for structured illumination and z-stack acquisition. To visualize nephrogenesis, transgenic zebrafish (Tg(wt1b:GFP)) with fluorescently labeled kidney structures were used. Renal defects were triggered by injection of an antisense morpholino oligonucleotide against the Wilms tumor gene wt1a, a factor known to be crucial for kidney development. The advantage of the experimental setup is the combination of a zoom microscope with simple strategies for re-adjusting movements in x, y or z direction without additional equipment. To circumvent focal drift that is induced by temperature variations and mechanical vibrations, an autofocus strategy was applied instead of utilizing a usually required environmental chamber. In order to re-adjust the positional changes due to a xy-drift, imaging chambers with imprinted relocation grids were employed. In comparison to more complex setups for time-lapse recording with optical sectioning such as confocal laser scanning or light sheet microscopes, a zoom microscope is easy to handle. Besides, it offers dissecting microscope-specific benefits such as high depth of field and an extended working distance. The method to study organogenesis presented here can also be used with fluorescence stereo microscopes not capable of optical sectioning. Although limited for high-throughput, this technique offers an alternative to more complex equipment that is normally used for time-lapse recording of developing tissues and organ dynamics.

  2. Could monopronucleated ICSI zygotes be considered for transfer? Analysis through time-lapse monitoring and PGS.

    Science.gov (United States)

    Mateo, S; Vidal, F; Parriego, M; Rodríguez, I; Montalvo, V; Veiga, A; Boada, M

    2017-07-01

    The purpose of this study was to investigate the chromosomal constitution and the developmental potential of intracytoplasmic sperm injection (ICSI) deriving embryos displaying a single pronucleus at the zygote stage. Eighty-eight embryos from single pronucleus (1PN) two polar bodies (2PB) ICSI zygotes from 64 preimplantational genetic screening (PGS) cycles (October 2012-December 2014), were retrospectively analyzed. Zygotes were cultured in a time-lapse incubator. Embryo biopsy was performed on day 3 and genetic analysis approached by array comparative genomic hybridization. Chromosomal analysis revealed that 17% (15/88) of embryos derived from 1PN 2PB zygotes were diagnosed as euploid. After blastomere biopsy at day 3, the blastocyst rate at day 5 was 3.4% (3/88). Only 2.3% (2/88) euploid blastocysts were obtained. In two couples and after counseling and patient agreement, the transfer of a euploid blastocyst from a 1PN 2PB ICSI zygote was performed resulting in the birth of a healthy child. These results open the possibility to consider embryos coming from 1PN 2PB ICSI zygotes for transfer when no other embryos from 2PN 2PB ICSI zygotes are available and if a PGS diagnosis of euploidy is obtained. Confirmation of biparental inheritance is strongly recommended.

  3. Thermal erosion of a permafrost coastline: Improving process-based models using time-lapse photography

    Science.gov (United States)

    Wobus, C.; Anderson, R.; Overeem, I.; Matell, N.; Clow, G.; Urban, F.

    2011-01-01

    Coastal erosion rates locally exceeding 30 m y-1 have been documented along Alaska's Beaufort Sea coastline, and a number of studies suggest that these erosion rates have accelerated as a result of climate change. However, a lack of direct observational evidence has limited our progress in quantifying the specific processes that connect climate change to coastal erosion rates in the Arctic. In particular, while longer ice-free periods are likely to lead to both warmer surface waters and longer fetch, the relative roles of thermal and mechanical (wave) erosion in driving coastal retreat have not been comprehensively quantified. We focus on a permafrost coastline in the northern National Petroleum Reserve-Alaska (NPR-A), where coastal erosion rates have averaged 10-15 m y-1 over two years of direct monitoring. We take advantage of these extraordinary rates of coastal erosion to observe and quantify coastal erosion directly via time-lapse photography in combination with meteorological observations. Our observations indicate that the erosion of these bluffs is largely thermally driven, but that surface winds play a crucial role in exposing the frozen bluffs to the radiatively warmed seawater that drives melting of interstitial ice. To first order, erosion in this setting can be modeled using formulations developed to describe iceberg deterioration in the open ocean. These simple models provide a conceptual framework for evaluating how climate-induced changes in thermal and wave energy might influence future erosion rates in this setting.

  4. Time-lapse imaging provides further evidence that planar arrangement of blastomeres is highly abnormal.

    Science.gov (United States)

    Ebner, Thomas; Höggerl, Alexandra; Oppelt, Peter; Radler, Elisabeth; Enzelsberger, Simon-Hermann; Mayer, Richard B; Petek, Erwin; Shebl, Omar

    2017-12-01

    Recently, guidelines on the annotation of dynamic human embryo monitoring recommended screening for the presence of planar blastomere arrangement at the 4-cell stage. This observational study was set up in order to analyze whether developmental kinetics of planar human embryos are different from tetrahedral ones. Therefore, embryos of 115 consecutive ICSI patients (showing 32 planar and 554 tetrahedral embryos) were cultured in a new time-lapse system (Miri TL) and their embryos were annotated for morphokinetic development and screened for irregular cleavages and morphological dysmorphisms. Significantly less planar embryos reached blastocyst stage and showed worse quality as compared to regular tetrahedral embryos. The rate of bi- and/or multinucleation was also significantly higher in the affected group. Irregular cleavages, particularly embryo rolling, were more often seen in planar embryos. Morphokinetics between planar and tetrahedral were distinguishable up to 4-cell stage (t2-t4), thereafter the observed delay in planar embryos (t8) was more likely the result of a higher rate of arrested embryos in the planar group. Planar embryos are associated with both a significant increase in irregular cleavage as well as a delay in preimplantation development. This indicates that planar embryos are rather abnormal and should only be considered for transfer if no other embryos are available.

  5. ESIAC: A data products system for ERTS imagery (time-lapse viewing and measuring)

    Science.gov (United States)

    Evans, W. E.; Serebreny, S. M.

    1974-01-01

    An Electronic Satellite Image Analysis Console (ESIAC) has been developed for visual analysis and objective measurement of earth resources imagery. The system is being employed to process imagery for use by USGS investigators in several different disciplines studying dynamic hydrologic conditions. The ESIAC provides facilities for storing registered image sequences in a magnetic video disc memory for subsequent recall, enhancement, and animated display in monochrome or color. The unique feature of the system is the capability to time-lapse the ERTS imagery and/or analytic displays of the imagery. Data products have included quantitative measurements of distances and areas, brightness profiles, and movie loops of selected themes. The applications of these data products are identified and include such diverse problem areas as measurement of snowfield extent, sediment plumes from estuary dicharge, playa inventory, phreatophyte and other vegetation changes. A comparative ranking of the electronic system in terms of accuracy, cost effectiveness and data output shows it to be a viable means of data analysis.

  6. Time-lapse resistivity analysis of Quaternary sediments in the Midlands of Ireland

    Science.gov (United States)

    Pellicer, Xavier M.; Zarroca, Mario; Gibson, Paul

    2012-07-01

    Electrical Resistivity Tomography (ERT) data are influenced by a number of factors associated with the subsurface such as porosity, moisture content and lithology; as well as external factors such as rainfall and temperature. Two time-lapse ERT profiles with 5 m and two with 2 m electrode spacings were acquired over a range of Quaternary sediment types encompassing till, esker gravel, glaciofluvial sand and silt and glaciolacustrine silt/clay. Data were collected on a monthly basis during 2006 at a site located in the Midlands of Ireland in order to evaluate the influence of such conditioning factors on the resistivity of the subsurface. Effective recharge, the depth of investigation, the texture and the internal architecture of the different sediment types and temperature variation are the main factors influencing the resistivity seasonal variation. The shallow subsurface (factors influencing the electrical response of the subsurface are the electrode spacing used for data collection and the seasonal temperature variation of the subsurface. Two methods for temperature correction of electrical resistivity data were tested in this study — both gave similar results. Resistivity values recorded in the shallow subsurface (< 5 m) show variations of over 15% subsequent to temperature correction. The results illustrate that seasonal temperature changes and their influence on subsurface temperature have to be accounted for in data interpretation and emphasise the potential of this technique for the estimation of the rate of movement of the wetting/drying front in soft sediments.

  7. Application of time-lapse seismic shear wave inversion to characterize the stimulated rock volume in the Niobrara and Codell Reservoirs, Wattenberg Field, CO

    Science.gov (United States)

    Mueller, Staci K.

    Advances in horizontal drilling and completions in shale reservoirs have allowed operators to extract hydrocarbons within low permeability reservoirs that were once impossible to access. The integration of time-lapse multicomponent seismic data with engineering technology aids in the characterization of these reservoirs through monitoring. This thesis investigates the fast and slow shear wave components of a time-lapse, nine-component seismic survey to determine the stimulated volume in the Niobrara and Codell reservoir intervals. The time-lapse post-stack inversions of the shear wave datasets provide insight into how the shear impedance is affected by hydraulic fracturing through the work of cross-equalized seismic shear impedances and shear wave splitting. The study area is the Wishbone Section within Wattenberg Field, CO, which is owned and operated by Anadarko Petroleum Corporation and contains eleven horizontal wells that vary in spacing and completion methods. Shear seismic data sets were acquired over this section before and after hydraulic stimulation. The time-lapse shear seismic inversions show an increase in fast shear wave velocity and a decrease in slow shear velocity after stimulation. The sensitivity of both the fast and slow shear seismic to stimulation correlates with the net pressure trends at each stage. Borehole image log interpretations are compared to the inversions to analyze the affect that a complex fracture network has on induced anisotropy. The stimulated volume for the Niobrara and Codell reservoir intervals are now more accurately defined. Time-lapse shear seismic is the only technology that is able to define the stimulated rock volume and reveal areas that are not being accessed by the wells currently drilled. These areas are now detected within the Wishbone section, and may be candidates for future re-completion.

  8. Maxillofacial injury: A retrospective analysis of time lapse between ...

    African Journals Online (AJOL)

    2013-11-04

    Nov 4, 2013 ... facial fractures in South Africa, no study of the timing of the stages from facial fracture to treatment has been reported from South. Africa or elsewhere. This investigation aimed to improve service planning and delivery in the DMFOS by examining where the primary cause of delayed treatment might lie – with ...

  9. Time-lapse resistivity surveys over simulated clandestine graves.

    Science.gov (United States)

    Jervis, John R; Pringle, Jamie K; Tuckwell, George W

    2009-11-20

    The aim of this study was to develop a better understanding of how electrical resistivity surveys can be used to locate clandestine graves. Resistivity surveys were conducted regularly over three simulated clandestine graves containing a pig cadaver, no cadaver and a pig cadaver wrapped in tarpaulin, respectively. Additionally, soil and groundwater samples were collected from two more simulated graves outside the survey area. The grave containing a pig cadaver was detectable from a low resistivity anomaly in the survey data. Groundwater data suggest that the resistivity anomaly associated with the surveyed pig grave was caused by a localised increase in groundwater conductivity. Wrapping a cadaver was found to initially change the resistivity response of a grave to a high resistivity anomaly. Resistivity surveys did not detect the disturbed soil in the grave that did not contain a cadaver. Although soil samples showed grave soil to be more porous than undisturbed soil, the lack of response from the grave that did not contain a cadaver suggests that disturbed soil was not responsible for the resistivity anomalies observed in this study. Resistivity surveys successfully detected all graves containing cadavers throughout the study, whilst also showing the potential to eliminate the need for mass excavation in a genuine search.

  10. Construction of an 8-mm time-lapse camera for biological research

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This report covers the construction of an 8mm camera for biological research. A time-lapse camera for use in biological research can be constructed from a super 8-mm...

  11. 3D lens-free time-lapse microscopy for 3D cell culture

    Science.gov (United States)

    Berdeu, Anthony; Momey, Fabien; Laperrousaz, Bastien; Bordy, Thomas; Gidrol, Xavier; Dinten, Jean-Marc; Picollet-D'hahan, Nathalie; Allier, Cédric

    2017-07-01

    We propose a new imaging platform based on lens-free time-lapse microscopy for 3D cell culture and its dedicated algorithm lying on a fully 3D regularized inverse problem approach. First 3D+t results are presented

  12. Exploiting the airwave for time-lapse reservoir monitoring with CSEM on land

    NARCIS (Netherlands)

    Wirianto, M.; Mulder, W.A.; Slob, E.C.

    2011-01-01

    In the application of controlled source electromagnetics for reservoir monitoring on land, repeatability errors in the source will mask the time-lapse signal due to hydrocarbon production when recording surface data close to the source. We demonstrate that at larger distances, the airwave will still

  13. Time-Lapse and Slow-Motion Tracking of Temperature Changes: Response Time of a Thermometer

    Science.gov (United States)

    Moggio, L.; Onorato, P.; Gratton, L. M.; Oss, S.

    2017-01-01

    We propose the use of a smartphone based time-lapse and slow-motion video techniques together with tracking analysis as valuable tools for investigating thermal processes such as the response time of a thermometer. The two simple experimental activities presented here, suitable also for high school and undergraduate students, allow one to measure…

  14. Latest time-lapse seismic data from Sleipner yield new insights into CO2 plume development

    NARCIS (Netherlands)

    Chadwick, R.A.; Noy, D.; Arts, R.; Eiken, O.

    2009-01-01

    Since its inception in 1996, the CO2 injection operation at Sleipner has been monitored by 3D time-lapse seismic surveys. Striking images of the CO2 plume have been obtained, showing a multi-tier feature of high reflectivity, interpreted as arising from a number of thin layers of CO2 trapped beneath

  15. Determination of Optimum Frame Rates for Observation of Construction Operations from Time-Lapse Movies

    Directory of Open Access Journals (Sweden)

    Y. M. Ibrahim

    2012-07-01

    Full Text Available Construction professionals have been using time-lapse movies in monitoring construction operations. However, some amount of detail is always lost in the interval between two consecutive frames in a time-lapse movie. This poses the question: By how much can the frame rate be lowered from the standard 30fps (frames per second to allow for the accurate observation of construction operations from a time-lapse movie? This paper addresses the problem by establishing the optimum frame rates for observation of activities related to mortar mixing and block handling. The activities were first recorded at the standard rate of 30fps. Using the Adobe Premier Pro video editing software, the records were then segregated into still images from which 15 different time-lapse movies of various time intervals were generated. The movies were then shown to 25 Construction Managers. A structured questionnaire was employed to capture the level of accuracy with which Construction Managers could interpret the job site situation from each movie. The results suggest that 1fpm (frame per minute is sufficient for the accurate tracking of labourers involved in mortar mixing while 1 frame in every 20 seconds is sufficient for accurate identification of number of cement bags used. However, for tracking number of blocks off-loaded, and those damaged, 1 frame in every 2 seconds is required.

  16. Integrated time-lapse geoelectrical imaging of wetland hydrological processes

    Science.gov (United States)

    Uhlemann, S. S.; Sorensen, J. P. R.; House, A. R.; Wilkinson, P. B.; Roberts, C.; Gooddy, D. C.; Binley, A. M.; Chambers, J. E.

    2016-03-01

    Wetlands provide crucial habitats, are critical in the global carbon cycle, and act as key biogeochemical and hydrological buffers. The effectiveness of these services is mainly controlled by hydrological processes, which can be highly variable both spatially and temporally due to structural complexity and seasonality. Spatial analysis of 2-D geoelectrical monitoring data integrated into the interpretation of conventional hydrological data has been implemented to provide a detailed understanding of hydrological processes in a riparian wetland. A two-layered hydrological system was observed in the peat. In the lower part of the peat, upwelling of deeper groundwater from underlying deposits was considered the driver for a 30% increase in peat resistivity during Winter/Spring. In Spring/Summer there was a 60% decrease in resistivity in the near-surface peats due to plant transpiration and/or microbial activity. Water exchange between the layers only appeared to be initiated following large drops in the encircling surface water stage. For the first time, we demonstrated that automated interpretation of geoelectrical data can be used to quantify ground movement in the vertical direction. Here, we applied this method to quantify shrink-swell of expandable soils, affecting hydrological parameters, such as, porosity and permeability. This study shows that an integrated interpretation of hydrological and geophysical data can significantly improve the understanding of wetland hydrological processes. Potentially, this approach can provide the basis for the evaluation of ecosystem services and may aid in the optimization of wetland management strategies.

  17. Fluorescence time-lapse imaging of single cells targeted with a focused scanning charged-particle microbeam

    Energy Technology Data Exchange (ETDEWEB)

    Bourret, Stéphane [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Vianna, François [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); IRSN, BP 3, F-13115 Saint-Paul Lez Durance (France); Devès, Guillaume [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Atallah, Vincent [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Department of Radiation Oncology, Institut Bergonié, Bordeaux (France); Univ. Victor Segalen, Bordeaux (France); Moretto, Philippe; Seznec, Hervé [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Barberet, Philippe, E-mail: barberet@cenbg.in2p3.fr [Univ. Bordeaux, CENBG, UMR 5797, F-33170 Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France)

    2014-04-01

    Charged particle microbeams provide unique features to study targeted and non-targeted radiation response and have recently emerged as a powerful tool to investigate radiation-induced DNA damage and repair. We have developed a charged particle microbeam delivering protons and alpha particles in the MeV energy range equipped with online time-lapse imaging capabilities. The beam is focused to a sub-micrometer beam spot under vacuum by means of a triplet of magnetic quadrupoles and extracted in air through a 200 nm Si{sub 3}N{sub 4} window. The end-station is equipped with an automated fluorescence microscope used for single cell targeting and online time-lapse imaging. Cells are kept in their medium during the irradiation procedure and the sample temperature is regulated to 37 °C. An overall targeting accuracy of 2.0 ± 0.7 μm has been measured by tracking the re-localization of the XRCC1 protein. First measurements of this re-localization shows the ability of our system to follow online the radiation-induced re-localization of proteins in the first minutes after irradiation.

  18. Time-lapse systems for embryo incubation and assessment in assisted reproduction.

    Science.gov (United States)

    Armstrong, Sarah; Arroll, Nicola; Cree, Lynsey M; Jordan, Vanessa; Farquhar, Cindy

    2015-02-27

    Embryo incubation and assessment is a vital step in assisted reproductive technology (ART). Traditionally, embryo assessment has been achieved by removing embryos from a conventional incubator daily for assessment of quality by an embryologist, under a light microscope. Over recent years time-lapse systems (TLSs) have been developed which can take digital images of embryos at frequent time intervals. This allows embryologists, with or without the assistance of computer algorithms, to assess the quality of the embryos without physically removing them from the incubator.The potential advantages of a TLS include the ability to maintain a stable culture environment, therefore limiting the exposure of embryos to changes in gas composition, temperature and movement. Additionally a TLS has the potential advantage of improving embryo selection for ART treatment by utilising additional information gained through monitoring embryo development. To determine the effect of a TLS compared to conventional embryo incubation and assessment on clinical outcomes in couples undergoing ART. A comprehensive search of all the major electronic databases, including grey literature, was undertaken in co-ordination with the Trials Search Co-ordinator of the Cochrane Menstrual Disorders and Subfertility Group in July 2014 and repeated in November 2014 to confirm that the review is up to date. Two authors (SA and NA) independently scanned the titles and abstracts of the articles retrieved by the search. Full texts of potentially eligible randomised controlled trials (RCTs) were obtained and examined independently by the authors for their suitability according to the review inclusion criteria. In the case of doubt between the two authors, a third author (LC) was consulted to gain consensus. The selection process is documented with a Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) flow chart. Data were obtained and extracted by two authors. Disagreement was resolved

  19. Automated Ground-based Time-lapse Camera Monitoring of West Greenland ice sheet outlet Glaciers: Challenges and Solutions

    Science.gov (United States)

    Ahn, Y.; Box, J. E.; Balog, J.; Lewinter, A.

    2008-12-01

    Monitoring Greenland outlet glaciers using remotely sensed data has drawn a great attention in earth science communities for decades and time series analysis of sensory data has provided important variability information of glacier flow by detecting speed and thickness changes, tracking features and acquiring model input. Thanks to advancements of commercial digital camera technology and increased solid state storage, we activated automatic ground-based time-lapse camera stations with high spatial/temporal resolution in west Greenland outlet and collected one-hour interval data continuous for more than one year at some but not all sites. We believe that important information of ice dynamics are contained in these data and that terrestrial mono-/stereo-photogrammetry can provide theoretical/practical fundamentals in data processing along with digital image processing techniques. Time-lapse images over periods in west Greenland indicate various phenomenon. Problematic is rain, snow, fog, shadows, freezing of water on camera enclosure window, image over-exposure, camera motion, sensor platform drift, and fox chewing of instrument cables, and the pecking of plastic window by ravens. Other problems include: feature identification, camera orientation, image registration, feature matching in image pairs, and feature tracking. Another obstacle is that non-metric digital camera contains large distortion to be compensated for precise photogrammetric use. Further, a massive number of images need to be processed in a way that is sufficiently computationally efficient. We meet these challenges by 1) identifying problems in possible photogrammetric processes, 2) categorizing them based on feasibility, and 3) clarifying limitation and alternatives, while emphasizing displacement computation and analyzing regional/temporal variability. We experiment with mono and stereo photogrammetric techniques in the aide of automatic correlation matching for efficiently handling the enormous

  20. A method for quantifying cloud immersion in a tropical mountain forest using time-lapse photography

    Science.gov (United States)

    Bassiouni, Maoya; Scholl, Martha A.; Torres-Sanchez, Angel J.; Murphy, Sheila F.

    2017-01-01

    Quantifying the frequency, duration, and elevation range of fog or cloud immersion is essential to estimate cloud water deposition in water budgets and to understand the ecohydrology of cloud forests. The goal of this study was to develop a low-cost and high spatial-coverage method to detect occurrence of cloud immersion within a mountain cloud forest by using time-lapse photography. Trail cameras and temperature/relative humidity sensors were deployed at five sites covering the elevation range from the assumed lifting condensation level to the mountain peaks in the Luquillo Mountains of Puerto Rico. Cloud-sensitive image characteristics (contrast, the coefficient of variation and the entropy of pixel luminance, and image colorfulness) were used with a k-means clustering approach to accurately detect cloud-immersed conditions in a time series of images from March 2014 to May 2016. Images provided hydrologically meaningful cloud-immersion information while temperature-relative humidity data were used to refine the image analysis using dew point information and provided temperature gradients along the elevation transect. Validation of the image processing method with human-judgment based classification generally indicated greater than 90% accuracy. Cloud-immersion frequency averaged 80% at sites above 900 m during nighttime hours and 49% during daytime hours, and was consistent with diurnal patterns of cloud immersion measured in a previous study. Results for the 617 m site demonstrated that cloud immersion in the Luquillo Mountains rarely occurs at the previously-reported cloud base elevation of about 600 m (11% during nighttime hours and 5% during daytime hours). The framework presented in this paper will be used to monitor at a low cost and high spatial resolution the long-term variability of cloud-immersion patterns in the Luquillo Mountains, and can be applied to ecohydrology research at other cloud-forest sites or in coastal ecosystems with advective sea

  1. On the feasibility of time-lapse superconducting gravimetry for reservoir monitoring

    Science.gov (United States)

    Elliott, Elizabeth Judith

    The feasibility of monitoring fluid flow subsurface processes that result in density changes, using the iGrav superconducting gravimeter, is investigated. Practical targets include steam-assisted gravity drainage (SAGD) bitumen depletion and water pumping from aquifers, for which there is currently a void in low-impact, inexpensive monitoring techniques. This study demonstrates that the iGrav has the potential to be applied to multi-scale and diverse reservoirs. Gravity and gravity gradient signals are forward modeled for a real SAGD reservoir at two time steps, and for surface-fed and groundwater-fed aquifer pumping models, to estimate signal strength and directional dependency of water flow. Time-lapse gravimetry on small-scale reservoirs exhibits two obstacles, namely, a microgal sensitivity requirement and high noise levels in the vicinity of the reservoir. In this study, both limitations are overcome by proposing (i) a portable superconducting gravimeter, and (ii) a pair of instruments under various baseline geometries. This results in improved spatial resolution for locating depletion zones, as well as the cancellation of noise common in both instruments. Results indicate that a pair of iGrav superconducting gravimeters meet the sensitivity requirements and the spatial focusing desired to monitor SAGD bitumen migration at the reservoir scales. For SAGD reservoirs, the well pair separation, reservoir depth, and survey sampling determine the resolvability of individual well pair depletion patterns during the steam chamber rising phase, and general reservoir depletion patterns during the steam chamber spreading phase. Results show that monitoring water table elevation changes due to pumping and tracking whether groundwater or surface water is being extracted are feasible.

  2. Time-Lapse Monitoring of Subsurface Fluid Flow using Parsimonious Seismic Interferometry

    KAUST Repository

    Hanafy, Sherif

    2017-04-21

    A typical small-scale seismic survey (such as 240 shot gathers) takes at least 16 working hours to be completed, which is a major obstacle in case of time-lapse monitoring experiments. This is especially true if the subject that needs to be monitored is rapidly changing. In this work, we will discuss how to decrease the recording time from 16 working hours to less than one hour of recording. Here, the virtual data has the same accuracy as the conventional data. We validate the efficacy of parsimonious seismic interferometry with the time-lapse mentoring idea with field examples, where we were able to record 30 different data sets within a 2-hour period. The recorded data are then processed to generate 30 snapshots that shows the spread of water from the ground surface down to a few meters.

  3. Probabilistic 3-D time-lapse inversion of magnetotelluric data: application to an enhanced geothermal system

    OpenAIRE

    Rosas-Carbajal, M; N. Linde; Peacock, J.; Zyserman, F. I.; Kalscheuer, Thomas; Thiel, S.

    2015-01-01

    Surface-based monitoring of mass transfer caused by injections and extractions in deep boreholes is crucial to maximize oil, gas and geothermal production. Inductive electromagnetic methods, such as magnetotellurics, are appealing for these applications due to their large penetration depths and sensitivity to changes in fluid conductivity and fracture connectivity. In this work, we propose a 3-D Markov chain Monte Carlo inversion of time-lapse magnetotelluric data to image mass transfer follo...

  4. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    OpenAIRE

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, J?r?me; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-01-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds withou...

  5. Unscented Kalman filter assimilation of time-lapse self-potential data for monitoring solute transport

    Science.gov (United States)

    Cui, Yi-an; Liu, Lanbo; Zhu, Xiaoxiong

    2017-08-01

    Monitoring the extent and evolution of contaminant plumes in local and regional groundwater systems from existing landfills is critical in contamination control and remediation. The self-potential survey is an efficient and economical nondestructive geophysical technique that can be used to investigate underground contaminant plumes. Based on the unscented transform, we have built a Kalman filtering cycle to conduct time-lapse data assimilation for monitoring the transport of solute based on the solute transport experiment using a bench-scale physical model. The data assimilation was formed by modeling the evolution based on the random walk model and observation correcting based on the self-potential forward. Thus, monitoring self-potential data can be inverted by the data assimilation technique. As a result, we can reconstruct the dynamic process of the contaminant plume instead of using traditional frame-to-frame static inversion, which may cause inversion artifacts. The data assimilation inversion algorithm was evaluated through noise-added synthetic time-lapse self-potential data. The result of the numerical experiment shows validity, accuracy and tolerance to the noise of the dynamic inversion. To validate the proposed algorithm, we conducted a scaled-down sandbox self-potential observation experiment to generate time-lapse data that closely mimics the real-world contaminant monitoring setup. The results of physical experiments support the idea that the data assimilation method is a potentially useful approach for characterizing the transport of contamination plumes using the unscented Kalman filter (UKF) data assimilation technique applied to field time-lapse self-potential data.

  6. Seismic time-lapse imaging using Interferometric least-squares migration

    KAUST Repository

    Sinha, Mrinal

    2016-09-06

    One of the problems with 4D surveys is that the environmental conditions change over time so that the experiment is insufficiently repeatable. To mitigate this problem, we propose the use of interferometric least-squares migration (ILSM) to estimate the migration image for the baseline and monitor surveys. Here, a known reflector is used as the reference reflector for ILSM. Results with synthetic and field data show that ILSM can eliminate artifacts caused by non-repeatability in time-lapse surveys.

  7. Unsupervised automated high throughput phenotyping of RNAi time-lapse movies.

    Science.gov (United States)

    Failmezger, Henrik; Fröhlich, Holger; Tresch, Achim

    2013-10-04

    Gene perturbation experiments in combination with fluorescence time-lapse cell imaging are a powerful tool in reverse genetics. High content applications require tools for the automated processing of the large amounts of data. These tools include in general several image processing steps, the extraction of morphological descriptors, and the grouping of cells into phenotype classes according to their descriptors. This phenotyping can be applied in a supervised or an unsupervised manner. Unsupervised methods are suitable for the discovery of formerly unknown phenotypes, which are expected to occur in high-throughput RNAi time-lapse screens. We developed an unsupervised phenotyping approach based on Hidden Markov Models (HMMs) with multivariate Gaussian emissions for the detection of knockdown-specific phenotypes in RNAi time-lapse movies. The automated detection of abnormal cell morphologies allows us to assign a phenotypic fingerprint to each gene knockdown. By applying our method to the Mitocheck database, we show that a phenotypic fingerprint is indicative of a gene's function. Our fully unsupervised HMM-based phenotyping is able to automatically identify cell morphologies that are specific for a certain knockdown. Beyond the identification of genes whose knockdown affects cell morphology, phenotypic fingerprints can be used to find modules of functionally related genes.

  8. Using time-lapse gravity for groundwater model calibration: An application to alluvial aquifer storage

    DEFF Research Database (Denmark)

    Christiansen, Lars; Binning, Philip John; Rosbjerg, Dan

    2011-01-01

    The estimation of hydrological model parameters by calibration to field data is a critical step in the modeling process. However, calibration often fails because of parameter correlation. Here it is shown that time-lapse gravity data can be combined with hydraulic head data in a coupled hydrogeop......The estimation of hydrological model parameters by calibration to field data is a critical step in the modeling process. However, calibration often fails because of parameter correlation. Here it is shown that time-lapse gravity data can be combined with hydraulic head data in a coupled...... shows that time-lapse gravity data are especially useful to constrain specific yield. Furthermore, we demonstrate that evapotranspiration, and riverbed conductance are better constrained by coupled inversion to gravity and head data than to head data alone. When estimating the four parameters...... simultaneously, the six correlation coefficients were reduced from unity when only head data were employed to significantly lower values when gravity and head data were combined. Our analysis reveals that the estimated parameter values are not very sensitive to the choice of weighting between head and gravity...

  9. Time-lapse seismic modeling and production data assimilation for enhanced oil recovery and carbon dioxide sequestration

    Science.gov (United States)

    Kumar, Ajitabh

    Production from a hydrocarbon reservoir is typically supported by water or carbon dioxide (CO2) injection. CO2 injection into hydrocarbon reservoirs is also a promising solution for reducing environmental hazards from the release of green house gases into the earth's atmosphere. Numerical simulators are used for designing and predicting the complex behavior of systems under such scenarios. Two key steps in such studies are forward modeling for performance prediction based on simulation studies using reservoir models and inverse modeling for updating reservoir models using the data collected from field. The viability of time-lapse seismic monitoring using an integrated modeling of fluid flow, including chemical reactions, and seismic response is examined. A comprehensive simulation of the gas injection process accounting for the phase behavior of CO2-reservoir fluids, the associated precipitation/dissolution reactions, and the accompanying changes in porosity and permeability is performed. The simulation results are then used to model the changes in seismic response with time. The general observation is that gas injection decreases bulk density and wave velocity of the host rock system. Another key topic covered in this work is the data assimilation study for hydrocarbon reservoirs using Ensemble Kalman Filter (EnKF). Some critical issues related to EnKF based history matching are explored, primarily for a large field with substantial production history. A novel and efficient approach based on spectral clustering to select 'optimal' initial ensemble members is proposed. Also, well-specific black-oil or compositional streamline trajectories are used for covariance localization. Approach is applied to the Weyburn field, a large carbonate reservoir in Canada. The approach for optimal member selection is found to be effective in reducing the ensemble size which was critical for this large-scale field application. Streamline-based covariance localization is shown to play

  10. A predictive model for blastocyst formation based on morphokinetic parameters in time-lapse monitoring of embryo development.

    Science.gov (United States)

    Milewski, Robert; Kuć, Paweł; Kuczyńska, Agnieszka; Stankiewicz, Bożena; Łukaszuk, Krzysztof; Kuczyński, Waldemar

    2015-04-01

    The aim of the study was to create a predictive model of blastocyst development based on morphokinetic parameters of time-lapse embryoscope monitoring. Time-lapse recordings of 432 embryos (obtained from 77 patients), monitored in Embryoscope, were involved in the study. Patients underwent in vitro fertilization according to standard procedure between June 2012 and April 2013. A retrospective analysis of morphokinetic features, focused on duration of time from the Intracytoplasmic Sperm Injection (ICSI) procedure to consecutive embryo division for 2, 3, 4 and 5 blastomeres, as well as time intervals between each division, was conducted. All embryos were observed for 5 days. Based on the distribution of analyzed morphokinetic parameters and number of embryos developed to blastocyst, a range denoting the possibility of an embryo reaching blastocyst stage was determined. According to the obtained results, univariate and multivariate logistic regression analyses were performed. Based on the times of division for two and five blastomeres and intervals between the second and third division, a multivariate predictive model was created. The predictive equation was constructed based on the parameters of logistic regression analysis (odds ratios). Statistically significant differences (p prediction parameter between the group of embryos developed to blastocyst (the median value: Me = 9.95, and quartiles: Q1 = 7.59, Q3 = 12.30) and embryos that did not develop to the blastocyst stage (Me = 4.66, Q1 = 2.33, Q3 = 8.19) were found. A Receiver Operating Characteristic (ROC) curve was created for the constructed predictive model. The Area Under the Curve was AUC = 0.806 with a 95 % confidence interval (0.747, 0.864). The predictive model constructed in this study has been validated using an independent data set, which indicates that the model is reliable and repeatable. Time-lapse imaging presents a new diagnostic tool for parametric evaluation of

  11. Modeling of time-lapse seismic reflection data from CO2 sequestration at West Pearl Queen Field

    Science.gov (United States)

    Bartel, L. C.; Haney, M. M.; Aldridge, D. F.; Symons, N. P.; Elbring, G. J.

    2006-12-01

    Sequestration of CO2 in depleted oil reservoirs, saline aquifers, or unminable coal sequences may prove to be an economical and environmentally safe means for long-term removal of carbon from the atmosphere. Requirements for storage of CO2 in subsurface geologic repositories (e.g., less than 0.1% per year leakage) pose significant challenges for geophysical remote sensing techniques. The many issues relevant to successful CO2 sequestration (volume in place, migration, leakage rate) require improved understanding of the advantages and pitfalls of potential monitoring methods. Advanced numerical modeling of time-lapse seismic reflection responses offers a controlled environment for testing hypotheses and exploring alternatives. The U.S. Department of Energy has conducted CO2 sequestration and monitoring tests at West Pearl Queen (WPQ) field in southeastern New Mexico. High-quality 9C/3D seismic reflection data were acquired before and after injection of ~2 kt of CO2 into a depleted sandstone unit at ~4200 ft depth. Images developed from time- lapse seismic data appear to reveal strong reflectivity changes attributed to displacement of brine by CO2. We are pursuing seismic numerical modeling studies with the goal of understanding and assessing the reliability and robustness of the time-lapse reflection responses. A 3D time-domain finite-difference isotropic elastic wave propagation algorithm generates realistic synthetic data. With this capability, we examine how various types of errors and noise in the 4D data degrade the ability to image a deep CO2 plume. Source/receiver sampling, subsurface illumination, correlated geologic heterogeneity, and static shifts are considered. As a result, we are able to make quantitative estimates of the tolerable errors for monitoring CO2 injection at WPQ field. Future plans include incorporating 3D poroelastic wave propagation modeling into the analysis. Sandia National Laboratories is a multiprogram science and engineering facility

  12. Acquiring fluorescence time-lapse movies of budding yeast and analyzing single-cell dynamics using GRAFTS.

    Science.gov (United States)

    Zopf, Christopher J; Maheshri, Narendra

    2013-07-18

    Fluorescence time-lapse microscopy has become a powerful tool in the study of many biological processes at the single-cell level. In particular, movies depicting the temporal dependence of gene expression provide insight into the dynamics of its regulation; however, there are many technical challenges to obtaining and analyzing fluorescence movies of single cells. We describe here a simple protocol using a commercially available microfluidic culture device to generate such data, and a MATLAB-based, graphical user interface (GUI) -based software package to quantify the fluorescence images. The software segments and tracks cells, enables the user to visually curate errors in the data, and automatically assigns lineage and division times. The GUI further analyzes the time series to produce whole cell traces as well as their first and second time derivatives. While the software was designed for S. cerevisiae, its modularity and versatility should allow it to serve as a platform for studying other cell types with few modifications.

  13. Isoniazid Killing of Mycobacterium smegmatis NADH Pyrophosphatase Mutant at Single-Cell Level using Microfluidics and Time-Lapse Microscopy.

    Science.gov (United States)

    Elitas, Meltem

    2017-09-07

    We introduce single-cell analysis for isoniazid-treated Mycobacterium smegmatis mutant, msm1946-NADH pyrophosphatase, using microfluidics and automated time-lapse microscopy. Mycobacterial NADH pyrophosphatase isoforms play an important role for the mechanism of isoniazid and ethionamide activation. Our single-cell analysis revealed important insights on isoniazid killing mechanism that was masked by traditional killing assays, raised significant questions related to viable but non-culturable subpopulation of cells, and existing methods that defines minimum inhibitory concentration of drugs. The major goal of this study was quantitatively analyze bacterial cell parameters to obtain high-resolution data for the time evolution of antibiotic killing at the single-cell level. The presented tools and methods could be applied to the closely related organisms to provide more detailed information for the design and employment of antibiotic treatments.

  14. Osteoclast Fusion: Time-Lapse Reveals Involvement of CD47 and Syncytin-1 at Different Stages of Nuclearity.

    Science.gov (United States)

    Møller, Anaïs Marie Julie; Delaissé, Jean-Marie; Søe, Kent

    2017-06-01

    Investigations addressing the molecular keys of osteoclast fusion are primarily based on end-point analyses. No matter if investigations are performed in vivo or in vitro the impact of a given factor is predominantly analyzed by counting the number of multi-nucleated cells, the number of nuclei per multinucleated cell or TRAcP activity. But end-point analyses do not show how the fusion came about. This would not be a problem if fusion of osteoclasts was a random process and occurred by the same molecular mechanism from beginning to end. However, we and others have in the recent period published data suggesting that fusion partners may specifically select each other and that heterogeneity between the partners seems to play a role. Therefore, we set out to directly test the hypothesis that fusion factors have a heterogenic involvement at different stages of nuclearity. Therefore, we have analyzed individual fusion events using time-lapse and antagonists of CD47 and syncytin-1. All time-lapse recordings have been studied by two independent observers. A total of 1808 fusion events were analyzed. The present study shows that CD47 and syncytin-1 have different roles in osteoclast fusion depending on the nuclearity of fusion partners. While CD47 promotes cell fusions involving mono-nucleated pre-osteoclasts, syncytin-1 promotes fusion of two multi-nucleated osteoclasts, but also reduces the number of fusions between mono-nucleated pre-osteoclasts. Furthermore, CD47 seems to mediate fusion mostly through broad contact surfaces between the partners' cell membrane while syncytin-1 mediate fusion through phagocytic-cup like structure. J. Cell. Physiol. 232: 1396-1403, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  15. Analysis of Snow Line and Albedo Conditions By Means of Time-Lapse Photography on Tapado Glacier, Chile

    Science.gov (United States)

    Vivero, S.; MacDonell, S.; McPhee, J. P.

    2014-12-01

    In the semiarid Coquimbo Region of Chile, high-altitude glaciers and seasonal snow are important sources of freshwater for irrigated agriculture and urban consumption. Due to the aridity of the environment, losses due to sublimation are large which means that accurate melt modelling is essential in order to reliably estimate streamflow. Since 2008, the CEAZA glaciology group has been studying the energy and mass balance of the largest glacier in the catchment, the Tapado Glacier using field and remote sensing measurements, and numerical modelling. The Tapado glacier system (30°08' S, 69°55' W) is a complex assemblage of uncovered and debris-covered ice located at the head of the Elqui basin between 4500 and 5536 m a.s.l. Energy balance modelling studies at the site have been limited in scope due to the development of ice pinnacles or penitentes on snow and ice surfaces. These features complicate energy distribution across the surface, due to modifications of parameters such as albedo. In this paper, we use time-lapse photography and automatic weather station (AWS) measurements to investigate how the development of penitentes impacts the spatial and temporal variability of albedo across the glacier surface and whether terrestrial photography is appropriate for use at such locations. Oblique photographs obtained from a high vantage point were georeferenced using a high resolution digital elevation model available for the entire glacier and its environs. By comparing the photographic data with point albedo measurements made at an AWS, distributed albedo maps were produced. Preliminary results suggest that distributed albedo values may be underestimated by the formation and development of penitentes during the ablation season. Moreover, it was observed that the evolution of the snow line during summer was not only topographically controlled but also modified by occasional convective snowfalls. Time-lapse photography provided to be a cost-effective tool for monitoring

  16. Water partitioning and storage via preferential pathways on the hillslope scale observed using time-lapse ERT

    Science.gov (United States)

    Kotikian, M.; Parsekian, A.; Paige, G. B.; Carey, A. M.

    2016-12-01

    Water in the west is primarily sourced from snowmelt in the mountainous alpine zone providing freshwater for rivers and recharge for groundwater aquifers. Subsurface water flow often moves through the soil and fractured rock although its storage, residence time, and partitioning have not been well documented at the hillslope scale. In this study we investigate water partitioning and preferential flow pathways using geophysical methods to complete the water balance. We hypothesize that preferential flow paths will indicate where water is partitioning into groundwater stores and will differ based on the vegetation cover and soil depth. We use daily time-lapse electric resistivity tomography (TL-ERT) to estimate moisture content on seasonal and annual time-scales. Water content is assumed to be the only variable to change over the duration of the measurement after temperature corrections. The ERT measurement is combined with other geophysical measurements including seismic refraction tomography for locating the weathering front, time-lapse borehole nuclear magnetic resonance (NMR) to directly measure changes in water content over the season, and 3D ERT as a control for out-of-plane effects of the 2D TL-ERT measurement. The results show that during snowmelt, the wetting front is heterogeneous and moves down at a rate up to 25 mm/day within the top 5m. A preferential flow path is observed to be moving water to at least 5m depth in one area. This preferential flow anomaly only occurred during snowmelt and was not observed during rainfall-driven infiltration. Heterogeneities in vegetation cover and soil depth result in different water flow behaviors. These results indicate that water storage increases during the snowmelt season and partitioning pathways differ seasonally and with precipitation type.

  17. Penicillin induced persistence in Chlamydia trachomatis: high quality time lapse video analysis of the developmental cycle.

    Directory of Open Access Journals (Sweden)

    Rachel J Skilton

    Full Text Available BACKGROUND: Chlamydia trachomatis is a major human pathogen with a unique obligate intracellular developmental cycle that takes place inside a modified cytoplasmic structure known as an inclusion. Following entry into a cell, the infectious elementary body (EB differentiates into a non-infectious replicative form known as a reticulate body (RB. RBs divide by binary fission and at the end of the cycle they redifferentiate into EBs. Treatment of C.trachomatis with penicillin prevents maturation of RBs which survive and enlarge to become aberrant RBs within the inclusion in a non-infective persistent state. Persistently infected individuals may be a reservoir for chlamydial infection. The C.trachomatis genome encodes the enzymes for peptidoglycan (PG biosynthesis but a PG sacculus has never been detected. This coupled to the action of penicillin is known as the chlamydial anomaly. We have applied video microscopy and quantitative DNA assays to the chlamydial developmental cycle to assess the effects of penicillin treatment and establish a framework for investigating penicillin induced chlamydial persistence. PRINCIPAL FINDINGS: Addition of penicillin at the time of cell infection does not prevent uptake and the establishment of an inclusion. EB to RB transition occurs but bacterial cytokinesis is arrested by the second binary fission. RBs continue to enlarge but not divide in the presence of penicillin. The normal developmental cycle can be recovered by the removal of penicillin although the large, aberrant RBs do not revert to the normal smaller size but remain present to the completion of the developmental cycle. Chromosomal and plasmid DNA replication is unaffected by the addition of penicillin but the arrest of bacterial cytokinesis under these conditions results in RBs accumulating multiple copies of the genome. CONCLUSIONS: We have applied video time lapse microscopy to the study of the chlamydial developmental cycle. Linked with accurate

  18. Time-lapse refraction seismic tomography for the detection of ground ice degradation

    Directory of Open Access Journals (Sweden)

    C. Hilbich

    2010-07-01

    Full Text Available The ice content of the subsurface is a major factor controlling the natural hazard potential of permafrost degradation in alpine terrain. Monitoring of changes in ice content is therefore similarly important as temperature monitoring in mountain permafrost. Although electrical resistivity tomography monitoring (ERTM proved to be a valuable tool for the observation of ice degradation, results are often ambiguous or contaminated by inversion artefacts. In theory, the sensitivity of P-wave velocity of seismic waves to phase changes between unfrozen water and ice is similar to the sensitivity of electric resistivity. Provided that the general conditions (lithology, stratigraphy, state of weathering, pore space remain unchanged over the observation period, temporal changes in the observed travel times of repeated seismic measurements should indicate changes in the ice and water content within the pores and fractures of the subsurface material. In this paper, a time-lapse refraction seismic tomography (TLST approach is applied as an independent method to ERTM at two test sites in the Swiss Alps. The approach was tested and validated based on a the comparison of time-lapse seismograms and analysis of reproducibility of the seismic signal, b the analysis of time-lapse travel time curves with respect to shifts in travel times and changes in P-wave velocities, and c the comparison of inverted tomograms including the quantification of velocity changes. Results show a high potential of the TLST approach concerning the detection of altered subsurface conditions caused by freezing and thawing processes. For velocity changes on the order of 3000 m/s even an unambiguous identification of significant ice loss is possible.

  19. 3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

    Science.gov (United States)

    Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

    2017-02-01

    We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume.

  20. A software solution for recording circadian oscillator features in time-lapse live cell microscopy

    Directory of Open Access Journals (Sweden)

    Salmon Patrick

    2010-07-01

    Full Text Available Abstract Background Fluorescent and bioluminescent time-lapse microscopy approaches have been successfully used to investigate molecular mechanisms underlying the mammalian circadian oscillator at the single cell level. However, most of the available software and common methods based on intensity-threshold segmentation and frame-to-frame tracking are not applicable in these experiments. This is due to cell movement and dramatic changes in the fluorescent/bioluminescent reporter protein during the circadian cycle, with the lowest expression level very close to the background intensity. At present, the standard approach to analyze data sets obtained from time lapse microscopy is either manual tracking or application of generic image-processing software/dedicated tracking software. To our knowledge, these existing software solutions for manual and automatic tracking have strong limitations in tracking individual cells if their plane shifts. Results In an attempt to improve existing methodology of time-lapse tracking of a large number of moving cells, we have developed a semi-automatic software package. It extracts the trajectory of the cells by tracking theirs displacements, makes the delineation of cell nucleus or whole cell, and finally yields measurements of various features, like reporter protein expression level or cell displacement. As an example, we present here single cell circadian pattern and motility analysis of NIH3T3 mouse fibroblasts expressing a fluorescent circadian reporter protein. Using Circadian Gene Express plugin, we performed fast and nonbiased analysis of large fluorescent time lapse microscopy datasets. Conclusions Our software solution, Circadian Gene Express (CGE, is easy to use and allows precise and semi-automatic tracking of moving cells over longer period of time. In spite of significant circadian variations in protein expression with extremely low expression levels at the valley phase, CGE allows accurate and

  1. Soil Contamination, Advanced integrated characterisation and time-lapse Monitoring, SoilCAM project highlights

    Science.gov (United States)

    French, H. K.; Van Der Zee, S. E.; Wehrer, M.; Godio, A.; Pedersen, L. B.; Tsocano, G.

    2013-12-01

    The SoilCAM project (2008- 2012, EU-FP7-212663) aimed at improving methods for monitoring subsurace contaminant distribution and biodegradation. Two test sites were chosen, Oslo airport Gardermoen, Norway where de-icing agents infiltrate the soil during snowmelt and the Trecate site in Italy where an inland crude oil spill occurred in 1994. A number of geophysical investigation techniques were combined with soil and water sampling techniques. Data obtained from time-lapse measurements were further analysed by numerical modelling of flow and transport at different scales in order to characterise transport processes in the unsaturated and saturated zones. Laboratory experiments provided physical and biogeochemical data for model parameterisation and to select remediation methods. The geophysical techniques were used to map geological heterogeneities and to conduct time-lapse measurements of processes in the unsaturated zone. Both cross borehole and surface electrodes were used for electrical resistivity and induced polarisation surveys. Results showed clear indications of areas highly affected by de-icing chemicals along the runway at Oslo airport. The time lapse measurements along the runway at the airport showed infiltration patterns during snowmelt and were used to validate 2D unsaturated flow and transport simulations using SUTRA. The simulations illustrate the effect of layering geological structures and membranes, buried parallel to the runway, on the flow pattern. Complex interaction between bio-geo-chemical processes in a 1D vertical profile along the runway were described with the ORCHESTRA model. Smaller scale field site measurements revealed increase of iron and manganese during degradation of de-icing chemicals. At the Trecate site a combination of georadar, electrical resistivity and radio magneto telluric provided a broad outline of the geology down to 50 m. Anomalies in the Induced polarisation and electrical resistivity data from the cross borehole

  2. Reconstructed imaging of acoustic cloak using time-lapse reversal method

    Science.gov (United States)

    Zhou, Chen; Cheng, Ying; Xu, Jian-yi; Li, Bo; Liu, Xiao-jun

    2014-08-01

    We proposed and investigated a solution to the inverse acoustic cloak problem, an anti-stealth technology to make cloaks visible, using the time-lapse reversal (TLR) method. The TLR method reconstructs the image of an unknown acoustic cloak by utilizing scattered acoustic waves. Compared to previous anti-stealth methods, the TLR method can determine not only the existence of a cloak but also its exact geometric information like definite shape, size, and position. Here, we present the process for TLR reconstruction based on time reversal invariance. This technology may have potential applications in detecting various types of cloaks with different geometric parameters.

  3. Intelligent data analysis to model and understand live cell time-lapse sequences.

    Science.gov (United States)

    Paterson, Allan; Ashtari, M; Ribé, D; Stenbeck, G; Tucker, A

    2012-01-01

    One important aspect of cellular function, which is at the basis of tissue homeostasis, is the delivery of proteins to their correct destinations. Significant advances in live cell microscopy have allowed tracking of these pathways by following the dynamics of fluorescently labelled proteins in living cells. This paper explores intelligent data analysis techniques to model the dynamic behavior of proteins in living cells as well as to classify different experimental conditions. We use a combination of decision tree classification and hidden Markov models. In particular, we introduce a novel approach to "align" hidden Markov models so that hidden states from different models can be cross-compared. Our models capture the dynamics of two experimental conditions accurately with a stable hidden state for control data and multiple (less stable) states for the experimental data recapitulating the behaviour of particle trajectories within live cell time-lapse data. In addition to having successfully developed an automated framework for the classification of protein transport dynamics from live cell time-lapse data our model allows us to understand the dynamics of a complex trafficking pathway in living cells in culture.

  4. Noise-free accurate count of microbial colonies by time-lapse shadow image analysis.

    Science.gov (United States)

    Ogawa, Hiroyuki; Nasu, Senshi; Takeshige, Motomu; Funabashi, Hisakage; Saito, Mikako; Matsuoka, Hideaki

    2012-12-01

    Microbial colonies in food matrices could be counted accurately by a novel noise-free method based on time-lapse shadow image analysis. An agar plate containing many clusters of microbial colonies and/or meat fragments was trans-illuminated to project their 2-dimensional (2D) shadow images on a color CCD camera. The 2D shadow images of every cluster distributed within a 3-mm thick agar layer were captured in focus simultaneously by means of a multiple focusing system, and were then converted to 3-dimensional (3D) shadow images. By time-lapse analysis of the 3D shadow images, it was determined whether each cluster comprised single or multiple colonies or a meat fragment. The analytical precision was high enough to be able to distinguish a microbial colony from a meat fragment, to recognize an oval image as two colonies contacting each other, and to detect microbial colonies hidden under a food fragment. The detection of hidden colonies is its outstanding performance in comparison with other systems. The present system attained accuracy for counting fewer than 5 colonies and is therefore of practical importance. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. The Extreme Ice Survey: Capturing and Conveying Glacial Processes Through Time-Lapse Imagery and Narration

    Science.gov (United States)

    Balog, J. D.; Box, J. E.; Pfeffer, W. T.; Hood, E. W.; Fagre, D. B.; Anker, C.; O'Neel, S.

    2010-12-01

    The Extreme Ice Survey (EIS) uses time-lapse photography, conventional photography, and video to document rapid change in the Earth's glacial ice. The EIS team currently has 38 time-lapse cameras at sites in Greenland, Iceland, Alaska, the Rocky Mountains and Nepal. EIS supplements this ongoing record with annual repeat photography in British Columbia, Iceland, the Alps, and Bolivia. EIS imagery supplies basic knowledge in glacier dynamics to the science community, as well as compelling, engaging narratives to the general public about the immediacy of the Anthropocene and climate change. Visual materials from EIS have impacted more than 150 million people, ranging from White House staff, the U. S. Congress and government agency officials to globally influential corporate officers and all age strata of the general public. Media products include a National Geographic/NOVA special, two National Geographic magazine articles, a feature in Parade magazine (circulation 71 million), and numerous presentations on CNN, NBC, BBC and National Public Radio. Columbia Glacier, Alaska, June 2006, May 2007, June 2008 terminus indicated.

  6. Comparative evaluation of performance measures for shading correction in time-lapse fluorescence microscopy.

    Science.gov (United States)

    Liu, L; Kan, A; Leckie, C; Hodgkin, P D

    2017-04-01

    Time-lapse fluorescence microscopy is a valuable technology in cell biology, but it suffers from the inherent problem of intensity inhomogeneity due to uneven illumination or camera nonlinearity, known as shading artefacts. This will lead to inaccurate estimates of single-cell features such as average and total intensity. Numerous shading correction methods have been proposed to remove this effect. In order to compare the performance of different methods, many quantitative performance measures have been developed. However, there is little discussion about which performance measure should be generally applied for evaluation on real data, where the ground truth is absent. In this paper, the state-of-the-art shading correction methods and performance evaluation methods are reviewed. We implement 10 popular shading correction methods on two artificial datasets and four real ones. In order to make an objective comparison between those methods, we employ a number of quantitative performance measures. Extensive validation demonstrates that the coefficient of joint variation (CJV) is the most applicable measure in time-lapse fluorescence images. Based on this measure, we have proposed a novel shading correction method that performs better compared to well-established methods for a range of real data tested. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

  7. Stochastic modeling of oligodendrocyte generation in cell culture: model validation with time-lapse data

    Directory of Open Access Journals (Sweden)

    Noble Mark

    2006-05-01

    Full Text Available Abstract Background The purpose of this paper is two-fold. The first objective is to validate the assumptions behind a stochastic model developed earlier by these authors to describe oligodendrocyte generation in cell culture. The second is to generate time-lapse data that may help biomathematicians to build stochastic models of cell proliferation and differentiation under other experimental scenarios. Results Using time-lapse video recording it is possible to follow the individual evolutions of different cells within each clone. This experimental technique is very laborious and cannot replace model-based quantitative inference from clonal data. However, it is unrivalled in validating the structure of a stochastic model intended to describe cell proliferation and differentiation at the clonal level. In this paper, such data are reported and analyzed for oligodendrocyte precursor cells cultured in vitro. Conclusion The results strongly support the validity of the most basic assumptions underpinning the previously proposed model of oligodendrocyte development in cell culture. However, there are some discrepancies; the most important is that the contribution of progenitor cell death to cell kinetics in this experimental system has been underestimated.

  8. A Sparse Bayesian Imaging Technique for Efficient Recovery of Reservoir Channels With Time-Lapse Seismic Measurements

    KAUST Repository

    Sana, Furrukh

    2016-06-01

    Subsurface reservoir flow channels are characterized by high-permeability values and serve as preferred pathways for fluid propagation. Accurate estimation of their geophysical structures is thus of great importance for the oil industry. The ensemble Kalman filter (EnKF) is a widely used statistical technique for estimating subsurface reservoir model parameters. However, accurate reconstruction of the subsurface geological features with the EnKF is challenging because of the limited measurements available from the wells and the smoothing effects imposed by the \\\\ell _{2} -norm nature of its update step. A new EnKF scheme based on sparse domain representation was introduced by Sana et al. (2015) to incorporate useful prior structural information in the estimation process for efficient recovery of subsurface channels. In this paper, we extend this work in two ways: 1) investigate the effects of incorporating time-lapse seismic data on the channel reconstruction; and 2) explore a Bayesian sparse reconstruction algorithm with the potential ability to reduce the computational requirements. Numerical results suggest that the performance of the new sparse Bayesian based EnKF scheme is enhanced with the availability of seismic measurements, leading to further improvement in the recovery of flow channels structures. The sparse Bayesian approach further provides a computationally efficient framework for enforcing a sparse solution, especially with the possibility of using high sparsity rates through the inclusion of seismic data.

  9. Time-lapse gravity and levelling in the sinkhole-endangered urban area of Bad Frankenhausen, Germany

    Science.gov (United States)

    Kobe, Martin; Gabriel, Gerald; Weise, Adelheid; Krawczyk, Charlotte; Vogel, Detlef

    2017-04-01

    Sinkholes, resulting from subrosion in the subsurface, can reach diameters of several hundred meters and thus pose a severe hazard for infrastructure and inhabitants in urban areas. Subrosion is the leaching of readily-soluble rocks, such as rock salt, gypsum, anhydrite and limestone by ground or meteoric water and leads to mass transport and relocation. Two scenarios of sinkhole evolution are conceivable: First, the surface subsides continuously in order to compensate for the mass loss. Second, the mass relocation leads to development of subsurface cavities. If they reach a critical size and the cover layers are not supported anymore, the surface collapses abruptly. To improve the understanding of subrosion processes and the related surface deformation a case study is conducted in Bad Frankenhausen, Germany, where subrosion leaches the Zechstein evaporates of the Permian. One part of the study is to analyse the spatiotemporal development of sinkholes by applying time-lapse observations. Therefore, we established a monitoring network consisting of 15 gravity and additional levelling points covering the main sinkhole areas in the city centre. In March 2014, the baseline survey was carried out. Since then, quarterly measurement campaigns are performed. In each campaign four different gravity meters are used to collect a statistical significant amount of data and to control the plausibility of our data. The gravity measurements are complemented by levelling surveys. The rectification of the time-lapse gravity data comprises the correction for jumps and systematic errors, as well as for well calculable influences, such as earth tides and air pressure changes. Furthermore, special interest was applied to seasonal changes of hydrological parameters such as soil moisture or groundwater level. We found the hydrological influence to be in the single digit up to the lower two-digit µGal range, depending on the season and the station. The standard deviations of the adjusted

  10. In vivo time-lapse imaging and serial section electron microscopy reveal developmental synaptic rearrangements

    Science.gov (United States)

    Li, Jianli; Erisir, Alev; Cline, Hollis

    2010-01-01

    Dendrites, axons and synapses are dynamic during circuit development, however changes in microcircuit connections as branches stabilize have not been directly demonstrated. By combining in vivo time-lapse imaging of Xenopus tectal neurons with electron microscope reconstructions of imaged neurons, we report for the first time the distribution and ultrastructure of synapses on individual vertebrate neurons and relate these synaptic properties to dynamics in dendritic and axonal arbor structure over hours or days of imaging. Dynamic dendrites have a high density of immature synapses whereas stable dendrites have sparser, mature synapses. Axons initiate contacts from multisynapse boutons on stable branches. Connections are refined by decreasing convergence from multiple inputs to postsynaptic dendrites and by decreasing divergence from multisynapse boutons to postsynaptic sites. Visual deprivation or NMDAR antagonists decreased synapse maturation and elimination, suggesting that coactive input activity promotes microcircuit development by concurrently regulating synapse elimination and maturation of remaining contacts. PMID:21262466

  11. Optimal Estimation of Diffusion Coefficients from Noisy Time-Lapse-Recorded Single-Particle Trajectories

    DEFF Research Database (Denmark)

    Vestergaard, Christian Lyngby

    2012-01-01

    Optimal Estimation of Diusion Coecients from Noisy Time-Lapse- Measurements of Single-Particle Trajectories Single-particle tracking techniques allow quantitative measurements of diusion at the single-molecule level. Recorded time-series are mostly short and contain considerable measurement noise...... estimator for the diusion coecient, valid for short time-series, along with an exact benchmark for the maximum precision attainable with any unbiased estimator, the Cramer-Rao bound. We propose a simple analytical and unbiased covariance-based estimator based on the autocovariance function and derive...... of diusion coecients of hOgg1 repair proteins diusing on stretched uctuating DNA from data previously analyzed using a suboptimal method. Our analysis shows that the proteins have dierent eective diusion coecients and that their diusion coecients are correlated with their residence time on DNA. These results...

  12. 3-D time-lapse electrical resistivity monitoring of injected CO2 in a shallow aquifer

    DEFF Research Database (Denmark)

    Doetsch, Joseph A. J.A.; Auken, Esben; Christiansen, Anders Vest C A.V.C.

    2013-01-01

    Contamination of potable groundwater by leaking CO2 is a potential risk of carbon sequestration. With the help of a field experiment, we investigate if surface electrical resistivity tomography (ERT) can detect dissolved CO2 in a shallow aquifer. For this purpose, we injected CO2 at a depth of 5...... and 10 m and monitored its migration using 320 surface electrodes on a 126 m × 20 m grid. A fully automated acquisition system continuously collected data and uploaded it into an online database. The large amount of data allows for time-series analysis for data quality and noise estimation. A baseline...... inversion reveals the geology at the site consisting of aeolian sands near the surface and glacial sands below 5 m depth. Time-lapse inversions clearly image the dissolved CO2 plume with decreased electrical resistivity values. We can follow the CO2 plume as it spreads and moves with the groundwater...

  13. In vivo time-lapse imaging of mitochondria in healthy and diseased peripheral myelin sheath.

    Science.gov (United States)

    Gonzalez, Sergio; Fernando, Ruani; Berthelot, Jade; Perrin-Tricaud, Claire; Sarzi, Emmanuelle; Chrast, Roman; Lenaers, Guy; Tricaud, Nicolas

    2015-07-01

    The myelin sheath that covers a large amount of neurons is critical for their homeostasis, and myelinating glia mitochondria have recently been shown to be essential for neuron survival. However morphological and physiological properties of these organelles remain elusive. Here we report a method to analyze mitochondrial dynamics and morphology in myelinating Schwann cells of living mice using viral transduction and time-lapse multiphoton microscopy. We describe the distribution, shape, size and dynamics of mitochondria in live cells. We also report mitochondrial alterations in Opa1(delTTAG) mutant mice cells at presymptomatic stages, suggesting that mitochondrial defects in myelin contribute to OPA1 related neuropathy and represent a biomarker for the disease. Copyright © 2015 © Elsevier B.V. and Mitochondria Research Society. Published by Elsevier B.V. All rights reserved.

  14. Time-lapse seismic analysis of the North Sea Fulmar Field

    Energy Technology Data Exchange (ETDEWEB)

    Johnston, David H.; McKenny, Robert S.; Burkhart, Tucker D.

    1998-12-31

    Time-lapse seismic analysis has been applied to two 3-D seismic surveys acquired over the central North Sea Fulmar field in a pre-production survey shot in 1977, reprocessed in 1987, and a survey in 1992. The Upper Jurassic reservoirs in the field have been under production since 1982. Differences in averaged impedance between the 1977 and 1992 surveys clearly show the effects of water influx and pressure decline. The changes observed in the seismic data are overall consistent with predictions obtained from a full-field, history-matched simulation. Differences in details may suggest areas of bypassed oil. Dta quality is not sufficient to serve as the sole basis for drilling decisions. 1 ref., 6 figs.

  15. Spectral-element simulations of carbon dioxide (CO2) sequestration time-lapse monitoring

    Science.gov (United States)

    Morency, C.; Luo, Y.; Tromp, J.

    2009-12-01

    Geologic sequestration of CO2, a green house gas, represents an effort to reduce the large amount of CO2 generated as a by-product of fossil fuels combustion and emitted into the atmosphere. This process of sequestration involves CO2 storage deep underground. There are three main storage options: injection into hydrocarbon reservoirs, injection into methane-bearing coal beds, or injection into deep saline aquifers, that is, highly permeable porous media. The key issues involve accurate monitoring of the CO2, from the injection stage to the prediction & verification of CO2 movement over time for environmental considerations. A natural non-intrusive monitoring technique is referred to as ``4D seismics'', which involves 3D time-lapse seismic surveys. The success of monitoring the CO2 movement is subject to a proper description of the physics of the problem. We propose to realize time-lapse migrations comparing acoustic, elastic, and poroelastic simulations of 4D seismic imaging to characterize the storage zone. This approach highlights the influence of using different physical theories on interpreting seismic data, and, more importantly, on extracting the CO2 signature from the seismic wave field. Our simulations are performed using a spectral-element method, which allows for highly accurate results. Biot's equations are implemented to account for poroelastic effects. Attenuation associated with the anelasticity of the rock frame and frequency-dependent viscous resistance of the pore fluid are accommodated based upon a memory variable approach. The sensitivity of observables to the model parameters is quantified based upon finite-frequency sensitivity kernels calculated using an adjoint method.

  16. Gliding motility of Babesia bovis merozoites visualized by time-lapse video microscopy.

    Directory of Open Access Journals (Sweden)

    Masahito Asada

    Full Text Available BACKGROUND: Babesia bovis is an apicomplexan intraerythrocytic protozoan parasite that induces babesiosis in cattle after transmission by ticks. During specific stages of the apicomplexan parasite lifecycle, such as the sporozoites of Plasmodium falciparum and tachyzoites of Toxoplasma gondii, host cells are targeted for invasion using a unique, active process termed "gliding motility". However, it is not thoroughly understood how the merozoites of B. bovis target and invade host red blood cells (RBCs, and gliding motility has so far not been observed in the parasite. METHODOLOGY/PRINCIPAL FINDINGS: Gliding motility of B. bovis merozoites was revealed by time-lapse video microscopy. The recorded images revealed that the process included egress of the merozoites from the infected RBC, gliding motility, and subsequent invasion into new RBCs. The gliding motility of B. bovis merozoites was similar to the helical gliding of Toxoplasma tachyzoites. The trails left by the merozoites were detected by indirect immunofluorescence assay using antiserum against B. bovis merozoite surface antigen 1. Inhibition of gliding motility by actin filament polymerization or depolymerization indicated that the gliding motility was driven by actomyosin dependent process. In addition, we revealed the timing of breakdown of the parasitophorous vacuole. Time-lapse image analysis of membrane-stained bovine RBCs showed formation and breakdown of the parasitophorous vacuole within ten minutes of invasion. CONCLUSIONS/SIGNIFICANCE: This is the first report of the gliding motility of B. bovis. Since merozoites of Plasmodium parasites do not glide on a substrate, the gliding motility of B. bovis merozoites is a notable finding.

  17. Field measurement of erosion rates: time-lapse monitoring of rapid stone flaking at Howden Minster, UK

    Science.gov (United States)

    Doehne, E.; Pinchin, S.

    2012-04-01

    The use of a solar-powered, field time-lapse camera and environmental monitoring system enabled measurements of the pattern and rate of loss of stone from the surface of Howden Minster, an abandoned monastery in Yorkshire dating to 1380 AD. Acquiring a photograph every 1-3 hours allowed the stone damage to be correlated with local environmental conditions. Image comparison techniques borrowed from observational astronomy, such as blink comparison, were used to determine what elements had changed from image to image. Results indicate that loss is episodic rather than continuous and in several cases is related to specific environmental conditions, such as condensation/dew formation or high winds. Damage was found also to be synchronous, with surface change (flaking, granular disintegration, and loss of flakes) occurring at the same time on different stone blocks. Crystallization pressure from magnesium sulfate phase transitions appear to be the main cause of the loss of stone surfaces. Significant variation in surface loss rates was observed and appears to be related to variations in salt concentration. An examination of stone texture by ESEM/EDS revealed signification variations and suggests that salt concentrations are controlled in part by stone micromorphology. Quantitative data on rates of surface loss are not available from most monuments. Time-lapse methods permit the relatively inexpensive acquisition of this type of data, which is needed to aid conservation decision-making and the evaluation of interventions. Such tools should also prove useful to geomorphologists studying honeycomb weathering, the moving rocks on Death Valley's Racetrack Playa, and other phenomena that are otherwise difficult to study. Context: The rapid deterioration of magnesian limestone structures in the north of England has been a serious problem for more than one hundred years. While air quality in England has improved during this period, the rate of stone loss in these carved stone

  18. Selected time-lapse movies of the east rift zone eruption of KĪlauea Volcano, 2004–2008

    Science.gov (United States)

    Orr, Tim R.

    2011-01-01

    Since 2004, the U.S. Geological Survey's Hawaiian Volcano Observatory has used mass-market digital time-lapse cameras and network-enabled Webcams for visual monitoring and research. The 26 time-lapse movies in this report were selected from the vast collection of images acquired by these camera systems during 2004–2008. Chosen for their content and broad aesthetic appeal, these image sequences document a variety of flow-field and vent processes from Kīlauea's east rift zone eruption, which began in 1983 and is still (as of 2011) ongoing.

  19. Formation and spreading of TDP-43 aggregates in cultured neuronal and glial cells demonstrated by time-lapse imaging.

    Directory of Open Access Journals (Sweden)

    Tomohiro Ishii

    Full Text Available TAR DNA-binding protein 43 (TDP-43 is a main constituent of cytoplasmic aggregates in neuronal and glial cells in cases of amyotrophic lateral sclerosis and frontotemporal lobar degeneration. We have previously demonstrated that adenovirus-transduced artificial TDP-43 cytoplasmic aggregates formation is enhanced by proteasome inhibition in vitro and in vivo. However, the relationship between cytoplasmic aggregate formation and cell death remains unclear. In the present study, rat neural stem cell lines stably transfected with EGFP- or Sirius-expression vectors under the control of tubulin beta III, glial fibrillary acidic protein, or 2',3'-cyclic nucleotide 3'-phosphodiesterase promoter were differentiated into neurons, astrocytes, and oligodendrocytes, respectively, in the presence of retinoic acid. The differentiated cells were then transduced with adenoviruses expressing DsRed-tagged human wild type and C-terminal fragment TDP-43 under the condition of proteasome inhibition. Time-lapse imaging analyses revealed growing cytoplasmic aggregates in the transduced neuronal and glial cells, followed by collapse of the cell. The aggregates remained insoluble in culture media, consisted of sarkosyl-insoluble granular materials, and contained phosphorylated TDP-43. Moreover, the released aggregates were incorporated into neighboring neuronal cells, suggesting cell-to-cell spreading. The present study provides a novel tool for analyzing the detailed molecular mechanisms of TDP-43 proteinopathy in vitro.

  20. Joint inversion of time-lapse VSP data for monitoring CO2 injection at the Farnsworth EOR field in Texas

    Science.gov (United States)

    Zhang, M.; Gao, K.; Balch, R. S.; Huang, L.

    2016-12-01

    During the Development Phase (Phase III) of the U.S. Southwest Regional Partnership on Carbon Sequestration (SWP), time-lapse 3D vertical seismic profiling (VSP) data were acquired to monitor CO2 injection/migration at the Farnsworth Enhanced Oil Recovery (EOR) field, in partnership with the industrial partner Chaparral Energy. The project is to inject a million tons of carbon dioxide into the target formation, the deep oil-bearing Morrow Formation in the Farnsworth Unit EOR field. Quantitative time-lapse seismic monitoring has the potential to track CO2 movement in geologic carbon storage sites. Los Alamos National Laboratory (LANL) has recently developed new full-waveform inversion methods to jointly invert time-lapse seismic data for changes in elastic and anisotropic parameters in target monitoring regions such as a CO2 reservoir. We apply our new joint inversion methods to time-lapse VSP data acquired at the Farnsworth EOR filed, and present some preliminary results showing geophysical properties changes in the reservoir.

  1. Time-lapse micro-tomography analysis of the deformation response of a gellan-gum-based scaffold

    Czech Academy of Sciences Publication Activity Database

    Kytýř, Daniel; Fenclová, Nela; Zlámal, Petr; Kumpová, Ivana; Fíla, Tomáš; Koudelka_ml., Petr; Gantar, A.; Novak, S.

    2017-01-01

    Roč. 51, č. 3 (2017), s. 397-402 ISSN 1580-2949 Institutional support: RVO:68378297 Keywords : bone scaffold * gellan gum * time-lapse micro CT * digital volume correlation Subject RIV: JJ - Other Materials Impact factor: 0.436, year: 2016 http://mit.imt.si/Revija/izvodi/mit173/kytyr.pdf

  2. How to connect time-lapse recorded trajectories of motile microorganisms with dynamical models in continuous time

    DEFF Research Database (Denmark)

    Pedersen, Jonas Nyvold; Li, Liang; Gradinaru, Cristian

    2016-01-01

    We provide a tool for data-driven modeling of motility, data being time-lapse recorded trajectories. Several mathematical properties of a model to be found can be gleaned from appropriate model-independent experimental statistics, if one understands how such statistics are distorted by the finite...

  3. Bayesian Markov chain Monte Carlo Inversion of Time-Lapse Geophysical Data To Characterize the Vadose Zone

    DEFF Research Database (Denmark)

    Scholer, Marie; Irving, James; Zibar, Majken Caroline Looms

    Geophysical methods have the potential to provide valuable information on hydrological properties in the unsaturated zone. In particular, time-lapse geophysical data, when coupled with a hydrological model and inverted stochastically, may allow for the effective estimation of subsurface hydraulic...

  4. Growth Rate and Morphology of a Single Calcium Carbonate Crystal on Polysulfone Film Measured with Time Lapse Raman Micro Spectroscopy

    NARCIS (Netherlands)

    Liszka, B.; Lenferink, Aufrid T.M.; Otto, Cornelis

    2016-01-01

    The growth of single, self- nucleated calcium carbonate crystals on a polysulfone (PSU) film was investigated with high resolution, time lapse Raman imaging. The Raman images were acquired on the interface of the polymer with the crystal. The growth of crystals could thus be followed in time. PSU is

  5. Time-Lapse Joint Inversion of Cross-Well DC Resistivity and Seismic Data: A Numerical Investigation

    Science.gov (United States)

    Time-lapse joint inversion of geophysical data is required to image the evolution of oil reservoirs during production and enhanced oil recovery, CO2 sequestration, geothermal fields during production, and to monitor the evolution of contaminant plumes. Joint inversion schemes red...

  6. ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments.

    Science.gov (United States)

    Hattab, Georges; Schlüter, Jan-Philip; Becker, Anke; Nattkemper, Tim W

    2017-01-01

    In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate). In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-)automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e.g., feature extraction or tracking). Image alignment faces two obstacles in this microscopic context: (a) highly dynamic structural changes in the sample (i.e., colony growth) and (b) an individual data set-specific sample environment which makes the application of landmarks-based alignments almost impossible. We present a computational image registration solution, we refer to as ViCAR: (Vi)sual (C)ues based (A)daptive (R)egistration, for such microfluidics experiments, consisting of (1) the detection of particular polygons (outlined and segmented ones, referred to as visual cues), (2) the adaptive retrieval of three coordinates throughout different sets of frames, and finally (3) an image registration based on the relation of these points correcting both rotation and translation. We tested ViCAR with different data sets and have found that it provides an effective spatial alignment thereby paving the way to extract temporal features pertinent to each resulting bacterial colony. By using ViCAR, we achieved an image registration with 99.9% of image closeness, based on the average rmsd of 4.10-2 pixels, and superior results compared to a state of the art algorithm.

  7. ViCAR: An Adaptive and Landmark-Free Registration of Time Lapse Image Data from Microfluidics Experiments

    Directory of Open Access Journals (Sweden)

    Georges Hattab

    2017-05-01

    Full Text Available In order to understand gene function in bacterial life cycles, time lapse bioimaging is applied in combination with different marker protocols in so called microfluidics chambers (i.e., a multi-well plate. In one experiment, a series of T images is recorded for one visual field, with a pixel resolution of 60 nm/px. Any (semi-automatic analysis of the data is hampered by a strong image noise, low contrast and, last but not least, considerable irregular shifts during the acquisition. Image registration corrects such shifts enabling next steps of the analysis (e.g., feature extraction or tracking. Image alignment faces two obstacles in this microscopic context: (a highly dynamic structural changes in the sample (i.e., colony growth and (b an individual data set-specific sample environment which makes the application of landmarks-based alignments almost impossible. We present a computational image registration solution, we refer to as ViCAR: (Visual (Cues based (Adaptive (Registration, for such microfluidics experiments, consisting of (1 the detection of particular polygons (outlined and segmented ones, referred to as visual cues, (2 the adaptive retrieval of three coordinates throughout different sets of frames, and finally (3 an image registration based on the relation of these points correcting both rotation and translation. We tested ViCAR with different data sets and have found that it provides an effective spatial alignment thereby paving the way to extract temporal features pertinent to each resulting bacterial colony. By using ViCAR, we achieved an image registration with 99.9% of image closeness, based on the average rmsd of 4.10−2 pixels, and superior results compared to a state of the art algorithm.

  8. Time-lapse analysis of potential cellular responsiveness to Johrei, a Japanese healing technique

    Directory of Open Access Journals (Sweden)

    Moore Dan

    2005-01-01

    Full Text Available Abstract Background Johrei is an alternative healing practice which involves the channeling of a purported universal healing energy to influence the health of another person. Despite little evidence to support the efficacy of such practices the use of such treatments is on the rise. Methods We assessed cultured human cancer cells for potential responsiveness to Johrei treatment from a short distance. Johrei treatment was delivered by practitioners who participated in teams of two, alternating every half hour for a total of four hours of treatment. The practitioners followed a defined set of mental procedures to minimize variability in mental states between experiments. An environmental chamber maintained optimal growth conditions for cells throughout the experiments. Computerized time-lapse microscopy allowed documentation of cancer cell proliferation and cell death before, during and after Johrei treatments. Results Comparing eight control experiments with eight Johrei intervention experiments, we found no evidence of a reproducible cellular response to Johrei treatment. Conclusion Cell death and proliferation rates of cultured human cancer cells do not appear responsive to Johrei treatment from a short distance.

  9. Untangling cell tracks: Quantifying cell migration by time lapse image data analysis.

    Science.gov (United States)

    Svensson, Carl-Magnus; Medyukhina, Anna; Belyaev, Ivan; Al-Zaben, Naim; Figge, Marc Thilo

    2017-10-04

    Automated microscopy has given researchers access to great amounts of live cell imaging data from in vitro and in vivo experiments. Much focus has been put on extracting cell tracks from such data using a plethora of segmentation and tracking algorithms, but further analysis is normally required to draw biologically relevant conclusions. Such relevant conclusions may be whether the migration is directed or not, whether the population has homogeneous or heterogeneous migration patterns. This review focuses on the analysis of cell migration data that are extracted from time lapse images. We discuss a range of measures and models used to analyze cell tracks independent of the biological system or the way the tracks were obtained. For single-cell migration, we focus on measures and models giving examples of biological systems where they have been applied, for example, migration of bacteria, fibroblasts, and immune cells. For collective migration, we describe the model systems wound healing, neural crest migration, and Drosophila gastrulation and discuss methods for cell migration within these systems. We also discuss the role of the extracellular matrix and subsequent differences between track analysis in vitro and in vivo. Besides methods and measures, we are putting special focus on the need for openly available data and code, as well as a lack of common vocabulary in cell track analysis. © 2017 International Society for Advancement of Cytometry. © 2017 International Society for Advancement of Cytometry.

  10. A time-lapse photography method for monitoring salmon (Oncorhynchus spp. passage and abundance in streams

    Directory of Open Access Journals (Sweden)

    William W. Deacy

    2016-06-01

    Full Text Available Accurately estimating population sizes is often a critical component of fisheries research and management. Although there is a growing appreciation of the importance of small-scale salmon population dynamics to the stability of salmon stock-complexes, our understanding of these populations is constrained by a lack of efficient and cost-effective monitoring tools for streams. Weirs are expensive, labor intensive, and can disrupt natural fish movements. While conventional video systems avoid some of these shortcomings, they are expensive and require excessive amounts of labor to review footage for data collection. Here, we present a novel method for quantifying salmon in small streams (<15 m wide, <1 m deep that uses both time-lapse photography and video in a model-based double sampling scheme. This method produces an escapement estimate nearly as accurate as a video-only approach, but with substantially less labor, money, and effort. It requires servicing only every 14 days, detects salmon 24 h/day, is inexpensive, and produces escapement estimates with confidence intervals. In addition to escapement estimation, we present a method for estimating in-stream salmon abundance across time, data needed by researchers interested in predator--prey interactions or nutrient subsidies. We combined daily salmon passage estimates with stream specific estimates of daily mortality developed using previously published data. To demonstrate proof of concept for these methods, we present results from two streams in southwest Kodiak Island, Alaska in which high densities of sockeye salmon spawn.

  11. Time-Lapse Dynamics of the Mouse Oocyte Chromatin Organisation during Meiotic Resumption

    Directory of Open Access Journals (Sweden)

    Martina Belli

    2014-01-01

    Full Text Available In the mammalian oocyte, distinct patterns of centromeres and pericentromeric heterochromatin localisation correlate with the gamete’s developmental competence. Mouse antral oocytes display two main types of chromatin organisation: SN oocytes, with a ring of Hoechst-positive chromatin surrounding the nucleolus, and NSN oocytes lacking this ring. When matured to MII and fertilised, only SN oocytes develop beyond the 2-cell, and reach full term. To give detailed information on the dynamics of the SN or NSN chromatin during meiosis resumption, we performed a 9 hr time-lapse observation. The main significant differences recorded are: (1 reduction of the nuclear area only in SN oocytes; (2 ~17 min delay of GVBD in NSN oocytes; (3 chromatin condensation, after GVBD, in SN oocytes; (4 formation of 4-5 CHCs in SN oocytes; (5 increase of the perivitelline space, ~57 min later in NSN oocytes; (6 formation of a rosette-like disposition of CHCs, ~84 min later in SN oocytes; (7 appearance of the MI plate ~40 min later in NSN oocytes. Overall, we described a pathway of transition from the GV to the MII stage that is punctuated of discrete recordable events showing their specificity and occurring with different time kinetics in the two types of oocytes.

  12. Adaptive time-lapse optimized survey design for electrical resistivity tomography monitoring

    Science.gov (United States)

    Wilkinson, Paul B.; Uhlemann, Sebastian; Meldrum, Philip I.; Chambers, Jonathan E.; Carrière, Simon; Oxby, Lucy S.; Loke, M. H.

    2015-10-01

    Adaptive optimal experimental design methods use previous data and results to guide the choice and design of future experiments. This paper describes the formulation of an adaptive survey design technique to produce optimal resistivity imaging surveys for time-lapse geoelectrical monitoring experiments. These survey designs are time-dependent and, compared to dipole-dipole or static optimized surveys that do not change over time, focus a greater degree of the image resolution on regions of the subsurface that are actively changing. The adaptive optimization method is validated using a controlled laboratory monitoring experiment comprising a well-defined cylindrical target moving along a trajectory that changes its depth and lateral position. The algorithm is implemented on a standard PC in conjunction with a modified automated multichannel resistivity imaging system. Data acquisition using the adaptive survey designs requires no more time or power than with comparable standard surveys, and the algorithm processing takes place while the system batteries recharge. The results show that adaptively designed optimal surveys yield a quantitative increase in image quality over and above that produced by using standard dipole-dipole or static (time-independent) optimized surveys.

  13. Incubator-independent cell-culture perfusion platform for continuous long-term microelectrode array electrophysiology and time-lapse imaging.

    Science.gov (United States)

    Saalfrank, Dirk; Konduri, Anil Krishna; Latifi, Shahrzad; Habibey, Rouhollah; Golabchi, Asiyeh; Martiniuc, Aurel Vasile; Knoll, Alois; Ingebrandt, Sven; Blau, Axel

    2015-06-01

    Most in vitro electrophysiology studies extract information and draw conclusions from representative, temporally limited snapshot experiments. This approach bears the risk of missing decisive moments that may make a difference in our understanding of physiological events. This feasibility study presents a simple benchtop cell-culture perfusion system adapted to commercial microelectrode arrays (MEAs), multichannel electrophysiology equipment and common inverted microscopy stages for simultaneous and uninterrupted extracellular electrophysiology and time-lapse imaging at ambient CO2 levels. The concept relies on a transparent, replica-casted polydimethylsiloxane perfusion cap, gravity- or syringe-pump-driven perfusion and preconditioning of pH-buffered serum-free cell-culture medium to ambient CO2 levels at physiological temperatures. The low-cost microfluidic in vitro enabling platform, which allows us to image cultures immediately after cell plating, is easy to reproduce and is adaptable to the geometries of different cell-culture containers. It permits the continuous and simultaneous multimodal long-term acquisition or manipulation of optical and electrophysiological parameter sets, thereby considerably widening the range of experimental possibilities. Two exemplary proof-of-concept long-term MEA studies on hippocampal networks illustrate system performance. Continuous extracellular recordings over a period of up to 70 days revealed details on both sudden and gradual neural activity changes in maturing cell ensembles with large intra-day fluctuations. Correlated time-lapse imaging unveiled rather static macroscopic network architectures with previously unreported local morphological oscillations on the timescale of minutes.

  14. BactImAS: a platform for processing and analysis of bacterial time-lapse microscopy movies.

    Science.gov (United States)

    Mekterović, Igor; Mekterović, Darko; Maglica, Zeljka

    2014-07-25

    The software available to date for analyzing image sequences from time-lapse microscopy works only for certain bacteria and under limited conditions. These programs, mostly MATLAB-based, fail for microbes with irregular shape, indistinct cell division sites, or that grow in closely packed microcolonies. Unfortunately, many organisms of interest have these characteristics, and analyzing their image sequences has been limited to time consuming manual processing. Here we describe BactImAS - a modular, multi-platform, open-source, Java-based software delivered both as a standalone program and as a plugin for Icy. The software is designed for extracting and visualizing quantitative data from bacterial time-lapse movies. BactImAS uses a semi-automated approach where the user defines initial cells, identifies cell division events, and, if necessary, manually corrects cell segmentation with the help of user-friendly GUI and incorporated ImageJ application. The program segments and tracks cells using a newly-developed algorithm designed for movies with difficult-to-segment cells that exhibit small frame-to-frame differences. Measurements are extracted from images in a configurable, automated fashion and an SQLite database is used to store, retrieve, and exchange all acquired data. Finally, the BactImAS can generate configurable lineage tree visualizations and export data as CSV files. We tested BactImAS on time-lapse movies of Mycobacterium smegmatis and achieved at least 10-fold reduction of processing time compared to manual analysis. We illustrate the power of the visualization tool by showing heterogeneity of both icl expression and cell growth atop of a lineage tree. The presented software simplifies quantitative analysis of time-lapse movies overall and is currently the only available software for the analysis of mycobacteria-like cells. It will be of interest to the community of both end-users and developers of time-lapse microscopy software.

  15. Human and Climate Amplified Rapid River Bluff Erosion: an Application of Terrestrial-Based Structure-from-Motion and Time-Lapse Photogrammetry in the Midwestern USA

    Science.gov (United States)

    Kelly, S. A.; Belmont, P.

    2016-12-01

    The Minnesota River Basin (MRB), south central Minnesota, is an extraordinary natural laboratory, and is currently impaired for excess sediments and nutrients. Tributaries of the Minnesota River have been actively incising and meandering into glacial tills for the last 13,400 years in response to a catastrophic base level drop. It is this geologic history combined with modern agricultural intensification and hydrologic change that provide a unique opportunity to study remarkably rapid bluff erosion using photogrammetry. Here we seek to understand the dominant mechanisms (fluvial toe erosion, freeze-thaw, groundwater sapping, tree throw, positive pore water pressures) and magnitude of bluff erosion using daily time-lapse photographs, repeat photo surveys, Structure-from-Motion (SfM), and calculations of bluff volumetric change through time. We expect for increased precipitation and streamflows in the basin to have accelerated bluff erosion via channel widening and migration. In general, we find that bluff failures occur during or immediately following (1-2 days) heavy rainfall events, especially during spring thaw, and the removal, or transport of the failed material out of the reach coincides with hydrograph flood peaks. Through the combined use of time-lapse and SfM photogrammetry we are able to identify the precipitation and flow events which occur with a frequency and magnitude large enough to effectively dominate bluff erosion. Identifying this `effective discharge' of bluff erosion is regionally important for sediment reduction strategies in the MRB.

  16. Heterogeneous cell-cycle behavior in response to UVB irradiation by a population of single cancer cells visualized by time-lapse FUCCI imaging.

    Science.gov (United States)

    Miwa, Shinji; Yano, Shuya; Kimura, Hiroaki; Yamamoto, Mako; Toneri, Makoto; Murakami, Takashi; Hayashi, Katsuhiro; Yamamoto, Norio; Fujiwara, Toshiyoshi; Tsuchiya, Hiroyuki; Hoffman, Robert M

    2015-01-01

    The present study analyzed the heterogeneous cell-cycle dependence and fate of single cancer cells in a population treated with UVB using a fluorescence ubiquitination-based cell-cycle (FUCCI) imaging system. HeLa cells expressing FUCCI were irradiated by 100 or 200 J/m(2) UVB. Modulation of the cell-cycle and apoptosis were observed by time-lapse confocal microscopy imaging every 30 min for 72 h. Correlation between cell survival and factors including cell-cycle phase at the time of the irradiation of UVB, mitosis and the G1/S transition were analyzed using the Kaplan-Meier method along with the log rank test. Time-lapse FUCCI imaging of HeLa cells demonstrated that UVB irradiation induced cell-cycle arrest in S/G2/M phase in the majority of the cells. The cells irradiated by 100 or 200 J/m(2) UVB during G0/G1 phase had a higher survival rate than the cells irradiated during S/G2/M phase. A minority of cells could escape S/G2/M arrest and undergo mitosis which significantly correlated with decreased survival of the cells. In contrast, G1/S transition significantly correlated with increased survival of the cells after UVB irradiation. UVB at 200 J/m(2) resulted in a greater number of apoptotic cells.

  17. Time lapse imaging of water content with geoelectrical methods: on the interest of working with absolute water content data

    Science.gov (United States)

    Dumont, Gaël; Pilawski, Tamara; Robert, Tanguy; Hermans, Thomas; Garré, Sarah; Nguyen, Frederic

    2016-04-01

    The electrical resistivity tomography is a suitable method to estimate the water content of a waste material and detect changes in water content. Various ERT profiles, both static data and time-lapse, where acquired on a landfill during the Minerve project. In the literature, the relative change of resistivity (Δρ/ρ) is generally computed. For saline or heat tracer tests in the saturated zone, the Δρ/ρ can be easily translated into pore water conductivity or underground temperature changes (provided that the initial salinity or temperature condition is homogeneous over the ERT panel extension). For water content changes in the vadose zone resulting of an infiltration event or injection experiment, many authors also work with the Δρ/ρ or relative changes of water content Δθ/θ (linked to the change of resistivity through one single parameter: the Archie's law exponent "m"). This parameter is not influenced by the underground temperature and pore fluid conductivity (ρ¬w) condition but is influenced by the initial water content distribution. Therefore, you never know if the loss of Δθ/θ signal is representative of the limit of the infiltration front or more humid initial condition. Another approach for the understanding of the infiltration process is the assessment of the absolute change of water content (Δθ). This requires the direct computation of the water content of the waste from the resistivity data. For that purpose, we used petrophysical laws calibrated with laboratory experiments and our knowledge of the in situ temperature and pore fluid conductivity parameters. Then, we investigated water content changes in the waste material after a rainfall event (Δθ= Δθ/θ* θ). This new observation is really representatives of the quantity of water infiltrated in the waste material. However, the uncertainty in the pore fluid conductivity value may influence the computed water changes (Δθ=k*m√(ρw) ; where "m" is the Archie's law exponent

  18. Overland flow dynamics through visual observation using time-lapse photographs

    Science.gov (United States)

    Silasari, Rasmiaditya; Blöschl, Günter

    2016-04-01

    Overland flow process on agricultural land is important to be investigated as it affects the stream discharge and water quality assessment. During rainfall events the formation of overland flow may happen through different processes (i.e. Hortonian or saturation excess overland flow) based on the governing soil hydraulic parameters (i.e. soil infiltration rate, soil water capacity). The dynamics of the soil water state and the processes will affect the surface runoff response which can be analyzed visually by observing the saturation patterns with a camera. Although visual observation was proven useful in laboratory experiments, the technique is not yet assessed for natural rainfall events. The aim of this work is to explore the use of time-lapse photographs of naturally occurring-saturation patterns in understanding the threshold processes of overland flow generation. The image processing produces orthographic projection of the saturation patterns which will be used to assess the dynamics of overland flow formation in relation with soil moisture state and rainfall magnitude. The camera observation was performed at Hydrological Open Air Laboratory (HOAL) catchment at Petzenkirchen, Lower Austria. The catchment covers an area of 66 ha dominated with agricultural land (87%). The mean annual precipitation and mean annual flow at catchment outlet are 750 mm and 4 l/s, respectively. The camera was set to observe the overland flow along a thalweg on an arable field which was drained in 1950s and has advantages of: (1) representing agricultural land as the dominant part of the catchment, (2) adjacent to the stream with clear visibility (no obstructing objects, such as trees), (3) drained area provides extra cases in understanding the response of tile drain outflow to overland flow formation and vice versa, and (4) in the vicinity of TDT soil moisture stations. The camera takes a picture with 1280 x 720 pixels resolution every minute and sends it directly in a PC via fiber

  19. Time lapse inversion of 2D ERT data for monitoring river water infiltration

    Science.gov (United States)

    Wallin, E. L.; Johnson, T. C.; Greenwood, W. J.

    2011-12-01

    Uranium transport in the 300 area is driven by both the chemical and physical effects of stage fluctuations in the Columbia River and resulting river water, ground water interaction. Because river water is less conductive than groundwater, it serves as a natural tracer that can be imaged using surface ERT. We've monitored 4 lines for 4 months over the high stage spring runoff interval to identify preferred flowpaths for river water intrusion. The four lines overlay former waste disposal sites including the processing ponds and sanitary leach trenches. We have used this ERT data set to investigate two methods of time lapse inversion, sequential and all-at-once. Each technique is a model difference approach as opposed to a data difference inversion approach. Both use a regularized inversion with model constraints that regularize spatially and temporally. For the sequential inversion, the starting and reference models are taken from the previous inversion. Both starting and reference models are taken from the first inversion for the all-at-once method. In either case an inversion is triggered if data misfit from the starting model exceeds the chi-squared convergence criteria. It was found that starting with a relatively smooth model provided better visualization of temporal conductivity changes when inverting all data sets with the same initial model, while an initial model exhibiting smaller data misfit may be used successfully as the starting point for sequential inversion. Inland conductivity changes within model cells were found to be highly correlated with river stage, and when paired with the characterization model, provide evidence of waste trenches, the processing pond, as well as the existence of a paleo-channel incised into the Ringold Formation and dipping structures on the Hanford-Ringold contact that provide preferred pathways for river water intrusion.

  20. Time lapse photography as an approach to understanding glide avalanche activity

    Science.gov (United States)

    Hendrikx, Jordy; Peitzsch, Erich H.; Fagre, Daniel B.

    2012-01-01

    Avalanches resulting from glide cracks are notoriously difficult to forecast, but are a recurring problem for numerous avalanche forecasting programs. In some cases glide cracks are observed to open and then melt away in situ. In other cases, they open and then fail catastrophically as large, full-depth avalanches. Our understanding and management of these phenomena are currently limited. It is thought that an increase in the rate of snow gliding occurs prior to full-depth avalanche activity so frequent observation of glide crack movement can provide an index of instability. During spring 2011 in Glacier National Park, Montana, USA, we began an approach to track glide crack avalanche activity using a time-lapse camera focused on a southwest facing glide crack. This crack melted in-situ without failing as a glide avalanche, while other nearby glide cracks on north through southeast aspects failed. In spring 2012, a camera was aimed at a large and productive glide crack adjacent to the Going to the Sun Road. We captured three unique glide events in the field of view. Unfortunately, all of them either failed very quickly, or during periods of obscured view, so measurements of glide rate could not be obtained. However, we compared the hourly meteorological variables during the period of glide activity to the same variables prior to glide activity. The variables air temperature, relative humidity, air pressure, incoming and reflected long wave radiation, SWE, total precipitation, and snow depth were found to be statistically different for our cases examined. We propose that these are some of the potential precursors for glide avalanche activity, but do urge caution in their use, due to the simple approach and small data set size. It is hoped that by introducing a workable method to easily record glide crack movement, combined with ongoing analysis of the associated meteorological data, we will improve our understanding of when, or if, glide avalanche activity will ensue.

  1. ENVIRONMENTAL MONITORING OF LEAKS USING TIME LAPSED LONG ELECTRODE ELECTRICAL RESISTIVITY

    Energy Technology Data Exchange (ETDEWEB)

    MYERS DA; RUCKER DF; FINK JB; LOKE MH

    2009-12-16

    Highly industrialized areas pose challenges for surface electrical resistivity characterization due to metallic infrastructure. The infrastructure is typically more conductive than the desired targets and will mask the deeper subsurface information. These challenges may be minimized if steel-cased wells are used as long electrodes in the area near the target. We demonstrate a method of using long electrodes to electrically monitor a simulated leak from an underground storage tank with both synthetic examples and a field demonstration. The synthetic examples place a simple target of varying electrical properties beneath a very low resistivity layer. The layer is meant to replicate the effects of infrastructure. Both surface and long electrodes are tested on the synthetic domain. The leak demonstration for the field experiment is simulated by injecting a high conductivity fluid in a perforated well within the S tank farm at Hanford, and the resistivity measurements are made before and after the leak test. All data are processed in four dimensions, where a regularization procedure is applied in both the time and space domains. The synthetic test case shows that the long electrode ERM could detect relative changes in resistivity that are commensurate with the differing target properties. The surface electrodes, on the other hand, had a more difficult time matching the original target's footprint. The field results shows a lowered resistivity feature develop south of the injection site after cessation of the injections. The time lapsed regularization parameter has a strong influence on the differences in inverted resistivity between the pre and post injection datasets, but the interpretation of the target is consistent across all values of the parameter. The long electrode ERM method may provide a tool for near real-time monitoring of leaking underground storage tanks.

  2. Single-cell time-lapse analysis of depletion of the universally conserved essential protein YgjD

    Directory of Open Access Journals (Sweden)

    Ackermann Martin

    2011-05-01

    Full Text Available Abstract Background The essential Escherichia coli gene ygjD belongs to a universally conserved group of genes whose function has been the focus of a number of recent studies. Here, we put ygjD under control of an inducible promoter, and used time-lapse microscopy and single cell analysis to investigate the phenotypic consequences of the depletion of YgjD protein from growing cells. Results We show that loss of YgjD leads to a marked decrease in cell size and termination of cell division. The transition towards smaller size occurs in a controlled manner: cell elongation and cell division remain coupled, but cell size at division decreases. We also find evidence that depletion of YgjD leads to the synthesis of the intracellular signaling molecule (pppGpp, inducing a cellular reaction resembling the stringent response. Concomitant deletion of the relA and spoT genes - leading to a strain that is uncapable of synthesizing (pppGpp - abrogates the decrease in cell size, but does not prevent termination of cell division upon YgjD depletion. Conclusions Depletion of YgjD protein from growing cells leads to a decrease in cell size that is contingent on (pppGpp, and to a termination of cell division. The combination of single-cell timelapse microscopy and statistical analysis can give detailed insights into the phenotypic consequences of the loss of essential genes, and can thus serve as a new tool to study the function of essential genes.

  3. Regularized focusing inversion of time-lapse electrical resistivity data: an approach to parametrize the minimum gradient support functional

    Science.gov (United States)

    Nguyen, Frédéric; Hermans, Thomas

    2015-04-01

    Inversion of time-lapse resistivity data allows obtaining 'snapshots' of changes occurring in monitored systems for applications such as aquifer storage, geothermal heat exchange, site remediation or tracer tests. Based on these snapshots, one can infer qualitative information on the location and morphology of changes occurring in the subsurface but also quantitative estimates on the degree of changes in certain property such as temperature or total dissolved solid content. Analysis of these changes can provide direct insight into flow and transport and associated processes and controlling parameters. However, the reliability of the analysis is dependent on survey geometry, measurement schemes, data error, and regularization. Survey design parameters may be optimized prior to the monitoring survey. Regularization, on the other hand, may be chosen depending on available information collected during the monitoring. Common approaches consider smoothing model changes both in space and time but it is often needed to obtain a sharp temporal anomaly, for example in fractured aquifers. We here propose to use the alternative regularization approach based on minimum gradient support (MGS) (Zhdanov, 2002) for time-lapse surveys which will focus the changes in tomograms snapshots. MGS will limit the occurrences of changes in electrical resistivity but will also restrict the variations of these changes inside the different zones. A commonly encountered difficulty by practitioners in this type of regularization is the choice of an additional parameter, the so-called β, required to define the MGS functional. To the best of our knowledge, there is no commonly accepted or standard methodology to optimize the MGS parameter β. The inversion algorithm used in this study is CRTomo (Kemna 2000). It uses a Gauss-Newton scheme to iteratively minimize an objective function which consists of a data misfit functional and a model constraint functional. A univariate line search is performed

  4. Segmentation of Environmental Time Lapse Image Sequences for the Determination of Shore Lines Captured by Hand-Held Smartphone Cameras

    Science.gov (United States)

    Kröhnert, M.; Meichsner, R.

    2017-09-01

    The relevance of globally environmental issues gains importance since the last years with still rising trends. Especially disastrous floods may cause in serious damage within very short times. Although conventional gauging stations provide reliable information about prevailing water levels, they are highly cost-intensive and thus just sparsely installed. Smartphones with inbuilt cameras, powerful processing units and low-cost positioning systems seem to be very suitable wide-spread measurement devices that could be used for geo-crowdsourcing purposes. Thus, we aim for the development of a versatile mobile water level measurement system to establish a densified hydrological network of water levels with high spatial and temporal resolution. This paper addresses a key issue of the entire system: the detection of running water shore lines in smartphone images. Flowing water never appears equally in close-range images even if the extrinsics remain unchanged. Its non-rigid behavior impedes the use of good practices for image segmentation as a prerequisite for water line detection. Consequently, we use a hand-held time lapse image sequence instead of a single image that provides the time component to determine a spatio-temporal texture image. Using a region growing concept, the texture is analyzed for immutable shore and dynamic water areas. Finally, the prevalent shore line is examined by the resultant shapes. For method validation, various study areas are observed from several distances covering urban and rural flowing waters with different characteristics. Future work provides a transformation of the water line into object space by image-to-geometry intersection.

  5. Gas piston activity of the Nyiragongo lava lake: First insights from a Stereographic Time-Lapse Camera system

    Science.gov (United States)

    Smets, Benoît; d'Oreye, Nicolas; Kervyn, Matthieu; Kervyn, François

    2017-10-01

    Nyiragongo volcano (D.R. Congo), in the western branch of the East African Rift System, is one of the most active volcanoes on Earth. Its eruptive activity is mainly characterized by the presence of a persistent lava lake in its main crater. As observed at other persistent lava lakes, the Nyiragongo lava lake level exhibits metric vertical variations in the form of minutes-to hour-long cycles, which we infer to be gas piston activity. To study this activity, we developed and tested a Stereographic Time-Lapse Camera (STLC) system, which takes stereo-pairs of photographs of the Nyiragongo crater at regular intervals. Each pair of gas- and steam-free images during daytime allows the production of a 3D point cloud. The comparison of the point clouds provides a measurement of topographic changes related to variations in lava lake level. The processing of a first dataset acquired between 18 and 20 September 2011, at an acquisition rate of 1 pair of images every 2 min, revealed cycles of vertical lava lake level variations reaching up to 3.8 m. Lava lake level variations >0.5 m are detected significantly. They are interpreted to result from gas accumulation and release in the lava lake itself. The limitations of the STLC approach are related to the number of cameras used and the atmospheric masking by steam and volcanic gas in the Nyiragongo crater. The proposed photogrammetric approach could be applied elsewhere or in other disciplines, where frequent topographic changes occur.

  6. SEGMENTATION OF ENVIRONMENTAL TIME LAPSE IMAGE SEQUENCES FOR THE DETERMINATION OF SHORE LINES CAPTURED BY HAND-HELD SMARTPHONE CAMERAS

    Directory of Open Access Journals (Sweden)

    M. Kröhnert

    2017-09-01

    Full Text Available The relevance of globally environmental issues gains importance since the last years with still rising trends. Especially disastrous floods may cause in serious damage within very short times. Although conventional gauging stations provide reliable information about prevailing water levels, they are highly cost-intensive and thus just sparsely installed. Smartphones with inbuilt cameras, powerful processing units and low-cost positioning systems seem to be very suitable wide-spread measurement devices that could be used for geo-crowdsourcing purposes. Thus, we aim for the development of a versatile mobile water level measurement system to establish a densified hydrological network of water levels with high spatial and temporal resolution. This paper addresses a key issue of the entire system: the detection of running water shore lines in smartphone images. Flowing water never appears equally in close-range images even if the extrinsics remain unchanged. Its non-rigid behavior impedes the use of good practices for image segmentation as a prerequisite for water line detection. Consequently, we use a hand-held time lapse image sequence instead of a single image that provides the time component to determine a spatio-temporal texture image. Using a region growing concept, the texture is analyzed for immutable shore and dynamic water areas. Finally, the prevalent shore line is examined by the resultant shapes. For method validation, various study areas are observed from several distances covering urban and rural flowing waters with different characteristics. Future work provides a transformation of the water line into object space by image-to-geometry intersection.

  7. Time-lapse Imaging of Primary Preneoplastic Mammary Epithelial Cells Derived from Genetically Engineered Mouse Models of Breast Cancer

    OpenAIRE

    Nakles, Rebecca E.; Millman, Sarah L.; Cabrera, M. Carla; Johnson, Peter; Mueller, Susette; Hoppe, Philipp S.; Schroeder, Timm; Furth, Priscilla A.

    2013-01-01

    Time-lapse imaging can be used to compare behavior of cultured primary preneoplastic mammary epithelial cells derived from different genetically engineered mouse models of breast cancer. For example, time between cell divisions (cell lifetimes), apoptotic cell numbers, evolution of morphological changes, and mechanism of colony formation can be quantified and compared in cells carrying specific genetic lesions. Primary mammary epithelial cell cultures are generated from mammary glands without...

  8. Time-lapse three-dimensional inversion of complex conductivity data using an active time constrained (ATC) approach

    Science.gov (United States)

    Karaoulis, M.; Revil, A.; Werkema, D.D.; Minsley, B.J.; Woodruff, W.F.; Kemna, A.

    2011-01-01

    Induced polarization (more precisely the magnitude and phase of impedance of the subsurface) is measured using a network of electrodes located at the ground surface or in boreholes. This method yields important information related to the distribution of permeability and contaminants in the shallow subsurface. We propose a new time-lapse 3-D modelling and inversion algorithm to image the evolution of complex conductivity over time. We discretize the subsurface using hexahedron cells. Each cell is assigned a complex resistivity or conductivity value. Using the finite-element approach, we model the in-phase and out-of-phase (quadrature) electrical potentials on the 3-D grid, which are then transformed into apparent complex resistivity. Inhomogeneous Dirichlet boundary conditions are used at the boundary of the domain. The calculation of the Jacobian matrix is based on the principles of reciprocity. The goal of time-lapse inversion is to determine the change in the complex resistivity of each cell of the spatial grid as a function of time. Each model along the time axis is called a 'reference space model'. This approach can be simplified into an inverse problem looking for the optimum of several reference space models using the approximation that the material properties vary linearly in time between two subsequent reference models. Regularizations in both space domain and time domain reduce inversion artefacts and improve the stability of the inversion problem. In addition, the use of the time-lapse equations allows the simultaneous inversion of data obtained at different times in just one inversion step (4-D inversion). The advantages of this new inversion algorithm are demonstrated on synthetic time-lapse data resulting from the simulation of a salt tracer test in a heterogeneous random material described by an anisotropic semi-variogram. ?? 2011 The Authors Geophysical Journal International ?? 2011 RAS.

  9. Imaging high stage river-water intrusion into a contaminated aquifer along a major river corridor using 2-D time-lapse surface electrical resistivity tomography

    Science.gov (United States)

    Wallin, E. L.; Johnson, T. C.; Greenwood, W. J.; Zachara, J. M.

    2013-03-01

    The Hanford 300 Area is located adjacent to the Columbia River in south-central Washington State, USA, and was a former site for nuclear fuel processing operations. Waste disposal practices resulted in persistent unsaturated zone and groundwater contamination, the primary contaminant of concern being uranium. Uranium behavior at the site is intimately linked with river stage driven groundwater-river water exchange such that understanding the nature of river water intrusion into the 300 Area is critical for predicting uranium desorption and transport. In this paper, we use 2-D surface-based time-lapse electrical resistivity tomography (ERT) to image the inland intrusion of river water during high stage conditions. We inverted approximately 1200 data sets (400 per line over three lines) using high performance computing resources to produce a time-lapse sequence of changes in bulk conductivity caused by river water intrusion during the 2011 spring runoff cycle over approximately 125 days. To invert the data, we use an image differencing approach that does not require regularization in the time dimension, enabling the inversion to accommodate the sharp, time varying contrasts in conductivity imposed by the moving water table. The resulting time series for each mesh element was then analyzed using common time series analysis to reveal the timing and location of river water intrusion beneath each line. The results reveal nonuniform flows characterized by preferred flow zones where river water enters and exits quickly with stage increase and decrease, and low permeability zones with broader bulk conductivity "break through" curves and longer river water residence times.

  10. A time-series method for automated measurement of changes in mitotic and interphase duration from time-lapse movies.

    Directory of Open Access Journals (Sweden)

    Frederic D Sigoillot

    Full Text Available Automated time-lapse microscopy can visualize proliferation of large numbers of individual cells, enabling accurate measurement of the frequency of cell division and the duration of interphase and mitosis. However, extraction of quantitative information by manual inspection of time-lapse movies is too time-consuming to be useful for analysis of large experiments.Here we present an automated time-series approach that can measure changes in the duration of mitosis and interphase in individual cells expressing fluorescent histone 2B. The approach requires analysis of only 2 features, nuclear area and average intensity. Compared to supervised learning approaches, this method reduces processing time and does not require generation of training data sets. We demonstrate that this method is as sensitive as manual analysis in identifying small changes in interphase or mitotic duration induced by drug or siRNA treatment.This approach should facilitate automated analysis of high-throughput time-lapse data sets to identify small molecules or gene products that influence timing of cell division.

  11. Globally referenced real time monitoring of mass movements using monoscopic time-lapse photography.

    Science.gov (United States)

    Kenner, Robert; Phillips, Marcia; Buchroithner, Manfred

    2016-04-01

    The creep movement of a rock glacier was monitored in daily resolution using images of an automatic in-situ time-lapse camera (AC). Displacements were calculated between the images in 2D image coordinates using the imaging velocimetry algorithm of Roesgen and Totaro, 1995. To georeference and scale these displacements, a creep velocity field captured once by a terrestrial laser scan (TLS) repeat measurement was used. The laser scan point cloud and the creep velocity vector field were projected in image coordinates of the AC to obtain a georeferencing mask, a scale mask and an azimuth mask for the 2D displacements calculated between two images. The scale mask was obtained by comparing the TLS derived displacement vectors with those of the AC, referring to a common measurement period. The automatic procedure includes the following work steps: 1. Offsets between two images are identified and corrected based on image parts representing unchanged terrain. 2. 2D displacements are calculated between all chronological image sequences. 3. Faulty displacement vectors are eliminated based on a predefined threshold for spatial direction differences. 4. The remaining displacements are georeferenced, scaled and attributed with individual displacement directions (azimuths) in global coordinates. 5. In addition to the displacement values, displacement velocities and accelerations are calculated using the date of the images. 6. For chronologically successive displacement vector fields, the spatial mean of the relative velocity is defined and expressed as a percentage of the first displacement velocity in the series. The time series of the relative velocities is expressed in chart form. 7. The spatial resolution of all georeferenced output data sets is homogenized, as they were influenced by the central projection of the photos. The described procedure proved to be a reliable, low cost method to monitor mass wasting processes. Even under difficult conditions, like thin snow coverage

  12. Unravelling complex processes during effusive volcanic eruptions using high resolution time-lapse imagery

    Science.gov (United States)

    Pinkerton, H.; James, M. R.; Applegarth, L. J.

    2010-12-01

    While lava flow models are being used successfully to predict areas that are liable to be covered during effusive eruptions, lavas that erupt for more than a few weeks have the potential to develop lava tubes, ephemeral vents and accidental breaches leading to new lava flow pathways. The processes resulting in each of these are not fully understood. Some of these may be related to variations in effusion rate during the eruption; others may be topographically-controlled. There is a therefore a need for a detailed analysis of the development of flow fields to improve our understanding of the factors that control maximum flow length of individual flows, ephemeral vent formation, accidental breaches, and the transition from channelled flows to tube-fed flows. During the final month of the 13 May 2008 to 6 July 2009 eruption into the Valle del Bove on Etna, four Canon EOS 450D cameras (3 visible and one modified to collect infrared images) were installed at critical locations around the rim of the Valle del Bove (Schiena dell’ Àsino, Monte Zoccolaro and Pizzi Deneri) to record the emplacement and development of lava flows erupted during this period. Some of the cameras collected images every 5 minutes, while others collected images every 15 minutes. During this time, active lava flows were restricted to the upper part of a large delta, individual flows lasted between a few hours and a few days and they had lengths ranging from tens to hundreds of metres. The resulting time-lapse images reveal significant reduction in mean flow lengths towards the end of the observation period; this is compatible with a marked decrease in effusion rate. Superimposed on this reduction, there were marked variations in effusion rate on shorter time periods. These short-term changes played a significant role in the development of breakouts and ephemeral vent formation and reactivation. The images also place constraints on the relative importance of factors controlling the maximum flow

  13. Live-cell time-lapse imaging and single-cell tracking of in vitro cultured neural stem cells - Tools for analyzing dynamics of cell cycle, migration, and lineage selection.

    Science.gov (United States)

    Piltti, Katja M; Cummings, Brian J; Carta, Krystal; Manughian-Peter, Ayla; Worne, Colleen L; Singh, Kulbir; Ong, Danier; Maksymyuk, Yuriy; Khine, Michelle; Anderson, Aileen J

    2018-01-15

    Neural stem cell (NSC) cultures have been considered technically challenging for time-lapse analysis due to high motility, photosensitivity, and growth at confluent densities. We have tested feasibility of long-term live-cell time-lapse analysis for NSC migration and differentiation studies. Here, we describe a method to study the dynamics of cell cycle, migration, and lineage selection in cultured multipotent mouse or human NSCs using single-cell tracking during a long-term, 7-14 day live-cell time-lapse analysis. We used in-house made PDMS inserts with five microwells on a glass coverslip petri-dish to constrain NSC into the area of acquisition during long-term live-cell imaging. In parallel, we have defined image acquisition settings for single-cell tracking of cell cycle dynamics using Fucci-reporter mouse NSC for 7 days as well as lineage selection and migration using human NSC for 14 days. Overall, we show that adjustments of live-cell analysis settings can extend the time period of single-cell tracking in mouse or human NSC from 24-72 h up to 7-14 days and potentially longer. However, we emphasize that experimental use of repeated fluorescence imaging will require careful consideration of controls during acquisition and analysis. Copyright © 2017. Published by Elsevier Inc.

  14. Noninferiority, randomized, controlled trial comparing embryo development using media developed for sequential or undisturbed culture in a time-lapse setup.

    Science.gov (United States)

    Hardarson, Thorir; Bungum, Mona; Conaghan, Joe; Meintjes, Marius; Chantilis, Samuel J; Molnar, Laszlo; Gunnarsson, Kristina; Wikland, Matts

    2015-12-01

    To study whether a culture medium that allows undisturbed culture supports human embryo development to the blastocyst stage equivalently to a well-established sequential media. Randomized, double-blinded sibling trial. Independent in vitro fertilization (IVF) clinics. One hundred twenty-eight patients, with 1,356 zygotes randomized into two study arms. Embryos randomly allocated into two study arms to compare embryo development on a time-lapse system using a single-step medium or sequential media. Percentage of good-quality blastocysts on day 5. Percentage of day 5 good-quality blastocysts was 21.1% (standard deviation [SD] ± 21.6%) and 22.2% (SD ± 22.1%) in the single-step time-lapse medium (G-TL) and the sequential media (G-1/G-2) groups, respectively. The mean difference (-1.2; 95% CI, -6.0; 3.6) between the two media systems for the primary end point was less than the noninferiority margin of -8%. There was a statistically significantly lower number of good-quality embryos on day 3 in the G-TL group [50.7% (SD ± 30.6%) vs. 60.8% (SD ± 30.7%)]. Four out of the 11 measured morphokinetic parameters were statistically significantly different for the two media used. The mean levels of ammonium concentration in the media at the end of the culture period was statistically significantly lower in the G-TL group as compared with the G-2 group. We have shown that a single-step culture medium supports blastocyst development equivalently to established sequential media. The ammonium concentrations were lower in the single-step media, and the measured morphokinetic parameters were modified somewhat. NCT01939626. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  15. In Vivo Time-Lapse Imaging in the Zebrafish Lateral Line: A Flexible, Open-Ended Research Project for an Undergraduate Neurobiology Laboratory Course.

    Science.gov (United States)

    Marra, Molly H; Tobias, Zachary J C; Cohen, Hannah R; Glover, Greta; Weissman, Tamily A

    2015-01-01

    The lateral line sensory system in fish detects movements in the water and allows fish to respond to predators, prey, and other stimuli. As the lateral line forms in the first two days of zebrafish development, axons extend caudally along the lateral surface of the fish, eventually forming synapses with hair cells of neuromasts. Growing lateral line axons are located superficially under the skin and can be labeled in living zebrafish using fluorescent protein expression. This system provides a relatively straightforward approach for in vivo time-lapse imaging of neuronal development in an undergraduate setting. Here we describe an upper-level neurobiology laboratory module in which students investigate aspects of axonal development in the zebrafish lateral line system. Students learn to handle and image living fish, collect time-lapse videos of moving mitochondria, and quantitatively measure mitochondrial dynamics by generating and analyzing kymographs of their movements. Energy demands may differ between axons with extending growth cones versus axons that have already reached their targets and are forming synapses. Since relatively little is known about this process in developing lateral line axons, students generate and test their own hypotheses regarding how mitochondrial dynamics may differ at two different time points in axonal development. Students also learn to incorporate into their analysis a powerful yet accessible quantitative tool, the kymograph, which is used to graph movement over time. After students measure and quantify dynamics in living fish at 1 and 2 days post fertilization, this module extends into independent projects, in which students can expand their studies in a number of different, inquiry-driven directions. The project can also be pared down for courses that wish to focus solely on the quantitative analysis (without fish handling), or vice versa. This research module provides a useful approach for the design of open-ended laboratory

  16. Spatiotemporal monitoring of soil water content profiles in an irrigated field using probabilistic inversion of time-lapse EMI data

    KAUST Repository

    Moghadas, Davood

    2017-10-17

    Monitoring spatiotemporal variations of soil water content (θ) is important across a range of research fields, including agricultural engineering, hydrology, meteorology and climatology. Low frequency electromagnetic induction (EMI) systems have proven to be useful tools in mapping soil apparent electrical conductivity (σa) and soil moisture. However, obtaining depth profile water content is an area that has not been fully explored using EMI. To examine this, we performed time-lapse EMI measurements using a CMD mini-Explorer sensor along a 10 m transect of a maize field over a 6 day period. Reference data were measured at the end of the profile via an excavated pit using 5TE capacitance sensors. In order to derive a time-lapse, depth-specific subsurface image of electrical conductivity (σ), we applied a probabilistic sampling approach, DREAM(ZS), on the measured EMI data. The inversely estimated σ values were subsequently converted to θ using the Rhoades et al. (1976) petrophysical relationship. The uncertainties in measured σa, as well as inaccuracies in the inverted data, introduced some discrepancies between estimated σ and reference values in time and space. Moreover, the disparity between the measurement footprints of the 5TE and CMD Mini-Explorer sensors also led to differences. The obtained θ permitted an accurate monitoring of the spatiotemporal distribution and variation of soil water content due to root water uptake and evaporation. The proposed EMI measurement and modeling technique also allowed for detecting temporal root zone soil moisture variations. The time-lapse θ monitoring approach developed using DREAM(ZS) thus appears to be a useful technique to understand spatiotemporal patterns of soil water content and provide insights into linked soil moisture vegetation processes and the dynamics of soil moisture/infiltration processes.

  17. Role of Interstitial Branching in the Development of Visual Corticocortical Connections: A Time-Lapse and Fixed-Tissue Analysis

    Science.gov (United States)

    Ruthazer, Edward S.; Bachleda, Amelia R.; Olavarria, Jaime F.

    2013-01-01

    We combined fixed-tissue and time-lapse analyses to investigate the axonal branching phenomena underlying the development of topographically organized ipsilateral projections from area 17 to area 18a in the rat. These complementary approaches allowed us to relate static, large-scale information provided by traditional fixed-tissue analysis to highly dynamic, local, small-scale branching phenomena observed with two-photon time-lapse microscopy in acute slices of visual cortex. Our fixed-tissue data revealed that labeled area 17 fibers invaded area 18a gray matter at topographically restricted sites, reaching superficial layers in significant numbers by postnatal day 6 (P6). Moreover, most parental axons gave rise to only one or occasionally a small number of closely spaced interstitial branches beneath 18a. Our time-lapse data showed that many filopodium-like branches emerged along parental axons in white matter or deep layers in area 18a. Most of these filopo-dial branches were transient, often disappearing after several minutes to hours of exploratory extension and retraction. These dynamic behaviors decreased significantly from P4, when the projection is first forming, through the second postnatal week, suggesting that the expression of, or sensitivity to, cortical cues promoting new branch addition in the white matter is developmentally down-regulated coincident with gray matter innervation. Together, these data demonstrate that the development of topographically organized corticocortical projections in rats involves extensive exploratory branching along parental axons and invasion of cortex by only a small number of interstitial branches, rather than the widespread innervation of superficial cortical layers by an initially exuberant population of branches. PMID:21031561

  18. Near real-time imaging of molasses injections using time-lapse electrical geophysics at the Brandywine DRMO, Brandywine, Maryland

    Science.gov (United States)

    Versteeg, R. J.; Johnson, T.; Major, B.; Day-Lewis, F. D.; Lane, J. W.

    2010-12-01

    Enhanced bioremediation, which involves introduction of amendments to promote biodegradation, increasingly is used to accelerate cleanup of recalcitrant compounds and has been identified as the preferred remedial treatment at many contaminated sites. Although blind introduction of amendments can lead to sub-optimal or ineffective remediation, the distribution of amendment throughout the treatment zone is difficult to measure using conventional sampling. Because amendments and their degradation products commonly have electrical properties that differ from those of ambient soil, time-lapse electrical geophysical monitoring has the potential to verify amendment emplacement and distribution. In order for geophysical monitoring to be useful, however, results of the injection ideally should be accessible in near real time. In August 2010, we demonstrated the feasibility of near real-time, autonomous electrical geophysical monitoring of amendment injections at the former Defense Reutilization and Marketing Office (DRMO) in Brandywine, Maryland. Two injections of about 1000 gallons each of molasses, a widely used amendment for enhanced bioremediation, were monitored using measurements taken with borehole and surface electrodes. During the injections, multi-channel resistance data were recorded; data were transmitted to a server and processed using a parallel resistivity inversion code; and results in the form of time-lapse imagery subsequently were posted to a website. This process occurred automatically without human intervention. The resulting time-lapse imagery clearly showed the evolution of the molasses plume. The delay between measurements and online delivery of images was between 45 and 60 minutes, thus providing actionable information that could support decisions about field procedures and a check on whether amendment reached target zones. This experiment demonstrates the feasibility of using electrical imaging as a monitoring tool both during amendment emplacement

  19. Spatiotemporal monitoring of soil water content profiles in an irrigated field using probabilistic inversion of time-lapse EMI data

    Science.gov (United States)

    Moghadas, Davood; Jadoon, Khan Zaib; McCabe, Matthew F.

    2017-12-01

    Monitoring spatiotemporal variations of soil water content (θ) is important across a range of research fields, including agricultural engineering, hydrology, meteorology and climatology. Low frequency electromagnetic induction (EMI) systems have proven to be useful tools in mapping soil apparent electrical conductivity (σa) and soil moisture. However, obtaining depth profile water content is an area that has not been fully explored using EMI. To examine this, we performed time-lapse EMI measurements using a CMD mini-Explorer sensor along a 10 m transect of a maize field over a 6 day period. Reference data were measured at the end of the profile via an excavated pit using 5TE capacitance sensors. In order to derive a time-lapse, depth-specific subsurface image of electrical conductivity (σ), we applied a probabilistic sampling approach, DREAM(ZS) , on the measured EMI data. The inversely estimated σ values were subsequently converted to θ using the Rhoades et al. (1976) petrophysical relationship. The uncertainties in measured σa, as well as inaccuracies in the inverted data, introduced some discrepancies between estimated σ and reference values in time and space. Moreover, the disparity between the measurement footprints of the 5TE and CMD Mini-Explorer sensors also led to differences. The obtained θ permitted an accurate monitoring of the spatiotemporal distribution and variation of soil water content due to root water uptake and evaporation. The proposed EMI measurement and modeling technique also allowed for detecting temporal root zone soil moisture variations. The time-lapse θ monitoring approach developed using DREAM(ZS) thus appears to be a useful technique to understand spatiotemporal patterns of soil water content and provide insights into linked soil moisture vegetation processes and the dynamics of soil moisture/infiltration processes.

  20. Coupled hydrogeophysical inversion using time-lapse magnetic resonance sounding and time-lapse gravity data for hydraulic aquifer testing: Will it work in practice?

    DEFF Research Database (Denmark)

    Herckenrath, Daan; Auken, Esben; Christiansen, Lars

    2012-01-01

    monitoring: partially penetrating pumping wells in anisotropic aquifers, delayed drainage effects, and typical data errors for TL-RG. Second, we introduce TL-MRS in a similar coupled hydrogeophysical inversion framework and compare the performance of TL-MRS and TL-RG for pumping test monitoring...... in an aquifer pumping test experiment when used in a coupled hydrogeophysical inversion approach. However, these studies considered highly idealized conditions. The aim of this paper is twofold: first, we investigate three major issues which likely limit the practical utility of TL-RG for pumping test....... For this purpose we consider a virtual pumping test, for which we generate synthetic drawdown, TL-MRS and TL-RG observations, and subsequently determine the aquifer parameters in an inverse parameter estimation approach. The inclusion of TL-RG and TL-MRS data did slightly improve parameter estimates...

  1. Time-lapse seismic study of levees in southern New Mexico

    Science.gov (United States)

    Ivanov, J.; Miller, R.D.; Stimac, N.; Ballard, R.F.; Dunbar, J. Joseph; Smullen, S. Steve

    2006-01-01

    The primary objective of this work was to measure changes in compressional- (Vp) and shear-wave (Vs) velocities in an earthen levee during a ponding experiment designed to simulate flood conditions on the Rio Grande in south New Mexico. Although similar to such experiment, performed an year earlier on the Rio Grande in south Texas, the levee seismic response results are different. This work was similar to previous Preliminary testing at three levee sites, all within a 1 km radius and each with unique physical, EM, and core characteristics, was completed and a single low-conductivity, highly fractured site was selected for investigation. Several different types of seismic data were recorded. Seismic data analysis techniques appraised included P-refraction tomography and Rayleigh surface-wave analysis using multichannel analysis of surface waves (MASW). P-wave velocity change (decrease) was rapid and isolated to one section within the pool confines, which already had anomalously high velocity most likely related to burrowing animals modification of the levee structure. S-wave velocity change was gradual and could be observed along the whole width of the pond within and below the levee. The results within the levee sand core were consistent with the observations of sand S-wave velocity changed due to saturation. ?? 2005 Society of Exploration Geophysicists.

  2. Individual cell motility studied by time-lapse video recording: influence of experimental conditions

    DEFF Research Database (Denmark)

    Hartmann-Petersen, R; Walmod, P S; Berezin, A

    2000-01-01

    line. Cellular morphology and organization of filamentous actin were assessed by means of phase-contrast and confocal laser scanning microscopy and compared to the corresponding motility data. RESULTS: Cell dissociation procedure, seeding density, time of cultivation, and substrate concentration were...... shown to affect cellular speed significantly. pH and temperature of the medium most profoundly influenced cell motility and morphology. Thus, the mean cell speed was 40% lower at pH 7.25 than at pH 7.6; at 29 degrees C, it was approximately four times lower than at 39 degrees C. CONCLUSION......: Of the parameters evaluated, cell motility was most strongly affected by changes in pH and temperature. In general, changes in cell speed were accompanied by alterations in cell morphology and organization of filamentous actin, although no consistent phenotypic characteristics could be demonstrated for cells...

  3. A feasibility study of time-lapse seismic noise interferometry for CO2 monitoring at Ketzin

    NARCIS (Netherlands)

    Boullenger, B.; Verdel, A.; Thorbecke, J.; Draganov, D.

    2013-01-01

    Since 2008, CO2 has been injected at the demonstration site for CO2 sequestration in Ketzin, Germany. Since 2009, a permanent array of seismic receivers installed by TNO at the injection site has recorded passive data continuously. It is the intention of TNO to use seismic interferometry (SI) by

  4. Application of Time-Lapse Seismic Monitoring for the Control and Optimization of CO2 Enhanced Oil Recovery Operations

    Energy Technology Data Exchange (ETDEWEB)

    Brian Toelle

    2008-11-30

    This project, 'Application of Time-Lapse Seismic Monitoring for the Control and Optimization of CO{sub 2} Enhanced Oil Recovery Operations', investigated the potential for monitoring CO{sub 2} floods in carbonate reservoirs through the use of standard p-wave seismic data. This primarily involved the use of 4D seismic (time lapse seismic) in an attempt to observe and map the movement of the injected CO{sub 2} through a carbonate reservoir. The differences between certain seismic attributes, such as amplitude, were used for this purpose. This technique has recently been shown to be effective in CO{sub 2} monitoring in Enhanced Oil Recovery (EOR) projects, such as Weyborne. This study was conducted in the Charlton 30/31 field in the northern Michigan Basin, which is a Silurian pinnacle reef that completed its primary production in 1997 and was scheduled for enhanced oil recovery using injected CO{sub 2}. Prior to injection an initial 'Base' 3D survey was obtained over the field and was then processed and interpreted. CO{sub 2} injection within the main portion of the reef was conducted intermittently during 13 months starting in August 2005. During this time, 29,000 tons of CO{sub 2} was injected into the Guelph formation, historically known as the Niagaran Brown formation. By September 2006, the reservoir pressure within the reef had risen to approximately 2000 lbs and oil and water production from the one producing well within the field had increased significantly. The determination of the reservoir's porosity distribution, a critical aspect of reservoir characterization and simulation, proved to be a significant portion of this project. In order to relate the differences observed between the seismic attributes seen on the multiple 3D seismic surveys and the actual location of the CO{sub 2}, a predictive reservoir simulation model was developed based on seismic attributes obtained from the base 3D seismic survey and available well data. This

  5. Time-lapse imaging of primary preneoplastic mammary epithelial cells derived from genetically engineered mouse models of breast cancer.

    Science.gov (United States)

    Nakles, Rebecca E; Millman, Sarah L; Cabrera, M Carla; Johnson, Peter; Mueller, Susette; Hoppe, Philipp S; Schroeder, Timm; Furth, Priscilla A

    2013-02-08

    Time-lapse imaging can be used to compare behavior of cultured primary preneoplastic mammary epithelial cells derived from different genetically engineered mouse models of breast cancer. For example, time between cell divisions (cell lifetimes), apoptotic cell numbers, evolution of morphological changes, and mechanism of colony formation can be quantified and compared in cells carrying specific genetic lesions. Primary mammary epithelial cell cultures are generated from mammary glands without palpable tumor. Glands are carefully resected with clear separation from adjacent muscle, lymph nodes are removed, and single-cell suspensions of enriched mammary epithelial cells are generated by mincing mammary tissue followed by enzymatic dissociation and filtration. Single-cell suspensions are plated and placed directly under a microscope within an incubator chamber for live-cell imaging. Sixteen 650 μm x 700 μm fields in a 4x4 configuration from each well of a 6-well plate are imaged every 15 min for 5 days. Time-lapse images are examined directly to measure cellular behaviors that can include mechanism and frequency of cell colony formation within the first 24 hr of plating the cells (aggregation versus cell proliferation), incidence of apoptosis, and phasing of morphological changes. Single-cell tracking is used to generate cell fate maps for measurement of individual cell lifetimes and investigation of cell division patterns. Quantitative data are statistically analyzed to assess for significant differences in behavior correlated with specific genetic lesions.

  6. IP4DI: A software for time-lapse 2D/3D DC-resistivity and induced polarization tomography

    Science.gov (United States)

    Karaoulis, M.; Revil, A.; Tsourlos, P.; Werkema, D. D.; Minsley, B. J.

    2013-04-01

    We propose a 2D/3D forward modelling and inversion package to invert direct current (DC)-resistivity, time-domain induced polarization (TDIP), and frequency-domain induced polarization (FDIP) data. Each cell used for the discretization of the 2D/3D problems is characterized by a DC-resistivity value and a chargeability or complex conductivity for TDIP/FDIP problems, respectively. The governing elliptic partial differential equations are solved with the finite element method, which can be applied for both real and complex numbers. The inversion can be performed either for a single snapshot of data or for a sequence of snapshots in order to monitor a dynamic process such as a salt tracer test. For the time-lapse inversion, we have developed an active time constrained (ATC) approach that is very efficient in filtering out noise in the data that is not correlated over time. The forward algorithm is benchmarked with simple analytical solutions. The inversion package IP4DI is benchmarked with three tests, two including simple geometries. The last one corresponds to a time-lapse resistivity problem for cross-well tomography during enhanced oil recovery. The algorithms are based on MATLAB® code package and a graphical user interface (GUI).

  7. A surge of the glaciers Skobreen–Paulabreen, Svalbard, observed by time-lapse photographs and remote sensing data

    Directory of Open Access Journals (Sweden)

    Lene Kristensen

    2012-11-01

    Full Text Available We present observations of a surge of the glaciers Skobreen–Paulabreen, Svalbard, during 2003–05, including a time-lapse movie of the frontal advance during 2005, Advanced Spaceborne Thermal Emission (ASTER imagery and oblique aerial photographs. The surge initiated in Skobreen, and then propagated downglacier into the lower parts of Paulabreen. ASTER satellite images from different stages of the surge are used to evaluate the surge progression. Features on the glacier surface advanced 2800 m over 2.4 yr, averaging 3.2 m/day, while the front advanced less (ca. 1300 m due to contemporaneous calving. The surge resulted in a lateral displacement of the medial moraines of Paulabreen of ca. 600 m at the glacier front. The time-lapse movie captured the advance of the frontal part of the glacier, and dramatically illustrates glacier dynamic processes in an accessible way. The movie documents a range of processes such as a plug-like flow of the glacier, proglacial thrusting, incorporation of old, dead ice at the margin, and calving into the fjord. The movie provides a useful resource for researchers, educators seeking to teach and inspire students, and those wishing to communicate the fascination of glacier science to a wider public.

  8. Estimation of soil hydraulic parameters by integrated hydrogeophysical inversion of time-lapse GPR data measured at Selhausen, Germany

    KAUST Repository

    Jadoon, Khan

    2012-06-01

    We present an integrated hydrogeophysical inversion approach that uses time-lapse off-ground ground-penetrating radar (GPR) data to estimate soil hydraulic parameters, and apply it to a dataset collected in the field. Off-ground GPR data are mainly sensitive to the near-surface water content profile and dynamics, and are thus related to soil hydraulic parameters, such as the parameters of the hydraulic conductivity and water retention functions. The hydrological simulator HYDRUS 1-D was used with a two-layer single- and dual-porosity model. To monitor the soil water content dynamics, time-lapse GPR and time domain reflectometry (TDR) measurements were performed, whereby only GPR data was used in the inversion. The dual porosity model provided better results compared to the single porosity model for describing the soil water dynamics, which is supported by field observations of macropores. Furthermore, the GPR-derived water content profiles reconstructed from the integrated hydrogeophysical inversion were in good agreement with TDR observations. These results suggest that the proposed method is promising for non-invasive characterization of the shallow subsurface hydraulic properties and monitoring water dynamics at the field scale.

  9. In situ visualization of magma deformation at high temperature using time-lapse 3D tomography

    Science.gov (United States)

    Godinho, jose; Lee, Peter; Lavallee, Yan; Kendrick, Jackie; Von-Aulock, Felix

    2016-04-01

    We use synchrotron based x-ray computed micro-tomography (sCT) to visualize, in situ, the microstructural evolution of magma samples 3 mm diameter with a resolution of 3 μm during heating and uniaxial compression at temperatures up to 1040 °C. The interaction between crystals, melt and gas bubbles is analysed in 4D (3D + time) during sample deformation. The ability to observe the changes of the microstructure as a function of time allow us to: a) study the effect of temperature in the ability of magma to fracture or deform; b) quantify bubble nucleation and growth rates during heating; c) study the relation between crystal displacement and volatile exsolution. We will show unique beautiful videos of how bubbles grow and coalescence, how samples and crystals within the sample fracture, heal and deform. Our study establishes in situ sCT as a powerful tool to quantify and visualize with micro-scale resolution fast processes taking place in magma that are essential to understand ascent in a volcanic conduit and validate existing models for determining the explosivity of volcanic eruptions. Tracking simultaneously the time and spatial changes of magma microstructures is shown to be primordial to study disequilibrium processes between crystals, melt and gas phases.

  10. Time-lapse electrical resistivity anomalies due to contaminant transport around landfills

    Directory of Open Access Journals (Sweden)

    J. Yang

    2007-06-01

    Full Text Available The extent of landfill leachate can be delineated by geo-electrical imaging as a response to the varying electrical resistivity in the contaminated area. This research was based on a combination of hydrogeological numerical simulation followed by geophysical forward and inversion modeling performed to evaluate the migration of a contaminant plume from a landfill. As a first step, groundwater flow and contaminant transport was simulated using the finite elements numerical modeling software FEFLOW. The extent of the contaminant plume was acquired through a hydrogeological model depicting the distributions of leachate concentration in the system. Next, based on the empirical relationship between the concentration and electrical conductivity of the leachate in the porous media, the corresponding geo-electrical structure was derived from the hydrogeological model. Finally, forward and inversion computations of geo-electrical anomalies were performed using the finite difference numerical modeling software DCIP2D/DCIP3D. The image obtained by geophysical inversion of the electric data was expected to be consistent with the initial hydrogeological model, as described by the distribution of leachate concentration. Numerical case studies were conducted for various geological conditions, hydraulic parameters and electrode arrays, from which conclusions were drawn regarding the suitability of the methodology to assess simple to more complex geo-electrical models. Thus, optimal mapping and monitoring configurations were determined.

  11. Evaluation and localization of an artificial drainage network by 3D time-lapse electrical resistivity tomography.

    Science.gov (United States)

    Jouen, T; Clément, R; Henine, H; Chaumont, C; Vincent, B; Tournebize, J

    2016-08-26

    In France, 10 % of total arable land is equipped with subsurface drainage systems, to control winter and spring waterlogging due to a temporary perched water table. Most of these systems were installed in the1980s and have aged since then and may now need maintenance. Sometimes, the location of the systems is known, but the standard situation in France is that the original as-built master sketches are no longer available. Performance assessment of drainage systems and curative actions are complicated since drain location is unknown. In this article, the authors test the application of a non-destructive drain detection method which consists in water injection at the outfall of the drainage network combined with time-lapse electrical resistivity tomography (ERT) monitoring. To assess the performance of this methodology, which consists in measuring electrical resistivity from electrodes placed at the nodes of a 1.2-m regular mesh, the authors interpreted the signal using a two-step approach. The first step is based on 3D ERT numerical modelling during a scenario of surface infiltration processes (forward modelling followed by geophysical inversion); this step optimizes the ERT method for locating the infiltration at depths below 1 m. The second step is the validation of the results obtained by numerical modelling with an experimental data set, using water injection into the drainage network combined with time-lapse ERT monitoring on an experimental field site. The results showed the relevance of time-lapse ERT monitoring on a small agricultural plot for locating the drainage network. The numerical results also showed several limitations of the combined methodology: (i) it is necessary to use an electrode spacing unit less than 1.20 m, which does not facilitate investigation on large agriculture plots, (ii) measurements must be taken when resistivity contrast is the strongest between the infiltration area and the soil and (iii) the volume of water needed for

  12. Highlights from the SoilCAM project: Soil Contamination, Advanced integrated characterisation and time-lapse Monitoring

    Science.gov (United States)

    French, H. K.; van der Zee, S. E. A. T. M.; Wehrer, M.; Godio, A.; Pedersen, L. B.; Toscano, G.

    2012-04-01

    The SoilCAM project (Soil Contamination, Advanced integrated characterisation and time-lapse Monitoring 2008-2012, EU-FP7-212663) is aimed at improving current methods for monitoring contaminant distribution and biodegradation in the subsurface. At two test sites, Oslo airport Gardermoen in Norway and the Trecate site in Italy, a number of geophysical techniques, lysimeter and other soil and water sampling techniques as well as numerical flow and transport modelling have been combined at different scales in order to characterise flow transport processes in the unsaturated and saturated zones. Laboratory experiments have provided data on physical and bio-geo-chemical parameters for use in models and to select remediation methods. The geophysical techniques were used to map geological heterogeneities and also conduct time-lapse measurements of processes in the unsaturated zone. Both cross borehole and surface electrodes were used for electrical resistivity and induced polarisation surveys. The geophysical surveys showed clear indications of areas highly affected by de-icing chemicals along the runway at Oslo airport. The time lapse measurements along the runway at the airport show infiltration patterns during snowmelt and are used to validate 2D unsaturated flow and transport simulations using SUTRA. The Orchestra model is used to describe the complex interaction between bio-geo-chemical processes in a 1D profile along the runway. The presence of installations such as a membrane along the runway highly affects the flow pattern and challenges the capacity of the numerical code. Smaller scale field site measurements have revealed the increase of iron and manganese during degradation of de-icing chemicals. The use of Nitrate to increase red-ox potential was tested, but results have not been analysed yet. So far it cannot be concluded that degradation process can be quantified indirectly by geophysical monitoring. At the Trecate site a combination of georadar, electrical

  13. Significantly improved precision of cell migration analysis in time-lapse video microscopy through use of a fully automated tracking system

    Directory of Open Access Journals (Sweden)

    Seufferlein Thomas

    2010-04-01

    Full Text Available Abstract Background Cell motility is a critical parameter in many physiological as well as pathophysiological processes. In time-lapse video microscopy, manual cell tracking remains the most common method of analyzing migratory behavior of cell populations. In addition to being labor-intensive, this method is susceptible to user-dependent errors regarding the selection of "representative" subsets of cells and manual determination of precise cell positions. Results We have quantitatively analyzed these error sources, demonstrating that manual cell tracking of pancreatic cancer cells lead to mis-calculation of migration rates of up to 410%. In order to provide for objective measurements of cell migration rates, we have employed multi-target tracking technologies commonly used in radar applications to develop fully automated cell identification and tracking system suitable for high throughput screening of video sequences of unstained living cells. Conclusion We demonstrate that our automatic multi target tracking system identifies cell objects, follows individual cells and computes migration rates with high precision, clearly outperforming manual procedures.

  14. Time-Lapse Micro-Tomography Measurements and Determination of Effective Transport Properties of Snow Metamorphism Under Advective Conditions

    Science.gov (United States)

    Ebner, P. P.; Grimm, S.; Steen-Larsen, H. C.; Schneebeli, M.; Steinfeld, A.

    2014-12-01

    The metamorphism of snow under advective air flow, with and without temperature gradient, was never experimentally investigated. We developed a new sample holder where metamorphism under advective conditions can be observed and measured using time-lapse micro-tomography [1]. Long-term experiments were performed and direct pore-level simulation (DPLS) [2,3] was directly applied on the extracted 3D digital geometry of the snow to calculate the effective transport properties by solving the governing fluid flow equations. The results showed no effect of isothermal advection, compared to rates typical for isothermal metamorphism. Appling a temperature gradient, the results showed increased snow metamorphism compared to rates typical for temperature gradient metamorphism. However, for both cases a change in the isotopic composition in the air as well as in the snow sample could be observed. These measurements could be influential to better understand snow-air exchange processes relevant for atmospheric chemistry and isotopic composition. REFERENCES[1] Ebner P. P., Grimm S., Schneebeli M., and Steinfeld A.: An instrumented sample holder for time-lapse micro-tomography measurements of snow under advective airflow. Geoscientific Instrumentation, Methods and Data Systems 4(2014), 353-373. [2] Zermatten E., Haussener S., Schneebeli M., and Steinfeld A.: Tomography-based determination of permeability and Dupuit-Forchheimer coefficient of characteristic snow samples. Journal of Glaciology 57(2011), 811-816. [3] Zermatten E., Schneebeli M., Arakawa H., and Steinfeld A.: Tomography-based determination of porosity, specific area and permeability of snow and comparison with measurements. Cold Regions Science and Technology 97 (2014), 33-40. Fig. 1: 3-D surface rendering of a refrozen wet snow sample with fluid flow streamline.

  15. Monitoring the geothermal fluid using time lapse electrical resistivity tomography: The Pisciarelli fumarolic field test site (Campi Flegrei, South Italy)

    Science.gov (United States)

    Fedele, Alessandro; Giulia Di Giuseppe, Maria; Troiano, Antonio; Somma, Reanto; Caputo, Teresa; Patella, Domenico; Troise, Claudia; De Natale, Giuseppe

    2015-04-01

    Pisciarelli area is a fumarolic field subject to very short time morphological changes. A number of critical problems affect this area, i.e. increase of temperature of the fumaroles above the average background temperature, local seismicity and occurrence of fumaroles mixed with jets of boiling water. The presence of a very shallow aquifer seem to have the control on the behavior and composition of the fumaroles. This fumarolic field is still largely unknown regarding geophysical surveys mainly because of its limited space, surrounded on the eastern side by intense urbanization inside the large Agnano crater (Troiano et al. 2014). Currently is mainly affected by geochemical, thermal and seismic monitoring which may not fully explain the behaviour of fluids surface. Many monitoring or time lapse (TL) applications are discussed in literature (e.g., White, 1994; Daily et al., 1995; Barker and Moore, 1998; Ramirez and Daily, 2001; Carter, 2002; Slater et al., 2002; Singha and Gorelick, 2005; Cassiani et al., 2006; Swarzenski et al., 2006; de Franco et al., 2009). However all these experiments are devoted to the use of the ERT for tracer tests or in contaminant hydrology and are characterized by a short monitoring period due to the complexity and problems of long-time instrument maintenance. We propose and present a first approach of a geophysical monitoring by time lapse electrical resistivity in a fumarolic field. The profiles were acquired in January 2013, in January, March, May, July, September and November 2014 respectively. They cross the Pisciarelli area following approximately the NS direction and were characterized by a 2.5 m electrode spacing and maximum penetration depth of about 20 m. and will supply fundamental evidences on the possible seasonal resistivity fluctuations or if the resistivity changes are indicative of an increase in volcanic gases present in the hydrothermal system.

  16. Time-lapse ultrashort pulse microscopy of infection in three-dimensional versus two-dimensional culture environments reveals enhanced extra-chromosomal virus replication compartment formation

    Science.gov (United States)

    Gibbs, Holly C.; Sing, Garwin; Armas, Juan Carlos González; Campbell, Colin J.; Ghazal, Peter; Yeh, Alvin T.

    2013-03-01

    The mechanisms that enable viruses to harness cellular machinery for their own survival are primarily studied in cell lines cultured in two-dimensional (2-D) environments. However, there are increasing reports of biological differences between cells cultured in 2-D versus three-dimensional (3-D) environments. Here we report differences in host-virus interactions based on differences in culture environment. Using ultrashort pulse microscopy (UPM), a form of two-photon microscopy that utilizes sub-10-fs pulses to efficiently excite fluorophores, we have shown that de novo development of extra-chromosomal virus replication compartments (VRCs) upon murine cytomegalovirus (mCMV) infection is markedly enhanced when host cells are cultured in 3-D collagen gels versus 2-D monolayers. In addition, time-lapse imaging revealed that mCMV-induced VRCs have the capacity to grow by coalescence. This work supports the future potential of 3-D culture as a useful bridge between traditional monolayer cultures and animal models to study host-virus interactions in a more physiologically relevant environment for the development of effective anti-viral therapeutics. These advances will require broader adoption of modalities, such as UPM, to image deep within scattering tissues.

  17. Vancomycin sorption on activated sludge Gram(+) bacteria rather than on EPS; 3D Confocal Laser Scanning Microscopy time-lapse imaging.

    Science.gov (United States)

    Louvet, J N; Carrion, C; Stalder, T; Alrhmoun, M; Casellas, M; Potier, O; Pons, M N; Dagot, C

    2017-11-01

    Antibiotics-bacteria interactions depend on antibiotic concentration at the scale of bacteria. This study investigates how vancomycin penetrates into activated sludge flocs and can be sorbed on the bacteria and extracellular polymeric substances (EPS). The 3D structure of flocs was imaged using EPS autofluorescence. The green fluorescent BODIPY(®) FL vancomycin was introduced in a microscopic chamber containing activated sludge and penetration of vancomycin into the flocs by diffusion was observed using time-lapse microscopy. The penetration depended on the floc structure, as long and large pores could go through the whole flocs making preferential path. The antibiotic concentration into the flocs was also found to depend on the sorption rate. BODIPY(®) FL vancomycin was found to bind preferentially into Gram(+) bacteria than on EPS. The vancomycin adsorption constant on bacteria according to the linear adsorption model, Kdbacteria was estimated to be 5 times higher (SD 2.6) than the adsorption constant on EPS KdEPS. These results suggest that antibiotic removal by sorption into wastewater treatment plants could change according to the amount of bacteria in the sludge. Moreover, antibiotic concentration at the scale of bacteria could be significantly higher than the concentration in the bulk solution and this should be taken into account when studying antibiotic activity or biodegradation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Background intensity correction for terabyte-sized time-lapse images.

    Science.gov (United States)

    Chalfoun, J; Majurski, M; Bhadriraju, K; Lund, S; Bajcsy, P; Brady, M

    2015-03-01

    Several computational challenges associated with large-scale background image correction of terabyte-sized fluorescent images are discussed and analysed in this paper. Dark current, flat-field and background correction models are applied over a mosaic of hundreds of spatially overlapping fields of view (FOVs) taken over the course of several days, during which the background diminishes as cell colonies grow. The motivation of our work comes from the need to quantify the dynamics of OCT-4 gene expression via a fluorescent reporter in human stem cell colonies. Our approach to background correction is formulated as an optimization problem over two image partitioning schemes and four analytical correction models. The optimization objective function is evaluated in terms of (1) the minimum root mean square (RMS) error remaining after image correction, (2) the maximum signal-to-noise ratio (SNR) reached after downsampling and (3) the minimum execution time. Based on the analyses with measured dark current noise and flat-field images, the most optimal GFP background correction is obtained by using a data partition based on forming a set of submosaic images with a polynomial surface background model. The resulting image after correction is characterized by an RMS of about 8, and an SNR value of a 4 × 4 downsampling above 5 by Rose criterion. The new technique generates an image with half RMS value and double SNR value when compared to an approach that assumes constant background throughout the mosaic. We show that the background noise in terabyte-sized fluorescent image mosaics can be corrected computationally with the optimized triplet (data partition, model, SNR driven downsampling) such that the total RMS value from background noise does not exceed the magnitude of the measured dark current noise. In this case, the dark current noise serves as a benchmark for the lowest noise level that an imaging system can achieve. In comparison to previous work, the past fluorescent

  19. New algorithm to determine true colocalization in combination with image restoration and time-lapse confocal microscopy to MAP kinases in mitochondria.

    Directory of Open Access Journals (Sweden)

    Jorge Ignacio Villalta

    Full Text Available The subcellular localization and physiological functions of biomolecules are closely related and thus it is crucial to precisely determine the distribution of different molecules inside the intracellular structures. This is frequently accomplished by fluorescence microscopy with well-characterized markers and posterior evaluation of the signal colocalization. Rigorous study of colocalization requires statistical analysis of the data, albeit yet no single technique has been established as a standard method. Indeed, the few methods currently available are only accurate in images with particular characteristics. Here, we introduce a new algorithm to automatically obtain the true colocalization between images that is suitable for a wide variety of biological situations. To proceed, the algorithm contemplates the individual contribution of each pixel's fluorescence intensity in a pair of images to the overall Pearsońs correlation and Manders' overlap coefficients. The accuracy and reliability of the algorithm was validated on both simulated and real images that reflected the characteristics of a range of biological samples. We used this algorithm in combination with image restoration by deconvolution and time-lapse confocal microscopy to address the localization of MEK1 in the mitochondria of different cell lines. Appraising the previously described behavior of Akt1 corroborated the reliability of the combined use of these techniques. Together, the present work provides a novel statistical approach to accurately and reliably determine the colocalization in a variety of biological images.

  20. Time-lapse imaging reveals highly dynamic structural maturation of postnatally born dentate granule cells in organotypic entorhino-hippocampal slice cultures.

    Science.gov (United States)

    Radic, Tijana; Jungenitz, Tassilo; Singer, Mathias; Beining, Marcel; Cuntz, Hermann; Vlachos, Andreas; Deller, Thomas; Schwarzacher, Stephan W

    2017-03-03

    Neurogenesis of hippocampal granule cells (GCs) persists throughout mammalian life and is important for learning and memory. How newborn GCs differentiate and mature into an existing circuit during this time period is not yet fully understood. We established a method to visualize postnatally generated GCs in organotypic entorhino-hippocampal slice cultures (OTCs) using retroviral (RV) GFP-labeling and performed time-lapse imaging to study their morphological development in vitro. Using anterograde tracing we could, furthermore, demonstrate that the postnatally generated GCs in OTCs, similar to adult born GCs, grow into an existing entorhino-dentate circuitry. RV-labeled GCs were identified and individual cells were followed for up to four weeks post injection. Postnatally born GCs exhibited highly dynamic structural changes, including dendritic growth spurts but also retraction of dendrites and phases of dendritic stabilization. In contrast, older, presumably prenatally born GCs labeled with an adeno-associated virus (AAV), were far less dynamic. We propose that the high degree of structural flexibility seen in our preparations is necessary for the integration of newborn granule cells into an already existing neuronal circuit of the dentate gyrus in which they have to compete for entorhinal input with cells generated and integrated earlier.

  1. Live Cell Imaging of Bacillus subtilis and Streptococcus pneumoniae using Automated Time-lapse Microscopy

    NARCIS (Netherlands)

    Jong, Imke G. de; Beilharz, Katrin; Kuipers, Oscar P.; Veening, Jan-Willem

    2011-01-01

    During the last few years scientists became increasingly aware that average data obtained from microbial population based experiments are not representative of the behavior, status or phenotype of single cells. Due to this new insight the number of single cell studies rises continuously. However,

  2. Influence of the geomembrane on time-lapse ERT measurements for leachate injection monitoring.

    Science.gov (United States)

    Audebert, M; Clément, R; Grossin-Debattista, J; Günther, T; Touze-Foltz, N; Moreau, S

    2014-04-01

    Leachate recirculation is a key process in the operation of municipal waste landfills as bioreactors. To quantify the water content and to evaluate the leachate injection system, in situ methods are required to obtain spatially distributed information, usually electrical resistivity tomography (ERT). However, this method can present false variations in the observations due to several parameters. This study investigates the impact of the geomembrane on ERT measurements. Indeed, the geomembrane tends to be ignored in the inversion process in most previously conducted studies. The presence of the geomembrane can change the boundary conditions of the inversion models, which have classically infinite boundary conditions. Using a numerical modelling approach, the authors demonstrate that a minimum distance is required between the electrode line and the geomembrane to satisfy the good conditions of use of the classical inversion tools. This distance is a function of the electrode line length (i.e. of the unit electrode spacing) used, the array type and the orientation of the electrode line. Moreover, this study shows that if this criterion on the minimum distance is not satisfied, it is possible to significantly improve the inversion process by introducing the complex geometry and the geomembrane location into the inversion tools. These results are finally validated on a field data set gathered on a small municipal solid waste landfill cell where this minimum distance criterion cannot be satisfied. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Remote estimation of the hydraulic properties of a sand using full-waveform integrated hydrogeophysical inversion of time-lapse, off-ground GPR data

    NARCIS (Netherlands)

    Lambot, S.; Slob, E.; Rhebergen, J.B.; Lopera, O.; Jadoon, K.Z.; Vereecken, H.

    2009-01-01

    We used integrated hydrogeophysical inversion of time-lapse, proximal ground penetrating radar (GPR) data to remotely infer the unsaturated soil hydraulic properties of a laboratory sand during an infiltration event. The inversion procedure involved full-waveform modeling of the radar signal and

  4. Monitoring an artificial tracer test within streambed sediments with time lapse underwater 3D ERT

    Science.gov (United States)

    Clémence, Houzé; Marc, Pessel; Véronique, Durand; Toihir, Ali

    2017-04-01

    The stream-aquifer interface is considered a hotspot for environmental and ecological issues. Due to their complexity, the exchange mechanisms occurring between groundwater and surface water at this interface are not yet fully understood. Many studies have focused on the characterization of the two-dimensional distribution of an artificial tracer (generally injected into the stream) within and outside the streambed, but there is insufficient information about the 3D spatial distribution of the tracer fluxes and their temporal variations. We monitored the transport of an artificial solute tracer transport with 3D electrical resistivity tomography (ERT) in order to improve the 3D spatial resolution in the imaging of the first tens of centimeters of streambed sediments and propose an innovative approach of the three-dimensional and temporal observation of the water fluxes. The hydro-geophysical field measurements were made on a small stream located within the Orgeval watershed (Seine et Marne, France). Using a resistivimeter connected to 180 electrodes, 3D electrical resistivity tomograms were made on a riverbed section, as a brine tracer was injected directly into the hyporheic zone. Before the tracer monitoring, the static 3D resistivity tomograms were consistent with the lithological heterogeneities identified at the site. However, this study defines some prerequisites to high-resolution 3D underwater resistivity measurements: for instance, a precise knowledge of an eventual weak electrode contact and a spatial resolution identical in every spatial direction. First results show a rapid development and persistence of a conductive plume around the injection point which disappears progressively after the injection. Within the sediments top layer, preferential flowpaths were highlighted due to the highly heterogeneous medium and hydraulic conductivity. The riverbed topography showed some pool-riffle sequences which conduct the formation of local entering and exiting

  5. Time Lapse Spectropolarimetry: Constraining the Nature and Progenitors of Interacting CCSNe

    Science.gov (United States)

    Huk, Leah

    2017-11-01

    SNe of Type IIn are among the brightest supernova explosions due to strong circumstellar interaction. Examining the geometric and optical properties of the circumstellar material (CSM) can help to identify the progenitors of individual IIn SNe. Polarimetry is the optimal method for constraining CSM characteristics, as polarimetric signals both depend upon and preserve geometric information from unresolved sources. I present the results of fitting an ensemble of simulated polarized Hα emission-line profiles of interacting SNe, created using a three-dimensional Monte Carlo radiative transfer code called SLIP, to the multi-epoch observed polarized spectra of the Type IIn SN 1997eg. Further study of this model ensemble will allow us to investigate relationships among SNe IIn based on viewing angle and consider how the category should be subdivided based on physical properties of the CSM and/or progenitor.

  6. Time-lapse imaging of in vitro myogenesis using atomic force microscopy.

    Science.gov (United States)

    Städler, B; Blättler, T M; Franco-Obregón, A

    2010-01-01

    Myoblast therapy relies on the integration of skeletal muscle stem cells into distinct muscular compartments for the prevention of clinical conditions such as heart failure, or bladder dysfunction. Understanding the fundamentals of myogenesis is hence crucial for the success of these potential medical therapies. In this report, we followed the rearrangement of the surface membrane structure and the actin cytoskeletal organization in C2C12 myoblasts at different stages of myogenesis using atomic force microscopy (AFM) and confocal laser scanning microscopy (CLSM). AFM imaging of living myoblasts undergoing fusion unveiled that within minutes of making cell-cell contact, membrane tubules appear that unite the myoblasts and increase in girth as fusion proceeds. CLSM identified these membrane tubules as built on scaffolds of actin filaments that nucleate at points of contact between fusing myoblasts. In contrast, similarly behaving membrane tubules are absent during cytokinesis. The results from our study in combination with recent findings in literature further expand the understanding of the biochemical and membrane structural rearrangements involved in the two fundamental cellular processes of division and fusion.

  7. Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies.

    Science.gov (United States)

    Bhadriraju, Kiran; Halter, Michael; Amelot, Julien; Bajcsy, Peter; Chalfoun, Joe; Vandecreme, Antoine; Mallon, Barbara S; Park, Kye-Yoon; Sista, Subhash; Elliott, John T; Plant, Anne L

    2016-07-01

    Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5days each, generating a total experimental dataset of 0.9 terabyte (TB). The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events. Copyright © 2016. Published by Elsevier B.V.

  8. Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies

    Directory of Open Access Journals (Sweden)

    Kiran Bhadriraju

    2016-07-01

    Full Text Available Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5 days each, generating a total experimental dataset of 0.9 terabyte (TB. The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events.

  9. Technical note: Stage and water width measurement of a mountain stream using a simple time-lapse camera

    Directory of Open Access Journals (Sweden)

    P. Leduc

    2018-01-01

    Full Text Available Remote sensing applied to river monitoring adds complementary information useful for understanding the system behaviour. In this paper, we present a method for visual stage gauging and water surface width measurement using a ground-based time-lapse camera and a fully automatic image analysis algorithm for flow monitoring at a river cross section of a steep, bouldery channel. The remote stage measurement was coupled with a water level logger (pressure transducer on site and shows that the image-based method gives a reliable estimate of the water height variation and daily flow record when validated against the pressure transducer (R = 0.91. From the remotely sensed pictures, we also extracted the water width and show that it is possible to correlate water surface width and stage. The images also provide valuable ancillary information for interpreting and understanding flow hydraulics and site weather conditions. This image-based gauging method is a reliable, informative and inexpensive alternative or adjunct to conventional stage measurement especially for remote sites.

  10. Technical note: Stage and water width measurement of a mountain stream using a simple time-lapse camera

    Science.gov (United States)

    Leduc, Pauline; Ashmore, Peter; Sjogren, Darren

    2018-01-01

    Remote sensing applied to river monitoring adds complementary information useful for understanding the system behaviour. In this paper, we present a method for visual stage gauging and water surface width measurement using a ground-based time-lapse camera and a fully automatic image analysis algorithm for flow monitoring at a river cross section of a steep, bouldery channel. The remote stage measurement was coupled with a water level logger (pressure transducer) on site and shows that the image-based method gives a reliable estimate of the water height variation and daily flow record when validated against the pressure transducer (R = 0.91). From the remotely sensed pictures, we also extracted the water width and show that it is possible to correlate water surface width and stage. The images also provide valuable ancillary information for interpreting and understanding flow hydraulics and site weather conditions. This image-based gauging method is a reliable, informative and inexpensive alternative or adjunct to conventional stage measurement especially for remote sites.

  11. Time-Lapse Geophysical Measurements targeting Spatial and Temporal Variability in Biogenic Gas Production from Peat Soils in a Hydrologically Controlled Wetland in the Florida Everglades

    Science.gov (United States)

    Wright, W. J.; Shahan, T.; Sharp, N.; Comas, X.

    2015-12-01

    Peat soils are known to release globally significant amounts of methane (CH4) and carbon dioxide (CO2) to the atmosphere. However, uncertainties still remain regarding the spatio-temporal distribution of gas accumulations and triggering mechanisms of gas releasing events. Furthermore, most research on peatland gas dynamics has traditionally been focused on high latitude peatlands. Therefore, understanding gas dynamics in low-latitude peatlands (e.g. the Florida Everglades) is key to global climate research. Recent studies in the Everglades have demonstrated that biogenic gas flux values may vary when considering different temporal and spatial scales of measurements. The work presented here targets spatial variability in gas production and release at the plot scale in an approximately 85 m2 area, and targets temporal variability with data collected during the spring months of two different years. This study is located in the Loxahatchee Impoundment Landscape Assessment (LILA), a hydrologically controlled, landscape scale (30 Ha) model of the Florida Everglades. Ground penetrating radar (GPR) has been used in the past to investigate biogenic gas dynamics in peat soils, and is used in this study to monitor changes of in situ gas storage. Each year, a grid of GPR profiles was collected to image changes in gas distribution in 2d on a weekly basis, and several flux chambers outfitted with time-lapse cameras captured high resolution (hourly) gas flux measurements inside the GPR grid. Combining these methods allows us to use a mass balance approach to estimate spatial variability in gas production rates, and capture temporal variability in gas flux rates.

  12. Time lapse imaging techniques for comparison of mineralization dynamics in primary murine osteoblasts and the late osteoblast/early osteocyte-like cell line MLO-A5.

    Science.gov (United States)

    Dallas, Sarah L; Veno, Patricia A; Rosser, Jennifer L; Barragan-Adjemian, Cielo; Rowe, David W; Kalajzic, Ivo; Bonewald, Lynda F

    2009-01-01

    Mineralization of bone matrix and osteocyte differentiation occur simultaneously and appear interrelated both spatially and temporally. Although these are dynamic events, their study has been limited to using static imaging approaches, either alone or in combination with chemical and biochemical analysis and/or genetic manipulation. Here we describe the application of live cell imaging techniques to study mineralization dynamics in primary osteoblast cultures compared to a late osteoblast/early osteocyte-like cell line, MLO-A5. Mineral deposition was monitored using alizarin red as a vital stain for calcium. To monitor differentiation into an osteocyte-like phenotype, the calvarial cells were isolated from transgenic mice expressing green fluorescent protein (GFP) driven by an 8-kb dentin matrix protein-1 (Dmp1) promoter that gives osteocyte-selective expression. Time lapse imaging showed that there was a lag phase of 15-20 h after beta-glycerophosphate addition, followed by mineral deposition that was rapid in primary osteoblast cultures but more gradual in MLO-A5 cultures. In primary osteoblast cultures, mineral was deposited exclusively in association with clusters of cells expressing Dmp1-GFP, suggesting that they were already differentiating into osteocyte-like cells. In MLO-A5 cells, the first indication of mineralization was the appearance of punctate areas of alizarin red fluorescence of 4-7 mum in diameter, followed by mineral deposition throughout the culture in association with collagen fibrils. A high amount of cell motility was observed within mineralizing nodules and in mineralizing MLO-A5 cultures. These studies provide a novel approach for analyzing mineralization kinetics that will enable us to dissect in a time-specific manner the essential players in the mineralization process. Copyright 2008 S. Karger AG, Basel.

  13. AnimalFinder: A semi-automated system for animal detection in time-lapse camera trap images

    Science.gov (United States)

    Price Tack, Jennifer L.; West, Brian S.; McGowan, Conor P.; Ditchkoff, Stephen S.; Reeves, Stanley J.; Keever, Allison; Grand, James B.

    2017-01-01

    Although the use of camera traps in wildlife management is well established, technologies to automate image processing have been much slower in development, despite their potential to drastically reduce personnel time and cost required to review photos. We developed AnimalFinder in MATLAB® to identify animal presence in time-lapse camera trap images by comparing individual photos to all images contained within the subset of images (i.e. photos from the same survey and site), with some manual processing required to remove false positives and collect other relevant data (species, sex, etc.). We tested AnimalFinder on a set of camera trap images and compared the presence/absence results with manual-only review with white-tailed deer (Odocoileus virginianus), wild pigs (Sus scrofa), and raccoons (Procyon lotor). We compared abundance estimates, model rankings, and coefficient estimates of detection and abundance for white-tailed deer using N-mixture models. AnimalFinder performance varied depending on a threshold value that affects program sensitivity to frequently occurring pixels in a series of images. Higher threshold values led to fewer false negatives (missed deer images) but increased manual processing time, but even at the highest threshold value, the program reduced the images requiring manual review by ~40% and correctly identified >90% of deer, raccoon, and wild pig images. Estimates of white-tailed deer were similar between AnimalFinder and the manual-only method (~1–2 deer difference, depending on the model), as were model rankings and coefficient estimates. Our results show that the program significantly reduced data processing time and may increase efficiency of camera trapping surveys.

  14. Documentation of normal and leukemic myelopoietic progenitor cells with high-resolution phase-contrast time-lapse cinematography.

    Science.gov (United States)

    Boll, I T

    2001-08-01

    The high-resolution phase-contrast, time-lapse cinematography using oil immersion lenses and 16-mm film demonstrates the kinetic cell events as maturation, locomotion, mitosis, and apoptosis of cells cultivated at 37 degrees C for up to 10 days. 0.5 v/v frozen-thawed sera with presumably high cytokine concentrations were added to the plasma or agar clot. Vital progenitor cells from human bone marrow and blood have a large, bright, unstructured nucleus with a large nucleolus and a narrow rim of cytoplasm (nuclear/cytoplasmic volume ratio = 0.7). Their nuclei are 6-14 micrometer in diameter and double their volume within 8 h. Many (70%) move at a mean speed of 2 micrometer/min, and many (30%) multiply with alpha-2alpha mitoses, generating progenitor cell families. Various disturbances during the course of mitosis lead to the formation of polyploid cells, thereby yielding the megakaryocytic cell line. Some of the progenitor cells undergo asymmetric alpha-alphan mitoses: One of the two initially identical daughter cells remains a progenitor cell in the morphological sense, whereas the other daughter cell - depending on the size of its mother cell - matures in the same culture medium to form a granulocytopoietic, monocytopoietic or erythrocytopoietic cell line. - In acute myeloid leukemias (AML), the blasts and their nuclei are slightly larger than the corresponding progenitor cells and move faster (5 micrometer/min). Symmetric alpha-2alpha mitoses permit unlimited multiplication of the leukemic blasts if contact with cytotoxic lymphocytes does not render them apoptotic. This results in more stromal cells than normal. Granulocytopenia, monocytopenia, and anemia occur due to the genetic impairment of signaling control for asymmetric alpha-alphan mitoses, and thrombocytopenia occurs due to the reduction in polyploidization. Copyright 2001 S. Karger GmbH, Freiburg

  15. Water content dynamics at plot scale - comparison of time-lapse electrical resistivity tomography monitoring and pore pressure modelling

    Science.gov (United States)

    Zieher, Thomas; Markart, Gerhard; Ottowitz, David; Römer, Alexander; Rutzinger, Martin; Meißl, Gertraud; Geitner, Clemens

    2017-01-01

    Physically-based dynamic modelling of shallow landslide susceptibility rests on several assumptions and simplifications. However, the applicability of physically-based models is only rarely tested in the field at the appropriate scale. This paper presents results of a spray irrigation experiment conducted on a plot of 100 m2 on an Alpine slope susceptible to shallow landsliding. Infiltrating precipitation applied at a constant rate (27.5 mm/h for 5.3 h) was monitored by means of 2D time-lapse electrical resistivity tomography, combined with time-domain reflectometry sensors installed at various depths. In addition, regolith characteristics were assessed by dynamic cone penetration tests using a light-weight cone penetrometer. The spray irrigation experiment resulted in a vertically progressing wetting front to a depth of 80-100 cm. Below that, the unconsolidated material was already saturated by rainfall in the previous days. The observed mean resistivity reduction attributed to infiltrating water during irrigation was scaled to pressure head. Mean variations in pore pressure were reproduced by a linear diffusion model also used in physically-based dynamic landslide susceptibility modelling. Sensitive parameters (hydraulic conductivity and specific storage) were tested over selected value ranges and calibrated. Calibrated parameter values are within published and experimentally derived ranges. The results of the comparison of observations and model results suggest that the model is capable of reproducing mean changes of pore pressure at a suitable scale for physically-based modelling of shallow landslide susceptibility. However, small-scale variations in pore pressure that may facilitate the triggering of shallow landslides are not captured by the model.

  16. In vivo time-lapse imaging of skin burn wound healing using second-harmonic generation microscopy

    Science.gov (United States)

    Yasui, Takeshi; Tanaka, Ryosuke; Hase, Eiji; Fukushima, Shu-ichiro; Araki, Tsutomu

    2014-02-01

    Wound healing is a process to repair the damaged tissue caused by thermal burn, incised wound, or stab wound. Although the wound healing has many aspects, it is common for dynamics of collagen fiber, such as decomposition, production, or growth, to be closely related with wound healing. If such the healing process can be visualized as a timelapse image of the collagen fiber in the same subject, one may obtain new findings regarding biological repairing mechanisms in the healing process. In this article, to investigate the temporal modoification of dermal collagen fiber in the burn wound healing, we used second-harmonic-generation (SHG) microscopy, showing high selectivity and good image contrast to collagen molecules as well as high spatial resolution, optical three-dimensional sectioning, minimal invasiveness, deep penetration, the absence of interference from background light, and in vivo measurement without additional staining. Since SHG light arises from a non-centrosymmetric triple helix of three polypeptide chains in the collagen molecule, SHG intensity sensitively reflects the structure maturity of collagen molecule and its aggregates. A series of time-lapse SHG images during the wound healing process of 2 weeks clearly indicated that condensation and melting of dermal collagen fibers by the deep dermal burn, decomposition of the damaged collagen fibers in the inflammation phase, production of new collagen fibers in the proliferation phase, and the growth of the new collagen fibers in the remodeling phase. These results show a high potential of SHG microscopy for optical assessment of the wound healing process in vivo.

  17. Is there any correlation between oocyte polarization microscopy findings with embryo time lapse monitoring in ICSI program?

    Science.gov (United States)

    Faramarzi, Azita; Khalili, Mohammad Ali; Agha-Rahimi, Azam; Omidi, Marjan

    2017-06-01

    The aim was to investigate the relationship between the presence of the meiotic spindle (MS) and zona pellucida (ZP) birefringence of MII oocytes with morphokinetics variables of derived embryos in ICSI setting. Using a polarization imaging system, the ZP birefringence and presence of MS were evaluated pre ICSI. Also, morphokinetics variables including time of second PB extrusion (tPB2), time of pronuclei appearance (tPNa), time of pronuclei fading (tPNf), time of two to eight discrete cells (t2-t8) ECC1 (t2-tPB2), cc2a (t3-t2), S2 (t4-t3) and S3 (t8-t5) as well as irregular cleavage events of 368 embryos were analyzed with time lapse monitoring (TLM). t5 occurred earlier in high birefringent ZP (HB-ZP) compared with low birefringent oocytes (LB-ZP; p = 0.001). In addition, t2 happened later in invisible MS compared to visible MS oocytes (p = 0.013). There were significantly lower rates of cell fusion (Fu) in oocytes with HB-ZP and also the Fu and trichotomous mitoses (TM) together in visible MS oocytes (p = 0.005, p = 0.001 and p = 0.001, respectively). Both t2 and t5 timings and irregular cleavage events of embryos were correlated with ZP birefringence and MS status, respectively. So, combining the information from both oocyte polarization microscopy imaging and embryo TLM can be a useful tool for single embryo transfer (SET) program.

  18. Monitoring field scale CO2 injection from time-lapse seismic and well log, integrating with advanced rock physics model at Cranfield EOR site

    Science.gov (United States)

    Ghosh, Ranjana

    2017-10-01

    Causes and effects of global warming have been highly debated in recent years. Nonetheless, injection and storage of CO2 (CO2 sequestration) in the subsurface is becoming increasingly accepted as a viable tool to reduce the amount of CO2 from the atmosphere, which is a primary contributor to global warming. Monitoring of CO2 movement with time is essential to ascertain that sequestration is not hazardous. A method is proposed here to appraise CO2 saturation from seismic attributes using differential effective medium theory modified for pressure (PDEM). The PDEM theory accounts pressure-induced fluid flow between cavities, which is a very important investigation in the CO2-sequestered regime of heterogeneous microstructure. The study area is the lower Tuscaloosa formation at Cranfield in Mississippi, USA, which is one of the active enhanced oil recovery (EOR), and CO2 capture and storage (CCS) fields. Injection well (F1) and two observation wells (F2 and F3) are present close (within 112 m) to the detailed area of study for this region. Since the three wells are closely situated, two wells, namely injection well F1 and the furthest observation well F3, have been focused on to monitor CO2 movement. Time-lapse (pre- and post-injection) log, core and surface seismic data are used in the quantitative assessment of CO2 saturation from the PDEM theory. It has been found that after approximately 9 months of injection, average CO2 saturations in F1 and F3 are estimated as 50% in a zone of thickness 25 m at a depth of 3 km.

  19. Monitoring the evolution and migration of a methane gas plume in an unconfined sandy aquifer using time-lapse GPR and ERT

    Science.gov (United States)

    Steelman, Colby M.; Klazinga, Dylan R.; Cahill, Aaron G.; Endres, Anthony L.; Parker, Beth L.

    2017-10-01

    Fugitive methane (CH4) leakage associated with conventional and unconventional petroleum development (e.g., shale gas) may pose significant risks to shallow groundwater. While the potential threat of stray (CH4) gas in aquifers has been acknowledged, few studies have examined the nature of its migration and fate in a shallow groundwater flow system. This study examines the geophysical responses observed from surface during a 72 day field-scale simulated CH4 leak in an unconfined sandy aquifer at Canadian Forces Base Borden, Canada, to better understand the transient behaviour of fugitive CH4 gas in the subsurface. Time-lapse ground-penetrating radar (GPR) and electrical resistivity tomography (ERT) were used to monitor the distribution and migration of the gas-phase and assess any impacts to groundwater hydrochemistry. Geophysical measurements captured the transient formation of a CH4 gas plume emanating from the injector, which was accompanied by an increase in total dissolved gas pressure (PTDG). Subsequent reductions in PTDG were accompanied by reduced bulk resistivity around the injector along with an increase in the GPR reflectivity along horizontal bedding reflectors farther downgradient. Repeat temporal GPR reflection profiling identified three events with major peaks in reflectivity, interpreted to represent episodic lateral CH4 gas release events into the aquifer. Here, a gradual increase in PTDG near the injector caused a sudden lateral breakthrough of gas in the direction of groundwater flow, causing free-phase CH4 to migrate much farther than anticipated based on groundwater advection. CH4 accumulated along subtle permeability boundaries demarcated by grain-scale bedding within the aquifer characteristic of numerous Borden-aquifer multi-phase flow experiments. Diminishing reflectivity over a period of days to weeks suggests buoyancy-driven migration to the vadose zone and/or CH4 dissolution into groundwater. Lateral and vertical CH4 migration was

  20. Monitoring field scale CO2 injection from time-lapse seismic and well log, integrating with advanced rock physics model at Cranfield EOR site

    Science.gov (United States)

    Ghosh, Ranjana

    2017-12-01

    Causes and effects of global warming have been highly debated in recent years. Nonetheless, injection and storage of CO2 (CO2 sequestration) in the subsurface is becoming increasingly accepted as a viable tool to reduce the amount of CO2 from the atmosphere, which is a primary contributor to global warming. Monitoring of CO2 movement with time is essential to ascertain that sequestration is not hazardous. A method is proposed here to appraise CO2 saturation from seismic attributes using differential effective medium theory modified for pressure (PDEM). The PDEM theory accounts pressure-induced fluid flow between cavities, which is a very important investigation in the CO2-sequestered regime of heterogeneous microstructure. The study area is the lower Tuscaloosa formation at Cranfield in Mississippi, USA, which is one of the active enhanced oil recovery (EOR), and CO2 capture and storage (CCS) fields. Injection well (F1) and two observation wells (F2 and F3) are present close (within 112 m) to the detailed area of study for this region. Since the three wells are closely situated, two wells, namely injection well F1 and the furthest observation well F3, have been focused on to monitor CO2 movement. Time-lapse (pre- and post-injection) log, core and surface seismic data are used in the quantitative assessment of CO2 saturation from the PDEM theory. It has been found that after approximately 9 months of injection, average CO2 saturations in F1 and F3 are estimated as 50% in a zone of thickness 25 m at a depth of 3 km.

  1. Assessing clogging processes caused by biofilm growth and organic particle accumulation in constructed wetlands using time-lapse electrical resistivity tomography method

    Science.gov (United States)

    Mahjoub, Himi; Tapias, Josefina C.; Lovera, Raúl; Rivero, Lluís; Font, Xavier; Casas, Albert

    2016-04-01

    Constructed wetlands for removing pollutants from wastewater in small communities are growing rapidly in many regions of the world. The advantages over conventional mechanical sanitation systems, where land availability is not a limiting factor, are low energy requirements, easy operation and maintenance, low sludge production and cost-effectivity. Nevertheless, with time the cleaning process can result in gradual clogging of the porous layer by suspended solids, bacterial film, chemical precipitates and compaction. The clogging development causes decrease of hydraulic conductivity, reduced oxygen supply and further leads to a rapid decrease of the treatment performance. As the investment involved in reversing clogging can represent a substantial fraction of the cost of a new system it is essential to assess in advance the evolution of clogging process and detect potential failures in the system. Since there is a lack of experiences for monitoring the functionality of constructed wetlands time-lapse electrical resistivity tomography studies have been conducted at horizontal sub-surface flow municipal wastewater treatment wetlands of Catalonia (Spain). The results of this research show that electrical resistivity tomography can be a very useful technique for assessing the extent of silting up processes that clog the subsurface flow constructed wetlands through the gravel layer. In the unsaturated zone, the electrical resistivity is greater at the end of the filter, since the pores contains air which is dielectric, while at the beginning of the filter the resistivity is lower because the electrical conduction of organic matter around the mineral grains. Conversely, in the saturated zone, the electrical resistivity is lower at the end of the filter, since pores contain a higher proportion of high ionic conductivity wastewater, while at the beginning of the filter the electrical resistivity is higher because of the lower porosity due to the clogging process.

  2. Understanding leachate flow in municipal solid waste landfills by combining time-lapse ERT and subsurface flow modelling - Part II: Constraint methodology of hydrodynamic models.

    Science.gov (United States)

    Audebert, M; Oxarango, L; Duquennoi, C; Touze-Foltz, N; Forquet, N; Clément, R

    2016-09-01

    Leachate recirculation is a key process in the operation of municipal solid waste landfills as bioreactors. To ensure optimal water content distribution, bioreactor operators need tools to design leachate injection systems. Prediction of leachate flow by subsurface flow modelling could provide useful information for the design of such systems. However, hydrodynamic models require additional data to constrain them and to assess hydrodynamic parameters. Electrical resistivity tomography (ERT) is a suitable method to study leachate infiltration at the landfill scale. It can provide spatially distributed information which is useful for constraining hydrodynamic models. However, this geophysical method does not allow ERT users to directly measure water content in waste. The MICS (multiple inversions and clustering strategy) methodology was proposed to delineate the infiltration area precisely during time-lapse ERT survey in order to avoid the use of empirical petrophysical relationships, which are not adapted to a heterogeneous medium such as waste. The infiltration shapes and hydrodynamic information extracted with MICS were used to constrain hydrodynamic models in assessing parameters. The constraint methodology developed in this paper was tested on two hydrodynamic models: an equilibrium model where, flow within the waste medium is estimated using a single continuum approach and a non-equilibrium model where flow is estimated using a dual continuum approach. The latter represents leachate flows into fractures. Finally, this methodology provides insight to identify the advantages and limitations of hydrodynamic models. Furthermore, we suggest an explanation for the large volume detected by MICS when a small volume of leachate is injected. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Hillslope-scale hydrological and snow cover dynamics derived from a wireless soil moisture and temperature monitoring network and time-lapse digital photography

    Science.gov (United States)

    Wollschläger, Ute; Vogt, Constantin; Kögler, Simon; Martini, Edoardo

    2015-04-01

    In mountainous catchments, snowmelt may be an important component of the water balance. We apply data from a wireless soil moisture and temperature monitoring network in combination with time-lapse digital photographs from a hillslope in the Schäfertal catchment, Lower Harz Mountains, to investigate interactions between hillslope-scale snow cover, soil moisture and soil temperature. The time series of digital photographs is evaluated using an automatic algorithm that estimates snow height at the position of several snow stakes placed along the hillslope using the green value of the RGB color cube. Inferred snow heights are applied to interpret near-subsurface soil moisture and soil temperature dynamics from the same time period including snow accumulation and melt. The combination of time-lapse digital photography, soil moisture and soil temperature monitoring clearly shows the strong influence of the snow cover on subsurface soil moisture and soil temperature dynamics. The shallow snow cover has a strong insulating effect on near-subsurface soil temperatures keeping the soil unfrozen even at air temperatures reaching down to less than -10 °C. The time-lapse photographs, soil moisture and soil temperature observations also show the different snowmelt behavior of the north- and south-exposed slopes. These observations are important information for future modelling of hillslope and catchment-scale hydrological dynamics.

  4. Time-Lapse Monitoring of an Engineering Scaled Excavation at Federal District, Brazil by Passive Ambient NoiseInterferometry

    Science.gov (United States)

    Cárdenas-Soto, M., Sr.; Hussain, Y.; Martinez-Carvajal, H., Sr.; Martino, S., Sr.; Rocha, M., Sr.

    2016-12-01

    gave Rayleigh wave velocity changes (dv/v=-dt/t). These changes correlated well with initiation and propagation of fracture at the face of this normal slope. It is concluded that cost effective technique, PANI has a good potential for the monitoring of time lapse changes of evolving fractures.

  5. A study of the progression of damage in an axially loaded Branta leucopsis femur using X-ray computed tomography and digital image correlation.

    Science.gov (United States)

    Mustansar, Zartasha; McDonald, Samuel A; Sellers, William Irvin; Manning, Phillip Lars; Lowe, Tristan; Withers, Philip J; Margetts, Lee

    2017-01-01

    This paper uses X-ray computed tomography to track the mechanical response of a vertebrate (Barnacle goose) long bone subjected to an axial compressive load, which is increased gradually until failure. A loading rig was mounted in an X-ray computed tomography system so that a time-lapse sequence of three-dimensional (3D) images of the bone's internal (cancellous or trabecular) structure could be recorded during loading. Five distinct types of deformation mechanism were observed in the cancellous part of the bone. These were (i) cracking, (ii) thinning (iii) tearing of cell walls and struts, (iv) notch formation, (v) necking and (vi) buckling. The results highlight that bone experiences brittle (notch formation and cracking), ductile (thinning, tearing and necking) and elastic (buckling) modes of deformation. Progressive deformation, leading to cracking was studied in detail using digital image correlation. The resulting strain maps were consistent with mechanisms occurring at a finer-length scale. This paper is the first to capture time-lapse 3D images of a whole long bone subject to loading until failure. The results serve as a unique reference for researchers interested in how bone responds to loading. For those using computer modelling, the study not only provides qualitative information for verification and validation of their simulations but also highlights that constitutive models for bone need to take into account a number of different deformation mechanisms.

  6. A study of the progression of damage in an axially loaded Branta leucopsis femur using X-ray computed tomography and digital image correlation

    Directory of Open Access Journals (Sweden)

    Zartasha Mustansar

    2017-06-01

    Full Text Available This paper uses X-ray computed tomography to track the mechanical response of a vertebrate (Barnacle goose long bone subjected to an axial compressive load, which is increased gradually until failure. A loading rig was mounted in an X-ray computed tomography system so that a time-lapse sequence of three-dimensional (3D images of the bone’s internal (cancellous or trabecular structure could be recorded during loading. Five distinct types of deformation mechanism were observed in the cancellous part of the bone. These were (i cracking, (ii thinning (iii tearing of cell walls and struts, (iv notch formation, (v necking and (vi buckling. The results highlight that bone experiences brittle (notch formation and cracking, ductile (thinning, tearing and necking and elastic (buckling modes of deformation. Progressive deformation, leading to cracking was studied in detail using digital image correlation. The resulting strain maps were consistent with mechanisms occurring at a finer-length scale. This paper is the first to capture time-lapse 3D images of a whole long bone subject to loading until failure. The results serve as a unique reference for researchers interested in how bone responds to loading. For those using computer modelling, the study not only provides qualitative information for verification and validation of their simulations but also highlights that constitutive models for bone need to take into account a number of different deformation mechanisms.

  7. Time-lapse resistivity measurements combined with soil water sampling to characterize solute movement in the unsaturated zone at Oslo airport, Gardermoen

    Science.gov (United States)

    Bloem, E.; French, H. K.; Binley, A.; Schotanus, D.; Eggen, G.

    2010-12-01

    Pollution of soils is a widespread problem and is an important part of the still to be implemented Soil Directive (EU). To improve risk assessment, monitoring, and treatment strategies for natural attenuation, we require a better understanding of the effect of soil heterogeneity on contaminant movement and methods for monitoring the effects of this heterogeneity at contaminated sites. Geophysical methods provide indirect measurements of subsurface properties over larger volumes than tradition techniques, and are potentially cost-efficient. However, the usefulness of any individual set of geophysical measurements (akin to a snapshot at one point in time) is severely limited by the problem of non-uniqueness or ambiguity when used to study contaminated sites, where the attendant processes vary in space and time. To make progress on soil contamination assessment and site characterization there is a strong need to integrate quasi field-scale, extensively instrumented tools, such as the multi-compartment sampler, with non-invasive (geophysical) and invasive (soil sampling, soil water sampling) methods. We illustrate this approach in an application to solute transport at Oslo airport, Norway. The impact of annual infiltration of large quantities of de-icing chemicals at Oslo airport, Gardermoen, represents common challenge for all airports with winter frost. It is also similar to the challenge posed by de-icing salt application along roads. At the research field station at Gardermoen, a degradable de-icing chemical and an inactive tracer were added to the snow cover prior to snowmelt and to the surface during an irrigation experiment performed after the snowmelt. In order to link geophysical measurements to solute transport processes in the unsaturated zone, time-lapse cross borehole resistivity as well as surface resistivity measurements were conducted at the same time as soil water samples were extracted. Measurements of soil temperature, and tension were also carried

  8. Estimation of soil hydraulic parameters in the field by integrated hydrogeophysical inversion of time-lapse ground-penetrating radar data

    KAUST Repository

    Jadoon, Khan

    2012-01-01

    An integrated hydrogeophysical inversion approach was used to remotely infer the unsaturated soil hydraulic parameters from time-lapse ground-penetrating radar (GPR) data collected at a fixed location over a bare agricultural field. The GPR model combines a full-waveform solution of Maxwell\\'s equations for three-dimensional wave propaga- tion in planar layered media together with global reflection and transmission functions to account for the antenna and its interactions with the medium. The hydrological simu- lator HYDRUS-1D was used with a two layer single- and dual-porosity model. The radar model was coupled to the hydrodynamic model, such that the soil electrical properties (permitivity and conductivity) that serve as input to the GPR model become a function of the hydrodynamic model output (water content), thereby permiting estimation of the soil hydraulic parameters from the GPR data in an inversion loop. To monitor the soil water con- tent dynamics, time-lapse GPR and time domain reflectometry (TDR) measurements were performed, whereby only GPR data was used in the inversion. Significant effects of water dynamics were observed in the time-lapse GPR data and in particular precipitation and evaporation events were clearly visible. The dual porosity model provided betier results compared to the single porosity model for describing the soil water dynamics, which is sup- ported by field observations of macropores. Furthermore, the GPR-derived water content profiles reconstructed from the integrated hydrogeophysical inversion were in good agree- ment with TDR observations. These results suggest that the proposed method is promising for non-invasive characterization of the shallow subsurface hydraulic properties and moni- toring water dynamics at the field scale. © Soil Science Society of America.

  9. Time-lapse microscopy and classification of 2D human mesenchymal stem cells based on cell shape picks up myogenic from osteogenic and adipogenic differentiation.

    Science.gov (United States)

    Seiler, Christof; Gazdhar, Amiq; Reyes, Mauricio; Benneker, Lorin M; Geiser, Thomas; Siebenrock, Klaus A; Gantenbein-Ritter, Benjamin

    2014-09-01

    Current methods to characterize mesenchymal stem cells (MSCs) are limited to CD marker expression, plastic adherence and their ability to differentiate into adipogenic, osteogenic and chondrogenic precursors. It seems evident that stem cells undergoing differentiation should differ in many aspects, such as morphology and possibly also behaviour; however, such a correlation has not yet been exploited for fate prediction of MSCs. Primary human MSCs from bone marrow were expanded and pelleted to form high-density cultures and were then randomly divided into four groups to differentiate into adipogenic, osteogenic chondrogenic and myogenic progenitor cells. The cells were expanded as heterogeneous and tracked with time-lapse microscopy to record cell shape, using phase-contrast microscopy. The cells were segmented using a custom-made image-processing pipeline. Seven morphological features were extracted for each of the segmented cells. Statistical analysis was performed on the seven-dimensional feature vectors, using a tree-like classification method. Differentiation of cells was monitored with key marker genes and histology. Cells in differentiation media were expressing the key genes for each of the three pathways after 21 days, i.e. adipogenic, osteogenic and chondrogenic, which was also confirmed by histological staining. Time-lapse microscopy data were obtained and contained new evidence that two cell shape features, eccentricity and filopodia (= 'fingers') are highly informative to classify myogenic differentiation from all others. However, no robust classifiers could be identified for the other cell differentiation paths. The results suggest that non-invasive automated time-lapse microscopy could potentially be used to predict the stem cell fate of hMSCs for clinical application, based on morphology for earlier time-points. The classification is challenged by cell density, proliferation and possible unknown donor-specific factors, which affect the performance of

  10. Deriving Macropore and Preferential Flow Parameters from Tracer and Time-lapse 3D GPR Experiments at the Plot-Scale

    Science.gov (United States)

    Jackisch, Conrad; Allroggen, Niklas; Tronicke, Jens; Zehe, Erwin

    2014-05-01

    "Hydrology - a science in which all processes are preferential" (Uhlenbrook, 2006) - as such preferential flow is known and discussed in hydrology since almost three decades. At the same time, preferential flow remains problematic as explicit descriptions are hard to define and upscale and implicit descriptions remain rather case sensitive. Moreover, our techniques to monitor preferential flow and especially flow structures are very limited. We conducted three multi-tracer plot-scale (1m x 1m) sprinkler experiments at a forested hillslope in the Attert Basin in Luxembourg with prevailing geogenic and biogenic preferential flow structures. It was accompanied by a 3D time-lapse GPR (Ground Penetrating Radar) survey covering an area of 3m x 3m. We present the results with special emphasis on the derivation of macropore parameters for further modelling. To do so, we developed an automated analysis of images from excavated Brilliant Blue stained profiles. Additionally, we analyse our time-lapse GPR data with respect to temporal changes and derive 3D strutural information of the preferential flow patterns. Superior to tracers, this high resolution subsurface imaging technique is non-invasive, repeatable and therefore helps to disentangle the dye stained patterns towards process observation. The results of the image analyses and the GPR surveys are compared and referenced to soil moisture monitoring, sampled Bromide profiles and stable isotope signatures. We further discuss implications for joint development of model concepts and observation methods.

  11. Time-Lapse Acoustic, Transport, and NMR Measurements to Monitor Induced Microstructural Changes of Carbonate Rocks During Injection of CO2-Rich Water

    Science.gov (United States)

    Grombacher, D.; Vanorio, T.; Ebert, Y.

    2011-12-01

    Geophysical monitoring during CO2 injection is necessary to ensure that 1) injected CO2 fills the reservoir as predicted, and that 2) injected CO2 does not migrate towards regions where it may escape. Injection of CO2 results in an altered equilibrium between the pore fluid and the host rock causing chemo-mechanical processes to occur which may impact rock frame properties. In order to improve monitoring techniques, further characterization of injection-induced microstructural changes due to chemo-mechanical processes is needed. We attempt to answer the following questions: How does injection alter the pore network, and how do injection-induced microstructural changes impact seismic properties? An experiment consisting of a suite of six concurrent and independent time-lapse measurements including permeability, porosity, acoustic, nuclear magnetic resonance (NMR) T2 relaxation, and scanning electron microscopy (SEM) and CT-scan images were conducted on two types of carbonate rocks (micritic limestones, and chalky, micritic carbonates). Measurements were taken as a function of the total injected volume of CO2-rich water (which mimics CO2 injection). Injections took place both under bench top conditions and under conditions of constant confining and pore pressures of 15MPa and 12MPa, respectively. Each measurement type is independent and sensitive to different pore properties, allowing us to determine how the microstructure is altered by considering the data from all measurement types simultaneously. Additionally, time-lapse measurements allow us to quantify induced pore structure changes. With increased injection of CO2-rich water, micritic limestones exhibit increased sensitivity of velocity to confining pressure, large permeability increases (~200%), and much variation in their T2 distribution. We hypothesize that injection alters the pore network by increasing pore connectivity and promoting the formation of more elongated pores. In contrast, chalkly, micritic

  12. Time lapse imaging analysis of the effect of ER stress modulators on apoptotic cell assessed by caspase3/7 activation in NG108-15 cells

    Directory of Open Access Journals (Sweden)

    Ayako Saito

    2016-03-01

    Full Text Available This paper reports the data from the long term time lapse imaging of neuronal cell line NG108-15 that were treated with apoptosis inducer or various ER stress inducers. Use of the fluorescent reporter for activated caspase3/7 in combination with the conventional light microscope allowed us to investigate the time course of apoptosis induction at the single cell level. Quantitative as well as qualitative data are presented here to show the effect of two different ER stress modulating chemical compounds on caspase3/7-dependent apoptosis in neuronal cell line NG108-15 cells. Additional results and interpretation of our data concerning ER stress and apoptosis in NG108-15 cells can be found in Suga et al. (2015 [1] and in Suga et al. (2015 [2].

  13. Bayesian Markov-Chain-Monte-Carlo inversion of time-lapse crosshole GPR data to characterize the vadose zone at the Arrenaes Site, Denmark

    DEFF Research Database (Denmark)

    Scholer, Marie; Irving, James; Zibar, Majken Caroline Looms

    2012-01-01

    -chain-Monte-Carlo inversion approach with different priors. The ground-penetrating radar (GPR) geophysical method has the potential to provide valuable information on the hydraulic properties of the vadose zone because of its strong sensitivity to soil water content. In particular, recent evidence has suggested...... that the stochastic inversion of crosshole GPR traveltime data can allow for a significant reduction in uncertainty regarding subsurface van Genuchten–Mualem (VGM) parameters. Much of the previous work on the stochastic estimation of VGM parameters from crosshole GPR data has considered the case of steady......-state infiltration conditions, which represent only a small fraction of practically relevant scenarios. We explored in detail the dynamic infiltration case, specifically examining to what extent time-lapse crosshole GPR traveltimes, measured during a forced infiltration experiment at the Arreneas field site...

  14. Time-lapse changes of P- and S-wave velocities and shear wave splitting in the first year after the 2011 Tohoku earthquake, Japan: shallow subsurface

    Science.gov (United States)

    Sawazaki, Kaoru; Snieder, Roel

    2013-04-01

    We detect time-lapse changes in P- and S-wave velocities (hereafter, VP and VS, respectively) and shear wave splitting parameters associated with the 2011 Tohoku earthquake, Japan, at depths between 0 and 504 m. We estimate not only medium parameters but also the 95 per cent confidence interval of the estimated velocity change by applying a new least squares inversion scheme to the deconvolution analysis of KiK-net vertical array records. Up to 6 per cent VS reduction is observed at more than half of the analysed KiK-net stations in northeastern Japan with over 95 per cent confidence in the first month after the main shock. There is a considerable correlation between the S-wave traveltime delay and the maximum horizontal dynamic strain (MDS) by the main shock motion when the strain exceeds 5 × 10- 4 on the ground surface. This correlation is not clearly observed for MDS at the borehole bottom. On the contrary, VP and shear wave splitting parameters do not show systematic changes after the Tohoku earthquake. These results indicate that the time-lapse change is concentrated near the ground surface, especially in loosely packed soil layers. We conclude that the behaviour of VP, VS and shear wave splitting parameters are explained by the generation of omnidirectional cracks near the ground surface and by the diffusion of water in the porous subsurface. Recovery of VS should be related to healing of the crack which is proportional to the logarithm of the lapse time after the main shock and/or to decompaction after shaking.

  15. Visualizing and quantifying movement from pre-recorded videos: The spectral time-lapse (STL algorithm [v1; ref status: indexed, http://f1000r.es/2qo

    Directory of Open Access Journals (Sweden)

    Christopher R Madan

    2014-01-01

    Full Text Available When studying animal behaviour within an open environment, movement-related data are often important for behavioural analyses. Therefore, simple and efficient techniques are needed to present and analyze the data of such movements. However, it is challenging to present both spatial and temporal information of movements within a two-dimensional image representation. To address this challenge, we developed the spectral time-lapse (STL algorithm that re-codes an animal’s position at every time point with a time-specific color, and overlays it with a reference frame of the video, to produce a summary image. We additionally incorporated automated motion tracking, such that the animal’s position can be extracted and summary statistics such as path length and duration can be calculated, as well as instantaneous velocity and acceleration. Here we describe the STL algorithm and offer a freely available MATLAB toolbox that implements the algorithm and allows for a large degree of end-user control and flexibility.

  16. Application of RVA and Time-Lapse Photography to Explore Effects of Extent of Chlorination, Milling Extraction Rate, and Particle-Size Reduction of Flour on Cake-Baking Functionality

    Science.gov (United States)

    Three factors (extent of chlorination, milling extraction rate and particle-size reduction) in the cake-bakeing functionality of Croplan 594W flour were explored by Rapid Visco-Analyzer (RVA) and time-lapse photography. The extent of chlorination and milling extraction rate showed dramatic effects,...

  17. Segmentation and tracking of stem cells in time lapse microscopy to quantify dynamic behavioral changes during spheroid formation.

    Science.gov (United States)

    Jiang, Ching-Fen; Hsu, Shan-hui; Tsai, Ka-Pei; Tsai, Ming-Hong

    2015-06-01

    Dynamic behavior of stem cells during in vitro development is diverse. Previous cell tracking studies have focused more on cell proliferation than on cell aggregation. However, the enhancement of cell proliferation in association with cell aggregation has been reported. In a previous study, we also demonstrated that the aggregation of adult human mesenchymal stem cells to form three-dimensional (3D) cellular spheroids helped maintain the expression of stemness marker genes in the cells. However, the dynamic behavioral changes triggered by spheroid formation remain to be investigated. A scheme of image processing techniques is proposed to meet this need. A hybrid-thresholding technique was first developed for efficient segmentation of cell clusters, after which a cell tracking method based on pair-matching with topological constraints was designed. Two morphological indices were derived to track the timing of 3D spheroid formation during the cellular aggregation process. Five cell motility indices measured from single cells and 3D spheroids were then compared. After confirmation of more than 90% correspondence between the results obtained by manual tracking and the proposed methods, an analysis of cellular behavior reveals a significant increase in motility in association with spheroid formation, consistent with a previous report that used a gene expression approach. This study proposed a systematic image analysis method to quantify the dynamic behavior of stem cells for stemness evaluation during cell culturing in vitro. Results demonstrated the validity of the developed platform in investigation of the dynamic behavior of cell aggregation in stem cell cultures in vitro. © 2015 International Society for Advancement of Cytometry.

  18. Efficacy of time-lapse photography and repeated counts abundance estimation for white-tailed deer populations

    Science.gov (United States)

    Keever, Allison; McGowan, Conor P.; Ditchkoff, Stephen S.; Acker, S.A.; Grand, James B.; Newbolt, Chad H.

    2017-01-01

    Automated cameras have become increasingly common for monitoring wildlife populations and estimating abundance. Most analytical methods, however, fail to account for incomplete and variable detection probabilities, which biases abundance estimates. Methods which do account for detection have not been thoroughly tested, and those that have been tested were compared to other methods of abundance estimation. The goal of this study was to evaluate the accuracy and effectiveness of the N-mixture method, which explicitly incorporates detection probability, to monitor white-tailed deer (Odocoileus virginianus) by using camera surveys and a known, marked population to collect data and estimate abundance. Motion-triggered camera surveys were conducted at Auburn University’s deer research facility in 2010. Abundance estimates were generated using N-mixture models and compared to the known number of marked deer in the population. We compared abundance estimates generated from a decreasing number of survey days used in analysis and by time periods (DAY, NIGHT, SUNRISE, SUNSET, CREPUSCULAR, ALL TIMES). Accurate abundance estimates were generated using 24 h of data and nighttime only data. Accuracy of abundance estimates increased with increasing number of survey days until day 5, and there was no improvement with additional data. This suggests that, for our system, 5-day camera surveys conducted at night were adequate for abundance estimation and population monitoring. Further, our study demonstrates that camera surveys and N-mixture models may be a highly effective method for estimation and monitoring of ungulate populations.

  19. Novel migrating mouse neural crest cell assay system utilizing P0-Cre/EGFP fluorescent time-lapse imaging

    Directory of Open Access Journals (Sweden)

    Kawakami Minoru

    2011-11-01

    Full Text Available Abstract Background Neural crest cells (NCCs are embryonic, multipotent stem cells. Their long-range and precision-guided migration is one of their most striking characteristics. We previously reported that P0-Cre/CAG-CAT-lacZ double-transgenic mice showed significant lacZ expression in tissues derived from NCCs. Results In this study, by embedding a P0-Cre/CAG-CAT-EGFP embryo at E9.5 in collagen gel inside a culture glass slide, we were able to keep the embryo developing ex vivo for more than 24 hours; this development was with enough NCC fluorescent signal intensity to enable single-cell resolution analysis, with the accompanying NCC migration potential intact and with the appropriate NCC response to the extracellular signal maintained. By implantation of beads with absorbed platelet-derived growth factor-AA (PDGF-AA, we demonstrated that PDGF-AA acts as an NCC-attractant in embryos. We also performed assays with NCCs isolated from P0-Cre/CAG-CAT-EGFP embryos on culture plates. The neuromediator 5-hydroxytryptamine (5-HT has been known to regulate NCC migration. We newly demonstrated that dopamine, in addition to 5-HT, stimulated NCC migration in vitro. Two NCC populations, with different axial levels of origins, showed unique distribution patterns regarding migration velocity and different dose-response patterns to both 5-HT and dopamine. Conclusions Although avian species predominated over the other species in the NCC study, our novel system should enable us to use mice to assay many different aspects of NCCs in embryos or on culture plates, such as migration, division, differentiation, and apoptosis.

  20. Time-lapse ERT interpretation methodology for leachate injection monitoring based on multiple inversions and a clustering strategy (MICS)

    Science.gov (United States)

    Audebert, M.; Clément, R.; Touze-Foltz, N.; Günther, T.; Moreau, S.; Duquennoi, C.

    2014-12-01

    Leachate recirculation is a key process in municipal waste landfills functioning as bioreactors. To quantify the water content and to assess the leachate injection system, in-situ methods are required to obtain spatially distributed information, usually electrical resistivity tomography (ERT). This geophysical method is based on the inversion process, which presents two major problems in terms of delimiting the infiltration area. First, it is difficult for ERT users to choose an appropriate inversion parameter set. Indeed, it might not be sufficient to interpret only the optimum model (i.e. the model with the chosen regularisation strength) because it is not necessarily the model which best represents the physical process studied. Second, it is difficult to delineate the infiltration front based on resistivity models because of the smoothness of the inversion results. This paper proposes a new methodology called MICS (multiple inversions and clustering strategy), which allows ERT users to improve the delimitation of the infiltration area in leachate injection monitoring. The MICS methodology is based on (i) a multiple inversion step by varying the inversion parameter values to take a wide range of resistivity models into account and (ii) a clustering strategy to improve the delineation of the infiltration front. In this paper, MICS was assessed on two types of data. First, a numerical assessment allows us to optimise and test MICS for different infiltration area sizes, contrasts and shapes. Second, MICS was applied to a field data set gathered during leachate recirculation on a bioreactor.

  1. Time-Lapse Monitoring of DNA Damage Colocalized With Particle Tracks in Single Living Cells

    Energy Technology Data Exchange (ETDEWEB)

    McFadden, Conor H. [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Hallacy, Timothy M. [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Department of Physics and Astronomy, Rice University, Houston, Texas (United States); Flint, David B. [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas (United States); Granville, Dal A. [Department of Medical Physics, The Ottawa Hospital Cancer Centre, Ottawa, Ontario (Canada); Asaithamby, Aroumougame [Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Centre, Dallas, Texas (United States); Sahoo, Narayan [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Akselrod, Mark S. [Crystal Growth Division, Landauer, Inc, Stillwater, Oklahoma (United States); Sawakuchi, Gabriel O., E-mail: gsawakuchi@mdanderson.org [Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Graduate School of Biomedical Sciences, The University of Texas, Houston, Texas (United States)

    2016-09-01

    Purpose: Understanding the DNA damage and repair induced by hadron therapy (HT) beams is crucial for developing novel strategies to maximize the use of HT beams to treat cancer patients. However, spatiotemporal studies of DNA damage and repair for beam energies relevant to HT have been challenging. We report a technique that enables spatiotemporal measurement of radiation-induced damage in live cells and colocalization of this damage with charged particle tracks over a broad range of clinically relevant beam energies. The technique uses novel fluorescence nuclear track detectors with fluorescence confocal laser scanning microscopy in the beam line to visualize particle track traversals within the subcellular compartments of live cells within seconds after injury. Methods and Materials: We designed and built a portable fluorescence confocal laser scanning microscope for use in the beam path, coated fluorescence nuclear track detectors with fluorescent-tagged live cells (HT1080 expressing enhanced green fluorescent protein tagged to XRCC1, a single-strand break repair protein), placed the entire assembly into a proton therapy beam line, and irradiated the cells with a fluence of ∼1 × 10{sup 6} protons/cm{sup 2}. Results: We successfully obtained confocal images of proton tracks and foci of DNA single-strand breaks immediately after irradiation. Conclusions: This technique represents an innovative method for analyzing biological responses in any HT beam line at energies and dose rates relevant to therapy. It allows precise determination of the number of tracks traversing a subcellular compartment and monitoring the cellular damage therein, and has the potential to measure the linear energy transfer of each track from therapeutic beams.

  2. Time-lapse effect of ancient plant coal biochar on some soil agrochemical parameters and soil characteristics.

    Science.gov (United States)

    Kocsis, Tamás; Biró, Borbála; Ulmer, Ákos; Szántó, Mónika; Kotroczó, Zsolt

    2018-01-01

    Biochar is a solid material obtained from reductive, oxygen-free processes, i.e. the thermo-chemical conversion of biomass in oxygen-limited environment. The obtained products have high carbon sequestration potential and strong nutrient-water absorption capacities because of the enlarged carbon surfaces. It is not yet clear how carbon stimulates agrochemical parameters in soil and how those characteristics are developing as time goes on a long-term basis. Samples of ancient (25, 35, 80 years old) plant coal-affected soils were collected in a temperate deciduous forest site located in the south part of the Bükk Mountains (in North Eastern Hungary). Physical-chemical soil characteristics, such as soil pH, cation exchange capacity (CEC), the organic and inorganic nitrogen (NH4+, NH3-) and the available nutrients (P2O5 and K2O), were estimated beside organic matter (SOM) content, measured by two different methods. Levels of polycyclic aromatic hydrocarbon (PAH) compounds in soil and in various biochar samples were assessed in relation with permissible limit values and potential toxicity. Positive correlation was found between the amount of available nutrients, total organic nitrogen content, cation exchange capacity and the age of plant coal-affected soils. The sample soils were exposed to continuous plant coal biochar effect for 25 years, during which macronutrients absorbed and accumulated in the plant coal surfaces. After this period, the degradation of carbon developed simultaneously with the reduction of the amount of available nutrients, till the end of the studied 80-year-affecting period. Measured CEC level indicated positive correlation with nutrient availability and the age of biochar-affected soils. Our results support the hypothesis that biochar in soil can improve its general agrochemical characteristics in relation with its persistence in a specific soil-plant system. Potential PAH content and toxicity of biochar products are key issues of developing

  3. Effect of Time Lapse between Endodontic and Periodontal Therapies on the Healing of Concurrent Endodontic-Periodontal Lesions without Communication: A Prospective Randomized Clinical Trial.

    Science.gov (United States)

    Gupta, Shilpi; Tewari, Sanjay; Tewari, Shikha; Mittal, Shweta

    2015-06-01

    The aim of this prospective randomized clinical trial was to evaluate the effect of a time lapse between endodontic treatment and nonsurgical periodontal treatment on periodontal healing of concurrent endodontic-periodontal lesions without communication. Thirty-one patients were randomly divided into 2 groups: group 1: endodontic treatment and scaling and root planning (SRP) were performed simultaneously and group 2: SRP was performed 3 months after endodontic treatment. Both groups were followed for 3 and 6 months after SRP. Primary outcome variables were the probing depth, clinical attachment level, and periapical index score. Both the groups showed a significant improvement in all the clinical parameters evaluated after the completion of endodontic and periodontal treatment (P .05). Periodontal healing responses were comparable in the 2 groups, with no apparent detriment resulting from simultaneous treatment. Improvements in periodontal parameters that were achieved in 6 months in group 2 were achieved only in 3 months in group 1 (P > .05). Nonsurgical periodontal treatment may be performed simultaneously with endodontic treatment in the management of concurrent endodontic-periodontal lesions without communication, and an observation period after endodontic treatment may not be required. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

  4. Exploring the breakdown of dairy protein gels during in vitro gastric digestion using time-lapse synchrotron deep-UV fluorescence microscopy.

    Science.gov (United States)

    Floury, Juliane; Bianchi, Tiago; Thévenot, Jonathan; Dupont, Didier; Jamme, Frédéric; Lutton, Evelyne; Panouillé, Maud; Boué, François; Le Feunteun, Steven

    2018-01-15

    A novel time-lapse synchrotron deep-UV microscopy methodology was developed that made use of the natural tryptophan fluorescence of proteins. It enabled the monitoring in situ of the microstructural changes of protein gels during simulated gastric digestion. Two dairy gels with an identical composition, but differing by the coagulation mode, were submitted to static in vitro gastric digestion. The kinetics of gel particle breakdown were quantified by image analysis and physico-chemical analyses of digesta. The results confirm the tendency of rennet gels, but not acid gels, to form compact protein aggregates under acidic conditions of the stomach. Consequently, the kinetics of proteolysis were much slower for the rennet gel, confirming the hypothesis of a reduced pepsin accessibility to its substrate. The particle shapes remained unchanged and the disintegration kinetics followed an exponential trend, suggesting that erosion was the predominant mechanism of the enzymatic breakdown of dairy gels in these experimental conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Live Cells as Dynamic Laboratories: Time Lapse Raman Spectral Microscopy of Nanoparticles with Both IgE Targeting and pH-Sensing Functions

    Directory of Open Access Journals (Sweden)

    Kristy L. Nowak-Lovato

    2012-01-01

    Full Text Available This review captures the use of live cells as dynamic microlaboratories through implementation of labeled nanoparticles (nanosensors that have both sensing and targeting functions. The addition of 2,4-ε-dinitrophenol-L-lysine (DNP as a FcεRI targeting ligand and 4-mercaptopyridine (4-MPy as a pH-sensing ligand enables spatial and temporal monitoring of FcεRI receptors and their pH environment within the endocytic pathway. To ensure reliability, the sensor is calibrated in vivo using the ionophore nigericin and standard buffer solutions to equilibrate the external [H+] concentration with that of the cell compartments. This review highlights the nanosensors, ability to traffic and respond to pH of receptor-bound nanosensors (1 at physiological temperature (37°C versus room temperature (25°C, (2 after pharmacological treatment with bafilomycin, an H+ ATPase pump inhibitor, or amiloride, an inhibitor of Na+/H+ exchange, and (3 in response to both temperature and pharmacological treatment. Whole-cell, time lapse images are demonstrated to show the ability to transform live cells into dynamic laboratories to monitor temporal and spatial endosomal pH. The versatility of these probes shows promise for future applications relevant to intracellular trafficking and intelligent drug design.

  6. Gigavision - A weatherproof, multibillion pixel resolution time-lapse camera system for recording and tracking phenology in every plant in a landscape

    Science.gov (United States)

    Brown, T.; Borevitz, J. O.; Zimmermann, C.

    2010-12-01

    retrieved at bi-weekly intervals. Our longer-term goal is to make gigapixel time-lapse datasets available online in an interactive interface that layers plant-level phenology data with gigapixel resolution images, genomic sequence data from individual plants with weather and other abitotic sensor data. Co-visualization of all of these data types provides researchers with a powerful new tool for examining complex ecological interactions across scales from the individual to the ecosystem. We will present detailed phenostage data from more than 100 plants of multiple species from our Gigavision timelapse camera at our “Big Blowout East” field site in the Indiana Dunes State Park, IN. This camera has been recording three to four 700 million pixel images a day since February 28, 2010. The camera field of view covers an area of about 7 hectares resulting in an average image resolution of about 1 pixel per centimeter over the entire site. We will also discuss some of the many technological challenges with developing and maintaining these types of hardware systems, collecting quantitative data from gigapixel resolution time-lapse data and effectively managing terabyte-sized datasets of millions of images.

  7. Vapor flux and recrystallization during dry snow metamorphism under a steady temperature gradient as observed by time-lapse micro-tomography

    Directory of Open Access Journals (Sweden)

    B. R. Pinzer

    2012-10-01

    Full Text Available Dry snow metamorphism under an external temperature gradient is the most common type of recrystallization of snow on the ground. The changes in snow microstructure modify the physical properties of snow, and therefore an understanding of this process is essential for many disciplines, from modeling the effects of snow on climate to assessing avalanche risk. We directly imaged the microstructural changes in snow during temperature gradient metamorphism (TGM under a constant gradient of 50 K m−1, using in situ time-lapse X-ray micro-tomography. This novel and non-destructive technique directly reveals the amount of ice that sublimates and is deposited during metamorphism, in addition to the exact locations of these phase changes. We calculated the average time that an ice volume stayed in place before it sublimated and found a characteristic residence time of 2–3 days. This means that most of the ice changes its phase from solid to vapor and back many times in a seasonal snowpack where similar temperature conditions can be found. Consistent with such a short timescale, we observed a mass turnover of up to 60% of the total ice mass per day. The concept of hand-to-hand transport for the water vapor flux describes the observed changes very well. However, we did not find evidence for a macroscopic vapor diffusion enhancement. The picture of {temperature gradient metamorphism} produced by directly observing the changing microstructure sheds light on the micro-physical processes and could help to improve models that predict the physical properties of snow.

  8. Characterizing a Mississippian Carbonate Reservoir for CO2-EOR and Carbon Geosequestration: Applicability of Existing Rock Physics Models and Implications to Feasibility of a Time Lapse Monitoring Program in the Wellington Oil Field, Sumner County, Kansas.

    Science.gov (United States)

    Lueck, A. J.; Raef, A. E.

    2015-12-01

    This study will focus on characterizing subsurface rock formations of the Wellington Field, in Sumner County, Kansas, for both geosequestration of carbon dioxide (CO2) in the saline Arbuckle formation and enhanced oil recovery of a depleting Mississippian oil reservoir. Multi-scale data including lithofacies core samples, X-ray diffraction, digital rock physics scans, scanning electron microscope (SEM) imaging, well log data including sonic and dipole sonic, and surface 3D seismic reflection data will be integrated to establish and/or validate a new or existing rock physics model that best represents our reservoir rock types and characteristics. We will acquire compressional wave velocity and shear wave velocity data from Mississippian and Arbuckle cores by running ultrasonic tests using an Ult 100 Ultrasonic System and a 12 ton hydraulic jack located in the geophysics lab in Thompson Hall at Kansas State University. The elastic constants Young's Modulus, Bulk Modulus, Shear (Rigidity) Modulus and Poisson's Ratio will be extracted from these velocity data. Ultrasonic velocities will also be compared to sonic and dipole sonic log data from the Wellington 1-32 well. These data will be integrated to validate a lithofacies classification statistical model, which will be and partially has been applied to the largely unknown saline Arbuckle formation, with hopes for a connection, perhaps via Poisson's ratio, allowing a time-lapse seismic feasibility assessment and potentially developing a transformation of compressional wave sonic velocities to shear wave sonic for all wells, where compressional wave sonic is available. We will also be testing our rock physics model by predicting effects of changing effective (brine + CO2 +hydrocarbon) fluid composition on seismic properties and the implications on feasibility of seismic monitoring. Lessons learned from characterizing the Mississippian are essential to understanding the potential of utilizing similar workflows for the

  9. Developments and field tests of low-frequency portable acoustic transducers for a mobile exploration and time lapse experiment of a sea-bottom reservoir

    Science.gov (United States)

    Tsuruga, K.; Kasahara, J.; Hasada, Y.; Kondo, H.

    2013-12-01

    Depth, scale and resolutions of geophysical explorations for mineral resources are controlled by transmitted seismic energy and wavelength (frequency range). Most explorations in marine have been conducted by survey ship system with arrayed acoustic sources whose dominant frequency range is about 10 to 500 Hz. On the other hand, for shallow parts of sea bottom structure survey, some sub-bottom profilers with frequency range around 3.5kHz are used. To monitor a time lapse of a sea bottom reservoir such as an oil, gas, or methane hydrate reservoir as well as to exploit a mobile survey near a sea bottom by AUVs, it is necessary to use a broadband portable acoustic transducer with a dominant frequency range of 500 Hz to 5 kHz. We have been developing several types of portable acoustic transducers and a transmitting and recording system which is accurately controlled by a GPS clock (Tsuruga et al., 2012). In this pater, we report the new broadband acoustic portable transducers which have larger power than the original cylindrical acoustic transducers in a low frequency range (4k-16kHz . We stacked 500-ms data by 28 times to obtain a transfer function of each source-receiver pair in the time and frequency domains. The preliminary results suggest as the follows: (i) it is successful to broaden the frequency bandwidth (i.e., 2k-10kHz) by extending a geometrical resonance length of a cylindrical acoustic transducers, and (ii) the observation at the sea bottom with accurately controlled timing systems of transmitter and data-logger is very useful to identify the stable and/or unstable seismic phases, that is, waves propagating in a underground and/or in a sea water as well as to reduce random noises caused by ocean waves over the data. In future works, we are planning to test a measurement at longer distance and moreover to develop a mobile type source-receiver array towed by an AUV to survey near sea bottom.

  10. Extreme Scale Computing Studies

    Science.gov (United States)

    2010-12-01

    survey, or locating dwarf galaxies in star counts. HOP [40] is a density-based clustering method, with poor scalability, that determines the location of...computers and servers. Today, the volume of electronics created for embedded systems, such as cell phones, dwarfs desktop and servers, and this trend...Defense reconnaissance satellites. In fact, the number of CPUs manufactured for embedded applications dwarfs those for desktops and servers. Embedded

  11. Fatigue damage assessment of uni-directional non-crimp fabric reinforced polyester composite using X-ray computed tomography

    DEFF Research Database (Denmark)

    Jespersen, Kristine Munk; Zangenberg Hansen, Jens; Lowe, Tristan

    2016-01-01

    In this study, the progression of tension-tension fatigue (R=0.1) damage in a unidirectional (UD) composite made from a non-crimp glass fibre fabric used for wind turbine blades is investigated using multi-scale 3D X-ray computed tomography (CT). Initially, a representative volume is examined...... fracture zone becomes more diffuse further from the backing layer. Our work supports a scheme explaining stiffness degradation in terms of UD fibre damage accumulation and demonstrates the importance of 3D and ideally time-lapse imaging studies....

  12. Temporal Characterization of Hydrates System Dynamics beneath Seafloor Mounds. Integrating Time-Lapse Electrical Resistivity Methods and In Situ Observations of Multiple Oceanographic Parameters

    Energy Technology Data Exchange (ETDEWEB)

    Lutken, Carol [Univ. of Mississippi, Oxford, MS (United States); Macelloni, Leonardo [Univ. of Mississippi, Oxford, MS (United States); D' Emidio, Marco [Univ. of Mississippi, Oxford, MS (United States); Dunbar, John [Univ. of Mississippi, Oxford, MS (United States); Higley, Paul [Univ. of Mississippi, Oxford, MS (United States)

    2015-01-31

    detect short-term changes within the hydrates system, identify relationships/impacts of local oceanographic parameters on the hydrates system, and improve our understanding of how seafloor instability is affected by hydrates-driven changes. A 2009 DCR survey of MC118 demonstrated that we could image resistivity anomalies to a depth of 75m below the seafloor in water depths of 1km. We reconfigured this system to operate autonomously on the seafloor in a pre-programmed mode, for periods of months. We designed and built a novel seafloor lander and deployment capability that would allow us to investigate the seafloor at potential deployment sites and deploy instruments only when conditions met our criteria. This lander held the DCR system, controlling computers, and battery power supply, as well as instruments to record oceanographic parameters. During the first of two cruises to the study site, we conducted resistivity surveying, selected a monitoring site, and deployed the instrumented lander and DCR, centered on what appeared to be the most active locations within the site, programmed to collect a DCR profile, weekly. After a 4.5-month residence on the seafloor, the team recovered all equipment. Unfortunately, several equipment failures occurred prior to recovery of the instrument packages. Prior to the failures, however, two resistivity profiles were collected together with oceanographic data. Results show, unequivocally, that significant changes can occur in both hydrate volume and distribution during time periods as brief as one week. Occurrences appear to be controlled by both deep and near-surface structure. Results have been integrated with seismic data from the area and show correspondence in space of hydrate and structures, including faults and gas chimneys.

  13. Impact of Delivery Modality, Student GPA, and Time-Lapse since High School on Successful Completion of College-Level Math after Taking Developmental Math

    Science.gov (United States)

    Acosta, Diane; North, Teresa Lynn; Avella, John

    2016-01-01

    This study considered whether delivery modality, student GPA, or time since high school affected whether 290 students who had completed a developmental math series as a community college were able to successfully complete college-level math. The data used in the study was comprised of a 4-year period historical student data from Odessa College…

  14. Studi Perbandingan Layanan Cloud Computing

    Directory of Open Access Journals (Sweden)

    Afdhal Afdhal

    2014-03-01

    Full Text Available In the past few years, cloud computing has became a dominant topic in the IT area. Cloud computing offers hardware, infrastructure, platform and applications without requiring end-users knowledge of the physical location and the configuration of providers who deliver the services. It has been a good solution to increase reliability, reduce computing cost, and make opportunities to IT industries to get more advantages. The purpose of this article is to present a better understanding of cloud delivery service, correlation and inter-dependency. This article compares and contrasts the different levels of delivery services and the development models, identify issues, and future directions on cloud computing. The end-users comprehension of cloud computing delivery service classification will equip them with knowledge to determine and decide which business model that will be chosen and adopted securely and comfortably. The last part of this article provides several recommendations for cloud computing service providers and end-users.

  15. Uniqueness and stability analysis of hydrogeophysical inversion for time-lapse ground-penetrating radar estimates of shallow soil hydraulic properties

    NARCIS (Netherlands)

    Jadoon, K.Z.; Slob, E.; Vanclooster, M.; Vereecken, H.; Lambot, S.

    2008-01-01

    Precise measurement of soil hydraulic properties at field scales is one of the prerequisites to simulate subsurface flow and transport processes, which is crucial in many research and engineering areas. In our study, we numerically analyze uniqueness and stability for integrated hydrogeophysical

  16. Time-Lapse Förster Resonance Energy Transfer Imaging by Confocal Laser Scanning Microscopy for Analyzing Dynamic Molecular Interactions in the Plasma Membrane of B Cells.

    Science.gov (United States)

    Sohn, Hae Won; Brzostowski, Joseph

    2018-01-01

    For decades, various Förster resonance energy transfer (FRET) techniques have been developed to measure the distance between interacting molecules. FRET imaging by the sensitized acceptor emission method has been widely applied to study the dynamical association between two molecules at a nanometer scale in live cells. Here, we provide a detailed protocol for FRET imaging by sensitized emission using a confocal laser scanning microscope to analyze the interaction of the B cell receptor (BCR) with the Lyn-enriched lipid microdomain on the plasma membrane of live cells upon antigen binding, one of the earliest signaling events in BCR-mediated B cell activation.

  17. Estimation of Biocompatibility of Nano-Sized Ceramic Particles with Osteoblasts, Osteosarcomas and Hepatocytes by Static and Time-Lapse Observation.

    Science.gov (United States)

    Abe, Shigeaki; Seitoku, Eri; Iwadera, Nobuki; Hamba, Yusuke; Yamagata, Shuichi; Akasaka, Tsukasa; Kusaka, Teruo; Inoue, Satoshi; Yawaka, Yasutaka; Iida, Junichiro; Sano, Hidehiko; Yonezawa, Tetsu; Yoshida, Yasuhiro

    2016-03-01

    We assessed the biocompatibility of nano-sized ceramic particles with several cells types. Though these particles have less than 100 nm in diameter, they act as submicron-sized particles in saline by aggregation that was estimated using laser diffraction particle size analysis (LDS). they act as submicro-sized particles in saline by aggregation based on laser diffraction particle size analysis (LDS). Several types of cells (osteoblasts, osteosarcoma and hepatocyte cells) were exposed to these particles and their cytocompatibility was estimated. Not only the cytotoxic assay but also their static and dynamic morphology under nanoparticles exposure were investigated. The intercellular uptake of particles was determined using a confocal fluorescence microscope. The particles used in this study did not inhibit cellular activity or growth even when their concentrations were high. Only copper oxide particles caused acute cytotoxicity depending on the particle size. The cytotoxicity assay, dynamic behavior of the nanoparticle-exposed cells and their examination under a confocal fluorescence microscope suggests that the irritative reaction was induced by contact between the cells and particles, whereas eluted copper ions are not dominant factor. These results indicate that nano-sized particles used in this study have excellent biocompatibility except copper oxide ones.

  18. Chloroplast to chromoplast transition in tomato fruit: spectral confocal microscopy analyses of carotenoids and chlorophylls in isolated plastids and time-lapse recording on intact live tissue.

    Science.gov (United States)

    Egea, Isabel; Bian, Wanping; Barsan, Cristina; Jauneau, Alain; Pech, Jean-Claude; Latché, Alain; Li, Zhengguo; Chervin, Christian

    2011-08-01

    There are several studies suggesting that tomato (Solanum lycopersicum) chromoplasts arise from chloroplasts, but there is still no report showing the fluorescence of both chlorophylls and carotenoids in an intermediate plastid, and no video showing this transition phase. Pigment fluorescence within individual plastids, isolated from tomato fruit using sucrose gradients, was observed at different ripening stages, and an in situ real-time recording of pigment fluorescence was performed on live tomato fruit slices. At the mature green and red stages, homogenous fractions of chloroplasts and chromoplasts were obtained, respectively. At the breaker stage, spectral confocal microscopy showed that intermediate plastids contained both chlorophylls and carotenoids. Furthermore, an in situ real-time recording (a) showed that the chloroplast to chromoplast transition was synchronous for all plastids of a single cell; and (b) confirmed that all chromoplasts derived from pre-existing chloroplasts. These results give details of the early steps of tomato chromoplast biogenesis from chloroplasts, with the formation of intermediate plastids containing both carotenoids and chlorophylls. They provide information at the sub-cellular level on the synchronism of plastid transition and pigment changes.

  19. Accurate, precise modeling of cell proliferation kinetics from time-lapse imaging and automated image analysis of agar yeast culture arrays

    Directory of Open Access Journals (Sweden)

    Zhao Lue

    2007-01-01

    Full Text Available Abstract Background Genome-wide mutant strain collections have increased demand for high throughput cellular phenotyping (HTCP. For example, investigators use HTCP to investigate interactions between gene deletion mutations and additional chemical or genetic perturbations by assessing differences in cell proliferation among the collection of 5000 S. cerevisiae gene deletion strains. Such studies have thus far been predominantly qualitative, using agar cell arrays to subjectively score growth differences. Quantitative systems level analysis of gene interactions would be enabled by more precise HTCP methods, such as kinetic analysis of cell proliferation in liquid culture by optical density. However, requirements for processing liquid cultures make them relatively cumbersome and low throughput compared to agar. To improve HTCP performance and advance capabilities for quantifying interactions, YeastXtract software was developed for automated analysis of cell array images. Results YeastXtract software was developed for kinetic growth curve analysis of spotted agar cultures. The accuracy and precision for image analysis of agar culture arrays was comparable to OD measurements of liquid cultures. Using YeastXtract, image intensity vs. biomass of spot cultures was linearly correlated over two orders of magnitude. Thus cell proliferation could be measured over about seven generations, including four to five generations of relatively constant exponential phase growth. Spot area normalization reduced the variation in measurements of total growth efficiency. A growth model, based on the logistic function, increased precision and accuracy of maximum specific rate measurements, compared to empirical methods. The logistic function model was also more robust against data sparseness, meaning that less data was required to obtain accurate, precise, quantitative growth phenotypes. Conclusion Microbial cultures spotted onto agar media are widely used for genotype

  20. Flight Trainer Digital Computer Study

    Science.gov (United States)

    1951-03-21

    speed „artet accuracy appear to-.depend on-in- creased size of units. Qn the ot;hgr^|Sg^d^ital cot"|wMr^ar^ stil ^ia-rr^-. their infancy and all...programming for onei .computation. cycle* The program ’diagrams are divided into numb erect frames , the first numb.er of ’.which specifies foe

  1. Computer technology forecast study for general aviation

    Science.gov (United States)

    Seacord, C. L.; Vaughn, D.

    1976-01-01

    A multi-year, multi-faceted program is underway to investigate and develop potential improvements in airframes, engines, and avionics for general aviation aircraft. The objective of this study was to assemble information that will allow the government to assess the trends in computer and computer/operator interface technology that may have application to general aviation in the 1980's and beyond. The current state of the art of computer hardware is assessed, technical developments in computer hardware are predicted, and nonaviation large volume users of computer hardware are identified.

  2. A Codesign Case Study in Computer Graphics

    DEFF Research Database (Denmark)

    Brage, Jens P.; Madsen, Jan

    1994-01-01

    The paper describes a codesign case study where a computer graphics application is examined with the intention to speed up its execution. The application is specified as a C program, and is characterized by the lack of a simple compute-intensive kernel. The hardware/software partitioning is based...

  3. Computational Studies of Drug Resistance

    DEFF Research Database (Denmark)

    da Silva Martins, João Miguel

    and bacterial resistance to common-use inhibitors, in such cases as multiple targeted proteins in the human immunode ciency virus infection and penicillinresistant Staphylococcus aureus. Thus, understanding the evolutionary pressures by which these arise and predicting future possible resistance mutations...... approaches that come together in the study of drug's and their in uence on proteins and vice-versa. In part I, I aim to understand through combined theoretical ensemble analysis and free energy calculations the e ects mutations have over the binding anity and function of the M2 proton channel. This research...... are included in this part's Supporting Information. While some correlation between experimental and theoretical results can be observed through the study of the proteins' ensembles and drugs' behavior in simulation, I also observe the limitations of the methods employed in distinguishing anities between low...

  4. Insights into enzymatic halogenation from computational studies

    Directory of Open Access Journals (Sweden)

    Hans Martin Senn

    2014-11-01

    Full Text Available The halogenases are a group of enzymes that have only come to the fore over the last ten years thanks to the discovery and characterization of several of novel representatives. They have re-vealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate and introduce halogens into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these stud-ies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein also serve to illustrate some of the limitations of the current computa-tional approaches and the challenges encountered in computational mechanistic enzymology.

  5. Degradation of metallic materials studied by correlative tomography

    Science.gov (United States)

    Burnett, T. L.; Holroyd, N. J. H.; Lewandowski, J. J.; Ogurreck, M.; Rau, C.; Kelley, R.; Pickering, E. J.; Daly, M.; Sherry, A. H.; Pawar, S.; Slater, T. J. A.; Withers, P. J.

    2017-07-01

    There are a huge array of characterization techniques available today and increasingly powerful computing resources allowing for the effective analysis and modelling of large datasets. However, each experimental and modelling tool only spans limited time and length scales. Correlative tomography can be thought of as the extension of correlative microscopy into three dimensions connecting different techniques, each providing different types of information, or covering different time or length scales. Here the focus is on the linking of time lapse X-ray computed tomography (CT) and serial section electron tomography using the focussed ion beam (FIB)-scanning electron microscope to study the degradation of metals. Correlative tomography can provide new levels of detail by delivering a multiscale 3D picture of key regions of interest. Specifically, the Xe+ Plasma FIB is used as an enabling tool for large-volume high-resolution serial sectioning of materials, and also as a tool for preparation of microscale test samples and samples for nanoscale X-ray CT imaging. The exemplars presented illustrate general aspects relating to correlative workflows, as well as to the time-lapse characterisation of metal microstructures during various failure mechanisms, including ductile fracture of steel and the corrosion of aluminium and magnesium alloys. Correlative tomography is already providing significant insights into materials behaviour, linking together information from different instruments across different scales. Multiscale and multifaceted work flows will become increasingly routine, providing a feed into multiscale materials models as well as illuminating other areas, particularly where hierarchical structures are of interest.

  6. Computer-Assisted Instruction on Study Skills.

    Science.gov (United States)

    Gadzella, Bernadette M.

    1982-01-01

    A computer-assisted instruction study skills program was presented to 88 college students, while a control group did not have access to it. Scores for the experimental group on the Survey of Study Habits and Attitudes increased during the semester, while scores for the control group decreased. (Author/BW)

  7. Computer Networks and African Studies Centers.

    Science.gov (United States)

    Kuntz, Patricia S.

    The use of electronic communication in the 12 Title VI African Studies Centers is discussed, and the networks available for their use are reviewed. It is argued that the African Studies Centers should be on the cutting edge of contemporary electronic communication and that computer networks should be a fundamental aspect of their programs. An…

  8. Computed Tomography Study Of Complicated Bacterial Meningitis ...

    African Journals Online (AJOL)

    To monitor the structural intracranial complications of bacterial meningitis using computed tomography (CT) scan. Retrospective study of medical and radiological records of patients who underwent CT scan over a 4 year period. AUniversityTeachingHospital in a developing country. Thirty three patients with clinically and ...

  9. Experimental and computational studies of polar solvation

    Energy Technology Data Exchange (ETDEWEB)

    1991-01-01

    Many articles and papers were published; a few are still in preparation or will be published. The solvation dynamics studies will be extended to ionic solutions. Computer simulations were also performed. A new line of research was begun on excited-state proton-transfer reactions catalyzed by alcohol solvents. (DLC)

  10. Computational Study of White Dwarf Stars

    Science.gov (United States)

    Pacheco, Jose; Hira, Ajit; Jaramillo, Danelle

    2014-03-01

    We begin our interest in the computational simulation of the astrophysical phenomena with a study of white dwarf stars. Of particular interest to astrophysicists are the conditions inside a white dwarf star in the time frame leading up to its explosive end as a Type Ia supernova, for an understanding of the massive stellar explosions. In addition, the studies of the evolution of white dwarfs could serve as promising probes of theories of gravitation. First, we set up the equations of equilibrium for the star of interest. Then we derived the appropriate equation of state. Next, a FORTRAN computer program was developed to implement our model for white dwarfs. This code allows for different sizes and masses of stars. Simulations were done in the mass interval from 0.4 to 0.8 solar masses. Our goal was to obtain both atmospheric and orbital parameters. The computational results thus obtained are compared with relevant observational data. The data are further analyzed to identify trends in terms of sizes and masses of stars. We hope to extend our computational studies to red giant stars in the future.

  11. Studying CO

    NARCIS (Netherlands)

    Boullenger, B.; Verdel, A.; Paap, B.; Thorbecke, J.; Draganov, D.

    2014-01-01

    Seismic interferometry applied to ambient-noise measurements allows the retrieval of the seismic response between pairs of receivers. We studied ambient-noise seismic interferometry (ANSI) to retrieve time-lapse reflection responses from a reservoir during CO2 geologic sequestration,

  12. National Computing Studies Summit: Open Learning Approaches to Computing Studies--An ACCE Discussion Paper

    Science.gov (United States)

    Webb, Ian

    2008-01-01

    In 2005 the Australian Council for Computers in Education (ACCE) was successful in obtaining a grant from National Centre of Science, Information and Communication Technology and Mathematics Education for Rural and Regional Australia (SiMERR) to undertake the Computing Studies Teachers Network Rural and Regional Focus Project. The project had five…

  13. Role of logic programming in computer studies

    Directory of Open Access Journals (Sweden)

    Nicolae PELIN

    2016-09-01

    Full Text Available The paper contains the analysis of the opinions of a number of scholars and specialists on the importance and the role in logic programming methodology of studying computer science, philosophy about the logic programs and interpreter, concerning the burden of which is opposite to the programmer if there is logic interpreter. The presented material is meant, according to the author, to help the reader to understand more easily the analyzed multilateral problem.

  14. The traveling salesman problem a computational study

    CERN Document Server

    Applegate, David L; Chvatal, Vasek; Cook, William J

    2006-01-01

    This book presents the latest findings on one of the most intensely investigated subjects in computational mathematics--the traveling salesman problem. It sounds simple enough: given a set of cities and the cost of travel between each pair of them, the problem challenges you to find the cheapest route by which to visit all the cities and return home to where you began. Though seemingly modest, this exercise has inspired studies by mathematicians, chemists, and physicists. Teachers use it in the classroom. It has practical applications in genetics, telecommunications, and neuroscience.

  15. Computer literacy study: report of qualitative findings.

    Science.gov (United States)

    McNeil, Barbara J; Elfrink, Victoria; Beyea, Suzanne C; Pierce, Susan T; Bickford, Carol J

    2006-01-01

    Computer literacy and information literacy are critical to the future of nursing. The very nature of health care is being transformed in response to environmental drivers such as the demands for cost-effective delivery of high quality services and enhanced patient safety. Facilitating the quality transformation depends on strategic changes such as implementing evidence-based practice (), promoting outcome research (), initiating interdisciplinary care coordination [Zwarenstein, M., Bryant, W. (2004). Interventions to promote collaboration between nurses and doctors. The Cochrane Library(I)], and implementing electronic health records (). Information management serves as a central premise of each of these strategies and is an essential tool to facilitate change. This report of the analysis of qualitative data from a national online survey of baccalaureate nursing education programs describes the current level of integration of the computer literacy and information literacy skills and competencies of nursing faculty, clinicians, and students in the United States. The outcomes of the study are important to guide curriculum development in meeting the changing health care environmental demands for quality, cost-effectiveness, and safety.

  16. Non-Determinism: An Abstract Concept in Computer Science Studies

    Science.gov (United States)

    Armoni, Michal; Gal-Ezer, Judith

    2007-01-01

    Non-determinism is one of the most important, yet abstract, recurring concepts of Computer Science. It plays an important role in Computer Science areas such as formal language theory, computability theory, distributed computing, and operating systems. We conducted a series of studies on the perception of non-determinism. In the current research,…

  17. COMPUTING

    CERN Multimedia

    P. McBride

    The Computing Project is preparing for a busy year where the primary emphasis of the project moves towards steady operations. Following the very successful completion of Computing Software and Analysis challenge, CSA06, last fall, we have reorganized and established four groups in computing area: Commissioning, User Support, Facility/Infrastructure Operations and Data Operations. These groups work closely together with groups from the Offline Project in planning for data processing and operations. Monte Carlo production has continued since CSA06, with about 30M events produced each month to be used for HLT studies and physics validation. Monte Carlo production will continue throughout the year in the preparation of large samples for physics and detector studies ramping to 50 M events/month for CSA07. Commissioning of the full CMS computing system is a major goal for 2007. Site monitoring is an important commissioning component and work is ongoing to devise CMS specific tests to be included in Service Availa...

  18. Study guide to accompany computers data and processing

    CERN Document Server

    Deitel, Harvey M

    1985-01-01

    Study Guide to Accompany Computer and Data Processing provides information pertinent to the fundamental aspects of computers and computer technology. This book presents the key benefits of using computers.Organized into five parts encompassing 19 chapters, this book begins with an overview of the evolution of modern computing systems from the earliest mechanical calculating devices to microchips. This text then introduces computer hardware and describes the processor. Other chapters describe how microprocessors are made and describe the physical operation of computers. This book discusses as w

  19. Using the Computer in Evolution Studies

    Science.gov (United States)

    Mariner, James L.

    1973-01-01

    Describes a high school biology exercise in which a computer greatly reduces time spent on calculations. Genetic equilibrium demonstrated by the Hardy-Weinberg principle and the subsequent effects of violating any of its premises are more readily understood when frequencies of alleles through many generations are calculated by the computer. (JR)

  20. Computational Studies of Magnetic Nozzle Performance

    Science.gov (United States)

    Ebersohn, Frans H.; Longmier, Benjamin W.; Sheehan, John P.; Shebalin, John B.; Raja, Laxminarayan

    2013-01-01

    An extensive literature review of magnetic nozzle research has been performed, examining previous work, as well as a review of fundamental principles. This has allow us to catalog all basic physical mechanisms which we believe underlie the thrust generation process. Energy conversion mechanisms include the approximate conservation of the magnetic moment adiabatic invariant, generalized hall and thermoelectric acceleration, swirl acceleration, thermal energy transformation into directed kinetic energy, and Joule heating. Momentum transfer results from the interaction of the applied magnetic field with currents induced in the plasma plume., while plasma detachment mechanisms include resistive diffusion, recombination and charge exchange collisions, magnetic reconnection, loss of adiabaticity, inertial forces, current closure, and self-field detachment. We have performed a preliminary study of Hall effects on magnetic nozzle jets with weak guiding magnetic fields and weak expansions (p(sub jet) approx. = P(sub background)). The conclusion from this study is that the Hall effect creates an azimuthal rotation of the plasma jet and, more generally, creates helical structures in the induced current, velocity field, and magnetic fields. We have studied plasma jet expansion to near vacuum without a guiding magnetic field, and are presently including a guiding magnetic field using a resistive MHD solver. This research is progressing toward the implementation of a full generalized Ohm's law solver. In our paper, we will summarize the basic principle, as well as the literature survey and briefly review our previous results. Our most recent results at the time of submittal will also be included. Efforts are currently underway to construct an experiment at the University of Michigan Plasmadynamics and Electric Propulsion Laboratory (PEPL) to study magnetic nozzle physics for a RF-thruster. Our computational study will work directly with this experiment to validate the numerical

  1. Computed tomographic study of maxillofacial gunshot injuries

    Energy Technology Data Exchange (ETDEWEB)

    Park, In Woo [Dept. of Dentistry, Capital Armed Forces General Hospital, Sungnam (Korea, Republic of)

    1996-08-15

    The purpose of this study was to evaluate the clinical and computed tomographic features of 7 cases of maxillofacial al gunshot injuries in the suicidal patients visited the emergency room, Capital Armed Forces General Hospital. The obtained results were as follows: 1. The gunshot wounds were directed from submental area to dorsum of nose (3 cases), frontal area (1 case), orbit (1 case), infraorbital area (1 case), and lateral to nasal wing (1 case), The shape of inlet in gunshot wounds were round (diameter : 13cm) and that of outlet were oval shape (size : inlet

  2. Computational Study of Multiple Hydrokinetic Turbine Performance

    Science.gov (United States)

    Jonas, Joseph David

    The k-omega Shear Stress Transport turbulence model was used to determine the performance of a pair of horizontal-axis hydrokinetic turbines. By varying the separation distance perpendicular to the flow direction between these turbines and computing both power and drag coefficients, the relationship between these outputs and the separation distance as an input was discovered. This study used a rotating reference frame, steady state approximation over three separation distances and two different mesh sizes to verify mesh independence. Once this meshing methodology was verified, two more separation distances were run using the same steady-state approximations at the coarse mesh size to better understand turbine performance at greater separation distances. The results of these simulations show that, at a given separation distance, the left and right turbines have very similar performance. The power and drag coefficients were both found to decrease on the order of 8% as the turbines are brought closer together, which means that, in an infinite and uniform flow field, turbines should be placed as far apart as is feasible to maximize resultant combined power output.

  3. Computational Studies of Strongly Correlated Quantum Matter

    Science.gov (United States)

    Shi, Hao

    The study of strongly correlated quantum many-body systems is an outstanding challenge. Highly accurate results are needed for the understanding of practical and fundamental problems in condensed-matter physics, high energy physics, material science, quantum chemistry and so on. Our familiar mean-field or perturbative methods tend to be ineffective. Numerical simulations provide a promising approach for studying such systems. The fundamental difficulty of numerical simulation is that the dimension of the Hilbert space needed to describe interacting systems increases exponentially with the system size. Quantum Monte Carlo (QMC) methods are one of the best approaches to tackle the problem of enormous Hilbert space. They have been highly successful for boson systems and unfrustrated spin models. For systems with fermions, the exchange symmetry in general causes the infamous sign problem, making the statistical noise in the computed results grow exponentially with the system size. This hinders our understanding of interesting physics such as high-temperature superconductivity, metal-insulator phase transition. In this thesis, we present a variety of new developments in the auxiliary-field quantum Monte Carlo (AFQMC) methods, including the incorporation of symmetry in both the trial wave function and the projector, developing the constraint release method, using the force-bias to drastically improve the efficiency in Metropolis framework, identifying and solving the infinite variance problem, and sampling Hartree-Fock-Bogoliubov wave function. With these developments, some of the most challenging many-electron problems are now under control. We obtain an exact numerical solution of two-dimensional strongly interacting Fermi atomic gas, determine the ground state properties of the 2D Fermi gas with Rashba spin-orbit coupling, provide benchmark results for the ground state of the two-dimensional Hubbard model, and establish that the Hubbard model has a stripe order in the

  4. Computational studies on intermolecular interactions in solvation

    Science.gov (United States)

    Song, Weiping

    This thesis presents the results of computational studies of intermolecular interactions in various contexts. We first investigated the relation between solute-solvent intermolecular interactions and local density augmentation in supercritical solvation. The phenomenon of interest is the excess density that exists in the neighborhood of an attractive solute in a supercritical solvent in the vicinity of the critical point. In Chapter 2, we examined the ability of various measures of the strength of solute-solvent interactions, calculated from all-atom potential functions, to correlate the extent of local density augmentation in both experimental and model solvents. The Gibbs Ensemble Monte Carlo (GEMC) method enables us to calculate phase equilibrium in pure substances and mixtures. It provides a convenient way to test and develop model potentials. In Chapter 3 we present some methodological aspects of such calculations, the issues related to approach to critical points and finite-size effects and applications to simple fluids. Chapter 4 then describes a simplified 2-site potential model for simulating supercritical fluoroform. The GEMC method was used to simulate the vapor-liquid coexistence curve of the model fluid and the dynamic properties were studied by performing NVT molecular dynamics (MD) simulations. The results show that despite its simplicity, this model is able to reproduce many important properties of supercritical fluoroform, making it useful in molecular simulations of supercritical solvation. In the above two studies, the intermolecular interactions are described by a sum of pair-wise additive Lennard-Jones + Coulomb terms. The standard Lorentz-Berthelot combining rules (geometric mean rule for well depth and arithmetic mean rule for collision diameter) are commonly applied to account for the unlike pair Lennard-Jones parameters. In Chapter 5, we examined the applicability of the combining rules for modeling alkane-perfluoroalkane interactions. It

  5. Multimodal computational microscopy based on transport of intensity equation.

    Science.gov (United States)

    Li, Jiaji; Chen, Qian; Sun, Jiasong; Zhang, Jialin; Zuo, Chao

    2016-12-01

    Transport of intensity equation (TIE) is a powerful tool for phase retrieval and quantitative phase imaging, which requires intensity measurements only at axially closely spaced planes without a separate reference beam. It does not require coherent illumination and works well on conventional bright-field microscopes. The quantitative phase reconstructed by TIE gives valuable information that has been encoded in the complex wave field by passage through a sample of interest. Such information may provide tremendous flexibility to emulate various microscopy modalities computationally without requiring specialized hardware components. We develop a requisite theory to describe such a hybrid computational multimodal imaging system, which yields quantitative phase, Zernike phase contrast, differential interference contrast, and light field moment imaging, simultaneously. It makes the various observations for biomedical samples easy. Then we give the experimental demonstration of these ideas by time-lapse imaging of live HeLa cell mitosis. Experimental results verify that a tunable lens-based TIE system, combined with the appropriate postprocessing algorithm, can achieve a variety of promising imaging modalities in parallel with the quantitative phase images for the dynamic study of cellular processes.

  6. Students' Computing Use and Study: When More is Less

    Directory of Open Access Journals (Sweden)

    Christine A McLachlan

    2016-02-01

    Full Text Available Since the turn of the century there has been a steady decline in enrolments of students in senior secondary computing classes in Australia. A flow on effect has seen reduced enrolments in tertiary computing courses and the subsequent predictions of shortages in skilled computing professionals. This paper investigates the relationship between students’ computing literacy levels, their use and access to computing tools, and students’ interest in and attitudes to formal computing study. Through the use of secondary data obtained from Australian and international reports, a reverse effect was discovered indicating that the more students used computing tools, the less interested they become in computing studies. Normal 0 false false false EN-AU X-NONE X-NONE

  7. A Study of Computing Undergraduates Undertaking a Systematic Literature Review

    Science.gov (United States)

    Brereton, P.

    2011-01-01

    Teaching computing students about the importance of evidence and about the use of empirical methods for evaluating computing technologies can be difficult, especially within dual honors undergraduate degree programs. The aims of this study were to explore the effectiveness of second-year undergraduate computing students in carrying out a…

  8. COMPUTING

    CERN Multimedia

    I. Fisk

    2013-01-01

    Computing activity had ramped down after the completion of the reprocessing of the 2012 data and parked data, but is increasing with new simulation samples for analysis and upgrade studies. Much of the Computing effort is currently involved in activities to improve the computing system in preparation for 2015. Operations Office Since the beginning of 2013, the Computing Operations team successfully re-processed the 2012 data in record time, not only by using opportunistic resources like the San Diego Supercomputer Center which was accessible, to re-process the primary datasets HTMHT and MultiJet in Run2012D much earlier than planned. The Heavy-Ion data-taking period was successfully concluded in February collecting almost 500 T. Figure 3: Number of events per month (data) In LS1, our emphasis is to increase efficiency and flexibility of the infrastructure and operation. Computing Operations is working on separating disk and tape at the Tier-1 sites and the full implementation of the xrootd federation ...

  9. Experimental and computational studies of nanofluids

    Science.gov (United States)

    Vajjha, Ravikanth S.

    The goals of this dissertation were (i) to experimentally investigate the fluid dynamic and heat transfer performance of nanofluids in a circular tube, (ii) to study the influence of temperature and particle volumetric concentration of nanofluids on thermophysical properties, heat transfer and pumping power, (iii) to measure the rheological properties of various nanofluids and (iv) to investigate using a computational fluid dynamic (CFD) technique the performance of nanofluids in the flat tube of a radiator. Nanofluids are a new class of fluids prepared by dispersing nanoparticles with average sizes of less than 100 nm in traditional heat transfer fluids such as water, oil, ethylene glycol and propylene glycol. In cold regions of the world, the choice of base fluid for heat transfer applications is an ethylene glycol or propylene glycol mixed with water in different proportions. In the present research, a 60% ethylene glycol (EG) or propylene glycol (PG) and 40% water (W) by mass fluid mixture (60:40 EG/W or 60:40 PG/W) was used as a base fluid, which provides freeze protection to a very low level of temperature. Experiments were conducted to measure the convective heat transfer coefficient and pressure loss of nanofluids flowing in a circular tube in the fully developed turbulent regime. The experimental measurements were carried out for aluminum oxide (Al2O3), copper oxide (CuO) and silicon dioxide (SiO2) nanoparticles dispersed in 60:40 EG/W base fluid. Experiments revealed that the heat transfer coefficient of nanofluids showed an increase with the particle volumetric concentration. Pressure loss was also observed to increase with the nanoparticle volumetric concentration. New correlations for the Nusselt number and the friction factor were developed. The effects of temperature and particle volumetric concentration on different thermophysical properties (e.g. viscosity, thermal conductivity, specific heat and density) and subsequently on the Prandtl number

  10. Where Computer Science and Cultural Studies Collide

    Science.gov (United States)

    Kirschenbaum, Matthew

    2009-01-01

    Most users have no more knowledge of what their computer or code is actually doing than most automobile owners have of their carburetor or catalytic converter. Nor is any such knowledge necessarily needed. But for academics, driven by an increasing emphasis on the materiality of new media--that is, the social, cultural, and economic factors…

  11. Biomedical Visual Computing: Case Studies and Challenges

    KAUST Repository

    Johnson, Christopher

    2012-01-01

    Advances in computational geometric modeling, imaging, and simulation let researchers build and test models of increasing complexity, generating unprecedented amounts of data. As recent research in biomedical applications illustrates, visualization will be critical in making this vast amount of data usable; it\\'s also fundamental to understanding models of complex phenomena. © 2012 IEEE.

  12. The effect of psychosocial stress on muscle activity during computer work: Comparative study between desktop computer and mobile computing products.

    Science.gov (United States)

    Taib, Mohd Firdaus Mohd; Bahn, Sangwoo; Yun, Myung Hwan

    2016-06-27

    The popularity of mobile computing products is well known. Thus, it is crucial to evaluate their contribution to musculoskeletal disorders during computer usage under both comfortable and stressful environments. This study explores the effect of different computer products' usages with different tasks used to induce psychosocial stress on muscle activity. Fourteen male subjects performed computer tasks: sixteen combinations of four different computer products with four different tasks used to induce stress. Electromyography for four muscles on the forearm, shoulder and neck regions and task performances were recorded. The increment of trapezius muscle activity was dependent on the task used to induce the stress where a higher level of stress made a greater increment. However, this relationship was not found in the other three muscles. Besides that, compared to desktop and laptop use, the lowest activity for all muscles was obtained during the use of a tablet or smart phone. The best net performance was obtained in a comfortable environment. However, during stressful conditions, the best performance can be obtained using the device that a user is most comfortable with or has the most experience with. Different computer products and different levels of stress play a big role in muscle activity during computer work. Both of these factors must be taken into account in order to reduce the occurrence of musculoskeletal disorders or problems.

  13. International Computer and Information Literacy Study: Assessment Framework

    Science.gov (United States)

    Fraillon, Julian; Schulz, Wolfram; Ainley, John

    2013-01-01

    The purpose of the International Computer and Information Literacy Study 2013 (ICILS 2013) is to investigate, in a range of countries, the ways in which young people are developing "computer and information literacy" (CIL) to support their capacity to participate in the digital age. To achieve this aim, the study will assess student…

  14. Children as Educational Computer Game Designers: An Exploratory Study

    Science.gov (United States)

    Baytak, Ahmet; Land, Susan M.; Smith, Brian K.

    2011-01-01

    This study investigated how children designed computer games as artifacts that reflected their understanding of nutrition. Ten 5th grade students were asked to design computer games with the software "Game Maker" for the purpose of teaching 1st graders about nutrition. The results from the case study show that students were able to…

  15. Computational and experimental study of laminar flames

    Energy Technology Data Exchange (ETDEWEB)

    Smooke, Mitchell [Yale Univ., New Haven, CT (United States)

    2015-05-29

    During the past three years, our research has centered on an investigation of the effects of complex chemistry and detailed transport on the structure and extinction of hydrocarbon flames in coflowing axisymmetric configurations. We have pursued both computational and experimental aspects of the research in parallel on both steady-state and time-dependent systems. The computational work has focused on the application of accurate and efficient numerical methods for the solution of the steady-state and time-dependent boundary value problems describing the various reacting systems. Detailed experimental measurements were performed on axisymmetric coflow flames using two-dimensional imaging techniques. Previously, spontaneous Raman scattering, chemiluminescence, and laser-induced fluorescence were used to measure the temperature, major and minor species profiles. Particle image velocimetry (PIV) has been used to investigate velocity distributions and for calibration of time-varying flames. Laser-induced incandescence (LII) with an extinction calibration was used to determine soot volume fractions, while soot surface temperatures were measured with three-color optical pyrometry using a color digital camera. A blackbody calibration of the camera allows for determination of soot volume fraction as well, which can be compared with the LII measurements. More recently, we have concentrated on a detailed characterization of soot using a variety of techniques including time-resolved LII (TiRe-LII) for soot primary particles sizes, multi-angle light scattering (MALS) for soot radius of gyration, and spectrally-resolved line of sight attenuation (spec-LOSA). Combining the information from all of these soot measurements can be used to determine the soot optical properties, which are observed to vary significantly depending on spatial location and fuel dilution. Our goal has been to obtain a more fundamental understanding of the important fluid dynamic and chemical interactions in

  16. Preferred computer activities among individuals with dementia: a pilot study.

    Science.gov (United States)

    Tak, Sunghee H; Zhang, Hongmei; Hong, Song Hee

    2015-03-01

    Computers offer new activities that are easily accessible, cognitively stimulating, and enjoyable for individuals with dementia. The current descriptive study examined preferred computer activities among nursing home residents with different severity levels of dementia. A secondary data analysis was conducted using activity observation logs from 15 study participants with dementia (severe = 115 logs, moderate = 234 logs, and mild = 124 logs) who participated in a computer activity program. Significant differences existed in preferred computer activities among groups with different severity levels of dementia. Participants with severe dementia spent significantly more time watching slide shows with music than those with both mild and moderate dementia (F [2,12] = 9.72, p = 0.003). Preference in playing games also differed significantly across the three groups. It is critical to consider individuals' interests and functional abilities when computer activities are provided for individuals with dementia. A practice guideline for tailoring computer activities is detailed. Copyright 2015, SLACK Incorporated.

  17. Maxillofacial injury: A retrospective analysis of time lapse between ...

    African Journals Online (AJOL)

    Objective. To investigate the number of days in seven patient management intervals from facial fracture occurrence to discharge from hospital, to gain insight into reasons for treatment delays. Results. Facial fractures were treated a mean of 20.4 days from occurrence. There was a mean of 10.3 days from fracture to hospital ...

  18. Integrated time-lapse geoelectrical imaging of wetland hydrological processes

    OpenAIRE

    Uhlemann, S. S.; Sorensen, J. P. R.; House, A. R.; Wilkinson, P. B.; ROBERTS, C.; D. C. Gooddy; Binley, A.M.; Chambers, J.E.

    2016-01-01

    Wetlands provide crucial habitats, are critical in the global carbon cycle, and act as key biogeochemical and hydrological buffers. The effectiveness of these services is mainly controlled by hydrological processes, which can be highly variable both spatially and temporally due to structural complexity and seasonality. Spatial analysis of 2D geoelectrical monitoring data integrated into the interpretation of conventional hydrological data has been implemented to provide a detailed understandi...

  19. An Exploratory Study of Apache Middle School Students' Computer Animation.

    Science.gov (United States)

    Stokrocki, Mary; Buckpitt, Marcia

    The paper describes a participant observation study of a 3 week summer art program for Apache middle school students on the White Mountain Reservation. Computer art skills, specifically animation using a menu-driven computer paint program, were the focus of the investigation. Because it was in the context of a summer program, instruction was…

  20. Gender Differences in Computer Education: A Costa Rican Case Study.

    Science.gov (United States)

    Huber, Brad R.; Scaglion, Richard

    1995-01-01

    Describes a time allocation study that was designed to determine how two types of teachers spent their time regarding gender differences in a primary school computer laboratory in Costa Rica. Topics include the sociocultural context of gender roles in Costa Rica, hypothesis testing, and the domination of boys in computer labs. Contains 101…

  1. Helping Students Deal with Computer Issues in Social Studies.

    Science.gov (United States)

    Schug, Mark C.; Kepner, Henry S., Jr.

    1985-01-01

    The special responsibility of the social studies program is to help students understand the personal and social issues related to computer technology. Students must understand how computer technology influences us in our roles as consumers, workers, citizens, and family members. Curriculum materials dealing with these topics need to be developed.…

  2. NASA Computational Case Study: The Flight of Friendship 7

    Science.gov (United States)

    Simpson, David G.

    2012-01-01

    In this case study, we learn how to compute the position of an Earth-orbiting spacecraft as a function of time. As an exercise, we compute the position of John Glenn's Mercury spacecraft Friendship 7 as it orbited the Earth during the third flight of NASA's Mercury program.

  3. Educational NASA Computational and Scientific Studies (enCOMPASS)

    Science.gov (United States)

    Memarsadeghi, Nargess

    2013-01-01

    Educational NASA Computational and Scientific Studies (enCOMPASS) is an educational project of NASA Goddard Space Flight Center aimed at bridging the gap between computational objectives and needs of NASA's scientific research, missions, and projects, and academia's latest advances in applied mathematics and computer science. enCOMPASS achieves this goal via bidirectional collaboration and communication between NASA and academia. Using developed NASA Computational Case Studies in university computer science/engineering and applied mathematics classes is a way of addressing NASA's goals of contributing to the Science, Technology, Education, and Math (STEM) National Objective. The enCOMPASS Web site at http://encompass.gsfc.nasa.gov provides additional information. There are currently nine enCOMPASS case studies developed in areas of earth sciences, planetary sciences, and astrophysics. Some of these case studies have been published in AIP and IEEE's Computing in Science and Engineering magazines. A few university professors have used enCOMPASS case studies in their computational classes and contributed their findings to NASA scientists. In these case studies, after introducing the science area, the specific problem, and related NASA missions, students are first asked to solve a known problem using NASA data and past approaches used and often published in a scientific/research paper. Then, after learning about the NASA application and related computational tools and approaches for solving the proposed problem, students are given a harder problem as a challenge for them to research and develop solutions for. This project provides a model for NASA scientists and engineers on one side, and university students, faculty, and researchers in computer science and applied mathematics on the other side, to learn from each other's areas of work, computational needs and solutions, and the latest advances in research and development. This innovation takes NASA science and

  4. Computational Study of Electron Delocalization in Hexaarylbenzenes

    Directory of Open Access Journals (Sweden)

    Citlalli Rios

    2014-03-01

    Full Text Available A number of hexaarylbenzene compounds were studied theoretically, in order to compare energy changes as a result of the toroidal delocalization effect that is characteristic of all these species. The energy was studied taking advantage of locally designed isodesmic reactions. Results indicate that the amount of aromaticity manifested by each substituent is a factor that should be considered when assessing the quantity of energy dissipated from each aromatic center. The influence of different substituents on electronic delocalization is also analyzed, as well as the role played by their frontier molecular orbitals.

  5. A study of computer-related upper limb discomfort and computer vision syndrome.

    Science.gov (United States)

    Sen, A; Richardson, Stanley

    2007-12-01

    Personal computers are one of the commonest office tools in Malaysia today. Their usage, even for three hours per day, leads to a health risk of developing Occupational Overuse Syndrome (OOS), Computer Vision Syndrome (CVS), low back pain, tension headaches and psychosocial stress. The study was conducted to investigate how a multiethnic society in Malaysia is coping with these problems that are increasing at a phenomenal rate in the west. This study investigated computer usage, awareness of ergonomic modifications of computer furniture and peripherals, symptoms of CVS and risk of developing OOS. A cross-sectional questionnaire study of 136 computer users was conducted on a sample population of university students and office staff. A 'Modified Rapid Upper Limb Assessment (RULA) for office work' technique was used for evaluation of OOS. The prevalence of CVS was surveyed incorporating a 10-point scoring system for each of its various symptoms. It was found that many were using standard keyboard and mouse without any ergonomic modifications. Around 50% of those with some low back pain did not have an adjustable backrest. Many users had higher RULA scores of the wrist and neck suggesting increased risk of developing OOS, which needed further intervention. Many (64%) were using refractive corrections and still had high scores of CVS commonly including eye fatigue, headache and burning sensation. The increase of CVS scores (suggesting more subjective symptoms) correlated with increase in computer usage spells. It was concluded that further onsite studies are needed, to follow up this survey to decrease the risks of developing CVS and OOS amongst young computer users.

  6. Computational Studies of Strongly Interacting Ultracold Atoms

    Science.gov (United States)

    2010-01-01

    The Journal of Chemical Physics , 124(22...Henry Krakauer, and Shiwei Zhang. Auxiliary-field quantum Monte Carlo study of first- and second-row post-d elements. The Journal of Chemical Physics , 125...quantum Monte Carlo with plane wave and Gaussian basis sets. The Journal of Chemical Physics , 126(19):194105, 2007. [10] Rodney J. Bartlett

  7. Answering Questions by Computer: A Logical Study.

    Science.gov (United States)

    Kuhns, J. L.

    This document is a study of the processing of questions input to computerized question-answering system such as the RAND Relational Data File. The process consists of (1)transforming the natural-language question into a symbolic question (i.e., a certain formula of predicate calculus) and (2)generating the answer by calculating the value set of…

  8. Enrique: A case study of a gifted computer user

    Energy Technology Data Exchange (ETDEWEB)

    Sesko, S C

    2000-03-17

    The author has been investigating the affective and intellectual views that gifted children have about computers. These studies have used various methodological approaches in order to develop a broad perspective on the issues involved in this topic. The author has used survey instruments (Sesko, 1998) and interview techniques (Sesko, 1999) to capture both statistical and narrative data. The objective of this study is to explore in depth the interactions that one student has with the machine and its applications. The driver for this and the previous studies was the paucity of research in the area of gifted and talented children and their involvement with what has become the primary intellectual tool of the century (Turkel, 1984). The second reason is that it has been posited that the intellectual characteristics of gifted children should enable those who are interested in computers to achieve a high level of proficiency with either computer applications or programming. Further, the ability to learn things at a young age should allow gifted children who use computers to develop a large variety of computer-based activities. The author has shown evidence to support these ideas in previous work. Finally, as Hausman (1985) claims, facilities with computers should allow these children to create new activities for using computers. The author found no published research to demonstrate whether they do; but still believes the results of this case study strongly support Hausman's contentions.

  9. Integrating user studies into computer graphics-related courses.

    Science.gov (United States)

    Santos, B S; Dias, P; Silva, S; Ferreira, C; Madeira, J

    2011-01-01

    This paper presents computer graphics. Computer graphics and visualization are essentially about producing images for a target audience, be it the millions watching a new CG-animated movie or the small group of researchers trying to gain insight into the large amount of numerical data resulting from a scientific experiment. To ascertain the final images' effectiveness for their intended audience or the designed visualizations' accuracy and expressiveness, formal user studies are often essential. In human-computer interaction (HCI), such user studies play a similar fundamental role in evaluating the usability and applicability of interaction methods and metaphors for the various devices and software systems we use.

  10. Osmosis : a molecular dynamics computer simulation study

    Science.gov (United States)

    Lion, Thomas

    Osmosis is a phenomenon of critical importance in a variety of processes ranging from the transport of ions across cell membranes and the regulation of blood salt levels by the kidneys to the desalination of water and the production of clean energy using potential osmotic power plants. However, despite its importance and over one hundred years of study, there is an ongoing confusion concerning the nature of the microscopic dynamics of the solvent particles in their transfer across the membrane. In this thesis the microscopic dynamical processes underlying osmotic pressure and concentration gradients are investigated using molecular dynamics (MD) simulations. I first present a new derivation for the local pressure that can be used for determining osmotic pressure gradients. Using this result, the steady-state osmotic pressure is studied in a minimal model for an osmotic system and the steady-state density gradients are explained using a simple mechanistic hopping model for the solvent particles. The simulation setup is then modified, allowing us to explore the timescales involved in the relaxation dynamics of the system in the period preceding the steady state. Further consideration is also given to the relative roles of diffusive and non-diffusive solvent transport in this period. Finally, in a novel modification to the classic osmosis experiment, the solute particles are driven out-of-equilibrium by the input of energy. The effect of this modification on the osmotic pressure and the osmotic ow is studied and we find that active solute particles can cause reverse osmosis to occur. The possibility of defining a new "osmotic effective temperature" is also considered and compared to the results of diffusive and kinetic temperatures..

  11. Experimental and computational study of thaumasite structure

    Energy Technology Data Exchange (ETDEWEB)

    Scholtzová, Eva, E-mail: Eva.Scholtzova@savba.sk [Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 36 Bratislava (Slovakia); Kucková, Lenka; Kožíšek, Jozef [Department of Physical Chemistry, Institute of Physical Chemistry and Chemical Physics, Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava, Radlinského 9, 812 37 Bratislava (Slovakia); Pálková, Helena [Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 36 Bratislava (Slovakia); Tunega, Daniel [Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 36 Bratislava (Slovakia); Institute for Soil Science, University of Natural Resources and Life Sciences, Peter-Jordanstrasse 82, A-1190 Wien (Austria)

    2014-05-01

    The structure of thaumasite has been studied experimentally by means of a single crystal X-ray diffraction and FTIR methods, and theoretically using density functional theory (DFT) method. Very good agreement was achieved between calculated and experimental structural parameters. In addition, calculations offered the refinement of the positions of the hydrogen atoms. The detailed analysis of the hydrogen bonds existing in the thaumasite structure has been performed. Several types of hydrogen bonds have been classified. The water molecules coordinating Ca{sup 2+} cation act as proton donors in moderate O-H···O hydrogen bonds formed with CO₃⁻²and SO₄⁻² anions. The multiple O-H···O hydrogen bonds exist among water molecules themselves. Finally, relatively weak hydrogen bonds form water molecules with the OH groups from the coordination sphere of the Si(OH)₆⁻² anion. Further, calculated vibrational spectrum allowed complete assignment of all vibrational modes which are not available from the experimental spectrum that has a complex structure with overlapped bands, especially below 1500 cm⁻¹. Highlights: • The thaumasite structure was studied experimentally and using DFT method. • We used DFT method for the refinement of the positions of hydrogen atoms. • A detailed analysis of the hydrogen bonds was done. • A complete assignment of all bands to particular types of vibrations was done.

  12. Hispanic women overcoming deterrents to computer science: A phenomenological study

    Science.gov (United States)

    Herling, Lourdes

    The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the U.S. population which they represent. The overall enrollment in computer science programs has continued to decline with the enrollment of women declining at a higher rate than that of men. This study addressed three aspects of underrepresentation about which there has been little previous research: addressing computing disciplines specifically rather than embedding them within the STEM disciplines, what attracts women and minorities to computer science, and addressing the issues of race/ethnicity and gender in conjunction rather than in isolation. Since women of underrepresented ethnicities are more severely underrepresented than women in general, it is important to consider whether race and ethnicity play a role in addition to gender as has been suggested by previous research. Therefore, this study examined what attracted Hispanic women to computer science specifically. The study determines whether being subjected to multiple marginalizations---female and Hispanic---played a role in the experiences of Hispanic women currently in computer science. The study found five emergent themes within the experiences of Hispanic women in computer science. Encouragement and role models strongly influenced not only the participants' choice to major in the field, but to persist as well. Most of the participants experienced a negative atmosphere and feelings of not fitting in while in college and industry. The interdisciplinary nature of computer science was the most common aspect that attracted the participants to computer science. The aptitudes participants commonly believed are needed for success in computer science are the Twenty

  13. Dynamics of Bottlebrush Networks: A Computational Study

    Science.gov (United States)

    Dobrynin, Andrey; Cao, Zhen; Sheiko, Sergei

    We study dynamics of deformation of bottlebrush networks using molecular dynamics simulations and theoretical calculations. Analysis of our simulation results show that the dynamics of bottlebrush network deformation can be described by a Rouse model for polydisperse networks with effective Rouse time of the bottlebrush network strand, τR =τ0Ns2 (Nsc + 1) where, Ns is the number-average degree of polymerization of the bottlebrush backbone strands between crosslinks, Nsc is the degree of polymerization of the side chains and τ0is a characteristic monomeric relaxation time. At time scales t smaller than the Rouse time, t crosslinks, the network response is pure elastic with shear modulus G (t) =G0 , where G0 is the equilibrium shear modulus at small deformation. The stress evolution in the bottlebrush networks can be described by a universal function of t /τR . NSF DMR-1409710.

  14. Computational study of vicarious nucleophilic substitution reactions.

    Science.gov (United States)

    Meneses, Lorena; Morocho, Shirley; Castellanos, Alejandra; Cuesta, Sebastián

    2017-10-02

    Vicarious nucleophilic substitution reactions are a versatile way of introducing substituents into aromatic and heteroaromatic electron-deficient compounds. In this project, a kinetic study of these reactions by applying quantum mechanics concepts, such as reaction force, force constant, and electronic reaction flow was proposed. Furthermore, absolute theoretical scales of electrophilicity by applying density functional theory electronic indices were established to classify a series of five and six-membered nitroheteroarenes, and nitrobenzenes with substituents in ortho, meta and para positions. The theoretical model was validated by comparison with experimental kinetic results. Calculations using B3LYP/6-311G(d,p) level of theory allowed analysis of the reactivity patterns and the mechanisms of these chemical reactions. The theoretical scale properly accounts for the activating/deactivating effects promoted by the substituents and agrees with the ability of these substituents to accept or donate electrons, electron acceptor substituents are those that increase electrophilicity, and electron donors those that reduce it.

  15. Computational Study of Combustor-Turbine Interactions

    Science.gov (United States)

    Miki, Kenji; Liou, Meng-Sing

    2017-01-01

    The Open National Combustion Code (OpenNCC) is applied to the simulation of a realisticcombustor configuration [Energy Efficient Engine (E(exp. 3))] in order to investigate the unsteady flow fields inside the combustor and around the first stage stator of a high pressure turbine (HPT). We consider one-twelfth (24 degrees) of the full annular E(exp. 3) combustor with three different geometries of the combustor exit: one without the vane, and two others with the vane set at different relative positions in relation to the fuel nozzle (clocking). Although it is common to take the exit flow profiles obtained by separately simulating the combustor and then feed it as the inflow profile when modeling the HPT, our studies show that the unsteady flow fields are influenced by the presence of the vane as well as clocking. More importantly, the characteristics (e.g., distribution and strength) of the high temperature spots (i.e., hot-streaks) appearing on the vane significantly alters. This indicates the importance of simultaneously modeling both the combustor and the HPT to understand the mechanics of the unsteady formulation of hot-streaks.

  16. Computational Study of Combustor-Turbine Interactions

    Science.gov (United States)

    Miki, Kenji; Liou, Meng-Sing

    2017-01-01

    The Open National Combustion Code (OpenNCC) is applied to the simulation of a realisticcombustor configuration (Energy Efficient Engine (E3)) in order to investigate the unsteady flow fields inside the combustor and around the first stage stator of a high pressure turbine (HPT). We consider one-twelfth (24 degrees) of the full annular E3 combustor with three different geometries of the combustor exit: one without the vane, and two others with the vane set at different relative positions in relation to the fuel nozzle (clocking). Although it is common to take the exit flow profiles obtained by separately simulating the combustor and then feed it as the inflow profile when modeling the HPT, our studies show that the unsteady flow fields are influenced by the presence of the vane as well as clocking. More importantly, the characteristics (e.g., distribution and strength) of the high temperature spots (i.e., hot-streaks) appearing on the vane significantly alters. This indicates the importance of simultaneously modeling both the combustor and the HPT to understand the mechanics of the unsteady formulation of hot-streaks.

  17. A Case Study on the Use of Blended Learning to Encourage Computer Science Students to Study

    Science.gov (United States)

    Perez-Marin, Diana; Pascual-Nieto, Ismael

    2012-01-01

    Students tend to procrastinate. In particular, Computer Science students tend to reduce the number of hours devoted to study concepts after class. In this paper, a case study on the use of Blended Learning to encourage Computer Science students to study is described. Furthermore, an experiment in which the reaction of 131 Computer Science…

  18. A computer study of air defense gun effectiveness.

    OpenAIRE

    Jung, Hyun Dae

    1987-01-01

    Approved for public release; distribution is unlimited This study describes the continuing development of a computer model for the simulation of burst kill probabilities for air defense gun systems firing projectiles at maneuvering aircraft. The computer simulation developed by Keeling is modified by adding a high explosive proximity and contact fuzed round to the simulation. The objective of this thesis is to develop and analyze the shipboard anti-air defense problem in ord...

  19. A Reflective Study into Children's Cognition When Making Computer Games

    Science.gov (United States)

    Allsop, Yasemin

    2016-01-01

    In this paper, children's mental activities when making digital games are explored. Where previous studies have mainly focused on children's learning, this study aimed to unfold the children's thinking process for learning when making computer games. As part of an ongoing larger scale study, which adopts an ethnographic approach, this research…

  20. A plea for neutral comparison studies in computational sciences.

    Directory of Open Access Journals (Sweden)

    Anne-Laure Boulesteix

    Full Text Available In computational science literature including, e.g., bioinformatics, computational statistics or machine learning, most published articles are devoted to the development of "new methods", while comparison studies are generally appreciated by readers but surprisingly given poor consideration by many journals. This paper stresses the importance of neutral comparison studies for the objective evaluation of existing methods and the establishment of standards by drawing parallels with clinical research. The goal of the paper is twofold. Firstly, we present a survey of recent computational papers on supervised classification published in seven high-ranking computational science journals. The aim is to provide an up-to-date picture of current scientific practice with respect to the comparison of methods in both articles presenting new methods and articles focusing on the comparison study itself. Secondly, based on the results of our survey we critically discuss the necessity, impact and limitations of neutral comparison studies in computational sciences. We define three reasonable criteria a comparison study has to fulfill in order to be considered as neutral, and explicate general considerations on the individual components of a "tidy neutral comparison study". R codes for completely replicating our statistical analyses and figures are available from the companion website http://www.ibe.med.uni-muenchen.de/organisation/mitarbeiter/020_professuren/boulesteix/plea2013.

  1. Dentomaxillofacial imaging with computed-radiography techniques: a preliminary study

    Science.gov (United States)

    Shaw, Chris C.; Kapa, Stanley F.; Furkart, Audrey J.; Gur, David

    1993-09-01

    A preliminary study was conducted to investigate the feasibility of using high resolution computed radiography techniques for dentomaxillofacial imaging. Storage phosphors were cut into various sizes and used with an experimental laser scanning reader for three different imaging procedures: intraoral, cephalometric and panoramic. Both phantom and patient images were obtained for comparing the computed radiography technique with the conventional screen/film or dental film techniques. It has been found that current computed radiography techniques are largely adequate for cephalometric and panoramic imaging but need further improvement on their spatial resolution capability for intraoral imaging. In this paper, the methods of applying the computer radiography techniques to dentomaxillofacial imaging are described and discussed. Images of phantoms, resolution bar patterns and patients are presented and compared. Issues on image quality and cost are discussed.

  2. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview In autumn the main focus was to process and handle CRAFT data and to perform the Summer08 MC production. The operational aspects were well covered by regular Computing Shifts, experts on duty and Computing Run Coordination. At the Computing Resource Board (CRB) in October a model to account for service work at Tier 2s was approved. The computing resources for 2009 were reviewed for presentation at the C-RRB. The quarterly resource monitoring is continuing. Facilities/Infrastructure operations Operations during CRAFT data taking ran fine. This proved to be a very valuable experience for T0 workflows and operations. The transfers of custodial data to most T1s went smoothly. A first round of reprocessing started at the Tier-1 centers end of November; it will take about two weeks. The Computing Shifts procedure was tested full scale during this period and proved to be very efficient: 30 Computing Shifts Persons (CSP) and 10 Computing Resources Coordinators (CRC). The shift program for the shut down w...

  3. Case studies in intelligent computing achievements and trends

    CERN Document Server

    Issac, Biju

    2014-01-01

    Although the field of intelligent systems has grown rapidly in recent years, there has been a need for a book that supplies a timely and accessible understanding of this important technology. Filling this need, Case Studies in Intelligent Computing: Achievements and Trends provides an up-to-date introduction to intelligent systems.This edited book captures the state of the art in intelligent computing research through case studies that examine recent developments, developmental tools, programming, and approaches related to artificial intelligence (AI). The case studies illustrate successful ma

  4. COMPUTING

    CERN Multimedia

    M. Kasemann

    Overview During the past three months activities were focused on data operations, testing and re-enforcing shift and operational procedures for data production and transfer, MC production and on user support. Planning of the computing resources in view of the new LHC calendar in ongoing. Two new task forces were created for supporting the integration work: Site Commissioning, which develops tools helping distributed sites to monitor job and data workflows, and Analysis Support, collecting the user experience and feedback during analysis activities and developing tools to increase efficiency. The development plan for DMWM for 2009/2011 was developed at the beginning of the year, based on the requirements from the Physics, Computing and Offline groups (see Offline section). The Computing management meeting at FermiLab on February 19th and 20th was an excellent opportunity discussing the impact and for addressing issues and solutions to the main challenges facing CMS computing. The lack of manpower is particul...

  5. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction CMS distributed computing system performed well during the 2011 start-up. The events in 2011 have more pile-up and are more complex than last year; this results in longer reconstruction times and harder events to simulate. Significant increases in computing capacity were delivered in April for all computing tiers, and the utilisation and load is close to the planning predictions. All computing centre tiers performed their expected functionalities. Heavy-Ion Programme The CMS Heavy-Ion Programme had a very strong showing at the Quark Matter conference. A large number of analyses were shown. The dedicated heavy-ion reconstruction facility at the Vanderbilt Tier-2 is still involved in some commissioning activities, but is available for processing and analysis. Facilities and Infrastructure Operations Facility and Infrastructure operations have been active with operations and several important deployment tasks. Facilities participated in the testing and deployment of WMAgent and WorkQueue+Request...

  6. Computational wing design studies relating to natural laminar flow

    Science.gov (United States)

    Waggoner, Edgar G.

    1986-01-01

    Two research studies are described which directly relate to the application of natural laminar flow (NLF) technology to transonic transport-type wing planforms. Each involved using state-of-the-art computational methods to design three-dimensional wing contours which generate significant runs of favorable pressure gradients. The first study supported the Variable Sweep Transition Flight Experiment and involves design of a full-span glove which extends from the leading edge to the spoiler hinge line on the upper surface of an F-14 outer wing panel. A wing was designed computationally for a corporate transport aircraft in the second study. The resulting wing design generated favorable pressure gradients from the leading edge aft to the mid-chord on both upper and lower surfaces at the cruise design point. Detailed descriptions of the computational design approach are presented along with the various constraints imposed on each of the designs.

  7. Doctors' experience with handheld computers in clinical practice: qualitative study.

    Science.gov (United States)

    McAlearney, Ann Scheck; Schweikhart, Sharon B; Medow, Mitchell A

    2004-05-15

    To examine doctors' perspectives about their experiences with handheld computers in clinical practice. Qualitative study of eight focus groups consisting of doctors with diverse training and practice patterns. Six practice settings across the United States and two additional focus group sessions held at a national meeting of general internists. 54 doctors who did or did not use handheld computers. Doctors who used handheld computers in clinical practice seemed generally satisfied with them and reported diverse patterns of use. Users perceived that the devices helped them increase productivity and improve patient care. Barriers to use concerned the device itself and personal and perceptual constraints, with perceptual factors such as comfort with technology, preference for paper, and the impression that the devices are not easy to use somewhat difficult to overcome. Participants suggested that organisations can help promote handheld computers by providing advice on purchase, usage, training, and user support. Participants expressed concern about reliability and security of the device but were particularly concerned about dependency on the device and over-reliance as a substitute for clinical thinking. Doctors expect handheld computers to become more useful, and most seem interested in leveraging (getting the most value from) their use. Key opportunities with handheld computers included their use as a stepping stone to build doctors' comfort with other information technology and ehealth initiatives and providing point of care support that helps improve patient care.

  8. Two Studies Examining Argumentation in Asynchronous Computer Mediated Communication

    Science.gov (United States)

    Joiner, Richard; Jones, Sarah; Doherty, John

    2008-01-01

    Asynchronous computer mediated communication (CMC) would seem to be an ideal medium for supporting development in student argumentation. This paper investigates this assumption through two studies. The first study compared asynchronous CMC with face-to-face discussions. The transactional and strategic level of the argumentation (i.e. measures of…

  9. Computing requirements for S. S. C. accelerator design and studies

    Energy Technology Data Exchange (ETDEWEB)

    Dragt, A.; Talman, R.; Siemann, R.; Dell, G.F.; Leemann, B.; Leemann, C.; Nauenberg, U.; Peggs, S.; Douglas, D.

    1984-01-01

    We estimate the computational hardware resources that will be required for accelerator physics studies during the design of the Superconducting SuperCollider. It is found that both Class IV and Class VI facilities (1) will be necessary. We describe a user environment for these facilities that is desirable within the context of accelerator studies. An acquisition scenario for these facilities is presented.

  10. Experiences of Computer Science Curriculum Design: A Phenomenological Study

    Science.gov (United States)

    Sloan, Arthur; Bowe, Brian

    2015-01-01

    This paper presents a qualitative study of 12 computer science lecturers' experiences of curriculum design of several degree programmes during a time of transition from year-long to semesterised courses, due to institutional policy change. The background to the study is outlined, as are the reasons for choosing the research methodology. The main…

  11. Brain-computer interfacing under distraction: an evaluation study

    DEFF Research Database (Denmark)

    Brandl, Stephanie; Frølich, Laura; Höhne, Johannes

    2016-01-01

    Objective. While motor-imagery based brain-computer interfaces (BCIs) have been studied over many years by now, most of these studies have taken place in controlled lab settings. Bringing BCI technology into everyday life is still one of the main challenges in this field of research. Approach...

  12. Student Engagement with Computer-Generated Feedback: A Case Study

    Science.gov (United States)

    Zhang, Zhe

    2017-01-01

    In order to benefit from feedback on their writing, students need to engage effectively with it. This article reports a case study on student engagement with computer-generated feedback, known as automated writing evaluation (AWE) feedback, in an EFL context. Differing from previous studies that explored commercially available AWE programs, this…

  13. Studying CO2 storage with ambient-noise seismic interferometry : A combined numerical feasibility study and field-data example for Ketzin, Germany

    NARCIS (Netherlands)

    Boullenger, B.; Verdel, A.; Paap, B.; Thorbecke, J.W.; Draganov, D.S.

    2015-01-01

    Seismic interferometry applied to ambient-noise measurements allows the retrieval of the seismic response between pairs of receivers. We studied ambient-noise seismic interferometry (ANSI) to retrieve time-lapse reflection responses from a reservoir during CO2 geologic sequestration, using the case

  14. Studying CO2 storage with ambient-noise seismic interferometry: A combined numerical feasibility study and field-data example for Ketzin, Germany

    NARCIS (Netherlands)

    Boullenger, B.; Verdel, A.R.; Paap, B.F.

    2015-01-01

    Seismic interferometry applied to ambient-noise measurements allows the retrieval of the seismic response between pairs of receivers. We studied ambient-noise seismic interferometry (ANSI) to retrieve time-lapse reflection responses from a reservoir during CO2 geologic sequestration, using the case

  15. Case studies of computer model applications in consulting practice

    Science.gov (United States)

    Siebein, Gary; Paek, Hyun; Lorang, Mark; McGuinnes, Courtney

    2002-05-01

    Six case studies of computer model applications in a consulting practice will be presented to present the range of issues that can be studied with computer models as well as to understand the limitations of the technique at the present time. Case studies of elliptical conference rooms demonstrate basic acoustic ray principles and suggest remediation strategies. Models of a large themed entertainment venue with multiple amplified sound sources show how visualization of the acoustic ray paths can assist a consultant and client in value engineering locations and amounts of acoustic materials. The acoustic problems with an angled ceiling and large rear wall were studied when an historic church was converted to a music performance hall. The computer model of an historic hall did not present enough detailed information and was supplemented with physical model studies and full size mock-up tests of the insertion of an elevator door that would open directly into the concert room. Studies to demonstrate the amount of room model detail to obtain realistic auralizations were also conducted. The integration of architectural acoustic design and audio system design were studied in computer models of a large church sanctuary.

  16. A Study of Student-Teachers' Readiness to Use Computers in Teaching: An Empirical Study

    Science.gov (United States)

    Padmavathi, M.

    2016-01-01

    This study attempts to analyze student-teachers' attitude towards the use of computers for classroom teaching. Four dimensions of computer attitude on a Likert-type five-point scale were used: Affect (liking), Perceived usefulness, Perceived Control, and Behaviour Intention to use computers. The effect of student-teachers' subject area, years of…

  17. Computer Assisted Instruction in Special Education Three Case Studies

    Directory of Open Access Journals (Sweden)

    İbrahim DOĞAN

    2015-09-01

    Full Text Available The purpose of this study is to investigate the computer use of three students attending the special education center. Students have mental retardation, hearing problem and physical handicap respectively. The maximum variation sampling is used to select the type of handicap while the convenience sampling is used to select the participants. Three widely encountered handicap types in special education are chosen to select the study participants. The multiple holistic case study design is used in the study. Results of the study indicate that teachers in special education prefer to use educational games and drill and practice type of computers programs. Also it is found that over use of the animation, text and symbols cause cognitive overload on the student with mental retardation. Additionally, it is also discovered that the student with hearing problem learn words better when the computers are used in education as compared to the traditional method. Furthermore the student with physical handicap improved his fine muscle control abilities besides planned course objectives when computers are used in special education.

  18. Study on the Computational Estimation Performance and Computational Estimation Attitude of Elementary School Fifth Graders in Taiwan

    Science.gov (United States)

    Tsao, Yea-Ling; Pan, Ting-Rung

    2011-01-01

    Main purpose of this study is to investigate what level of computational estimation performance is possessed by fifth graders and explore computational estimation attitude towards fifth graders. Two hundred and thirty-five Grade-5 students from four elementary schools in Taipei City were selected for "Computational Estimation Test" and…

  19. ANIMATED COMPUTER GRAPHICS FOR THE STUDY OF MECHANICAL VIBRATIONS

    OpenAIRE

    Crăifăleanu Andrei; ION George Cătălin

    2006-01-01

    The paper presents a computer code developed by the authors for the study of the small oscillations of a system of two pendulums, coupled one to each other, as well as to the fixed element, with linear springs and with linear viscous dampers. The code has an advanced Windows interface.

  20. Nanoscale energy transport and harvesting a computational study

    CERN Document Server

    Gang, Zhang

    2014-01-01

    Molecular Dynamics Simulations for Computing Thermal Conductivity of Nano MaterialsNonequilibrium Phonon Green's Function Simulation and Its Application to Carbon NanotubesThermal Conduction of GrapheneBallistic Thermal Transport by Phonons at Low Temperatures in Low-Dimensional Quantum StructuresSurface functionalization induced thermal conductivity attenuation in silicon nanowires: A molecular dynamics study

  1. Merging Computers and Communication: A Case Study in Latin America.

    Science.gov (United States)

    Oeffinger, John C.

    1987-01-01

    Discusses access to information through merging computers and new communications technology and its influence in developing nations. Highlights include a case study of InterNet/LACRIP (Latin American Cancer Research Information Project), a microcomputer-based international network involving institutions in the United States and Latin America that…

  2. It Pays to Compare: An Experimental Study on Computational Estimation

    Science.gov (United States)

    Star, Jon R.; Rittle-Johnson, Bethany

    2009-01-01

    Comparing and contrasting examples is a core cognitive process that supports learning in children and adults across a variety of topics. In this experimental study, we evaluated the benefits of supporting comparison in a classroom context for children learning about computational estimation. Fifth- and sixth-grade students (N = 157) learned about…

  3. Defining Effectiveness Using Finite Sets A Study on Computability

    DEFF Research Database (Denmark)

    Macedo, Hugo Daniel dos Santos; Haeusler, Edward H.; Garcia, Alex

    2016-01-01

    This paper studies effectiveness in the domain of computability. In the context of model-theoretical approaches to effectiveness, where a function is considered effective if there is a model containing a representation of such function, our definition relies on a model provided by functions betwe...

  4. Computational and experimental studies on oxalic acid imprinted ...

    Indian Academy of Sciences (India)

    imprinted polymer. KIRAN KUMAR TADI and R V MOTGHARE. ∗. Department of Chemistry, Visvesvaraya National Institute of Technology, South Ambazari Road,. Nagpur 440 ... Keywords. Computational approach; molecularly imprinted polymer; oxalic acid; adsorption studies. ... High levels of oxalic acid remove calcium ...

  5. Computational studies of third-order nonlinear optical properties of ...

    Indian Academy of Sciences (India)

    2017-06-20

    Jun 20, 2017 ... Home; Journals; Pramana – Journal of Physics; Volume 89; Issue 1. Computational studies of third-order nonlinear optical properties of pyridine derivative 2-aminopyridinium p-toluenesulphonate crystal. ANUJ KUMAR MAHESH PAL SINGH YADAV. Special Issue Volume 89 Issue 1 July 2017 Article ID 7 ...

  6. Computer simulation study of water using a fluctuating charge model

    Indian Academy of Sciences (India)

    Unknown

    Abstract. Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Rick et al (S W Rick, S J Stuart and B J Berne 1994 J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to ...

  7. Crew/computer communications study. Volume 2: Appendixes

    Science.gov (United States)

    Johannes, J. D.

    1974-01-01

    The software routines developed during the crew/computer communications study are described to provide the user with an understanding of each routine, any restrictions in use, the required input data, and expected results after executing the routines. The combination of routines to generate a crew/computer communications application is also explained. The programmable keyboard and display used by the program is described, and an experiment scenario is provided to illustrate the relationship between the program frames when they are grouped into activity phases. Program descriptions and a user's guide are also presented. For Vol. 1, see N74-18843.

  8. A Study on Parallel Computation Tools on Networked PCs

    Directory of Open Access Journals (Sweden)

    Heru Suhartanto

    2010-10-01

    Full Text Available Many models for natural phenomena, engineering applications and industries need powerfull computing resources to solve their problems. High Performance Computing resources were introduced by many researchers. This comes in the form of Supercomputers and with operating systems and tools for development such as parallel compiler and its library. However, these resources are  expensive for the investation and maintenance, hence people need some alternatives. Many people then introduced parallel distributed computing by using available computing resource such as PCs. Each of these PCs is treated  s a processors, hence the cluster of the PC behaves as Multiprocessors Computer. Many tools are developed for such purposes. This paper studies the peformance of the currently popular tools such as Parallel Virta\\ual Machine (PVM, Message Passing Interface (MPI, Java Remote Method Invocation (RMI and Java Common Object Request Broker Architecture (CORBA. Some experiments were conducted on a cluster of PCs, the results show significant speed up. Each of those tools are identified suitable for a certain implementation and programming purposes.

  9. Electromagnetic computation methods for lightning surge protection studies

    CERN Document Server

    Baba, Yoshihiro

    2016-01-01

    This book is the first to consolidate current research and to examine the theories of electromagnetic computation methods in relation to lightning surge protection. The authors introduce and compare existing electromagnetic computation methods such as the method of moments (MOM), the partial element equivalent circuit (PEEC), the finite element method (FEM), the transmission-line modeling (TLM) method, and the finite-difference time-domain (FDTD) method. The application of FDTD method to lightning protection studies is a topic that has matured through many practical applications in the past decade, and the authors explain the derivation of Maxwell's equations required by the FDTD, and modeling of various electrical components needed in computing lightning electromagnetic fields and surges with the FDTD method. The book describes the application of FDTD method to current and emerging problems of lightning surge protection of continuously more complex installations, particularly in critical infrastructures of e...

  10. COMPUTING

    CERN Multimedia

    I. Fisk

    2010-01-01

    Introduction It has been a very active quarter in Computing with interesting progress in all areas. The activity level at the computing facilities, driven by both organised processing from data operations and user analysis, has been steadily increasing. The large-scale production of simulated events that has been progressing throughout the fall is wrapping-up and reprocessing with pile-up will continue. A large reprocessing of all the proton-proton data has just been released and another will follow shortly. The number of analysis jobs by users each day, that was already hitting the computing model expectations at the time of ICHEP, is now 33% higher. We are expecting a busy holiday break to ensure samples are ready in time for the winter conferences. Heavy Ion An activity that is still in progress is computing for the heavy-ion program. The heavy-ion events are collected without zero suppression, so the event size is much large at roughly 11 MB per event of RAW. The central collisions are more complex and...

  11. COMPUTING

    CERN Multimedia

    M. Kasemann P. McBride Edited by M-C. Sawley with contributions from: P. Kreuzer D. Bonacorsi S. Belforte F. Wuerthwein L. Bauerdick K. Lassila-Perini M-C. Sawley

    Introduction More than seventy CMS collaborators attended the Computing and Offline Workshop in San Diego, California, April 20-24th to discuss the state of readiness of software and computing for collisions. Focus and priority were given to preparations for data taking and providing room for ample dialog between groups involved in Commissioning, Data Operations, Analysis and MC Production. Throughout the workshop, aspects of software, operating procedures and issues addressing all parts of the computing model were discussed. Plans for the CMS participation in STEP’09, the combined scale testing for all four experiments due in June 2009, were refined. The article in CMS Times by Frank Wuerthwein gave a good recap of the highly collaborative atmosphere of the workshop. Many thanks to UCSD and to the organizers for taking care of this workshop, which resulted in a long list of action items and was definitely a success. A considerable amount of effort and care is invested in the estimate of the comput...

  12. Computer Simulation for Pain Management Education: A Pilot Study.

    Science.gov (United States)

    Allred, Kelly; Gerardi, Nicole

    2017-10-01

    Effective pain management is an elusive concept in acute care. Inadequate knowledge has been identified as a barrier to providing optimal pain management. This study aimed to determine student perceptions of an interactive computer simulation as a potential method for learning pain management, as a motivator to read and learn more about pain management, preference over traditional lecture, and its potential to change nursing practice. A post-computer simulation survey with a mixed-methods descriptive design was used in this study. A college of nursing in a large metropolitan university in the Southeast United States. A convenience sample of 30 nursing students in a Bachelor of Science nursing program. An interactive computer simulation was developed as a potential alternative method of teaching pain management to nursing students. Increases in educational gain as well as its potential to change practice were explored. Each participant was asked to complete a survey consisting of 10 standard 5-point Likert scale items and 5 open-ended questions. The survey was used to evaluate the students' perception of the simulation, specifically related to educational benefit, preference compared with traditional teaching methods, and perceived potential to change nursing practice. Data provided descriptive statistics for initial evaluation of the computer simulation. The responses on the survey suggest nursing students perceive the computer simulation to be entertaining, fun, educational, occasionally preferred over regular lecture, and with potential to change practice. Preliminary data support the use of computer simulation in educating nursing students about pain management. Copyright © 2017 American Society for Pain Management Nursing. Published by Elsevier Inc. All rights reserved.

  13. Identifying a Computer Forensics Expert: A Study to Measure the Characteristics of Forensic Computer Examiners

    Directory of Open Access Journals (Sweden)

    Gregory H. Carlton

    2010-03-01

    Full Text Available Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 The usage of digital evidence from electronic devices has been rapidly expanding within litigation, and along with this increased usage, the reliance upon forensic computer examiners to acquire, analyze, and report upon this evidence is also rapidly growing. This growing demand for forensic computer examiners raises questions concerning the selection of individuals qualified to perform this work. While courts have mechanisms for qualifying witnesses that provide testimony based on scientific data, such as digital data, the qualifying criteria covers a wide variety of characteristics including, education, experience, training, professional certifications, or other special skills. In this study, we compare task performance responses from forensic computer examiners with an expert review panel and measure the relationship with the characteristics of the examiners to their quality responses. The results of this analysis provide insight into identifying forensic computer examiners that provide high-quality responses. /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

  14. CFD Vision 2030 Study: A Path to Revolutionary Computational Aerosciences

    Science.gov (United States)

    Slotnick, Jeffrey; Khodadoust, Abdollah; Alonso, Juan; Darmofal, David; Gropp, William; Lurie, Elizabeth; Mavriplis, Dimitri

    2014-01-01

    This report documents the results of a study to address the long range, strategic planning required by NASA's Revolutionary Computational Aerosciences (RCA) program in the area of computational fluid dynamics (CFD), including future software and hardware requirements for High Performance Computing (HPC). Specifically, the "Vision 2030" CFD study is to provide a knowledge-based forecast of the future computational capabilities required for turbulent, transitional, and reacting flow simulations across a broad Mach number regime, and to lay the foundation for the development of a future framework and/or environment where physics-based, accurate predictions of complex turbulent flows, including flow separation, can be accomplished routinely and efficiently in cooperation with other physics-based simulations to enable multi-physics analysis and design. Specific technical requirements from the aerospace industrial and scientific communities were obtained to determine critical capability gaps, anticipated technical challenges, and impediments to achieving the target CFD capability in 2030. A preliminary development plan and roadmap were created to help focus investments in technology development to help achieve the CFD vision in 2030.

  15. COMPUTING

    CERN Multimedia

    P. McBride

    It has been a very active year for the computing project with strong contributions from members of the global community. The project has focused on site preparation and Monte Carlo production. The operations group has begun processing data from P5 as part of the global data commissioning. Improvements in transfer rates and site availability have been seen as computing sites across the globe prepare for large scale production and analysis as part of CSA07. Preparations for the upcoming Computing Software and Analysis Challenge CSA07 are progressing. Ian Fisk and Neil Geddes have been appointed as coordinators for the challenge. CSA07 will include production tests of the Tier-0 production system, reprocessing at the Tier-1 sites and Monte Carlo production at the Tier-2 sites. At the same time there will be a large analysis exercise at the Tier-2 centres. Pre-production simulation of the Monte Carlo events for the challenge is beginning. Scale tests of the Tier-0 will begin in mid-July and the challenge it...

  16. COMPUTING

    CERN Multimedia

    I. Fisk

    2012-01-01

    Introduction Computing continued with a high level of activity over the winter in preparation for conferences and the start of the 2012 run. 2012 brings new challenges with a new energy, more complex events, and the need to make the best use of the available time before the Long Shutdown. We expect to be resource constrained on all tiers of the computing system in 2012 and are working to ensure the high-priority goals of CMS are not impacted. Heavy ions After a successful 2011 heavy-ion run, the programme is moving to analysis. During the run, the CAF resources were well used for prompt analysis. Since then in 2012 on average 200 job slots have been used continuously at Vanderbilt for analysis workflows. Operations Office As of 2012, the Computing Project emphasis has moved from commissioning to operation of the various systems. This is reflected in the new organisation structure where the Facilities and Data Operations tasks have been merged into a common Operations Office, which now covers everything ...

  17. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction It has been a very active quarter in Computing with interesting progress in all areas. The activity level at the computing facilities, driven by both organised processing from data operations and user analysis, has been steadily increasing. The large-scale production of simulated events that has been progressing throughout the fall is wrapping-up and reprocessing with pile-up will continue. A large reprocessing of all the proton-proton data has just been released and another will follow shortly. The number of analysis jobs by users each day, that was already hitting the computing model expectations at the time of ICHEP, is now 33% higher. We are expecting a busy holiday break to ensure samples are ready in time for the winter conferences. Heavy Ion The Tier 0 infrastructure was able to repack and promptly reconstruct heavy-ion collision data. Two copies were made of the data at CERN using a large CASTOR disk pool, and the core physics sample was replicated ...

  18. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction More than seventy CMS collaborators attended the Computing and Offline Workshop in San Diego, California, April 20-24th to discuss the state of readiness of software and computing for collisions. Focus and priority were given to preparations for data taking and providing room for ample dialog between groups involved in Commissioning, Data Operations, Analysis and MC Production. Throughout the workshop, aspects of software, operating procedures and issues addressing all parts of the computing model were discussed. Plans for the CMS participation in STEP’09, the combined scale testing for all four experiments due in June 2009, were refined. The article in CMS Times by Frank Wuerthwein gave a good recap of the highly collaborative atmosphere of the workshop. Many thanks to UCSD and to the organizers for taking care of this workshop, which resulted in a long list of action items and was definitely a success. A considerable amount of effort and care is invested in the estimate of the co...

  19. COMPUTING

    CERN Multimedia

    M. Kasemann

    CCRC’08 challenges and CSA08 During the February campaign of the Common Computing readiness challenges (CCRC’08), the CMS computing team had achieved very good results. The link between the detector site and the Tier0 was tested by gradually increasing the number of parallel transfer streams well beyond the target. Tests covered the global robustness at the Tier0, processing a massive number of very large files and with a high writing speed to tapes.  Other tests covered the links between the different Tiers of the distributed infrastructure and the pre-staging and reprocessing capacity of the Tier1’s: response time, data transfer rate and success rate for Tape to Buffer staging of files kept exclusively on Tape were measured. In all cases, coordination with the sites was efficient and no serious problem was found. These successful preparations prepared the ground for the second phase of the CCRC’08 campaign, in May. The Computing Software and Analysis challen...

  20. COMPUTING

    CERN Multimedia

    I. Fisk

    2010-01-01

    Introduction The first data taking period of November produced a first scientific paper, and this is a very satisfactory step for Computing. It also gave the invaluable opportunity to learn and debrief from this first, intense period, and make the necessary adaptations. The alarm procedures between different groups (DAQ, Physics, T0 processing, Alignment/calibration, T1 and T2 communications) have been reinforced. A major effort has also been invested into remodeling and optimizing operator tasks in all activities in Computing, in parallel with the recruitment of new Cat A operators. The teams are being completed and by mid year the new tasks will have been assigned. CRB (Computing Resource Board) The Board met twice since last CMS week. In December it reviewed the experience of the November data-taking period and could measure the positive improvements made for the site readiness. It also reviewed the policy under which Tier-2 are associated with Physics Groups. Such associations are decided twice per ye...

  1. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction During the past six months, Computing participated in the STEP09 exercise, had a major involvement in the October exercise and has been working with CMS sites on improving open issues relevant for data taking. At the same time operations for MC production, real data reconstruction and re-reconstructions and data transfers at large scales were performed. STEP09 was successfully conducted in June as a joint exercise with ATLAS and the other experiments. It gave good indication about the readiness of the WLCG infrastructure with the two major LHC experiments stressing the reading, writing and processing of physics data. The October Exercise, in contrast, was conducted as an all-CMS exercise, where Physics, Computing and Offline worked on a common plan to exercise all steps to efficiently access and analyze data. As one of the major results, the CMS Tier-2s demonstrated to be fully capable for performing data analysis. In recent weeks, efforts were devoted to CMS Computing readiness. All th...

  2. NATO Advanced Study Institute on Methods in Computational Molecular Physics

    CERN Document Server

    Diercksen, Geerd

    1992-01-01

    This volume records the lectures given at a NATO Advanced Study Institute on Methods in Computational Molecular Physics held in Bad Windsheim, Germany, from 22nd July until 2nd. August, 1991. This NATO Advanced Study Institute sought to bridge the quite considerable gap which exist between the presentation of molecular electronic structure theory found in contemporary monographs such as, for example, McWeeny's Methods 0/ Molecular Quantum Mechanics (Academic Press, London, 1989) or Wilson's Electron correlation in moleeules (Clarendon Press, Oxford, 1984) and the realization of the sophisticated computational algorithms required for their practical application. It sought to underline the relation between the electronic structure problem and the study of nuc1ear motion. Software for performing molecular electronic structure calculations is now being applied in an increasingly wide range of fields in both the academic and the commercial sectors. Numerous applications are reported in areas as diverse as catalysi...

  3. Cloud Computing as Evolution of Distributed Computing – A Case Study for SlapOS Distributed Cloud Computing Platform

    Directory of Open Access Journals (Sweden)

    George SUCIU

    2013-01-01

    Full Text Available The cloud computing paradigm has been defined from several points of view, the main two directions being either as an evolution of the grid and distributed computing paradigm, or, on the contrary, as a disruptive revolution in the classical paradigms of operating systems, network layers and web applications. This paper presents a distributed cloud computing platform called SlapOS, which unifies technologies and communication protocols into a new technology model for offering any application as a service. Both cloud and distributed computing can be efficient methods for optimizing resources that are aggregated from a grid of standard PCs hosted in homes, offices and small data centers. The paper fills a gap in the existing distributed computing literature by providing a distributed cloud computing model which can be applied for deploying various applications.

  4. Computational Study of Scenarios Regarding Explosion Risk Mitigation

    Science.gov (United States)

    Vlasin, Nicolae-Ioan; Mihai Pasculescu, Vlad; Florea, Gheorghe-Daniel; Cornel Suvar, Marius

    2016-10-01

    Exploration in order to discover new deposits of natural gas, upgrading techniques to exploit these resources and new ways to convert the heat capacity of these gases into industrial usable energy is the research areas of great interest around the globe. But all activities involving the handling of natural gas (exploitation, transport, combustion) are subjected to the same type of risk: the risk to explosion. Experiments carried out physical scenarios to determine ways to reduce this risk can be extremely costly, requiring suitable premises, equipment and apparatus, manpower, time and, not least, presenting the risk of personnel injury. Taking in account the above mentioned, the present paper deals with the possibility of studying the scenarios of gas explosion type events in virtual domain, exemplifying by performing a computer simulation of a stoichiometric air - methane explosion (methane is the main component of natural gas). The advantages of computer-assisted imply are the possibility of using complex virtual geometries of any form as the area of deployment phenomenon, the use of the same geometry for an infinite number of settings of initial parameters as input, total elimination the risk of personnel injury, decrease the execution time etc. Although computer simulations are hardware resources consuming and require specialized personnel to use the CFD (Computational Fluid Dynamics) techniques, the costs and risks associated with these methods are greatly diminished, presenting, in the same time, a major benefit in terms of execution time.

  5. Heavy Lift Vehicle (HLV) Avionics Flight Computing Architecture Study

    Science.gov (United States)

    Hodson, Robert F.; Chen, Yuan; Morgan, Dwayne R.; Butler, A. Marc; Sdhuh, Joseph M.; Petelle, Jennifer K.; Gwaltney, David A.; Coe, Lisa D.; Koelbl, Terry G.; Nguyen, Hai D.

    2011-01-01

    A NASA multi-Center study team was assembled from LaRC, MSFC, KSC, JSC and WFF to examine potential flight computing architectures for a Heavy Lift Vehicle (HLV) to better understand avionics drivers. The study examined Design Reference Missions (DRMs) and vehicle requirements that could impact the vehicles avionics. The study considered multiple self-checking and voting architectural variants and examined reliability, fault-tolerance, mass, power, and redundancy management impacts. Furthermore, a goal of the study was to develop the skills and tools needed to rapidly assess additional architectures should requirements or assumptions change.

  6. Computational study of noise in a large signal transduction network

    Directory of Open Access Journals (Sweden)

    Ruohonen Keijo

    2011-06-01

    Full Text Available Abstract Background Biochemical systems are inherently noisy due to the discrete reaction events that occur in a random manner. Although noise is often perceived as a disturbing factor, the system might actually benefit from it. In order to understand the role of noise better, its quality must be studied in a quantitative manner. Computational analysis and modeling play an essential role in this demanding endeavor. Results We implemented a large nonlinear signal transduction network combining protein kinase C, mitogen-activated protein kinase, phospholipase A2, and β isoform of phospholipase C networks. We simulated the network in 300 different cellular volumes using the exact Gillespie stochastic simulation algorithm and analyzed the results in both the time and frequency domain. In order to perform simulations in a reasonable time, we used modern parallel computing techniques. The analysis revealed that time and frequency domain characteristics depend on the system volume. The simulation results also indicated that there are several kinds of noise processes in the network, all of them representing different kinds of low-frequency fluctuations. In the simulations, the power of noise decreased on all frequencies when the system volume was increased. Conclusions We concluded that basic frequency domain techniques can be applied to the analysis of simulation results produced by the Gillespie stochastic simulation algorithm. This approach is suited not only to the study of fluctuations but also to the study of pure noise processes. Noise seems to have an important role in biochemical systems and its properties can be numerically studied by simulating the reacting system in different cellular volumes. Parallel computing techniques make it possible to run massive simulations in hundreds of volumes and, as a result, accurate statistics can be obtained from computational studies.

  7. Reverse running pumps analytical, experimental and computational study: A review

    Energy Technology Data Exchange (ETDEWEB)

    Nautiyal, Himanshu; Varun; Kumar, Anoop [Department of Mechanical Engineering, National Institute of Technology, Hamirpur (India)

    2010-09-15

    A pump can be used as turbine and has good application in micro-hydropower schemes. Pump as turbine (PAT) is one of the best alternatives for fulfilling the energy demands and providing the electricity in remote and rural areas. In this study a review on the work done in the area of pump working as turbine has been explained. Based upon the literature survey, analytical, experimental and computational works on pump as turbine have been discussed. Several methods for predicting the behaviour of pumps in turbine mode have been developed but no method is appropriate for the entire range of specific speeds. Computational fluid dynamics (CFD) is also used to study the reverse operation of centrifugal pumps, but still results are not yet acceptable. (author)

  8. A computational study of routing algorithms for realistic transportation networks

    Energy Technology Data Exchange (ETDEWEB)

    Jacob, R.; Marathe, M.V.; Nagel, K.

    1998-12-01

    The authors carry out an experimental analysis of a number of shortest path (routing) algorithms investigated in the context of the TRANSIMS (Transportation Analysis and Simulation System) project. The main focus of the paper is to study how various heuristic and exact solutions, associated data structures affected the computational performance of the software developed especially for realistic transportation networks. For this purpose the authors have used Dallas Fort-Worth road network with very high degree of resolution. The following general results are obtained: (1) they discuss and experimentally analyze various one-one shortest path algorithms, which include classical exact algorithms studied in the literature as well as heuristic solutions that are designed to take into account the geometric structure of the input instances; (2) they describe a number of extensions to the basic shortest path algorithm. These extensions were primarily motivated by practical problems arising in TRANSIMS and ITS (Intelligent Transportation Systems) related technologies. Extensions discussed include--(i) time dependent networks, (ii) multi-modal networks, (iii) networks with public transportation and associated schedules. Computational results are provided to empirically compare the efficiency of various algorithms. The studies indicate that a modified Dijkstra`s algorithm is computationally fast and an excellent candidate for use in various transportation planning applications as well as ITS related technologies.

  9. COMPUTING

    CERN Multimedia

    I. Fisk

    2013-01-01

    Computing operation has been lower as the Run 1 samples are completing and smaller samples for upgrades and preparations are ramping up. Much of the computing activity is focusing on preparations for Run 2 and improvements in data access and flexibility of using resources. Operations Office Data processing was slow in the second half of 2013 with only the legacy re-reconstruction pass of 2011 data being processed at the sites.   Figure 1: MC production and processing was more in demand with a peak of over 750 Million GEN-SIM events in a single month.   Figure 2: The transfer system worked reliably and efficiently and transferred on average close to 520 TB per week with peaks at close to 1.2 PB.   Figure 3: The volume of data moved between CMS sites in the last six months   The tape utilisation was a focus for the operation teams with frequent deletion campaigns from deprecated 7 TeV MC GEN-SIM samples to INVALID datasets, which could be cleaned up...

  10. COMPUTING

    CERN Multimedia

    I. Fisk

    2012-01-01

      Introduction Computing activity has been running at a sustained, high rate as we collect data at high luminosity, process simulation, and begin to process the parked data. The system is functional, though a number of improvements are planned during LS1. Many of the changes will impact users, we hope only in positive ways. We are trying to improve the distributed analysis tools as well as the ability to access more data samples more transparently.  Operations Office Figure 2: Number of events per month, for 2012 Since the June CMS Week, Computing Operations teams successfully completed data re-reconstruction passes and finished the CMSSW_53X MC campaign with over three billion events available in AOD format. Recorded data was successfully processed in parallel, exceeding 1.2 billion raw physics events per month for the first time in October 2012 due to the increase in data-parking rate. In parallel, large efforts were dedicated to WMAgent development and integrati...

  11. COMPUTING

    CERN Multimedia

    2010-01-01

    Introduction Just two months after the “LHC First Physics” event of 30th March, the analysis of the O(200) million 7 TeV collision events in CMS accumulated during the first 60 days is well under way. The consistency of the CMS computing model has been confirmed during these first weeks of data taking. This model is based on a hierarchy of use-cases deployed between the different tiers and, in particular, the distribution of RECO data to T1s, who then serve data on request to T2s, along a topology known as “fat tree”. Indeed, during this period this model was further extended by almost full “mesh” commissioning, meaning that RECO data were shipped to T2s whenever possible, enabling additional physics analyses compared with the “fat tree” model. Computing activities at the CMS Analysis Facility (CAF) have been marked by a good time response for a load almost evenly shared between ALCA (Alignment and Calibration tasks - highest p...

  12. COMPUTING

    CERN Multimedia

    Matthias Kasemann

    Overview The main focus during the summer was to handle data coming from the detector and to perform Monte Carlo production. The lessons learned during the CCRC and CSA08 challenges in May were addressed by dedicated PADA campaigns lead by the Integration team. Big improvements were achieved in the stability and reliability of the CMS Tier1 and Tier2 centres by regular and systematic follow-up of faults and errors with the help of the Savannah bug tracking system. In preparation for data taking the roles of a Computing Run Coordinator and regular computing shifts monitoring the services and infrastructure as well as interfacing to the data operations tasks are being defined. The shift plan until the end of 2008 is being put together. User support worked on documentation and organized several training sessions. The ECoM task force delivered the report on “Use Cases for Start-up of pp Data-Taking” with recommendations and a set of tests to be performed for trigger rates much higher than the ...

  13. COMPUTING

    CERN Multimedia

    M. Kasemann

    Introduction A large fraction of the effort was focused during the last period into the preparation and monitoring of the February tests of Common VO Computing Readiness Challenge 08. CCRC08 is being run by the WLCG collaboration in two phases, between the centres and all experiments. The February test is dedicated to functionality tests, while the May challenge will consist of running at all centres and with full workflows. For this first period, a number of functionality checks of the computing power, data repositories and archives as well as network links are planned. This will help assess the reliability of the systems under a variety of loads, and identifying possible bottlenecks. Many tests are scheduled together with other VOs, allowing the full scale stress test. The data rates (writing, accessing and transfer¬ring) are being checked under a variety of loads and operating conditions, as well as the reliability and transfer rates of the links between Tier-0 and Tier-1s. In addition, the capa...

  14. COMPUTING

    CERN Multimedia

    Contributions from I. Fisk

    2012-01-01

    Introduction The start of the 2012 run has been busy for Computing. We have reconstructed, archived, and served a larger sample of new data than in 2011, and we are in the process of producing an even larger new sample of simulations at 8 TeV. The running conditions and system performance are largely what was anticipated in the plan, thanks to the hard work and preparation of many people. Heavy ions Heavy Ions has been actively analysing data and preparing for conferences.  Operations Office Figure 6: Transfers from all sites in the last 90 days For ICHEP and the Upgrade efforts, we needed to produce and process record amounts of MC samples while supporting the very successful data-taking. This was a large burden, especially on the team members. Nevertheless the last three months were very successful and the total output was phenomenal, thanks to our dedicated site admins who keep the sites operational and the computing project members who spend countless hours nursing the...

  15. COMPUTING

    CERN Multimedia

    P. MacBride

    The Computing Software and Analysis Challenge CSA07 has been the main focus of the Computing Project for the past few months. Activities began over the summer with the preparation of the Monte Carlo data sets for the challenge and tests of the new production system at the Tier-0 at CERN. The pre-challenge Monte Carlo production was done in several steps: physics generation, detector simulation, digitization, conversion to RAW format and the samples were run through the High Level Trigger (HLT). The data was then merged into three "Soups": Chowder (ALPGEN), Stew (Filtered Pythia) and Gumbo (Pythia). The challenge officially started when the first Chowder events were reconstructed on the Tier-0 on October 3rd. The data operations teams were very busy during the the challenge period. The MC production teams continued with signal production and processing while the Tier-0 and Tier-1 teams worked on splitting the Soups into Primary Data Sets (PDS), reconstruction and skimming. The storage sys...

  16. Central Computer Science Concepts to Research-Based Teacher Training in Computer Science: An Experimental Study

    Science.gov (United States)

    Zendler, Andreas; Klaudt, Dieter

    2012-01-01

    The significance of computer science for economics and society is undisputed. In particular, computer science is acknowledged to play a key role in schools (e.g., by opening multiple career paths). The provision of effective computer science education in schools is dependent on teachers who are able to properly represent the discipline and whose…

  17. Fluid Dynamics of Competitive Swimming: A Computational Study

    Science.gov (United States)

    Mittal, Rajat; Loebbeck, Alfred; Singh, Hersh; Mark, Russell; Wei, Timothy

    2004-11-01

    The dolphin kick is an important component in competitive swimming and is used extensively by swimmers immediately following the starting dive as well as after turns. In this stroke, the swimmer swims about three feet under the water surface and the stroke is executed by performing an undulating wave-like motion of the body that is quite similar to the anguilliform propulsion mode in fish. Despite the relatively simple kinematics of this stoke, considerable variability in style and performance is observed even among Olympic level swimmers. Motivated by this, a joint experimental-numerical study has been initiated to examine the fluid-dynamics of this stroke. The current presentation will describe the computational portion of this study. The computations employ a sharp interface immersed boundary method (IBM) which allows us to simulate flows with complex moving boudnaries on stationary Cartesian grids. 3D body scans of male and female Olympic swimmers have been obtained and these are used in conjuction with high speed videos to recreate a realistic dolphin kick for the IBM solver. Preliminary results from these computations will be presented.

  18. Study of tip loss corrections using CFD rotor computations

    DEFF Research Database (Denmark)

    Shen, Wen Zhong; Zhu, Wei Jun; Sørensen, Jens Nørkær

    2014-01-01

    computations for wind turbines with sharp tip. Using the technique of determination of angle of attack and the CFD results for a NordTank 500 kW rotor, airfoil data are extracted and a new tip loss function on airfoil data is derived. To validate, BEM computations with the new tip loss function are carried out...... and compared with CFD results for the NordTank 500 kW turbine and the NREL 5 MW turbine. Comparisons show that BEM with the new tip loss function can predict correctly the loading near the blade tip.......Tip loss correction is known to play an important role for engineering prediction of wind turbine performance. There are two different types of tip loss corrections: tip corrections on momentum theory and tip corrections on airfoil data. In this paper, we study the latter using detailed CFD...

  19. Logic as Marr's Computational Level: Four Case Studies.

    Science.gov (United States)

    Baggio, Giosuè; van Lambalgen, Michiel; Hagoort, Peter

    2015-04-01

    We sketch four applications of Marr's levels-of-analysis methodology to the relations between logic and experimental data in the cognitive neuroscience of language and reasoning. The first part of the paper illustrates the explanatory power of computational level theories based on logic. We show that a Bayesian treatment of the suppression task in reasoning with conditionals is ruled out by EEG data, supporting instead an analysis based on defeasible logic. Further, we describe how results from an EEG study on temporal prepositions can be reanalyzed using formal semantics, addressing a potential confound. The second part of the article demonstrates the predictive power of logical theories drawing on EEG data on processing progressive constructions and on behavioral data on conditional reasoning in people with autism. Logical theories can constrain processing hypotheses all the way down to neurophysiology, and conversely neuroscience data can guide the selection of alternative computational level models of cognition. Copyright © 2014 Cognitive Science Society, Inc.

  20. COMPUTING

    CERN Multimedia

    I. Fisk

    2011-01-01

    Introduction The Computing Team successfully completed the storage, initial processing, and distribution for analysis of proton-proton data in 2011. There are still a variety of activities ongoing to support winter conference activities and preparations for 2012. Heavy ions The heavy-ion run for 2011 started in early November and has already demonstrated good machine performance and success of some of the more advanced workflows planned for 2011. Data collection will continue until early December. Facilities and Infrastructure Operations Operational and deployment support for WMAgent and WorkQueue+Request Manager components, routinely used in production by Data Operations, are provided. The GlideInWMS and components installation are now deployed at CERN, which is added to the GlideInWMS factory placed in the US. There has been new operational collaboration between the CERN team and the UCSD GlideIn factory operators, covering each others time zones by monitoring/debugging pilot jobs sent from the facto...

  1. Penerapan Teknologi Cloud Computing Di Universitas Studi Kasus: Fakultas Teknologi Informasi Ukdw

    OpenAIRE

    Kurniawan, Erick

    2015-01-01

    Teknologi Cloud Computing adalah paradigma baru dalam penyampaian layanan komputasi. Cloud Computing memiliki banyak kelebihan dibandingkan dengan sistem konvensional. Artikel ini membahas tentang arsitektur cloud computing secara umum dan beberapa contoh penerapan layanan cloud computing beserta manfaatnya di lingkungan universitas. Studi kasus yang diambil adalah penerapan layanan cloud computing di Fakultas Teknologi Informasi UKDW.

  2. Identification of Enhancers In Human: Advances In Computational Studies

    KAUST Repository

    Kleftogiannis, Dimitrios A.

    2016-03-24

    Roughly ~50% of the human genome, contains noncoding sequences serving as regulatory elements responsible for the diverse gene expression of the cells in the body. One very well studied category of regulatory elements is the category of enhancers. Enhancers increase the transcriptional output in cells through chromatin remodeling or recruitment of complexes of binding proteins. Identification of enhancer using computational techniques is an interesting area of research and up to now several approaches have been proposed. However, the current state-of-the-art methods face limitations since the function of enhancers is clarified, but their mechanism of function is not well understood. This PhD thesis presents a bioinformatics/computer science study that focuses on the problem of identifying enhancers in different human cells using computational techniques. The dissertation is decomposed into four main tasks that we present in different chapters. First, since many of the enhancer’s functions are not well understood, we study the basic biological models by which enhancers trigger transcriptional functions and we survey comprehensively over 30 bioinformatics approaches for identifying enhancers. Next, we elaborate more on the availability of enhancer data as produced by different enhancer identification methods and experimental procedures. In particular, we analyze advantages and disadvantages of existing solutions and we report obstacles that require further consideration. To mitigate these problems we developed the Database of Integrated Human Enhancers (DENdb), a centralized online repository that archives enhancer data from 16 ENCODE cell-lines. The integrated enhancer data are also combined with many other experimental data that can be used to interpret the enhancers content and generate a novel enhancer annotation that complements the existing integrative annotation proposed by the ENCODE consortium. Next, we propose the first deep-learning computational

  3. Toward Computational Spectroscopy Studies for Large Molecular Systems

    Science.gov (United States)

    Biczysko, Malgorzata; Bloino, Julien; Barone, Vincenzo

    2013-06-01

    Integrated computational approaches built on quantum mechanical (QM) methods combined with time-independent schemes to account for nuclear motion effects are applied to the spectroscopic investigation of molecular systems, from large biomolecules to hybrid supra-molecular systems. Within the time-independent approaches, vibrational spectra are computed including anharmonicities through perturbative corrections while UV-vis line-shapes are simulated accounting for the vibrational structure; in both cases, the environmental effects are taken into account by explicit or continuum models. Extension to larger systems relies on reduced dimensionality approaches and effective schemes to select transitions of interest, available for both vibrational and vibronic spectra. Such procedures are exploited to simulate IR and UV-vis spectra leading in all cases to good agreement with experimental observations and allowing to dissect different effects underlying spectral phenomena, finally, paving a feasible route toward the state-of-the-art computational spectroscopy studies, even for relatively large molecular systems [1,2]. 1. V. Barone, A. Baiardi, M. Biczysko, J. Bloino, C. Cappelli, F. Lipparini Phys. Chem. Chem. Phys, 14, 12404, 2012 2. V. Barone, M. Biczysko, J. Bloino, M. Borkowska-Panek, I. Carnimeo, P. Panek, Int. J. Quantum Chem. 112, 2185, 2012

  4. COMPUTING

    CERN Multimedia

    M. Kasemann

    CMS relies on a well functioning, distributed computing infrastructure. The Site Availability Monitoring (SAM) and the Job Robot submission have been very instrumental for site commissioning in order to increase availability of more sites such that they are available to participate in CSA07 and are ready to be used for analysis. The commissioning process has been further developed, including "lessons learned" documentation via the CMS twiki. Recently the visualization, presentation and summarizing of SAM tests for sites has been redesigned, it is now developed by the central ARDA project of WLCG. Work to test the new gLite Workload Management System was performed; a 4 times increase in throughput with respect to LCG Resource Broker is observed. CMS has designed and launched a new-generation traffic load generator called "LoadTest" to commission and to keep exercised all data transfer routes in the CMS PhE-DEx topology. Since mid-February, a transfer volume of about 12 P...

  5. In-situ assessment of biofilm formation in submerged membrane system using optical coherence tomography and computational fluid dynamics

    KAUST Repository

    Fortunato, Luca

    2016-09-09

    This paper introduces a novel approach to study the biofouling development on gravity driven submerged membrane bioreactor (SMBR). The on-line monitoring of biofilm formation on a flat sheet membrane was conducted non-destructively using optical coherence tomography (OCT), allowing the in-situ investigation of the biofilm structure for 43 d. The OCT enabled to obtain a time-lapse of biofilm development on the membrane under the continuous operation. Acquired real-time information on the biofilm structure related to the change in the flux profile confirming the successful monitoring of the dynamic evolution of the biofouling layer. Four different phases were observed linking the permeate flux with the change of biofilm morphology. In particular, a stable flux of 2.1±0.1 L/m2 h was achieved with the achievement of steady biofilm morphology after 30 d of operation. Biofilm descriptors, such as thickness, biofilm area, macro-porosity and roughness (absolute and relative), were calculated for each OCT acquired scans. Interestingly, relative roughness was correlated with the flux decrease. Furthermore, the precise biofilm morphology obtained from the OCT scans was used in computational fluid dynamics (CFD) simulation to better understand the role of biofilm structure on the filtration mechanism. © 2016 Elsevier B.V.

  6. 3D ultrasound computer tomography: update from a clinical study

    Science.gov (United States)

    Hopp, T.; Zapf, M.; Kretzek, E.; Henrich, J.; Tukalo, A.; Gemmeke, H.; Kaiser, C.; Knaudt, J.; Ruiter, N. V.

    2016-04-01

    Ultrasound Computer Tomography (USCT) is a promising new imaging method for breast cancer diagnosis. We developed a 3D USCT system and tested it in a pilot study with encouraging results: 3D USCT was able to depict two carcinomas, which were present in contrast enhanced MRI volumes serving as ground truth. To overcome severe differences in the breast shape, an image registration was applied. We analyzed the correlation between average sound speed in the breast and the breast density estimated from segmented MRIs and found a positive correlation with R=0.70. Based on the results of the pilot study we now carry out a successive clinical study with 200 patients. For this we integrated our reconstruction methods and image post-processing into a comprehensive workflow. It includes a dedicated DICOM viewer for interactive assessment of fused USCT images. A new preview mode now allows intuitive and faster patient positioning. We updated the USCT system to decrease the data acquisition time by approximately factor two and to increase the penetration depth of the breast into the USCT aperture by 1 cm. Furthermore the compute-intensive reflectivity reconstruction was considerably accelerated, now allowing a sub-millimeter volume reconstruction in approximately 16 minutes. The updates made it possible to successfully image first patients in our ongoing clinical study.

  7. Dandy-Walker syndrome studied by computed tomography and pneumoencephalography

    Energy Technology Data Exchange (ETDEWEB)

    Masdeu, J.C. (Hines Veterans Administration Hospital, Maywood, IL); Dobben, G.D.; Azar-Kia, B.

    1983-04-01

    Based on air studies, some authors have disputed the ability of computed tomography (CT) to diagnose posterior fossa cysts. The authors correlated the pneumoencephalographic, CT, and pathological findings in 4 patients with classic Dandy-Walker syndrome. Three cases had been misdiagnosed as retrocerebellar arachnoid cysts because the fourth ventricle was incorrectly considered normal on brow-up or erect air studies, reflecting the inability of such studies to evaluate an agenetic vermis and deficient posterior medullary velum which are characteristic of Dandy-Walker malformation. Careful correlation with autopsy findings showed that even with complete agenesis of the inferior vermis, if the slit between the cerebellar hemispheres is narrow, the fourth ventricle could be misinterpreted as normal on pneumoencephalography and sagittal CT. Radionuclide studies, a small amount of air, or metrizamide may be needed to determine whether the cyst communicates with the subarachnoid space.

  8. Student Perceptions in the Design of a Computer Card Game for Learning Computer Literacy Issues: A Case Study

    Science.gov (United States)

    Kordaki, Maria; Papastergiou, Marina; Psomos, Panagiotis

    2016-01-01

    The aim of this work was twofold. First, an empirical study was designed aimed at investigating the perceptions that entry-level non-computing majors--namely Physical Education and Sport Science (PESS) undergraduate students--hold about basic Computer Literacy (CL) issues. The participants were 90 first-year PESS students, and their perceptions…

  9. Advances in the computational study of language acquisition.

    Science.gov (United States)

    Brent, M R

    1996-01-01

    This paper provides a tutorial introduction to computational studies of how children learn their native languages. Its aim is to make recent advances accessible to the broader research community, and to place them in the context of current theoretical issues. The first section locates computational studies and behavioral studies within a common theoretical framework. The next two sections review two papers that appear in this volume: one on learning the meanings of words and one or learning the sounds of words. The following section highlights an idea which emerges independently in these two papers and which I have dubbed autonomous bootstrapping. Classical bootstrapping hypotheses propose that children begin to get a toc-hold in a particular linguistic domain, such as syntax, by exploiting information from another domain, such as semantics. Autonomous bootstrapping complements the cross-domain acquisition strategies of classical bootstrapping with strategies that apply within a single domain. Autonomous bootstrapping strategies work by representing partial and/or uncertain linguistic knowledge and using it to analyze the input. The next two sections review two more more contributions to this special issue: one on learning word meanings via selectional preferences and one on algorithms for setting grammatical parameters. The final section suggests directions for future research.

  10. Computational Study on Chemical Reaction Mechanisms of Octafluorocarbon Molecules

    Science.gov (United States)

    Choi, Heechol; Song, Mi-Young; Yoon, Jung-Sik; Plasma Fundamental Technology Research Team

    2015-09-01

    Saturated or unsaturated octafluorocarbons(OFCs) have been used extensively in dry etching processes due to their relatively low global warming potential and their high CF2 radical levels in commercial plasma treatments. Many experimental and theoretical studies of these species have been performed for useful information about physical and chemical properties of OFCs. However, direct experimental studies of these chemicals are difficult because of their high reactivity in plasma state and high-level theoretical approaches such as G3(MP2) and CCSD(T)/CBS need huge computational cost. Recently, it has been shown that the ωB97X-D/aVTZ method is strongly recommended as the best practical density functional theory(DFT) for rigorous and extensive studies of OFCs because of its high performance and reliability for van der Waals interactions. All the feasible isomerization and dissociation paths of OFCs were investigated at ωB97X-D/aVTZ and rate constants of their chemical reactions were computed by using variational transition-state theory(VTST) for a deep insight into OFCs' reaction mechanisms. Fates and roles of OFCs and their fragments in plasma phases could be clearly explained based on the obtained reaction mechanisms. This work was supported by R&D Program of ``Plasma Convergence & Fundamental Research'' through NFRI of Korea funded by the Government funds.

  11. Mathematical and computational modeling and simulation fundamentals and case studies

    CERN Document Server

    Moeller, Dietmar P F

    2004-01-01

    Mathematical and Computational Modeling and Simulation - a highly multi-disciplinary field with ubiquitous applications in science and engineering - is one of the key enabling technologies of the 21st century. This book introduces to the use of Mathematical and Computational Modeling and Simulation in order to develop an understanding of the solution characteristics of a broad class of real-world problems. The relevant basic and advanced methodologies are explained in detail, with special emphasis on ill-defined problems. Some 15 simulation systems are presented on the language and the logical level. Moreover, the reader can accumulate experience by studying a wide variety of case studies. The latter are briefly described within the book but their full versions as well as some simulation software demos are available on the Web. The book can be used for University courses of different level as well as for self-study. Advanced sections are marked and can be skipped in a first reading or in undergraduate courses...

  12. Computer Assisted Language Learning. Routledge Studies in Computer Assisted Language Learning

    Science.gov (United States)

    Pennington, Martha

    2011-01-01

    Computer-assisted language learning (CALL) is an approach to language teaching and learning in which computer technology is used as an aid to the presentation, reinforcement and assessment of material to be learned, usually including a substantial interactive element. This books provides an up-to date and comprehensive overview of…

  13. Study on the application of mobile internet cloud computing platform

    Science.gov (United States)

    Gong, Songchun; Fu, Songyin; Chen, Zheng

    2012-04-01

    The innovative development of computer technology promotes the application of the cloud computing platform, which actually is the substitution and exchange of a sort of resource service models and meets the needs of users on the utilization of different resources after changes and adjustments of multiple aspects. "Cloud computing" owns advantages in many aspects which not merely reduce the difficulties to apply the operating system and also make it easy for users to search, acquire and process the resources. In accordance with this point, the author takes the management of digital libraries as the research focus in this paper, and analyzes the key technologies of the mobile internet cloud computing platform in the operation process. The popularization and promotion of computer technology drive people to create the digital library models, and its core idea is to strengthen the optimal management of the library resource information through computers and construct an inquiry and search platform with high performance, allowing the users to access to the necessary information resources at any time. However, the cloud computing is able to promote the computations within the computers to distribute in a large number of distributed computers, and hence implement the connection service of multiple computers. The digital libraries, as a typical representative of the applications of the cloud computing, can be used to carry out an analysis on the key technologies of the cloud computing.

  14. To What Degree Are Undergraduate Students Using Their Personal Computers to Support Their Daily Study Practices?

    Science.gov (United States)

    Sim, KwongNui; Butson, Russell

    2014-01-01

    This scoping study examines the degree to which twenty two undergraduate students used their personal computers to support their academic study. The students were selected based on their responses to a questionnaire aimed at gauging their degree of computer skill. Computer activity data was harvested from the personal computers of eighteen…

  15. Degeneration in dysplastic hips. A computer tomography study

    DEFF Research Database (Denmark)

    Jacobsen, Steffen; Rømer, Lone; Søballe, Kjeld

    2005-01-01

    with moderate to severe dysplasia, and 78 hips with normal morphology in the study cohort, whilst 111 hip joints were borderline dysplastic according to preset definitions. Comparative analyses of anatomy and distribution of degeneration between dysplastic and normal hips in the study cohort were performed......-referred younger patients with hip pain believed to be caused by hip dysplasia constituted the study cohort. The average age was 35.5 years (range, 15-61 years). They were examined by close-cut transverse pelvic and knee computed tomography and antero-posterior radiographs (CT). We identified 197 hips...... ranging from -0.8 to 0.7). Fifty-one hips were subluxated (24R/27L). There were no cases of complete dislocation. The formation of subchondral cysts or osteophytes in dysplastic hips was significantly associated with reduced minimum joint space width (p ranging from 0.005 to 0.02). However, in 67 hips...

  16. Dimensions Of Security Threats In Cloud Computing: A Case Study

    National Research Council Canada - National Science Library

    Mathew Nicho; Mahmoud Hendy

    2013-01-01

      Even though cloud computing, as a model, is not new, organizations are increasingly implementing it because of its large-scale computation and data storage, flexible scalability, relative reliability...

  17. Size effects on insect hovering aerodynamics: an integrated computational study

    Energy Technology Data Exchange (ETDEWEB)

    Liu, H [Graduate School of Engineering, Chiba University, Chiba, 263-8522 (Japan); Aono, H [Department of Aerospace Engineering, University of Michigan, Ann Arbor, MI48109 (United States)], E-mail: hliu@faculty.chiba-u.jp, E-mail: aonoh@umich.edu

    2009-03-01

    Hovering is a miracle of insects that is observed for all sizes of flying insects. Sizing effect in insect hovering on flapping-wing aerodynamics is of interest to both the micro-air-vehicle (MAV) community and also of importance to comparative morphologists. In this study, we present an integrated computational study of such size effects on insect hovering aerodynamics, which is performed using a biology-inspired dynamic flight simulator that integrates the modelling of realistic wing-body morphology, the modelling of flapping-wing and body kinematics and an in-house Navier-Stokes solver. Results of four typical insect hovering flights including a hawkmoth, a honeybee, a fruit fly and a thrips, over a wide range of Reynolds numbers from O(10{sup 4}) to O(10{sup 1}) are presented, which demonstrate the feasibility of the present integrated computational methods in quantitatively modelling and evaluating the unsteady aerodynamics in insect flapping flight. Our results based on realistically modelling of insect hovering therefore offer an integrated understanding of the near-field vortex dynamics, the far-field wake and downwash structures, and their correlation with the force production in terms of sizing and Reynolds number as well as wing kinematics. Our results not only give an integrated interpretation on the similarity and discrepancy of the near- and far-field vortex structures in insect hovering but also demonstrate that our methods can be an effective tool in the MAVs design.

  18. Size effects on insect hovering aerodynamics: an integrated computational study.

    Science.gov (United States)

    Liu, H; Aono, H

    2009-03-01

    Hovering is a miracle of insects that is observed for all sizes of flying insects. Sizing effect in insect hovering on flapping-wing aerodynamics is of interest to both the micro-air-vehicle (MAV) community and also of importance to comparative morphologists. In this study, we present an integrated computational study of such size effects on insect hovering aerodynamics, which is performed using a biology-inspired dynamic flight simulator that integrates the modelling of realistic wing-body morphology, the modelling of flapping-wing and body kinematics and an in-house Navier-Stokes solver. Results of four typical insect hovering flights including a hawkmoth, a honeybee, a fruit fly and a thrips, over a wide range of Reynolds numbers from O(10(4)) to O(10(1)) are presented, which demonstrate the feasibility of the present integrated computational methods in quantitatively modelling and evaluating the unsteady aerodynamics in insect flapping flight. Our results based on realistically modelling of insect hovering therefore offer an integrated understanding of the near-field vortex dynamics, the far-field wake and downwash structures, and their correlation with the force production in terms of sizing and Reynolds number as well as wing kinematics. Our results not only give an integrated interpretation on the similarity and discrepancy of the near- and far-field vortex structures in insect hovering but also demonstrate that our methods can be an effective tool in the MAVs design.

  19. A Study on the Role of Computers in Adult Education

    Science.gov (United States)

    Giannoukos, Georgios; Besas, Georgios; Hioctour, Vasilios; Georgas, Thomas

    2016-01-01

    This paper discusses how knowledge of computers can affect our daily personal life as well as in the workplace in Greece. Our research is concerned with how useful the knowledge of computers is in the everyday life and work of adults and attempts to investigate the interest of adults for learning computer programmes and different subjects via…

  20. A Study of Computer Security Policies for the Indonesian Navy

    Science.gov (United States)

    1993-06-01

    The Indonesian Navy recognized the need for a computer security program over ten years ago. They published their first computer security regulation...terrorist, and disgruntled employees. This thesis demonstrates the need for an updated computer security regulation. To add in meeting that need, the thesis

  1. Hispanic Women Overcoming Deterrents to Computer Science: A Phenomenological Study

    Science.gov (United States)

    Herling, Lourdes

    2011-01-01

    The products of computer science are important to all aspects of society and are tools in the solution of the world's problems. It is, therefore, troubling that the United States faces a shortage in qualified graduates in computer science. The number of women and minorities in computer science is significantly lower than the percentage of the…

  2. Assessing stapes piston position using computed tomography: a cadaveric study.

    Science.gov (United States)

    Hahn, Yoav; Diaz, Rodney; Hartman, Jonathan; Bobinski, Matthew; Brodie, Hilary

    2009-02-01

    Temporal bone computed tomographic (CT) scanning in the postoperative stapedotomy patient is inaccurate in assessing stapes piston position within the vestibule. Poststapedotomy patients that have persistent vertigo may undergo CT scanning to assess the position of the stapes piston within the vestibule to rule out overly deep insertion. Vertigo is a recognized complication of the deep piston, and CT evaluation is often recommended. The accuracy of CT scan in this setting is unestablished. Stapedotomy was performed on 12 cadaver ears, and stainless steel McGee pistons were placed. The cadaver heads were then scanned using a fine-cut temporal bone protocol. Temporal bone dissection was performed with microscopic measurement of the piston depth in the vestibule. These values were compared with depth of intravestibular penetration measured on CT scan by 4 independent measurements. The intravestibular penetration as assessed by computed tomography was consistently greater than the value found on cadaveric anatomic dissection. The radiographic bias was greater when piston location within the vestibule was shallower. The axial CT scan measurement was 0.53 mm greater, on average, than the anatomic measurement. On average, the coronal CT measurement was 0.68 mm greater than the anatomic measurement. The degree of overestimation of penetration, however, was highly inconsistent. Standard temporal bone CT scan is neither an accurate nor precise examination of stapes piston depth within the vestibule. We found that CT measurement consistently overstated intravestibular piston depth. Computed tomography is not a useful study in the evaluation of piston depth for poststapedectomy vertigo and is of limited value in this setting.

  3. The utilization of Computer Mediated Communication for case study collaboration.

    Science.gov (United States)

    Gwozdek, Anne E; Klausner, Christine P; Kerschbaum, Wendy E

    2008-01-01

    Computer Mediated Communication (CMC) can be used as an effective tool for student communication and collaboration. First-year, first-semester dental hygiene students self-selected groups to develop dental hygiene process of care treatment plans, written reports, and oral case presentations based on assigned clinical cases. In consultation with the University of Michigan (UM) Digital Media Commons Collaborative Technologies Teams, CMC options were identified. Two chat rooms were established within the UM's Course Management System (CTools) to provide opportunities for synchronous (simultaneous, real-time) communication. One course blog site and 8 case blog sites were developed to provide students and instructors with electronic asynchronous (nonsimultaneous) communication formats. The purpose of this study was to evaluate the effectiveness of these technologies during group case study projects. CMC has the potential to provide an effective means of collaboration and communication when the technologies align with the purpose of the project and compliment the dynamics of student groups.

  4. Computational studies of polysiloxanes : oxidation potentials and decomposition reactions.

    Energy Technology Data Exchange (ETDEWEB)

    Assary, R. S.; Curtiss, L. A.; Redfern, P. C.; Zhang, Z.; Amine, K. (Center for Nanoscale Materials); ( CSE); ( MSD); (Northwestern Univ.)

    2011-06-23

    Silicon-containing solvents have tremendous potential for application as electrolytes for electrical energy storage devices such as lithium-ion (air) batteries and supercapacitors. Quantum chemical methods were employed to investigate trends in oxidation potentials and decomposition reactions of a series of polysiloxanes. Various electron-donating and -withdrawing substituents can be used to tune the oxidation potential in shorter chain siloxanes but not in longer ones. Decomposition reactions of siloxanes in their oxidized states were investigated and compared against their carbon analogues. These studies suggest that the Si-O group provides added stability for siloxanes over their carbon analogues. Computational studies have also been performed for various disiloxanes and siloxanes with spacer groups to understand their thermochemical stability and oxidation potentials.

  5. Conversion of eugenol to methyleugenol: Computational study and experimental

    Science.gov (United States)

    Kurniawan, Muhammad Arsyik; Matsjeh, Sabirin; Triono, Sugeng

    2017-03-01

    This study provides comprehensive benchmark calculations for the computational study and experimental research on conversion of eugenol to methyleugenol with different pathway of the transition state compounds. First-principle calculation (DFT) were used to generate the structure optimization, energies of species. The calculation parameter are used to predict reactant, product and transition state species as guide to predict the experimental development of chemical characterization method including NMR and IR. The calculation showed significant effect of NaOH in formation of transition state in reaction. Experimentally, the step was nucleophilic substitution reaction of eugenolate ion to dimethylsulfate compound, it was obtained methyleugenol compound with purity of 90.73 %, which analyzed by Infrared and H-NMR spectrometer.

  6. Computational study of anterior communicating artery hemodynamics before aneurysm formation

    Science.gov (United States)

    Castro, Marcelo A.; Putman, Christopher M.; Cebral, Juan R.

    2012-03-01

    It is widely accepted that complexity in the flow pattern at the anterior communicating artery (AComA) is associated with the high rate of aneurysm formation in that location observed in large studies. A previous computational hemodynamic study showed a possible association between high maximum intraaneurysmal wall shear stress (WSS) at the systolic peak with rupture in a cohort of AComA aneurysms. In another study it was observed a connection between location of aneurysm blebs and regions of high WSS in models where blebs were virtually removed. However, others reported associations between low WSS and either rupture or blister formation. The purpose of this work is to study associations between hemodynamic patterns and AComA aneurysm initiation by comparing hemodynamics in the aneurysm and the normal model where the aneurysm was computationally removed. Vascular models of both right and left circulation were independently reconstructed from three-dimensional rotational angiography images using deformable models, and fused using a surface merging algorithm. The geometric models were then used to generate high-quality volumetric finite element grids of tetrahedra with an advancing front technique. For each patient, the second anatomical model was created by digitally removing the aneurysm. It was iteratively achieved by applying a Laplacian smoothing filter and remeshing the surface. Finite element blood flow numerical simulations were performed. It was observed that aneurysms initiated in regions of high and moderate WSS in the counterpart normal models. Adjacent or close to those regions, low WSS portions of the arterial wall were not affected by the disease.

  7. A study of kinematic cues and anticipatory performance in tennis using computational manipulation and computer graphics.

    Science.gov (United States)

    Ida, Hirofumi; Fukuhara, Kazunobu; Kusubori, Seiji; Ishii, Motonobu

    2011-09-01

    Computer graphics of digital human models can be used to display human motions as visual stimuli. This study presents our technique for manipulating human motion with a forward kinematics calculation without violating anatomical constraints. A motion modulation of the upper extremity was conducted by proportionally modulating the anatomical joint angular velocity calculated by motion analysis. The effect of this manipulation was examined in a tennis situation--that is, the receiver's performance of predicting ball direction when viewing a digital model of the server's motion derived by modulating the angular velocities of the forearm or that of the elbow during the forward swing. The results showed that the faster the server's forearm pronated, the more the receiver's anticipation of the ball direction tended to the left side of the serve box. In contrast, the faster the server's elbow extended, the more the receiver's anticipation of the ball direction tended to the right. This suggests that tennis players are sensitive to the motion modulation of their opponent's racket-arm.

  8. How common standards can diminish collective intelligence: a computational study.

    Science.gov (United States)

    Morreau, Michael; Lyon, Aidan

    2016-08-01

    Making good decisions depends on having accurate information - quickly, and in a form in which it can be readily communicated and acted upon. Two features of medical practice can help: deliberation in groups and the use of scores and grades in evaluation. We study the contributions of these features using a multi-agent computer simulation of groups of physicians. One might expect individual differences in members' grading standards to reduce the capacity of the group to discover the facts on which well-informed decisions depend. Observations of the simulated groups suggest on the contrary that this kind of diversity can in fact be conducive to epistemic performance. Sometimes, it is adopting common standards that may be expected to result in poor decisions. © 2016 John Wiley & Sons, Ltd.

  9. Cogeneration technology alternatives study. Volume 6: Computer data

    Science.gov (United States)

    1980-01-01

    The potential technical capabilities of energy conversion systems in the 1985 - 2000 time period were defined with emphasis on systems using coal, coal-derived fuels or alternate fuels. Industrial process data developed for the large energy consuming industries serve as a framework for the cogeneration applications. Ground rules for the study were established and other necessary equipment (balance-of-plant) was defined. This combination of technical information, energy conversion system data ground rules, industrial process information and balance-of-plant characteristics was analyzed to evaluate energy consumption, capital and operating costs and emissions. Data in the form of computer printouts developed for 3000 energy conversion system-industrial process combinations are presented.

  10. Computational Modeling Studies of Peptides and Proteins on Inorganic Surfaces

    Science.gov (United States)

    Farmer, Barry

    2013-03-01

    Biological moieties offer exquisite sensitivity and selectivity in their interactions with small molecules, offering considerable potential in applications as chemical sensors. To detect binding events between the peptide and the intended molecule, a transduction mechanism is needed. This often involves an association of the peptide with an inorganic surface, such as a metal nanoparticle, a carbon nanotube, or graphene. Understanding the nature of the association of the peptide with the surface and its effect on the conformational (and thus, binding) properties of the peptide are key to optimizing the sensing mechanism. We utilized computational approaches ranging from ab initio to molecular dynamics to bond-fluctuation Monte Carlo methods to study the adsorption of peptides and proteins on inorganic surfaces to develop an understanding of the role that composition and substrate character plays in the adsorption process, and in turn, the effects on the binding events with the molecules of interest.

  11. Anethole-Water a Combined Jet, Matrix, and Computational Study

    Science.gov (United States)

    Newby, Josh; Nesheiwat, Jackleen

    2016-06-01

    Anethole [(E)-1-methoxy-4-(1-propenyl)benzene] is a natural product molecule that is commonly recognized as the flavor component of anise, fennel, and licorice. Previously, we reported the jet-cooled, laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) spectra of anethole. In this work, several weak bands were observed and were tentatively assigned as van der Waals clusters of anethole with water. We have since confirmed this assignment and have conducted a more detailed study to determine the geometry of these clusters. Results from LIF, SVLF, and matrix isolation FTIR spectroscopy, as well as computational results will be presented in this talk. J. Phys. Chem. A, 2013, 117 (48), 12831-12841 Newly built system at Hobart and William Smith Colleges

  12. Computational study of performance characteristics for truncated conical aerospike nozzles

    Science.gov (United States)

    Nair, Prasanth P.; Suryan, Abhilash; Kim, Heuy Dong

    2017-12-01

    Aerospike nozzles are advanced rocket nozzles that can maintain its aerodynamic efficiency over a wide range of altitudes. It belongs to class of altitude compensating nozzles. A vehicle with an aerospike nozzle uses less fuel at low altitudes due to its altitude adaptability, where most missions have the greatest need for thrust. Aerospike nozzles are better suited to Single Stage to Orbit (SSTO) missions compared to conventional nozzles. In the current study, the flow through 20% and 40% aerospike nozzle is analyzed in detail using computational fluid dynamics technique. Steady state analysis with implicit formulation is carried out. Reynolds averaged Navier-Stokes equations are solved with the Spalart-Allmaras turbulence model. The results are compared with experimental results from previous work. The transition from open wake to closed wake happens in lower Nozzle Pressure Ratio for 20% as compared to 40% aerospike nozzle.

  13. Computational Interpersonal Communication: Communication Studies and Spoken Dialogue Systems

    Directory of Open Access Journals (Sweden)

    David J. Gunkel

    2016-09-01

    Full Text Available With the advent of spoken dialogue systems (SDS, communication can no longer be considered a human-to-human transaction. It now involves machines. These mechanisms are not just a medium through which human messages pass, but now occupy the position of the other in social interactions. But the development of robust and efficient conversational agents is not just an engineering challenge. It also depends on research in human conversational behavior. It is the thesis of this paper that communication studies is best situated to respond to this need. The paper argues: 1 that research in communication can supply the information necessary to respond to and resolve many of the open problems in SDS engineering, and 2 that the development of SDS applications can provide the discipline of communication with unique opportunities to test extant theory and verify experimental results. We call this new area of interdisciplinary collaboration “computational interpersonal communication” (CIC

  14. Patterned corneal collagen crosslinking for astigmatism: computational modeling study.

    Science.gov (United States)

    Seven, Ibrahim; Sinha Roy, Abhijit; Dupps, William J

    2014-06-01

    To test the hypothesis that spatially selective corneal stromal stiffening can alter corneal astigmatism and assess the effects of treatment orientation, pattern, and material model complexity in computational models using patient-specific geometries. Cornea and Refractive Surgery Service, Academic Eye Institute, Cleveland, Ohio, USA. Computational modeling study. Three-dimensional corneal geometries from 10 patients with corneal astigmatism were exported from a clinical tomography system (Pentacam). Corneoscleral finite element models of each eye were generated. Four candidate treatment patterns were simulated, and the effects of treatment orientation and magnitude of stiffening on anterior curvature and aberrations were studied. The effect of material model complexity on simulated outcomes was also assessed. Pretreatment anterior corneal astigmatism ranged from 1.22 to 3.92 diopters (D) in a series that included regular and irregular astigmatic patterns. All simulated treatment patterns oriented on the flat axis resulted in mean reductions in corneal astigmatism and depended on the pattern geometry. The linear bow-tie pattern produced a greater mean reduction in astigmatism (1.08 D ± 0.13 [SD]; range 0.74 to 1.23 D) than other patterns tested under an assumed 2-times increase in corneal stiffness, and it had a nonlinear relationship to the degree of stiffening. The mean astigmatic effect did not change significantly with a fiber- or depth-dependent model, but it did affect the coupling ratio. In silico simulations based on patient-specific geometries suggest that clinically significant reductions in astigmatism are possible with patterned collagen crosslinking. Effect magnitude was dependent on patient-specific geometry, effective stiffening pattern, and treatment orientation. Proprietary or commercial disclosures are listed after the references. Copyright © 2014 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

  15. X-ray luminescence computed tomography: a sensitivity study

    Science.gov (United States)

    Lun, Michael C.; Zhang, Wei; Li, Changqing

    2017-03-01

    X-ray luminescence computed tomography (XLCT) is a hybrid molecular imaging modality that uses high energy x-ray photons to excite nanophosphors (e.g. Europium doped Gadolinium Oxysulfide - GOS: Eu3+) emitting optical photons to be measured by a sensitive detector for image reconstruction. XLCT has potentials to combine both the merits of x-ray imaging (high spatial resolution) and optical imaging (high sensitivity), which makes XLCT an attractive imaging modality to image nanophosphor targets deeply embedded in turbid media. In this study, we have evaluated the sensitivity of XLCT with phantom experiments by scanning targets of different phosphor concentrations at different depths. Cylindrical phantoms embedded with a cylindrical target with varying concentrations of GOS: Eu3+ (27.6 mM, 2.76 mM, 276 μM, and 27.6 μM) were scanned inside our lab made XLCT imaging system for varying scanning depths (6, 11, 16, and 21 mm). We found that XLCT is capable of imaging targets of very low concentrations (27.6 μM or 0.01 mg/mL) at significant depths, such as 21 mm. Our results demonstrate that there is also little variation in the reconstructed target size for different imaging depths for XLCT. We have for the first time, compared the sensitivity of XLCT with that of traditional computed tomography (CT) for phosphor targets. We found that XLCT's use of x-ray induced photons provides much higher measurement sensitivity and contrast compared to CT which provides image contrast solely based on x-ray attenuation.

  16. A bioinformatic and computational study of myosin phosphatase subunit diversity.

    Science.gov (United States)

    Dippold, Rachael P; Fisher, Steven A

    2014-08-01

    Variability in myosin phosphatase (MP) subunits may provide specificity in signaling pathways that regulate muscle tone. We utilized public databases and computational algorithms to investigate the phylogenetic diversity of MP regulatory (PPP1R12A-C) and inhibitory (PPP1R14A-D) subunits. The comparison of exonic coding sequences and expression data confirmed or refuted the existence of isoforms and their tissue-specific expression in different model organisms. The comparison of intronic and exonic sequences identified potential expressional regulatory elements. As examples, smooth muscle MP regulatory subunit (PPP1R12A) is highly conserved through evolution. Its alternative exon E24 is present in fish through mammals with two invariant features: 1) a reading frame shift generating a premature termination codon and 2) a hexanucleotide sequence adjacent to the 3' splice site hypothesized to be a novel suppressor of exon splicing. A characteristic of the striated muscle MP regulatory subunit (PPP1R12B) locus is numerous and phylogenetically variable transcriptional start sites. In fish this locus only codes for the small (M21) subunit, suggesting the primordial function of this gene. Inhibitory subunits show little intragenic variability; their diversity is thought to have arisen by expansion and tissue-specific expression of different gene family members. We demonstrate differences in the regulatory landscape between smooth muscle enriched (PPP1R14A) and more ubiquitously expressed (PPP1R14B) family members and identify deeply conserved intronic sequence and predicted transcriptional cis-regulatory elements. This bioinformatic and computational study has uncovered a number of attributes of MP subunits that supports selection of ideal model organisms and testing of hypotheses regarding their physiological significance and regulated expression. Copyright © 2014 the American Physiological Society.

  17. Integrated databases and computer systems for studying eukaryotic gene expression.

    Science.gov (United States)

    Kolchanov, N A; Ponomarenko, M P; Frolov, A S; Ananko, E A; Kolpakov, F A; Ignatieva, E V; Podkolodnaya, O A; Goryachkovskaya, T N; Stepanenko, I L; Merkulova, T I; Babenko, V V; Ponomarenko, Y V; Kochetov, A V; Podkolodny, N L; Vorobiev, D V; Lavryushev, S V; Grigorovich, D A; Kondrakhin, Y V; Milanesi, L; Wingender, E; Solovyev, V; Overton, G C

    1999-01-01

    The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences. The GeneExpress system developed includes the following major informational and software modules: (1) Transcription Regulation (TRRD) module, which contains the databases on transcription regulatory regions of eukaryotic genes and TRRD Viewer for data visualization; (2) Site Activity Prediction (ACTIVITY), the module for analysis of functional site activity and its prediction; (3) Site Recognition module, which comprises (a) B-DNA-VIDEO system for detecting the conformational and physicochemical properties of DNA sites significant for their recognition, (b) Consensus and Weight Matrices (ConsFrec) and (c) Transcription Factor Binding Sites Recognition (TFBSR) systems for detecting conservative contextual regions of functional sites and their recognition; (4) Gene Networks (GeneNet), which contains an object-oriented database accumulating the data on gene networks and signal transduction pathways, and the Java-based Viewer for exploration and visualization of the GeneNet information; (5) mRNA Translation (Leader mRNA), designed to analyze structural and contextual properties of mRNA 5'-untranslated regions (5'-UTRs) and predict their translation efficiency; (6) other program modules designed to study the structure-function organization of regulatory genomic sequences and regulatory proteins. GeneExpress is available at http://wwwmgs.bionet.nsc. ru/systems/GeneExpress/ and the links to the mirror site(s) can be found at http://wwwmgs.bionet.nsc.ru/mgs/links/mirrors.html+ ++.

  18. Computational fluid dynamics (CFD) studies of a miniaturized dissolution system.

    Science.gov (United States)

    Frenning, G; Ahnfelt, E; Sjögren, E; Lennernäs, H

    2017-04-15

    Dissolution testing is an important tool that has applications ranging from fundamental studies of drug-release mechanisms to quality control of the final product. The rate of release of the drug from the delivery system is known to be affected by hydrodynamics. In this study we used computational fluid dynamics to simulate and investigate the hydrodynamics in a novel miniaturized dissolution method for parenteral formulations. The dissolution method is based on a rotating disc system and uses a rotating sample reservoir which is separated from the remaining dissolution medium by a nylon screen. Sample reservoirs of two sizes were investigated (SR6 and SR8) and the hydrodynamic studies were performed at rotation rates of 100, 200 and 400rpm. The overall fluid flow was similar for all investigated cases, with a lateral upward spiraling motion and central downward motion in the form of a vortex to and through the screen. The simulations indicated that the exchange of dissolution medium between the sample reservoir and the remaining release medium was rapid for typical screens, for which almost complete mixing would be expected to occur within less than one minute at 400rpm. The local hydrodynamic conditions in the sample reservoirs depended on their size; SR8 appeared to be relatively more affected than SR6 by the resistance to liquid flow resulting from the screen. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Computational study of precision nitrogen doping on graphene nanoribbon edges

    Science.gov (United States)

    Dong, Yuan; Gahl, Martha T.; Zhang, Chi; Lin, Jian

    2017-12-01

    Nitrogen doping in graphene is important for applications spanning from electronics to metal-free electrocatalysts. Despite much experimental study, limited theoretic work has been done in understanding the mechanism of the doping process, especially from a precision perspective. Herein, we present a computational study on precision nitrogen doping on edges of graphene nanoribbons (GNRs) by combining molecular dynamics (MD) simulation at a time scale of 40 ns and density function theory (DFT) calculation. In the MD study both ammonia and acetonitrile were used as nitrogen sources. MD results revealed that the ammonia produces almost all amine-type dopants, while the acetonitrile produces a considerable amount of pyrrolic and pyridinic nitrogen dopants which are beneficial to electronics and electrocatalysts. Results also show that the concentration of pyrrolic and pyridinic dopants can be precisely controlled by the edge geometries of the GNRs. Furthermore, DFT calculation illustrated the reaction mechanism in these different types of the GNRs when using acetonitrile as the nitrogen source. The calculated energies in different reaction stages indicate the stability of dopants on various GNRs, agreeing well with the MD results. The disclosed mechanism of controllable nitrogen doping on the edges of the GNRs would provide guidance to experimental realization, paving new routes to widespread applications.

  20. Interactive design computation : A case study on quantum design paradigm

    NARCIS (Netherlands)

    Feng, H.

    2013-01-01

    The ever-increasing complexity of design processes fosters novel design computation models to be employed in architectural research and design in order to facilitate accurate data processing and refined decision making. These computation models have enabled designers to work with complex geometry

  1. Secure Cloud Computing Implementation Study For Singapore Military Operations

    Science.gov (United States)

    2016-09-01

    Computing in Healthcare. Adapted from [13]. Benefits Cloud Computing  Clinical Research  Electronic Medical Records  Collaboration Solutions...medium to send orders to tactical action units, the cloud should also contain a feature to verify that the action units have received and understood the...NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. SECURE CLOUD

  2. Exploring Computer Science: A Case Study of School Reform

    Science.gov (United States)

    Goode, Joanna; Margolis, Jane

    2011-01-01

    This article will detail efforts to broaden participation in computing in urban schools through a comprehensive reform effort of curricular development, teacher professional development, and policy changes. Beginning with an account of the curricular development of "Exploring Computer Science", we will describe the inquiry-based research…

  3. Case Studies of Liberal Arts Computer Science Programs

    Science.gov (United States)

    Baldwin, D.; Brady, A.; Danyluk, A.; Adams, J.; Lawrence, A.

    2010-01-01

    Many undergraduate liberal arts institutions offer computer science majors. This article illustrates how quality computer science programs can be realized in a wide variety of liberal arts settings by describing and contrasting the actual programs at five liberal arts colleges: Williams College, Kalamazoo College, the State University of New York…

  4. Promoting High-Performance Computing and Communications. A CBO Study.

    Science.gov (United States)

    Webre, Philip

    In 1991 the Federal Government initiated the multiagency High Performance Computing and Communications program (HPCC) to further the development of U.S. supercomputer technology and high-speed computer network technology. This overview by the Congressional Budget Office (CBO) concentrates on obstacles that might prevent the growth of the…

  5. A study of ergonomic factors leading to computer vision syndrome ...

    African Journals Online (AJOL)

    An observation and measurement of the participant's computer workstation was then made in order to identify the risk factors leading to CVS. Data were analysed with descriptive statistics. 72% of participants reported taking breaks after 2 hours while 28% reported taking breaks after every hour of computer use. Eye strain ...

  6. Computer model for economic study of unbleached kraft paperboard production

    Science.gov (United States)

    Peter J. Ince

    1984-01-01

    Unbleached kraft paperboard is produced from wood fiber in an industrial papermaking process. A highly specific and detailed model of the process is presented. The model is also presented as a working computer program. A user of the computer program will provide data on physical parameters of the process and on prices of material inputs and outputs. The program is then...

  7. Virtual Computing Laboratories: A Case Study with Comparisons to Physical Computing Laboratories

    Science.gov (United States)

    Burd, Stephen D.; Seazzu, Alessandro F.; Conway, Christopher

    2009-01-01

    Current technology enables schools to provide remote or virtual computing labs that can be implemented in multiple ways ranging from remote access to banks of dedicated workstations to sophisticated access to large-scale servers hosting virtualized workstations. This paper reports on the implementation of a specific lab using remote access to…

  8. Computer Science Lesson Study: Building Computing Skills among Elementary School Teachers

    Science.gov (United States)

    Newman, Thomas R.

    2017-01-01

    The lack of diversity in the technology workforce in the United States has proven to be a stubborn problem, resisting even the most well-funded reform efforts. With the absence of computer science education in the mainstream K-12 curriculum, only a narrow band of students in public schools go on to careers in technology. The problem persists…

  9. A computational study of liposome logic: towards cellular computing from the bottom up.

    Science.gov (United States)

    Smaldon, James; Romero-Campero, Francisco J; Fernández Trillo, Francisco; Gheorghe, Marian; Alexander, Cameron; Krasnogor, Natalio

    2010-09-01

    In this paper we propose a new bottom-up approach to cellular computing, in which computational chemical processes are encapsulated within liposomes. This "liposome logic" approach (also called vesicle computing) makes use of supra-molecular chemistry constructs, e.g. protocells, chells, etc. as minimal cellular platforms to which logical functionality can be added. Modeling and simulations feature prominently in "top-down" synthetic biology, particularly in the specification, design and implementation of logic circuits through bacterial genome reengineering. The second contribution in this paper is the demonstration of a novel set of tools for the specification, modelling and analysis of "bottom-up" liposome logic. In particular, simulation and modelling techniques are used to analyse some example liposome logic designs, ranging from relatively simple NOT gates and NAND gates to SR-Latches, D Flip-Flops all the way to 3 bit ripple counters. The approach we propose consists of specifying, by means of P systems, gene regulatory network-like systems operating inside proto-membranes. This P systems specification can be automatically translated and executed through a multiscaled pipeline composed of dissipative particle dynamics (DPD) simulator and Gillespie's stochastic simulation algorithm (SSA). Finally, model selection and analysis can be performed through a model checking phase. This is the first paper we are aware of that brings to bear formal specifications, DPD, SSA and model checking to the problem of modeling target computational functionality in protocells. Potential chemical routes for the laboratory implementation of these simulations are also discussed thus for the first time suggesting a potentially realistic physiochemical implementation for membrane computing from the bottom-up.

  10. Brain-computer interfacing under distraction: an evaluation study

    Science.gov (United States)

    Brandl, Stephanie; Frølich, Laura; Höhne, Johannes; Müller, Klaus-Robert; Samek, Wojciech

    2016-10-01

    Objective. While motor-imagery based brain-computer interfaces (BCIs) have been studied over many years by now, most of these studies have taken place in controlled lab settings. Bringing BCI technology into everyday life is still one of the main challenges in this field of research. Approach. This paper systematically investigates BCI performance under 6 types of distractions that mimic out-of-lab environments. Main results. We report results of 16 participants and show that the performance of the standard common spatial patterns (CSP) + regularized linear discriminant analysis classification pipeline drops significantly in this ‘simulated’ out-of-lab setting. We then investigate three methods for improving the performance: (1) artifact removal, (2) ensemble classification, and (3) a 2-step classification approach. While artifact removal does not enhance the BCI performance significantly, both ensemble classification and the 2-step classification combined with CSP significantly improve the performance compared to the standard procedure. Significance. Systematically analyzing out-of-lab scenarios is crucial when bringing BCI into everyday life. Algorithms must be adapted to overcome nonstationary environments in order to tackle real-world challenges.

  11. Focal spinal arachnoiditis increases subarachnoid space pressure: a computational study.

    Science.gov (United States)

    Bilston, L E; Fletcher, D F; Stoodley, M A

    2006-07-01

    Enlarging fluid filled cystic cavitations form within the spinal cord in up to 28% of spinal cord injured patients. These post-traumatic syrinxes can cause neurological deterioration and current treatment results are unsatisfactory. Localized scar tissue (arachnoiditis) within the subarachnoid space at the level of injury has been suggested to be involved in the pathogenesis of syrinx formation. This study tests the hypothesis that pressure pulses in the subarachnoid space are accentuated adjacent to regions of arachnoiditis, which may drive fluid into the spinal cord and contribute to syrinx formation. An axisymmetric, cylindrical computational fluid dynamics model was developed to represent the subarachnoid space under normal physiological conditions and in the presence of arachnoiditis. Cerebrospinal fluid flow into the model was estimated from magnetic resonance imaging flow studies. Arachnoiditis was modelled as a porous obstruction in the subarachnoid space. Peak fluid pressures were higher above the obstruction than in the absence of obstruction. The peak pressures were strongly dependent on the permeability of the obstruction. Elevations in subarachnoid space pressures due to arachnoiditis may facilitate fluid flow into the spinal cord, enhancing syrinx formation. This suggests that it may be worthwhile to investigate strategies that inhibit arachnoiditis or minimize systolic pressure peaks for treating or preventing syringomyelia.

  12. A study of the effectiveness of an interactive computer classroom.

    Science.gov (United States)

    Ayoub, J L; Vanderboom, C; Knight, M; Walsh, K; Briggs, R; Grekin, K

    1998-01-01

    This study examined the use of an interactive computer classroom (ICC) compared with a traditional lecture/discussion format (LD) for a nursing management course taught from fall semester 1994 through fall semester 1996. The ICC was structured around a group systems support software, a tool previously used in business settings for group decision-making activities. Structured learning activities allowed all students to participate simultaneously and anonymously. Data were collected during the second and final semesters of the study. The outcomes included academic performance, measured by course exams; class participation, measured by direct observation; and attendance records. The control group was a concurrent management course taught with the same objectives and evaluated by identical examinations. The examination scores and the frequency of class participation of the ICC group were significantly higher than those measures of the LD group. There was no significant difference in class attendance. Evaluation forms with open-ended questions were completed by the ICC students and revealed that the students believed that the process enhanced application and understanding. The negative aspects of the ICC experience were the need for increased preparation time for faculty and the students' lack of tolerance when technical difficulties caused delays.

  13. Studying allosteric regulation in metal sensor proteins using computational methods.

    Science.gov (United States)

    Chakravorty, Dhruva K; Merz, Kenneth M

    2014-01-01

    In this chapter, we describe advances made in understanding the mechanism of allosteric regulation of DNA operator binding in the ArsR/SmtB family of metal-sensing proteins using computational methods. The paradigm, zinc-sensing transcriptional repressor Staphylococcus aureus CzrA represents an excellent model system to understand how metal sensor proteins maintain cellular metal homeostasis. Here, we discuss studies that helped to characterize a metal ion-mediated hydrogen-bonding pathway (HBP) that plays a dominant role in the allosteric mechanism of DNA operator binding in these proteins. The chapter discusses computational methods used to provide a molecular basis for the large conformational motions and allosteric coupling free energy (~6kcal/mol) associated with Zn(II) binding in CzrA. We present an accurate and convenient means by which to include metal ions in the nuclear magnetic resonance (NMR) structure determination process using molecular dynamics (MD) constrained by NMR-derived data. The method provides a realistic and physically viable description of the metal-binding site(s) and has potentially broad applicability in the structure determination of metal ion-bound proteins, protein folding, and metal template protein-design studies. Finally, our simulations provide strong support for a proposed HBP that physically connects the metal-binding residue, His97, to the DNA-binding interface through the αR helix that is present only in the Zn(II)-bound state. We find the interprotomer hydrogen bond interaction to be significantly stronger (~8kcal/mol) at functional allosteric metal-binding sites compared to the apo proteins. This interaction works to overcome the considerable disorder at these hydrogen-bonding sites in apo protein and functions as a "switch" to lock in a weak DNA-binding conformation once metal is bound. This interaction is found to be considerably weaker in nonresponsive metal-binding sites. These findings suggest a conserved functional

  14. Helicopter mission optimization study. [portable computer technology for flight optimization

    Science.gov (United States)

    Olson, J. R.

    1978-01-01

    The feasibility of using low-cost, portable computer technology to help a helicopter pilot optimize flight parameters to minimize fuel consumption and takeoff and landing noise was demonstrated. Eight separate computer programs were developed for use in the helicopter cockpit using a hand-held computer. The programs provide the helicopter pilot with the ability to calculate power required, minimum fuel consumption for both range and endurance, maximum speed and a minimum noise profile for both takeoff and landing. Each program is defined by a maximum of two magnetic cards. The helicopter pilot is required to key in the proper input parameter such as gross weight, outside air temperature or pressure altitude.

  15. Usability Studies in Virtual and Traditional Computer Aided Design Environments for Fault Identification

    Science.gov (United States)

    2017-08-08

    Usability Studies In Virtual And Traditional Computer Aided Design Environments For Fault Identification Dr. Syed Adeel Ahmed, Xavier University...the differences in interaction when compared with traditional human computer interfaces. This paper provides analysis via usability study methods...communicate their subjective opinions. Keywords: Usability Analysis; CAVETM (Cave Automatic Virtual Environments); Human Computer Interface (HCI

  16. Usability Studies In Virtual And Traditional Computer Aided Design Environments For Spatial Awareness

    Science.gov (United States)

    2017-08-08

    differences in interaction when compared with traditional human computer interfaces . This paper provides analysis via usability study methods...communicate their subjective opinions. Keywords: Usability Analysis; CAVETM (Cave Automatic Virtual Environments); Human Computer Interface (HCI...Usability Studies In Virtual And Traditional Computer Aided Design Environments For Spatial Awareness Dr. Syed Adeel Ahmed, Xavier University of

  17. Ethics and Computer-Assisted Assessment: Three Case Studies.

    Science.gov (United States)

    Jacob, Susan; Brantley, John C.

    1989-01-01

    Three ethical-legal case incidents involving computer-assisted psychodiagnostic assessment in the schools are presented. Each case is analyzed in terms of applicable laws, ethical codes, and standards for professional practice. (Author)

  18. Center for Advanced Energy Studies: Computer Assisted Virtual Environment (CAVE)

    Data.gov (United States)

    Federal Laboratory Consortium — The laboratory contains a four-walled 3D computer assisted virtual environment - or CAVE TM — that allows scientists and engineers to literally walk into their data...

  19. Computed tomographic study of the complication of head injury

    Energy Technology Data Exchange (ETDEWEB)

    Kojima, T.; Waga, S. (Mie Univ., Tsu (Japan). School of Medicine)

    1982-08-01

    Computed tomography (CT) is quite effective in the diagnosis of traumatic intracranial hemorrhage and cerebral contusion. Two hundred and nine consecutive patients with head injury were admitted to the hospital and studied by CT in the year from 1977 to 1980. Fourty-seven of 209 patients had the complications of head injury, including 6 patients with carotidcavernous fistula (CCF), 6 with traumatic aneurysm, 10 with pneumocephalus, 4 with intracranial foreign body, 15 with optic nerve injury, and 14 with other cranial nerve palsy. Five patients with CCF had abnormal finding on CT. Two traumatic aneurysms of the superficial temporal artery were visualized on CT after injection of contrast material, but all traumatic aneurysms of the carotid siphon were not seen on CT. CT in all 10 patients with pneumocephalus and in all 4 patients with intracranial foreign body was of diagnostic value: On CT in two patients even small air bubbles were seen in details. In the CT examination of 29 patients who presented with cranial nerve injury, we could not find out any abnormality on CT. We emphasize that CT is much less effective in the diagnosis of vascular complication of head injury and traumatic cranial nerve injury.

  20. Computational Study on a PTAS for Planar Dominating Set Problem

    Directory of Open Access Journals (Sweden)

    Qian-Ping Gu

    2013-01-01

    Full Text Available The dominating set problem is a core NP-hard problem in combinatorial optimization and graph theory, and has many important applications. Baker [JACM 41,1994] introduces a k-outer planar graph decomposition-based framework for designing polynomial time approximation scheme (PTAS for a class of NP-hard problems in planar graphs. It is mentioned that the framework can be applied to obtain an O(2ckn time, c is a constant, (1+1/k-approximation algorithm for the planar dominating set problem. We show that the approximation ratio achieved by the mentioned application of the framework is not bounded by any constant for the planar dominating set problem. We modify the application of the framework to give a PTAS for the planar dominating set problem. With k-outer planar graph decompositions, the modified PTAS has an approximation ratio (1 + 2/k. Using 2k-outer planar graph decompositions, the modified PTAS achieves the approximation ratio (1+1/k in O(22ckn time. We report a computational study on the modified PTAS. Our results show that the modified PTAS is practical.

  1. Accuracy study of new computer-assisted orthopedic surgery software

    Energy Technology Data Exchange (ETDEWEB)

    Sidon, Eli [Department of Orthopaedic Surgery, Beilinson-Rabin Medical Center, Petach Tikva (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel); Steinberg, Ely L., E-mail: steinberge@tasmc.health.gov.il [Department of Orthopaedic Surgery, Tel-Aviv Medical Center, Tel Aviv (Israel); Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv (Israel)

    2012-12-15

    Purpose: The new computerized system is based on image analysis and designed to aid in orthopedic surgeries by virtual trajectory of the guide wire, intra-operative planning and various measurements. Validation of the accuracy and safety of any computer-aided surgery system is essential before implementing it clinically. We examined the accuracy of guide-wire length and angle measurements and fusion of multiple adjacent images (panoramic view image, PVI{sup ®}) of the new software. Methods: This is a 2-part study. Part I: twenty guide wires were drilled to various depths in a synthetic femur model and the results obtained by the software measurements were compared with manual measurements by a caliper and a depth gauge. Part II: a sawbone femur shaft was osteotomized and various inclinations of >10° to the varus or valgus angles were tested. The manually obtained measurements of angles and lengths were compared to the new computerized system software PVI. Results: There was a significant positive linear correlation between all groups of the computerized length and the control measurements (r > 0.983, p < 0.01). There was no significant difference among different distances, angles or positions from the image intensifier. There was a significant positive linear correlation between the angle and length measurement on the PVI and the control measurement (r > 0.993, p < 0.01). Conclusions: The new computerized software has high reliability in performing measurements of length using an aiming, positioning and referring device intra-operatively.

  2. Tautomerism of 4-hydrazinoquinazolines: vibrational spectra and computational study

    Directory of Open Access Journals (Sweden)

    Tetiana Yu. Sergeieva

    2014-03-01

    Full Text Available The tautomerism of 4-hydrazinoquinazoline and its derivatives was investigated. Geometry and thermodynamic parameters were computed theoretically using Gaussian 03 software. All calculations were performed at the MP2 level of theory using the standard 6-31G(d basis. Energetics and relative stabilities of tautomers were compared and analyzed in a gas phase. The effect of solvents (1,4-dioxane, acetic acid, ethanol and water on the tautomeric equlibria was evaluated using PCM. It was determined that solvents induced slight changes in the relative stability. In all cases 4-hydrazinoquinazoline exists predominantly as the amino form. The variation of dipole moments was studied. The anharmonic vibrational wavenumbers for unsubstituted 4-hydrazinoquinazoline were calculated at MP2/6-31G(d level and compared with experimental data. The modes of IR spectra were assigned. The calculated herein wavenumbers and intensities of amino form are in good agreement with those observed experimentally.      

  3. Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study.

    Science.gov (United States)

    Yao, Yuan; Zhang, Hui; Li, Ze-Sheng

    2013-11-01

    Chalcone isomerase (CHI) catalyzes the intramolecular cyclization of chalcones into flavonoids. The activity of CHI is essential for the biosynthesis of flavonoids precursors of floral pigments and phenylpropanoid plant defense compounds. In the present study, we explored the detailed binding structures and binding free energies for two different active site conformations of CHI with s-cis/s-trans conformers of three chalcone compounds by performing molecular dynamics (MD) simulations and binding free energy calculations. The computational results indicate that s-cis/s-trans conformers of chalcone compounds are orientated in the similar binding position in the active site of CHI and stabilized by the different first hydrogen bond network and the same second hydrogen bond network. The first hydrogen bond network results in much lower binding affinity of s-trans conformer of chalcone compound with CHI than that of s-cis conformer. The conformational change of the active site residue T48 from indirectly interacting with the substrate via the second hydrogen bond network to directly forming the hydrogen bond with the substrates cannot affect the binding mode of both conformers of chalcone compounds, but remarkably improves the binding affinity. These results show that CHI has a strong stereoselectivity. The calculated binding free energies for three chalcone compounds with CHI are consistent with the experimental activity data. In addition, several valuable insights are suggested for future rational design and discovery of high-efficiency mutants of CHI.

  4. A computational study on outliers in world music

    Science.gov (United States)

    Benetos, Emmanouil; Dixon, Simon

    2017-01-01

    The comparative analysis of world music cultures has been the focus of several ethnomusicological studies in the last century. With the advances of Music Information Retrieval and the increased accessibility of sound archives, large-scale analysis of world music with computational tools is today feasible. We investigate music similarity in a corpus of 8200 recordings of folk and traditional music from 137 countries around the world. In particular, we aim to identify music recordings that are most distinct compared to the rest of our corpus. We refer to these recordings as ‘outliers’. We use signal processing tools to extract music information from audio recordings, data mining to quantify similarity and detect outliers, and spatial statistics to account for geographical correlation. Our findings suggest that Botswana is the country with the most distinct recordings in the corpus and China is the country with the most distinct recordings when considering spatial correlation. Our analysis includes a comparison of musical attributes and styles that contribute to the ‘uniqueness’ of the music of each country. PMID:29253027

  5. Computational study of putative functional variants in human kisspeptin

    Directory of Open Access Journals (Sweden)

    Esmaeil Samadian

    2017-12-01

    Full Text Available Non-synonymous single nucleotide polymorphisms (nsSNPs are a type of genetic mutations that result in amino acid substitution of the encoded proteins that may potentially affect its function and phenotype. An In Silico assay has been carried out by using bioinformatics prediction tools to identify nsSNPs which are responsible for important disorders in human kisspeptin (KISS1 gene. In this study, for the first time, KISS1 amino acid changes were discovered by tBlastn for EST database. A list of nsSNPs in human KISS1 gene from dbSNP, dbEST and UniProt databases were prepared. Computational analysis was performed using SIFT (Sorting Intolerant From Tolerant and PolyPhen (Polymorphism Phenotyping programs. Of the total 92 nsSNPs, 20 were found to be damaged by both servers. Six nsSNPs (P97L, G122R, W114C, R92C, R120H and N115K are predicted with the highest damaging scores (SIFT = 0, PolyPhen = 1. These intolerant changes may suggest their functional significance in critical regions which may affect the function and stability of KISS1 protein. Identifying these nsSNPs among the thousands of them make an opportunity to screen only those predicted deleterious by programs.

  6. [Diagnosis. Radiological study. Ultrasound, computed tomography and magnetic resonance imaging].

    Science.gov (United States)

    Gallo Vallejo, Francisco Javier; Giner Ruiz, Vicente

    2014-01-01

    Because of its low cost, availability in primary care and ease of interpretation, simple X-ray should be the first-line imaging technique used by family physicians for the diagnosis and/or follow-up of patients with osteoarthritis. Nevertheless, this technique should only be used if there are sound indications and if the results will influence decision-making. Despite the increase of indications in patients with rheumatological disease, the role of ultrasound in patients with osteoarthritis continues to be limited. Computed tomography (CT) is of some -although limited- use in osteoarthritis, especially in the study of complex joints (such as the sacroiliac joint and facet joints). Magnetic resonance imaging (MRI) has represented a major advance in the evaluation of joint cartilage and subchondral bone in patients with osteoarthritis but, because of its high cost and diagnostic-prognostic yield, this technique should only be used in highly selected patients. The indications for ultrasound, CT and MRI in patients with osteoarthritis continue to be limited in primary care and often coincide with situations in which the patient may require hospital referral. Patient safety should be bourne in mind. Patients should be protected from excessive ionizing radiation due to unnecessary repeat X-rays or inadequate views or to requests for tests such as CT, when not indicated. Copyright © 2014 Elsevier España, S.L. All rights reserved.

  7. A computational study on outliers in world music.

    Science.gov (United States)

    Panteli, Maria; Benetos, Emmanouil; Dixon, Simon

    2017-01-01

    The comparative analysis of world music cultures has been the focus of several ethnomusicological studies in the last century. With the advances of Music Information Retrieval and the increased accessibility of sound archives, large-scale analysis of world music with computational tools is today feasible. We investigate music similarity in a corpus of 8200 recordings of folk and traditional music from 137 countries around the world. In particular, we aim to identify music recordings that are most distinct compared to the rest of our corpus. We refer to these recordings as 'outliers'. We use signal processing tools to extract music information from audio recordings, data mining to quantify similarity and detect outliers, and spatial statistics to account for geographical correlation. Our findings suggest that Botswana is the country with the most distinct recordings in the corpus and China is the country with the most distinct recordings when considering spatial correlation. Our analysis includes a comparison of musical attributes and styles that contribute to the 'uniqueness' of the music of each country.

  8. A computational study on outliers in world music.

    Directory of Open Access Journals (Sweden)

    Maria Panteli

    Full Text Available The comparative analysis of world music cultures has been the focus of several ethnomusicological studies in the last century. With the advances of Music Information Retrieval and the increased accessibility of sound archives, large-scale analysis of world music with computational tools is today feasible. We investigate music similarity in a corpus of 8200 recordings of folk and traditional music from 137 countries around the world. In particular, we aim to identify music recordings that are most distinct compared to the rest of our corpus. We refer to these recordings as 'outliers'. We use signal processing tools to extract music information from audio recordings, data mining to quantify similarity and detect outliers, and spatial statistics to account for geographical correlation. Our findings suggest that Botswana is the country with the most distinct recordings in the corpus and China is the country with the most distinct recordings when considering spatial correlation. Our analysis includes a comparison of musical attributes and styles that contribute to the 'uniqueness' of the music of each country.

  9. High Performance Computing Innovation Service Portal Study (HPC-ISP)

    Science.gov (United States)

    2009-04-01

    based electronic commerce interface for the goods and services available through the brokerage service. This infrastructure will also support the... electronic commerce backend functionality for third parties that want to sell custom computing services. • Tailored Industry Portals are web portals for...broker shown in Figure 8 is essentially a web server that provides remote access to computing and software resources through an electronic commerce

  10. Computing and information sciences preliminary engineering design study

    Energy Technology Data Exchange (ETDEWEB)

    Schroeder, J O; Pearson, E W; Thomas, J J; Brothers, J W; Campbell, W K; DeVaney, D M; Jones, D R; Littlefield, R J; Peterson, M J

    1991-04-01

    This document presents the preliminary design concept for the integrated computing and information system to be included in the Environmental and Molecular Sciences Laboratory (EMSL) at the Pacific Northwest Laboratory, Richland, Washington, for the US Department of Energy (DOE). The EMSL is scheduled for completion and occupancy in 1994 or 1995 and will support the DOE environmental mission, in particular hazardous waste remediation. The focus of the report is on the Computing and Information Sciences engineering task of providing a fully integrated state-of-the-art computing environment for simulation, experimentation and analysis in support of molecular research. The EMSL will house two major research organizations, the Molecular Sciences Research Center (MSRC) and part of the Environmental Sciences Research Center (ESRC). Included in the report is a preliminary description of the computing and information system to be included. The proposed system architecture is based on a preliminary understanding of the EMSL users' needs for computational resources. As users understand more about the scientific challenges they face, the definition of the functional requirements will change. At the same time, the engineering team will be gaining experience with new computing technologies. Accordingly, the design architecture must evolve to reflect this new understanding of functional requirements and enabling technologies. 3 figs., 2 tabs.

  11. Life cycle assessment study of a Chinese desktop personal computer.

    Science.gov (United States)

    Duan, Huabo; Eugster, Martin; Hischier, Roland; Streicher-Porte, Martin; Li, Jinhui

    2009-02-15

    Associated with the tremendous prosperity in world electronic information and telecommunication industry, there continues to be an increasing awareness of the environmental impacts related to the accelerating mass production, electricity use, and waste management of electronic and electric products (e-products). China's importance as both a consumer and supplier of e-products has grown at an unprecedented pace in recent decade. Hence, this paper aims to describe the application of life cycle assessment (LCA) to investigate the environmental performance of Chinese e-products from a global level. A desktop personal computer system has been selected to carry out a detailed and modular LCA which follows the ISO 14040 series. The LCA is constructed by SimaPro software version 7.0 and expressed with the Eco-indicator'99 life cycle impact assessment method. For a sensitivity analysis of the overall LCA results, the so-called CML method is used in order to estimate the influence of the choice of the assessment method on the result. Life cycle inventory information is complied by ecoinvent 1.3 databases, combined with literature and field investigations on the present Chinese situation. The established LCA study shows that that the manufacturing and the use of such devices are of the highest environmental importance. In the manufacturing of such devices, the integrated circuits (ICs) and the Liquid Crystal Display (LCD) are those parts contributing most to the impact. As no other aspects are taken into account during the use phase, the impact is due to the way how the electricity is produced. The final process steps--i.e. the end of life phase--lead to a clear environmental benefit if a formal and modern, up-to-date technical system is assumed, like here in this study.

  12. Pulmonary emphysema subtypes on computed tomography: the MESA COPD study.

    Science.gov (United States)

    Smith, Benjamin M; Austin, John H M; Newell, John D; D'Souza, Belinda M; Rozenshtein, Anna; Hoffman, Eric A; Ahmed, Firas; Barr, R Graham

    2014-01-01

    Pulmonary emphysema is divided into 3 major subtypes at autopsy: centrilobular, paraseptal, and panlobular emphysema. These subtypes can be defined by visual assessment on computed tomography (CT); however, clinical characteristics of emphysema subtypes on CT are not well defined. We developed a reliable approach to visual assessment of emphysema subtypes on CT and examined if emphysema subtypes have distinct characteristics. The Multi-Ethnic Study of Atherosclerosis COPD Study recruited smokers with chronic obstructive pulmonary disease (COPD) and controls ages 50-79 years with ≥ 10 pack-years. Participants underwent CT following a standardized protocol. Definitions of centrilobular, paraseptal, and panlobular emphysema were obtained by literature review. Six-minute walk distance and pulmonary function were performed following guidelines. Twenty-seven percent of 318 smokers had emphysema on CT. Interrater reliability of emphysema subtype was substantial (K: 0.70). Compared with participants without emphysema, individuals with centrilobular or panlobular emphysema had greater dyspnea, reduced walk distance, greater hyperinflation, and lower diffusing capacity. In contrast, individuals with paraseptal emphysema were similar to controls, except for male predominance. Centrilobular, but not panlobular or paraseptal, emphysema was associated with greater smoking history (+21 pack-years P emphysema, was associated with reduced body mass index (-5 kg/m(2); P = .01). Other than for dyspnea, these findings were independent of the forced expiratory volume in 1 second. Seventeen percent of smokers without COPD on spirometry had emphysema, which was independently associated with reduced walk distance. Emphysema subtypes on CT are common in smokers with and without COPD. Centrilobular and panlobular emphysema, but not paraseptal emphysema, have considerable symptomatic and physiological consequences. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. A computed tomography phantom study of foam earplugs

    Science.gov (United States)

    Hsu, Li-Sheng; Yen, Ju-Bei; Wang, Shie-Shan; Liao, Chien-Lin

    2016-01-01

    Abstract Ingestion of a foreign body is common among children. However, ingestion of foam earplugs (FEPs) has not been reported previously. A 7-month-old female infant presented with small bowel obstruction, which was finally proved to be a case of FEP ingestion. Computed tomography (CT) phantom study was performed to examine the imaging features of FEPs. We studied the following dry and fully wet FEPs, FEPs squeezed in pure water to varying degrees, and FEPs with different degrees of compression in the dry and wet states from day 0 to 6 and all scanned with a CT scanner. The density of a dry FEP is −843.5 ± 4.5 Hounsfield units (HU) and it increases to 0.76 ± 9.3 HU when fully wet. The densities of FEPs ranged from −844.2 to 1.0 HU with different water/air ratios, and some showed a heterogeneous geographic pattern. The densities of FEPs increase due to compression and gradual water absorption. FEPs can be potentially hazardous objects to children. Owing to the special foam structure of the FEP, it can mimic a fatty lesion if the density ranges from −100 to −50 HU; moreover, it can hide in the water if fully wet. However, it should not be mistaken as air, as the density of a dry FEP is −843.5 HU, and the contour can be observed if the window level is set appropriately. Because of its soft texture, the surgeon should be careful not to miss an FEP during the operation. Moreover, radiologists should be familiar with the CT features of FEPs so that they can be identified before surgery. PMID:27583901

  14. Scheduling of a computer integrated manufacturing system: A simulation study

    Directory of Open Access Journals (Sweden)

    Nadia Bhuiyan

    2011-12-01

    Full Text Available Purpose: The purpose of this paper is to study the effect of selected scheduling dispatching rules on the performance of an actual CIM system using different performance measures and to compare the results with the literature.Design/methodology/approach: To achieve this objective, a computer simulation model of the existing CIM system is developed to test the performance of different scheduling rules with respect to mean flow time, machine efficiency and total run time as performance measures.Findings: Results suggest that the system performs much better considering the machine efficiency when the initial number of parts released is maximum and the buffer size is minimum. Furthermore, considering the average flow time, the system performs much better when the selected dispatching rule is either Earliest Due Date (EDD or Shortest Process Time (SPT with buffer size of five and the initial number of parts released of eight.Research limitations/implications: In this research, some limitations are: a limited number of factors and levels were considered for the experiment set-up; however the flexibility of the model allows experimenting with additional factors and levels. In the simulation experiments of this research, three scheduling dispatching rules (First In/First Out (FIFO, EDD, SPT were used. In future research, the effect of other dispatching rules on the system performance can be compared. Some assumptions can be relaxed in future work.Practical implications: This research helps to identify the potential effect of a selected number of dispatching rules and two other factors, the number of buffers and initial number of parts released, on the performance of the existing CIM systems with different part types where the machines are the major resource constraints.Originality/value: This research is among the few to study the effect of the dispatching rules on the performance of the CIM systems with use of terminating simulation analysis. This is

  15. A study on the GPU based parallel computation of a projection image

    Science.gov (United States)

    Lee, Hyunjeong; Han, Miseon; Kim, Jeongtae

    2017-05-01

    Fast computation of projection images is crucial in many applications such as medical image reconstruction and light field image processing. To do that, parallelization of the computation and efficient implementation of the computation using a parallel processor such as GPGPU (General-Purpose computing on Graphics Processing Units) is essential. In this research, we investigate methods for parallel computation of projection images and efficient implementation of the methods using CUDA (Compute Unified Device Architecture). We also study how to efficiently use the memory of GPU for the parallel processing.

  16. Noncontrast computed tomography in obstructive anuria: a prospective study.

    Science.gov (United States)

    Shokeir, Ahmed A; Shoma, Ahmed M; Mosbah, Ahmed; Mansour, Osama; Abol-Ghar, Mohamed; Eassa, Waleed; El-Asmy, Ahmed

    2002-06-01

    To evaluate the role of noncontrast computed tomography (NCCT) in the determination of the cause of obstructive anuria and to compare its accuracy with that of the traditional methods of combined plain abdominal x-ray (KUB) and gray-scale abdominal ultrasonography (US). The study included 40 consecutive patients with obstructive anuria. In addition to the routine evaluation, which included history, clinical examination, biochemical profile, KUB, and US, all patients underwent NCCT. The study patients were tested against an age and sex-matched control group that included the normal contralateral kidneys of 57 consecutive patients who underwent KUB, US, and NCCT for acute flank pain during the same study period. The reference standard for the determination of the cause of obstruction was retrograde or antegrade ureterography with or without ureteroscopy or open surgery. The absence of obstruction in the control group was confirmed by nonequivocal normal intravenous urography of the side free of flank pain. Both NCCT and combined KUB and US were compared regarding the sensitivity, specificity, and overall accuracy. The study group had 48 renal units, because obstruction was bilateral in 8 patients and of a solitary kidney in 32. Of the 42 renal units with calculus obstruction, the site of stone impaction was identified in all renal units by NCCT (sensitivity 100%) and in only 25 by combined KUB and US (sensitivity 59.5%)-a significant difference (P = 0.0001). Of the 6 renal units with noncalcular obstruction, both NCCT and US diagnosed the cause of obstruction in 3. The overall sensitivity of NCCT in the determination of the cause of obstructive anuria was 94% and that of combined KUB and US was 58%-a significant difference (P = 0.0001). The specificity of NCCT was not significantly different from that of combined KUB and US (96.5% versus 93%, respectively). The overall accuracy of NCCT was 95% and that of combined KUB and US was 77%-a significant difference (P = 0

  17. Fault-tolerant building-block computer study

    Science.gov (United States)

    Rennels, D. A.

    1978-01-01

    Ultra-reliable core computers are required for improving the reliability of complex military systems. Such computers can provide reliable fault diagnosis, failure circumvention, and, in some cases serve as an automated repairman for their host systems. A small set of building-block circuits which can be implemented as single very large integration devices, and which can be used with off-the-shelf microprocessors and memories to build self checking computer modules (SCCM) is described. Each SCCM is a microcomputer which is capable of detecting its own faults during normal operation and is described to communicate with other identical modules over one or more Mil Standard 1553A buses. Several SCCMs can be connected into a network with backup spares to provide fault-tolerant operation, i.e. automated recovery from faults. Alternative fault-tolerant SCCM configurations are discussed along with the cost and reliability associated with their implementation.

  18. Life under tension: Computational studies of proteins involved in mechanotransduction

    Science.gov (United States)

    Sotomayor, Marcos Manuel

    Living organisms rely on macroscopic and microscopic structures that produce and transform force: from mechanical motion of our muscles and bones to sound transduction and cell volume regulation, handling of forces is essential to life. Investigation of the microscopic machinery behind force generation and transduction in the cell has only become possible with recent advances in x-ray crystallography, nuclear magnetic resonance spectroscopy, single-molecule force spectroscopy, and computer modeling. In this thesis, molecular dynamics simulations have been used to study proteins that transform forces into biochemical signals (mechanotransduction). The first protein studied is the mechanosensitive channel of small conductance MscS. This membrane channel has been proposed to act as a safety valve during osmotic shock, facilitating the release of ions and small solutes upon increase in membrane tension, thereby preventing bacterial cells from bursting. The second set of proteins studied are ankyrin and cadherin repeats, likely forming part of the transduction apparatus in hearing and other mechanical senses. Simulations of all these proteins went beyond the standard approach in which only equilibrium properties are monitored; we adopted and developed strategies in which external electric fields and forces are used to probe their response and function and at the same time produce verifiable predictions. The outcome of the simulations performed on MscS, in close collaborations with experimentalists, allowed us to establish conduction properties of different conformations and propose structural models of MscS's open and closed states. Simulations of ankyrin and cadherin repeats focused on their elastic properties, resulting in the discovery and prediction of ankyrin's tertiary and secondary structure elasticity (later on corroborated by atomic force microscopy experiments), and the discovery of a novel form of secondary structure elasticity mediated by calcium ions in

  19. Educational Computer Use in Leisure Contexts: A Phenomenological Study of Adolescents' Experiences at Internet Cafes

    Science.gov (United States)

    Cilesiz, Sebnem

    2009-01-01

    Computer use is a widespread leisure activity for adolescents. Leisure contexts, such as Internet cafes, constitute specific social environments for computer use and may hold significant educational potential. This article reports a phenomenological study of adolescents' experiences of educational computer use at Internet cafes in Turkey. The…

  20. The International Computer and Information Literacy Study from a European Perspective: Introduction to the Special Issue

    Science.gov (United States)

    Gerick, Julia; Eickelmann, Birgit; Bos, Wilfried

    2017-01-01

    The "International Computer and Information Literacy Study" (ICILS 2013) provides, for the first time, information about students' computer and information literacy (CIL), as well as its acquisition, based on a computer-based test for students and background questionnaires. Among the 21 education systems that participated in ICILS 2013,…

  1. Developing Computer Model-Based Assessment of Chemical Reasoning: A Feasibility Study

    Science.gov (United States)

    Liu, Xiufeng; Waight, Noemi; Gregorius, Roberto; Smith, Erica; Park, Mihwa

    2012-01-01

    This paper reports a feasibility study on developing computer model-based assessments of chemical reasoning at the high school level. Computer models are flash and NetLogo environments to make simultaneously available three domains in chemistry: macroscopic, submicroscopic, and symbolic. Students interact with computer models to answer assessment…

  2. The Effects of Integrating Service Learning into Computer Science: An Inter-Institutional Longitudinal Study

    Science.gov (United States)

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-01-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of…

  3. HIGH-PERFORMANCE COMPUTING FOR THE STUDY OF EARTH AND ENVIRONMENTAL SCIENCE MATERIALS USING SYNCHROTRON X-RAY COMPUTED MICROTOMOGRAPHY.

    Energy Technology Data Exchange (ETDEWEB)

    FENG,H.; JONES,K.W.; MCGUIGAN,M.; SMITH,G.J.; SPILETIC,J.

    2001-10-12

    Synchrotron x-ray computed microtomography (CMT) is a non-destructive method for examination of rock, soil, and other types of samples studied in the earth and environmental sciences. The high x-ray intensities of the synchrotron source make possible the acquisition of tomographic volumes at a high rate that requires the application of high-performance computing techniques for data reconstruction to produce the three-dimensional volumes, for their visualization, and for data analysis. These problems are exacerbated by the need to share information between collaborators at widely separated locations over both local and tide-area networks. A summary of the CMT technique and examples of applications are given here together with a discussion of the applications of high-performance computing methods to improve the experimental techniques and analysis of the data.

  4. Studying Collective Human Decision Making and Creativity with Evolutionary Computation.

    Science.gov (United States)

    Sayama, Hiroki; Dionne, Shelley D

    2015-01-01

    We report a summary of our interdisciplinary research project "Evolutionary Perspective on Collective Decision Making" that was conducted through close collaboration between computational, organizational, and social scientists at Binghamton University. We redefined collective human decision making and creativity as evolution of ecologies of ideas, where populations of ideas evolve via continual applications of evolutionary operators such as reproduction, recombination, mutation, selection, and migration of ideas, each conducted by participating humans. Based on this evolutionary perspective, we generated hypotheses about collective human decision making, using agent-based computer simulations. The hypotheses were then tested through several experiments with real human subjects. Throughout this project, we utilized evolutionary computation (EC) in non-traditional ways-(1) as a theoretical framework for reinterpreting the dynamics of idea generation and selection, (2) as a computational simulation model of collective human decision-making processes, and (3) as a research tool for collecting high-resolution experimental data on actual collaborative design and decision making from human subjects. We believe our work demonstrates untapped potential of EC for interdisciplinary research involving human and social dynamics.

  5. Computational and Experimental Studies on the Hetero-Diels-Alder ...

    African Journals Online (AJOL)

    NJD

    hetero-Diels-Alder (DTHDA) reactions emerged as an efficient methodology for the construction of ring fused ... explore the energetics of all reactants (1 and sulphene) and the corresponding cycloadducts (2 and 3) with ... large systems due to its computational efficiency compared with the MP2 level and above. Frequency ...

  6. A Successful Course of Study in Computer Programming

    Science.gov (United States)

    Seeger, David H.

    1977-01-01

    Three keys to the successful development of the program of the computer programming department of the Technical Institute of Oklahoma State University are discussed: Community involvement, faculty/administration commitment to the basic principles of technical career education, and availability of appropriate equipment for student use. (HD)

  7. Logic as Marr's computational level: Four case studies

    NARCIS (Netherlands)

    Baggio, G.; Lambalgen, M. van; Hagoort, P.

    2015-01-01

    We sketch four applications of Marr's levels-of-analysis methodology to the relations between logic and experimental data in the cognitive neuroscience of language and reasoning. The first part of the paper illustrates the explanatory power of computational level theories based on logic. We show

  8. The effects of integrating service learning into computer science: an inter-institutional longitudinal study

    Science.gov (United States)

    Payton, Jamie; Barnes, Tiffany; Buch, Kim; Rorrer, Audrey; Zuo, Huifang

    2015-07-01

    This study is a follow-up to one published in computer science education in 2010 that reported preliminary results showing a positive impact of service learning on student attitudes associated with success and retention in computer science. That paper described how service learning was incorporated into a computer science course in the context of the Students & Technology in Academia, Research, and Service (STARS) Alliance, an NSF-supported broadening participation in computing initiative that aims to diversify the computer science pipeline through innovative pedagogy and inter-institutional partnerships. The current paper describes how the STARS Alliance has expanded to diverse institutions, all using service learning as a vehicle for broadening participation in computing and enhancing attitudes and behaviors associated with student success. Results supported the STARS model of service learning for enhancing computing efficacy and computing commitment and for providing diverse students with many personal and professional development benefits.

  9. Computational method for multi-modal microscopy based on transport of intensity equation

    Science.gov (United States)

    Li, Jiaji; Chen, Qian; Sun, Jiasong; Zhang, Jialin; Zuo, Chao

    2017-02-01

    In this paper, we develop the requisite theory to describe a hybrid virtual-physical multi-modal imaging system which yields quantitative phase, Zernike phase contrast, differential interference contrast (DIC), and light field moment imaging simultaneously based on transport of intensity equation(TIE). We then give the experimental demonstration of these ideas by time-lapse imaging of live HeLa cell mitosis. Experimental results verify that a tunable lens based TIE system, combined with the appropriate post-processing algorithm, can achieve a variety of promising imaging modalities in parallel with the quantitative phase images for the dynamic study of cellular processes.

  10. An Integrated Computer-Aided Approach for Environmental Studies

    DEFF Research Database (Denmark)

    Gani, Rafiqul; Chen, Fei; Jaksland, Cecilia

    1997-01-01

    A general framework for an integrated computer-aided approach to solve process design, control, and environmental problems simultaneously is presented. Physicochemical properties and their relationships to the molecular structure play an important role in the proposed integrated approach. The sco...... and applicability of the integrated approach is highlighted through examples involving estimation of properties and environmental pollution prevention. The importance of mixture effects on some environmentally important properties is also demonstrated.......A general framework for an integrated computer-aided approach to solve process design, control, and environmental problems simultaneously is presented. Physicochemical properties and their relationships to the molecular structure play an important role in the proposed integrated approach. The scope...

  11. Computer tomographic and angiographic studies of histologically confirmed intrahepatic masses

    Energy Technology Data Exchange (ETDEWEB)

    Janson, R.; Lackner, K.; Paquet, K.J.; Thelen, M.; Thurn, P.

    1980-06-01

    The computer tomographic and angiographic findings in 53 patients with intrahepatic masses were compared. The histological findings show that 17 were due to echinococcus, 12 were due to hepatic carcinoma, ten were metastases, five patients had focal nodular hyperplasia, three an alveolar echinococcus and there were three cases with an haemangioma of the liver and a further three liver abscesses. Computer tomography proved superior in peripherally situated lesions, and in those in the left lobe of the liver. Arteriography was better at demonstrating lesions below 2 cm in size, particularly vascular tumours. As a pre-operative measure, angiography is to be preferred since it is able to demonstrate anatomic anomalies and variations in the blood supply, as well as invasion of the portal vein or of the inferior vena cava.

  12. Web OS in Cloud Computing: A Case study

    OpenAIRE

    Ranjan Kumar Mondal; Debabrata Sarddar

    2016-01-01

    Like a Server Operating System (SOS) and a Cloud Operating System (COS) are responsible for computing resources. In a server the OS is responsible for managing the various hardware resources inside a server’s frame. A Web Operating System serves the same purpose like traditional server does. Instead of managing a single machine’s resources, a cloud Operating System is responsible for managing the cloud infrastructure. But unlike a traditional Operating System, a Web Operating System has to...

  13. A study on strategic provisioning of cloud computing services.

    Science.gov (United States)

    Whaiduzzaman, Md; Haque, Mohammad Nazmul; Rejaul Karim Chowdhury, Md; Gani, Abdullah

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models "everything-as-a-service." Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified.

  14. A Study on Strategic Provisioning of Cloud Computing Services

    Directory of Open Access Journals (Sweden)

    Md Whaiduzzaman

    2014-01-01

    Full Text Available Cloud computing is currently emerging as an ever-changing, growing paradigm that models “everything-as-a-service.” Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified.

  15. HEP Computing Tools, Grid and Supercomputers for Genome Sequencing Studies

    Science.gov (United States)

    De, K.; Klimentov, A.; Maeno, T.; Mashinistov, R.; Novikov, A.; Poyda, A.; Tertychnyy, I.; Wenaus, T.

    2017-10-01

    PanDA - Production and Distributed Analysis Workload Management System has been developed to address ATLAS experiment at LHC data processing and analysis challenges. Recently PanDA has been extended to run HEP scientific applications on Leadership Class Facilities and supercomputers. The success of the projects to use PanDA beyond HEP and Grid has drawn attention from other compute intensive sciences such as bioinformatics. Recent advances of Next Generation Genome Sequencing (NGS) technology led to increasing streams of sequencing data that need to be processed, analysed and made available for bioinformaticians worldwide. Analysis of genomes sequencing data using popular software pipeline PALEOMIX can take a month even running it on the powerful computer resource. In this paper we will describe the adaptation the PALEOMIX pipeline to run it on a distributed computing environment powered by PanDA. To run pipeline we split input files into chunks which are run separately on different nodes as separate inputs for PALEOMIX and finally merge output file, it is very similar to what it done by ATLAS to process and to simulate data. We dramatically decreased the total walltime because of jobs (re)submission automation and brokering within PanDA. Using software tools developed initially for HEP and Grid can reduce payload execution time for Mammoths DNA samples from weeks to days.

  16. A Study on Strategic Provisioning of Cloud Computing Services

    Science.gov (United States)

    Rejaul Karim Chowdhury, Md

    2014-01-01

    Cloud computing is currently emerging as an ever-changing, growing paradigm that models “everything-as-a-service.” Virtualised physical resources, infrastructure, and applications are supplied by service provisioning in the cloud. The evolution in the adoption of cloud computing is driven by clear and distinct promising features for both cloud users and cloud providers. However, the increasing number of cloud providers and the variety of service offerings have made it difficult for the customers to choose the best services. By employing successful service provisioning, the essential services required by customers, such as agility and availability, pricing, security and trust, and user metrics can be guaranteed by service provisioning. Hence, continuous service provisioning that satisfies the user requirements is a mandatory feature for the cloud user and vitally important in cloud computing service offerings. Therefore, we aim to review the state-of-the-art service provisioning objectives, essential services, topologies, user requirements, necessary metrics, and pricing mechanisms. We synthesize and summarize different provision techniques, approaches, and models through a comprehensive literature review. A thematic taxonomy of cloud service provisioning is presented after the systematic review. Finally, future research directions and open research issues are identified. PMID:25032243

  17. Computational Studies of Marine Toxins Targeting Ion Channels

    Directory of Open Access Journals (Sweden)

    Serdar Kuyucak

    2013-03-01

    Full Text Available Toxins from marine animals offer novel drug leads for treatment of diseases involving ion channels. Computational methods could be very helpful in this endeavour in several ways, e.g., (i constructing accurate models of the channel-toxin complexes using docking and molecular dynamics (MD simulations; (ii determining the binding free energies of toxins from umbrella sampling MD simulations; (iii predicting the effect of mutations from free energy MD simulations. Using these methods, one can design new analogs of toxins with improved affinity and selectivity properties. Here we present a review of the computational methods and discuss their applications to marine toxins targeting potassium and sodium channels. Detailed examples from the potassium channel toxins—ShK from sea anemone and κ-conotoxin PVIIA—are provided to demonstrate capabilities of the computational methods to give accurate descriptions of the channel-toxin complexes and the energetics of their binding. An example is also given from sodium channel toxins (μ-conotoxin GIIIA to illustrate the differences between the toxin binding modes in potassium and sodium channels.

  18. Computer literacy among first year medical students in a developing country: A cross sectional study

    Science.gov (United States)

    2012-01-01

    Background The use of computer assisted learning (CAL) has enhanced undergraduate medical education. CAL improves performance at examinations, develops problem solving skills and increases student satisfaction. The study evaluates computer literacy among first year medical students in Sri Lanka. Methods The study was conducted at Faculty of Medicine, University of Colombo, Sri Lanka between August-September 2008. First year medical students (n = 190) were invited for the study. Data on computer literacy and associated factors were collected by an expert-validated pre-tested self-administered questionnaire. Computer literacy was evaluated by testing knowledge on 6 domains; common software packages, operating systems, database management and the usage of internet and E-mail. A linear regression was conducted using total score for computer literacy as the continuous dependant variable and other independent covariates. Results Sample size-181 (Response rate-95.3%), 49.7% were Males. Majority of the students (77.3%) owned a computer (Males-74.4%, Females-80.2%). Students have gained their present computer knowledge by; a formal training programme (64.1%), self learning (63.0%) or by peer learning (49.2%). The students used computers for predominately; word processing (95.6%), entertainment (95.0%), web browsing (80.1%) and preparing presentations (76.8%). Majority of the students (75.7%) expressed their willingness for a formal computer training programme at the faculty. Mean score for the computer literacy questionnaire was 48.4 ± 20.3, with no significant gender difference (Males-47.8 ± 21.1, Females-48.9 ± 19.6). There were 47.9% students that had a score less than 50% for the computer literacy questionnaire. Students from Colombo district, Western Province and Student owning a computer had a significantly higher mean score in comparison to other students (p computer training was the strongest predictor of computer literacy (β = 13.034), followed by using

  19. Computer literacy among first year medical students in a developing country: a cross sectional study.

    Science.gov (United States)

    Ranasinghe, Priyanga; Wickramasinghe, Sashimali A; Pieris, Wa Rasanga; Karunathilake, Indika; Constantine, Godwin R

    2012-09-14

    The use of computer assisted learning (CAL) has enhanced undergraduate medical education. CAL improves performance at examinations, develops problem solving skills and increases student satisfaction. The study evaluates computer literacy among first year medical students in Sri Lanka. The study was conducted at Faculty of Medicine, University of Colombo, Sri Lanka between August-September 2008. First year medical students (n = 190) were invited for the study. Data on computer literacy and associated factors were collected by an expert-validated pre-tested self-administered questionnaire. Computer literacy was evaluated by testing knowledge on 6 domains; common software packages, operating systems, database management and the usage of internet and E-mail. A linear regression was conducted using total score for computer literacy as the continuous dependant variable and other independent covariates. Sample size-181 (Response rate-95.3%), 49.7% were Males. Majority of the students (77.3%) owned a computer (Males-74.4%, Females-80.2%). Students have gained their present computer knowledge by; a formal training programme (64.1%), self learning (63.0%) or by peer learning (49.2%). The students used computers for predominately; word processing (95.6%), entertainment (95.0%), web browsing (80.1%) and preparing presentations (76.8%). Majority of the students (75.7%) expressed their willingness for a formal computer training programme at the faculty.Mean score for the computer literacy questionnaire was 48.4 ± 20.3, with no significant gender difference (Males-47.8 ± 21.1, Females-48.9 ± 19.6). There were 47.9% students that had a score less than 50% for the computer literacy questionnaire. Students from Colombo district, Western Province and Student owning a computer had a significantly higher mean score in comparison to other students (p computer training was the strongest predictor of computer literacy (β = 13.034), followed by using internet facility, being from

  20. Theoretical and computational studies in protein folding, design, and function

    Science.gov (United States)

    Morrissey, Michael Patrick

    2000-10-01

    In this work, simplified statistical models are used to understand an array of processes related to protein folding and design. In Part I, lattice models are utilized to test several theories about the statistical properties of protein-like systems. In Part II, sequence analysis and all-atom simulations are used to advance a novel theory for the behavior of a particular protein. Part I is divided into five chapters. In Chapter 2, a method of sequence design for model proteins, based on statistical mechanical first-principles, is developed. The cumulant design method uses a mean-field approximation to expand the free energy of a sequence in temperature. The method successfully designs sequences which fold to a target lattice structure at a specific temperature, a feat which was not possible using previous design methods. The next three chapters are computational studies of the double mutant cycle, which has been used experimentally to predict intra-protein interactions. Complete structure prediction is demonstrated for a model system using exhaustive, and also sub-exhaustive, double mutants. Nonadditivity of enthalpy, rather than of free energy, is proposed and demonstrated to be a superior marker for inter-residue contact. Next, a new double mutant protocol, called exchange mutation, is introduced. Although simple statistical arguments predict exchange mutation to be a more accurate contact predictor than standard mutant cycles, this hypothesis was not upheld in lattice simulations. Reasons for this inconsistency will be discussed. Finally, a multi-chain folding algorithm is introduced. Known as LINKS, this algorithm was developed to test a method of structure prediction which utilizes chain-break mutants. While structure prediction was not successful, LINKS should nevertheless be a useful tool for the study of protein-protein and protein-ligand interactions. The last chapter of Part I utilizes the lattice to explore the differences between standard folding, from